ScientificPythonLectures Simple

SciKits Numpy Matplotlib
2024
SciPy Python EDITION
IP[y]:
Cython IPython
Edited by
Scien�fic Python Gaël Varoquaux

Emmanuelle Gouillart
Olaf Vahtras
Lectures
Pierre de Buyl
K. Jarrod Millman
Stéfan van der Walt
lectures.scientific-python.org
Gaël Varoquaux • Emmanuelle Gouillart • Olav Vahtras

Pierre de Buyl • K. Jarrod Millman • Stéfan van der Walt
Christopher Burns • Adrian Chauve • Robert Cimrman • Christophe Combelles
Ralf Gommers • André Espaze • Zbigniew Jędrzejewski-Szmek
Valen� n Haenel • Michael Hartmann • Gert-Ludwig Ingold • Fabian Pedregosa
Didrik Pinte • Nicolas P. Rougier • Joris Van den Bossche • Pauli Virtanen
and many others...
Contents
I Getting started with Python for science 2

1 Python scientific computing ecosystem 4
1.1 Why Python? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.2 The scientific Python ecosystem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
1.3 Before starting: Installing a working environment . . . . . . . . . . . . . . . . . . . . . . 7
1.4 The workflow: interactive environments and text editors . . . . . . . . . . . . . . . . . . 8
2 The Python language 12

2.1 First steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2 Basic types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.3 Control Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.4 Defining functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.5 Reusing code: scripts and modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.6 Input and Output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
2.7 Standard Library . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
2.8 Exception handling in Python . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
2.9 Object-oriented programming (OOP) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3 NumPy: creating and manipulating numerical data 54

3.1 The NumPy array object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
3.2 Numerical operations on arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
3.3 More elaborate arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
3.4 Advanced operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
3.5 Some exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.6 Full code examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
4 Matplotlib: plotting 107

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.2 Simple plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
4.3 Figures, Subplots, Axes and Ticks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
4.4 Other Types of Plots: examples and exercises . . . . . . . . . . . . . . . . . . . . . . . . . 119
4.5 Beyond this tutorial . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
4.6 Quick references . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5 SciPy : high-level scientific computing 211

5.1 File input/output: scipy.io . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
5.2 Special functions: scipy.special . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
i
5.3 Linear algebra operations: scipy.linalg . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
5.4 Interpolation: scipy.interpolate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
5.5 Optimization and fit: scipy.optimize . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
5.6 Statistics and random numbers: scipy.stats . . . . . . . . . . . . . . . . . . . . . . . . 221
5.7 Numerical integration: scipy.integrate . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
5.8 Fast Fourier transforms: scipy.fft . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
5.9 Signal processing: scipy.signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
5.10 Image manipulation: scipy.ndimage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
5.11 Summary exercises on scientific computing . . . . . . . . . . . . . . . . . . . . . . . . . . 236
5.12 Full code examples for the SciPy chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
6 Getting help and finding documentation 291
II Advanced topics 294

7 Advanced Python Constructs 296
7.1 Iterators, generator expressions and generators . . . . . . . . . . . . . . . . . . . . . . . . 297
7.2 Decorators . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
7.3 Context managers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
8 Advanced NumPy 314

8.1 Life of ndarray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
8.2 Universal functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
8.3 Interoperability features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
8.4 Array siblings: chararray, maskedarray . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
8.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
8.6 Contributing to NumPy/SciPy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
9 Debugging code 348

9.1 Avoiding bugs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349
9.2 Debugging workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
9.3 Using the Python debugger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
9.4 Debugging segmentation faults using gdb . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
10 Optimizing code 360

10.1 Optimization workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
10.2 Profiling Python code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
10.3 Making code go faster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
10.4 Writing faster numerical code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
11 Sparse Arrays in SciPy 368

11.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368
11.2 Storage Schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371
11.3 Linear System Solvers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
11.4 Other Interesting Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378
12 Image manipulation and processing using NumPy and SciPy 379

12.1 Opening and writing to image files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
12.2 Displaying images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382
12.3 Basic manipulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383
12.4 Image filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385
12.5 Feature extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391
12.6 Measuring objects properties: scipy.ndimage.measurements . . . . . . . . . . . . . . . . 394
12.8 Examples for the image processing chapter . . . . . . . . . . . . . . . . . . . . . . . . . . 397
13 Mathematical optimization: finding minima of functions 424

13.1 Knowing your problem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
13.2 A review of the different optimizers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428
ii
13.4 Examples for the mathematical optimization chapter . . . . . . . . . . . . . . . . . . . . 434
13.5 Practical guide to optimization with SciPy . . . . . . . . . . . . . . . . . . . . . . . . . . 474
13.6 Special case: non-linear least-squares . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
13.7 Optimization with constraints . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478
13.9 Examples for the mathematical optimization chapter . . . . . . . . . . . . . . . . . . . . 479
14 Interfacing with C 480

14.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
14.2 Python-C-Api . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
14.3 Ctypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489
14.4 SWIG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493
14.5 Cython . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498
14.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503
14.7 Further Reading and References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503
14.8 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503
III Packages and applications 505

15 Statistics in Python 507
15.1 Data representation and interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 508
15.2 Hypothesis testing: comparing two groups . . . . . . . . . . . . . . . . . . . . . . . . . . 513
15.3 Linear models, multiple factors, and analysis of variance . . . . . . . . . . . . . . . . . . . 516
15.4 More visualization: seaborn for statistical exploration . . . . . . . . . . . . . . . . . . . . 522
15.5 Testing for interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525
15.6 Full code for the figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
15.7 Solutions to this chapter’s exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
16 Sympy : Symbolic Mathematics in Python 557

16.1 First Steps with SymPy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 558
16.2 Algebraic manipulations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 559
16.3 Calculus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560
16.4 Equation solving . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 563
16.5 Linear Algebra . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 564
17 scikit-image: image processing 566

17.1 Introduction and concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 567
17.2 Importing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 569
17.3 Example data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570
17.4 Input/output, data types and colorspaces . . . . . . . . . . . . . . . . . . . . . . . . . . . 570
17.5 Image preprocessing / enhancement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 572
17.6 Image segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 576
17.7 Measuring regions’ properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579
17.8 Data visualization and interaction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579
17.9 Feature extraction for computer vision . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580
17.11 Examples for the scikit-image chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 581
18 scikit-learn: machine learning in Python 593

18.1 Introduction: problem settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 594
18.2 Basic principles of machine learning with scikit-learn . . . . . . . . . . . . . . . . . . . . 598
18.3 Supervised Learning: Classification of Handwritten Digits . . . . . . . . . . . . . . . . . . 604
18.4 Supervised Learning: Regression of Housing Data . . . . . . . . . . . . . . . . . . . . . . 608
18.5 Measuring prediction performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613
18.6 Unsupervised Learning: Dimensionality Reduction and Visualization . . . . . . . . . . . . 619
18.7 Parameter selection, Validation, and Testing . . . . . . . . . . . . . . . . . . . . . . . . . 622
18.8 Examples for the scikit-learn chapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630
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IV About the Scientific Python Lectures 678
19 About the Scientific Python Lectures 679
19.1 Authors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 679
Index 682
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Scientific Python Lectures, Edition 2024.1rc0
Contents 1
Part I
Getting started with Python for

science
2
This part of the Scientific Python Lectures is a self-contained introduction to everything that is needed
to use Python for science, from the language itself, to numerical computing or plotting.
3
CHAPTER 1
Python scientific computing ecosystem
Authors: Fernando Perez, Emmanuelle Gouillart, Gaël Varoquaux, Valentin Haenel
1.1 Why Python?
1.1.1 The scientist’s needs
• Get data (simulation, experiment control),

• Manipulate and process data,
• Visualize results, quickly to understand, but also with high quality figures, for reports or publica-
tions.
1.1.2 Python’s strengths
• Batteries included Rich collection of already existing bricks of classic numerical methods, plot-
ting or data processing tools. We don’t want to re-program the plotting of a curve, a Fourier
transform or a fitting algorithm. Don’t reinvent the wheel!
• Easy to learn Most scientists are not paid as programmers, neither have they been trained so.
They need to be able to draw a curve, smooth a signal, do a Fourier transform in a few minutes.
• Easy communication To keep code alive within a lab or a company it should be as readable
as a book by collaborators, students, or maybe customers. Python syntax is simple, avoiding
strange symbols or lengthy routine specifications that would divert the reader from mathematical
or scientific understanding of the code.
4
• Efficient code Python numerical modules are computationally efficient. But needless to say that
a very fast code becomes useless if too much time is spent writing it. Python aims for quick
development times and quick execution times.
• Universal Python is a language used for many different problems. Learning Python avoids learning
a new software for each new problem.
1.1.3 How does Python compare to other solutions?
Compiled languages: C, C++, Fortran. . .
Pros
• Very fast. For heavy computations, it’s difficult to outperform these languages.
Cons
• Painful usage: no interactivity during development, mandatory compilation steps,
verbose syntax, manual memory management. These are difficult languages for
non programmers.
Matlab scripting language
Pros
• Very rich collection of libraries with numerous algorithms, for many different do-
mains. Fast execution because these libraries are often written in a compiled lan-
guage.
• Pleasant development environment: comprehensive and help, integrated editor, etc.
• Commercial support is available.
Cons
• Base language is quite poor and can become restrictive for advanced users.
• Not free and not everything is open sourced.
Julia
Pros
• Fast code, yet interactive and simple.
• Easily connects to Python or C.
Cons
• Ecosystem limited to numerical computing.
• Still young.
1.1. Why Python? 5

Other scripting languages: Scilab, Octave, R, IDL, etc.
Pros
• Open-source, free, or at least cheaper than Matlab.
• Some features can be very advanced (statistics in R, etc.)
Cons
• Fewer available algorithms than in Matlab, and the language is not more advanced.
• Some software are dedicated to one domain. Ex: Gnuplot to draw curves. These
programs are very powerful, but they are restricted to a single type of usage, such
as plotting.
Python
Pros
• Very rich scientific computing libraries
• Well thought out language, allowing to write very readable and well structured code:
we “code what we think”.
• Many libraries beyond scientific computing (web server, serial port access, etc.)
• Free and open-source software, widely spread, with a vibrant community.
• A variety of powerful environments to work in, such as IPython, Spyder, Jupyter
notebooks, Pycharm, Visual Studio Code
Cons
• Not all the algorithms that can be found in more specialized software or toolboxes.
1.2 The scientific Python ecosystem
Unlike Matlab, or R, Python does not come with a pre-bundled set of modules for scientific computing.
Below are the basic building blocks that can be combined to obtain a scientific computing environment:
Python, a generic and modern computing language

• The language: flow control, data types (string, int), data collections (lists, dictionaries), etc.
• Modules of the standard library: string processing, file management, simple network protocols.
• A large number of specialized modules or applications written in Python: web framework, etc. . . .
and scientific computing.
• Development tools (automatic testing, documentation generation)
See also:
chapter on Python language
Core numeric libraries
1.2. The scientific Python ecosystem 6

• NumPy: numerical computing with powerful numerical arrays objects, and routines to manip-
ulate them. https://numpy.org/
See also:
chapter on numpy
• SciPy : high-level numerical routines. Optimization, regression, interpolation, etc https://scipy.
org/
See also:
chapter on SciPy
• Matplotlib : 2-D visualization, “publication-ready” plots https://matplotlib.org/
See also:
chapter on matplotlib
Advanced interactive environments:
• IPython, an advanced Python console https://ipython.org/
• Jupyter, notebooks in the browser https://jupyter.org/
Domain-specific packages,
• pandas, statsmodels, seaborn for statistics
• sympy for symbolic computing
• scikit-image for image processing
• scikit-learn for machine learning
and many more packages not documented in the Scientific Python Lectures.
See also:
chapters on advanced topics
chapters on packages and applications
1.3 Before starting: Installing a working environment
Python comes in many flavors, and there are many ways to install it. However, we recommend to install
a scientific-computing distribution, that comes readily with optimized versions of scientific modules.
Under Linux
If you have a recent distribution, most of the tools are probably packaged, and it is recommended to use
your package manager.
Other systems
There are several fully-featured scientific Python distributions:
• Anaconda
• WinPython
1.3. Before starting: Installing a working environment 7

1.4 The workflow: interactive environments and text editors
Interactive work to test and understand algorithms: In this section, we describe a workflow
combining interactive work and consolidation.
Python is a general-purpose language. As such, there is not one blessed environment to work in, and
not only one way of using it. Although this makes it harder for beginners to find their way, it makes it
possible for Python to be used for programs, in web servers, or embedded devices.
1.4.1 Interactive work
We recommend an interactive work with the IPython console, or its offspring, the Jupyter notebook.
They are handy to explore and understand algorithms.
Under the notebook
To execute code, press “shift enter”
Start ipython:
In [1]: print('Hello world')

Hello world
Getting help by using the ? operator after an object:
In [2]: print?
Signature: print(*args, sep=' ', end='\n', file=None, flush=False)
Docstring:
Prints the values to a stream, or to sys.stdout by default.
sep
string inserted between values, default a space.
end
string appended after the last value, default a newline.
file
a file-like object (stream); defaults to the current sys.stdout.
flush
whether to forcibly flush the stream.
Type: builtin_function_or_method
See also:
• IPython user manual: https://ipython.readthedocs.io/en/stable/
• Jupyter Notebook QuickStart: https://docs.jupyter.org/en/latest/start/index.html
1.4.2 Elaboration of the work in an editor
As you move forward, it will be important to not only work interactively, but also to create and reuse
Python files. For this, a powerful code editor will get you far. Here are several good easy-to-use editors:
• Spyder: integrates an IPython console, a debugger, a profiler. . .
• PyCharm: integrates an IPython console, notebooks, a debugger. . . (freely available, but commer-
cial)
• Visual Studio Code: integrates a Python console, notebooks, a debugger, . . .
1.4. The workflow: interactive environments and text editors 8

Some of these are shipped by the various scientific Python distributions, and you can find them in the
menus.
As an exercise, create a file my_file.py in a code editor, and add the following lines:
s = 'Hello world'
print(s)
Now, you can run it in IPython console or a notebook and explore the resulting variables:
In [3]: %run my_file.py

Hello world
In [4]: s
Out[4]: 'Hello world'
In [5]: %whos
Variable Type Data/Info
----------------------------
s str Hello world
From a script to functions
While it is tempting to work only with scripts, that is a file full of instructions following each other,
do plan to progressively evolve the script to a set of functions:
• A script is not reusable, functions are.
• Thinking in terms of functions helps breaking the problem in small blocks.
1.4.3 IPython and Jupyter Tips and Tricks
The user manuals contain a wealth of information. Here we give a quick introduction to four useful
features: history, tab completion, magic functions, and aliases.
Command history Like a UNIX shell, the IPython console supports command history. Type up and
down to navigate previously typed commands:
In [6]: x = 10
In [7]: <UP>
In [8]: x = 10
Tab completion Tab completion, is a convenient way to explore the structure of any object you’re
dealing with. Simply type object_name.<TAB> to view the object’s attributes. Besides Python objects
and keywords, tab completion also works on file and directory names.*

In [9]: x = 10
In [10]: x.<TAB>
as_integer_ratio() conjugate() imag to_bytes()
bit_count() denominator numerator
bit_length() from_bytes() real
Magic functions The console and the notebooks support so-called magic functions by prefixing a
command with the % character. For example, the run and whos functions from the previous section are
magic functions. Note that, the setting automagic, which is enabled by default, allows you to omit the
preceding % sign. Thus, you can just type the magic function and it will work.
Other useful magic functions are:
• %cd to change the current directory.
In [11]: cd /tmp
/tmp
• %cpaste allows you to paste code, especially code from websites which has been prefixed with the
standard Python prompt (e.g. >>>) or with an ipython prompt, (e.g. in [3]):
In [12]: %cpaste
• %timeit allows you to time the execution of short snippets using the timeit module from the
standard library:
In [12]: %timeit x = 10
10.6 ns +- 1.37 ns per loop (mean +- std. dev. of 7 runs, 100,000,000 loops each)
See also:
Chapter on optimizing code
• %debug allows you to enter post-mortem debugging. That is to say, if the code you try to execute,
raises an exception, using %debug will enter the debugger at the point where the exception was
thrown.
In [13]: x === 10
Cell In[13], line 1
x === 10
^
SyntaxError: invalid syntax
In [14]: %debug
> /home/jarrod/.venv/lectures/lib64/python3.11/site-packages/IPython/core/
˓→compilerop.py(86)ast_parse()
84 Arguments are exactly the same as ast.parse (in the standard␣

˓→library),
85 and are passed to the built-in compile function."""

---> 86 return compile(source, filename, symbol, self.flags | PyCF_ONLY_
˓→AST, 1)
87
88 def reset_compiler_flags(self):
(continues on next page)

(continued from previous page)

ipdb> locals()
{'self': <IPython.core.compilerop.CachingCompiler object at 0x7f30d02efc10>,
˓→'source': 'x === 10\n', 'filename': '<ipython-input-1-8e8bc565444b>', 'symbol
˓→': 'exec'}
ipdb>
See also:
Chapter on debugging
Aliases Furthermore IPython ships with various aliases which emulate common UNIX command line
tools such as ls to list files, cp to copy files and rm to remove files (a full list of aliases is shown when
typing alias).
Getting help
• The built-in cheat-sheet is accessible via the %quickref magic function.

• A list of all available magic functions is shown when typing %magic.

CHAPTER 2
The Python language
Authors: Chris Burns, Christophe Combelles, Emmanuelle Gouillart, Gaël Varoquaux
Python for scientific computing
We introduce here the Python language. Only the bare minimum necessary for getting started with
NumPy and SciPy is addressed here. To learn more about the language, consider going through the
excellent tutorial https://docs.python.org/3/tutorial. Dedicated books are also available, such as Dive
into Python 3.
Tip: Python is a programming language, as are C, Fortran, BASIC, PHP, etc. Some specific
features of Python are as follows:
• an interpreted (as opposed to compiled) language. Contrary to e.g. C or Fortran, one does not
compile Python code before executing it. In addition, Python can be used interactively: many
Python interpreters are available, from which commands and scripts can be executed.
• a free software released under an open-source license: Python can be used and distributed free
of charge, even for building commercial software.
• multi-platform: Python is available for all major operating systems, Windows, Linux/Unix,
MacOS X, most likely your mobile phone OS, etc.
• a very readable language with clear non-verbose syntax
12
• a language for which a large variety of high-quality packages are available for various applications,
from web frameworks to scientific computing.
• a language very easy to interface with other languages, in particular C and C++.
• Some other features of the language are illustrated just below. For example, Python is an object-
oriented language, with dynamic typing (the same variable can contain objects of different types
during the course of a program).
See https://www.python.org/about/ for more information about distinguishing features of Python.
2.1 First steps
Start the Ipython shell (an enhanced interactive Python shell):

• by typing “ipython” from a Linux/Mac terminal, or from the Windows cmd shell,
• or by starting the program from a menu, e.g. the Anaconda Navigator, the Python(x,y) menu if
you have installed one of these scientific-Python suites.
Tip: If you don’t have Ipython installed on your computer, other Python shells are available, such
as the plain Python shell started by typing “python” in a terminal, or the Idle interpreter. However,
we advise to use the Ipython shell because of its enhanced features, especially for interactive scientific
computing.
Once you have started the interpreter, type
>>> print("Hello, world!")

Hello, world!
Tip: The message “Hello, world!” is then displayed. You just executed your first Python instruction,
congratulations!
To get yourself started, type the following stack of instructions
>>> a = 3
>>> b = 2*a
>>> type(b)
<class 'int'>
>>> print(b)
6
>>> a*b
18
>>> b = 'hello'
>>> type(b)
<class 'str'>
>>> b + b
'hellohello'
>>> 2*b
'hellohello'
Tip: Two variables a and b have been defined above. Note that one does not declare the type of a
variable before assigning its value. In C, conversely, one should write:
2.1. First steps 13

int a = 3;
In addition, the type of a variable may change, in the sense that at one point in time it can be equal
to a value of a certain type, and a second point in time, it can be equal to a value of a different type.
b was first equal to an integer, but it became equal to a string when it was assigned the value ‘hello’.
Operations on integers (b=2*a) are coded natively in Python, and so are some operations on strings such
as additions and multiplications, which amount respectively to concatenation and repetition.
2.2 Basic types
2.2.1 Numerical types
Tip: Python supports the following numerical, scalar types:
Integer
>>> 1 + 1
2
>>> a = 4
>>> type(a)
<class 'int'>
Floats
>>> c = 2.1
>>> type(c)
<class 'float'>
Complex
>>> a = 1.5 + 0.5j

>>> a.real
1.5
>>> a.imag
0.5
>>> type(1. + 0j)
<class 'complex'>
Booleans
>>> 3 > 4
False
>>> test = (3 > 4)
>>> test
False
>>> type(test)
<class 'bool'>
Tip: A Python shell can therefore replace your pocket calculator, with the basic arithmetic operations
+, -, *, /, % (modulo) natively implemented
2.2. Basic types 14

>>> 7 * 3.
21.0
>>> 2**10
1024
>>> 8 % 3
2
Type conversion (casting):
>>> float(1)
1.0
2.2.2 Containers
Tip: Python provides many efficient types of containers, in which collections of objects can be stored.
Lists
Tip: A list is an ordered collection of objects, that may have different types. For example:
>>> colors = ['red', 'blue', 'green', 'black', 'white']

>>> type(colors)
<class 'list'>
Indexing: accessing individual objects contained in the list:
>>> colors[2]
'green'
Counting from the end with negative indices:
>>> colors[-1]
'white'
>>> colors[-2]
'black'
Warning: Indexing starts at 0 (as in C), not at 1 (as in Fortran or Matlab)!
Slicing: obtaining sublists of regularly-spaced elements:
>>> colors
['red', 'blue', 'green', 'black', 'white']
>>> colors[2:4]
['green', 'black']
Warning: Note that colors[start:stop] contains the elements with indices i such as start<=
i < stop (i ranging from start to stop-1). Therefore, colors[start:stop] has (stop - start)
elements.
2.2. Basic types 15

Slicing syntax: colors[start:stop:stride]
Tip: All slicing parameters are optional:

>>> colors
>>> colors[3:]
['black', 'white']
>>> colors[:3]
['red', 'blue', 'green']
>>> colors[::2]
['red', 'green', 'white']
Lists are mutable objects and can be modified:

>>> colors[0] = 'yellow'
>>> colors
['yellow', 'blue', 'green', 'black', 'white']
>>> colors[2:4] = ['gray', 'purple']
>>> colors
['yellow', 'blue', 'gray', 'purple', 'white']
Note: The elements of a list may have different types:

>>> colors = [3, -200, 'hello']
>>> colors
[3, -200, 'hello']
>>> colors[1], colors[2]
(-200, 'hello')
Tip: For collections of numerical data that all have the same type, it is often more efficient to use the
array type provided by the numpy module. A NumPy array is a chunk of memory containing fixed-sized
items. With NumPy arrays, operations on elements can be faster because elements are regularly spaced
in memory and more operations are performed through specialized C functions instead of Python loops.
Tip: Python offers a large panel of functions to modify lists, or query them. Here are a few examples;
for more details, see https://docs.python.org/3/tutorial/datastructures.html#more-on-lists
Add and remove elements:
>>> colors = ['red', 'blue', 'green', 'black', 'white']

>>> colors.append('pink')
>>> colors
['red', 'blue', 'green', 'black', 'white', 'pink']
>>> colors.pop() # removes and returns the last item
'pink'
>>> colors
>>> colors.extend(['pink', 'purple']) # extend colors, in-place
>>> colors
['red', 'blue', 'green', 'black', 'white', 'pink', 'purple']
>>> colors = colors[:-2]
2.2. Basic types 16


>>> colors
Reverse:
>>> rcolors = colors[::-1]

>>> rcolors
['white', 'black', 'green', 'blue', 'red']
>>> rcolors2 = list(colors) # new object that is a copy of colors in a different␣
˓→memory area
>>> rcolors2
>>> rcolors2.reverse() # in-place; reversing rcolors2 does not affect colors
>>> rcolors2
Concatenate and repeat lists:
>>> rcolors + colors

['white', 'black', 'green', 'blue', 'red', 'red', 'blue', 'green', 'black', 'white']
>>> rcolors * 2
['white', 'black', 'green', 'blue', 'red', 'white', 'black', 'green', 'blue', 'red']
Tip: Sort:
>>> sorted(rcolors) # new object

['black', 'blue', 'green', 'red', 'white']
>>> rcolors
>>> rcolors.sort() # in-place
>>> rcolors
['black', 'blue', 'green', 'red', 'white']
Methods and Object-Oriented Programming
The notation rcolors.method() (e.g. rcolors.append(3) and colors.pop()) is our first example
of object-oriented programming (OOP). Being a list, the object rcolors owns the method function
that is called using the notation .. No further knowledge of OOP than understanding the notation .
is necessary for going through this tutorial.
Discovering methods:
Reminder: in Ipython: tab-completion (press tab)

In [1]: rcolors.<TAB>
append() count() insert() reverse()
clear() extend() pop() sort()
copy() index() remove()
2.2. Basic types 17

Strings
Different string syntaxes (simple, double or triple quotes):
s = 'Hello, how are you?'

s = "Hi, what's up"
s = '''Hello,
how are you''' # tripling the quotes allows the
# string to span more than one line
s = """Hi,
what's up?"""
In [2]: 'Hi, what's up?'

Cell In[2], line 1
'Hi, what's up?'
^
SyntaxError: unterminated string literal (detected at line 1)
This syntax error can be avoided by enclosing the string in double quotes instead of single quotes.
Alternatively, one can prepend a backslash to the second single quote. Other uses of the backslash are,
e.g., the newline character \n and the tab character \t.
Tip: Strings are collections like lists. Hence they can be indexed and sliced, using the same syntax and
rules.
Indexing:
>>> a = "hello"
>>> a[0]
'h'
>>> a[1]
'e'
>>> a[-1]
'o'
Tip: (Remember that negative indices correspond to counting from the right end.)
Slicing:
>>> a = "hello, world!"

>>> a[3:6] # 3rd to 6th (excluded) elements: elements 3, 4, 5
'lo,'
>>> a[2:10:2] # Syntax: a[start:stop:step]
'lo o'
>>> a[::3] # every three characters, from beginning to end
'hl r!'
Tip: Accents and special characters can also be handled as in Python 3 strings consist of Unicode
characters.
A string is an immutable object and it is not possible to modify its contents. One may however create
new strings from the original one.
2.2. Basic types 18

In [3]: a = "hello, world!"
In [4]: a.replace('l', 'z', 1)

Out[4]: 'hezlo, world!'
Tip: Strings have many useful methods, such as a.replace as seen above. Remember the a. object-
oriented notation and use tab completion or help(str) to search for new methods.
See also:
Python offers advanced possibilities for manipulating strings, looking for patterns or formatting. The
interested reader is referred to https://docs.python.org/3/library/stdtypes.html#string-methods and
https://docs.python.org/3/library/string.html#format-string-syntax
String formatting:
>>> 'An integer: %i ; a float: %f ; another string: %s ' % (1, 0.1, 'string') # with␣
˓→more values use tuple after %
'An integer: 1; a float: 0.100000; another string: string'
>>> i = 102
>>> filename = 'processing_of_dataset_%d .txt' % i # no need for tuples with just␣
˓→one value after %
>>> filename
'processing_of_dataset_102.txt'
Dictionaries
Tip: A dictionary is basically an efficient table that maps keys to values.
>>> tel = {'emmanuelle': 5752, 'sebastian': 5578}

>>> tel['francis'] = 5915
>>> tel
{'emmanuelle': 5752, 'sebastian': 5578, 'francis': 5915}
>>> tel['sebastian']
5578
>>> tel.keys()
dict_keys(['emmanuelle', 'sebastian', 'francis'])
>>> tel.values()
dict_values([5752, 5578, 5915])
>>> 'francis' in tel
True
Tip: It can be used to conveniently store and retrieve values associated with a name (a string for a
date, a name, etc.). See https://docs.python.org/3/tutorial/datastructures.html#dictionaries for more
information.
A dictionary can have keys (resp. values) with different types:
>>> d = {'a':1, 'b':2, 3:'hello'}

>>> d
{'a': 1, 'b': 2, 3: 'hello'}
2.2. Basic types 19

More container types
Tuples
Tuples are basically immutable lists. The elements of a tuple are written between parentheses, or just
separated by commas:
>>> t = 12345, 54321, 'hello!'

>>> t[0]
12345
>>> t
(12345, 54321, 'hello!')
>>> u = (0, 2)
Sets: unordered, unique items:
>>> s = set(('a', 'b', 'c', 'a'))

>>> s
{'a', 'b', 'c'}
>>> s.difference(('a', 'b'))
{'c'}
2.2.3 Assignment operator
Tip: Python library reference says:

Assignment statements are used to (re)bind names to values and to modify attributes or
items of mutable objects.
In short, it works as follows (simple assignment):
1. an expression on the right hand side is evaluated, the corresponding object is created/obtained
2. a name on the left hand side is assigned, or bound, to the r.h.s. object
Things to note:
• a single object can have several names bound to it:
In [5]: a = [1, 2, 3]
• to change a list in place, use indexing/slices:
In [6]: a = [1, 2, 3]
• the key concept here is mutable vs. immutable

– mutable objects can be changed in place
– immutable objects cannot be modified once created
See also:
A very good and detailed explanation of the above issues can be found in David M. Beazley’s article
Types and Objects in Python.
2.2. Basic types 20

2.3 Control Flow
Controls the order in which the code is executed.
2.3.1 if/elif/else
>>> if 2**2 == 4:
... print("Obvious!")
...
Obvious!
Blocks are delimited by indentation
Tip: Type the following lines in your Python interpreter, and be careful to respect the indentation
depth. The Ipython shell automatically increases the indentation depth after a colon : sign; to decrease
the indentation depth, go four spaces to the left with the Backspace key. Press the Enter key twice to
leave the logical block.
>>> a = 10
>>> if a == 1:
... print(1)
... elif a == 2:
... print(2)
... else:
... print("A lot")
...
A lot
Indentation is compulsory in scripts as well. As an exercise, re-type the previous lines with the same
indentation in a script condition.py, and execute the script with run condition.py in Ipython.
2.3.2 for/range
Iterating with an index:
>>> for i in range(4):

... print(i)
0
1
2
3
But most often, it is more readable to iterate over values:
>>> for word in ('cool', 'powerful', 'readable'):

... print('Python is %s ' % word)
Python is cool
Python is powerful
Python is readable
2.3. Control Flow 21

2.3.3 while/break/continue
Typical C-style while loop (Mandelbrot problem):
>>> z = 1 + 1j
>>> while abs(z) < 100:
... z = z**2 + 1
>>> z
(-134+352j)
More advanced features

break out of enclosing for/while loop:
>>> z = 1 + 1j
>>> while abs(z) < 100:

... if z.imag == 0:
... break
... z = z**2 + 1
continue the next iteration of a loop.:
>>> a = [1, 0, 2, 4]
>>> for element in a:
... if element == 0:
... continue
... print(1. / element)
1.0
0.5
0.25
2.3.4 Conditional Expressions
if <OBJECT>
Evaluates to False:
• any number equal to zero (0, 0.0, 0+0j)
• an empty container (list, tuple, set, dictionary, . . . )
• False, None
Evaluates to True:
• everything else
a == b
Tests equality, with logics:
>>> 1 == 1.
True
a is b
Tests identity: both sides are the same object:
>>> a = 1
>>> b = 1.
>>> a == b
True


>>> a is b
False
>>> a = 1
>>> b = 1
>>> a is b
True
a in b
For any collection b: b contains a
>>> b = [1, 2, 3]
>>> 2 in b
True
>>> 5 in b
False
If b is a dictionary, this tests that a is a key of b.
2.3.5 Advanced iteration
Iterate over any sequence
You can iterate over any sequence (string, list, keys in a dictionary, lines in a file, . . . ):
>>> vowels = 'aeiouy'
>>> for i in 'powerful':

... if i in vowels:
... print(i)
o
e
u
>>> message = "Hello how are you?"

>>> message.split() # returns a list
['Hello', 'how', 'are', 'you?']
>>> for word in message.split():
... print(word)
...
Hello
how
are
you?
Tip: Few languages (in particular, languages for scientific computing) allow to loop over anything but
integers/indices. With Python it is possible to loop exactly over the objects of interest without bothering
with indices you often don’t care about. This feature can often be used to make code more readable.
Warning: Not safe to modify the sequence you are iterating over.

Keeping track of enumeration number
Common task is to iterate over a sequence while keeping track of the item number.
• Could use while loop with a counter as above. Or a for loop:
>>> words = ('cool', 'powerful', 'readable')

>>> for i in range(0, len(words)):
... print((i, words[i]))
(0, 'cool')
(1, 'powerful')
(2, 'readable')
• But, Python provides a built-in function - enumerate - for this:
>>> for index, item in enumerate(words):

... print((index, item))
(0, 'cool')
(1, 'powerful')
(2, 'readable')
Looping over a dictionary
Use items:
>>> d = {'a': 1, 'b':1.2, 'c':1j}
>>> for key, val in sorted(d.items()):

... print('Key: %s has value: %s ' % (key, val))
Key: a has value: 1
Key: b has value: 1.2
Key: c has value: 1j
Note: The ordering of a dictionary is random, thus we use sorted() which will sort on the keys.
2.3.6 List Comprehensions
Instead of creating a list by means of a loop, one can make use of a list comprehension with a rather
self-explaining syntax.
>>> [i**2 for i in range(4)]

[0, 1, 4, 9]
Exercise
Compute the decimals of Pi using the Wallis formula:

∞
∏︁ 4𝑖2
𝜋=2
𝑖=1
4𝑖2 − 1

2.4 Defining functions
2.4.1 Function definition
In [1]: def test():

...: print('in test function')
...:
...:
In [2]: test()
in test function
Warning: Function blocks must be indented as other control-flow blocks.
2.4.2 Return statement
Functions can optionally return values.
In [3]: def disk_area(radius):

...: return 3.14 * radius * radius
...:
In [4]: disk_area(1.5)
Out[4]: 7.0649999999999995
Note: By default, functions return None.
Note: Note the syntax to define a function:

• the def keyword;
• is followed by the function’s name, then
• the arguments of the function are given between parentheses followed by a colon.
• the function body;
• and return object for optionally returning values.
2.4.3 Parameters
Mandatory parameters (positional arguments)
In [5]: def double_it(x):

...: return x * 2
...:
In [6]: double_it(3)
Out[6]: 6
In [7]: double_it()
---------------------------------------------------------------------------
2.4. Defining functions 25


TypeError Traceback (most recent call last)
Cell In[7], line 1
----> 1 double_it()
TypeError: double_it() missing 1 required positional argument: 'x'
Optional parameters (keyword or named arguments)
In [8]: def double_it(x=2):

...: return x * 2
...:
In [9]: double_it()
Out[9]: 4
In [10]: double_it(3)
Out[10]: 6
Keyword arguments allow you to specify default values.
Warning: Default values are evaluated when the function is defined, not when it is called. This
can be problematic when using mutable types (e.g. dictionary or list) and modifying them in the
function body, since the modifications will be persistent across invocations of the function.
Using an immutable type in a keyword argument:
In [11]: bigx = 10
In [12]: def double_it(x=bigx):

....: return x * 2
....:
In [13]: bigx = 1e9 # Now really big
In [14]: double_it()
Out[14]: 20
Using an mutable type in a keyword argument (and modifying it inside the function body):
In [15]: def add_to_dict(args={'a': 1, 'b': 2}):
....: for i in args.keys():
....: args[i] += 1
....: print(args)
....:
In [16]: add_to_dict
Out[16]: <function __main__.add_to_dict(args={'a': 1, 'b': 2})>
In [17]: add_to_dict()
{'a': 2, 'b': 3}
{'a': 3, 'b': 4}
{'a': 4, 'b': 5}

Tip: More involved example implementing python’s slicing:

In [20]: def slicer(seq, start=None, stop=None, step=None):
....: """Implement basic python slicing."""
....: return seq[start:stop:step]
....:
In [21]: rhyme = 'one fish, two fish, red fish, blue fish'.split()
In [22]: rhyme
Out[22]: ['one', 'fish,', 'two', 'fish,', 'red', 'fish,', 'blue', 'fish']
In [23]: slicer(rhyme)
Out[23]: ['one', 'fish,', 'two', 'fish,', 'red', 'fish,', 'blue', 'fish']
In [24]: slicer(rhyme, step=2)

Out[24]: ['one', 'two', 'red', 'blue']
In [25]: slicer(rhyme, 1, step=2)

Out[25]: ['fish,', 'fish,', 'fish,', 'fish']
In [26]: slicer(rhyme, start=1, stop=4, step=2)

Out[26]: ['fish,', 'fish,']
The order of the keyword arguments does not matter:
In [27]: slicer(rhyme, step=2, start=1, stop=4)

Out[27]: ['fish,', 'fish,']
but it is good practice to use the same ordering as the function’s definition.
Keyword arguments are a very convenient feature for defining functions with a variable number of argu-
ments, especially when default values are to be used in most calls to the function.
2.4.4 Passing by value
Tip: Can you modify the value of a variable inside a function? Most languages (C, Java, . . . ) distinguish
“passing by value” and “passing by reference”. In Python, such a distinction is somewhat artificial, and
it is a bit subtle whether your variables are going to be modified or not. Fortunately, there exist clear
rules.
Parameters to functions are references to objects, which are passed by value. When you pass a variable
to a function, python passes the reference to the object to which the variable refers (the value). Not the
variable itself.
If the value passed in a function is immutable, the function does not modify the caller’s variable. If the
value is mutable, the function may modify the caller’s variable in-place:
>>> def try_to_modify(x, y, z):
... x = 23
... y.append(42)
... z = [99] # new reference
... print(x)
... print(y)
... print(z)


...
>>> a = 77 # immutable variable
>>> b = [99] # mutable variable
>>> c = [28]
>>> try_to_modify(a, b, c)
23
[99, 42]
[99]
>>> print(a)
77
>>> print(b)
[99, 42]
>>> print(c)
[28]
Functions have a local variable table called a local namespace.

The variable x only exists within the function try_to_modify.
2.4.5 Global variables
Variables declared outside the function can be referenced within the function:
In [28]: x = 5
In [29]: def addx(y):

....: return x + y
....:
In [30]: addx(10)
Out[30]: 15
But these “global” variables cannot be modified within the function, unless declared global in the
function.
This doesn’t work:
In [31]: def setx(y):

....: x = y
....: print('x is %d ' % x)
....:
....:
In [32]: setx(10)
x is 10
In [33]: x
Out[33]: 5
This works:
In [34]: def setx(y):

....: global x
....: x = y
....: print('x is %d ' % x)
....:
....:

In [35]: setx(10)
x is 10
In [36]: x
Out[36]: 10
2.4.6 Variable number of parameters
Special forms of parameters:

• *args: any number of positional arguments packed into a tuple
• **kwargs: any number of keyword arguments packed into a dictionary
In [37]: def variable_args(*args, **kwargs):

....: print('args is', args)
....: print('kwargs is', kwargs)
....:
In [38]: variable_args('one', 'two', x=1, y=2, z=3)

args is ('one', 'two')
kwargs is {'x': 1, 'y': 2, 'z': 3}
2.4.7 Docstrings
Documentation about what the function does and its parameters. General convention:
In [39]: def funcname(params):

....: """Concise one-line sentence describing the function.
....:
....: Extended summary which can contain multiple paragraphs.
....: """
....: # function body
....: pass
....:
In [40]: funcname?
Signature: funcname(params)
Docstring:
Concise one-line sentence describing the function.
Extended summary which can contain multiple paragraphs.
File: ~/src/scientific-python-lectures/<ipython-input-13-64e466df6d64>
Type: function
Note: Docstring guidelines

For the sake of standardization, the Docstring Conventions webpage documents the semantics and con-
ventions associated with Python docstrings.
Also, the NumPy and SciPy modules have defined a precise standard for documenting scientific functions,
that you may want to follow for your own functions, with a Parameters section, an Examples section,
etc. See https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard

2.4.8 Functions are objects
Functions are first-class objects, which means they can be:

• assigned to a variable
• an item in a list (or any collection)
• passed as an argument to another function.
In [41]: va = variable_args
In [42]: va('three', x=1, y=2)

args is ('three',)
kwargs is {'x': 1, 'y': 2}
2.4.9 Methods
Methods are functions attached to objects. You’ve seen these in our examples on lists, dictionaries,
strings, etc. . .
2.4.10 Exercises
Exercise: Fibonacci sequence
Write a function that displays the n first terms of the Fibonacci sequence, defined by:
⎧
⎨ 𝑈0 = 0
𝑈1 = 1
𝑈𝑛+2 = 𝑈𝑛+1 + 𝑈𝑛
⎩
Exercise: Quicksort
Implement the quicksort algorithm, as defined by wikipedia
function quicksort(array)
var list less, greater
if length(array) < 2
return array
select and remove a pivot value pivot from array
for each x in array
if x < pivot + 1 then append x to less
else append x to greater
return concatenate(quicksort(less), pivot, quicksort(greater))

2.5 Reusing code: scripts and modules
For now, we have typed all instructions in the interpreter. For longer sets of instructions we need to
change track and write the code in text files (using a text editor), that we will call either scripts or
modules. Use your favorite text editor (provided it offers syntax highlighting for Python), or the editor
that comes with the Scientific Python Suite you may be using.
2.5.1 Scripts
Tip: Let us first write a script, that is a file with a sequence of instructions that are executed each
time the script is called. Instructions may be e.g. copied-and-pasted from the interpreter (but take care
to respect indentation rules!).
The extension for Python files is .py. Write or copy-and-paste the following lines in a file called test.py
message = "Hello how are you?"

for word in message.split():
print(word)
Tip: Let us now execute the script interactively, that is inside the Ipython interpreter. This is maybe
the most common use of scripts in scientific computing.
Note: in Ipython, the syntax to execute a script is %run script.py. For example,
In [1]: %run test.py

Hello
how
are
you?
In [2]: message
Out[2]: 'Hello how are you?'
The script has been executed. Moreover the variables defined in the script (such as message) are now
available inside the interpreter’s namespace.
Tip: Other interpreters also offer the possibility to execute scripts (e.g., execfile in the plain Python
interpreter, etc.).
It is also possible In order to execute this script as a standalone program, by executing the script inside
a shell terminal (Linux/Mac console or cmd Windows console). For example, if we are in the same
directory as the test.py file, we can execute this in a console:
$ python test.py
Hello
how
are
you?
Tip: Standalone scripts may also take command-line arguments
2.5. Reusing code: scripts and modules 31

In file.py:
import sys
print(sys.argv)
$ python file.py test arguments

['file.py', 'test', 'arguments']
Warning: Don’t implement option parsing yourself. Use a dedicated module such as argparse.
2.5.2 Importing objects from modules
In [3]: import os
In [4]: os
Out[4]: <module 'os' (frozen)>
In [5]: os.listdir('.')
Out[5]:
['profile_ck2k8f7z',
'profile_26m682xb',
'profile_9uubmu6o',
'profile_7mq49vl8',
'profile_3rb9vdbi',
'profile_y1p3rvyo',
'profile_kyykqxou',
'profile_dpqx0_vw',
'profile_pwzbmtp3',
'profile_4_9n3ryf',
'profile_9b7x_pag',
'clr-debug-pipe-1617-5179-in',
'profile_pc7fylc7',
'profile__p5h5ppc',
'profile_x4mstgaw',
'profile_310tdq6r',
'profile_pebpmsqb',
'profile__ywru9nv',
'profile_9chgyidj',
'profile_jwax2bhl',
'profile_qcv2_jni',
'profile_oc_h6zir',
'profile_t_0h4o8i',
'profile_c_2eyrp8',
'profile_lkjppp5x',
'clr-debug-pipe-1601-4963-out',
'profile_x2t_oxup',
'profile_hbj21aea',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-chrony.service-8HHZaX',
'profile_cesu8d60',
'profile_apx_iqtc',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-systemd-logind.service-n77a4k',


'profile_hljp9ndj',
'.font-unix',
'profile_odnphug0',
'profile_z8fuwnu4',
'profile_xdxzjzz7',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-haveged.service-xQvBRa',
'profile_6clt2rjv',
'profile_s4jdupe7',
'profile_2ezqschg',
'profile_pvbtrkwv',
'profile_mpl_stbo',
'profile_4eyx_j57',
'.X11-unix',
'profile_rqiwxfvj',
'profile_peqvaz3i',
'dotnet-diagnostic-1601-4963-socket',
'profile_zz6rwara',
'profile_f75dn8vq',
'profile_jux17vrr',
'.XIM-unix',
'profile_crzc5e8o',
'snap-private-tmp',
'profile_12eedl69',
'profile_5nrrvojn',
'profile_64yeljxq',
'profile_325dps4w',
'profile_7317plqv',
'profile_bdozhfn9',
'profile_h926ob79',
'www-data-temp-aspnet-0',
'profile_4n9he534',
'.ICE-unix',
'profile_b4xeiklx',
'profile_69sm2u8_',
'.Test-unix',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-systemd-resolved.service-4jB2qV',
'profile_et_7iubf',
'profile_rsy5e_95',
'profile_ua_gk06t',
'profile_e7z7326y',
'profile_lf71uewc',
'profile_mfkryvja',
'profile_zuw06usv']
And also:
In [6]: from os import listdir
Importing shorthands:
In [7]: import numpy as np

Warning:
from os import *
This is called the star import and please, Do not use it

• Makes the code harder to read and understand: where do symbols come from?
• Makes it impossible to guess the functionality by the context and the name (hint: os.name is
the name of the OS), and to profit usefully from tab completion.
• Restricts the variable names you can use: os.name might override name, or vise-versa.
• Creates possible name clashes between modules.
• Makes the code impossible to statically check for undefined symbols.
Tip: Modules are thus a good way to organize code in a hierarchical way. Actually, all the scientific
computing tools we are going to use are modules:
>>> import numpy as np # data arrays

>>> np.linspace(0, 10, 6)
array([ 0., 2., 4., 6., 8., 10.])
>>> import scipy as sp # scientific computing
2.5.3 Creating modules
Tip: If we want to write larger and better organized programs (compared to simple scripts), where
some objects are defined, (variables, functions, classes) and that we want to reuse several times, we have
to create our own modules.
Let us create a module demo contained in the file demo.py:
"A demo module."
def print_b():
"Prints b."
print("b")
def print_a():
"Prints a."
print("a")
c = 2
d = 2
Tip: In this file, we defined two functions print_a and print_b. Suppose we want to call the print_a
function from the interpreter. We could execute the file as a script, but since we just want to have access
to the function print_a, we are rather going to import it as a module. The syntax is as follows.

In [8]: import demo
In [9]: demo.print_a()
a
In [10]: demo.print_b()
b
Importing the module gives access to its objects, using the module.object syntax. Don’t forget to put
the module’s name before the object’s name, otherwise Python won’t recognize the instruction.
Introspection
In [11]: demo?
Type: module
Base Class: <type 'module'>
String Form: <module 'demo' from 'demo.py'>
Namespace: Interactive
File: /home/varoquau/Projects/Python_talks/scipy_2009_tutorial/source/
˓→demo.py
Docstring:
A demo module.
In [12]: who
demo
In [13]: whos
------------------------------
demo module <module 'demo' from 'demo.py'>
In [14]: dir(demo)
Out[14]:
['__builtins__',
'__doc__',
'__file__',
'__name__',
'__package__',
'c',
'd',
'print_a',
'print_b']
In [15]: demo.<TAB>
demo.c demo.print_a demo.py
demo.d demo.print_b demo.pyc
Importing objects from modules into the main namespace

In [16]: from demo import print_a, print_b
In [17]: whos
--------------------------------
demo module <module 'demo' from 'demo.py'>
print_a function <function print_a at 0xb7421534>
print_b function <function print_b at 0xb74214c4>


In [18]: print_a()
a
Warning: Module caching

Modules are cached: if you modify demo.py and re-import it in the old session, you will
get the old one.
Solution:
In [10]: importlib.reload(demo)
2.5.4 ‘__main__’ and module loading
Tip: Sometimes we want code to be executed when a module is run directly, but not when it is imported
by another module. if __name__ == '__main__' allows us to check whether the module is being run
directly.
File demo2.py:
def print_b():
"Prints b."
print("b")
def print_a():
"Prints a."
print("a")
# print_b() runs on import

print_b()
if __name__ == "__main__":
# print_a() is only executed when the module is run directly.
print_a()
Importing it:
In [19]: import demo2

b
In [20]: import demo2
Running it:
In [21]: %run demo2

b
a

2.5.5 Scripts or modules? How to organize your code
Note: Rule of thumb

• Sets of instructions that are called several times should be written inside functions for better code
reusability.
• Functions (or other bits of code) that are called from several scripts should be written inside a
module, so that only the module is imported in the different scripts (do not copy-and-paste your
functions in the different scripts!).
How modules are found and imported
When the import mymodule statement is executed, the module mymodule is searched in a given list of
directories. This list includes a list of installation-dependent default path (e.g., /usr/lib64/python3.
11) as well as the list of directories specified by the environment variable PYTHONPATH.
The list of directories searched by Python is given by the sys.path variable
In [22]: import sys
In [23]: sys.path
Out[23]:
['/home/runner/work/scientific-python-lectures/scientific-python-lectures',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python311.zip',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/lib-dynload',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages']
Modules must be located in the search path, therefore you can:

• write your own modules within directories already defined in the search path (e.g. $HOME/.venv/
lectures/lib64/python3.11/site-packages). You may use symbolic links (on Linux) to keep
the code somewhere else.
• modify the environment variable PYTHONPATH to include the directories containing the user-defined
modules.
Tip: On Linux/Unix, add the following line to a file read by the shell at startup (e.g. /etc/profile,
.profile)
export PYTHONPATH=$PYTHONPATH:/home/emma/user_defined_modules
On Windows, https://support.microsoft.com/kb/310519 explains how to handle environment vari-

ables.
• or modify the sys.path variable itself within a Python script.
Tip:
import sys
new_path = '/home/emma/user_defined_modules'
if new_path not in sys.path:
sys.path.append(new_path)

This method is not very robust, however, because it makes the code less portable (user-dependent
path) and because you have to add the directory to your sys.path each time you want to import
from a module in this directory.
See also:
See https://docs.python.org/3/tutorial/modules.html for more information about modules.
2.5.6 Packages
A directory that contains many modules is called a package. A package is a module with submodules
(which can have submodules themselves, etc.). A special file called __init__.py (which may be empty)
tells Python that the directory is a Python package, from which modules can be imported.
$ ls
_build_utils/ fft/ _lib/ odr/ spatial/
cluster/ fftpack/ linalg/ optimize/ special/
conftest.py __init__.py linalg.pxd optimize.pxd special.pxd
constants/ integrate/ meson.build setup.py stats/
datasets/ interpolate/ misc/ signal/
_distributor_init.py io/ ndimage/ sparse/
$ cd ndimage
$ ls
_filters.py __init__.py _measurements.py morphology.py src/
filters.py _interpolation.py measurements.py _ni_docstrings.py tests/
_fourier.py interpolation.py meson.build _ni_support.py utils/
fourier.py LICENSE.txt _morphology.py setup.py
From Ipython:
In [24]: import scipy as sp
In [25]: sp.__file__
Out[25]: '/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/scipy/__
˓→init__.py'
In [26]: sp.version.version
Out[26]: '1.12.0'
In [27]: sp.ndimage.morphology.binary_dilation?
Signature:
sp.ndimage.morphology.binary_dilation(
input,
structure=None,
iterations=1,
mask=None,
output=None,
border_value=0,
origin=0,
brute_force=False,
)
Docstring:
Multidimensional binary dilation with the given structuring element.
...

2.5.7 Good practices
• Use meaningful object names

• Indentation: no choice!
Tip: Indenting is compulsory in Python! Every command block following a colon bears an
additional indentation level with respect to the previous line with a colon. One must therefore
indent after def f(): or while:. At the end of such logical blocks, one decreases the indentation
depth (and re-increases it if a new block is entered, etc.)
Strict respect of indentation is the price to pay for getting rid of { or ; characters that delineate
logical blocks in other languages. Improper indentation leads to errors such as
------------------------------------------------------------
IndentationError: unexpected indent (test.py, line 2)
All this indentation business can be a bit confusing in the beginning. However, with the clear
indentation, and in the absence of extra characters, the resulting code is very nice to read compared
to other languages.
• Indentation depth: Inside your text editor, you may choose to indent with any positive number
of spaces (1, 2, 3, 4, . . . ). However, it is considered good practice to indent with 4 spaces. You
may configure your editor to map the Tab key to a 4-space indentation.
• Style guidelines
Long lines: you should not write very long lines that span over more than (e.g.) 80 characters.
Long lines can be broken with the \ character
>>> long_line = "Here is a very very long line \

... that we break in two parts."
Spaces
Write well-spaced code: put whitespaces after commas, around arithmetic operators, etc.:
>>> a = 1 # yes
>>> a=1 # too cramped
A certain number of rules for writing “beautiful” code (and more importantly using the same
conventions as anybody else!) are given in the Style Guide for Python Code.
Quick read
If you want to do a first quick pass through the Scientific Python Lectures to learn the ecosystem, you
can directly skip to the next chapter: NumPy: creating and manipulating numerical data.
The remainder of this chapter is not necessary to follow the rest of the intro part. But be sure to
come back and finish this chapter later.

2.6 Input and Output
To be exhaustive, here are some information about input and output in Python. Since we will use the
NumPy methods to read and write files, you may skip this chapter at first reading.
We write or read strings to/from files (other types must be converted to strings). To write in a file:
>>> f = open('workfile', 'w') # opens the workfile file

>>> type(f)
<class '_io.TextIOWrapper'>
>>> f.write('This is a test \nand another test')
>>> f.close()
To read from a file
In [1]: f = open('workfile', 'r')
In [2]: s = f.read()
In [3]: print(s)
This is a test
and another test
In [4]: f.close()
See also:
For more details: https://docs.python.org/3/tutorial/inputoutput.html
2.6.1 Iterating over a file
In [5]: f = open('workfile', 'r')
In [6]: for line in f:

...: print(line)
...:
This is a test
and another test
In [7]: f.close()
File modes
• Read-only: r
• Write-only: w
– Note: Create a new file or overwrite existing file.
• Append a file: a
• Read and Write: r+
• Binary mode: b
– Note: Use for binary files, especially on Windows.
2.6. Input and Output 40

2.7 Standard Library
Note: Reference document for this section:

• The Python Standard Library documentation: https://docs.python.org/3/library/index.html
• Python Essential Reference, David Beazley, Addison-Wesley Professional
2.7.1 os module: operating system functionality
“A portable way of using operating system dependent functionality.”
Directory and file manipulation
Current directory:
In [1]: os.getcwd()
Out[1]: '/tmp'
List a directory:
In [2]: os.listdir(os.curdir)
Out[2]:
['profile_ck2k8f7z',
'profile_26m682xb',
'profile_9uubmu6o',
'profile_7mq49vl8',
'profile_3rb9vdbi',
'profile_y1p3rvyo',
'profile_kyykqxou',
'profile_dpqx0_vw',
'profile_pwzbmtp3',
'profile_ihf87a62',
'profile_hwt5gl3k',
'profile_4_9n3ryf',
'profile_vla8egnu',
'profile_9b7x_pag',
'profile_pc7fylc7',
'profile__p5h5ppc',
'profile_x4mstgaw',
'profile_310tdq6r',
'profile_pebpmsqb',
'profile__ywru9nv',
'profile_9chgyidj',
'profile_jwax2bhl',
'profile_qcv2_jni',
'profile_i9q659ew',
'profile_oc_h6zir',
'profile_t_0h4o8i',
'profile_c_2eyrp8',
'profile_lkjppp5x',
'profile_x2t_oxup',
2.7. Standard Library 41


'profile_hbj21aea',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-chrony.service-8HHZaX',
'profile_cesu8d60',
'profile_spqcyhij',
'profile_apx_iqtc',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-systemd-logind.service-n77a4k',
'profile_4alaajpc',
'profile_hljp9ndj',
'.font-unix',
'profile_odnphug0',
'profile_z8fuwnu4',
'profile_xdxzjzz7',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-haveged.service-xQvBRa',
'profile_6clt2rjv',
'profile_s4jdupe7',
'profile_2ezqschg',
'profile_lyr8jq60',
'profile_7laigamd',
'profile_pvbtrkwv',
'profile_2t63ypn4',
'profile_mpl_stbo',
'profile_4eyx_j57',
'.X11-unix',
'profile_rqiwxfvj',
'profile_peqvaz3i',
'profile_zz6rwara',
'profile_f75dn8vq',
'profile_jux17vrr',
'.XIM-unix',
'profile_2f16_1a8',
'profile_crzc5e8o',
'snap-private-tmp',
'profile_12eedl69',
'profile_5nrrvojn',
'profile_64yeljxq',
'profile_325dps4w',
'profile_7317plqv',
'profile_bdozhfn9',
'profile_h926ob79',
'www-data-temp-aspnet-0',
'profile_4n9he534',
'.ICE-unix',
'profile_b4xeiklx',
'profile_69sm2u8_',
'.Test-unix',
'systemd-private-3795adbe5b1b42309183d6a067bccaf5-systemd-resolved.service-4jB2qV',
'profile_et_7iubf',
'profile_rsy5e_95',
'profile_ua_gk06t',
'profile_e7z7326y',


'profile_lf71uewc',
'profile_mfkryvja',
'profile_pe2iwp3d',
'profile_zuw06usv']
Make a directory:
In [3]: os.mkdir('junkdir')
In [4]: 'junkdir' in os.listdir(os.curdir)

Out[4]: True
Rename the directory:

In [5]: os.rename('junkdir', 'foodir')
In [6]: 'junkdir' in os.listdir(os.curdir)

Out[6]: False
In [7]: 'foodir' in os.listdir(os.curdir)

Out[7]: True
In [8]: os.rmdir('foodir')
In [9]: 'foodir' in os.listdir(os.curdir)

Out[9]: False
Delete a file:
In [10]: fp = open('junk.txt', 'w')
In [11]: fp.close()
In [12]: 'junk.txt' in os.listdir(os.curdir)

Out[12]: True
In [13]: os.remove('junk.txt')
In [14]: 'junk.txt' in os.listdir(os.curdir)

Out[14]: False
os.path: path manipulations
os.path provides common operations on pathnames.
In [15]: fp = open('junk.txt', 'w')
In [16]: fp.close()
In [17]: a = os.path.abspath('junk.txt')
In [18]: a
Out[18]: '/tmp/junk.txt'
In [19]: os.path.split(a)
Out[19]: ('/tmp', 'junk.txt')

In [20]: os.path.dirname(a)
Out[20]: '/tmp'
In [21]: os.path.basename(a)
Out[21]: 'junk.txt'
In [22]: os.path.splitext(os.path.basename(a))
Out[22]: ('junk', '.txt')
In [23]: os.path.exists('junk.txt')
Out[23]: True
In [24]: os.path.isfile('junk.txt')
Out[24]: True
In [25]: os.path.isdir('junk.txt')
Out[25]: False
In [26]: os.path.expanduser('~/local')
Out[26]: '/home/runner/local'
In [27]: os.path.join(os.path.expanduser('~'), 'local', 'bin')

Out[27]: '/home/runner/local/bin'
Running an external command
In [28]: os.system('ls')
Out[28]: 0
Note: Alternative to os.system

A noteworthy alternative to os.system is the sh module. Which provides much more convenient ways
to obtain the output, error stream and exit code of the external command.
In [29]: import sh
In [20]: com = sh.ls()
In [30]: print(com)
basic_types.rst exceptions.rst oop.rst standard_library.rst
control_flow.rst first_steps.rst python_language.rst
demo2.py functions.rst python-logo.png
demo.py io.rst reusing_code.rst
In [31]: print(com.exit_code)
0
In [23]: type(com)
Out[31]: sh.RunningCommand

Walking a directory
os.path.walk generates a list of filenames in a directory tree.
In [32]: for dirpath, dirnames, filenames in os.walk(os.curdir):

....: for fp in filenames:
....: print(os.path.abspath(fp))
....:
....:
/tmp/clr-debug-pipe-1617-5179-in
/tmp/clr-debug-pipe-1601-4963-out
/tmp/dotnet-diagnostic-1601-4963-socket
/tmp/junk.txt
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README


/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/dhist
/tmp/bookmarks
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
/tmp/README
Environment variables:
In [33]: import os
In [34]: os.environ.keys()
Out[34]:
['_',
'FSLDIR',
'TERM_PROGRAM_VERSION',
'FSLREMOTECALL',
'USER',


'HOME',
'PATH',
'PS1',
'SHELL',
'EDITOR',
'WORKON_HOME',
'PYTHONPATH',
...
In [35]: os.environ['PYTHONPATH']
Out[35]: '.:/Users/cburns/src/utils:/Users/cburns/src/nitools:
/Users/cburns/local/lib/python2.5/site-packages/:
/usr/local/lib/python2.5/site-packages/:
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5'
In [36]: os.getenv('PYTHONPATH')
Out[36]: '.:/Users/cburns/src/utils:/Users/cburns/src/nitools:
/Users/cburns/local/lib/python2.5/site-packages/:
/usr/local/lib/python2.5/site-packages/:
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5'
2.7.2 shutil: high-level file operations
The shutil provides useful file operations:

• shutil.rmtree: Recursively delete a directory tree.
• shutil.move: Recursively move a file or directory to another location.
• shutil.copy: Copy files or directories.
2.7.3 glob: Pattern matching on files
The glob module provides convenient file pattern matching.

Find all files ending in .txt:
In [37]: import glob
In [38]: glob.glob('*.txt')
Out[38]: ['junk.txt']
2.7.4 sys module: system-specific information
System-specific information related to the Python interpreter.

• Which version of python are you running and where is it installed:
In [39]: sys.platform
Out[39]: 'linux'
In [40]: sys.version
Out[40]: '3.11.8 (main, Feb 7 2024, 04:02:05) [GCC 11.4.0]'
In [41]: sys.prefix
Out[41]: '/opt/hostedtoolcache/Python/3.11.8/x64'

• List of command line arguments passed to a Python script:
In [42]: sys.argv
Out[42]:
['/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/sphinx/__
˓→main__.py',
'-b',
'latex',
'-d',
'build/doctrees',
'.',
'build/latex']
sys.path is a list of strings that specifies the search path for modules. Initialized from PYTHONPATH:
In [43]: sys.path
Out[43]:
['/home/runner/work/scientific-python-lectures/scientific-python-lectures',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python311.zip',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/lib-dynload',
'/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages']
2.7.5 pickle: easy persistence
Useful to store arbitrary objects to a file. Not safe or fast!
In [44]: import pickle
In [45]: l = [1, None, 'Stan']
In [46]: with open('test.pkl', 'wb') as file:

....: pickle.dump(l, file)
....:
In [47]: with open('test.pkl', 'rb') as file:

....: out = pickle.load(file)
....:
In [48]: out
Out[48]: [1, None, 'Stan']
Exercise
Write a program to search your PYTHONPATH for the module site.py.
path_site

2.8 Exception handling in Python
It is likely that you have raised Exceptions if you have typed all the previous commands of the tutorial.
For example, you may have raised an exception if you entered a command with a typo.
Exceptions are raised by different kinds of errors arising when executing Python code. In your own code,
you may also catch errors, or define custom error types. You may want to look at the descriptions of the
the built-in Exceptions when looking for the right exception type.
2.8.1 Exceptions
Exceptions are raised by errors in Python:
In [1]: 1/0
---------------------------------------------------------------------------
ZeroDivisionError Traceback (most recent call last)
Cell In[1], line 1
----> 1 1/0
ZeroDivisionError: division by zero
In [2]: 1 + 'e'
---------------------------------------------------------------------------
Cell In[2], line 1
----> 1 1 + 'e'
TypeError: unsupported operand type(s) for +: 'int' and 'str'
In [3]: d = {1:1, 2:2}
In [4]: d[3]
---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
Cell In[4], line 1
----> 1 d[3]
KeyError: 3
In [5]: l = [1, 2, 3]
In [6]: l[4]
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
Cell In[6], line 1
----> 1 l[4]
IndexError: list index out of range
In [7]: l.foobar
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[7], line 1
----> 1 l.foobar
AttributeError: 'list' object has no attribute 'foobar'
2.8. Exception handling in Python 49

As you can see, there are different types of exceptions for different errors.
2.8.2 Catching exceptions
try/except
In [8]: while True:

...: try:
...: x = int(input('Please enter a number: '))
...: break
...: except ValueError:
...: print('That was no valid number. Try again...')
...:
Please enter a number: a
That was no valid number. Try again...
Please enter a number: 1
In [9]: x
Out[9]: 1
try/finally
In [10]: try:
....: x = int(input('Please enter a number: '))
....: finally:
....: print('Thank you for your input')
....:
Please enter a number: a
Thank you for your input
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[10], line 2
1 try:
----> 2 x = int(input('Please enter a number: '))
3 finally:
4 print('Thank you for your input')
ValueError: invalid literal for int() with base 10: 'a'
Important for resource management (e.g. closing a file)
Easier to ask for forgiveness than for permission
In [11]: def print_sorted(collection):

....: try:
....: collection.sort()
....: except AttributeError:
....: pass # The pass statement does nothing
....: print(collection)
....:
In [12]: print_sorted([1, 3, 2])

[1, 2, 3]


In [13]: print_sorted(set((1, 3, 2)))
{1, 2, 3}
In [14]: print_sorted('132')
132
2.8.3 Raising exceptions
• Capturing and reraising an exception:
In [15]: def filter_name(name):

....: try:
....: name = name.encode('ascii')
....: except UnicodeError as e:
....: if name == 'Gaël':
....: print('OK, Gaël')
....: else:
....: raise e
....: return name
....:
In [16]: filter_name('Gaël')
OK, Gaël
Out[16]: 'Gaël'
In [17]: filter_name('Stéfan')
---------------------------------------------------------------------------
UnicodeEncodeError Traceback (most recent call last)
Cell In[17], line 1
----> 1 filter_name('Stéfan')
Cell In[15], line 8, in filter_name(name)

6 print('OK, Gaël')
7 else:
----> 8 raise e
9 return name
Cell In[15], line 3, in filter_name(name)

1 def filter_name(name):
2 try:
----> 3 name = name.encode('ascii')
4 except UnicodeError as e:
5 if name == 'Gaël':
UnicodeEncodeError: 'ascii' codec can't encode character '\xe9' in position 2:␣

˓→ordinal not in range(128)
• Exceptions to pass messages between parts of the code:
In [18]: def achilles_arrow(x):

....: if abs(x - 1) < 1e-3:
....: raise StopIteration
....: x = 1 - (1-x)/2.
....: return x
....:

In [19]: x = 0
In [20]: while True:

....: try:
....: x = achilles_arrow(x)
....: except StopIteration:
....: break
....:
....:
In [21]: x
Out[21]: 0.9990234375
Use exceptions to notify certain conditions are met (e.g. StopIteration) or not (e.g. custom error raising)
2.9 Object-oriented programming (OOP)
Python supports object-oriented programming (OOP). The goals of OOP are:

• to organize the code, and
• to reuse code in similar contexts.
Here is a small example: we create a Student class, which is an object gathering several custom functions
(methods) and variables (attributes), we will be able to use:
>>> class Student(object):

... def __init__(self, name):
... self.name = name
... def set_age(self, age):
... self.age = age
... def set_major(self, major):
... self.major = major
...
>>> anna = Student('anna')
>>> anna.set_age(21)
>>> anna.set_major('physics')
In the previous example, the Student class has __init__, set_age and set_major methods. Its at-
tributes are name, age and major. We can call these methods and attributes with the following notation:
classinstance.method or classinstance.attribute. The __init__ constructor is a special method
we call with: MyClass(init parameters if any).
Now, suppose we want to create a new class MasterStudent with the same methods and attributes as
the previous one, but with an additional internship attribute. We won’t copy the previous class, but
inherit from it:
>>> class MasterStudent(Student):

... internship = 'mandatory, from March to June'
...
>>> james = MasterStudent('james')
>>> james.internship
'mandatory, from March to June'
>>> james.set_age(23)
2.9. Object-oriented programming (OOP) 52


>>> james.age
23
The MasterStudent class inherited from the Student attributes and methods.
Thanks to classes and object-oriented programming, we can organize code with different classes corre-
sponding to different objects we encounter (an Experiment class, an Image class, a Flow class, etc.), with
their own methods and attributes. Then we can use inheritance to consider variations around a base
class and reuse code. Ex : from a Flow base class, we can create derived StokesFlow, TurbulentFlow,
PotentialFlow, etc.
2.9. Object-oriented programming (OOP) 53

CHAPTER 3
NumPy: creating and manipulating
numerical data
Authors: Emmanuelle Gouillart, Didrik Pinte, Gaël Varoquaux, and Pauli Virtanen
This chapter gives an overview of NumPy, the core tool for performant numerical computing with Python.
3.1 The NumPy array object
Section contents
• What are NumPy and NumPy arrays?

• Creating arrays
• Basic data types
• Basic visualization
• Indexing and slicing
• Copies and views
• Fancy indexing
54
3.1.1 What are NumPy and NumPy arrays?
NumPy arrays
Python objects
• high-level number objects: integers, floating point
• containers: lists (costless insertion and append), dictionaries (fast lookup)
NumPy provides
• extension package to Python for multi-dimensional arrays
• closer to hardware (efficiency)
• designed for scientific computation (convenience)
• Also known as array oriented computing
>>> import numpy as np

>>> a = np.array([0, 1, 2, 3])
>>> a
array([0, 1, 2, 3])
Tip: For example, An array containing:

• values of an experiment/simulation at discrete time steps
• signal recorded by a measurement device, e.g. sound wave
• pixels of an image, grey-level or colour
• 3-D data measured at different X-Y-Z positions, e.g. MRI scan
• ...
Why it is useful: Memory-efficient container that provides fast numerical operations.
In [1]: L = range(1000)
In [2]: %timeit [i**2 for i in L]

41.5 us +- 103 ns per loop (mean +- std. dev. of 7 runs, 10,000 loops each)
In [3]: a = np.arange(1000)
In [4]: %timeit a**2

883 ns +- 0.95 ns per loop (mean +- std. dev. of 7 runs, 1,000,000 loops each)
3.1. The NumPy array object 55

NumPy Reference documentation
• On the web: https://numpy.org/doc/

• Interactive help:
In [5]: np.array?
Docstring:
array(object, dtype=None, *, copy=True, order='K', subok=False, ndmin=0,
like=None)
Create an array.
Parameters
----------
object : array_like
An array, any object exposing the array interface, an object whose
``__array__`` method returns an array, or any (nested) sequence.
If object is a scalar, a 0-dimensional array containing object is
returned.
dtype : data-type, optional
The desired data-type for the array. If not given, NumPy will try to use
a default ``dtype`` that can represent the values (by applying promotion
rules when necessary.)
copy : bool, optional
If true (default), then the object is copied. Otherwise, a copy will
only be made if ``__array__`` returns a copy, if obj is a nested
sequence, or if a copy is needed to satisfy any of the other
requirements (``dtype``, `òrder``, etc.).
order : {'K', 'A', 'C', 'F'}, optional
Specify the memory layout of the array. If object is not an array, the
newly created array will be in C order (row major) unless 'F' is
specified, in which case it will be in Fortran order (column major).
If object is an array the following holds.
===== ========= ===================================================

order no copy copy=True
===== ========= ===================================================
'K' unchanged F & C order preserved, otherwise most similar order
'A' unchanged F order if input is F and not C, otherwise C order
'C' C order C order
'F' F order F order
===== ========= ===================================================
When ``copy=False`` and a copy is made for other reasons, the result is
the same as if ``copy=True``, with some exceptions for 'A', see the
Notes section. The default order is 'K'.
subok : bool, optional
If True, then sub-classes will be passed-through, otherwise
the returned array will be forced to be a base-class array (default).
ndmin : int, optional
Specifies the minimum number of dimensions that the resulting
array should have. Ones will be prepended to the shape as
needed to meet this requirement.
like : array_like, optional
Reference object to allow the creation of arrays which are not
NumPy arrays. If an array-like passed in as ``like`` supports
the ``__array_function__`` protocol, the result will be defined


by it. In this case, it ensures the creation of an array object
compatible with that passed in via this argument.
.. versionadded:: 1.20.0
Returns
-------
out : ndarray
An array object satisfying the specified requirements.
See Also
--------
empty_like : Return an empty array with shape and type of input.
ones_like : Return an array of ones with shape and type of input.
zeros_like : Return an array of zeros with shape and type of input.
full_like : Return a new array with shape of input filled with value.
empty : Return a new uninitialized array.
ones : Return a new array setting values to one.
zeros : Return a new array setting values to zero.
full : Return a new array of given shape filled with value.
Notes
-----
When order is 'A' and `òbject`` is an array in neither 'C' nor 'F' order,
and a copy is forced by a change in dtype, then the order of the result is
not necessarily 'C' as expected. This is likely a bug.
Examples
--------
>>> np.array([1, 2, 3])
array([1, 2, 3])
Upcasting:
>>> np.array([1, 2, 3.0])

array([ 1., 2., 3.])
More than one dimension:
>>> np.array([[1, 2], [3, 4]])

array([[1, 2],
[3, 4]])
Minimum dimensions 2:
>>> np.array([1, 2, 3], ndmin=2)

array([[1, 2, 3]])
Type provided:
>>> np.array([1, 2, 3], dtype=complex)

array([ 1.+0.j, 2.+0.j, 3.+0.j])
Data-type consisting of more than one element:


>>> x = np.array([(1,2),(3,4)],dtype=[('a','<i4'),('b','<i4')])
>>> x['a']
array([1, 3])
Creating an array from sub-classes:
>>> np.array(np.mat('1 2; 3 4'))

array([[1, 2],
[3, 4]])
>>> np.array(np.mat('1 2; 3 4'), subok=True)

matrix([[1, 2],
[3, 4]])
Type: builtin_function_or_method
• Looking for something:
>>> np.lookfor('create array')

Search results for 'create array'
---------------------------------
numpy.array
Create an array.
numpy.memmap
Create a memory-map to an array stored in a *binary* file on disk.
In [6]: np.con*?
np.concatenate
np.conj
np.conjugate
np.convolve
Import conventions
The recommended convention to import NumPy is:
3.1.2 Creating arrays
Manual construction of arrays
• 1-D:
>>> a = np.array([0, 1, 2, 3])

>>> a
array([0, 1, 2, 3])
>>> a.ndim
1
>>> a.shape
(4,)
>>> len(a)
4
• 2-D, 3-D, . . . :

>>> b = np.array([[0, 1, 2], [3, 4, 5]]) # 2 x 3 array

>>> b
array([[0, 1, 2],
[3, 4, 5]])
>>> b.ndim
2
>>> b.shape
(2, 3)
>>> len(b) # returns the size of the first dimension
2
>>> c = np.array([[[1], [2]], [[3], [4]]])

>>> c
array([[[1],
[2]],
[[3],
[4]]])
>>> c.shape
(2, 2, 1)
Exercise: Simple arrays
• Create a simple two dimensional array. First, redo the examples from above. And then create
your own: how about odd numbers counting backwards on the first row, and even numbers on
the second?
• Use the functions len(), numpy.shape() on these arrays. How do they relate to each other?
And to the ndim attribute of the arrays?
Functions for creating arrays
Tip: In practice, we rarely enter items one by one. . .
• Evenly spaced:
>>> a = np.arange(10) # 0 .. n-1 (!)

>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> b = np.arange(1, 9, 2) # start, end (exclusive), step
>>> b
array([1, 3, 5, 7])
• or by number of points:
>>> c = np.linspace(0, 1, 6) # start, end, num-points

>>> c
array([0. , 0.2, 0.4, 0.6, 0.8, 1. ])
>>> d = np.linspace(0, 1, 5, endpoint=False)
>>> d
array([0. , 0.2, 0.4, 0.6, 0.8])
• Common arrays:

>>> a = np.ones((3, 3)) # reminder: (3, 3) is a tuple

>>> a
array([[1., 1., 1.],
[1., 1., 1.],
[1., 1., 1.]])
>>> b = np.zeros((2, 2))
>>> b
array([[0., 0.],
[0., 0.]])
>>> c = np.eye(3)
>>> c
array([[1., 0., 0.],
[0., 1., 0.],
[0., 0., 1.]])
>>> d = np.diag(np.array([1, 2, 3, 4]))
>>> d
array([[1, 0, 0, 0],
[0, 2, 0, 0],
[0, 0, 3, 0],
[0, 0, 0, 4]])
• np.random: random numbers (Mersenne Twister PRNG):
>>> rng = np.random.default_rng(27446968)

>>> a = rng.random(4) # uniform in [0, 1]
>>> a
array([0.64613018, 0.48984931, 0.50851229, 0.22563948])
>>> b = rng.standard_normal(4) # Gaussian

>>> b
array([-0.38250769, -0.61536465, 0.98131732, 0.59353096])
Exercise: Creating arrays using functions
• Experiment with arange, linspace, ones, zeros, eye and diag.

• Create different kinds of arrays with random numbers.
• Try setting the seed before creating an array with random values.
• Look at the function np.empty. What does it do? When might this be useful?
3.1.3 Basic data types
You may have noticed that, in some instances, array elements are displayed with a trailing dot (e.g. 2.
vs 2). This is due to a difference in the data-type used:
>>> a = np.array([1, 2, 3])

>>> a.dtype
dtype('int64')
>>> b = np.array([1., 2., 3.])

>>> b.dtype
dtype('float64')
Tip: Different data-types allow us to store data more compactly in memory, but most of the time we

simply work with floating point numbers. Note that, in the example above, NumPy auto-detects the
data-type from the input.
You can explicitly specify which data-type you want:
>>> c = np.array([1, 2, 3], dtype=float)

>>> c.dtype
dtype('float64')
The default data type is floating point:
>>> a = np.ones((3, 3))

>>> a.dtype
dtype('float64')
There are also other types:

Complex
>>> d = np.array([1+2j, 3+4j, 5+6*1j])

>>> d.dtype
dtype('complex128')
Bool
>>> e = np.array([True, False, False, True])

>>> e.dtype
dtype('bool')
Strings
>>> f = np.array(['Bonjour', 'Hello', 'Hallo'])

>>> f.dtype # <--- strings containing max. 7 letters
dtype('<U7')
Much more
• int32
• int64
• uint32
• uint64
3.1.4 Basic visualization
Now that we have our first data arrays, we are going to visualize them.
Start by launching IPython:
$ ipython # or ipython3 depending on your install
Or the notebook:
$ jupyter notebook
Once IPython has started, enable interactive plots:

>>> %matplotlib
Or, from the notebook, enable plots in the notebook:
>>> %matplotlib inline
The inline is important for the notebook, so that plots are displayed in the notebook and not in a new
window.
Matplotlib is a 2D plotting package. We can import its functions as below:
>>> import matplotlib.pyplot as plt # the tidy way
And then use (note that you have to use show explicitly if you have not enabled interactive plots with
%matplotlib):
>>> plt.plot(x, y) # line plot

>>> plt.show() # <-- shows the plot (not needed with interactive plots)
Or, if you have enabled interactive plots with %matplotlib:
• 1D plotting:
>>> x = np.linspace(0, 3, 20)

>>> y = np.linspace(0, 9, 20)
[<matplotlib.lines.Line2D object at ...>]
>>> plt.plot(x, y, 'o') # dot plot
• 2D arrays (such as images):

>>> image = rng.random((30, 30))
>>> plt.imshow(image, cmap=plt.cm.hot)
<matplotlib.image.AxesImage object at ...>
>>> plt.colorbar()
<matplotlib.colorbar.Colorbar object at ...>

See also:
More in the: matplotlib chapter
Exercise: Simple visualizations
• Plot some simple arrays: a cosine as a function of time and a 2D matrix.

• Try using the gray colormap on the 2D matrix.
3.1.5 Indexing and slicing
The items of an array can be accessed and assigned to the same way as other Python sequences (e.g.
lists):
>>> a = np.arange(10)
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> a[0], a[2], a[-1]
(0, 2, 9)
Warning: Indices begin at 0, like other Python sequences (and C/C++). In contrast, in Fortran
or Matlab, indices begin at 1.
The usual python idiom for reversing a sequence is supported:
>>> a[::-1]
array([9, 8, 7, 6, 5, 4, 3, 2, 1, 0])
For multidimensional arrays, indices are tuples of integers:
>>> a = np.diag(np.arange(3))
>>> a
array([[0, 0, 0],
[0, 1, 0],
[0, 0, 2]])
>>> a[1, 1]
1
>>> a[2, 1] = 10 # third line, second column
>>> a


array([[ 0, 0, 0],
[ 0, 1, 0],
[ 0, 10, 2]])
>>> a[1]
array([0, 1, 0])
Note:
• In 2D, the first dimension corresponds to rows, the second to columns.
• for multidimensional a, a[0] is interpreted by taking all elements in the unspecified dimensions.
Slicing: Arrays, like other Python sequences can also be sliced:

>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> a[2:9:3] # [start:end:step]
array([2, 5, 8])
Note that the last index is not included! :
>>> a[:4]
array([0, 1, 2, 3])
All three slice components are not required: by default, start is 0, end is the last and step is 1:
>>> a[1:3]
array([1, 2])
>>> a[::2]
array([0, 2, 4, 6, 8])
>>> a[3:]
array([3, 4, 5, 6, 7, 8, 9])
A small illustrated summary of NumPy indexing and slicing. . .

>>> a[0, 3:5]
array([3, 4]) 0 1 2 3 4 5
>>> a[4:, 4:]
10 11 12 13 14 15
array([[44, 55],
[54, 55]]) 20 21 22 23 24 25
>>> a[:, 2]
30 31 32 33 34 35
a([2, 12, 22, 32, 42, 52])
>>> a[2::2, ::2] 40 41 42 43 44 45

array([[20, 22, 24],
50 51 52 53 54 55
[40, 42, 44]])
You can also combine assignment and slicing:

>>> a[5:] = 10
>>> a


array([ 0, 1, 2, 3, 4, 10, 10, 10, 10, 10])
>>> b = np.arange(5)
>>> a[5:] = b[::-1]
>>> a
array([0, 1, 2, 3, 4, 4, 3, 2, 1, 0])
Exercise: Indexing and slicing
• Try the different flavours of slicing, using start, end and step: starting from a linspace, try to
obtain odd numbers counting backwards, and even numbers counting forwards.
• Reproduce the slices in the diagram above. You may use the following expression to create the
array:
>>> np.arange(6) + np.arange(0, 51, 10)[:, np.newaxis]
array([[ 0, 1, 2, 3, 4, 5],
[10, 11, 12, 13, 14, 15],
[20, 21, 22, 23, 24, 25],
[30, 31, 32, 33, 34, 35],
[40, 41, 42, 43, 44, 45],
[50, 51, 52, 53, 54, 55]])
Exercise: Array creation
Create the following arrays (with correct data types):

[[1, 1, 1, 1],
[1, 1, 1, 1],
[1, 1, 1, 2],
[1, 6, 1, 1]]
[[0., 0., 0., 0., 0.],

[2., 0., 0., 0., 0.],
[0., 3., 0., 0., 0.],
[0., 0., 4., 0., 0.],
[0., 0., 0., 5., 0.],
[0., 0., 0., 0., 6.]]
Par on course: 3 statements for each

Hint: Individual array elements can be accessed similarly to a list, e.g. a[1] or a[1, 2].
Hint: Examine the docstring for diag.
Exercise: Tiling for array creation
Skim through the documentation for np.tile, and use this function to construct the array:
[[4, 3, 4, 3, 4, 3],
[2, 1, 2, 1, 2, 1],
[4, 3, 4, 3, 4, 3],
[2, 1, 2, 1, 2, 1]]

3.1.6 Copies and views
A slicing operation creates a view on the original array, which is just a way of accessing array data.
Thus the original array is not copied in memory. You can use np.may_share_memory() to check if two
arrays share the same memory block. Note however, that this uses heuristics and may give you false
positives.
When modifying the view, the original array is modified as well:
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> b = a[::2]
>>> b
array([0, 2, 4, 6, 8])
>>> np.may_share_memory(a, b)
True
>>> b[0] = 12
>>> b
array([12, 2, 4, 6, 8])
>>> a # (!)
array([12, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> c = a[::2].copy() # force a copy
>>> c[0] = 12
>>> a
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
>>> np.may_share_memory(a, c)
False
This behavior can be surprising at first sight. . . but it allows to save both memory and time.
Worked example: Prime number sieve
Compute prime numbers in 0–99, with a sieve

• Construct a shape (100,) boolean array is_prime, filled with True in the beginning:
>>> is_prime = np.ones((100,), dtype=bool)

• Cross out 0 and 1 which are not primes:

>>> is_prime[:2] = 0
• For each integer j starting from 2, cross out its higher multiples:
>>> N_max = int(np.sqrt(len(is_prime) - 1))
>>> for j in range(2, N_max + 1):
... is_prime[2*j::j] = False
• Skim through help(np.nonzero), and print the prime numbers

• Follow-up:
– Move the above code into a script file named prime_sieve.py
– Run it to check it works
– Use the optimization suggested in the sieve of Eratosthenes:
1. Skip j which are already known to not be primes
2. The first number to cross out is 𝑗 2
3.1.7 Fancy indexing
Tip: NumPy arrays can be indexed with slices, but also with boolean or integer arrays (masks). This
method is called fancy indexing. It creates copies not views.
Using boolean masks

>>> a = rng.integers(0, 21, 15)
>>> a
array([ 3, 13, 12, 10, 10, 10, 18, 4, 8, 5, 6, 11, 12, 17, 3])
>>> (a % 3 == 0)
array([ True, False, True, False, False, False, True, False, False,
False, True, False, True, False, True])
>>> mask = (a % 3 == 0)
>>> extract_from_a = a[mask] # or, a[a%3==0]
>>> extract_from_a # extract a sub-array with the mask
array([ 3, 12, 18, 6, 12, 3])
Indexing with a mask can be very useful to assign a new value to a sub-array:
>>> a[a % 3 == 0] = -1
>>> a
array([-1, 13, -1, 10, 10, 10, -1, 4, 8, 5, -1, 11, -1, 17, -1])

Indexing with an array of integers
>>> a = np.arange(0, 100, 10)

>>> a
array([ 0, 10, 20, 30, 40, 50, 60, 70, 80, 90])
Indexing can be done with an array of integers, where the same index is repeated several time:
>>> a[[2, 3, 2, 4, 2]] # note: [2, 3, 2, 4, 2] is a Python list

array([20, 30, 20, 40, 20])
New values can be assigned with this kind of indexing:
>>> a[[9, 7]] = -100

>>> a
array([ 0, 10, 20, 30, 40, 50, 60, -100, 80, -100])
Tip: When a new array is created by indexing with an array of integers, the new array has the same
shape as the array of integers:
>>> idx = np.array([[3, 4], [9, 7]])
>>> idx.shape
(2, 2)
>>> a[idx]
array([[3, 4],
[9, 7]])
The image below illustrates various fancy indexing applications
>>> a[(0,1,2,3,4), (1,2,3,4,5)]

0 1 2 3 4 5
array([1, 12, 23, 34, 45])
>>> a[3:, [0,2,5]] 10 11 12 13 14 15

array([[30, 32, 35],
20 21 22 23 24 25
[40, 42, 45],
[50, 52, 55]])
30 31 32 33 34 35
>>> mask = np.array([1,0,1,0,0,1], dtype=bool)
>>> a[mask, 2] 40 41 42 43 44 45
array([2, 22, 52])
50 51 52 53 54 55
Exercise: Fancy indexing
• Again, reproduce the fancy indexing shown in the diagram above.

• Use fancy indexing on the left and array creation on the right to assign values into an array, for
instance by setting parts of the array in the diagram above to zero.

3.2 Numerical operations on arrays
Section contents
• Elementwise operations
• Basic reductions
• Broadcasting
• Array shape manipulation
• Sorting data
• Summary
3.2.1 Elementwise operations
Basic operations
With scalars:
>>> a = np.array([1, 2, 3, 4])

>>> a + 1
array([2, 3, 4, 5])
>>> 2**a
array([ 2, 4, 8, 16])
All arithmetic operates elementwise:
>>> b = np.ones(4) + 1
>>> a - b
array([-1., 0., 1., 2.])
>>> a * b
array([2., 4., 6., 8.])
>>> j = np.arange(5)
>>> 2**(j + 1) - j
array([ 2, 3, 6, 13, 28])
These operations are of course much faster than if you did them in pure python:
>>> a = np.arange(10000)
>>> %timeit a + 1
10000 loops, best of 3: 24.3 us per loop
>>> l = range(10000)
>>> %timeit [i+1 for i in l]
1000 loops, best of 3: 861 us per loop
Warning: Array multiplication is not matrix multiplication:

>>> c = np.ones((3, 3))
>>> c * c # NOT matrix multiplication!
array([[1., 1., 1.],
[1., 1., 1.],
[1., 1., 1.]])
3.2. Numerical operations on arrays 69

Note: Matrix multiplication:
>>> c @ c
array([[3., 3., 3.],
[3., 3., 3.],
[3., 3., 3.]])
Exercise: Elementwise operations
• Try simple arithmetic elementwise operations: add even elements with odd elements
• Time them against their pure python counterparts using %timeit.
• Generate:
– [2**0, 2**1, 2**2, 2**3, 2**4]
– a_j = 2^(3*j) - j
Other operations
Comparisons:
>>> a = np.array([1, 2, 3, 4])

>>> b = np.array([4, 2, 2, 4])
>>> a == b
array([False, True, False, True])
>>> a > b
array([False, False, True, False])
Tip: Array-wise comparisons:
>>> a = np.array([1, 2, 3, 4])

>>> b = np.array([4, 2, 2, 4])
>>> c = np.array([1, 2, 3, 4])
>>> np.array_equal(a, b)
False
>>> np.array_equal(a, c)
True
Logical operations:
>>> a = np.array([1, 1, 0, 0], dtype=bool)

>>> b = np.array([1, 0, 1, 0], dtype=bool)
>>> np.logical_or(a, b)
array([ True, True, True, False])
>>> np.logical_and(a, b)
array([ True, False, False, False])
Transcendental functions:
>>> np.sin(a)
array([ 0. , 0.84147098, 0.90929743, 0.14112001, -0.7568025 ])


>>> np.exp(a)
array([ 1. , 2.71828183, 7.3890561 , 20.08553692, 54.59815003])
>>> np.log(np.exp(a))
array([0., 1., 2., 3., 4.])
Shape mismatches
>>> a + np.array([1, 2])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ValueError: operands could not be broadcast together with shapes (4,) (2,)
Broadcasting? We’ll return to that later.

Transposition:
>>> a = np.triu(np.ones((3, 3)), 1) # see help(np.triu)

>>> a
array([[0., 1., 1.],
[0., 0., 1.],
[0., 0., 0.]])
>>> a.T
array([[0., 0., 0.],
[1., 0., 0.],
[1., 1., 0.]])
Note: The transposition is a view

The transpose returns a view of the original array:
>>> a = np.arange(9).reshape(3, 3)
>>> a.T[0, 2] = 999
>>> a.T
array([[ 0, 3, 999],
[ 1, 4, 7],
[ 2, 5, 8]])
>>> a
array([[ 0, 1, 2],
[ 3, 4, 5],
[999, 7, 8]])
Note: Linear algebra

The sub-module numpy.linalg implements basic linear algebra, such as solving linear systems, singular
value decomposition, etc. However, it is not guaranteed to be compiled using efficient routines, and thus
we recommend the use of scipy.linalg, as detailed in section Linear algebra operations: scipy.linalg
Exercise other operations
• Look at the help for np.allclose. When might this be useful?

• Look at the help for np.triu and np.tril.

3.2.2 Basic reductions
Computing sums
>>> x = np.array([1, 2, 3, 4])

>>> np.sum(x)
10
>>> x.sum()
10
Sum by rows and by columns:
>>> x = np.array([[1, 1], [2, 2]])

>>> x
array([[1, 1],
[2, 2]])
>>> x.sum(axis=0) # columns (first dimension)
array([3, 3])
>>> x[:, 0].sum(), x[:, 1].sum()
(3, 3)
>>> x.sum(axis=1) # rows (second dimension)
array([2, 4])
>>> x[0, :].sum(), x[1, :].sum()
(2, 4)
Tip: Same idea in higher dimensions:

>>> x = rng.random((2, 2, 2))
>>> x.sum(axis=2)[0, 1]
0.73415...
>>> x[0, 1, :].sum()
0.73415...

Other reductions
— works the same way (and take axis=)

Extrema:
>>> x = np.array([1, 3, 2])

>>> x.min()
1
>>> x.max()
3
>>> x.argmin() # index of minimum

0
>>> x.argmax() # index of maximum
1
Logical operations:
>>> np.all([True, True, False])

False
>>> np.any([True, True, False])
True
Note: Can be used for array comparisons:
>>> a = np.zeros((100, 100))

>>> np.any(a != 0)
False
>>> np.all(a == a)
True
>>> a = np.array([1, 2, 3, 2])

>>> b = np.array([2, 2, 3, 2])
>>> c = np.array([6, 4, 4, 5])
>>> ((a <= b) & (b <= c)).all()
True
Statistics:
>>> x = np.array([1, 2, 3, 1])

>>> y = np.array([[1, 2, 3], [5, 6, 1]])
>>> x.mean()
1.75
>>> np.median(x)
1.5
>>> np.median(y, axis=-1) # last axis
array([2., 5.])
>>> x.std() # full population standard dev.

0.82915619758884995
. . . and many more (best to learn as you go).
Exercise: Reductions

• Given there is a sum, what other function might you expect to see?
• What is the difference between sum and cumsum?
Worked Example: diffusion using a random walk algorithm
Tip: Let us consider a simple 1D random walk process: at each time step a walker jumps right or
left with equal probability.
We are interested in finding the typical distance from the origin of a random walker after t left or
right jumps? We are going to simulate many “walkers” to find this law, and we are going to do so
using array computing tricks: we are going to create a 2D array with the “stories” (each walker has a
story) in one direction, and the time in the other:
>>> n_stories = 1000 # number of walkers

>>> t_max = 200 # time during which we follow the walker
We randomly choose all the steps 1 or -1 of the walk:

>>> t = np.arange(t_max)
>>> rng = np.random.default_rng()
>>> steps = 2 * rng.integers(0, 1 + 1, (n_stories, t_max)) - 1 # +1 because the␣
˓→high value is exclusive
>>> np.unique(steps) # Verification: all steps are 1 or -1

array([-1, 1])
We build the walks by summing steps along the time:

>>> positions = np.cumsum(steps, axis=1) # axis = 1: dimension of time
>>> sq_distance = positions**2
We get the mean in the axis of the stories:

>>> mean_sq_distance = np.mean(sq_distance, axis=0)
Plot the results:

>>> plt.figure(figsize=(4, 3))
<Figure size ... with 0 Axes>
>>> plt.plot(t, np.sqrt(mean_sq_distance), 'g.', t, np.sqrt(t), 'y-')
[<matplotlib.lines.Line2D object at ...>, <matplotlib.lines.Line2D object at ...>]
>>> plt.xlabel(r"$t$")
Text(...'$t$')
>>> plt.ylabel(r"$\sqrt{\langle (\delta x)^2 \rangle}$")
Text(...'$\\sqrt{\\langle (\\delta x)^2 \\rangle}$')
>>> Numerical
3.2. plt.tight_layout()
operations #onprovide
arrays sufficient space for labels 74
We find a well-known result in physics: the RMS distance grows as the square root of the time!
3.2.3 Broadcasting
• Basic operations on numpy arrays (addition, etc.) are elementwise

• This works on arrays of the same size.
Nevertheless, It’s also possible to do operations on arrays of different
sizes if NumPy can transform these arrays so that they all have
the same size: this conversion is called broadcasting.
The image below gives an example of broadcasting:
Let’s verify:

>>> a = np.tile(np.arange(0, 40, 10), (3, 1)).T

>>> a
array([[ 0, 0, 0],
[10, 10, 10],
[20, 20, 20],
[30, 30, 30]])
>>> b = np.array([0, 1, 2])
>>> a + b
array([[ 0, 1, 2],
[10, 11, 12],
[20, 21, 22],
[30, 31, 32]])
We have already used broadcasting without knowing it!:

>>> a = np.ones((4, 5))
>>> a[0] = 2 # we assign an array of dimension 0 to an array of dimension 1
>>> a
array([[2., 2., 2., 2., 2.],
[1., 1., 1., 1., 1.],
[1., 1., 1., 1., 1.],
[1., 1., 1., 1., 1.]])
A useful trick:
>>> a = np.arange(0, 40, 10)
>>> a.shape
(4,)
>>> a = a[:, np.newaxis] # adds a new axis -> 2D array
>>> a.shape
(4, 1)
>>> a
array([[ 0],
[10],
[20],
[30]])
>>> a + b
array([[ 0, 1, 2],
[10, 11, 12],
[20, 21, 22],
[30, 31, 32]])
Tip: Broadcasting seems a bit magical, but it is actually quite natural to use it when we want to solve
a problem whose output data is an array with more dimensions than input data.
Worked Example: Broadcasting
Let’s construct an array of distances (in miles) between cities of Route 66: Chicago, Springfield,
Saint-Louis, Tulsa, Oklahoma City, Amarillo, Santa Fe, Albuquerque, Flagstaff and Los Angeles.
>>> mileposts = np.array([0, 198, 303, 736, 871, 1175, 1475, 1544,
... 1913, 2448])
>>> distance_array = np.abs(mileposts - mileposts[:, np.newaxis])
>>> distance_array
array([[ 0, 198, 303, 736, 871, 1175, 1475, 1544, 1913, 2448],
[ 198, 0, 105, 538, 673, 977, 1277, 1346, 1715, 2250],

[ 303, 105, 0, 433, 568, 872, 1172, 1241, 1610, 2145],

[ 736, 538, 433, 0, 135, 439, 739, 808, 1177, 1712],
[ 871, 673, 568, 135, 0, 304, 604, 673, 1042, 1577],
[1175, 977, 872, 439, 304, 0, 300, 369, 738, 1273],
[1475, 1277, 1172, 739, 604, 300, 0, 69, 438, 973],
[1544, 1346, 1241, 808, 673, 369, 69, 0, 369, 904],
[1913, 1715, 1610, 1177, 1042, 738, 438, 369, 0, 535],
[2448, 2250, 2145, 1712, 1577, 1273, 973, 904, 535, 0]])
A lot of grid-based or network-based problems can also use broadcasting. For instance, if we want to
compute the distance from the origin of points on a 5x5 grid, we can do
>>> x, y = np.arange(5), np.arange(5)[:, np.newaxis]

>>> distance = np.sqrt(x ** 2 + y ** 2)
>>> distance
array([[0. , 1. , 2. , 3. , 4. ],
[1. , 1.41421356, 2.23606798, 3.16227766, 4.12310563],
[2. , 2.23606798, 2.82842712, 3.60555128, 4.47213595],
[3. , 3.16227766, 3.60555128, 4.24264069, 5. ],
[4. , 4.12310563, 4.47213595, 5. , 5.65685425]])
Or in color:
>>> plt.pcolor(distance)
<matplotlib.collections.PolyQuadMesh object at ...>
>>> plt.colorbar()

Remark : the numpy.ogrid() function allows to directly create vectors x and y of the previous example,
with two “significant dimensions”:
>>> x, y = np.ogrid[0:5, 0:5]

>>> x, y
(array([[0],
[1],
[2],
[3],
[4]]), array([[0, 1, 2, 3, 4]]))
>>> x.shape, y.shape
((5, 1), (1, 5))
>>> distance = np.sqrt(x ** 2 + y ** 2)
Tip: So, np.ogrid is very useful as soon as we have to handle computations on a grid. On the other
hand, np.mgrid directly provides matrices full of indices for cases where we can’t (or don’t want to)
benefit from broadcasting:
>>> x, y = np.mgrid[0:4, 0:4]

>>> x
array([[0, 0, 0, 0],
[1, 1, 1, 1],
[2, 2, 2, 2],
[3, 3, 3, 3]])
>>> y
array([[0, 1, 2, 3],
[0, 1, 2, 3],
[0, 1, 2, 3],
[0, 1, 2, 3]])
See also:
Broadcasting: discussion of broadcasting in the Advanced NumPy chapter.

3.2.4 Array shape manipulation
Flattening
>>> a = np.array([[1, 2, 3], [4, 5, 6]])

>>> a.ravel()
array([1, 2, 3, 4, 5, 6])
>>> a.T
array([[1, 4],
[2, 5],
[3, 6]])
>>> a.T.ravel()
array([1, 4, 2, 5, 3, 6])
Higher dimensions: last dimensions ravel out “first”.
Reshaping
The inverse operation to flattening:
>>> a.shape
(2, 3)
>>> b = a.ravel()
>>> b = b.reshape((2, 3))
>>> b
array([[1, 2, 3],
[4, 5, 6]])
Or,
>>> a.reshape((2, -1)) # unspecified (-1) value is inferred

array([[1, 2, 3],
[4, 5, 6]])
Warning: ndarray.reshape may return a view (cf help(np.reshape))), or copy
Tip:
>>> b[0, 0] = 99
>>> a
array([[99, 2, 3],
[ 4, 5, 6]])
Beware: reshape may also return a copy!:
>>> a = np.zeros((3, 2))

>>> b = a.T.reshape(3*2)
>>> b[0] = 9
>>> a
array([[0., 0.],
[0., 0.],
[0., 0.]])
To understand this you need to learn more about the memory layout of a NumPy array.

Adding a dimension
Indexing with the np.newaxis object allows us to add an axis to an array (you have seen this already
above in the broadcasting section):
>>> z = np.array([1, 2, 3])

>>> z
array([1, 2, 3])
>>> z[:, np.newaxis]

array([[1],
[2],
[3]])
>>> z[np.newaxis, :]
array([[1, 2, 3]])
Dimension shuffling
>>> a = np.arange(4*3*2).reshape(4, 3, 2)
>>> a.shape
(4, 3, 2)
>>> a[0, 2, 1]
5
>>> b = a.transpose(1, 2, 0)
>>> b.shape
(3, 2, 4)
>>> b[2, 1, 0]
5
Also creates a view:
>>> b[2, 1, 0] = -1
>>> a[0, 2, 1]
-1
Resizing
Size of an array can be changed with ndarray.resize:
>>> a.resize((8,))
>>> a
array([0, 1, 2, 3, 0, 0, 0, 0])
However, it must not be referred to somewhere else:
>>> b = a
>>> a.resize((4,))
ValueError: cannot resize an array that references or is referenced
by another array in this way.
Use the np.resize function or refcheck=False

Exercise: Shape manipulations
• Look at the docstring for reshape, especially the notes section which has some more information
about copies and views.
• Use flatten as an alternative to ravel. What is the difference? (Hint: check which one returns
a view and which a copy)
• Experiment with transpose for dimension shuffling.
3.2.5 Sorting data
Sorting along an axis:
>>> a = np.array([[4, 3, 5], [1, 2, 1]])

>>> b = np.sort(a, axis=1)
>>> b
array([[3, 4, 5],
[1, 1, 2]])
Note: Sorts each row separately!
In-place sort:
>>> a.sort(axis=1)
>>> a
array([[3, 4, 5],
[1, 1, 2]])
Sorting with fancy indexing:
>>> a = np.array([4, 3, 1, 2])

>>> j = np.argsort(a)
>>> j
array([2, 3, 1, 0])
>>> a[j]
array([1, 2, 3, 4])
Finding minima and maxima:
>>> a = np.array([4, 3, 1, 2])

>>> j_max = np.argmax(a)
>>> j_min = np.argmin(a)
>>> j_max, j_min
(0, 2)
Exercise: Sorting
• Try both in-place and out-of-place sorting.

• Try creating arrays with different dtypes and sorting them.
• Use all or array_equal to check the results.
• Look at np.random.shuffle for a way to create sortable input quicker.
• Combine ravel, sort and reshape.

• Look at the axis keyword for sort and rewrite the previous exercise.
3.2.6 Summary
What do you need to know to get started?

• Know how to create arrays : array, arange, ones, zeros.
• Know the shape of the array with array.shape, then use slicing to obtain different views of the
array: array[::2], etc. Adjust the shape of the array using reshape or flatten it with ravel.
• Obtain a subset of the elements of an array and/or modify their values with masks
>>> a[a < 0] = 0
• Know miscellaneous operations on arrays, such as finding the mean or max (array.max(), array.
mean()). No need to retain everything, but have the reflex to search in the documentation (online
docs, help(), lookfor())!!
• For advanced use: master the indexing with arrays of integers, as well as broadcasting. Know more
NumPy functions to handle various array operations.
Quick read
can directly skip to the next chapter: Matplotlib: plotting.
come back and finish this chapter, as well as to do some more exercices.
3.3 More elaborate arrays
Section contents
• More data types

• Structured data types
• maskedarray: dealing with (propagation of) missing data
3.3.1 More data types
Casting
“Bigger” type wins in mixed-type operations:
>>> np.array([1, 2, 3]) + 1.5

array([2.5, 3.5, 4.5])
Assignment never changes the type!
3.3. More elaborate arrays 82

>>> a = np.array([1, 2, 3])

>>> a.dtype
dtype('int64')
>>> a[0] = 1.9 # <-- float is truncated to integer
>>> a
array([1, 2, 3])
Forced casts:
>>> a = np.array([1.7, 1.2, 1.6])

>>> b = a.astype(int) # <-- truncates to integer
>>> b
array([1, 1, 1])
Rounding:
>>> a = np.array([1.2, 1.5, 1.6, 2.5, 3.5, 4.5])

>>> b = np.around(a)
>>> b # still floating-point
array([1., 2., 2., 2., 4., 4.])
>>> c = np.around(a).astype(int)
>>> c
array([1, 2, 2, 2, 4, 4])
Different data type sizes
Integers (signed):
int8 8 bits
int16 16 bits
int32 32 bits (same as int on 32-bit platform)
int64 64 bits (same as int on 64-bit platform)
>>> np.array([1], dtype=int).dtype

dtype('int64')
>>> np.iinfo(np.int32).max, 2**31 - 1
(2147483647, 2147483647)
Unsigned integers:
uint8 8 bits
uint16 16 bits
uint32 32 bits
uint64 64 bits
>>> np.iinfo(np.uint32).max, 2**32 - 1

(4294967295, 4294967295)
Floating-point numbers:

float16 16 bits
float32 32 bits
float64 64 bits (same as float)
float96 96 bits, platform-dependent (same as np.longdouble)
float128 128 bits, platform-dependent (same as np.longdouble)
>>> np.finfo(np.float32).eps
1.1920929e-07
>>> np.finfo(np.float64).eps
2.2204460492503131e-16
>>> np.float32(1e-8) + np.float32(1) == 1

True
>>> np.float64(1e-8) + np.float64(1) == 1
False
Complex floating-point numbers:
complex64 two 32-bit floats

complex128 two 64-bit floats
complex192 two 96-bit floats, platform-dependent
complex256 two 128-bit floats, platform-dependent
Smaller data types
If you don’t know you need special data types, then you probably don’t.
Comparison on using float32 instead of float64:
• Half the size in memory and on disk
• Half the memory bandwidth required (may be a bit faster in some operations)
In [1]: a = np.zeros((int(1e6),), dtype=np.float64)
In [2]: b = np.zeros((int(1e6),), dtype=np.float32)
In [3]: %timeit a*a

267 us +- 1.76 us per loop (mean +- std. dev. of 7 runs, 1,000 loops each)
In [4]: %timeit b*b

133 us +- 176 ns per loop (mean +- std. dev. of 7 runs, 10,000 loops each)
• But: bigger rounding errors — sometimes in surprising places (i.e., don’t use them unless you
really need them)

3.3.2 Structured data types
sensor_code (4-character string)

position (float)
value (float)
>>> samples = np.zeros((6,), dtype=[('sensor_code', 'S4'),

... ('position', float), ('value', float)])
>>> samples.ndim
1
>>> samples.shape
(6,)
>>> samples.dtype.names
('sensor_code', 'position', 'value')
>>> samples[:] = [('ALFA', 1, 0.37), ('BETA', 1, 0.11), ('TAU', 1, 0.13),
... ('ALFA', 1.5, 0.37), ('ALFA', 3, 0.11), ('TAU', 1.2, 0.13)]
>>> samples
array([(b'ALFA', 1. , 0.37), (b'BETA', 1. , 0.11), (b'TAU', 1. , 0.13),
(b'ALFA', 1.5, 0.37), (b'ALFA', 3. , 0.11), (b'TAU', 1.2, 0.13)],
dtype=[('sensor_code', 'S4'), ('position', '<f8'), ('value', '<f8')])
Field access works by indexing with field names:
>>> samples['sensor_code']
array([b'ALFA', b'BETA', b'TAU', b'ALFA', b'ALFA', b'TAU'], dtype='|S4')
>>> samples['value']
array([0.37, 0.11, 0.13, 0.37, 0.11, 0.13])
>>> samples[0]
(b'ALFA', 1., 0.37)
>>> samples[0]['sensor_code'] = 'TAU'

>>> samples[0]
(b'TAU', 1., 0.37)
Multiple fields at once:
>>> samples[['position', 'value']]

array([(1. , 0.37), (1. , 0.11), (1. , 0.13), (1.5, 0.37),
(3. , 0.11), (1.2, 0.13)],
dtype={'names': ['position', 'value'], 'formats': ['<f8', '<f8'], 'offsets': [4,
˓→ 12], 'itemsize': 20})
Fancy indexing works, as usual:
>>> samples[samples['sensor_code'] == b'ALFA']

array([(b'ALFA', 1.5, 0.37), (b'ALFA', 3. , 0.11)],
dtype=[('sensor_code', 'S4'), ('position', '<f8'), ('value', '<f8')])
Note: There are a bunch of other syntaxes for constructing structured arrays, see here and here.

3.3.3 maskedarray: dealing with (propagation of) missing data
• For floats one could use NaN’s, but masks work for all types:
>>> x = np.ma.array([1, 2, 3, 4], mask=[0, 1, 0, 1])

>>> x
masked_array(data=[1, --, 3, --],
mask=[False, True, False, True],
fill_value=999999)
>>> y = np.ma.array([1, 2, 3, 4], mask=[0, 1, 1, 1])

>>> x + y
masked_array(data=[2, --, --, --],
mask=[False, True, True, True],
fill_value=999999)
• Masking versions of common functions:
>>> np.ma.sqrt([1, -1, 2, -2])

masked_array(data=[1.0, --, 1.41421356237... --],
mask=[False, True, False, True],
fill_value=1e+20)
Note: There are other useful array siblings
While it is off topic in a chapter on NumPy, let’s take a moment to recall good coding practice, which
really do pay off in the long run:
Good practices
• Explicit variable names (no need of a comment to explain what is in the variable)
• Style: spaces after commas, around =, etc.
A certain number of rules for writing “beautiful” code (and, more importantly, using the same
conventions as everybody else!) are given in the Style Guide for Python Code and the Docstring
Conventions page (to manage help strings).
• Except some rare cases, variable names and comments in English.
3.4 Advanced operations
Section contents
• Polynomials
• Loading data files
3.4. Advanced operations 86

3.4.1 Polynomials
NumPy also contains polynomials in different bases:

For example, 3𝑥2 + 2𝑥 − 1:
>>> p = np.poly1d([3, 2, -1])

>>> p(0)
-1
>>> p.roots
array([-1. , 0.33333333])
>>> p.order
2
>>> x = np.linspace(0, 1, 20)

>>> y = np.cos(x) + 0.3*rng.random(20)
>>> p = np.poly1d(np.polyfit(x, y, 3))
>>> t = np.linspace(0, 1, 200) # use a larger number of points for smoother plotting
>>> plt.plot(x, y, 'o', t, p(t), '-')
[<matplotlib.lines.Line2D object at ...>, <matplotlib.lines.Line2D object at ...>]
See https://numpy.org/doc/stable/reference/routines.polynomials.poly1d.html for more.
More polynomials (with more bases)
NumPy also has a more sophisticated polynomial interface, which supports e.g. the Chebyshev basis.
3𝑥2 + 2𝑥 − 1:
>>> p = np.polynomial.Polynomial([-1, 2, 3]) # coefs in different order!

>>> p(0)
-1.0
>>> p.roots()
array([-1. , 0.33333333])
>>> p.degree() # In general polynomials do not always expose 'order'
2
Example using polynomials in Chebyshev basis, for polynomials in range [-1, 1]:
>>> x = np.linspace(-1, 1, 2000)



>>> y = np.cos(x) + 0.3*rng.random(2000)
>>> p = np.polynomial.Chebyshev.fit(x, y, 90)
>>> plt.plot(x, y, 'r.')

>>> plt.plot(x, p(x), 'k-', lw=3)
The Chebyshev polynomials have some advantages in interpolation.
3.4.2 Loading data files
Text files
Example: populations.txt:
# year hare lynx carrot
1900 30e3 4e3 48300
1901 47.2e3 6.1e3 48200
1902 70.2e3 9.8e3 41500
1903 77.4e3 35.2e3 38200
>>> data = np.loadtxt('data/populations.txt')

>>> data
array([[ 1900., 30000., 4000., 48300.],
[ 1901., 47200., 6100., 48200.],
[ 1902., 70200., 9800., 41500.],
...
>>> np.savetxt('pop2.txt', data)

>>> data2 = np.loadtxt('pop2.txt')
Note: If you have a complicated text file, what you can try are:
• np.genfromtxt
• Using Python’s I/O functions and e.g. regexps for parsing (Python is quite well suited for this)

Reminder: Navigating the filesystem with IPython
In [1]: pwd # show current directory

Out[1]: '/tmp'
Images
Using Matplotlib:
>>> img = plt.imread('data/elephant.png')

>>> img.shape, img.dtype
((200, 300, 3), dtype('float32'))
>>> plt.imshow(img)
>>> plt.savefig('plot.png')
>>> plt.imsave('red_elephant.png', img[:,:,0], cmap=plt.cm.gray)
This saved only one channel (of RGB):
>>> plt.imshow(plt.imread('red_elephant.png'))
Other libraries:

>>> import imageio.v3 as iio

>>> iio.imwrite('tiny_elephant.png', (img[::6,::6] * 255).astype(np.uint8))
>>> plt.imshow(plt.imread('tiny_elephant.png'), interpolation='nearest')
NumPy’s own format
NumPy has its own binary format, not portable but with efficient I/O:
>>> data = np.ones((3, 3))

>>> np.save('pop.npy', data)
>>> data3 = np.load('pop.npy')
Well-known (& more obscure) file formats
• HDF5: h5py, PyTables

• NetCDF: scipy.io.netcdf_file, netcdf4-python, . . .
• Matlab: scipy.io.loadmat, scipy.io.savemat
• MatrixMarket: scipy.io.mmread, scipy.io.mmwrite
• IDL: scipy.io.readsav
. . . if somebody uses it, there’s probably also a Python library for it.
Exercise: Text data files
Write a Python script that loads data from populations.txt:: and drop the last column and the first
5 rows. Save the smaller dataset to pop2.txt.
NumPy internals
If you are interested in the NumPy internals, there is a good discussion in Advanced NumPy.

3.5 Some exercises
3.5.1 Array manipulations
1. Form the 2-D array (without typing it in explicitly):
[[1, 6, 11],
[2, 7, 12],
[3, 8, 13],
[4, 9, 14],
[5, 10, 15]]
and generate a new array containing its 2nd and 4th rows.
2. Divide each column of the array:

>>> a = np.arange(25).reshape(5, 5)
elementwise with the array b = np.array([1., 5, 10, 15, 20]). (Hint: np.newaxis).
3. Harder one: Generate a 10 x 3 array of random numbers (in range [0,1]). For each row, pick the
number closest to 0.5.
• Use abs and argmin to find the column j closest for each row.
• Use fancy indexing to extract the numbers. (Hint: a[i,j] – the array i must contain the
row numbers corresponding to stuff in j.)
3.5.2 Picture manipulation: Framing a Face
Let’s do some manipulations on NumPy arrays by starting with an image of a raccoon. scipy provides
a 2D array of this image with the scipy.datasets.face function:
>>> import scipy as sp

>>> face = sp.datasets.face(gray=True) # 2D grayscale image
Here are a few images we will be able to obtain with our manipulations: use different colormaps, crop
the image, change some parts of the image.
• Let’s use the imshow function of matplotlib to display the image.
>>> import matplotlib.pyplot as plt

>>> face = sp.datasets.face(gray=True)
>>> plt.imshow(face)
<matplotlib.image.AxesImage object at 0x...>
• The face is displayed in false colors. A colormap must be

specified for it to be displayed in grey.
>>> plt.imshow(face, cmap=plt.cm.gray)

3.5. Some exercises 91

• Create an array of the image with a narrower centering

[for example,] remove 100 pixels from all the borders of the image. To check the result, display
this new array with imshow.
>>> crop_face = face[100:-100, 100:-100]
• We will now frame the face with a black locket. For this, we
need to create a mask corresponding to the pixels we want to be black. The center of the face
is around (660, 330), so we defined the mask by this condition (y-300)**2 + (x-660)**2
>>> sy, sx = face.shape
>>> y, x = np.ogrid[0:sy, 0:sx] # x and y indices of pixels
>>> y.shape, x.shape
((768, 1), (1, 1024))
>>> centerx, centery = (660, 300) # center of the image
>>> mask = ((y - centery)**2 + (x - centerx)**2) > 230**2 # circle
then we assign the value 0 to the pixels of the image corresponding to the mask. The syntax
is extremely simple and intuitive:
>>> face[mask] = 0
>>> plt.imshow(face)
• Follow-up: copy all instructions of this exercise in a script called

face_locket.py then execute this script in IPython with %run face_locket.py.
Change the circle to an ellipsoid.
3.5.3 Data statistics
The data in populations.txt describes the populations of hares and lynxes (and carrots) in northern
Canada during 20 years:
>>> year, hares, lynxes, carrots = data.T # trick: columns to variables

>>> plt.axes([0.2, 0.1, 0.5, 0.8])
<Axes: >
>>> plt.plot(year, hares, year, lynxes, year, carrots)
[<matplotlib.lines.Line2D object at ...>, ...]
>>> plt.legend(('Hare', 'Lynx', 'Carrot'), loc=(1.05, 0.5))
<matplotlib.legend.Legend object at ...>

Computes and print, based on the data in populations.txt. . .

1. The mean and std of the populations of each species for the years in the period.
2. Which year each species had the largest population.
3. Which species has the largest population for each year. (Hint: argsort & fancy indexing of
np.array(['H', 'L', 'C']))
4. Which years any of the populations is above 50000. (Hint: comparisons and np.any)
5. The top 2 years for each species when they had the lowest populations. (Hint: argsort, fancy
indexing)
6. Compare (plot) the change in hare population (see help(np.gradient)) and the number of lynxes.
Check correlation (see help(np.corrcoef)).
. . . all without for-loops.
Solution: Python source file
3.5.4 Crude integral approximations
Write a function f(a, b, c) that returns 𝑎𝑏 −𝑐. Form a 24x12x6 array containing its values in parameter
ranges [0,1] x [0,1] x [0,1].
Approximate the 3-d integral
∫︁ 1 ∫︁ 1 ∫︁ 1
(𝑎𝑏 − 𝑐)𝑑𝑎 𝑑𝑏 𝑑𝑐
0 0 0
over this volume with the mean. The exact result is: ln 2 − 21 ≈ 0.1931 . . . — what is your relative error?
(Hints: use elementwise operations and broadcasting. You can make np.ogrid give a number of points
in given range with np.ogrid[0:1:20j].)
Reminder Python functions:
def f(a, b, c):

return some_result
3.5.5 Mandelbrot set
Write a script that computes the Mandelbrot fractal. The Mandelbrot iteration:

N_max = 50
some_threshold = 50
c = x + 1j*y
z = 0
for j in range(N_max):
z = z**2 + c
Point (x, y) belongs to the Mandelbrot set if |𝑧| < some_threshold.

Do this computation by:
1. Construct a grid of c = x + 1j*y values in range [-2, 1] x [-1.5, 1.5]
2. Do the iteration
3. Form the 2-d boolean mask indicating which points are in the set
4. Save the result to an image with:

>>> plt.imshow(mask.T, extent=[-2, 1, -1.5, 1.5])
>>> plt.gray()
>>> plt.savefig('mandelbrot.png')
3.5.6 Markov chain
Markov chain transition matrix P, and probability distribution on the states p:

1. 0 <= P[i,j] <= 1: probability to go from state i to state j
2. Transition rule: 𝑝𝑛𝑒𝑤 = 𝑃 𝑇 𝑝𝑜𝑙𝑑
3. all(sum(P, axis=1) == 1), p.sum() == 1: normalization
Write a script that works with 5 states, and:
• Constructs a random matrix, and normalizes each row so that it is a transition matrix.
• Starts from a random (normalized) probability distribution p and takes 50 steps => p_50

• Computes the stationary distribution: the eigenvector of P.T with eigenvalue 1 (numerically: closest
to 1) => p_stationary
Remember to normalize the eigenvector — I didn’t. . .
• Checks if p_50 and p_stationary are equal to tolerance 1e-5
Toolbox: np.random, @, np.linalg.eig, reductions, abs(), argmin, comparisons, all, np.linalg.norm,
etc.
3.6 Full code examples
3.6.1 Full code examples for the numpy chapter
1D plotting
Plot a basic 1D figure
import numpy as np
import matplotlib.pyplot as plt
x = np.linspace(0, 3, 20)
y = np.linspace(0, 9, 20)
plt.plot(x, y)
3.6. Full code examples 95


plt.plot(x, y, "o")
plt.show()
Total running time of the script: (0 minutes 0.056 seconds)
2D plotting
Plot a basic 2D figure
import numpy as np
rng = np.random.default_rng()
image = rng.random((30, 30))
plt.imshow(image, cmap=plt.cm.hot)
plt.colorbar()
plt.show()

Distances exercise
Plot distances in a grid
import numpy as np
x, y = np.arange(5), np.arange(5)[:, np.newaxis]

distance = np.sqrt(x**2 + y**2)
plt.pcolor(distance)
plt.colorbar()
plt.show()

Fitting to polynomial
Plot noisy data and their polynomial fit
import numpy as np
rng = np.random.default_rng(27446968)
y = np.cos(x) + 0.3 * rng.random(20)
p = np.poly1d(np.polyfit(x, y, 3))
t = np.linspace(0, 1, 200)
plt.plot(x, y, "o", t, p(t), "-")
plt.show()

Fitting in Chebyshev basis
Plot noisy data and their polynomial fit in a Chebyshev basis
import numpy as np
x = np.linspace(-1, 1, 2000)
y = np.cos(x) + 0.3 * rng.random(2000)
p = np.polynomial.Chebyshev.fit(x, y, 90)
plt.plot(x, y, "r.")
plt.plot(x, p(x), "k-", lw=3)
plt.show()

Population exercise
Plot populations of hares, lynxes, and carrots
import numpy as np
data = np.loadtxt("../../../data/populations.txt")
year, hares, lynxes, carrots = data.T
plt.axes([0.2, 0.1, 0.5, 0.8])

plt.plot(year, hares, year, lynxes, year, carrots)
plt.legend(("Hare", "Lynx", "Carrot"), loc=(1.05, 0.5))
plt.show()

Reading and writing an elephant
Read and write images
import numpy as np
original figure
plt.figure()
img = plt.imread("../../../data/elephant.png")
plt.imshow(img)
<matplotlib.image.AxesImage object at 0x7f9c882ae3d0>
red channel displayed in grey
plt.figure()
img_red = img[:, :, 0]
plt.imshow(img_red, cmap=plt.cm.gray)

<matplotlib.image.AxesImage object at 0x7f9c7dcee3d0>
lower resolution
plt.figure()
img_tiny = img[::6, ::6]
plt.imshow(img_tiny, interpolation="nearest")
plt.show()

Mandelbrot set
Compute the Mandelbrot fractal and plot it

import numpy as np
from numpy import newaxis
import warnings
def compute_mandelbrot(N_max, some_threshold, nx, ny):

# A grid of c-values
x = np.linspace(-2, 1, nx)
y = np.linspace(-1.5, 1.5, ny)
c = x[:, newaxis] + 1j * y[newaxis, :]
# Mandelbrot iteration
z = c
# The code below overflows in many regions of the x-y grid, suppress
# warnings temporarily
with warnings.catch_warnings():
warnings.simplefilter("ignore")
for j in range(N_max):
z = z**2 + c
mandelbrot_set = abs(z) < some_threshold
return mandelbrot_set


mandelbrot_set = compute_mandelbrot(50, 50.0, 601, 401)
plt.imshow(mandelbrot_set.T, extent=[-2, 1, -1.5, 1.5])

plt.gray()
plt.show()
Random walk exercise
Plot distance as a function of time for a random walk together with the theoretical result
import numpy as np
# We create 1000 realizations with 200 steps each

n_stories = 1000
t_max = 200
t = np.arange(t_max)
# Steps can be -1 or 1 (note that randint excludes the upper limit)
steps = 2 * rng.integers(0, 1 + 1, (n_stories, t_max)) - 1
# The time evolution of the position is obtained by successively

# summing up individual steps. This is done for each of the
# realizations, i.e. along axis 1.
positions = np.cumsum(steps, axis=1)
# Determine the time evolution of the mean square distance.

sq_distance = positions**2
mean_sq_distance = np.mean(sq_distance, axis=0)
# Plot the distance d from the origin as a function of time and

# compare with the theoretically expected result where d(t)


# grows as a square root of time t.
plt.figure(figsize=(4, 3))
plt.plot(t, np.sqrt(mean_sq_distance), "g.", t, np.sqrt(t), "y-")
plt.xlabel(r"$t$")
plt.ylabel(r"$\sqrt{\langle (\delta x)^2 \rangle}$")
plt.tight_layout()
plt.show()

CHAPTER 4
Matplotlib: plotting
Thanks
Many thanks to Bill Wing and Christoph Deil for review and corrections.
Authors: Nicolas Rougier, Mike Müller, Gaël Varoquaux
Chapter contents
• Introduction
• Simple plot
• Figures, Subplots, Axes and Ticks
• Other Types of Plots: examples and exercises
• Beyond this tutorial
• Quick references
• Full code examples
107
4.1 Introduction
Tip: Matplotlib is probably the most used Python package for 2D-graphics. It provides both a quick
way to visualize data from Python and publication-quality figures in many formats. We are going to
explore matplotlib in interactive mode covering most common cases.
4.1.1 IPython, Jupyter, and matplotlib modes
Tip: The Jupyter notebook and the IPython enhanced interactive Python, are tuned for the scientific-
computing workflow in Python, in combination with Matplotlib:
For interactive matplotlib sessions, turn on the matplotlib mode

IPython console
When using the IPython console, use:
In [1]: %matplotlib
Jupyter notebook
In the notebook, insert, at the beginning of the notebook the following magic:
%matplotlib inline
4.1.2 pyplot
Tip: pyplot provides a procedural interface to the matplotlib object-oriented plotting library. It is
modeled closely after Matlab™. Therefore, the majority of plotting commands in pyplot have Matlab™
analogs with similar arguments. Important commands are explained with interactive examples.
4.2 Simple plot
Tip: In this section, we want to draw the cosine and sine functions on the same plot. Starting from
the default settings, we’ll enrich the figure step by step to make it nicer.
First step is to get the data for the sine and cosine functions:
import numpy as np
X = np.linspace(-np.pi, np.pi, 256)

C, S = np.cos(X), np.sin(X)
X is now a numpy array with 256 values ranging from −𝜋 to +𝜋 (included). C is the cosine (256 values)
and S is the sine (256 values).
To run the example, you can type them in an IPython interactive session:
4.1. Introduction 108

$ ipython --matplotlib
This brings us to the IPython prompt:
IPython 0.13 -- An enhanced Interactive Python.

? -> Introduction to IPython's features.
%magic -> Information about IPython's 'magic' % functions.
help -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.
Tip: You can also download each of the examples and run it using regular python, but you will lose
interactive data manipulation:
$ python plot_exercise_1.py
You can get source for each step by clicking on the corresponding figure.
4.2.1 Plotting with default settings
Hint: Documentation
• plot tutorial
• plot() command
Tip: Matplotlib comes with a set of default settings that allow customizing all kinds of properties. You
can control the defaults of almost every property in matplotlib: figure size and dpi, line width, color and
style, axes, axis and grid properties, text and font properties and so on.
import numpy as np

plt.plot(X, C)
plt.plot(X, S)
plt.show()
4.2. Simple plot 109

4.2.2 Instantiating defaults
Hint: Documentation
• Customizing matplotlib
In the script below, we’ve instantiated (and commented) all the figure settings that influence the ap-
pearance of the plot.
Tip: The settings have been explicitly set to their default values, but now you can interactively play
with the values to explore their affect (see Line properties and Line styles below).
import numpy as np
# Create a figure of size 8x6 inches, 80 dots per inch

plt.figure(figsize=(8, 6), dpi=80)
# Create a new subplot from a grid of 1x1

plt.subplot(1, 1, 1)

# Plot cosine with a blue continuous line of width 1 (pixels)

plt.plot(X, C, color="blue", linewidth=1.0, linestyle="-")
# Plot sine with a green continuous line of width 1 (pixels)

plt.plot(X, S, color="green", linewidth=1.0, linestyle="-")
# Set x limits
plt.xlim(-4.0, 4.0)
# Set x ticks
plt.xticks(np.linspace(-4, 4, 9))
# Set y limits
plt.ylim(-1.0, 1.0)
# Set y ticks


plt.yticks(np.linspace(-1, 1, 5))
# Save figure using 72 dots per inch

# plt.savefig("exercise_2.png", dpi=72)
# Show result on screen

plt.show()
4.2.3 Changing colors and line widths
Hint: Documentation
• Controlling line properties
• Line2D API
Tip: First step, we want to have the cosine in blue and the sine in red and a slightly thicker line for
both of them. We’ll also slightly alter the figure size to make it more horizontal.
...
plt.plot(X, S, color="red", linewidth=2.5, linestyle="-")
...
4.2.4 Setting limits

Hint: Documentation
• xlim() command
• ylim() command
Tip: Current limits of the figure are a bit too tight and we want to make some space in order to clearly
see all data points.
...
plt.xlim(X.min() * 1.1, X.max() * 1.1)
plt.ylim(C.min() * 1.1, C.max() * 1.1)
...
4.2.5 Setting ticks
Hint: Documentation
• xticks() command
• yticks() command
• Tick container
• Tick locating and formatting
Tip: Current ticks are not ideal because they do not show the interesting values (±𝜋,:math:pm pi/2)
for sine and cosine. We’ll change them such that they show only these values.
...
plt.xticks([-np.pi, -np.pi/2, 0, np.pi/2, np.pi])
plt.yticks([-1, 0, +1])
...

4.2.6 Setting tick labels
Hint: Documentation
• Working with text
• xticks() command
• yticks() command
• set_xticklabels()
• set_yticklabels()
Tip: Ticks are now properly placed but their label is not very explicit. We could guess that 3.142 is 𝜋
but it would be better to make it explicit. When we set tick values, we can also provide a corresponding
label in the second argument list. Note that we’ll use latex to allow for nice rendering of the label.
...
plt.xticks([-np.pi, -np.pi/2, 0, np.pi/2, np.pi],
[r'$-\pi$', r'$-\pi/2$', r'$0$', r'$+\pi/2$', r'$+\pi$'])
plt.yticks([-1, 0, +1],
[r'$-1$', r'$0$', r'$+1$'])
...
4.2.7 Moving spines
Hint: Documentation
• spines API

• Axis container
• Transformations tutorial
Tip: Spines are the lines connecting the axis tick marks and noting the boundaries of the data area.
They can be placed at arbitrary positions and until now, they were on the border of the axis. We’ll change
that since we want to have them in the middle. Since there are four of them (top/bottom/left/right),
we’ll discard the top and right by setting their color to none and we’ll move the bottom and left ones to
coordinate 0 in data space coordinates.
...
ax = plt.gca() # gca stands for 'get current axis'
ax.spines['right'].set_color('none')
ax.spines['top'].set_color('none')
ax.xaxis.set_ticks_position('bottom')
ax.spines['bottom'].set_position(('data',0))
ax.yaxis.set_ticks_position('left')
ax.spines['left'].set_position(('data',0))
...
4.2.8 Adding a legend
Hint: Documentation
• Legend guide
• legend() command
• legend API
Tip: Let’s add a legend in the upper left corner. This only requires adding the keyword argument label
(that will be used in the legend box) to the plot commands.
...
plt.plot(X, C, color="blue", linewidth=2.5, linestyle="-", label="cosine")
plt.plot(X, S, color="red", linewidth=2.5, linestyle="-", label="sine")


plt.legend(loc='upper left')
...
4.2.9 Annotate some points
Hint: Documentation
• Annotating axis
• annotate() command
Tip: Let’s annotate some interesting points using the annotate command. We chose the 2𝜋/3 value
and we want to annotate both the sine and the cosine. We’ll first draw a marker on the curve as well as
a straight dotted line. Then, we’ll use the annotate command to display some text with an arrow.
...
t = 2 * np.pi / 3
plt.plot([t, t], [0, np.cos(t)], color='blue', linewidth=2.5, linestyle="--")
plt.scatter([t, ], [np.cos(t), ], 50, color='blue')
plt.annotate(r'$cos(\frac{2\pi}{3} )=-\frac{1} {2} $',

xy=(t, np.cos(t)), xycoords='data',
xytext=(-90, -50), textcoords='offset points', fontsize=16,
arrowprops=dict(arrowstyle="->", connectionstyle="arc3,rad=.2"))
plt.plot([t, t],[0, np.sin(t)], color='red', linewidth=2.5, linestyle="--")

plt.scatter([t, ],[np.sin(t), ], 50, color='red')
plt.annotate(r'$sin(\frac{2\pi}{3} )=\frac{\sqrt{3} }{2} $',

xy=(t, np.sin(t)), xycoords='data',
xytext=(+10, +30), textcoords='offset points', fontsize=16,
arrowprops=dict(arrowstyle="->", connectionstyle="arc3,rad=.2"))
...

4.2.10 Devil is in the details
Hint: Documentation
• artist API
• set_bbox() method
Tip: The tick labels are now hardly visible because of the blue and red lines. We can make them
bigger and we can also adjust their properties such that they’ll be rendered on a semi-transparent white
background. This will allow us to see both the data and the labels.
...
for label in ax.get_xticklabels() + ax.get_yticklabels():
label.set_fontsize(16)
label.set_bbox(dict(facecolor='white', edgecolor='None', alpha=0.65))
...
4.3 Figures, Subplots, Axes and Ticks
A “figure” in matplotlib means the whole window in the user interface. Within this figure there can be
“subplots”.
Tip: So far we have used implicit figure and axes creation. This is handy for fast plots. We can have
more control over the display using figure, subplot, and axes explicitly. While subplot positions the plots
in a regular grid, axes allows free placement within the figure. Both can be useful depending on your
intention. We’ve already worked with figures and subplots without explicitly calling them. When we
call plot, matplotlib calls gca() to get the current axes and gca in turn calls gcf() to get the current
figure. If there is none it calls figure() to make one, strictly speaking, to make a subplot(111). Let’s
look at the details.
4.3. Figures, Subplots, Axes and Ticks 116

4.3.1 Figures
Tip: A figure is the windows in the GUI that has “Figure #” as title. Figures are numbered starting
from 1 as opposed to the normal Python way starting from 0. This is clearly MATLAB-style. There are
several parameters that determine what the figure looks like:
Argument Default Description

num 1 number of figure
figsize figure.figsize figure size in inches (width, height)
dpi figure.dpi resolution in dots per inch
facecolor figure.facecolor color of the drawing background
edgecolor figure.edgecolor color of edge around the drawing background
frameon True draw figure frame or not
Tip: The defaults can be specified in the resource file and will be used most of the time. Only the
number of the figure is frequently changed.
As with other objects, you can set figure properties also setp or with the set_something methods.
When you work with the GUI you can close a figure by clicking on the x in the upper right corner. But
you can close a figure programmatically by calling close. Depending on the argument it closes (1) the
current figure (no argument), (2) a specific figure (figure number or figure instance as argument), or (3)
all figures ("all" as argument).
plt.close(1) # Closes figure 1
4.3.2 Subplots
Tip: With subplot you can arrange plots in a regular grid. You need to specify the number of rows and
columns and the number of the plot. Note that the gridspec command is a more powerful alternative.

4.3.3 Axes
Axes are very similar to subplots but allow placement of plots at any location in the figure. So if we
want to put a smaller plot inside a bigger one we do so with axes.

4.3.4 Ticks
Well formatted ticks are an important part of publishing-ready figures. Matplotlib provides a totally
configurable system for ticks. There are tick locators to specify where ticks should appear and tick
formatters to give ticks the appearance you want. Major and minor ticks can be located and formatted
independently from each other. Per default minor ticks are not shown, i.e. there is only an empty list
for them because it is as NullLocator (see below).
Tick Locators
Tick locators control the positions of the ticks. They are set as follows:
ax = plt.gca()
ax.xaxis.set_major_locator(eval(locator))
There are several locators for different kind of requirements:
All of these locators derive from the base class matplotlib.ticker.Locator. You can make your own
locator deriving from it. Handling dates as ticks can be especially tricky. Therefore, matplotlib provides
special locators in matplotlib.dates.
4.4 Other Types of Plots: examples and exercises
4.4. Other Types of Plots: examples and exercises 119



4.4.1 Regular Plots
Starting from the code below, try to reproduce the graphic taking care of filled areas:
Hint: You need to use the fill_between() command.
n = 256
X = np.linspace(-np.pi, np.pi, n)


Y = np.sin(2 * X)
plt.plot(X, Y + 1, color='blue', alpha=1.00)

plt.plot(X, Y - 1, color='blue', alpha=1.00)
Click on the figure for solution.
4.4.2 Scatter Plots
Starting from the code below, try to reproduce the graphic taking care of marker size, color and trans-
parency.
Hint: Color is given by angle of (X,Y).
n = 1024
X = rng.normal(0,1,n)
Y = rng.normal(0,1,n)
plt.scatter(X,Y)
Click on figure for solution.
4.4.3 Bar Plots
Starting from the code below, try to reproduce the graphic by adding labels for red bars.
Hint: You need to take care of text alignment.

n = 12
X = np.arange(n)
Y1 = (1 - X / float(n)) * rng.uniform(0.5, 1.0, n)
plt.bar(X, +Y1, facecolor='#9999ff', edgecolor='white')

plt.bar(X, -Y2, facecolor='#ff9999', edgecolor='white')
for x, y in zip(X, Y1):

plt.text(x + 0.4, y + 0.05, '%.2f ' % y, ha='center', va='bottom')
plt.ylim(-1.25, +1.25)
4.4.4 Contour Plots
Starting from the code below, try to reproduce the graphic taking care of the colormap (see Colormaps
below).
Hint: You need to use the clabel() command.
def f(x, y):

return (1 - x / 2 + x ** 5 + y ** 3) * np.exp(-x ** 2 -y ** 2)
n = 256
x = np.linspace(-3, 3, n)
y = np.linspace(-3, 3, n)
X, Y = np.meshgrid(x, y)
plt.contourf(X, Y, f(X, Y), 8, alpha=.75, cmap='jet')

C = plt.contour(X, Y, f(X, Y), 8, colors='black', linewidth=.5)

4.4.5 Imshow
Starting from the code below, try to reproduce the graphic taking care of colormap, image interpolation
and origin.
Hint: You need to take care of the origin of the image in the imshow command and use a colorbar()
def f(x, y):

return (1 - x / 2 + x ** 5 + y ** 3) * np.exp(-x ** 2 - y ** 2)
n = 10
x = np.linspace(-3, 3, 4 * n)
y = np.linspace(-3, 3, 3 * n)
plt.imshow(f(X, Y))
Click on the figure for the solution.
4.4.6 Pie Charts
Starting from the code below, try to reproduce the graphic taking care of colors and slices size.
Hint: You need to modify Z.
Z = rng.uniform(0, 1, 20)
plt.pie(Z)
Click on the figure for the solution.

4.4.7 Quiver Plots
Starting from the code below, try to reproduce the graphic taking care of colors and orientations.
Hint: You need to draw arrows twice.
n = 8
X, Y = np.mgrid[0:n, 0:n]
plt.quiver(X, Y)
4.4.8 Grids
Starting from the code below, try to reproduce the graphic taking care of line styles.
axes = plt.gca()
axes.set_xlim(0, 4)
axes.set_ylim(0, 3)
axes.set_xticklabels([])
axes.set_yticklabels([])

4.4.9 Multi Plots
Starting from the code below, try to reproduce the graphic.
Hint: You can use several subplots with different partition.
4.4.10 Polar Axis
Hint: You only need to modify the axes line
plt.axes([0, 0, 1, 1])
N = 20
theta = np.arange(0., 2 * np.pi, 2 * np.pi / N)
radii = 10 * rng.random(N)
width = np.pi / 4 * rng.random(N)
bars = plt.bar(theta, radii, width=width, bottom=0.0)
for r, bar in zip(radii, bars):

bar.set_facecolor(plt.cm.jet(r / 10.))
bar.set_alpha(0.5)

4.4.11 3D Plots
Hint: You need to use contourf()
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = Axes3D(fig)
X = np.arange(-4, 4, 0.25)
Y = np.arange(-4, 4, 0.25)
X, Y = np.meshgrid(X, Y)
R = np.sqrt(X**2 + Y**2)
Z = np.sin(R)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap='hot')
4.4.12 Text
Try to do the same from scratch !
Hint: Have a look at the matplotlib logo.

Quick read
can directly skip to the next chapter: SciPy : high-level scientific computing.
come back and finish this chapter later.
4.5 Beyond this tutorial
Matplotlib benefits from extensive documentation as well as a large community of users and developers.
Here are some links of interest:
4.5.1 Tutorials
• Pyplot tutorial • Customizing your objects

• Introduction • Object containers
• Controlling line properties • Figure container
• Working with multiple figures and axes • Axes container
• Working with text • Axis containers
• Image tutorial • Tick containers
• Startup commands • Path tutorial
• Importing image data into NumPy arrays • Introduction
• Plotting NumPy arrays as images • Bézier example
• Text tutorial • Compound paths
• Text introduction • Transforms tutorial
• Basic text commands • Introduction
• Text properties and layout • Data coordinates
• Writing mathematical expressions • Axes coordinates
• Text rendering With LaTeX • Blended transformations
• Annotating text • Using offset transforms to create a shadow
• Artist tutorial effect
• Introduction • The transformation pipeline
4.5.2 Matplotlib documentation
• User guide • How-To

• FAQ • Troubleshooting
• Installation • Environment Variables
• Usage • Screenshots
4.5. Beyond this tutorial 129

4.5.3 Code documentation
The code is well documented and you can quickly access a specific command from within a python
session:

>>> help(plt.plot)
Help on function plot in module matplotlib.pyplot:
plot(*args: ...) -> 'list[Line2D]'

Plot y versus x as lines and/or markers.
Call signatures::
plot([x], y, [fmt], *, data=None, **kwargs)

plot([x], y, [fmt], [x2], y2, [fmt2], ..., **kwargs)
...
4.5.4 Galleries
The matplotlib gallery is also incredibly useful when you search how to render a given graphic. Each
example comes with its source.
4.5.5 Mailing lists
Finally, there is a user mailing list where you can ask for help and a developers mailing list that is more
technical.
4.6 Quick references
Here is a set of tables that show main properties and styles.
4.6. Quick references 130

4.6.1 Line properties
Property Description Appearance
alpha (or a) alpha transparency on 0-1

scale
antialiased True or False - use antialised
rendering
color (or c) matplotlib color arg

linestyle (or ls) see Line properties
linewidth (or lw) float, the line width in points
solid_capstyle Cap style for solid lines
solid_joinstyle Join style for solid lines
dash_capstyle Cap style for dashes
dash_joinstyle Join style for dashes
marker see Markers
markeredgewidth line width around the
(mew) marker symbol
markeredgecolor edge color if a marker is used
(mec)
markerfacecolor face color if a marker is used
(mfc)
markersize (ms) size of the marker in points
4.6.2 Line styles

4.6.3 Markers
4.6.4 Colormaps
All colormaps can be reversed by appending _r. For instance, gray_r is the reverse of gray.
If you want to know more about colormaps, check the documentation on Colormaps in matplotlib.

4.7.1 Code samples for Matplotlib
The examples here are only examples relevant to the points raised in this chapter. The matplotlib
documentation comes with a much more exhaustive gallery.
Pie chart
A simple pie chart example with matplotlib.
import numpy as np
n = 20
Z = np.ones(n)
Z[-1] *= 2
plt.axes([0.025, 0.025, 0.95, 0.95])
plt.pie(Z, explode=Z * 0.05, colors=[f"{ i / float(n): f} " for i in range(n)])

plt.axis("equal")
plt.xticks([])
plt.yticks()
plt.show()

A simple, good-looking plot
Demoing some simple features of matplotlib
import numpy as np
import matplotlib
matplotlib.use("Agg")
fig = plt.figure(figsize=(5, 4), dpi=72)

axes = fig.add_axes([0.01, 0.01, 0.98, 0.98])
X = np.linspace(0, 2, 200)
Y = np.sin(2 * np.pi * X)
plt.plot(X, Y, lw=2)
plt.ylim(-1.1, 1.1)
plt.grid()
plt.show()

Plotting a scatter of points
A simple example showing how to plot a scatter of points with matplotlib.
import numpy as np
n = 1024
X = rng.normal(0, 1, n)
Y = rng.normal(0, 1, n)
T = np.arctan2(Y, X)
plt.axes([0.025, 0.025, 0.95, 0.95])

plt.scatter(X, Y, s=75, c=T, alpha=0.5)
plt.xlim(-1.5, 1.5)
plt.xticks([])
plt.ylim(-1.5, 1.5)
plt.yticks([])
plt.show()

Subplots
Show multiple subplots in matplotlib.
fig = plt.figure()
fig.subplots_adjust(bottom=0.025, left=0.025, top=0.975, right=0.975)
plt.xticks([]), plt.yticks([])
plt.xticks([])
plt.yticks([])
plt.xticks([])
plt.yticks([])
plt.xticks([])
plt.yticks([])
plt.show()

Horizontal arrangement of subplots
An example showing horizontal arrangement of subplots with matplotlib.
plt.xticks([])
plt.yticks([])
plt.text(0.5, 0.5, "subplot(2,1,1)", ha="center", va="center", size=24, alpha=0.5)
plt.xticks([])
plt.yticks([])
plt.tight_layout()
plt.show()

Subplot plot arrangement vertical
An example showing vertical arrangement of subplots with matplotlib.
plt.xticks([])
plt.yticks([])
plt.xticks([])
plt.yticks([])
plt.tight_layout()
plt.show()

A simple plotting example
A plotting example with a few simple tweaks
import numpy as np
import matplotlib

axes = fig.add_axes([0.01, 0.01, 0.98, 0.98])
y = np.sin(2 * np.pi * x)
plt.plot(x, y, lw=0.25, c="k")
plt.xticks(np.arange(0.0, 2.0, 0.1))
plt.yticks(np.arange(-1.0, 1.0, 0.1))
plt.grid()
plt.show()

Simple axes example
This example shows a couple of simple usage of axes.
plt.axes([0.1, 0.1, 0.8, 0.8])

plt.xticks([])
plt.yticks([])
plt.text(
0.6, 0.6, "axes([0.1, 0.1, 0.8, 0.8])", ha="center", va="center", size=20,␣
˓→alpha=0.5
plt.axes([0.2, 0.2, 0.3, 0.3])

plt.xticks([])
plt.yticks([])
plt.text(
0.5, 0.5, "axes([0.2, 0.2, 0.3, 0.3])", ha="center", va="center", size=16,␣
˓→alpha=0.5
plt.show()

3D plotting
A simple example of 3D plotting.
import numpy as np
ax = plt.figure().add_subplot(projection="3d")
X = np.arange(-4, 4, 0.25)
Y = np.arange(-4, 4, 0.25)
R = np.sqrt(X**2 + Y**2)
Z = np.sin(R)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=plt.cm.hot)

ax.contourf(X, Y, Z, zdir="z", offset=-2, cmap=plt.cm.hot)
ax.set_zlim(-2, 2)
plt.show()

Imshow elaborate
An example demoing imshow and styling the figure.
import numpy as np
def f(x, y):

return (1 - x / 2 + x**5 + y**3) * np.exp(-(x**2) - y**2)
n = 10
x = np.linspace(-3, 3, int(3.5 * n))
y = np.linspace(-3, 3, int(3.0 * n))
Z = f(X, Y)
plt.axes([0.025, 0.025, 0.95, 0.95])

plt.imshow(Z, interpolation="nearest", cmap="bone", origin="lower")
plt.colorbar(shrink=0.92)
plt.xticks([])
plt.yticks([])
plt.show()

Plotting a vector field: quiver
A simple example showing how to plot a vector field (quiver) with matplotlib.
import numpy as np
n = 8
T = np.arctan2(Y - n / 2.0, X - n / 2.0)
R = 10 + np.sqrt((Y - n / 2.0) ** 2 + (X - n / 2.0) ** 2)
U, V = R * np.cos(T), R * np.sin(T)
plt.axes([0.025, 0.025, 0.95, 0.95])

plt.quiver(X, Y, U, V, R, alpha=0.5)
plt.quiver(X, Y, U, V, edgecolor="k", facecolor="None", linewidth=0.5)
plt.xlim(-1, n)
plt.xticks([])
plt.ylim(-1, n)
plt.yticks([])
plt.show()

A example of plotting not quite right
An “ugly” example of plotting.
import numpy as np
import matplotlib
matplotlib.rc("grid", color="black", linestyle="-", linewidth=1)

axes = fig.add_axes([0.01, 0.01, 0.98, 0.98], facecolor=".75")
X = np.linspace(0, 2, 40)
plt.plot(X, Y, lw=0.05, c="b", antialiased=False)
plt.xticks([])
plt.yticks(np.arange(-1.0, 1.0, 0.2))
plt.grid()
ax = plt.gca()
plt.show()

Displaying the contours of a function
An example showing how to display the contours of a function with matplotlib.
import numpy as np
def f(x, y):

n = 256
plt.axes([0.025, 0.025, 0.95, 0.95])
plt.contourf(X, Y, f(X, Y), 8, alpha=0.75, cmap=plt.cm.hot)

C = plt.contour(X, Y, f(X, Y), 8, colors="black", linewidths=0.5)
plt.clabel(C, inline=1, fontsize=10)
plt.xticks([])
plt.yticks([])
plt.show()

Plotting in polar coordinates
A simple example showing how to plot in polar coordinates with matplotlib.
import numpy as np
ax = plt.axes([0.025, 0.025, 0.95, 0.95], polar=True)
N = 20
theta = np.arange(0.0, 2 * np.pi, 2 * np.pi / N)

bar.set_facecolor(plt.cm.jet(r / 10.0))
bar.set_alpha(0.5)
ax.set_xticklabels([])
ax.set_yticklabels([])
plt.show()

Plot and filled plots
Simple example of plots and filling between them with matplotlib.
import numpy as np
n = 256
X = np.linspace(-np.pi, np.pi, n)
Y = np.sin(2 * X)
plt.axes([0.025, 0.025, 0.95, 0.95])
plt.plot(X, Y + 1, color="blue", alpha=1.00)

plt.fill_between(X, 1, Y + 1, color="blue", alpha=0.25)
plt.plot(X, Y - 1, color="blue", alpha=1.00)

plt.fill_between(X, -1, Y - 1, (Y - 1) > -1, color="blue", alpha=0.25)
plt.fill_between(X, -1, Y - 1, (Y - 1) < -1, color="red", alpha=0.25)
plt.xlim(-np.pi, np.pi)
plt.xticks([])
plt.ylim(-2.5, 2.5)
plt.yticks([])
plt.show()

Bar plots
An example of bar plots with matplotlib.
import numpy as np
n = 12
X = np.arange(n)
plt.axes([0.025, 0.025, 0.95, 0.95])

plt.bar(X, +Y1, facecolor="#9999ff", edgecolor="white")
plt.bar(X, -Y2, facecolor="#ff9999", edgecolor="white")

plt.text(x + 0.4, y + 0.05, f"{ y: .2f} ", ha="center", va="bottom")

plt.text(x + 0.4, -y - 0.05, f"{ y: .2f} ", ha="center", va="top")
plt.xlim(-0.5, n)
plt.xticks([])
plt.ylim(-1.25, 1.25)
plt.yticks([])
plt.show()

Subplot grid
An example showing the subplot grid in matplotlib.
plt.xticks([])
plt.yticks([])
plt.xticks([])
plt.yticks([])
plt.xticks([])
plt.yticks([])
plt.xticks([])
plt.yticks([])


plt.tight_layout()
plt.show()
Axes
This example shows various axes command to position matplotlib axes.
plt.axes([0.1, 0.1, 0.5, 0.5])

plt.xticks([])
plt.yticks([])
plt.text(
0.1, 0.1, "axes([0.1, 0.1, 0.5, 0.5])", ha="left", va="center", size=16, alpha=0.5
)
plt.axes([0.2, 0.2, 0.5, 0.5])

plt.xticks([])
plt.yticks([])
plt.text(
)


plt.axes([0.3, 0.3, 0.5, 0.5])
plt.xticks([])
plt.yticks([])
plt.text(
)
plt.axes([0.4, 0.4, 0.5, 0.5])

plt.xticks([])
plt.yticks([])
plt.text(
)
plt.show()
Grid
Displaying a grid on the axes in matploblib.
ax = plt.axes([0.025, 0.025, 0.95, 0.95])


ax.set_xlim(0, 4)
ax.set_ylim(0, 3)
ax.xaxis.set_major_locator(plt.MultipleLocator(1.0))
ax.xaxis.set_minor_locator(plt.MultipleLocator(0.1))
ax.yaxis.set_major_locator(plt.MultipleLocator(1.0))
ax.yaxis.set_minor_locator(plt.MultipleLocator(0.1))
ax.grid(which="major", axis="x", linewidth=0.75, linestyle="-", color="0.75")
ax.grid(which="minor", axis="x", linewidth=0.25, linestyle="-", color="0.75")
ax.grid(which="major", axis="y", linewidth=0.75, linestyle="-", color="0.75")
ax.grid(which="minor", axis="y", linewidth=0.25, linestyle="-", color="0.75")
plt.show()
3D plotting
Demo 3D plotting with matplotlib and style the figure.

from mpl_toolkits.mplot3d import axes3d


X, Y, Z = axes3d.get_test_data(0.05)
cset = ax.contourf(X, Y, Z)
ax.clabel(cset, fontsize=9, inline=1)
plt.xticks([])
plt.yticks([])
ax.set_zticks([])
ax.text2D(
-0.05,
1.05,
" 3D plots \n",
horizontalalignment="left",
verticalalignment="top",
bbox={"facecolor": "white", "alpha": 1.0},
family="DejaVu Sans",
size="x-large",
transform=plt.gca().transAxes,
)
ax.text2D(
-0.05,
0.975,
" Plot 2D or 3D data",
size="medium",
)
plt.show()
GridSpec
An example demoing gridspec


from matplotlib import gridspec
G = gridspec.GridSpec(3, 3)
axes_1 = plt.subplot(G[0, :])

plt.xticks([])
plt.yticks([])
plt.text(0.5, 0.5, "Axes 1", ha="center", va="center", size=24, alpha=0.5)
axes_2 = plt.subplot(G[1, :-1])

plt.xticks([])
plt.yticks([])
axes_3 = plt.subplot(G[1:, -1])

plt.xticks([])
plt.yticks([])
axes_4 = plt.subplot(G[-1, 0])

plt.xticks([])
plt.yticks([])
axes_5 = plt.subplot(G[-1, -2])

plt.xticks([])
plt.yticks([])
plt.tight_layout()
plt.show()

Demo text printing
A example showing off elaborate text printing with matplotlib.
import numpy as np
eqs = []
eqs.append(
r"$W^{3\beta}_{\delta_1 \rho_1 \sigma_2} = U^{3\beta}_{\delta_1 \rho_1} + \frac{1}
˓→ {8 \pi 2} \int^{\alpha_2}_{\alpha_2} d \alpha^\prime_2 \left[\frac{ U^{2\beta}_{\
˓→delta_1 \rho_1} - \alpha^\prime_2U^{1\beta}_{\rho_1 \sigma_2} }{U^{0\beta}_{\rho_1 \
˓→sigma_2}}\right]$"
)
eqs.append(
r"$\frac{d\rho}{d t} + \rho \vec{v} \cdot\nabla\vec{v} = -\nabla p + \mu\nabla^2 \
˓→vec{v} + \rho \vec{g} $"
)
eqs.append(r"$\int_{-\infty}^\infty e^{-x^2}dx=\sqrt{\pi}$")
eqs.append(r"$E = mc^2 = \sqrt{{m_0}^2c^4 + p^2c^2}$")
eqs.append(r"$F_G = G\frac{m_1m_2} {r^2}$")
plt.axes([0.025, 0.025, 0.95, 0.95])


for i in range(24):
index = rng.integers(0, len(eqs))
eq = eqs[index]
size = np.random.uniform(12, 32)
x, y = np.random.uniform(0, 1, 2)
alpha = np.random.uniform(0.25, 0.75)
plt.text(
x,
y,
eq,
ha="center",
va="center",
color="#11557c",
alpha=alpha,
fontsize=size,
clip_on=True,
)
plt.xticks([])
plt.yticks([])
plt.show()
4.7.2 Code for the chapter’s exercises
4.7.3 Example demoing choices for an option
4.7.4 Code generating the summary figures with a title
Code for the chapter’s exercises
Exercise 1
Solution of the exercise 1 with matplotlib.

import numpy as np
n = 256
plt.plot(X, C)
plt.plot(X, S)
plt.show()

Exercise 4
Exercise 4 with matplotlib.
import numpy as np

plt.subplot(111)

S = np.sin(X)
C = np.cos(X)


plt.show()

Exercise 3
import numpy as np

plt.subplot(111)


plt.xlim(-4.0, 4.0)
plt.ylim(-1.0, 1.0)
plt.show()

Exercise 5
import numpy as np

plt.subplot(111)

S = np.sin(X)
C = np.cos(X)


plt.xticks([-np.pi, -np.pi / 2, 0, np.pi / 2, np.pi])

plt.yticks([-1, 0, +1])
plt.show()

Exercise 6
import numpy as np

plt.subplot(111)

C = np.cos(X)
S = np.sin(X)


plt.xticks(
[-np.pi, -np.pi / 2, 0, np.pi / 2, np.pi],
[r"$-\pi$", r"$-\pi/2$", r"$0$", r"$+\pi/2$", r"$+\pi$"],
)

plt.yticks([-1, 0, +1], [r"$-1$", r"$0$", r"$+1$"])
plt.show()

Exercise 2
import numpy as np
# Create a new figure of size 8x6 points, using 100 dots per inch
# Create a new subplot from a grid of 1x1

plt.subplot(111)

# Plot cosine using blue color with a continuous line of width 1 (pixels)
# Plot sine using green color with a continuous line of width 1 (pixels)
plt.plot(X, S, color="green", linewidth=1.0, linestyle="-")
# Set x limits
plt.xlim(-4.0, 4.0)
# Set x ticks


# Set y limits
plt.ylim(-1.0, 1.0)
# Set y ticks
# Show result on screen

plt.show()
Exercise 7
Exercise 7 with matplotlib
import numpy as np

plt.subplot(111)
X = np.linspace(-np.pi, np.pi, 256, endpoint=True)

C = np.cos(X)
S = np.sin(X)

ax = plt.gca()


ax.spines["right"].set_color("none")
ax.spines["top"].set_color("none")
ax.xaxis.set_ticks_position("bottom")
ax.spines["bottom"].set_position(("data", 0))
ax.yaxis.set_ticks_position("left")
ax.spines["left"].set_position(("data", 0))

plt.xticks(
[r"$-\pi$", r"$-\pi/2$", r"$0$", r"$+\pi/2$", r"$+\pi$"],
)

plt.yticks([-1, 0, +1], [r"$-1$", r"$0$", r"$+1$"])
plt.show()
Exercise 8
import numpy as np

plt.subplot(111)


C = np.cos(X)
S = np.sin(X)

ax = plt.gca()

plt.xticks(
[r"$-\pi$", r"$-\pi/2$", r"$0$", r"$+\pi/2$", r"$+\pi$"],
)

plt.yticks([-1, +1], [r"$-1$", r"$+1$"])
plt.legend(loc="upper left")
plt.show()
Exercise 9

import numpy as np

plt.subplot(111)

C = np.cos(X)
S = np.sin(X)

ax = plt.gca()

plt.xticks(
[r"$-\pi$", r"$-\pi/2$", r"$0$", r"$+\pi/2$", r"$+\pi$"],
)

plt.yticks([-1, +1], [r"$-1$", r"$+1$"])
t = 2 * np.pi / 3
plt.plot([t, t], [0, np.cos(t)], color="blue", linewidth=1.5, linestyle="--")
plt.scatter(


[
t,
],
[
np.cos(t),
],
50,
color="blue",
)
plt.annotate(
r"$sin(\frac{2\pi}{3} )=\frac{\sqrt{3} }{2} $",
xy=(t, np.sin(t)),
xycoords="data",
xytext=(+10, +30),
textcoords="offset points",
fontsize=16,
arrowprops={"arrowstyle": "->", "connectionstyle": "arc3,rad=.2"},
)
plt.plot([t, t], [0, np.sin(t)], color="red", linewidth=1.5, linestyle="--")

plt.scatter(
[
t,
],
[
np.sin(t),
],
50,
color="red",
)
plt.annotate(
r"$cos(\frac{2\pi}{3} )=-\frac{1} {2} $",
xy=(t, np.cos(t)),
xycoords="data",
xytext=(-90, -50),
fontsize=16,
)
plt.show()

Exercise
Exercises with matplotlib.
import numpy as np

plt.subplot(111)


ax = plt.gca()

plt.xticks(
[r"$-\pi$", r"$-\pi/2$", r"$0$", r"$+\pi/2$", r"$+\pi$"],
)

plt.yticks([-1, 1], [r"$-1$", r"$+1$"])


t = 2 * np.pi / 3
plt.plot([t, t], [0, np.cos(t)], color="blue", linewidth=1.5, linestyle="--")
plt.scatter(
[
t,
],
[
np.cos(t),
],
50,
color="blue",
)
plt.annotate(
r"$sin(\frac{2\pi}{3} )=\frac{\sqrt{3} }{2} $",
xy=(t, np.sin(t)),
xycoords="data",
xytext=(10, 30),
fontsize=16,
)
plt.plot([t, t], [0, np.sin(t)], color="red", linewidth=1.5, linestyle="--")

plt.scatter(
[
t,
],
[
np.sin(t),
],
50,
color="red",
)
plt.annotate(
r"$cos(\frac{2\pi}{3} )=-\frac{1} {2} $",
xy=(t, np.cos(t)),
xycoords="data",
xytext=(-90, -50),
fontsize=16,
)
for label in ax.get_xticklabels() + ax.get_yticklabels():

label.set_fontsize(16)
label.set_bbox({"facecolor": "white", "edgecolor": "None", "alpha": 0.65})
plt.show()

Example demoing choices for an option
The colors matplotlib line plots
An example demoing the various colors taken by matplotlib’s plot.
size = 256, 16
dpi = 72.0
figsize = size[0] / float(dpi), size[1] / float(dpi)
fig = plt.figure(figsize=figsize, dpi=dpi)
fig.patch.set_alpha(0)
plt.axes([0, 0.1, 1, 0.8], frameon=False)
for i in range(1, 11):

plt.plot([i, i], [0, 1], lw=1.5)
plt.xlim(0, 11)
plt.xticks([])
plt.yticks([])
plt.show()
Linewidth
Plot various linewidth with matplotlib.
size = 256, 16
dpi = 72.0

plt.plot([i, i], [0, 1], color="b", lw=i / 2.0)
plt.xlim(0, 11)
plt.ylim(0, 1)
plt.xticks([])
plt.yticks([])
plt.show()

Alpha: transparency
This example demonstrates using alpha for transparency.
size = 256, 16
dpi = 72.0

plt.axvline(i, linewidth=1, color="blue", alpha=0.25 + 0.75 * i / 10.0)
plt.xlim(0, 11)
plt.xticks([])
plt.yticks([])
plt.show()
Aliased versus anti-aliased
This example demonstrates aliased versus anti-aliased text.
size = 128, 16
dpi = 72.0
plt.axes([0, 0, 1, 1], frameon=False)
plt.rcParams["text.antialiased"] = False
plt.text(0.5, 0.5, "Aliased", ha="center", va="center")
plt.xlim(0, 1)
plt.ylim(0, 1)
plt.xticks([])
plt.yticks([])
plt.show()

Aliased versus anti-aliased
The example shows aliased versus anti-aliased text.
size = 128, 16
dpi = 72.0
plt.rcParams["text.antialiased"] = True
plt.text(0.5, 0.5, "Anti-aliased", ha="center", va="center")
plt.xlim(0, 1)
plt.ylim(0, 1)
plt.xticks([])
plt.yticks([])
plt.show()
Marker size
Demo the marker size control in matplotlib.
size = 256, 16
dpi = 72.0

plt.plot(
[
i,
],
[
1,
],
"s",
markersize=i,
markerfacecolor="w",
markeredgewidth=0.5,
markeredgecolor="k",


)
plt.xlim(0, 11)
plt.xticks([])
plt.yticks([])
plt.show()
Marker edge width
Demo the marker edge widths of matplotlib’s markers.
size = 256, 16
dpi = 72.0

plt.plot(
[
i,
],
[
1,
],
"s",
markersize=5,
markeredgewidth=1 + i / 10.0,
markeredgecolor="k",
)
plt.xlim(0, 11)
plt.xticks([])
plt.yticks([])
plt.show()

Colormaps
An example plotting the matplotlib colormaps.
import numpy as np
plt.rc("text", usetex=False)
a = np.outer(np.arange(0, 1, 0.01), np.ones(10))
plt.subplots_adjust(top=0.8, bottom=0.05, left=0.01, right=0.99)
maps = [m for m in plt.cm.datad if not m.endswith("_r")]
maps.sort()
l = len(maps) + 1
for i, m in enumerate(maps):
plt.subplot(1, l, i + 1)
plt.axis("off")
plt.imshow(a, aspect="auto", cmap=plt.get_cmap(m), origin="lower")
plt.title(m, rotation=90, fontsize=10, va="bottom")
plt.show()

Solid joint style
An example showing the different solid joint styles in matplotlib.
import numpy as np
size = 256, 16
dpi = 72.0
plt.plot(np.arange(3), [0, 1, 0], color="blue", linewidth=8, solid_joinstyle="miter")

plt.plot(
4 + np.arange(3), [0, 1, 0], color="blue", linewidth=8, solid_joinstyle="bevel"
)
plt.plot(
8 + np.arange(3), [0, 1, 0], color="blue", linewidth=8, solid_joinstyle="round"
)
plt.xlim(0, 12)
plt.ylim(-1, 2)
plt.xticks([])
plt.yticks([])
plt.show()
Solid cap style
An example demoing the solide cap style in matplotlib.
import numpy as np
size = 256, 16
dpi = 72.0
plt.plot(np.arange(4), np.ones(4), color="blue", linewidth=8, solid_capstyle="butt")
plt.plot(
5 + np.arange(4), np.ones(4), color="blue", linewidth=8, solid_capstyle="round"
)


plt.plot(
10 + np.arange(4),
np.ones(4),
color="blue",
linewidth=8,
solid_capstyle="projecting",
)
plt.xlim(0, 14)
plt.xticks([])
plt.yticks([])
plt.show()
Marker edge color
Demo the marker edge color of matplotlib’s markers.
import numpy as np
size = 256, 16
dpi = 72.0

r, g, b = np.random.uniform(0, 1, 3)
plt.plot(
[
i,
],
[
1,
],
"s",
markersize=5,
markeredgecolor=(r, g, b, 1),
)
plt.xlim(0, 11)
plt.xticks([])
plt.yticks([])

plt.show()
Marker face color
Demo the marker face color of matplotlib’s markers.
import numpy as np
size = 256, 16
dpi = 72.0

r, g, b = np.random.uniform(0, 1, 3)
plt.plot(
[
i,
],
[
1,
],
"s",
markersize=8,
markerfacecolor=(r, g, b, 1),
markeredgecolor=(0, 0, 0, 0.5),
)
plt.xlim(0, 11)
plt.xticks([])
plt.yticks([])
plt.show()

Dash capstyle
An example demoing the dash capstyle.
import numpy as np
size = 256, 16
dpi = 72.0
plt.plot(
np.arange(4),
np.ones(4),
color="blue",
dashes=[15, 15],
linewidth=8,
dash_capstyle="butt",
)
plt.plot(
5 + np.arange(4),
np.ones(4),
color="blue",
dashes=[15, 15],
linewidth=8,
dash_capstyle="round",
)
plt.plot(
10 + np.arange(4),
np.ones(4),
color="blue",
dashes=[15, 15],
linewidth=8,
dash_capstyle="projecting",
)
plt.xlim(0, 14)
plt.xticks([])
plt.yticks([])
plt.show()

Dash join style
Example demoing the dash join style.
import numpy as np
size = 256, 16
dpi = 72.0
plt.plot(
np.arange(3),
[0, 1, 0],
color="blue",
dashes=[12, 5],
linewidth=8,
dash_joinstyle="miter",
)
plt.plot(
4 + np.arange(3),
[0, 1, 0],
color="blue",
dashes=[12, 5],
linewidth=8,
dash_joinstyle="bevel",
)
plt.plot(
8 + np.arange(3),
[0, 1, 0],
color="blue",
dashes=[12, 5],
linewidth=8,
dash_joinstyle="round",
)
plt.xlim(0, 12)
plt.ylim(-1, 2)
plt.xticks([])
plt.yticks([])
plt.show()

Markers
Show the different markers of matplotlib.
import numpy as np
def marker(m, i):

X = i * 0.5 * np.ones(11)
Y = np.arange(11)
plt.plot(X, Y, lw=1, marker=m, ms=10, mfc=(0.75, 0.75, 1, 1), mec=(0, 0, 1, 1))

plt.text(0.5 * i, 10.25, repr(m), rotation=90, fontsize=15, va="bottom")
markers = [
0,
1,
2,
3,
4,
5,
6,
7,
"o",
"h",
"_",
"1",
"2",
"3",
"4",
"8",
"p",
"^",
"v",
"<",
">",
"|",


"d",
",",
"+",
"s",
"*",
"|",
"x",
"D",
"H",
".",
]
n_markers = len(markers)
size = 20 * n_markers, 300

dpi = 72.0
for i, m in enumerate(markers):
marker(m, i)
plt.xlim(-0.2, 0.2 + 0.5 * n_markers)

plt.xticks([])
plt.yticks([])
plt.show()
Linestyles
Plot the different line styles.

import numpy as np
def linestyle(ls, i):

X = i * 0.5 * np.ones(11)
Y = np.arange(11)
plt.plot(
X,
Y,
ls,
color=(0.0, 0.0, 1, 1),
lw=3,
ms=8,
mfc=(0.75, 0.75, 1, 1),
mec=(0, 0, 1, 1),
)
plt.text(0.5 * i, 10.25, ls, rotation=90, fontsize=15, va="bottom")
linestyles = [
"-",
"--",
":",
"-.",
".",
",",
"o",
"^",
"v",
"<",
">",
"s",
"+",


"x",
"d",
"1",
"2",
"3",
"4",
"h",
"p",
"|",
"_",
"D",
"H",
]
n_lines = len(linestyles)
size = 20 * n_lines, 300

dpi = 72.0
for i, ls in enumerate(linestyles):
linestyle(ls, i)
plt.xlim(-0.2, 0.2 + 0.5 * n_lines)

plt.xticks([])
plt.yticks([])
plt.show()
Locators for tick on axis
An example demoing different locators to position ticks on axis for matplotlib.

import numpy as np
def tickline():
plt.xlim(0, 10), plt.ylim(-1, 1), plt.yticks([])
ax = plt.gca()
ax.spines["left"].set_color("none")
ax.yaxis.set_ticks_position("none")
ax.xaxis.set_minor_locator(plt.MultipleLocator(0.1))
ax.plot(np.arange(11), np.zeros(11))
return ax
locators = [
"plt.NullLocator()",
"plt.MultipleLocator(1.0)",
"plt.FixedLocator([0, 2, 8, 9, 10])",
"plt.IndexLocator(3, 1)",
"plt.LinearLocator(5)",
"plt.LogLocator(2, [1.0])",
"plt.AutoLocator()",
]
n_locators = len(locators)
size = 512, 40 * n_locators

dpi = 72.0

for i, locator in enumerate(locators):

plt.subplot(n_locators, 1, i + 1)
ax = tickline()
ax.xaxis.set_major_locator(eval(locator))
plt.text(5, 0.3, locator[3:], ha="center")
plt.subplots_adjust(bottom=0.01, top=0.99, left=0.01, right=0.99)

plt.show()
Code generating the summary figures with a title
3D plotting vignette
Demo 3D plotting with matplotlib and decorate the figure.
import numpy as np
fig = plt.figure()


ax = Axes3D(fig)
X = np.arange(-4, 4, 0.25)
Y = np.arange(-4, 4, 0.25)
R = np.sqrt(X**2 + Y**2)
Z = np.sin(R)
ax.plot_surface(X, Y, Z, rstride=1, cstride=1, cmap=plt.cm.hot)

ax.contourf(X, Y, Z, zdir="z", offset=-2, cmap=plt.cm.hot)
ax.set_zlim(-2, 2)
plt.xticks([])
plt.yticks([])
ax.set_zticks([])
ax.text2D(
0.05,
0.93,
" 3D plots \n",
size="xx-large",
)
ax.text2D(
0.05,
0.87,
" Plot 2D or 3D data",
size="large",
)
plt.show()
Plotting in polar, decorated
An example showing how to plot in polar coordinate, and some decorations.

import numpy as np
plt.subplot(1, 1, 1, polar=True)
N = 20
theta = np.arange(0.0, 2 * np.pi, 2 * np.pi / N)
bar.set_facecolor(plt.cm.jet(r / 10.0))
bar.set_alpha(0.5)
plt.gca().set_xticklabels([])
plt.gca().set_yticklabels([])
plt.text(
-0.2,
1.02,
" Polar Axis \n",
size="xx-large",
)

plt.text(
-0.2,
1.01,
"\n\n Plot anything using polar axis ",
size="large",
)
plt.show()
Plot example vignette
An example of plots with matplotlib, and added annotations.
import numpy as np
n = 256
X = np.linspace(0, 2, n)

plt.plot(X, Y, lw=2, color="violet")

plt.xlim(-0.2, 2.2)
plt.xticks([])
plt.ylim(-1.2, 1.2)
plt.yticks([])
# Add a title and a box around it

from matplotlib.patches import FancyBboxPatch
ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,
boxstyle="square,pad=0",
zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Regular Plot: plt.plot(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Plot lines and/or markers ",
size="large",
)
plt.show()

Multiple plots vignette
Demo multiple plots and style the figure.
ax = plt.subplot(2, 1, 1)

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.72),
width=0.66,
height=0.34,
clip_on=False,
zorder=3,
facecolor="white",
alpha=1.0,
)
)

plt.text(
-0.05,
1.02,
" Multiplot: plt.subplot(...)\n",
size="xx-large",
transform=ax.transAxes,
)
plt.text(
-0.05,
1.01,
"\n\n Plot several plots at once ",
size="large",
transform=ax.transAxes,
)
plt.show()
Boxplot with matplotlib
An example of doing box plots with matplotlib

import numpy as np
fig = plt.figure(figsize=(8, 5))

axes = plt.subplot(111)
n = 5
Z = np.zeros((n, 4))
X = np.linspace(0, 2, n)
Y = rng.random((n, 4))
plt.boxplot(Y)
plt.xticks([])
plt.yticks([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,
zorder=3,
facecolor="white",
alpha=1.0,


)
)
plt.text(
-0.05,
1.02,
" Box Plot: plt.boxplot(...)\n ",
size="xx-large",
transform=axes.transAxes,
)
plt.text(
-0.04,
0.98,
"\n Make a box and whisker plot ",
size="large",
)
plt.show()
Plot scatter decorated
An example showing the scatter function, with decorations.

import numpy as np
n = 1024
X = rng.normal(0, 1, n)
Y = rng.normal(0, 1, n)
T = np.arctan2(Y, X)
plt.scatter(X, Y, s=75, c=T, alpha=0.5)

plt.xlim(-1.5, 1.5)
plt.xticks([])
plt.ylim(-1.5, 1.5)
plt.yticks([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,


zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Scatter Plot: plt.scatter(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Make a scatter plot of x versus y ",
size="large",
)
plt.show()
Pie chart vignette
Demo pie chart with matplotlib and style the figure.

import numpy as np
n = 20
X = np.ones(n)
X[-1] *= 2
plt.pie(X, explode=X * 0.05, colors=[f"{ i / float(n): f} " for i in range(n)])
fig = plt.gcf()
w, h = fig.get_figwidth(), fig.get_figheight()
r = h / float(w)
plt.xlim(-1.5, 1.5)
plt.ylim(-1.5 * r, 1.5 * r)
plt.xticks([])
plt.yticks([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,


zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Pie Chart: plt.pie(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Make a pie chart of an array ",
size="large",
)
plt.show()
Imshow demo
Demoing imshow

import numpy as np
def f(x, y):

n = 10
x = np.linspace(-3, 3, 8 * n)
y = np.linspace(-3, 3, 6 * n)
Z = f(X, Y)
plt.imshow(Z, interpolation="nearest", cmap="bone", origin="lower")
plt.xticks([])
plt.yticks([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,


zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Imshow: plt.imshow(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Display an image to current axes ",
size="large",
)
plt.show()
Bar plot advanced
An more elaborate bar plot example

import numpy as np
n = 16
X = np.arange(n)
Y1 = (1 - X / float(n)) * np.random.uniform(0.5, 1.0, n)
Y2 = (1 - X / float(n)) * np.random.uniform(0.5, 1.0, n)
plt.bar(X, Y1, facecolor="#9999ff", edgecolor="white")
plt.bar(X, -Y2, facecolor="#ff9999", edgecolor="white")
plt.xlim(-0.5, n)
plt.xticks([])
plt.ylim(-1, 1)
plt.yticks([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,
zorder=3,
facecolor="white",


alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Bar Plot: plt.bar(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Make a bar plot with rectangles ",
size="large",
)
plt.show()
Plotting quiver decorated
An example showing quiver with decorations.

import numpy as np
n = 8
T = np.arctan2(Y - n / 2.0, X - n / 2.0)
R = 10 + np.sqrt((Y - n / 2.0) ** 2 + (X - n / 2.0) ** 2)
U, V = R * np.cos(T), R * np.sin(T)
plt.quiver(X, Y, U, V, R, alpha=0.5)
plt.quiver(X, Y, U, V, edgecolor="k", facecolor="None", linewidth=0.5)
plt.xlim(-1, n)
plt.xticks([])
plt.ylim(-1, n)
plt.yticks([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,


zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Quiver Plot: plt.quiver(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Plot a 2-D field of arrows ",
size="large",
)
plt.show()
Display the contours of a function
An example demoing how to plot the contours of a function, with additional layout tweaks.

/home/runner/work/scientific-python-lectures/scientific-python-lectures/intro/
˓→matplotlib/examples/pretty_plots/plot_contour_ext.py:24: UserWarning: The following␣
˓→kwargs were not used by contour: 'linewidth'
C = plt.contour(X, Y, f(X, Y), 8, colors="black", linewidth=0.5)
import numpy as np
def f(x, y):

n = 256
plt.contourf(X, Y, f(X, Y), 8, alpha=0.75, cmap=plt.cm.hot)

C = plt.contour(X, Y, f(X, Y), 8, colors="black", linewidth=0.5)
plt.clabel(C, inline=1, fontsize=10)
plt.xticks([])
plt.yticks([])


ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,
zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Contour Plot: plt.contour(..)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Draw contour lines and filled contours ",
size="large",
)
plt.show()

Grid elaborate
An example displaying a grid on the axes and tweaking the layout.
Text(-0.05, 1.01, '\n\n Draw ticks and grid ')

from matplotlib.ticker import MultipleLocator
fig = plt.figure(figsize=(8, 6), dpi=72, facecolor="white")

axes = plt.subplot(111)
axes.set_xlim(0, 4)
axes.set_ylim(0, 3)
axes.xaxis.set_major_locator(MultipleLocator(1.0))
axes.xaxis.set_minor_locator(MultipleLocator(0.1))
axes.yaxis.set_major_locator(MultipleLocator(1.0))
axes.yaxis.set_minor_locator(MultipleLocator(0.1))
axes.grid(which="major", axis="x", linewidth=0.75, linestyle="-", color="0.75")
axes.grid(which="minor", axis="x", linewidth=0.25, linestyle="-", color="0.75")
axes.grid(which="major", axis="y", linewidth=0.75, linestyle="-", color="0.75")
axes.grid(which="minor", axis="y", linewidth=0.25, linestyle="-", color="0.75")
axes.set_xticklabels([])


axes.set_yticklabels([])

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,
zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Grid: plt.grid(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Draw ticks and grid ",
size="large",
)

Text printing decorated
An example showing text printing and decorating the resulting figure.
import numpy as np
fig = plt.figure()
plt.xticks([])
plt.yticks([])
eqs = []
eqs.append(
r"$W^{3\beta}_{\delta_1 \rho_1 \sigma_2} = U^{3\beta}_{\delta_1 \rho_1} + \frac{1}
˓→ {8 \pi 2} \int^{\alpha_2}_{\alpha_2} d \alpha^\prime_2 \left[\frac{ U^{2\beta}_{\
˓→delta_1 \rho_1} - \alpha^\prime_2U^{1\beta}_{\rho_1 \sigma_2} }{U^{0\beta}_{\rho_1 \
˓→sigma_2}}\right]$"
)
eqs.append(
r"$\frac{d\rho}{d t} + \rho \vec{v} \cdot\nabla\vec{v} = -\nabla p + \mu\nabla^2 \
˓→vec{v} + \rho \vec{g} $"
)
eqs.append(r"$\int_{-\infty}^\infty e^{-x^2}dx=\sqrt{\pi}$")
eqs.append(r"$E = mc^2 = \sqrt{{m_0}^2c^4 + p^2c^2}$")
eqs.append(r"$F_G = G\frac{m_1m_2} {r^2}$")


for i in range(24):
index = rng.integers(0, len(eqs))
eq = eqs[index]
size = rng.uniform(12, 32)
x, y = rng.uniform(0, 1, 2)
alpha = rng.uniform(0.25, 0.75)
plt.text(
x,
y,
eq,
ha="center",
va="center",
color="#11557c",
alpha=alpha,
fontsize=size,
clip_on=True,
)

ax = plt.gca()
ax.add_patch(
FancyBboxPatch(
(-0.05, 0.87),
width=0.66,
height=0.165,
clip_on=False,
zorder=3,
facecolor="white",
alpha=1.0,
)
)
plt.text(
-0.05,
1.02,
" Text: plt.text(...)\n",
size="xx-large",
)
plt.text(
-0.05,
1.01,
"\n\n Draw any kind of text ",
size="large",


)
plt.show()

CHAPTER 5
SciPy : high-level scientific computing
Authors: Gaël Varoquaux, Adrien Chauve, Andre Espaze, Emmanuelle Gouillart, Ralf Gommers
Scipy
The scipy package contains various toolboxes dedicated to common issues in scientific computing.
Its different submodules correspond to different applications, such as interpolation, integration, opti-
mization, image processing, statistics, special functions, etc.
Tip: scipy can be compared to other standard scientific-computing libraries, such as the GSL (GNU
Scientific Library for C and C++), or Matlab’s toolboxes. scipy is the core package for scientific routines
in Python; it is meant to operate efficiently on numpy arrays, so that NumPy and SciPy work hand in
hand.
Before implementing a routine, it is worth checking if the desired data processing is not already imple-
mented in SciPy. As non-professional programmers, scientists often tend to re-invent the wheel, which
leads to buggy, non-optimal, difficult-to-share and unmaintainable code. By contrast, SciPy’s routines
are optimized and tested, and should therefore be used when possible.
Chapters contents
• File input/output: scipy.io

• Special functions: scipy.special
• Linear algebra operations: scipy.linalg
• Interpolation: scipy.interpolate
211
• Optimization and fit: scipy.optimize

• Statistics and random numbers: scipy.stats
• Numerical integration: scipy.integrate
• Fast Fourier transforms: scipy.fft
• Signal processing: scipy.signal
• Image manipulation: scipy.ndimage
• Summary exercises on scientific computing
• Full code examples for the SciPy chapter
Warning: This tutorial is far from an introduction to numerical computing. As enumerating the
different submodules and functions in SciPy would be very boring, we concentrate instead on a few
examples to give a general idea of how to use scipy for scientific computing.
scipy is composed of task-specific sub-modules:
Tip: They all depend on numpy, but are mostly independent of each other. The standard way of
importing NumPy and these SciPy modules is:

5.1 File input/output: scipy.io
scipy.io contains functions for loading and saving data in several common formats including Matlab,
IDL, Matrix Market, and Harwell-Boeing.
Matlab files: Loading and saving:

>>> a = np.ones((3, 3))
>>> sp.io.savemat('file.mat', {'a': a}) # savemat expects a dictionary
>>> data = sp.io.loadmat('file.mat')
>>> data['a']
array([[1., 1., 1.],
[1., 1., 1.],
[1., 1., 1.]])
Warning: Python / Matlab mismatch: The Matlab file format does not support 1D arrays.
>>> a = np.ones(3)
>>> a
array([1., 1., 1.])
>>> a.shape
(3,)
>>> sp.io.savemat('file.mat', {'a': a})
>>> a2 = sp.io.loadmat('file.mat')['a']
>>> a2
array([[1., 1., 1.]])
5.1. File input/output: scipy.io 212

>>> a2.shape
(1, 3)
Notice that the original array was a one-dimensional array, whereas the saved and reloaded array is
a two-dimensional array with a single row.
For other formats, see the scipy.io documentation.
See also:
• Load text files: numpy.loadtxt()/numpy.savetxt()
• Clever loading of text/csv files: numpy.genfromtxt()
• Fast and efficient, but NumPy-specific, binary format: numpy.save()/numpy.load()
• Basic input/output of images in Matplotlib: matplotlib.pyplot.imread()/matplotlib.pyplot.
imsave()
• More advanced input/output of images: imageio
5.2 Special functions: scipy.special
“Special” functions are functions commonly used in science and mathematics that are not considered to
be “elementary” functions. Examples include
• the gamma function, scipy.special.gamma(),
• the error function, scipy.special.erf(),
• Bessel functions, such as scipy.special.jv() (Bessel functions of the first kind), and
• elliptic functions, such as scipy.special.ellipj() (Jacobian elliptic functions).
Other special functions are combinations of familiar elementary functions, but they offer better accuracy
or robustness than their naive implementations would.
Most of these function are computed elementwise and follow standard NumPy broadcasting rules when
the input arrays have different shapes. For example, scipy.special.xlog1py() is mathematically
equivalent to 𝑥 log(1 + 𝑦).

>>> x = np.asarray([1, 2])
>>> y = np.asarray([[3], [4], [5]])
>>> res = sp.special.xlog1py(x, y)
>>> res.shape
(3, 2)
>>> ref = x * np.log(1 + y)
>>> np.allclose(res, ref)
True
However, it is numerically favorable for small 𝑦, when explicit addition of 1 would lead to loss of precision
due to floating point truncation error.
>>> x = 2.5
>>> y = 1e-18
>>> x * np.log(1 + y)
0.0
>>> sp.special.xlog1py(x, y)
2.5e-18
5.2. Special functions: scipy.special 213

Many special functions also have “logarithmized” variants. For instance, the gamma function Γ(·) is
related to the factorial function by 𝑛! = Γ(𝑛 + 1), but it extends the domain from the positive integers
to the complex plane.
>>> x = np.arange(10)
>>> np.allclose(sp.special.gamma(x + 1), sp.special.factorial(x))
True
>>> sp.special.gamma(5) < sp.special.gamma(5.5) < sp.special.gamma(6)
True
The factorial function grows quickly, and so the gamma function overflows for moderate values of the
argument. However, sometimes only the logarithm of the gamma function is needed. In such cases, we
can compute the logarithm of the gamma function directly using scipy.special.gammaln().
>>> x = [5, 50, 500]

>>> np.log(sp.special.gamma(x))
array([ 3.17805383, 144.56574395, inf])
>>> sp.special.gammaln(x)
array([ 3.17805383, 144.56574395, 2605.11585036])
Such functions can often be used when the intermediate components of a calculation would overflow
or underflow, but the final result would not. For example, suppose we wish to compute the ratio
Γ(500)/Γ(499).
>>> a = sp.special.gamma(500)
>>> b = sp.special.gamma(499)
>>> a, b
(inf, inf)
Both the numerator and denominator overflow, so performing $a / b$ will not return the result we seek.
However, the magnitude of the result should be moderate, so the use of logarithms comes to mind.
Combining the identities log(𝑎/𝑏) = log(𝑎) − log(𝑏) and exp(log(𝑥)) = 𝑥, we get:
>>> log_a = sp.special.gammaln(500)

>>> log_b = sp.special.gammaln(499)
>>> log_res = log_a - log_b
>>> res = np.exp(log_res)
>>> res
499.0000000...
Similarly, suppose we wish to compute the difference log(Γ(500) − Γ(499)). For this, we use scipy.
special.logsumexp(), which computes log(exp(𝑥)+exp(𝑦)) using a numerical trick that avoids overflow.
>>> res = sp.special.logsumexp([log_a, log_b],

... b=[1, -1]) # weights the terms of the sum
>>> res
2605.113844343...
For more information about these and many other special functions, see the documentation of scipy.
special.
5.2. Special functions: scipy.special 214

5.3 Linear algebra operations: scipy.linalg
scipy.linalg provides a Python interface to efficient, compiled implementations of standard linear alge-
bra operations: the BLAS (Basic Linear Algebra Subroutines) and LAPACK (Linear Algebra PACKage)
libraries.
For example, the scipy.linalg.det() function computes the determinant of a square matrix:

>>> arr = np.array([[1, 2],
... [3, 4]])
>>> sp.linalg.det(arr)
-2.0
Mathematically, the solution of a linear system 𝐴𝑥 = 𝑏 is 𝑥 = 𝐴−1 𝑏, but explicit inversion of a matrix is
numerically unstable and should be avoided. Instead, use scipy.linalg.solve():
>>> A = np.array([[1, 2],

... [2, 3]])
>>> b = np.array([14, 23])
>>> x = sp.linalg.solve(A, b)
>>> x
array([4., 5.])
>>> np.allclose(A @ x, b)
True
Linear systems with special structure can often be solved more efficiently than more general systems. For
example, systems with triangular matrices can be solved using scipy.linalg.solve_triangular():
>>> A_upper = np.triu(A)

>>> A_upper
array([[1, 2],
[0, 3]])
>>> np.allclose(sp.linalg.solve_triangular(A_upper, b, lower=False),
... sp.linalg.solve(A_upper, b))
True
scipy.linalg also features matrix factorizations/decompositions such as the singular value decomposi-
tion.
>>> A = np.array([[1, 2],

... [2, 3]])
>>> U, s, Vh = sp.linalg.svd(A)
>>> s # singular values
array([4.23606798, 0.23606798])
The original matrix can be recovered by matrix multiplication of the factors:
>>> S = np.diag(s) # convert to diagonal matrix before matrix multiplication

>>> A2 = U @ S @ Vh
>>> np.allclose(A2, A)
True
>>> A3 = (U * s) @ Vh # more efficient: use array math broadcasting rules!
>>> np.allclose(A3, A)
True
Many other decompositions (e.g. LU, Cholesky, QR), solvers for structured linear systems (e.g. triangu-
lar, circulant), eigenvalue problem algorithms, matrix functions (e.g. matrix exponential), and routines
for special matrix creation (e.g. block diagonal, toeplitz) are available in scipy.linalg.
5.3. Linear algebra operations: scipy.linalg 215

5.4 Interpolation: scipy.interpolate
scipy.interpolate is useful for fitting a function from experimental data and thus evaluating points
where no reference value exists. The module includes, but not limited to FITPACK Fortran subroutines.
By imagining experimental data close to a sine function:
>>> measured_time = np.linspace(0, 1, 10)

>>> noise = (rng.random(10)*2 - 1) * 1e-1
>>> measures = np.sin(2 * np.pi * measured_time) + noise
scipy.interpolate has many interpolation methods which need to be chosen based on the data. See
the tutorial for some guidelines:
>>> spline = sp.interpolate.CubicSpline(measured_time, measures)
Then the result can be evaluated at the time of interest:
>>> interpolation_time = np.linspace(0, 1, 50)

>>> linear_results = spline(interpolation_time)
scipy.interpolate.CloughTocher2DInterpolator is similar to scipy.interpolate.CubicSpline,

but for 2-D arrays. See the summary exercise on Maximum wind speed prediction at the Sprogø sta-
tion for a more advanced spline interpolation example.
5.5 Optimization and fit: scipy.optimize
scipy.optimize provides algorithms for root finding, curve fitting, and more general optimization.
5.5.1 Root Finding
scipy.optimize.root_scalar() attempts to find a root of a specified scalar-valued function (i.e., an

argument at which the function value is zero). Like many scipy.optimize functions, the function needs
an initial guess of the solution, which the algorithm will refine until it converges or recognizes failure.
We also provide the derivative to improve the rate of convergence.
>>> def f(x):

... return (x-1)*(x-2)
>>> def df(x):
5.4. Interpolation: scipy.interpolate 216


... return 2*x - 3
>>> x0 = 0 # guess
>>> res = sp.optimize.root_scalar(f, x0=x0, fprime=df)
>>> res
converged: True
flag: converged
function_calls: 12
iterations: 6
root: 1.0
method: newton
Warning: None of the functions in scipy.optimize that accept a guess are guaranteed to converge
for all possible guesses! (For example, try x0=1.5 in the example above, where the derivative of
the function is exactly zero.) If this occurs, try a different guess, adjust the options (like providing
a bracket as shown below), or consider whether SciPy offers a more appropriate method for the
problem.
Note that only one the root at 1.0 is found. By inspection, we can tell that there is a second root at
2.0. We can direct the function toward a particular root by changing the guess or by passing a bracket
that contains only the root we seek.
>>> res = sp.optimize.root_scalar(f, bracket=(1.5, 10))

>>> res.root
2.0
For multivariate problems, use scipy.optimize.root().
>>> def f(x):

... # intersection of unit circle and line from origin
... return [x[0]**2 + x[1]**2 - 1,
... x[1] - x[0]]
>>> res = sp.optimize.root(f, x0=[0, 0])
>>> np.allclose(f(res.x), 0, atol=1e-10)
True
>>> np.allclose(res.x, np.sqrt(2)/2)
True
Over-constrained problems can be solved in the least-squares sense using scipy.optimize.root() with
method='lm' (Levenberg-Marquardt).
>>> def f(x):

... # intersection of unit circle, line from origin, and parabola
... return [x[0]**2 + x[1]**2 - 1,
... x[1] - x[0],
... x[1] - x[0]**2]
>>> res = sp.optimize.root(f, x0=[1, 1], method='lm')
>>> res.success
True
>>> res.x
array([0.76096066, 0.66017736])
See the documentation of scipy.optimize.root_scalar() and scipy.optimize.root() for a variety

of other solution algorithms and options.
5.5. Optimization and fit: scipy.optimize 217

5.5.2 Curve fitting
Suppose we have data that is sinusoidal but noisy:

>>> x = np.linspace(-5, 5, num=50) # 50 values between -5 and 5
>>> noise = 0.01 * np.cos(100 * x)
>>> a, b = 2.9, 1.5
>>> y = a * np.cos(b * x) + noise
We can approximate the underlying amplitude, frequency, and phase from the data by least squares
curve fitting. To begin, we write a function that accepts the independent variable as the first argument
and all parameters to fit as separate arguments:
>>> def f(x, a, b, c):
... return a * np.sin(b * x + c)
We then use scipy.optimize.curve_fit() to find 𝑎 and 𝑏:
>>> params, _ = sp.optimize.curve_fit(f, x, y, p0=[2, 1, 3])

>>> params
array([2.900026 , 1.50012043, 1.57079633])
>>> ref = [a, b, np.pi/2] # what we'd expect
>>> np.allclose(params, ref, rtol=1e-3)
True
Exercise: Curve fitting of temperature data
The temperature extremes in Alaska for each month, starting in January, are given by (in
degrees Celsius):
max: 17, 19, 21, 28, 33, 38, 37, 37, 31, 23, 19, 18
min: -62, -59, -56, -46, -32, -18, -9, -13, -25, -46, -52, -58

1. Plot these temperature extremes.

2. Define a function that can describe min and max temperatures. Hint: this function
has to have a period of 1 year. Hint: include a time offset.
3. Fit this function to the data with scipy.optimize.curve_fit().
4. Plot the result. Is the fit reasonable? If not, why?
5. Is the time offset for min and max temperatures the same within the fit accuracy?
solution
5.5.3 Optimization
Suppose we wish to minimize the scalar-valued function of a single variable 𝑓 (𝑥) = 𝑥2 + 10 sin(𝑥):
>>> def f(x):

... return x**2 + 10*np.sin(x)
>>> x = np.arange(-5, 5, 0.1)
>>> plt.plot(x, f(x))
>>> plt.show()
We can see that the function has a local minimizer near 𝑥 = 3.8 and a global minimizer near 𝑥 = −1.3,
but the precise values cannot be determined from the plot.
The most appropriate function for this purpose is scipy.optimize.minimize_scalar(). Since we know
the approximate locations of the minima, we will provide bounds that restrict the search to the vicinity
of the global minimum.
>>> res = sp.optimize.minimize_scalar(f, bounds=(-2, -1))

>>> res
message: Solution found.
success: True
status: 0
fun: -7.9458233756...
x: -1.306440997...
nit: 8
nfev: 8
>>> res.fun == f(res.x)
True
If we did not already know the approximate location of the global minimum, we could use one of

SciPy’s global minimizers, such as scipy.optimize.differential_evolution(). We are required to

pass bounds, but they do not need to be tight.
>>> bounds=[(-5, 5)] # list of lower, upper bound for each variable
>>> res = sp.optimize.differential_evolution(f, bounds=bounds)
>>> res
message: Optimization terminated successfully.
success: True
fun: -7.9458233756...
x: [-1.306e+00]
nit: 6
nfev: 111
jac: [ 9.948e-06]
For multivariate optimization, a good choice for many problems is scipy.optimize.minimize(). Sup-
pose we wish to find the minimum of a quadratic function of two variables, 𝑓 (𝑥0 , 𝑥1 ) = (𝑥0 −1)2 +(𝑥1 −2)2 .
>>> def f(x):

... return (x[0] - 1)**2 + (x[1] - 2)**2
Like scipy.optimize.root(), scipy.optimize.minimize() requires a guess x0. (Note that this is the
initial value of both variables rather than the value of the variable we happened to label 𝑥0 .)
>>> res = sp.optimize.minimize(f, x0=[0, 0])

>>> res
success: True
status: 0
fun: 1.70578...e-16
x: [ 1.000e+00 2.000e+00]
nit: 2
jac: [ 3.219e-09 -8.462e-09]
hess_inv: [[ 9.000e-01 -2.000e-01]
[-2.000e-01 6.000e-01]]
nfev: 9
njev: 3
Maximization?
Is scipy.optimize.minimize() restricted to the solution of minimization problems? Nope! To solve

a maximization problem, simply minimize the negative of the original objective function.
This barely scratches the surface of SciPy’s optimization features, which include mixed integer linear
programming, constrained nonlinear programming, and the solution of assignment problems. For much
more information, see the documentation of scipy.optimize and the advanced chapter Mathematical
optimization: finding minima of functions.
Exercise: 2-D minimization

The six-hump camelback function
𝑥4 2
𝑓 (𝑥, 𝑦) = (4 − 2.1𝑥2 + )𝑥 + 𝑥𝑦 + (4𝑦 2 − 4)𝑦 2
3
has multiple local minima. Find a global minimum (there is more than one, each with the
same value of the objective function) and at least one other local minimum.
Hints:
• Variables can be restricted to −2 < 𝑥 < 2 and −1 < 𝑦 < 1.
• numpy.meshgrid() and matplotlib.pyplot.imshow() can help with visualization.
• Try minimizing with scipy.optimize.minimize() with an initial guess of (𝑥, 𝑦) =
(0, 0). Does it find the global minimum, or converge to a local minimum? What about
other initial guesses?
• Try minimizing with scipy.optimize.differential_evolution().
solution
See the summary exercise on Non linear least squares curve fitting: application to point extraction in
topographical lidar data for another, more advanced example.
5.6 Statistics and random numbers: scipy.stats
scipy.stats contains fundamental tools for statistics in Python.
5.6.1 Statistical Distributions
Consider a random variable distributed according to the standard normal. We draw a sample consisting
of 100000 observations from the random variable. The normalized histogram of the sample is an estimator
of the random variable’s probability density function (PDF):
>>> dist = sp.stats.norm(loc=0, scale=1) # standard normal distribution

>>> sample = dist.rvs(size=100000) # "random variate sample"
>>> plt.hist(sample, bins=50, density=True, label='normalized histogram')
>>> x = np.linspace(-5, 5)
>>> plt.plot(x, dist.pdf(x), label='PDF')
>>> plt.legend()
5.6. Statistics and random numbers: scipy.stats 221

Distribution objects and frozen distributions
Each of the 100+ scipy.stats distribution families is represented by an object with a __call__
method. Here, we call the scipy.stats.norm object to specify its location and scale, and it returns a
frozen distribution: a particular element of a distribution family with all parameters fixed. The frozen
distribution object has methods to compute essential functions of the particular distribution.
Suppose we knew that the sample had been drawn from a distribution belonging to the family of normal
distributions, but we did not know the particular distribution’s location (mean) and scale (standard
deviation). We perform maximum likelihood estimation of the unknown parameters using the distribution
family’s fit method:
>>> loc, scale = sp.stats.norm.fit(sample)

>>> loc
0.0015767005...
>>> scale
0.9973396878...
Since we know the true parameters of the distribution from which the sample was drawn, we are not
surprised that these estimates are similar.
Exercise: Probability distributions
Generate 1000 random variates from a gamma distribution with a shape parameter of 1. Hint: the
shape parameter is passed as the first argument when freezing the distribution. Plot the histogram of
the sample, and overlay the distribution’s PDF. Estimate the shape parameter from the sample using
the fit method.
Extra: the distributions have many useful methods. Explore them using tab completion. Plot the
cumulative density function of the distribution, and compute the variance.
5.6. Statistics and random numbers: scipy.stats 222

5.6.2 Sample Statistics and Hypothesis Tests
The sample mean is an estimator of the mean of the distribution from which the sample was drawn:
>>> np.mean(sample)
0.001576700508...
NumPy includes some of the most fundamental sample statistics (e.g. numpy.mean(), numpy.var(),
numpy.percentile()); scipy.stats includes many more. For instance, the geometric mean is a common
measure of central tendency for data that tends to be distributed over many orders of magnitude.
>>> sp.stats.gmean(2**sample)
1.0010934829...
SciPy also includes a variety of hypothesis tests that produce a sample statistic and a p-value. For
instance, suppose we wish to test the null hypothesis that sample was drawn from a normal distribution:
>>> res = sp.stats.normaltest(sample)

>>> res.statistic
5.20841759...
>>> res.pvalue
0.07396163283...
Here, statistic is a sample statistic that tends to be high for samples that are drawn from non-normal
distributions. pvalue is the probability of observing such a high value of the statistic for a sample
that has been drawn from a normal distribution. If the p-value is unusually small, this may be taken
as evidence that sample was not drawn from the normal distribution. Our statistic and p-value are
moderate, so the test is inconclusive.
There are many other features of scipy.stats, including circular statistics, quasi-Monte Carlo methods,
and resampling methods. For much more information, see the documentation of scipy.stats and the
advanced chapter statistics.
5.7 Numerical integration: scipy.integrate
5.7.1 Quadrature
∫︀ 𝜋/2
Suppose we wish to compute the definite integral 0 sin(𝑡)𝑑𝑡 numerically. scipy.integrate.quad()
chooses one of several adaptive techniques depending on the parameters, and is therefore the recom-
mended first choice for integration of function of a single variable:
>>> integral, error_estimate = sp.integrate.quad(np.sin, 0, np.pi/2)

>>> np.allclose(integral, 1) # numerical result ~ analytical result
True
>>> abs(integral - 1) < error_estimate # actual error < estimated error
True
Other functions for numerical quadrature, including integration of multivariate functions and approxi-
mating integrals from samples, are available in scipy.integrate.
5.7. Numerical integration: scipy.integrate 223

5.7.2 Initial Value Problems
scipy.integrate also features routines for integrating Ordinary Differential Equations (ODE). For
example, scipy.integrate.solve_ivp() integrates ODEs of the form:
𝑑𝑦
= 𝑓 (𝑡, 𝑦(𝑡))
𝑑𝑡
from an initial time 𝑡0 and initial state 𝑦(𝑡 = 𝑡0 ) = 𝑡0 to a final time 𝑡𝑓 or until an event occurs (e.g. a
specified state is reached).
As an introduction, consider the initial value problem given by 𝑑𝑦 𝑑𝑡 = −2𝑦 and the initial condition
𝑦(𝑡 = 0) = 1 on the interval 𝑡 = 0 . . . 4. We begin by defining a callable that computes 𝑓 (𝑡, 𝑦(𝑡)) given
the current time and state.
>>> def f(t, y):

... return -2 * y
Then, to compute y as a function of time:
>>> t_span = (0, 4) # time interval

>>> t_eval = np.linspace(*t_span) # times at which to evaluate `y`
>>> y0 = [1,] # initial state
>>> res = sp.integrate.solve_ivp(f, t_span=t_span, y0=y0, t_eval=t_eval)
and plot the result:
>>> plt.plot(res.t, res.y[0])

>>> plt.xlabel('t')
Text(0.5, ..., 't')
>>> plt.ylabel('y')
Text(..., 0.5, 'y')
>>> plt.title('Solution of Initial Value Problem')
Text(0.5, 1.0, 'Solution of Initial Value Problem')
Let us integrate a more complex ODE: a damped spring-mass oscillator. The position of√︀ a mass attached
to a spring obeys the 2nd order ODE 𝑦¨ + 2𝜁𝜔0 𝑦˙ + 𝜔02 𝑦 = 0 with natural frequency 𝜔0 = 𝑘/𝑚, damping
ratio 𝜁 = 𝑐/(2𝑚𝜔0 ), spring constant 𝑘, mass 𝑚, and damping coefficient 𝑐.
Before using scipy.integrate.solve_ivp(), the 2nd order ODE needs to be transformed into a system
of first-order ODEs. Note that
𝑑𝑦 𝑑𝑦˙
= 𝑦˙ = 𝑦¨ = −(2𝜁𝜔0 𝑦˙ + 𝜔02 𝑦)
𝑑𝑡 𝑑𝑡
If we define 𝑧 = [𝑧0 , 𝑧1 ] where 𝑧0 = 𝑦 and 𝑧1 = 𝑦,˙ then the first order equation:
[︂ 𝑑𝑧0 ]︂ [︂ ]︂
𝑑𝑧 𝑑𝑡 𝑧1
= 𝑑𝑧1 =
𝑑𝑡 𝑑𝑡
−(2𝜁𝜔0 𝑧1 + 𝜔02 𝑧0 )
5.7. Numerical integration: scipy.integrate 224

is equivalent to the original second order equation.

We set:
>>> m = 0.5 # kg
>>> k = 4 # N/m
>>> c = 0.4 # N s/m
>>> zeta = c / (2 * m * np.sqrt(k/m))
>>> omega = np.sqrt(k / m)
and define the function that computes 𝑧˙ = 𝑓 (𝑡, 𝑧(𝑡)):
>>> def f(t, z, zeta, omega):

... return (z[1], -2.0 * zeta * omega * z[1] - omega**2 * z[0])
Integration of the system follows:
>>> t_span = (0, 10)

>>> t_eval = np.linspace(*t_span, 100)
>>> z0 = [1, 0]
>>> res = sp.integrate.solve_ivp(f, t_span, z0, t_eval=t_eval,
... args=(zeta, omega), method='LSODA')
Tip: With the option method=’LSODA’, scipy.integrate.solve_ivp() uses the LSODA (Liver-
more Solver for Ordinary Differential equations with Automatic method switching for stiff and non-stiff
problems). See the ODEPACK Fortran library for more details.
See also:
Partial Differental Equations
There is no Partial Differential Equations (PDE) solver in SciPy. Some Python packages for solving
PDE’s are available, such as fipy or SfePy.
5.8 Fast Fourier transforms: scipy.fft
The scipy.fft module computes fast Fourier transforms (FFTs) and offers utilities to handle them.
Some important functions are:
• scipy.fft.fft() to compute the FFT
• scipy.fft.fftfreq() to generate the sampling frequencies
• scipy.fft.ifft() to compute the inverse FFT, from frequency space to signal space
5.8. Fast Fourier transforms: scipy.fft 225

As an illustration, a (noisy) input signal (sig), and its FFT:
>>> sig_fft = sp.fft.fft(sig)

>>> freqs = sp.fft.fftfreq(sig.size, d=time_step)
Signal FFT
As the signal comes from a real-valued function, the Fourier transform is symmetric.
The peak signal frequency can be found with freqs[power.argmax()]
Setting the Fourier component above this frequency to zero and inverting the FFT with scipy.fft.
ifft(), gives a filtered signal.
Note: The code of this example can be found here

numpy.fft
NumPy also has an implementation of FFT (numpy.fft). However, the SciPy one should be preferred,
as it uses more efficient underlying implementations.
Fully worked examples:
Crude periodicity finding (link) Gaussian image blur (link)
Exercise: Denoise moon landing image

1. Examine the provided image moonlanding.png, which is heavily contaminated with periodic
noise. In this exercise, we aim to clean up the noise using the Fast Fourier Transform.
2. Load the image using matplotlib.pyplot.imread().
3. Find and use the 2-D FFT function in scipy.fft, and plot the spectrum (Fourier transform of)
the image. Do you have any trouble visualising the spectrum? If so, why?
4. The spectrum consists of high and low frequency components. The noise is contained in the
high-frequency part of the spectrum, so set some of those components to zero (use array slicing).
5. Apply the inverse Fourier transform to see the resulting image.
Solution

5.9 Signal processing: scipy.signal
Tip: scipy.signal is for typical signal processing: 1D, regularly-sampled signals.
Resampling scipy.signal.resample(): resample a signal to n points using FFT.
>>> t = np.linspace(0, 5, 100)

>>> x = np.sin(t)
>>> x_resampled = sp.signal.resample(x, 25)
>>> plt.plot(t, x)
>>> plt.plot(t[::4], x_resampled, 'ko')
Tip: Notice how on the side of the window the resampling is less accurate and has a rippling effect.
This resampling is different from the interpolation provided by scipy.interpolate as it only applies to
regularly sampled data.
Detrending scipy.signal.detrend(): remove linear trend from signal:
5.9. Signal processing: scipy.signal 229

>>> t = np.linspace(0, 5, 100)

>>> x = t + rng.normal(size=100)
>>> x_detrended = sp.signal.detrend(x)
>>> plt.plot(t, x)
>>> plt.plot(t, x_detrended)
Filtering: For non-linear filtering, scipy.signal has filtering (median filter scipy.signal.medfilt(),
Wiener scipy.signal.wiener()), but we will discuss this in the image section.
Tip: scipy.signal also has a full-blown set of tools for the design of linear filter (finite and infinite
response filters), but this is out of the scope of this tutorial.
Spectral analysis: scipy.signal.spectrogram() compute a spectrogram –frequency spectrums over

consecutive time windows–, while scipy.signal.welch() comptes a power spectrum density (PSD).
5.9. Signal processing: scipy.signal 230

5.10 Image manipulation: scipy.ndimage
scipy.ndimage provides manipulation of n-dimensional arrays as images.
5.10.1 Geometrical transformations on images
Changing orientation, resolution, ..
>>> # Load an image

>>> # Shift, rotate and zoom it

>>> shifted_face = sp.ndimage.shift(face, (50, 50))
>>> shifted_face2 = sp.ndimage.shift(face, (50, 50), mode='nearest')
>>> rotated_face = sp.ndimage.rotate(face, 30)
>>> cropped_face = face[50:-50, 50:-50]
>>> zoomed_face = sp.ndimage.zoom(face, 2)
>>> zoomed_face.shape
(1536, 2048)
>>> plt.subplot(151)
<Axes: >
>>> plt.imshow(shifted_face, cmap=plt.cm.gray)

>>> plt.axis('off')
(-0.5, 1023.5, 767.5, -0.5)
>>> # etc.
5.10.2 Image filtering
Generate a noisy face:

>>> face = face[:512, -512:] # crop out square on right
>>> noisy_face = np.copy(face).astype(float)
>>> noisy_face += face.std() * 0.5 * rng.standard_normal(face.shape)
Apply a variety of filters on it:
5.10. Image manipulation: scipy.ndimage 231

>>> blurred_face = sp.ndimage.gaussian_filter(noisy_face, sigma=3)

>>> median_face = sp.ndimage.median_filter(noisy_face, size=5)
>>> wiener_face = sp.signal.wiener(noisy_face, (5, 5))
Other filters in scipy.ndimage.filters and scipy.signal can be applied to images.
Exercise
Compare histograms for the different filtered images.
5.10.3 Mathematical morphology
Tip: Mathematical morphology stems from set theory. It characterizes and transforms geometrical
structures. Binary (black and white) images, in particular, can be transformed using this theory: the
sets to be transformed are the sets of neighboring non-zero-valued pixels. The theory was also extended
to gray-valued images.
Mathematical-morphology operations use a structuring element in order to modify geometrical structures.

Let us first generate a structuring element:
>>> el = sp.ndimage.generate_binary_structure(2, 1)
>>> el
array([[False, True, False],
[...True, True, True],
[False, True, False]])
>>> el.astype(int)
array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]])

• Erosion scipy.ndimage.binary_erosion()
>>> a = np.zeros((7, 7), dtype=int)

>>> a[1:6, 2:5] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> sp.ndimage.binary_erosion(a).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> # Erosion removes objects smaller than the structure
>>> sp.ndimage.binary_erosion(a, structure=np.ones((5,5))).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
• Dilation scipy.ndimage.binary_dilation()
>>> a = np.zeros((5, 5))

>>> a[2, 2] = 1
>>> a
array([[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 1., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])
>>> sp.ndimage.binary_dilation(a).astype(a.dtype)
array([[0., 0., 0., 0., 0.],
[0., 0., 1., 0., 0.],
[0., 1., 1., 1., 0.],
[0., 0., 1., 0., 0.],
[0., 0., 0., 0., 0.]])
• Opening scipy.ndimage.binary_opening()

>>> a[1:4, 1:4] = 1
>>> a[4, 4] = 1
>>> a
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 1]])


>>> # Opening removes small objects
>>> sp.ndimage.binary_opening(a, structure=np.ones((3, 3))).astype(int)
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 0]])
>>> # Opening can also smooth corners
>>> sp.ndimage.binary_opening(a).astype(int)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]])
• Closing: scipy.ndimage.binary_closing()
Exercise
Check that opening amounts to eroding, then dilating.
An opening operation removes small structures, while a closing operation fills small holes. Such opera-
tions can therefore be used to “clean” an image.
>>> a = np.zeros((50, 50))

>>> a[10:-10, 10:-10] = 1
>>> a += 0.25 * rng.standard_normal(a.shape)
>>> mask = a>=0.5
>>> opened_mask = sp.ndimage.binary_opening(mask)
>>> closed_mask = sp.ndimage.binary_closing(opened_mask)
Exercise
Check that the area of the reconstructed square is smaller than the area of the initial
square. (The opposite would occur if the closing step was performed before the opening).
For gray-valued images, eroding (resp. dilating) amounts to replacing a pixel by the minimal (resp.
maximal) value among pixels covered by the structuring element centered on the pixel of interest.

>>> a[1:6, 1:6] = 3


>>> a[4, 4] = 2; a[2, 3] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 3, 3, 3, 3, 3, 0],
[0, 3, 3, 1, 3, 3, 0],
[0, 3, 3, 3, 3, 3, 0],
[0, 3, 3, 3, 2, 3, 0],
[0, 3, 3, 3, 3, 3, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> sp.ndimage.grey_erosion(a, size=(3, 3))
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 3, 2, 2, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
5.10.4 Connected components and measurements on images
Let us first generate a nice synthetic binary image.
>>> x, y = np.indices((100, 100))

>>> sig = np.sin(2*np.pi*x/50.) * np.sin(2*np.pi*y/50.) * (1+x*y/50.**2)**2
>>> mask = sig > 1
scipy.ndimage.label() assigns a different label to each connected component:

>>> labels, nb = sp.ndimage.label(mask)

>>> nb
8
Now compute measurements on each connected component:
>>> areas = sp.ndimage.sum(mask, labels, range(1, labels.max()+1))

>>> areas # The number of pixels in each connected component
array([190., 45., 424., 278., 459., 190., 549., 424.])
>>> maxima = sp.ndimage.maximum(sig, labels, range(1, labels.max()+1))
>>> maxima # The maximum signal in each connected component
array([ 1.80238238, 1.13527605, 5.51954079, 2.49611818, 6.71673619,
1.80238238, 16.76547217, 5.51954079])
Extract the 4th connected component, and crop the array around it:
>>> sp.ndimage.find_objects(labels)[3]
(slice(30, 48, None), slice(30, 48, None))
>>> sl = sp.ndimage.find_objects(labels)[3]
>>> plt.imshow(sig[sl])
See the summary exercise on Image processing application: counting bubbles and unmolten grains for a
more advanced example.
5.11 Summary exercises on scientific computing
The summary exercises use mainly NumPy, SciPy and Matplotlib. They provide some real-life examples
of scientific computing with Python. Now that the basics of working with NumPy and SciPy have been
introduced, the interested user is invited to try these exercises.
5.11. Summary exercises on scientific computing 236

5.11.1 Maximum wind speed prediction at the Sprogø station
The exercise goal is to predict the maximum wind speed occurring every 50 years even if no measure
exists for such a period. The available data are only measured over 21 years at the Sprogø meteorological
station located in Denmark. First, the statistical steps will be given and then illustrated with functions
from the scipy.interpolate module. At the end the interested readers are invited to compute results from
raw data and in a slightly different approach.
Statistical approach
The annual maxima are supposed to fit a normal probability density function. However such function
is not going to be estimated because it gives a probability from a wind speed maxima. Finding the
maximum wind speed occurring every 50 years requires the opposite approach, the result needs to be
found from a defined probability. That is the quantile function role and the exercise goal will be to find
it. In the current model, it is supposed that the maximum wind speed occurring every 50 years is defined
as the upper 2% quantile.
By definition, the quantile function is the inverse of the cumulative distribution function. The latter
describes the probability distribution of an annual maxima. In the exercise, the cumulative probability
p_i for a given year i is defined as p_i = i/(N+1) with N = 21, the number of measured years. Thus
it will be possible to calculate the cumulative probability of every measured wind speed maxima. From
those experimental points, the scipy.interpolate module will be very useful for fitting the quantile function.
Finally the 50 years maxima is going to be evaluated from the cumulative probability of the 2% quantile.
Computing the cumulative probabilities
The annual wind speeds maxima have already been computed and saved in the NumPy format in the
file examples/max-speeds.npy, thus they will be loaded by using NumPy:

>>> max_speeds = np.load('intro/scipy/summary-exercises/examples/max-speeds.npy')
>>> years_nb = max_speeds.shape[0]
Following the cumulative probability definition p_i from the previous section, the corresponding values
will be:
>>> cprob = (np.arange(years_nb, dtype=np.float32) + 1)/(years_nb + 1)
and they are assumed to fit the given wind speeds:
>>> sorted_max_speeds = np.sort(max_speeds)
Prediction with UnivariateSpline
In this section the quantile function will be estimated by using the UnivariateSpline class which can
represent a spline from points. The default behavior is to build a spline of degree 3 and points can
have different weights according to their reliability. Variants are InterpolatedUnivariateSpline and
LSQUnivariateSpline on which errors checking is going to change. In case a 2D spline is wanted, the
BivariateSpline class family is provided. All those classes for 1D and 2D splines use the FITPACK
Fortran subroutines, that’s why a lower library access is available through the splrep and splev functions
for respectively representing and evaluating a spline. Moreover interpolation functions without the use
of FITPACK parameters are also provided for simpler use.
For the Sprogø maxima wind speeds, the UnivariateSpline will be used because a spline of degree 3
seems to correctly fit the data:


>>> quantile_func = sp.interpolate.UnivariateSpline(cprob, sorted_max_speeds)
The quantile function is now going to be evaluated from the full range of probabilities:
>>> nprob = np.linspace(0, 1, 100)

>>> fitted_max_speeds = quantile_func(nprob)
In the current model, the maximum wind speed occurring every 50 years is defined as the upper 2%
quantile. As a result, the cumulative probability value will be:
>>> fifty_prob = 1. - 0.02
So the storm wind speed occurring every 50 years can be guessed by:
>>> fifty_wind = quantile_func(fifty_prob)

>>> fifty_wind
array(32.97989825...)
The results are now gathered on a Matplotlib figure:
Fig. 1: Solution: Python source file

Exercise with the Gumbell distribution
The interested readers are now invited to make an exercise by using the wind speeds measured over 21
years. The measurement period is around 90 minutes (the original period was around 10 minutes but the
file size has been reduced for making the exercise setup easier). The data are stored in NumPy format
inside the file examples/sprog-windspeeds.npy. Do not look at the source code for the plots until you
have completed the exercise.
• The first step will be to find the annual maxima by using NumPy and plot them as a matplotlib
bar figure.
• The second step will be to use the Gumbell distribution on cumulative probabilities p_i defined as
-log( -log(p_i) ) for fitting a linear quantile function (remember that you can define the degree
of the UnivariateSpline). Plotting the annual maxima versus the Gumbell distribution should
give you the following figure.
• The last step will be to find 34.23 m/s for the maximum wind speed occurring every 50 years.


5.11.2 Non linear least squares curve fitting: application to point extraction in
topographical lidar data
The goal of this exercise is to fit a model to some data. The data used in this tutorial are lidar data
and are described in details in the following introductory paragraph. If you’re impatient and want to
practice now, please skip it and go directly to Loading and visualization.
Introduction
Lidars systems are optical rangefinders that analyze property of scattered light to measure distances.
Most of them emit a short light impulsion towards a target and record the reflected signal. This signal
is then processed to extract the distance between the lidar system and the target.
Topographical lidar systems are such systems embedded in airborne platforms. They measure distances
between the platform and the Earth, so as to deliver information on the Earth’s topography (see1 for
more details).
In this tutorial, the goal is to analyze the waveform recorded by the lidar system2 . Such a signal
contains peaks whose center and amplitude permit to compute the position and some characteristics of
the hit target. When the footprint of the laser beam is around 1m on the Earth surface, the beam can
hit multiple targets during the two-way propagation (for example the ground and the top of a tree or
building). The sum of the contributions of each target hit by the laser beam then produces a complex
signal with multiple peaks, each one containing information about one target.
One state of the art method to extract information from these data is to decompose them in a sum of
Gaussian functions where each function represents the contribution of a target hit by the laser beam.
Therefore, we use the scipy.optimize module to fit a waveform to one or a sum of Gaussian functions.
Loading and visualization
Load the first waveform using:

>>> waveform_1 = np.load('intro/scipy/summary-exercises/examples/waveform_1.npy')
and visualize it:

>>> t = np.arange(len(waveform_1))
>>> plt.plot(t, waveform_1)
>>> plt.show()
As shown below, this waveform is a 80-bin-length signal with a single peak with an amplitude of ap-
proximately 30 in the 15 nanosecond bin. Additionally, the base level of noise is approximately 3. These
values can be used in the initial solution.
1 Mallet, C. and Bretar, F. Full-Waveform Topographic Lidar: State-of-the-Art. ISPRS Journal of Photogrammetry
and Remote Sensing 64(1), pp.1-16, January 2009 http://dx.doi.org/10.1016/j.isprsjprs.2008.09.007

2 The data used for this tutorial are part of the demonstration data available for the FullAnalyze software and were
kindly provided by the GIS DRAIX.

Fitting a waveform with a simple Gaussian model
The signal is very simple and can be modeled as a single Gaussian function and an offset corresponding
to the background noise. To fit the signal with the function, we must:
• define the model
• propose an initial solution
• call scipy.optimize.leastsq
Model
A Gaussian function defined by

{︃ (︂ )︂2 }︃
𝑡−𝜇
𝐵 + 𝐴 exp −
𝜎
can be defined in python by:
>>> def model(t, coeffs):

... return coeffs[0] + coeffs[1] * np.exp( - ((t-coeffs[2])/coeffs[3])**2 )
where
• coeffs[0] is 𝐵 (noise)
• coeffs[1] is 𝐴 (amplitude)
• coeffs[2] is 𝜇 (center)

• coeffs[3] is 𝜎 (width)
Initial solution
One possible initial solution that we determine by inspection is:
>>> x0 = np.array([3, 30, 15, 1], dtype=float)
Fit
scipy.optimize.leastsq minimizes the sum of squares of the function given as an argument. Basically,
the function to minimize is the residuals (the difference between the data and the model):
>>> def residuals(coeffs, y, t):

... return y - model(t, coeffs)
So let’s get our solution by calling scipy.optimize.leastsq() with the following arguments:
• the function to minimize
• an initial solution
• the additional arguments to pass to the function

>>> t = np.arange(len(waveform_1))
>>> x, flag = sp.optimize.leastsq(residuals, x0, args=(waveform_1, t))
>>> x
array([ 2.70363, 27.82020, 15.47924, 3.05636])
And visualize the solution:
fig, ax = plt.subplots(figsize=(8, 6))

plt.plot(t, waveform_1, t, model(t, x))
plt.xlabel("Time [ns]")
plt.ylabel("Amplitude [bins]")
plt.legend(["Waveform", "Model"])
plt.show()
Remark: from scipy v0.8 and above, you should rather use scipy.optimize.curve_fit() which takes
the model and the data as arguments, so you don’t need to define the residuals any more.
Going further
• Try with a more complex waveform (for instance waveform_2.npy) that contains three significant
peaks. You must adapt the model which is now a sum of Gaussian functions instead of only one
Gaussian peak.
• In some cases, writing an explicit function to compute the Jacobian is faster than letting leastsq
estimate it numerically. Create a function to compute the Jacobian of the residuals and use it as
an input for leastsq.
• When we want to detect very small peaks in the signal, or when the initial guess is too far from a
good solution, the result given by the algorithm is often not satisfying. Adding constraints to the
parameters of the model enables to overcome such limitations. An example of a priori knowledge
we can add is the sign of our variables (which are all positive).
• See the solution.


• Further exercise: compare the result of scipy.optimize.leastsq() and what you can get with
scipy.optimize.fmin_slsqp() when adding boundary constraints.
5.11.3 Image processing application: counting bubbles and unmolten grains
Statement of the problem
1. Open the image file MV_HFV_012.jpg and display it. Browse through the keyword arguments
in the docstring of imshow to display the image with the “right” orientation (origin in the bottom
left corner, and not the upper left corner as for standard arrays).
This Scanning Element Microscopy image shows a glass sample (light gray matrix) with some
bubbles (on black) and unmolten sand grains (dark gray). We wish to determine the fraction
of the sample covered by these three phases, and to estimate the typical size of sand grains and
bubbles, their sizes, etc.
2. Crop the image to remove the lower panel with measure information.
3. Slightly filter the image with a median filter in order to refine its histogram. Check how the
histogram changes.

4. Using the histogram of the filtered image, determine thresholds that allow to define masks for sand
pixels, glass pixels and bubble pixels. Other option (homework): write a function that determines
automatically the thresholds from the minima of the histogram.
5. Display an image in which the three phases are colored with three different colors.
6. Use mathematical morphology to clean the different phases.
7. Attribute labels to all bubbles and sand grains, and remove from the sand mask grains that are
smaller than 10 pixels. To do so, use ndimage.sum or np.bincount to compute the grain sizes.
8. Compute the mean size of bubbles.
5.11.4 Example of solution for the image processing exercise: unmolten grains in
glass
1. Open the image file MV_HFV_012.jpg and display it. Browse through the keyword arguments
in the docstring of imshow to display the image with the “right” orientation (origin in the bottom
left corner, and not the upper left corner as for standard arrays).
>>> dat = plt.imread('data/MV_HFV_012.jpg')

2. Crop the image to remove the lower panel with measure information.
>>> dat = dat[:-60]
3. Slightly filter the image with a median filter in order to refine its histogram. Check how the
histogram changes.
>>> filtdat = sp.ndimage.median_filter(dat, size=(7,7))

>>> hi_dat = np.histogram(dat, bins=np.arange(256))
>>> hi_filtdat = np.histogram(filtdat, bins=np.arange(256))
4. Using the histogram of the filtered image, determine thresholds that allow to define masks for sand
pixels, glass pixels and bubble pixels. Other option (homework): write a function that determines
automatically the thresholds from the minima of the histogram.
>>> void = filtdat <= 50

>>> sand = np.logical_and(filtdat > 50, filtdat <= 114)
>>> glass = filtdat > 114
5. Display an image in which the three phases are colored with three different colors.
>>> phases = void.astype(int) + 2*glass.astype(int) + 3*sand.astype(int)

6. Use mathematical morphology to clean the different phases.
>>> sand_op = sp.ndimage.binary_opening(sand, iterations=2)
7. Attribute labels to all bubbles and sand grains, and remove from the sand mask grains that are
smaller than 10 pixels. To do so, use sp.ndimage.sum or np.bincount to compute the grain sizes.
>>> sand_labels, sand_nb = sp.ndimage.label(sand_op)

>>> sand_areas = np.array(sp.ndimage.sum(sand_op, sand_labels, np.arange(sand_
˓→labels.max()+1)))
>>> mask = sand_areas > 100

>>> remove_small_sand = mask[sand_labels.ravel()].reshape(sand_labels.shape)
8. Compute the mean size of bubbles.
>>> bubbles_labels, bubbles_nb = sp.ndimage.label(void)

>>> bubbles_areas = np.bincount(bubbles_labels.ravel())[1:]
>>> mean_bubble_size = bubbles_areas.mean()
>>> median_bubble_size = np.median(bubbles_areas)


>>> mean_bubble_size, median_bubble_size
(1699.875, 65.0)
5.12 Full code examples for the SciPy chapter
5.12.1 Finding the minimum of a smooth function
Demos various methods to find the minimum of a function.
import numpy as np
def f(x):
return x**2 + 10 * np.sin(x)
x = np.arange(-5, 5, 0.1)
plt.plot(x, f(x))
[<matplotlib.lines.Line2D object at 0x7f9c88eb9350>]
Now find the minimum with a few methods
5.12. Full code examples for the SciPy chapter 249

import scipy as sp
# The default (Nelder Mead)

print(sp.optimize.minimize(f, x0=0))

success: True
status: 0
fun: -7.945823375615215
x: [-1.306e+00]
nit: 5
jac: [-1.192e-06]
hess_inv: [[ 8.589e-02]]
nfev: 12
njev: 6
plt.show()
5.12.2 Resample a signal with scipy.signal.resample
scipy.signal.resample() uses FFT to resample a 1D signal.

Generate a signal with 100 data point
import numpy as np
x = np.sin(t)
Downsample it by a factor of 4
import scipy as sp
x_resampled = sp.signal.resample(x, 25)
Plot
plt.plot(t, x, label="Original signal")
plt.plot(t[::4], x_resampled, "ko", label="Resampled signal")
plt.legend(loc="best")
plt.show()

5.12.3 Detrending a signal
scipy.signal.detrend() removes a linear trend.

Generate a random signal with a trend
import numpy as np
x = t + rng.normal(size=100)
Detrend
import scipy as sp
x_detrended = sp.signal.detrend(x)
Plot
plt.plot(t, x, label="x")
plt.plot(t, x_detrended, label="x_detrended")
plt.show()

5.12.4 Integrating a simple ODE
Solve the ODE dy/dt = -2y between t = 0..4, with the initial condition y(t=0) = 1.
import numpy as np
import scipy as sp


def f(t, y):
return -2 * y
t_span = (0, 4) # time interval

t_eval = np.linspace(*t_span) # times at which to evaluate `y`
y0 = [
1,
] # initial state
res = sp.integrate.solve_ivp(f, t_span=t_span, y0=y0, t_eval=t_eval)
plt.plot(res.t, res.y[0])
plt.xlabel("t")
plt.ylabel("y")
plt.title("Solution of Initial Value Problem")
plt.tight_layout()
plt.show()
5.12.5 Normal distribution: histogram and PDF
Explore the normal distribution: a histogram built from samples and the PDF (probability density
function).

import numpy as np
import scipy as sp
dist = sp.stats.norm(loc=0, scale=1) # standard normal distribution

sample = dist.rvs(size=100000) # "random variate sample"
plt.hist(
sample,
bins=51, # group the observations into 50 bins
density=True, # normalize the frequencies
label="normalized histogram",
)
x = np.linspace(-5, 5) # possible values of the random variable

plt.plot(x, dist.pdf(x), label="PDF")
plt.legend()
plt.show()
5.12.6 Integrate the Damped spring-mass oscillator
import numpy as np
import scipy as sp
m = 0.5 # kg
k = 4 # N/m
c = 0.4 # N s/m
zeta = c / (2 * m * np.sqrt(k / m))

omega = np.sqrt(k / m)
def f(t, z, zeta, omega):



return (z[1], -zeta * omega * z[1] - omega**2 * z[0])
t_span = (0, 10)

t_eval = np.linspace(*t_span, 100)
z0 = [1, 0]
res = sp.integrate.solve_ivp(
f, t_span, z0, t_eval=t_eval, args=(zeta, omega), method="LSODA"
)
plt.plot(res.t, res.y[0], label="y")
plt.plot(res.t, res.y[1], label="dy/dt")
plt.show()
5.12.7 Comparing 2 sets of samples from Gaussians
import numpy as np
# Generates 2 sets of observations

samples1 = rng.normal(0, size=1000)
samples2 = rng.normal(1, size=1000)


# Compute a histogram of the sample
bins = np.linspace(-4, 4, 30)
histogram1, bins = np.histogram(samples1, bins=bins, density=True)
histogram2, bins = np.histogram(samples2, bins=bins, density=True)
plt.hist(samples1, bins=bins, density=True, label="Samples 1")
plt.hist(samples2, bins=bins, density=True, label="Samples 2")
plt.show()
5.12.8 Curve fitting
Demos a simple curve fitting

First generate some data
import numpy as np
# Seed the random number generator for reproducibility

x_data = np.linspace(-5, 5, num=50)

noise = 0.01 * np.cos(100 * x_data)
a, b = 2.9, 1.5
y_data = a * np.cos(b * x_data) + noise
# And plot it
plt.scatter(x_data, y_data)

<matplotlib.collections.PathCollection object at 0x7f9c88181f10>
Now fit a simple sine function to the data
import scipy as sp
def test_func(x, a, b, c):

return a * np.sin(b * x + c)
params, params_covariance = sp.optimize.curve_fit(

test_func, x_data, y_data, p0=[2, 1, 3]
)
print(params)
[2.900026 1.50012043 1.57079633]
And plot the resulting curve on the data
plt.scatter(x_data, y_data, label="Data")
plt.plot(x_data, test_func(x_data, *params), label="Fitted function")
plt.show()

5.12.9 Spectrogram, power spectral density
Demo spectrogram and power spectral density on a frequency chirp.
import numpy as np
Generate a chirp signal
# Seed the random number generator

np.random.seed(0)
time_step = 0.01
time_vec = np.arange(0, 70, time_step)
# A signal with a small frequency chirp

sig = np.sin(0.5 * np.pi * time_vec * (1 + 0.1 * time_vec))
plt.plot(time_vec, sig)

[<matplotlib.lines.Line2D object at 0x7f9c7d769310>]
Compute and plot the spectrogram
The spectrum of the signal on consecutive time windows
import scipy as sp
freqs, times, spectrogram = sp.signal.spectrogram(sig)
plt.imshow(spectrogram, aspect="auto", cmap="hot_r", origin="lower")
plt.title("Spectrogram")
plt.ylabel("Frequency band")
plt.xlabel("Time window")
plt.tight_layout()

Compute and plot the power spectral density (PSD)
The power of the signal per frequency band
freqs, psd = sp.signal.welch(sig)
plt.semilogx(freqs, psd)
plt.title("PSD: power spectral density")
plt.xlabel("Frequency")
plt.ylabel("Power")
plt.tight_layout()

plt.show()
5.12.10 Demo mathematical morphology
A basic demo of binary opening and closing.
# Generate some binary data

import numpy as np
np.random.seed(0)
a = np.zeros((50, 50))
a[10:-10, 10:-10] = 1
a += 0.25 * np.random.standard_normal(a.shape)
mask = a >= 0.5
# Apply mathematical morphology



import scipy as sp
opened_mask = sp.ndimage.binary_opening(mask)
closed_mask = sp.ndimage.binary_closing(opened_mask)
# Plot
plt.figure(figsize=(12, 3.5))
plt.subplot(141)
plt.imshow(a, cmap=plt.cm.gray)
plt.axis("off")
plt.title("a")
plt.subplot(142)
plt.imshow(mask, cmap=plt.cm.gray)
plt.axis("off")
plt.title("mask")
plt.subplot(143)
plt.imshow(opened_mask, cmap=plt.cm.gray)
plt.axis("off")
plt.title("opened_mask")
plt.subplot(144)
plt.imshow(closed_mask, cmap=plt.cm.gray)
plt.title("closed_mask")
plt.axis("off")
plt.subplots_adjust(wspace=0.05, left=0.01, bottom=0.01, right=0.99, top=0.99)
plt.show()

5.12.11 A demo of 1D interpolation
# Generate data
import numpy as np
measured_time = np.linspace(0, 1, 10)
noise = 1e-1 * (rng.random(10) * 2 - 1)
measures = np.sin(2 * np.pi * measured_time) + noise
# Interpolate it to new time points

import scipy as sp
linear_interp = sp.interpolate.interp1d(measured_time, measures)

interpolation_time = np.linspace(0, 1, 50)
linear_results = linear_interp(interpolation_time)
cubic_interp = sp.interpolate.interp1d(measured_time, measures, kind="cubic")
cubic_results = cubic_interp(interpolation_time)
# Plot the data and the interpolation

plt.plot(measured_time, measures, "o", ms=6, label="measures")
plt.plot(interpolation_time, linear_results, label="linear interp")
plt.plot(interpolation_time, cubic_results, label="cubic interp")
plt.legend()
plt.show()

5.12.12 Plot geometrical transformations on images
Demo geometrical transformations of images.
Downloading file 'face.dat' from 'https://raw.githubusercontent.com/scipy/dataset-

˓→face/main/face.dat' to '/home/runner/.cache/scipy-data'.
# Load some data

import scipy as sp
face = sp.datasets.face(gray=True)
# Apply a variety of transformations

shifted_face = sp.ndimage.shift(face, (50, 50))

shifted_face2 = sp.ndimage.shift(face, (50, 50), mode="nearest")
rotated_face = sp.ndimage.rotate(face, 30)
cropped_face = face[50:-50, 50:-50]
zoomed_face = sp.ndimage.zoom(face, 2)
zoomed_face.shape
plt.subplot(151)
plt.imshow(shifted_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(152)
plt.imshow(shifted_face2, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(153)
plt.imshow(rotated_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(154)
plt.imshow(cropped_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(155)
plt.imshow(zoomed_face, cmap=plt.cm.gray)
plt.axis("off")


plt.show()
5.12.13 Demo connected components
Extracting and labeling connected components in a 2D array
import numpy as np
Generate some binary data
x, y = np.indices((100, 100))
sig = (
np.sin(2 * np.pi * x / 50.0)
* np.sin(2 * np.pi * y / 50.0)
* (1 + x * y / 50.0**2) ** 2
)
mask = sig > 1
plt.imshow(sig)
plt.axis("off")
plt.title("sig")
plt.axis("off")
plt.title("mask")
Label connected components

import scipy as sp
labels, nb = sp.ndimage.label(mask)
plt.figure(figsize=(3.5, 3.5))
plt.imshow(labels)
plt.title("label")
plt.axis("off")
Extract the 4th connected component, and crop the array around it
sl = sp.ndimage.find_objects(labels == 4)
plt.imshow(sig[sl[0]])
plt.title("Cropped connected component")
plt.axis("off")
plt.show()

5.12.14 Minima and roots of a function
Demos finding minima and roots of a function.
Define the function
import numpy as np
x = np.arange(-10, 10, 0.1)
def f(x):
return x**2 + 10 * np.sin(x)
Find minima
import scipy as sp
# Global optimization
grid = (-10, 10, 0.1)
xmin_global = sp.optimize.brute(f, (grid,))
print(f"Global minima found { xmin_global} ")
# Constrain optimization
xmin_local = sp.optimize.fminbound(f, 0, 10)
print(f"Local minimum found { xmin_local} ")
Global minima found [-1.30641113]

Local minimum found 3.8374671194983834

Root finding
root = sp.optimize.root(f, 1) # our initial guess is 1

print(f"First root found { root.x} ")
root2 = sp.optimize.root(f, -2.5)
print(f"Second root found { root2.x} ")
First root found [0.]

Second root found [-2.47948183]
Plot function, minima, and roots

ax = fig.add_subplot(111)
# Plot the function

ax.plot(x, f(x), "b-", label="f(x)")
# Plot the minima

xmins = np.array([xmin_global[0], xmin_local])
ax.plot(xmins, f(xmins), "go", label="Minima")
# Plot the roots

roots = np.array([root.x, root2.x])
ax.plot(roots, f(roots), "kv", label="Roots")
# Decorate the figure

ax.legend(loc="best")
ax.set_xlabel("x")
ax.set_ylabel("f(x)")
ax.axhline(0, color="gray")
plt.show()

5.12.15 Plot filtering on images
Demo filtering for denoising of images.
# Load some data

import scipy as sp
face = face[:512, -512:] # crop out square on right
# Apply a variety of filters

import numpy as np
noisy_face = np.copy(face).astype(float)


noisy_face += face.std() * 0.5 * rng.standard_normal(face.shape)
blurred_face = sp.ndimage.gaussian_filter(noisy_face, sigma=3)
median_face = sp.ndimage.median_filter(noisy_face, size=5)
wiener_face = sp.signal.wiener(noisy_face, (5, 5))
plt.subplot(141)
plt.imshow(noisy_face, cmap=plt.cm.gray)
plt.axis("off")
plt.title("noisy")
plt.subplot(142)
plt.imshow(blurred_face, cmap=plt.cm.gray)
plt.axis("off")
plt.title("Gaussian filter")
plt.subplot(143)
plt.imshow(median_face, cmap=plt.cm.gray)
plt.axis("off")
plt.title("median filter")
plt.subplot(144)
plt.imshow(wiener_face, cmap=plt.cm.gray)
plt.title("Wiener filter")
plt.axis("off")
plt.show()
5.12.16 Optimization of a two-parameter function
import numpy as np
# Define the function that we are interested in

def sixhump(x):
return (
(4 - 2.1 * x[0] ** 2 + x[0] ** 4 / 3) * x[0] ** 2
+ x[0] * x[1]
+ (-4 + 4 * x[1] ** 2) * x[1] ** 2
)
# Make a grid to evaluate the function (for plotting)

xlim = [-2, 2]
ylim = [-1, 1]
x = np.linspace(*xlim)
y = np.linspace(*ylim)
xg, yg = np.meshgrid(x, y)

A 2D image plot of the function
Simple visualization in 2D
plt.figure()
plt.imshow(sixhump([xg, yg]), extent=xlim + ylim, origin="lower")
plt.colorbar()
<matplotlib.colorbar.Colorbar object at 0x7f9c8863a310>
A 3D surface plot of the function
fig = plt.figure()
ax = fig.add_subplot(111, projection="3d")
surf = ax.plot_surface(
xg,
yg,
sixhump([xg, yg]),
rstride=1,
cstride=1,
cmap=plt.cm.viridis,
linewidth=0,
antialiased=False,


)
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.set_zlabel("f(x, y)")
ax.set_title("Six-hump Camelback function")
Text(0.5, 1.0, 'Six-hump Camelback function')
Find minima
import scipy as sp
# local minimization
res_local = sp.optimize.minimize(sixhump, x0=[0, 0])
# global minimization
res_global = sp.optimize.differential_evolution(sixhump, bounds=[xlim, ylim])
plt.figure()
# Show the function in 2D
plt.imshow(sixhump([xg, yg]), extent=xlim + ylim, origin="lower")
plt.colorbar()
# Mark the minima
plt.scatter(res_local.x[0], res_local.x[1], label="local minimizer")


plt.scatter(res_global.x[0], res_global.x[1], label="global minimizer")
plt.legend()
plt.show()
5.12.17 Plotting and manipulating FFTs for filtering
Plot the power of the FFT of a signal and inverse FFT back to reconstruct a signal.
This example demonstrate scipy.fft.fft(), scipy.fft.fftfreq() and scipy.fft.ifft(). It imple-
ments a basic filter that is very suboptimal, and should not be used.
import numpy as np
import scipy as sp

Generate the signal
# Seed the random number generator

time_step = 0.02
period = 5.0
time_vec = np.arange(0, 20, time_step)

sig = np.sin(2 * np.pi / period * time_vec) + 0.5 * rng.normal(size=time_vec.size)
plt.plot(time_vec, sig, label="Original signal")
[<matplotlib.lines.Line2D object at 0x7f9c889405d0>]

Compute and plot the power
# The FFT of the signal

sig_fft = sp.fft.fft(sig)
# And the power (sig_fft is of complex dtype)

power = np.abs(sig_fft) ** 2
# The corresponding frequencies

sample_freq = sp.fft.fftfreq(sig.size, d=time_step)
# Plot the FFT power

plt.plot(sample_freq, power)
plt.xlabel("Frequency [Hz]")
plt.ylabel("plower")
# Find the peak frequency: we can focus on only the positive frequencies
pos_mask = np.where(sample_freq > 0)
freqs = sample_freq[pos_mask]
peak_freq = freqs[power[pos_mask].argmax()]
# Check that it does indeed correspond to the frequency that we generate

# the signal with
np.allclose(peak_freq, 1.0 / period)
# An inner plot to show the peak frequency

axes = plt.axes([0.55, 0.3, 0.3, 0.5])
plt.title("Peak frequency")
plt.plot(freqs[:8], power[pos_mask][:8])
plt.setp(axes, yticks=[])
# scipy.signal.find_peaks_cwt can also be used for more advanced

# peak detection

[]
Remove all the high frequencies
We now remove all the high frequencies and transform back from frequencies to signal.
high_freq_fft = sig_fft.copy()
high_freq_fft[np.abs(sample_freq) > peak_freq] = 0
filtered_sig = sp.fft.ifft(high_freq_fft)
plt.plot(time_vec, sig, label="Original signal")
plt.plot(time_vec, filtered_sig, linewidth=3, label="Filtered signal")
plt.xlabel("Time [s]")
plt.ylabel("Amplitude")

/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/matplotlib/cbook.
˓→py:1699: ComplexWarning: Casting complex values to real discards the imaginary part
return math.isfinite(val)
/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/matplotlib/cbook.
˓→py:1345: ComplexWarning: Casting complex values to real discards the imaginary part
return np.asarray(x, float)
<matplotlib.legend.Legend object at 0x7f9c7d534c10>
Note This is actually a bad way of creating a filter: such brutal cut-off in frequency space does not
control distortion on the signal.
Filters should be created using the SciPy filter design code
plt.show()

5.12.18 Solutions of the exercises for SciPy
Solutions of the exercises for SciPy
Crude periodicity finding
Discover the periods in evolution of animal populations (../../../../data/populations.txt)
Load the data
import numpy as np
data = np.loadtxt("../../../../data/populations.txt")
years = data[:, 0]
populations = data[:, 1:]
Plot the data
plt.figure()
plt.plot(years, populations * 1e-3)
plt.xlabel("Year")
plt.ylabel(r"Population number ($\cdot10^3$)")
plt.legend(["hare", "lynx", "carrot"], loc=1)

<matplotlib.legend.Legend object at 0x7f9c88886990>
Plot its periods
import scipy as sp
ft_populations = sp.fft.fft(populations, axis=0)

frequencies = sp.fft.fftfreq(populations.shape[0], years[1] - years[0])
periods = 1 / frequencies
plt.figure()
plt.plot(periods, abs(ft_populations) * 1e-3, "o")
plt.xlim(0, 22)
plt.xlabel("Period")
plt.ylabel(r"Power ($\cdot10^3$)")
plt.show()
/home/runner/work/scientific-python-lectures/scientific-python-lectures/intro/scipy/
˓→examples/solutions/plot_periodicity_finder.py:39: RuntimeWarning: divide by zero␣
˓→encountered in divide
periods = 1 / frequencies
There’s probably a period of around 10 years (obvious from the plot), but for this crude a method,
there’s not enough data to say much more.

Curve fitting: temperature as a function of month of the year
We have the min and max temperatures in Alaska for each months of the year. We would like to find a
function to describe this yearly evolution.
For this, we will fit a periodic function.
The data
import numpy as np
temp_max = np.array([17, 19, 21, 28, 33, 38, 37, 37, 31, 23, 19, 18])
temp_min = np.array([-62, -59, -56, -46, -32, -18, -9, -13, -25, -46, -52, -58])
months = np.arange(12)
plt.plot(months, temp_max, "ro")
plt.plot(months, temp_min, "bo")
plt.xlabel("Month")
plt.ylabel("Min and max temperature")
Text(35.472222222222214, 0.5, 'Min and max temperature')

Fitting it to a periodic function
import scipy as sp
def yearly_temps(times, avg, ampl, time_offset):

return avg + ampl * np.cos((times + time_offset) * 2 * np.pi / times.max())
res_max, cov_max = sp.optimize.curve_fit(yearly_temps, months, temp_max, [20, 10, 0])

res_min, cov_min = sp.optimize.curve_fit(yearly_temps, months, temp_min, [-40, 20, 0])
Plotting the fit
days = np.linspace(0, 12, num=365)
plt.figure()
plt.plot(months, temp_max, "ro")
plt.plot(days, yearly_temps(days, *res_max), "r-")
plt.plot(months, temp_min, "bo")
plt.plot(days, yearly_temps(days, *res_min), "b-")
plt.xlabel("Month")
plt.ylabel(r"Temperature ($^\circ$C)")
plt.show()

Simple image blur by convolution with a Gaussian kernel
Blur an an image (../../../../data/elephant.png) using a Gaussian kernel.

Convolution is easy to perform with FFT: convolving two signals boils down to multiplying their FFTs
(and performing an inverse FFT).
import numpy as np
import scipy as sp
The original image
# read image
img = plt.imread("../../../../data/elephant.png")
plt.figure()
plt.imshow(img)
<matplotlib.image.AxesImage object at 0x7f9c882f9bd0>

Prepare an Gaussian convolution kernel
# First a 1-D Gaussian

t = np.linspace(-10, 10, 30)
bump = np.exp(-0.1 * t**2)
bump /= np.trapz(bump) # normalize the integral to 1
# make a 2-D kernel out of it

kernel = bump[:, np.newaxis] * bump[np.newaxis, :]
Implement convolution via FFT
# Padded fourier transform, with the same shape as the image

# We use :func:`scipy.fft.fft2` to have a 2D FFT
kernel_ft = sp.fft.fft2(kernel, s=img.shape[:2], axes=(0, 1))
# convolve
img_ft = sp.fft.fft2(img, axes=(0, 1))
# the 'newaxis' is to match to color direction
img2_ft = kernel_ft[:, :, np.newaxis] * img_ft
img2 = sp.fft.ifft2(img2_ft, axes=(0, 1)).real
# clip values to range

img2 = np.clip(img2, 0, 1)
# plot output
plt.figure()
plt.imshow(img2)

<matplotlib.image.AxesImage object at 0x7f9c88bb0c50>
Further exercise (only if you are familiar with this stuff):

A “wrapped border” appears in the upper left and top edges of the image. This is because the padding
is not done correctly, and does not take the kernel size into account (so the convolution “flows out of
bounds of the image”). Try to remove this artifact.
A function to do it: scipy.signal.fftconvolve()
The above exercise was only for didactic reasons: there exists a function in scipy that will do
this for us, and probably do a better job: scipy.signal.fftconvolve()
# mode='same' is there to enforce the same output shape as input arrays

# (ie avoid border effects)
img3 = sp.signal.fftconvolve(img, kernel[:, :, np.newaxis], mode="same")
plt.figure()
plt.imshow(img3)

<matplotlib.image.AxesImage object at 0x7f9c887e5c50>
Note that we still have a decay to zero at the border of the image. Using scipy.ndimage.
gaussian_filter() would get rid of this artifact
plt.show()
Image denoising by FFT
Denoise an image (../../../../data/moonlanding.png) by implementing a blur with an FFT.

Implements, via FFT, the following convolution:
∫︁
𝑓1 (𝑡) = 𝑑𝑡′ 𝐾(𝑡 − 𝑡′ )𝑓0 (𝑡′ )
𝑓˜1 (𝜔) = 𝐾(𝜔)

˜ 𝑓˜0 (𝜔)

Read and plot the image
import numpy as np
im = plt.imread("../../../../data/moonlanding.png").astype(float)
plt.figure()
plt.imshow(im, plt.cm.gray)
plt.title("Original image")
Text(0.5, 1.0, 'Original image')
Compute the 2d FFT of the input image
import scipy as sp
im_fft = sp.fft.fft2(im)
# Show the results
def plot_spectrum(im_fft):
from matplotlib.colors import LogNorm
# A logarithmic colormap


plt.imshow(np.abs(im_fft), norm=LogNorm(vmin=5))
plt.colorbar()
plt.figure()
plot_spectrum(im_fft)
plt.title("Fourier transform")
Text(0.5, 1.0, 'Fourier transform')
Filter in FFT
# In the lines following, we'll make a copy of the original spectrum and
# truncate coefficients.
# Define the fraction of coefficients (in each direction) we keep

keep_fraction = 0.1
# Call ff a copy of the original transform. NumPy arrays have a copy

# method for this purpose.
im_fft2 = im_fft.copy()
# Set r and c to be the number of rows and columns of the array.

r, c = im_fft2.shape


# Set to zero all rows with indices between r*keep_fraction and
# r*(1-keep_fraction):
im_fft2[int(r * keep_fraction) : int(r * (1 - keep_fraction))] = 0
# Similarly with the columns:

im_fft2[:, int(c * keep_fraction) : int(c * (1 - keep_fraction))] = 0
plt.figure()
plot_spectrum(im_fft2)
plt.title("Filtered Spectrum")
Text(0.5, 1.0, 'Filtered Spectrum')
Reconstruct the final image
# Reconstruct the denoised image from the filtered spectrum, keep only the
# real part for display.
im_new = sp.fft.ifft2(im_fft2).real
plt.figure()
plt.imshow(im_new, plt.cm.gray)
plt.title("Reconstructed Image")

Text(0.5, 1.0, 'Reconstructed Image')
Easier and better: scipy.ndimage.gaussian_filter()
Implementing filtering directly with FFTs is tricky and time consuming. We can use the
Gaussian filter from scipy.ndimage
im_blur = sp.ndimage.gaussian_filter(im, 4)
plt.figure()
plt.imshow(im_blur, plt.cm.gray)
plt.title("Blurred image")
plt.show()

See also:
References to go further
• Some chapters of the advanced and the packages and applications parts of the SciPy lectures
• The SciPy cookbook

CHAPTER 6
Getting help and finding documentation
Author: Emmanuelle Gouillart

Rather than knowing all functions in NumPy and SciPy, it is important to find rapidly information
throughout the documentation and the available help. Here are some ways to get information:
• In Ipython, help function opens the docstring of the function. Only type the beginning of the
function’s name and use tab completion to display the matching functions.
In [1]: help(np.van<TAB>
In [2]: help(np.vander)
Help on _ArrayFunctionDispatcher in module numpy:
vander(x, N=None, increasing=False)

Generate a Vandermonde matrix.
The columns of the output matrix are powers of the input vector. The
order of the powers is determined by the ìncreasing` boolean argument.
Specifically, when ìncreasing` is False, the ì`-th output column is
the input vector raised element-wise to the power of ``N - i - 1``. Such
a matrix with a geometric progression in each row is named for Alexandre-
Theophile Vandermonde.
Parameters
----------
x : array_like
1-D input array.
N : int, optional
Number of columns in the output. If `N` is not specified, a square
array is returned (``N = len(x)``).
291

increasing : bool, optional
Order of the powers of the columns. If True, the powers increase
from left to right, if False (the default) they are reversed.
.. versionadded:: 1.9.0
Returns
-------
out : ndarray
Vandermonde matrix. If ìncreasing` is False, the first column is
``x^(N-1)``, the second ``x^(N-2)`` and so forth. If ìncreasing` is
True, the columns are ``x^0, x^1, ..., x^(N-1)``.
See Also
--------
polynomial.polynomial.polyvander
Examples
--------
>>> x = np.array([1, 2, 3, 5])
>>> N = 3
>>> np.vander(x, N)
array([[ 1, 1, 1],
[ 4, 2, 1],
[ 9, 3, 1],
[25, 5, 1]])
>>> np.column_stack([x**(N-1-i) for i in range(N)])

array([[ 1, 1, 1],
[ 4, 2, 1],
[ 9, 3, 1],
[25, 5, 1]])
>>> x = np.array([1, 2, 3, 5])

>>> np.vander(x)
array([[ 1, 1, 1, 1],
[ 8, 4, 2, 1],
[ 27, 9, 3, 1],
[125, 25, 5, 1]])
>>> np.vander(x, increasing=True)
array([[ 1, 1, 1, 1],
[ 1, 2, 4, 8],
[ 1, 3, 9, 27],
[ 1, 5, 25, 125]])
The determinant of a square Vandermonde matrix is the product

of the differences between the values of the input vector:
>>> np.linalg.det(np.vander(x))
48.000000000000043 # may vary
>>> (5-3)*(5-2)*(5-1)*(3-2)*(3-1)*(2-1)
48
In Ipython it is not possible to open a separated window for help and documentation; however one can
always open a second Ipython shell just to display help and docstrings. . .
• Numpy’s and Scipy’s documentations can be browsed online on https://scipy.org and https://
292
numpy.org. The search button is quite useful inside the reference documentation of the two
packages.
Tutorials on various topics as well as the complete API with all docstrings are found on this website.
• Numpy’s and Scipy’s documentation is enriched and updated on a regular basis by users on a wiki
https://numpy.org/doc/stable/. As a result, some docstrings are clearer or more detailed on the
wiki, and you may want to read directly the documentation on the wiki instead of the official
documentation website. Note that anyone can create an account on the wiki and write better
documentation; this is an easy way to contribute to an open-source project and improve the tools
you are using!
• The SciPy Cookbook https://scipy-cookbook.readthedocs.io gives recipes on many common prob-
lems frequently encountered, such as fitting data points, solving ODE, etc.
• Matplotlib’s website https://matplotlib.org/ features a very nice gallery with a large number of
plots, each of them shows both the source code and the resulting plot. This is very useful for
learning by example. More standard documentation is also available.
Finally, two more “technical” possibilities are useful as well:
• In Ipython, the magical function %psearch search for objects matching patterns. This is useful if,
for example, one does not know the exact name of a function.
• numpy.lookfor looks for keywords inside the docstrings of specified modules.
In [4]: np.lookfor('convolution')
Search results for 'convolution'
--------------------------------
numpy.convolve
Returns the discrete, linear convolution of two one-dimensional sequences.
numpy.ma.convolve
Returns the discrete, linear convolution of two one-dimensional sequences.
numpy.polymul
Find the product of two polynomials.
numpy.bartlett
Return the Bartlett window.
numpy.correlate
Cross-correlation of two 1-dimensional sequences.
numpy.vectorize
vectorize(pyfunc=np._NoValue, otypes=None, doc=None, excluded=None,
• If everything listed above fails (and Google doesn’t have the answer). . . don’t despair! There is
a vibrant Scientific Python community. Scientific Python is present on various platform. https:
//scientific-python.org/community/
Packages like SciPy and NumPy also have their own channels. Have a look at their respective
websites to find out how to engage with users and maintainers.
293
Part II
Advanced topics
294
This part of the Scientific Python Lectures is dedicated to advanced usage. It strives to educate the
proficient Python coder to be an expert and tackles various specific topics.
295
CHAPTER 7
Advanced Python Constructs
Author Zbigniew Jędrzejewski-Szmek

This section covers some features of the Python language which can be considered advanced — in
the sense that not every language has them, and also in the sense that they are more useful in more
complicated programs or libraries, but not in the sense of being particularly specialized, or particularly
complicated.
It is important to underline that this chapter is purely about the language itself — about features
supported through special syntax complemented by functionality of the Python stdlib, which could not
be implemented through clever external modules.
The process of developing the Python programming language, its syntax, is very transparent; proposed
changes are evaluated from various angles and discussed via Python Enhancement Proposals — PEPs.
As a result, features described in this chapter were added after it was shown that they indeed solve real
problems and that their use is as simple as possible.
Chapter contents
• Iterators, generator expressions and generators

– Iterators
– Generator expressions
– Generators
– Bidirectional communication
– Chaining generators
• Decorators
– Replacing or tweaking the original object
296
– Decorators implemented as classes and as functions

– Copying the docstring and other attributes of the original function
– Examples in the standard library
– Deprecation of functions
– A while-loop removing decorator
– A plugin registration system
• Context managers
– Catching exceptions
– Using generators to define context managers
7.1 Iterators, generator expressions and generators
7.1.1 Iterators
Simplicity
Duplication of effort is wasteful, and replacing the various home-grown approaches with a standard
feature usually ends up making things more readable, and interoperable as well.
Guido van Rossum — Adding Optional Static Typing to Python
An iterator is an object adhering to the iterator protocol — basically this means that it has a next
method, which, when called, returns the next item in the sequence, and when there’s nothing to return,
raises the StopIteration exception.
An iterator object allows to loop just once. It holds the state (position) of a single iteration, or from the
other side, each loop over a sequence requires a single iterator object. This means that we can iterate
over the same sequence more than once concurrently. Separating the iteration logic from the sequence
allows us to have more than one way of iteration.
Calling the __iter__ method on a container to create an iterator object is the most straightforward way
to get hold of an iterator. The iter function does that for us, saving a few keystrokes.
>>> nums = [1, 2, 3] # note that ... varies: these are different objects
>>> iter(nums)
<...iterator object at ...>
>>> nums.__iter__()
<...iterator object at ...>
>>> nums.__reversed__()
<...reverseiterator object at ...>
>>> it = iter(nums)
>>> next(it)
1
>>> next(it)
2
>>> next(it)
3
>>> next(it)
7.1. Iterators, generator expressions and generators 297


StopIteration
When used in a loop, StopIteration is swallowed and causes the loop to finish. But with explicit
invocation, we can see that once the iterator is exhausted, accessing it raises an exception.
Using the for..in loop also uses the __iter__ method. This allows us to transparently start the iteration
over a sequence. But if we already have the iterator, we want to be able to use it in an for loop in
the same way. In order to achieve this, iterators in addition to next are also required to have a method
called __iter__ which returns the iterator (self).
Support for iteration is pervasive in Python: all sequences and unordered containers in the standard
library allow this. The concept is also stretched to other things: e.g. file objects support iteration over
lines.
>>> with open("/etc/fstab") as f:

... f is f.__iter__()
...
True
The file is an iterator itself and it’s __iter__ method doesn’t create a separate object: only a single
thread of sequential access is allowed.
7.1.2 Generator expressions
A second way in which iterator objects are created is through generator expressions, the basis for list
comprehensions. To increase clarity, a generator expression must always be enclosed in parentheses
or an expression. If round parentheses are used, then a generator iterator is created. If rectangular
parentheses are used, the process is short-circuited and we get a list.
>>> (i for i in nums)

<generator object <genexpr> at 0x...>
>>> [i for i in nums]
[1, 2, 3]
>>> list(i for i in nums)
[1, 2, 3]
The list comprehension syntax also extends to dictionary and set comprehensions. A set is cre-
ated when the generator expression is enclosed in curly braces. A dict is created when the generator
expression contains “pairs” of the form key:value:
>>> {i for i in range(3)}

{0, 1, 2}
>>> {i:i**2 for i in range(3)}
{0: 0, 1: 1, 2: 4}
One gotcha should be mentioned: in old Pythons the index variable (i) would leak, and in versions >=
3 this is fixed.

7.1.3 Generators
Generators
A generator is a function that produces a sequence of results instead of a single value.

David Beazley — A Curious Course on Coroutines and Concurrency
A third way to create iterator objects is to call a generator function. A generator is a function containing
the keyword yield. It must be noted that the mere presence of this keyword completely changes the
nature of the function: this yield statement doesn’t have to be invoked, or even reachable, but causes
the function to be marked as a generator. When a normal function is called, the instructions contained in
the body start to be executed. When a generator is called, the execution stops before the first instruction
in the body. An invocation of a generator function creates a generator object, adhering to the iterator
protocol. As with normal function invocations, concurrent and recursive invocations are allowed.
When next is called, the function is executed until the first yield. Each encountered yield statement
gives a value becomes the return value of next. After executing the yield statement, the execution of
this function is suspended.
>>> def f():

... yield 1
... yield 2
>>> f()
<generator object f at 0x...>
>>> gen = f()
>>> next(gen)
1
>>> next(gen)
2
>>> next(gen)
StopIteration
Let’s go over the life of the single invocation of the generator function.
>>> def f():

... print("-- start --")
... yield 3
... print("-- finish --")
... yield 4
>>> gen = f()
>>> next(gen)
-- start --
3
>>> next(gen)
-- finish --
4
>>> next(gen)
...
StopIteration
Contrary to a normal function, where executing f() would immediately cause the first print to be
executed, gen is assigned without executing any statements in the function body. Only when gen.
__next__() is invoked by next, the statements up to the first yield are executed. The second next
prints -- finish -- and execution halts on the second yield. The third next falls of the end of the

function. Since no yield was reached, an exception is raised.

What happens with the function after a yield, when the control passes to the caller? The state of
each generator is stored in the generator object. From the point of view of the generator function, is
looks almost as if it was running in a separate thread, but this is just an illusion: execution is strictly
single-threaded, but the interpreter keeps and restores the state in between the requests for the next
value.
Why are generators useful? As noted in the parts about iterators, a generator function is just a different
way to create an iterator object. Everything that can be done with yield statements, could also be
done with next methods. Nevertheless, using a function and having the interpreter perform its magic
to create an iterator has advantages. A function can be much shorter than the definition of a class with
the required next and __iter__ methods. What is more important, it is easier for the author of the
generator to understand the state which is kept in local variables, as opposed to instance attributes,
which have to be used to pass data between consecutive invocations of next on an iterator object.
A broader question is why are iterators useful? When an iterator is used to power a loop, the loop
becomes very simple. The code to initialise the state, to decide if the loop is finished, and to find the
next value is extracted into a separate place. This highlights the body of the loop — the interesting
part. In addition, it is possible to reuse the iterator code in other places.
7.1.4 Bidirectional communication
Each yield statement causes a value to be passed to the caller. This is the reason for the introduction
of generators by PEP 255. But communication in the reverse direction is also useful. One obvious way
would be some external state, either a global variable or a shared mutable object. Direct communication
is possible thanks to PEP 342. It is achieved by turning the previously boring yield statement into an
expression. When the generator resumes execution after a yield statement, the caller can call a method
on the generator object to either pass a value into the generator, which then is returned by the yield
statement, or a different method to inject an exception into the generator.
The first of the new methods is send(value), which is similar to next(), but passes value into the
generator to be used for the value of the yield expression. In fact, g.next() and g.send(None) are
equivalent.
The second of the new methods is throw(type, value=None, traceback=None) which is equivalent to:
raise type, value, traceback
at the point of the yield statement.

Unlike raise (which immediately raises an exception from the current execution point), throw() first
resumes the generator, and only then raises the exception. The word throw was picked because it
is suggestive of putting the exception in another location, and is associated with exceptions in other
languages.
What happens when an exception is raised inside the generator? It can be either raised explicitly or
when executing some statements or it can be injected at the point of a yield statement by means of
the throw() method. In either case, such an exception propagates in the standard manner: it can
be intercepted by an except or finally clause, or otherwise it causes the execution of the generator
function to be aborted and propagates in the caller.
For completeness’ sake, it’s worth mentioning that generator iterators also have a close() method,
which can be used to force a generator that would otherwise be able to provide more values to finish
immediately. It allows the generator __del__ method to destroy objects holding the state of generator.
Let’s define a generator which just prints what is passed in through send and throw.
>>> import itertools

>>> def g():
... print('--start--')
... for i in itertools.count():


... print('--yielding %i --' % i)
... try:
... ans = yield i
... except GeneratorExit:
... print('--closing--')
... raise
... except Exception as e:
... print('--yield raised %r --' % e)
... else:
... print('--yield returned %s --' % ans)
>>> it = g()
>>> next(it)
--start--
--yielding 0--
0
>>> it.send(11)
--yield returned 11--
--yielding 1--
1
>>> it.throw(IndexError)
--yield raised IndexError()--
--yielding 2--
2
>>> it.close()
--closing--
7.1.5 Chaining generators
Note: This is a preview of PEP 380 (not yet implemented, but accepted for Python 3.3).
Let’s say we are writing a generator and we want to yield a number of values generated by a second
generator, a subgenerator. If yielding of values is the only concern, this can be performed without
much difficulty using a loop such as
subgen = some_other_generator()
for v in subgen:
yield v
However, if the subgenerator is to interact properly with the caller in the case of calls to send(), throw()
and close(), things become considerably more difficult. The yield statement has to be guarded by a
try..except..finally structure similar to the one defined in the previous section to “debug” the generator
function. Such code is provided in PEP 380#id13, here it suffices to say that new syntax to properly
yield from a subgenerator is being introduced in Python 3.3:
yield from some_other_generator()
This behaves like the explicit loop above, repeatedly yielding values from some_other_generator until
it is exhausted, but also forwards send, throw and close to the subgenerator.

7.2 Decorators
Summary
This amazing feature appeared in the language almost apologetically and with concern that it might
not be that useful.
Bruce Eckel — An Introduction to Python Decorators
Since functions and classes are objects, they can be passed around. Since they are mutable objects, they
can be modified. The act of altering a function or class object after it has been constructed but before
is is bound to its name is called decorating.
There are two things hiding behind the name “decorator” — one is the function which does the work of
decorating, i.e. performs the real work, and the other one is the expression adhering to the decorator
syntax, i.e. an at-symbol and the name of the decorating function.
Function can be decorated by using the decorator syntax for functions:
@decorator # ❷
def function(): # ❶
pass
• A function is defined in the standard way. ❶

• An expression starting with @ placed before the function definition is the decorator ❷. The part
after @ must be a simple expression, usually this is just the name of a function or class. This part is
evaluated first, and after the function defined below is ready, the decorator is called with the newly
defined function object as the single argument. The value returned by the decorator is attached to
the original name of the function.
Decorators can be applied to functions and to classes. For classes the semantics are identical — the
original class definition is used as an argument to call the decorator and whatever is returned is assigned
under the original name.
Before the decorator syntax was implemented (PEP 318), it was possible to achieve the same effect by
assigning the function or class object to a temporary variable and then invoking the decorator explicitly
and then assigning the return value to the name of the function. This sounds like more typing, and it
is, and also the name of the decorated function doubling as a temporary variable must be used at least
three times, which is prone to errors. Nevertheless, the example above is equivalent to:
def function(): # ❶
pass
function = decorator(function) # ❷
Decorators can be stacked — the order of application is bottom-to-top, or inside-out. The semantics
are such that the originally defined function is used as an argument for the first decorator, whatever is
returned by the first decorator is used as an argument for the second decorator, . . . , and whatever is
returned by the last decorator is attached under the name of the original function.
The decorator syntax was chosen for its readability. Since the decorator is specified before the header
of the function, it is obvious that its is not a part of the function body and its clear that it can only
operate on the whole function. Because the expression is prefixed with @ is stands out and is hard to
miss (“in your face”, according to the PEP :) ). When more than one decorator is applied, each one is
placed on a separate line in an easy to read way.
7.2. Decorators 302

7.2.1 Replacing or tweaking the original object
Decorators can either return the same function or class object or they can return a completely different
object. In the first case, the decorator can exploit the fact that function and class objects are mutable
and add attributes, e.g. add a docstring to a class. A decorator might do something useful even without
modifying the object, for example register the decorated class in a global registry. In the second case,
virtually anything is possible: when something different is substituted for the original function or class,
the new object can be completely different. Nevertheless, such behaviour is not the purpose of decorators:
they are intended to tweak the decorated object, not do something unpredictable. Therefore, when a
function is “decorated” by replacing it with a different function, the new function usually calls the original
function, after doing some preparatory work. Likewise, when a class is “decorated” by replacing if with
a new class, the new class is usually derived from the original class. When the purpose of the decorator
is to do something “every time”, like to log every call to a decorated function, only the second type of
decorators can be used. On the other hand, if the first type is sufficient, it is better to use it, because it
is simpler.
7.2.2 Decorators implemented as classes and as functions
The only requirement on decorators is that they can be called with a single argument. This means that
decorators can be implemented as normal functions, or as classes with a __call__ method, or in theory,
even as lambda functions.
Let’s compare the function and class approaches. The decorator expression (the part after @) can be
either just a name, or a call. The bare-name approach is nice (less to type, looks cleaner, etc.), but is
only possible when no arguments are needed to customise the decorator. Decorators written as functions
can be used in those two cases:
>>> def simple_decorator(function):

... print("doing decoration")
... return function
>>> @simple_decorator
... def function():
... print("inside function")
doing decoration
>>> function()
inside function
>>> def decorator_with_arguments(arg):

... print("defining the decorator")
... def _decorator(function):
... # in this inner function, arg is available too
... print("doing decoration, %r " % arg)
... return function
... return _decorator
>>> @decorator_with_arguments("abc")
... def function():
defining the decorator
doing decoration, 'abc'
>>> function()
inside function
The two trivial decorators above fall into the category of decorators which return the original function.
If they were to return a new function, an extra level of nestedness would be required. In the worst case,
three levels of nested functions.
7.2. Decorators 303

>>> def replacing_decorator_with_args(arg):

... # in this inner function, arg is available too
... def _wrapper(*args, **kwargs):
... print("inside wrapper, %r %r " % (args, kwargs))
... return function(*args, **kwargs)
... return _wrapper
>>> @replacing_decorator_with_args("abc")
... def function(*args, **kwargs):
... print("inside function, %r %r " % (args, kwargs))
... return 14
>>> function(11, 12)
inside wrapper, (11, 12) {}
inside function, (11, 12) {}
14
The _wrapper function is defined to accept all positional and keyword arguments. In general we cannot
know what arguments the decorated function is supposed to accept, so the wrapper function just passes
everything to the wrapped function. One unfortunate consequence is that the apparent argument list is
misleading.
Compared to decorators defined as functions, complex decorators defined as classes are simpler. When
an object is created, the __init__ method is only allowed to return None, and the type of the created
object cannot be changed. This means that when a decorator is defined as a class, it doesn’t make
much sense to use the argument-less form: the final decorated object would just be an instance of the
decorating class, returned by the constructor call, which is not very useful. Therefore it’s enough to
discuss class-based decorators where arguments are given in the decorator expression and the decorator
__init__ method is used for decorator construction.
>>> class decorator_class(object):

... def __init__(self, arg):
... # this method is called in the decorator expression
... print("in decorator init, %s " % arg)
... self.arg = arg
... def __call__(self, function):
... # this method is called to do the job
... print("in decorator call, %s " % self.arg)
... return function
>>> deco_instance = decorator_class('foo')
in decorator init, foo
>>> @deco_instance
... print("in function, %s %s " % (args, kwargs))
in decorator call, foo
>>> function()
in function, () {}
Contrary to normal rules (PEP 8) decorators written as classes behave more like functions and therefore
their name often starts with a lowercase letter.
In reality, it doesn’t make much sense to create a new class just to have a decorator which returns the
original function. Objects are supposed to hold state, and such decorators are more useful when the
decorator returns a new object.
7.2. Decorators 304

>>> class replacing_decorator_class(object):

... def __init__(self, arg):
... # this method is called in the decorator expression
... print("in decorator init, %s " % arg)
... self.arg = arg
... def __call__(self, function):
... # this method is called to do the job
... print("in decorator call, %s " % self.arg)
... self.function = function
... return self._wrapper
... def _wrapper(self, *args, **kwargs):
... print("in the wrapper, %s %s " % (args, kwargs))
... return self.function(*args, **kwargs)
>>> deco_instance = replacing_decorator_class('foo')
in decorator init, foo
>>> @deco_instance
... print("in function, %s %s " % (args, kwargs))
in decorator call, foo
>>> function(11, 12)
in the wrapper, (11, 12) {}
in function, (11, 12) {}
A decorator like this can do pretty much anything, since it can modify the original function object and
mangle the arguments, call the original function or not, and afterwards mangle the return value.
7.2.3 Copying the docstring and other attributes of the original function
When a new function is returned by the decorator to replace the original function, an unfortunate
consequence is that the original function name, the original docstring, the original argument list are
lost. Those attributes of the original function can partially be “transplanted” to the new function
by setting __doc__ (the docstring), __module__ and __name__ (the full name of the function), and
__annotations__ (extra information about arguments and the return value of the function available in
Python 3). This can be done automatically by using functools.update_wrapper.
functools.update_wrapper(wrapper, wrapped)
“Update a wrapper function to look like the wrapped function.”

>>> import functools
>>> def replacing_decorator_with_args(arg):
... def _wrapper(*args, **kwargs):
... print("inside wrapper, %r %r " % (args, kwargs))
... return function(*args, **kwargs)
... return functools.update_wrapper(_wrapper, function)
>>> @replacing_decorator_with_args("abc")
... def function():
... "extensive documentation"
... return 14
7.2. Decorators 305

>>> function
<function function at 0x...>
>>> print(function.__doc__)
extensive documentation
One important thing is missing from the list of attributes which can be copied to the replacement
function: the argument list. The default values for arguments can be modified through the __defaults__,
__kwdefaults__ attributes, but unfortunately the argument list itself cannot be set as an attribute. This
means that help(function) will display a useless argument list which will be confusing for the user of
the function. An effective but ugly way around this problem is to create the wrapper dynamically, using
eval. This can be automated by using the external decorator module. It provides support for the
decorator decorator, which takes a wrapper and turns it into a decorator which preserves the function
signature.
To sum things up, decorators should always use functools.update_wrapper or some other means of
copying function attributes.
7.2.4 Examples in the standard library
First, it should be mentioned that there’s a number of useful decorators available in the standard library.
There are three decorators which really form a part of the language:
• classmethod causes a method to become a “class method”, which means that it can be invoked
without creating an instance of the class. When a normal method is invoked, the interpreter inserts
the instance object as the first positional parameter, self. When a class method is invoked, the
class itself is given as the first parameter, often called cls.
Class methods are still accessible through the class’ namespace, so they don’t pollute the module’s
namespace. Class methods can be used to provide alternative constructors:
class Array(object):
def __init__(self, data):
self.data = data
@classmethod
def fromfile(cls, file):
data = numpy.load(file)
return cls(data)
This is cleaner than using a multitude of flags to __init__.

• staticmethod is applied to methods to make them “static”, i.e. basically a normal function, but
accessible through the class namespace. This can be useful when the function is only needed inside
this class (its name would then be prefixed with _), or when we want the user to think of the
method as connected to the class, despite an implementation which doesn’t require this.
• property is the pythonic answer to the problem of getters and setters. A method decorated with
property becomes a getter which is automatically called on attribute access.
>>> class A(object):

... @property
... def a(self):
... "an important attribute"
... return "a value"
>>> A.a
<property object at 0x...>
>>> A().a
'a value'
7.2. Decorators 306

In this example, A.a is an read-only attribute. It is also documented: help(A) includes the
docstring for attribute a taken from the getter method. Defining a as a property allows it to be a
calculated on the fly, and has the side effect of making it read-only, because no setter is defined.
To have a setter and a getter, two methods are required, obviously:
class Rectangle(object):
def __init__(self, edge):
self.edge = edge
@property
def area(self):
"""Computed area.
Setting this updates the edge length to the proper value.

"""
return self.edge**2
@area.setter
def area(self, area):
self.edge = area ** 0.5
The way that this works, is that the property decorator replaces the getter method with a property
object. This object in turn has three methods, getter, setter, and deleter, which can be used
as decorators. Their job is to set the getter, setter and deleter of the property object (stored as
attributes fget, fset, and fdel). The getter can be set like in the example above, when creating
the object. When defining the setter, we already have the property object under area, and we add
the setter to it by using the setter method. All this happens when we are creating the class.
Afterwards, when an instance of the class has been created, the property object is special. When the
interpreter executes attribute access, assignment, or deletion, the job is delegated to the methods
of the property object.
To make everything crystal clear, let’s define a “debug” example:
>>> class D(object):

... @property
... def a(self):
... print("getting 1")
... return 1
... @a.setter
... def a(self, value):
... print("setting %r " % value)
... @a.deleter
... def a(self):
... print("deleting")
>>> D.a
<property object at 0x...>
>>> D.a.fget
<function ...>
>>> D.a.fset
<function ...>
>>> D.a.fdel
<function ...>
>>> d = D() # ... varies, this is not the same à` function
>>> d.a
getting 1
1
>>> d.a = 2
7.2. Decorators 307


setting 2
>>> del d.a
deleting
>>> d.a
getting 1
1
Properties are a bit of a stretch for the decorator syntax. One of the premises of the decorator
syntax — that the name is not duplicated — is violated, but nothing better has been invented so
far. It is just good style to use the same name for the getter, setter, and deleter methods.
Some newer examples include:
• functools.lru_cache memoizes an arbitrary function maintaining a limited cache of argu-
ments:answer pairs (Python 3.2)
• functools.total_ordering is a class decorator which fills in missing ordering methods (__lt__,
__gt__, __le__, . . . ) based on a single available one.
7.2.5 Deprecation of functions
Let’s say we want to print a deprecation warning on stderr on the first invocation of a function we don’t
like anymore. If we don’t want to modify the function, we can use a decorator:
class deprecated(object):
"""Print a deprecation warning once on first use of the function.
>>> @deprecated() # doctest: +SKIP

... def f():
... pass
>>> f() # doctest: +SKIP
f is deprecated
"""
def __call__(self, func):
self.func = func
self.count = 0
return self._wrapper
def _wrapper(self, *args, **kwargs):
self.count += 1
if self.count == 1:
print(self.func.__name__, 'is deprecated')
return self.func(*args, **kwargs)
It can also be implemented as a function:
def deprecated(func):
"""Print a deprecation warning once on first use of the function.
>>> @deprecated # doctest: +SKIP

... def f():
... pass
>>> f() # doctest: +SKIP
f is deprecated
"""
count = [0]
def wrapper(*args, **kwargs):
count[0] += 1
7.2. Decorators 308


if count[0] == 1:
print(func.__name__, 'is deprecated')
return func(*args, **kwargs)
return wrapper
7.2.6 A while-loop removing decorator
Let’s say we have function which returns a lists of things, and this list created by running a loop. If we
don’t know how many objects will be needed, the standard way to do this is something like:
def find_answers():
answers = []
while True:
ans = look_for_next_answer()
if ans is None:
break
answers.append(ans)
return answers
This is fine, as long as the body of the loop is fairly compact. Once it becomes more complicated, as
often happens in real code, this becomes pretty unreadable. We could simplify this by using yield
statements, but then the user would have to explicitly call list(find_answers()).
We can define a decorator which constructs the list for us:
def vectorized(generator_func):
def wrapper(*args, **kwargs):
return list(generator_func(*args, **kwargs))
return functools.update_wrapper(wrapper, generator_func)
Our function then becomes:

@vectorized
def find_answers():
while True:
ans = look_for_next_answer()
if ans is None:
break
yield ans
7.2.7 A plugin registration system
This is a class decorator which doesn’t modify the class, but just puts it in a global registry. It falls into
the category of decorators returning the original object:
class WordProcessor(object):
PLUGINS = []
def process(self, text):
for plugin in self.PLUGINS:
text = plugin().cleanup(text)
return text
@classmethod
def plugin(cls, plugin):
cls.PLUGINS.append(plugin)
7.2. Decorators 309

@WordProcessor.plugin
class CleanMdashesExtension(object):
def cleanup(self, text):
return text.replace('—', u'\N{em dash}')
Here we use a decorator to decentralise the registration of plugins. We call our decorator with a noun,
instead of a verb, because we use it to declare that our class is a plugin for WordProcessor. Method
plugin simply appends the class to the list of plugins.
A word about the plugin itself: it replaces HTML entity for em-dash with a real Unicode em-dash
character. It exploits the unicode literal notation to insert a character by using its name in the unicode
database (“EM DASH”). If the Unicode character was inserted directly, it would be impossible to
distinguish it from an en-dash in the source of a program.
See also:
More examples and reading
• PEP 318 (function and method decorator syntax)
• PEP 3129 (class decorator syntax)
• https://wiki.python.org/moin/PythonDecoratorLibrary
• https://docs.python.org/dev/library/functools.html
• https://pypi.org/project/decorator
• Bruce Eckel
– Decorators I: Introduction to Python Decorators
– Python Decorators II: Decorator Arguments
– Python Decorators III: A Decorator-Based Build System
7.3 Context managers
A context manager is an object with __enter__ and __exit__ methods which can be used in the with
statement:
with manager as var:

do_something(var)
is in the simplest case equivalent to
var = manager.__enter__()
try:
do_something(var)
finally:
manager.__exit__()
In other words, the context manager protocol defined in PEP 343 permits the extraction of the boring
part of a try..except..finally structure into a separate class leaving only the interesting do_something
block.
1. The __enter__ method is called first. It can return a value which will be assigned to var. The
as-part is optional: if it isn’t present, the value returned by __enter__ is simply ignored.
2. The block of code underneath with is executed. Just like with try clauses, it can either execute
successfully to the end, or it can break, continue or return, or it can throw an exception. Either
7.3. Context managers 310

way, after the block is finished, the __exit__ method is called. If an exception was thrown,
the information about the exception is passed to __exit__, which is described below in the next
subsection. In the normal case, exceptions can be ignored, just like in a finally clause, and will
be rethrown after __exit__ is finished.
Let’s say we want to make sure that a file is closed immediately after we are done writing to it:
>>> class closing(object):

... def __init__(self, obj):
... self.obj = obj
... def __enter__(self):
... return self.obj
... def __exit__(self, *args):
... self.obj.close()
>>> with closing(open('/tmp/file', 'w')) as f:
... f.write('the contents\n')
Here we have made sure that the f.close() is called when the with block is exited. Since closing files is
such a common operation, the support for this is already present in the file class. It has an __exit__
method which calls close and can be used as a context manager itself:
>>> with open('/tmp/file', 'a') as f:

... f.write('more contents\n')
The common use for try..finally is releasing resources. Various different cases are implemented
similarly: in the __enter__ phase the resource is acquired, in the __exit__ phase it is released, and the
exception, if thrown, is propagated. As with files, there’s often a natural operation to perform after the
object has been used and it is most convenient to have the support built in. With each release, Python
provides support in more places:
• all file-like objects:
– file ➥ automatically closed
– fileinput, tempfile
– bz2.BZ2File, gzip.GzipFile, tarfile.TarFile, zipfile.ZipFile
– ftplib, nntplib ➥ close connection
• locks
– multiprocessing.RLock ➥ lock and unlock
– multiprocessing.Semaphore
– memoryview ➥ automatically release
• decimal.localcontext ➥ modify precision of computations temporarily
• _winreg.PyHKEY ➥ open and close hive key
• warnings.catch_warnings ➥ kill warnings temporarily
• contextlib.closing ➥ the same as the example above, call close
• parallel programming
– concurrent.futures.ThreadPoolExecutor ➥ invoke in parallel then kill thread pool
– concurrent.futures.ProcessPoolExecutor ➥ invoke in parallel then kill process pool
– nogil ➥ solve the GIL problem temporarily (cython only :( )

7.3.1 Catching exceptions
When an exception is thrown in the with-block, it is passed as arguments to __exit__. Three arguments
are used, the same as returned by sys.exc_info(): type, value, traceback. When no exception is thrown,
None is used for all three arguments. The context manager can “swallow” the exception by returning a
true value from __exit__. Exceptions can be easily ignored, because if __exit__ doesn’t use return
and just falls of the end, None is returned, a false value, and therefore the exception is rethrown after
__exit__ is finished.
The ability to catch exceptions opens interesting possibilities. A classic example comes from unit-tests
— we want to make sure that some code throws the right kind of exception:
class assert_raises(object):
# based on pytest and unittest.TestCase
def __init__(self, type):
self.type = type
def __enter__(self):
pass
def __exit__(self, type, value, traceback):
if type is None:
raise AssertionError('exception expected')
if issubclass(type, self.type):
return True # swallow the expected exception
raise AssertionError('wrong exception type')
with assert_raises(KeyError):
{}['foo']
7.3.2 Using generators to define context managers
When discussing generators, it was said that we prefer generators to iterators implemented as classes
because they are shorter, sweeter, and the state is stored as local, not instance, variables. On the other
hand, as described in Bidirectional communication, the flow of data between the generator and its caller
can be bidirectional. This includes exceptions, which can be thrown into the generator. We would like to
implement context managers as special generator functions. In fact, the generator protocol was designed
to support this use case.
@contextlib.contextmanager
def some_generator(<arguments>):
<setup>
try:
yield <value>
finally:
<cleanup>
The contextlib.contextmanager helper takes a generator and turns it into a context manager. The
generator has to obey some rules which are enforced by the wrapper function — most importantly it
must yield exactly once. The part before the yield is executed from __enter__, the block of code
protected by the context manager is executed when the generator is suspended in yield, and the rest
is executed in __exit__. If an exception is thrown, the interpreter hands it to the wrapper through
__exit__ arguments, and the wrapper function then throws it at the point of the yield statement.
Through the use of generators, the context manager is shorter and simpler.
Let’s rewrite the closing example as a generator:
def closing(obj):


try:
yield obj
finally:
obj.close()
Let’s rewrite the assert_raises example as a generator:
def assert_raises(type):
try:
yield
except type:
return
except Exception as value:
raise AssertionError('wrong exception type')
else:
raise AssertionError('exception expected')
Here we use a decorator to turn generator functions into context managers!

CHAPTER 8
Advanced NumPy
Author: Pauli Virtanen

NumPy is at the base of Python’s scientific stack of tools. Its purpose to implement efficient operations
on many items in a block of memory. Understanding how it works in detail helps in making efficient use
of its flexibility, taking useful shortcuts.
This section covers:
• Anatomy of NumPy arrays, and its consequences. Tips and tricks.
• Universal functions: what, why, and what to do if you want a new one.
• Integration with other tools: NumPy offers several ways to wrap any data in an ndarray, without
unnecessary copies.
• Recently added features, and what’s in them: PEP 3118 buffers, generalized ufuncs, . . .
Prerequisites
• NumPy
• Cython
• Pillow (Python imaging library, used in a couple of examples)
Chapter contents
• Life of ndarray
– It’s. . .
314
– Block of memory
– Data types
– Indexing scheme: strides
– Findings in dissection
• Universal functions
– What they are?
– Exercise: building an ufunc from scratch
– Solution: building an ufunc from scratch
– Generalized ufuncs
• Interoperability features
– Sharing multidimensional, typed data
– The old buffer protocol
– The old buffer protocol
– Array interface protocol
• Array siblings: chararray, maskedarray
– chararray: vectorized string operations
– masked_array missing data
– recarray: purely convenience
• Summary
• Contributing to NumPy/SciPy
– Why
– Reporting bugs
– Contributing to documentation
– Contributing features
– How to help, in general
Tip: In this section, NumPy will be imported as follows:
8.1 Life of ndarray
8.1.1 It’s. . .
ndarray =
block of memory + indexing scheme + data type descriptor
• raw data
• how to locate an element
• how to interpret an element
8.1. Life of ndarray 315

typedef struct PyArrayObject {

PyObject_HEAD
/* Block of memory */
char *data;
/* Data type descriptor */

PyArray_Descr *descr;
/* Indexing scheme */
int nd;
npy_intp *dimensions;
npy_intp *strides;
/* Other stuff */
PyObject *base;
int flags;
PyObject *weakreflist;
} PyArrayObject;
8.1.2 Block of memory
>>> x = np.array([1, 2, 3], dtype=np.int32)

>>> x.data
<... at ...>
>>> bytes(x.data)
b'\x01\x00\x00\x00\x02\x00\x00\x00\x03\x00\x00\x00'
Memory address of the data:
>>> x.__array_interface__['data'][0]
64803824
The whole __array_interface__:
>>> x.__array_interface__
{'data': (..., False), 'strides': None, 'descr': [('', '<i4')], 'typestr': '<i4',
˓→'shape': (3,), 'version': 3}
Reminder: two ndarrays may share the same memory:
>>> x = np.array([1, 2, 3, 4])

>>> y = x[:-1]
>>> x[0] = 9
>>> y
array([9, 2, 3])

Memory does not need to be owned by an ndarray:
>>> x = b'1234'
x is a string (in Python 3 a bytes), we can represent its data as an array of ints:
>>> y = np.frombuffer(x, dtype=np.int8)

>>> y.data
<... at ...>
>>> y.base is x
True
>>> y.flags
C_CONTIGUOUS : True
F_CONTIGUOUS : True
OWNDATA : False
WRITEABLE : False
ALIGNED : True
WRITEBACKIFCOPY : False
The owndata and writeable flags indicate status of the memory block.
See also:
array interface
8.1.3 Data types
The descriptor
dtype describes a single item in the array:
type scalar type of the data, one of:

int8, int16, float64, et al. (fixed size)
str, unicode, void (flexible size)
itemsize size of the data block
byte- byte order: big-endian > / little-endian < / not applicable |
order
fields sub-dtypes, if it’s a structured data type
shape shape of the array, if it’s a sub-array
>>> np.dtype(int).type
<class 'numpy.int64'>
>>> np.dtype(int).itemsize
8
>>> np.dtype(int).byteorder
'='

Example: reading .wav files
The .wav file header:
chunk_id "RIFF"
chunk_size 4-byte unsigned little-endian integer
format "WAVE"
fmt_id "fmt "
fmt_size 4-byte unsigned little-endian integer
audio_fmt 2-byte unsigned little-endian integer
num_channels 2-byte unsigned little-endian integer
sample_rate 4-byte unsigned little-endian integer
byte_rate 4-byte unsigned little-endian integer
block_align 2-byte unsigned little-endian integer
bits_per_sample 2-byte unsigned little-endian integer
data_id "data"
data_size 4-byte unsigned little-endian integer
• 44-byte block of raw data (in the beginning of the file)

• . . . followed by data_size bytes of actual sound data.
The .wav file header as a NumPy structured data type:
>>> wav_header_dtype = np.dtype([

... ("chunk_id", (bytes, 4)), # flexible-sized scalar type, item size 4
... ("chunk_size", "<u4"), # little-endian unsigned 32-bit integer
... ("format", "S4"), # 4-byte string
... ("fmt_id", "S4"),
... ("fmt_size", "<u4"),
... ("audio_fmt", "<u2"), #
... ("num_channels", "<u2"), # .. more of the same ...
... ("sample_rate", "<u4"), #
... ("byte_rate", "<u4"),
... ("block_align", "<u2"),
... ("bits_per_sample", "<u2"),
... ("data_id", ("S1", (2, 2))), # sub-array, just for fun!
... ("data_size", "u4"),
... #
... # the sound data itself cannot be represented here:
... # it does not have a fixed size
... ])
See also:
wavreader.py
>>> wav_header_dtype['format']
dtype('S4')
>>> wav_header_dtype.fields
mappingproxy({'chunk_id': (dtype('S4'), 0), 'chunk_size': (dtype('uint32'), 4),
˓→'format': (dtype('S4'), 8), 'fmt_id': (dtype('S4'), 12), 'fmt_size': (dtype('uint32
˓→'), 16), 'audio_fmt': (dtype('uint16'), 20), 'num_channels': (dtype('uint16'), 22),
˓→'sample_rate': (dtype('uint32'), 24), 'byte_rate': (dtype('uint32'), 28), 'block_
˓→align': (dtype('uint16'), 32), 'bits_per_sample': (dtype('uint16'), 34), 'data_id':␣
˓→(dtype(('S1', (2, 2))), 36), 'data_size': (dtype('uint32'), 40)})
>>> wav_header_dtype.fields['format']
(dtype('S4'), 8)
• The first element is the sub-dtype in the structured data, corresponding to the name format

• The second one is its offset (in bytes) from the beginning of the item
Exercise
Mini-exercise, make a “sparse” dtype by using offsets, and only some of the fields:
>>> wav_header_dtype = np.dtype(dict(
... names=['format', 'sample_rate', 'data_id'],
... offsets=[offset_1, offset_2, offset_3], # counted from start of structure in␣
˓→bytes
... formats=list of dtypes for each of the fields,

... ))
and use that to read the sample rate, and data_id (as sub-array).
>>> f = open('data/test.wav', 'r')

>>> wav_header = np.fromfile(f, dtype=wav_header_dtype, count=1)
>>> f.close()
>>> print(wav_header)
[ ('RIFF', 17402L, 'WAVE', 'fmt ', 16L, 1, 1, 16000L, 32000L, 2, 16, [['d', 'a'], ['t
˓→', 'a']], 17366L)]
>>> wav_header['sample_rate']
array([16000], dtype=uint32)
Let’s try accessing the sub-array:
>>> wav_header['data_id']
array([[['d', 'a'],
['t', 'a']]],
dtype='|S1')
>>> wav_header.shape
(1,)
>>> wav_header['data_id'].shape
(1, 2, 2)
When accessing sub-arrays, the dimensions get added to the end!
Note: There are existing modules such as wavfile, audiolab, etc. for loading sound data. . .
Casting and re-interpretation/views
casting
• on assignment
• on array construction
• on arithmetic
• etc.
• and manually: .astype(dtype)
data re-interpretation
• manually: .view(dtype)

Casting
• Casting in arithmetic, in nutshell:

– only type (not value!) of operands matters
– largest “safe” type able to represent both is picked
– scalars can “lose” to arrays in some situations
• Casting in general copies data:
>>> x = np.array([1, 2, 3, 4], dtype=float)

>>> x
array([1., 2., 3., 4.])
>>> y = x.astype(np.int8)
>>> y
array([1, 2, 3, 4], dtype=int8)
>>> y + 1
>>> y + 256
array([257, 258, 259, 260], dtype=int16)
>>> y + 256.0
array([257., 258., 259., 260.])
>>> y + np.array([256], dtype=np.int32)
array([257, 258, 259, 260], dtype=int32)
• Casting on setitem: dtype of the array is not changed on item assignment:
>>> y[:] = y + 1.5

>>> y
Note: Exact rules: see NumPy documentation
Re-interpretation / viewing
• Data block in memory (4 bytes)
0x01 || 0x02 || 0x03 || 0x04
– 4 of uint8, OR,
– 4 of int8, OR,
– 2 of int16, OR,
– 1 of int32, OR,
– 1 of float32, OR,
– ...
How to switch from one to another?
1. Switch the dtype:
>>> x = np.array([1, 2, 3, 4], dtype=np.uint8)

>>> x.dtype = "<i2"
>>> x


array([ 513, 1027], dtype=int16)
>>> 0x0201, 0x0403
(513, 1027)
0x01 0x02 || 0x03 0x04
Note: little-endian: least significant byte is on the left in memory
2. Create a new view of type uint32, shorthand i4:
>>> y = x.view("<i4")
>>> y
array([67305985], dtype=int32)
>>> 0x04030201
67305985
0x01 0x02 0x03 0x04
Note:
• .view() makes views, does not copy (or alter) the memory block
• only changes the dtype (and adjusts array shape):
>>> x[1] = 5
>>> y
array([328193], dtype=int32)
>>> y.base is x
True
Mini-exercise: data re-interpretation
See also:
view-colors.py
You have RGBA data in an array:
>>> x = np.zeros((10, 10, 4), dtype=np.int8)

>>> x[:, :, 0] = 1
>>> x[:, :, 1] = 2
>>> x[:, :, 2] = 3
>>> x[:, :, 3] = 4
where the last three dimensions are the R, B, and G, and alpha channels.
How to make a (10, 10) structured array with field names ‘r’, ‘g’, ‘b’, ‘a’ without copying data?
>>> y = ...
>>> assert (y['r'] == 1).all()

>>> assert (y['g'] == 2).all()


>>> assert (y['b'] == 3).all()
>>> assert (y['a'] == 4).all()
Solution
>>> y = x.view([('r', 'i1'),

... ('g', 'i1'),
... ('b', 'i1'),
... ('a', 'i1')]
... )[:, :, 0]
Warning: Another two arrays, each occupying exactly 4 bytes of memory:

>>> x = np.array([[1, 3], [2, 4]], dtype=np.uint8)
>>> x
array([[1, 3],
[2, 4]], dtype=uint8)
>>> y = x.transpose()
>>> y
array([[1, 2],
[3, 4]], dtype=uint8)
We view the elements of x (1 byte each) as int16 (2 bytes each):

>>> x.view(np.int16)
array([[ 769],
[1026]], dtype=int16)
What is happening here? Take a look at the bytes stored in memory by x:

>>> x.tobytes()
b'\x01\x03\x02\x04'
The \x stands for heXadecimal, so what we are seeing is:

0x01 0x03 0x02 0x04
We ask NumPy to interpret these bytes as elements of dtype int16—each of which occupies two
bytes in memory. Therefore, 0x01 0x03 becomes the first uint16 and 0x02 0x04 the second.
You may then expect to see 0x0103 (259, when converting from hexadecimal to decimal) as the first
result. But your computer likely stores most significant bytes first, and as such reads the number as
0x0301 or 769 (go on and type 0x0301 into your Python terminal to verify).
We can do the same on a copy of y (why doesn’t it work on y directly?):
>>> y.copy().view(np.int16)
array([[ 513],
[1027]], dtype=int16)
Can you explain these numbers, 513 and 1027, as well as the output shape of the resulting array?

8.1.4 Indexing scheme: strides
Main point
The question:
>>> x = np.array([[1, 2, 3],

... [4, 5, 6],
... [7, 8, 9]], dtype=np.int8)
>>> x.tobytes('A')
b'\x01\x02\x03\x04\x05\x06\x07\x08\t'
At which byte in ``x.data`` does the item ``x[1, 2]`` begin?
The answer (in NumPy)

• strides: the number of bytes to jump to find the next element
• 1 stride per dimension
>>> x.strides
(3, 1)
>>> byte_offset = 3 * 1 + 1 * 2 # to find x[1, 2]
>>> x.flat[byte_offset]
6
>>> x[1, 2]
6
simple, flexible
C and Fortran order
Note: The Python built-in bytes returns bytes in C-order by default which can cause confusion when
trying to inspect memory layout. We use numpy.ndarray.tobytes() with order=A instead, which
preserves the C or F ordering of the bytes in memory.
>>> x = np.array([[1, 2, 3],

... [4, 5, 6]], dtype=np.int16, order='C')
>>> x.strides
(6, 2)
>>> x.tobytes('A')
b'\x01\x00\x02\x00\x03\x00\x04\x00\x05\x00\x06\x00'
• Need to jump 6 bytes to find the next row

• Need to jump 2 bytes to find the next column
>>> y = np.array(x, order='F')

>>> y.strides
(2, 4)
>>> y.tobytes('A')
b'\x01\x00\x04\x00\x02\x00\x05\x00\x03\x00\x06\x00'
• Need to jump 2 bytes to find the next row

• Need to jump 4 bytes to find the next column
• Similarly to higher dimensions:

– C: last dimensions vary fastest (= smaller strides)

– F: first dimensions vary fastest
shape = (𝑑1 , 𝑑2 , ..., 𝑑𝑛 )
strides = (𝑠1 , 𝑠2 , ..., 𝑠𝑛 )
𝑠𝐶
𝑗 = 𝑑𝑗+1 𝑑𝑗+2 ...𝑑𝑛 × itemsize
𝑠𝐹
𝑗 = 𝑑1 𝑑2 ...𝑑𝑗−1 × itemsize
Note: Now we can understand the behavior of .view():
>>> y = np.array([[1, 3], [2, 4]], dtype=np.uint8).transpose()

>>> x = y.copy()
Transposition does not affect the memory layout of the data, only strides
>>> x.strides
(2, 1)
>>> y.strides
(1, 2)
>>> x.tobytes('A')
b'\x01\x02\x03\x04'
>>> y.tobytes('A')
b'\x01\x03\x02\x04'
• the results are different when interpreted as 2 of int16

• .copy() creates new arrays in the C order (by default)
Note: In-place operations with views

Prior to NumPy version 1.13, in-place operations with views could result in incorrect results for large
arrays. Since version 1.13, NumPy includes checks for memory overlap to guarantee that results are
consistent with the non in-place version (e.g. a = a + a.T produces the same result as a += a.T).
Note however that this may result in the data being copied (as if using a += a.T.copy()), ultimately
resulting in more memory being used than might otherwise be expected for in-place operations!
Slicing with integers
• Everything can be represented by changing only shape, strides, and possibly adjusting the data
pointer!
• Never makes copies of the data
>>> x = np.array([1, 2, 3, 4, 5, 6], dtype=np.int32)

>>> y = x[::-1]
>>> y
array([6, 5, 4, 3, 2, 1], dtype=int32)
>>> y.strides
(-4,)
>>> y = x[2:]
>>> y.__array_interface__['data'][0] - x.__array_interface__['data'][0]
8

>>> x = np.zeros((10, 10, 10), dtype=float)

>>> x.strides
(800, 80, 8)
>>> x[::2,::3,::4].strides
(1600, 240, 32)
• Similarly, transposes never make copies (it just swaps strides):
>>> x = np.zeros((10, 10, 10), dtype=float)

>>> x.strides
(800, 80, 8)
>>> x.T.strides
(8, 80, 800)
But: not all reshaping operations can be represented by playing with strides:
>>> a = np.arange(6, dtype=np.int8).reshape(3, 2)

>>> b = a.T
>>> b.strides
(1, 2)
So far, so good. However:
>>> bytes(a.data)
b'\x00\x01\x02\x03\x04\x05'
>>> b
array([[0, 2, 4],
[1, 3, 5]], dtype=int8)
>>> c = b.reshape(3*2)
>>> c
array([0, 2, 4, 1, 3, 5], dtype=int8)
Here, there is no way to represent the array c given one stride and the block of memory for a. Therefore,
the reshape operation needs to make a copy here.
Example: fake dimensions with strides
Stride manipulation
>>> from numpy.lib.stride_tricks import as_strided

>>> help(as_strided)
Help on function as_strided in module numpy.lib.stride_tricks:
...
Warning: as_strided does not check that you stay inside the memory block bounds. . .
>>> x = np.array([1, 2, 3, 4], dtype=np.int16)

>>> as_strided(x, strides=(2*2, ), shape=(2, ))
array([1, 3], dtype=int16)
>>> x[::2]

See also:
stride-fakedims.py
Exercise
array([1, 2, 3, 4], dtype=np.int8)
-> array([[1, 2, 3, 4],

[1, 2, 3, 4],
[1, 2, 3, 4]], dtype=np.int8)
using only as_strided.:
Hint: byte_offset = stride[0]*index[0] + stride[1]*index[1] + ...
Spoiler
Stride can also be 0 :

>>> y = as_strided(x, strides=(0, 1), shape=(3, 4))
>>> y
array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]], dtype=int8)
>>> y.base.base is x
True
Broadcasting
• Doing something useful with it: outer product of [1, 2, 3, 4] and [5, 6, 7]

>>> x2 = as_strided(x, strides=(0, 1*2), shape=(3, 4))
>>> x2
array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]], dtype=int16)
>>> y = np.array([5, 6, 7], dtype=np.int16)

>>> y2 = as_strided(y, strides=(1*2, 0), shape=(3, 4))
>>> y2
array([[5, 5, 5, 5],
[6, 6, 6, 6],
[7, 7, 7, 7]], dtype=int16)
>>> x2 * y2
array([[ 5, 10, 15, 20],
[ 6, 12, 18, 24],
[ 7, 14, 21, 28]], dtype=int16)

. . . seems somehow familiar . . .

>>> y = np.array([5, 6, 7], dtype=np.int16)
>>> x[np.newaxis,:] * y[:,np.newaxis]
array([[ 5, 10, 15, 20],
[ 6, 12, 18, 24],
[ 7, 14, 21, 28]], dtype=int16)
• Internally, array broadcasting is indeed implemented using 0-strides.
More tricks: diagonals
See also:
stride-diagonals.py
Challenge
• Pick diagonal entries of the matrix: (assume C memory order):
>>> x = np.array([[1, 2, 3],

... [4, 5, 6],
... [7, 8, 9]], dtype=np.int32)
>>> x_diag = as_strided(x, shape=(3,), strides=(???,))
• Pick the first super-diagonal entries [2, 6].

• And the sub-diagonals?
(Hint to the last two: slicing first moves the point where striding
starts from.)
Solution
Pick diagonals:
>>> x_diag = as_strided(x, shape=(3, ), strides=((3+1)*x.itemsize, ))

>>> x_diag
array([1, 5, 9], dtype=int32)
Slice first, to adjust the data pointer:
>>> as_strided(x[0, 1:], shape=(2, ), strides=((3+1)*x.itemsize, ))

>>> as_strided(x[1:, 0], shape=(2, ), strides=((3+1)*x.itemsize, ))

Note: Using np.diag
>>> y = np.diag(x, k=1)

>>> y
However,
>>> y.flags.owndata
False

See also:
stride-diagonals.py
Challenge
Compute the tensor trace:
>>> x = np.arange(5*5*5*5).reshape(5, 5, 5, 5)
>>> s = 0
... for j in range(5):
... s += x[j, i, j, i]
by striding, and using sum() on the result.
>>> y = as_strided(x, shape=(5, 5), strides=(TODO, TODO))

>>> s2 = ...
>>> assert s == s2
Solution
>>> y = as_strided(x, shape=(5, 5), strides=((5*5*5 + 5)*x.itemsize,

... (5*5 + 1)*x.itemsize))
>>> s2 = y.sum()
CPU cache effects
Memory layout can affect performance:
In [1]: x = np.zeros((20000,))
In [2]: y = np.zeros((20000*67,))[::67]
In [3]: x.shape, y.shape

Out[3]: ((20000,), (20000,))
In [4]: %timeit x.sum()

5.17 us +- 9.39 ns per loop (mean +- std. dev. of 7 runs, 100,000 loops each)
In [5]: %timeit y.sum()

In [6]: x.strides, y.strides

Out[6]: ((8,), (536,))
Smaller strides are faster?

• CPU pulls data from main memory to its cache in blocks

• If many array items consecutively operated on fit in a single block (small stride):
– ⇒ fewer transfers needed
– ⇒ faster
See also:
• numexpr is designed to mitigate cache effects when evaluating array expressions.
• numba is a compiler for Python code, that is aware of numpy arrays.
8.1.5 Findings in dissection
• memory block: may be shared, .base, .data

• data type descriptor: structured data, sub-arrays, byte order, casting, viewing, .astype(), .view()
• strided indexing: strides, C/F-order, slicing w/ integers, as_strided, broadcasting, stride tricks,
diag, CPU cache coherence
8.2 Universal functions
8.2.1 What they are?
• Ufunc performs and elementwise operation on all elements of an array.

Examples:
np.add, np.subtract, scipy.special.*, ...
• Automatically support: broadcasting, casting, . . .

• The author of an ufunc only has to supply the elementwise operation, NumPy takes care of the
rest.
• The elementwise operation needs to be implemented in C (or, e.g., Cython)
8.2. Universal functions 329

Parts of an Ufunc
1. Provided by user
void ufunc_loop(void **args, int *dimensions, int *steps, void *data)

{
/*
* int8 output = elementwise_function(int8 input_1, int8 input_2)
*
* This function must compute the ufunc for many values at once,
* in the way shown below.
*/
char *input_1 = (char*)args[0];
char *output = (char*)args[2];
int i;
for (i = 0; i < dimensions[0]; ++i) {

*output = elementwise_function(*input_1, *input_2);
input_1 += steps[0];
output += steps[2];
}
}
2. The NumPy part, built by
char types[3]
types[0] = NPY_BYTE /* type of first input arg */

types[1] = NPY_BYTE /* type of second input arg */
types[2] = NPY_BYTE /* type of third input arg */
PyObject *python_ufunc = PyUFunc_FromFuncAndData(

ufunc_loop,
NULL,
types,
1, /* ntypes */
2, /* num_inputs */
1, /* num_outputs */
identity_element,
name,
docstring,
unused)
• A ufunc can also support multiple different input-output type combinations.

Making it easier
3. ufunc_loop is of very generic form, and NumPy provides pre-made ones
PyUfunc_f_f float elementwise_func(float input_1)

PyUfunc_ff_f float elementwise_func(float input_1, float input_2)
PyUfunc_d_d double elementwise_func(double input_1)
PyUfunc_dd_d double elementwise_func(double input_1, double input_2)
PyUfunc_D_D elementwise_func(npy_cdouble *input, npy_cdouble* output)
PyUfunc_DD_D elementwise_func(npy_cdouble *in1, npy_cdouble *in2, npy_cdouble*
out)
• Only elementwise_func needs to be supplied

• . . . except when your elementwise function is not in one of the above forms
8.2.2 Exercise: building an ufunc from scratch
The Mandelbrot fractal is defined by the iteration
𝑧 ← 𝑧2 + 𝑐
where 𝑐 = 𝑥 + 𝑖𝑦 is a complex number. This iteration is repeated – if 𝑧 stays finite no matter how long
the iteration runs, 𝑐 belongs to the Mandelbrot set.
• Make ufunc called mandel(z0, c) that computes:
z = z0
for k in range(iterations):
z = z*z + c
say, 100 iterations or until z.real**2 + z.imag**2 > 1000. Use it to determine which c are in
the Mandelbrot set.
• Our function is a simple one, so make use of the PyUFunc_* helpers.
• Write it in Cython
See also:
mandel.pyx, mandelplot.py
#
# Fix the parts marked by TODO
#
#
# Compile this file by (Cython >= 0.12 required because of the complex vars)
#
# cython mandel.pyx
# python setup.py build_ext -i
#
# and try it out with, in this directory,
#
# >>> import mandel
# >>> mandel.mandel(0, 1 + 2j)
#
#


# The elementwise function
# ------------------------
cdef void mandel_single_point(double complex *z_in,

double complex *c_in,
double complex *z_out) nogil:
#
# The Mandelbrot iteration
#
#
# Some points of note:
#
# - It's *NOT* allowed to call any Python functions here.
#
# The Ufunc loop runs with the Python Global Interpreter Lock released.
# Hence, the ``nogil``.
#
# - And so all local variables must be declared with ``cdef``
#
# - Note also that this function receives *pointers* to the data
#
cdef double complex z = z_in[0]

cdef double complex c = c_in[0]
cdef int k # the integer we use in the for loop
#
# TODO: write the Mandelbrot iteration for one point here,
# as you would write it in Python.
#
# Say, use 100 as the maximum number of iterations, and 1000
# as the cutoff for z.real**2 + z.imag**2.
#
TODO: mandelbrot iteration should go here
# Return the answer for this point

z_out[0] = z
# Boilerplate Cython definitions

#
# Pulls definitions from the NumPy C headers.
# -------------------------------------------
from numpy cimport import_array, import_ufunc

from numpy cimport (PyUFunc_FromFuncAndData,
PyUFuncGenericFunction)
from numpy cimport NPY_CDOUBLE, NP_DOUBLE, NPY_LONG
# Import all pre-defined loop functions

# you won't need all of them - keep the relevant ones
from numpy cimport (

PyUFunc_f_f_As_d_d,


PyUFunc_d_d,
PyUFunc_f_f,
PyUFunc_g_g,
PyUFunc_F_F_As_D_D,
PyUFunc_F_F,
PyUFunc_D_D,
PyUFunc_G_G,
PyUFunc_ff_f_As_dd_d,
PyUFunc_ff_f,
PyUFunc_dd_d,
PyUFunc_gg_g,
PyUFunc_FF_F_As_DD_D,
PyUFunc_DD_D,
PyUFunc_FF_F,
PyUFunc_GG_G)
# Required module initialization

# ------------------------------
import_array()
import_ufunc()
# The actual ufunc declaration

# ----------------------------
cdef PyUFuncGenericFunction loop_func[1]

cdef char input_output_types[3]
cdef void *elementwise_funcs[1]
#
# Reminder: some pre-made Ufunc loops:
#
# ================ =======================================================
# ``PyUfunc_f_f`` ``float elementwise_func(float input_1)``
# ``PyUfunc_ff_f`` ``float elementwise_func(float input_1, float input_2)``
# ``PyUfunc_d_d`` ``double elementwise_func(double input_1)``
# ``PyUfunc_dd_d`` ``double elementwise_func(double input_1, double input_2)``
# ``PyUfunc_D_D`` `èlementwise_func(complex_double *input, complex_double* complex_
˓→double)``
# ``PyUfunc_DD_D`` `èlementwise_func(complex_double *in1, complex_double *in2,␣

˓→complex_double* out)``
# ================ =======================================================
#
# The full list is above.
#
#
# Type codes:
#
# NPY_BOOL, NPY_BYTE, NPY_UBYTE, NPY_SHORT, NPY_USHORT, NPY_INT, NPY_UINT,
# NPY_LONG, NPY_ULONG, NPY_LONGLONG, NPY_ULONGLONG, NPY_FLOAT, NPY_DOUBLE,
# NPY_LONGDOUBLE, NPY_CFLOAT, NPY_CDOUBLE, NPY_CLONGDOUBLE, NPY_DATETIME,
# NPY_TIMEDELTA, NPY_OBJECT, NPY_STRING, NPY_UNICODE, NPY_VOID
#


loop_func[0] = ... TODO: suitable PyUFunc_* ...
input_output_types[0] = ... TODO ...
... TODO: fill in rest of input_output_types ...
# This thing is passed as the ``data`` parameter for the generic

# PyUFunc_* loop, to let it know which function it should call.
elementwise_funcs[0] = <void*>mandel_single_point
# Construct the ufunc:
mandel = PyUFunc_FromFuncAndData(
loop_func,
elementwise_funcs,
input_output_types,
1, # number of supported input types
TODO, # number of input args
TODO, # number of output args
0, # ìdentity` element, never mind this
"mandel", # function name
"mandel(z, c) -> computes z*z + c", # docstring
0 # unused
)
Reminder: some pre-made Ufunc loops:
PyUfunc_f_f float elementwise_func(float input_1)

PyUfunc_ff_f float elementwise_func(float input_1, float input_2)
PyUfunc_d_d double elementwise_func(double input_1)
PyUfunc_dd_d double elementwise_func(double input_1, double input_2)
PyUfunc_D_D elementwise_func(complex_double *input, complex_double* output)
PyUfunc_DD_D elementwise_func(complex_double *in1, complex_double *in2,
complex_double* out)
Type codes:
NPY_BOOL, NPY_BYTE, NPY_UBYTE, NPY_SHORT, NPY_USHORT, NPY_INT, NPY_UINT,
NPY_LONG, NPY_ULONG, NPY_LONGLONG, NPY_ULONGLONG, NPY_FLOAT, NPY_DOUBLE,
NPY_LONGDOUBLE, NPY_CFLOAT, NPY_CDOUBLE, NPY_CLONGDOUBLE, NPY_DATETIME,
NPY_TIMEDELTA, NPY_OBJECT, NPY_STRING, NPY_UNICODE, NPY_VOID
8.2.3 Solution: building an ufunc from scratch
# The elementwise function

# ------------------------

#
# The Mandelbrot iteration
#
#
# Some points of note:


#
# - It's *NOT* allowed to call any Python functions here.
#
# The Ufunc loop runs with the Python Global Interpreter Lock released.
# Hence, the ``nogil``.
#
# - And so all local variables must be declared with ``cdef``
#
# - Note also that this function receives *pointers* to the data;
# the "traditional" solution to passing complex variables around
#
cdef double complex z = z_in[0]

cdef double complex c = c_in[0]
cdef int k # the integer we use in the for loop
# Straightforward iteration
for k in range(100):
z = z*z + c
if z.real**2 + z.imag**2 > 1000:
break
# Return the answer for this point

z_out[0] = z
# Boilerplate Cython definitions

#
# Pulls definitions from the NumPy C headers.
# -------------------------------------------
from numpy cimport import_array, import_ufunc

from numpy cimport (PyUFunc_FromFuncAndData,
PyUFuncGenericFunction)
from numpy cimport NPY_CDOUBLE
from numpy cimport PyUFunc_DD_D
# Required module initialization

# ------------------------------
import_array()
import_ufunc()
# The actual ufunc declaration

# ----------------------------
cdef PyUFuncGenericFunction loop_func[1]

cdef char input_output_types[3]
cdef void *elementwise_funcs[1]
loop_func[0] = PyUFunc_DD_D
input_output_types[0] = NPY_CDOUBLE


loop_func,
elementwise_funcs,
input_output_types,
1, # number of supported input types
2, # number of input args
1, # number of output args
"mandel(z, c) -> computes iterated z*z + c", # docstring
0 # unused
)
"""
Plot Mandelbrot
================
Plot the Mandelbrot ensemble.
"""
import numpy as np
import mandel
x = np.linspace(-1.7, 0.6, 1000)

y = np.linspace(-1.4, 1.4, 1000)
c = x[None, :] + 1j * y[:, None]
z = mandel.mandel(c, c)
plt.imshow(abs(z) ** 2 < 1000, extent=[-1.7, 0.6, -1.4, 1.4])

plt.gray()
plt.show()
Note: Most of the boilerplate could be automated by these Cython modules:

https://github.com/cython/cython/wiki/MarkLodato-CreatingUfuncs
Several accepted input types
E.g. supporting both single- and double-precision versions

...
cdef void mandel_single_point_singleprec(float complex *z_in,

float complex *c_in,
float complex *z_out) nogil:
...
cdef PyUFuncGenericFunction loop_funcs[2]

cdef char input_output_types[3*2]
cdef void *elementwise_funcs[1*2]
loop_funcs[0] = PyUFunc_DD_D
loop_funcs[1] = PyUFunc_FF_F
input_output_types[3] = NPY_CFLOAT
elementwise_funcs[1] = <void*>mandel_single_point_singleprec
loop_func,
elementwise_funcs,
input_output_types,
2, # number of supported input types <----------------
2, # number of input args
1, # number of output args
"mandel(z, c) -> computes iterated z*z + c", # docstring
0 # unused
)

8.2.4 Generalized ufuncs
ufunc
output = elementwise_function(input)
Both output and input can be a single array element only.
generalized ufunc
output and input can be arrays with a fixed number of dimensions
For example, matrix trace (sum of diag elements):
input shape = (n, n)

output shape = () i.e. scalar
(n, n) -> ()
Matrix product:
input_1 shape = (m, n)

input_2 shape = (n, p)
output shape = (m, p)
(m, n), (n, p) -> (m, p)
• This is called the “signature” of the generalized ufunc

• The dimensions on which the g-ufunc acts, are “core dimensions”
Status in NumPy
• g-ufuncs are in NumPy already . . .

• new ones can be created with PyUFunc_FromFuncAndDataAndSignature
• most linear-algebra functions are implemented as g-ufuncs to enable working with stacked arrays:

>>> np.linalg.det(rng.random((3, 5, 5)))
array([ 0.01829761, -0.0077266 , -0.05336566])
>>> np.linalg._umath_linalg.det.signature
'(m,m)->()'
• matrix multiplication this way could be useful for operating on many small matrices at once
• Also see tensordot and einsum
Generalized ufunc loop
Matrix multiplication (m,n),(n,p) -> (m,p)
void gufunc_loop(void **args, int *dimensions, int *steps, void *data)

{
char *input_1 = (char*)args[0]; /* these are as previously */
char *output = (char*)args[2];
int input_1_stride_m = steps[3]; /* strides for the core dimensions */



int input_1_stride_n = steps[4]; /* are added after the non-core */
int input_2_strides_n = steps[5]; /* steps */
int input_2_strides_p = steps[6];
int output_strides_n = steps[7];
int output_strides_p = steps[8];
int m = dimension[1]; /* core dimensions are added after */

int n = dimension[2]; /* the main dimension; order as in */
int p = dimension[3]; /* signature */
int i;
for (i = 0; i < dimensions[0]; ++i) {

matmul_for_strided_matrices(input_1, input_2, output,
strides for each array...);
output += steps[2];
}
}
8.3 Interoperability features
8.3.1 Sharing multidimensional, typed data
Suppose you
1. Write a library than handles (multidimensional) binary data,
2. Want to make it easy to manipulate the data with NumPy, or whatever other library,
3. . . . but would not like to have NumPy as a dependency.
Currently, 3 solutions:
1. the “old” buffer interface
2. the array interface
3. the “new” buffer interface (PEP 3118)
8.3.2 The old buffer protocol
• Only 1-D buffers

• No data type information
• C-level interface; PyBufferProcs tp_as_buffer in the type object
• But it’s integrated into Python (e.g. strings support it)
Mini-exercise using Pillow (Python Imaging Library):
See also:
pilbuffer.py
8.3. Interoperability features 339

>>> from PIL import Image

>>> data = np.zeros((200, 200, 4), dtype=np.uint8)
>>> data[:, :] = [255, 0, 0, 255] # Red
>>> # In PIL, RGBA images consist of 32-bit integers whose bytes are [RR,GG,BB,AA]
>>> data = data.view(np.int32).squeeze()
>>> img = Image.frombuffer("RGBA", (200, 200), data, "raw", "RGBA", 0, 1)
>>> img.save('test.png')
Q:
Check what happens if data is now modified, and img saved again.
8.3.3 The old buffer protocol
"""
From buffer
============
Show how to exchange data between numpy and a library that only knows
the buffer interface.
"""
import numpy as np
import Image
# Let's make a sample image, RGBA format
x = np.zeros((200, 200, 4), dtype=np.int8)
x[:, :, 0] = 254 # red

x[:, :, 3] = 255 # opaque
data = x.view(np.int32) # Check that you understand why this is OK!
img = Image.frombuffer("RGBA", (200, 200), data)

img.save("test.png")
#
# Modify the original data, and save again.
#
# It turns out that PIL, which knows next to nothing about NumPy,
# happily shares the same data.
#
x[:, :, 1] = 254
img.save("test2.png")

8.3.4 Array interface protocol
• Multidimensional buffers
• Data type information present
• NumPy-specific approach; slowly deprecated (but not going away)
• Not integrated in Python otherwise
See also:
Documentation: https://numpy.org/doc/stable/reference/arrays.interface.html
>>> x = np.array([[1, 2], [3, 4]])

>>> x.__array_interface__
{'data': (171694552, False), # memory address of data, is readonly?
'descr': [('', '<i4')], # data type descriptor
'typestr': '<i4', # same, in another form
'strides': None, # strides; or None if in C-order
'shape': (2, 2),
'version': 3,
}
::
>>> from PIL import Image

>>> img = Image.open('data/test.png')
>>> img.__array_interface__
{'version': 3,
'data': ...,
'shape': (200, 200, 4),


'typestr': '|u1'}
>>> x = np.asarray(img)
>>> x.shape
(200, 200, 4)
Note: A more C-friendly variant of the array interface is also defined.
8.4 Array siblings: chararray, maskedarray
8.4.1 chararray: vectorized string operations
>>> x = np.array(['a', ' bbb', ' ccc']).view(np.chararray)

>>> x.lstrip(' ')
chararray(['a', 'bbb', 'ccc'],
dtype='...')
>>> x.upper()
chararray(['A', ' BBB', ' CCC'],
dtype='...')
Note: .view() has a second meaning: it can make an ndarray an instance of a specialized ndarray
subclass
8.4.2 masked_array missing data
Masked arrays are arrays that may have missing or invalid entries.
For example, suppose we have an array where the fourth entry is invalid:
>>> x = np.array([1, 2, 3, -99, 5])
One way to describe this is to create a masked array:
>>> mx = np.ma.masked_array(x, mask=[0, 0, 0, 1, 0])

>>> mx
masked_array(data=[1, 2, 3, --, 5],
mask=[False, False, False, True, False],
fill_value=999999)
Masked mean ignores masked data:
>>> mx.mean()
2.75
>>> np.mean(mx)
2.75
Warning: Not all NumPy functions respect masks, for instance np.dot, so check the return types.
The masked_array returns a view to the original array:
8.4. Array siblings: chararray, maskedarray 342

>>> mx[1] = 9
>>> x
array([ 1, 9, 3, -99, 5])
The mask
You can modify the mask by assigning:
>>> mx[1] = np.ma.masked

>>> mx
masked_array(data=[1, --, 3, --, 5],
mask=[False, True, False, True, False],
fill_value=999999)
The mask is cleared on assignment:
>>> mx[1] = 9
>>> mx
masked_array(data=[1, 9, 3, --, 5],
mask=[False, False, False, True, False],
fill_value=999999)
The mask is also available directly:
>>> mx.mask
array([False, False, False, True, False])
The masked entries can be filled with a given value to get an usual array back:
>>> x2 = mx.filled(-1)
>>> x2
array([ 1, 9, 3, -1, 5])
The mask can also be cleared:
>>> mx.mask = np.ma.nomask

>>> mx
masked_array(data=[1, 9, 3, -99, 5],
mask=[False, False, False, False, False],
fill_value=999999)
Domain-aware functions
The masked array package also contains domain-aware functions:
>>> np.ma.log(np.array([1, 2, -1, -2, 3, -5]))

masked_array(data=[0.0, 0.693147180559..., --, --, 1.098612288668..., --],
mask=[False, False, True, True, False, True],
fill_value=1e+20)
Note: Streamlined and more seamless support for dealing with missing data in arrays is making its
way into NumPy 1.7. Stay tuned!

Example: Masked statistics
Canadian rangers were distracted when counting hares and lynxes in 1903-1910 and 1917-1918, and
got the numbers are wrong. (Carrot farmers stayed alert, though.) Compute the mean populations
over time, ignoring the invalid numbers.
>>> populations = np.ma.masked_array(data[:,1:])
>>> year = data[:, 0]
>>> bad_years = (((year >= 1903) & (year <= 1910))

... | ((year >= 1917) & (year <= 1918)))
>>> # '&' means 'and' and '|' means 'or'
>>> populations[bad_years, 0] = np.ma.masked
>>> populations[bad_years, 1] = np.ma.masked
>>> populations.mean(axis=0)
masked_array(data=[40472.72727272727, 18627.272727272728, 42400.0],
mask=[False, False, False],
fill_value=1e+20)
>>> populations.std(axis=0)
masked_array(data=[21087.656489006717, 15625.799814240254, 3322.5062255844787],
mask=[False, False, False],
fill_value=1e+20)
Note that Matplotlib knows about masked arrays:

>>> plt.plot(year, populations, 'o-')
[<matplotlib.lines.Line2D object at ...>, ...]
8.4.3 recarray: purely convenience
>>> arr = np.array([('a', 1), ('b', 2)], dtype=[('x', 'S1'), ('y', int)])
>>> arr2 = arr.view(np.recarray)
>>> arr2.x
array([b'a', b'b'], dtype='|S1')
>>> arr2.y
array([1, 2])

8.5 Summary
• Anatomy of the ndarray: data, dtype, strides.

• Universal functions: elementwise operations, how to make new ones
• Ndarray subclasses
• Various buffer interfaces for integration with other tools
• Recent additions: PEP 3118, generalized ufuncs
8.6 Contributing to NumPy/SciPy
Get this tutorial: https://www.euroscipy.org/talk/882
8.6.1 Why
• “There’s a bug?”
• “I don’t understand what this is supposed to do?”
• “I have this fancy code. Would you like to have it?”
• “I’d like to help! What can I do?”
8.6.2 Reporting bugs
• Bug tracker (prefer this)

– https://github.com/numpy/numpy/issues
– https://github.com/scipy/scipy/issues
– Click the “Sign up” link to get an account
• Mailing lists (https://numpy.org/community/)
– If you’re unsure
– No replies in a week or so? Just file a bug ticket.
Good bug report
Title: numpy.random.permutations fails for non-integer arguments
I'm trying to generate random permutations, using numpy.random.permutations
When calling numpy.random.permutation with non-integer arguments

it fails with a cryptic error message::
>>> rng.permutation(12)
array([ 2, 6, 4, 1, 8, 11, 10, 5, 9, 3, 7, 0])
>>> rng.permutation(12.) #doctest: +SKIP
File "_generator.pyx", line 4844, in numpy.random._generator.Generator.permutation
numpy.exceptions.AxisError: axis 0 is out of bounds for array of dimension 0
8.5. Summary 345


This also happens with long arguments, and so
np.random.permutation(X.shape[0]) where X is an array fails on 64
bit windows (where shape is a tuple of longs).
It would be great if it could cast to integer or at least raise a

proper error for non-integer types.
I'm using NumPy 1.4.1, built from the official tarball, on Windows
64 with Visual studio 2008, on Python.org 64-bit Python.
0. What are you trying to do?

1. Small code snippet reproducing the bug (if possible)
• What actually happens
• What you’d expect
2. Platform (Windows / Linux / OSX, 32/64 bits, x86/PPC, . . . )
3. Version of NumPy/SciPy
>>> print(np.__version__)
1...
Check that the following is what you expect
>>> print(np.__file__)
/...
In case you have old/broken NumPy installations lying around.

If unsure, try to remove existing NumPy installations, and reinstall. . .
8.6.3 Contributing to documentation
1. Documentation editor
• https://numpy.org/doc/stable/
• Registration
– Register an account
– Subscribe to scipy-dev mailing list (subscribers-only)
– Problem with mailing lists: you get mail
∗ But: you can turn mail delivery off
∗ “change your subscription options”, at the bottom of
https://mail.python.org/mailman3/lists/scipy-dev.python.org/
– Send a mail @ scipy-dev mailing list; ask for activation:
To: scipy-dev@scipy.org
Hi,
I'd like to edit NumPy/SciPy docstrings. My account is XXXXX
Cheers,
N. N.
8.6. Contributing to NumPy/SciPy 346

• Check the style guide:

– https://numpy.org/doc/stable/
– Don’t be intimidated; to fix a small thing, just fix it
• Edit
2. Edit sources and send patches (as for bugs)
3. Complain on the mailing list
8.6.4 Contributing features
The contribution of features is documented on https://numpy.org/doc/stable/dev/
8.6.5 How to help, in general
• Bug fixes always welcome!

– What irks you most
– Browse the tracker
• Documentation work
– API docs: improvements to docstrings
∗ Know some SciPy module well?
– User guide
∗ https://numpy.org/doc/stable/user/
• Ask on communication channels:
– numpy-discussion list
– scipy-dev list
8.6. Contributing to NumPy/SciPy 347

CHAPTER 9
Debugging code
Author: Gaël Varoquaux

This section explores tools to understand better your code base: debugging, to find and fix bugs.
It is not specific to the scientific Python community, but the strategies that we will employ are tailored
to its needs.
Prerequisites
• NumPy
• IPython
• nosetests
• pyflakes
• gdb for the C-debugging part.
Chapter contents
• Avoiding bugs
– Coding best practices to avoid getting in trouble
– pyflakes: fast static analysis
• Debugging workflow
• Using the Python debugger
– Invoking the debugger
348
– Debugger commands and interaction

• Debugging segmentation faults using gdb
9.1 Avoiding bugs
9.1.1 Coding best practices to avoid getting in trouble
Brian Kernighan
“Everyone knows that debugging is twice as hard as writing a program in the first place. So if you’re
as clever as you can be when you write it, how will you ever debug it?”
• We all write buggy code. Accept it. Deal with it.

• Write your code with testing and debugging in mind.
• Keep It Simple, Stupid (KISS).
– What is the simplest thing that could possibly work?
• Don’t Repeat Yourself (DRY).
– Every piece of knowledge must have a single, unambiguous, authoritative representation within
a system.
– Constants, algorithms, etc. . .
• Try to limit interdependencies of your code. (Loose Coupling)
• Give your variables, functions and modules meaningful names (not mathematics names)
9.1.2 pyflakes: fast static analysis
They are several static analysis tools in Python; to name a few:

• pylint
• pychecker
• pyflakes
• flake8
Here we focus on pyflakes, which is the simplest tool.
• Fast, simple
• Detects syntax errors, missing imports, typos on names.
Another good recommendation is the flake8 tool which is a combination of pyflakes and pep8. Thus, in
addition to the types of errors that pyflakes catches, flake8 detects violations of the recommendation in
PEP8 style guide.
Integrating pyflakes (or flake8) in your editor or IDE is highly recommended, it does yield productivity
gains.
9.1. Avoiding bugs 349

Running pyflakes on the current edited file
You can bind a key to run pyflakes in the current buffer.

• In kate Menu: ‘settings -> configure kate
– In plugins enable ‘external tools’
– In external Tools’, add pyflakes:
kdialog --title "pyflakes %f ilename" --msgbox "$(pyflakes %f ilename)"
• In TextMate
Menu: TextMate -> Preferences -> Advanced -> Shell variables, add a shell variable:
TM_PYCHECKER = /Library/Frameworks/Python.framework/Versions/Current/bin/pyflakes
Then Ctrl-Shift-V is binded to a pyflakes report

• In vim In your .vimrc (binds F5 to pyflakes):
autocmd FileType python let &mp = 'echo "*** running % ***" ; pyflakes %'
autocmd FileType tex,mp,rst,python imap <Esc>[15~ <C-O>:make!^M
autocmd FileType tex,mp,rst,python map <Esc>[15~ :make!^M
autocmd FileType tex,mp,rst,python set autowrite
• In emacs In your .emacs (binds F5 to pyflakes):
(defun pyflakes-thisfile () (interactive)

(compile (format "pyflakes %s " (buffer-file-name)))
)
(define-minor-mode pyflakes-mode
"Toggle pyflakes mode.
With no argument, this command toggles the mode.
Non-null prefix argument turns on the mode.
Null prefix argument turns off the mode."
;; The initial value.
nil
;; The indicator for the mode line.
" Pyflakes"
;; The minor mode bindings.
'( ([f5] . pyflakes-thisfile) )
)
(add-hook 'python-mode-hook (lambda () (pyflakes-mode t)))
A type-as-go spell-checker like integration
• In vim
– Use the pyflakes.vim plugin:
1. download the zip file from https://www.vim.org/scripts/script.php?script_id=2441
2. extract the files in ~/.vim/ftplugin/python
3. make sure your vimrc has filetype plugin indent on
9.1. Avoiding bugs 350

– Alternatively: use the syntastic plugin. This can be configured to use flake8 too and also
handles on-the-fly checking for many other languages.
• In emacs
Use the flymake mode with pyflakes, documented on https://www.emacswiki.org/emacs/FlyMake
and included in Emacs 26 and more recent. To activate it, use M-x (meta-key then x) and enter
flymake-mode at the prompt. To enable it automatically when opening a Python file, add the
following line to your .emacs file:
(add-hook 'python-mode-hook '(lambda () (flymake-mode)))
9.2 Debugging workflow
If you do have a non trivial bug, this is when debugging strategies kick in. There is no silver bullet. Yet,
strategies help:
For debugging a given problem, the favorable situation is when the problem is
isolated in a small number of lines of code, outside framework or application
code, with short modify-run-fail cycles
1. Make it fail reliably. Find a test case that makes the code fail every time.
2. Divide and Conquer. Once you have a failing test case, isolate the failing code.
• Which module.
• Which function.
• Which line of code.
=> isolate a small reproducible failure: a test case
3. Change one thing at a time and re-run the failing test case.
4. Use the debugger to understand what is going wrong.
5. Take notes and be patient. It may take a while.
Note: Once you have gone through this process: isolated a tight piece of code reproducing the bug
and fix the bug using this piece of code, add the corresponding code to your test suite.
9.2. Debugging workflow 351

9.3 Using the Python debugger
The python debugger, pdb: https://docs.python.org/3/library/pdb.html, allows you to inspect your code
interactively.
Specifically it allows you to:
• View the source code.
• Walk up and down the call stack.
• Inspect values of variables.
• Modify values of variables.
• Set breakpoints.
print
Yes, print statements do work as a debugging tool. However to inspect runtime, it is often more
efficient to use the debugger.
9.3.1 Invoking the debugger
Ways to launch the debugger:

1. Postmortem, launch debugger after module errors.
2. Launch the module with the debugger.
3. Call the debugger inside the module
Postmortem
Situation: You’re working in IPython and you get a traceback.

Here we debug the file index_error.py. When running it, an IndexError is raised. Type %debug and
drop into the debugger.
In [1]: %run index_error.py

---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
File ~/src/scientific-python-lectures/advanced/debugging/index_error.py:10
6 print(lst[len(lst)])
9 if __name__ == "__main__":
---> 10 index_error()
File ~/src/scientific-python-lectures/advanced/debugging/index_error.py:6, in index_

˓→error()
4 def index_error():
5 lst = list("foobar")
----> 6 print(lst[len(lst)])
In [61]: :q
Cell In[61], line 1
:q
^
9.3. Using the Python debugger 352


SyntaxError: invalid syntax
In [2]: %debug
> /home/jarrod/src/scientific-python-lectures/advanced/debugging/index_error.
˓→py(6)index_error()
7
8
ipdb> list
1 """Small snippet to raise an IndexError."""
2
3
7
8
9 if __name__ == "__main__":
10 index_error()
ipdb> len(lst)
6
ipdb> print(lst[len(lst)-1])
r
ipdb> quit
Post-mortem debugging without IPython
In some situations you cannot use IPython, for instance to debug a script that wants to be called from
the command line. In this case, you can call the script with python -m pdb script.py:
$ python -m pdb index_error.py
> /home/varoquau/dev/scientific-python-lectures/advanced/optimizing/index_error.
˓→py(1)<module>()
-> """Small snippet to raise an IndexError."""

(Pdb) continue
File "/usr/lib/python2.6/pdb.py", line 1296, in main
pdb._runscript(mainpyfile)
File "/usr/lib/python2.6/pdb.py", line 1215, in _runscript
self.run(statement)
File "/usr/lib/python2.6/bdb.py", line 372, in run
exec cmd in globals, locals
File "<string>", line 1, in <module>
File "index_error.py", line 8, in <module>
index_error()
File "index_error.py", line 5, in index_error
print lst[len(lst)]
Uncaught exception. Entering post mortem debugging
Running 'cont' or 'step' will restart the program
> /home/varoquau/dev/scientific-python-lectures/advanced/optimizing/index_error.
˓→py(5)index_error()

-> print(lst[len(lst)])
(Pdb)
Step-by-step execution
Situation: You believe a bug exists in a module but are not sure where.
For instance we are trying to debug wiener_filtering.py. Indeed the code runs, but the filtering does
not work well.
• Run the script in IPython with the debugger using %run -d wiener_filtering.py :
In [1]: %run -d wiener_filtering.py

*** Blank or comment
NOTE: Enter 'c' at the ipdb> prompt to continue execution.
> /home/jarrod/src/scientific-python-lectures/advanced/debugging/wiener_
˓→filtering.py(1)<module>()
----> 1 """ Wiener filtering a noisy raccoon face: this module is buggy
2 """
3
4 import numpy as np
5 import scipy as sp
• Set a break point at line 34 using b 34:
ipdb> n
> /home/varoquau/dev/scientific-python-lectures/advanced/optimizing/wiener_
˓→filtering.py(4)<module>()
3
1---> 4 import numpy as np
5 import scipy as sp
ipdb> b 34
Breakpoint 2 at /home/varoquau/dev/scientific-python-lectures/advanced/
˓→optimizing/wiener_filtering.py:34
• Continue execution to next breakpoint with c(ont(inue)):
ipdb> c
˓→filtering.py(34)iterated_wiener()
33 """
2--> 34 noisy_img = noisy_img
35 denoised_img = local_mean(noisy_img, size=size)
• Step into code with n(ext) and s(tep): next jumps to the next statement in the current execution
context, while step will go across execution contexts, i.e. enable exploring inside function calls:
ipdb> s
2 34 noisy_img = noisy_img
---> 35 denoised_img = local_mean(noisy_img, size=size)
36 l_var = local_var(noisy_img, size=size)
ipdb> n


35 denoised_img = local_mean(noisy_img, size=size)

---> 36 l_var = local_var(noisy_img, size=size)
37 for i in range(3):
• Step a few lines and explore the local variables:
ipdb> n
36 l_var = local_var(noisy_img, size=size)

---> 37 for i in range(3):
38 res = noisy_img - denoised_img
ipdb> print(l_var)
[[5868 5379 5316 ..., 5071 4799 5149]
[5013 363 437 ..., 346 262 4355]
[5379 410 344 ..., 392 604 3377]
...,
[ 435 362 308 ..., 275 198 1632]
[ 548 392 290 ..., 248 263 1653]
[ 466 789 736 ..., 1835 1725 1940]]
ipdb> print(l_var.min())
0
Oh dear, nothing but integers, and 0 variation. Here is our bug, we are doing integer arithmetic.
Raising exception on numerical errors
When we run the wiener_filtering.py file, the following warnings are raised:
In [2]: %run wiener_filtering.py
wiener_filtering.py:40: RuntimeWarning: divide by zero encountered in divide
noise_level = (1 - noise/l_var )
We can turn these warnings in exception, which enables us to do post-mortem debugging on them,
and find our problem more quickly:
In [1]: np.seterr(all='raise')
Out[1]: {'divide': 'print', 'invalid': 'print', 'over': 'print', 'under': 'ignore'}
In [4]: %run wiener_filtering.py
---------------------------------------------------------------------------
FloatingPointError Traceback (most recent call last)
/home/esc/anaconda/lib/python2.7/site-packages/IPython/utils/py3compat.pyc in␣
˓→execfile(fname, *where)
176 else:
177 filename = fname
--> 178 __builtin__.execfile(filename, *where)
/home/esc/physique-cuso-python-2013/scientific-python-lectures/advanced/debugging/
˓→wiener_filtering.py in <module>()
55 pl.matshow(noisy_face[cut], cmap=pl.cm.gray)
56
---> 57 denoised_face = iterated_wiener(noisy_face)
58 pl.matshow(denoised_face[cut], cmap=pl.cm.gray)
59
/home/esc/physique-cuso-python-2013/scientific-python-lectures/advanced/debugging/
˓→wiener_filtering.py in iterated_wiener(noisy_img, size)
38 res = noisy_img - denoised_img

39 noise = (res**2).sum()/res.size
---> 40 noise_level = (1 - noise/l_var )
41 the Python
9.3. Using noise_level[noise_level<0]
debugger = 0 355
42 denoised_img += noise_level*res
FloatingPointError: divide by zero encountered in divide
Other ways of starting a debugger
• Raising an exception as a poor man break point

If you find it tedious to note the line number to set a break point, you can simply raise an exception
at the point that you want to inspect and use IPython’s %debug. Note that in this case you cannot
step or continue the execution.
• Debugging test failures using nosetests
You can run nosetests --pdb to drop in post-mortem debugging on exceptions, and nosetests
--pdb-failure to inspect test failures using the debugger.
In addition, you can use the IPython interface for the debugger in nose by installing the nose plugin
ipdbplugin. You can than pass --ipdb and --ipdb-failure options to nosetests.
• Calling the debugger explicitly
Insert the following line where you want to drop in the debugger:
import pdb; pdb.set_trace()
Warning: When running nosetests, the output is captured, and thus it seems that the debugger
does not work. Simply run the nosetests with the -s flag.
Graphical debuggers and alternatives
• pudb is a good semi-graphical debugger with a text user interface in the console.
• The Visual Studio Code integrated development environment includes a debugging mode.
• The Mu editor is a simple Python editor that includes a debugging mode.
9.3.2 Debugger commands and interaction
l(list) Lists the code at the current position

u(p) Walk up the call stack
d(own) Walk down the call stack
n(ext) Execute the next line (does not go down in new functions)
s(tep) Execute the next statement (goes down in new functions)
bt Print the call stack
a Print the local variables
!command Execute the given Python command (by opposition to pdb commands
Warning: Debugger commands are not Python code

You cannot name the variables the way you want. For instance, if in you cannot override the variables
in the current frame with the same name: use different names than your local variable when
typing code in the debugger.

Getting help when in the debugger
Type h or help to access the interactive help:
ipdb> help
Documented commands (type help <topic>):

========================================
EOF bt cont enable jump pdef r tbreak w
a c continue exit l pdoc restart u whatis
alias cl d h list pinfo return unalias where
args clear debug help n pp run unt
b commands disable ignore next q s until
break condition down j p quit step up
Miscellaneous help topics:

==========================
exec pdb
Undocumented commands:
======================
retval rv
9.4 Debugging segmentation faults using gdb
If you have a segmentation fault, you cannot debug it with pdb, as it crashes the Python interpreter
before it can drop in the debugger. Similarly, if you have a bug in C code embedded in Python, pdb is
useless. For this we turn to the gnu debugger, gdb, available on Linux.
Before we start with gdb, let us add a few Python-specific tools to it. For this we add a few macros to
our ~/.gdbinit. The optimal choice of macro depends on your Python version and your gdb version. I
have added a simplified version in gdbinit, but feel free to read DebuggingWithGdb.
To debug with gdb the Python script segfault.py, we can run the script in gdb as follows
$ gdb python
...
(gdb) run segfault.py
Starting program: /usr/bin/python segfault.py
[Thread debugging using libthread_db enabled]
Program received signal SIGSEGV, Segmentation fault.

_strided_byte_copy (dst=0x8537478 "\360\343G", outstrides=4, src=
0x86c0690 <Address 0x86c0690 out of bounds>, instrides=32, N=3,
elsize=4)
at numpy/core/src/multiarray/ctors.c:365
365 _FAST_MOVE(Int32);
(gdb)
We get a segfault, and gdb captures it for post-mortem debugging in the C level stack (not the Python
call stack). We can debug the C call stack using gdb’s commands:
(gdb) up
#1 0x004af4f5 in _copy_from_same_shape (dest=<value optimized out>,
src=<value optimized out>, myfunc=0x496780 <_strided_byte_copy>,
swap=0)
9.4. Debugging segmentation faults using gdb 357


at numpy/core/src/multiarray/ctors.c:748
748 myfunc(dit->dataptr, dest->strides[maxaxis],
As you can see, right now, we are in the C code of numpy. We would like to know what is the Python
code that triggers this segfault, so we go up the stack until we hit the Python execution loop:
(gdb) up
#8 0x080ddd23 in call_function (f=
Frame 0x85371ec, for file /home/varoquau/usr/lib/python2.6/site-packages/numpy/
˓→core/arrayprint.py, line 156, in _leading_trailing (a=<numpy.ndarray at remote␣
˓→0x85371b0>, _nc=<module at remote 0xb7f93a64>), throwflag=0)
at ../Python/ceval.c:3750
3750 ../Python/ceval.c: No such file or directory.
in ../Python/ceval.c
(gdb) up
#9 PyEval_EvalFrameEx (f=
Frame 0x85371ec, for file /home/varoquau/usr/lib/python2.6/site-packages/numpy/
˓→core/arrayprint.py, line 156, in _leading_trailing (a=<numpy.ndarray at remote␣
˓→0x85371b0>, _nc=<module at remote 0xb7f93a64>), throwflag=0)
at ../Python/ceval.c:2412
2412 in ../Python/ceval.c
(gdb)
Once we are in the Python execution loop, we can use our special Python helper function. For instance
we can find the corresponding Python code:
(gdb) pyframe
/home/varoquau/usr/lib/python2.6/site-packages/numpy/core/arrayprint.py (158): _
˓→leading_trailing
(gdb)
This is numpy code, we need to go up until we find code that we have written:
(gdb) up
...
(gdb) up
#34 0x080dc97a in PyEval_EvalFrameEx (f=
Frame 0x82f064c, for file segfault.py, line 11, in print_big_array (small_array=
˓→<numpy.ndarray at remote 0x853ecf0>, big_array=<numpy.ndarray at remote 0x853ed20>),
˓→ throwflag=0) at ../Python/ceval.c:1630
1630 ../Python/ceval.c: No such file or directory.

in ../Python/ceval.c
(gdb) pyframe
segfault.py (12): print_big_array
The corresponding code is:
def make_big_array(small_array):
big_array = stride_tricks.as_strided(
small_array, shape=(2e6, 2e6), strides=(32, 32)
)
return big_array
Thus the segfault happens when printing big_array[-10:]. The reason is simply that big_array has
been allocated with its end outside the program memory.

Note: For a list of Python-specific commands defined in the gdbinit, read the source of this file.
Wrap up exercise
The following script is well documented and hopefully legible. It seeks to answer a problem of actual
interest for numerical computing, but it does not work. . . Can you debug it?
Python source code: to_debug.py

CHAPTER 10
Optimizing code
Donald Knuth
“Premature optimization is the root of all evil”

This chapter deals with strategies to make Python code go faster.
Prerequisites
• line_profiler
Chapters contents
• Optimization workflow
• Profiling Python code
– Timeit
– Profiler
– Line-profiler
• Making code go faster
– Algorithmic optimization
∗ Example of the SVD
360
• Writing faster numerical code

– Additional Links
10.1 Optimization workflow
1. Make it work: write the code in a simple legible ways.

2. Make it work reliably: write automated test cases, make really sure that your algorithm is right
and that if you break it, the tests will capture the breakage.
3. Optimize the code by profiling simple use-cases to find the bottlenecks and speeding up these
bottleneck, finding a better algorithm or implementation. Keep in mind that a trade off should
be found between profiling on a realistic example and the simplicity and speed of execution of the
code. For efficient work, it is best to work with profiling runs lasting around 10s.
10.2 Profiling Python code
No optimization without measuring!
• Measure: profiling, timing

• You’ll have surprises: the fastest code is not always what you think
10.2.1 Timeit
In IPython, use timeit (https://docs.python.org/3/library/timeit.html) to time elementary operations:
In [2]: a = np.arange(1000)
In [3]: %timeit a ** 2
871 ns +- 3.75 ns per loop (mean +- std. dev. of 7 runs, 1,000,000 loops each)
In [4]: %timeit a ** 2.1

In [5]: %timeit a * a
1 us +- 2.23 ns per loop (mean +- std. dev. of 7 runs, 1,000,000 loops each)
Use this to guide your choice between strategies.
Note: For long running calls, using %time instead of %timeit; it is less precise but faster
10.1. Optimization workflow 361

10.2.2 Profiler
Useful when you have a large program to profile, for example the following file:
# For this example to run, you also need the 'ica.py' file
import numpy as np
import scipy as sp
from ica import fastica
# @profile # uncomment this line to run with line_profiler

def test():
data = rng.random((5000, 100))
u, s, v = sp.linalg.svd(data)
pca = u[:, :10].T @ data
results = fastica(pca.T, whiten=False)
if __name__ == "__main__":
test()
Note: This is a combination of two unsupervised learning techniques, principal component analysis
(PCA) and independent component analysis (ICA). PCA is a technique for dimensionality reduction,
i.e. an algorithm to explain the observed variance in your data using less dimensions. ICA is a source
separation technique, for example to unmix multiple signals that have been recorded through multiple
sensors. Doing a PCA first and then an ICA can be useful if you have more sensors than signals. For
more information see: the FastICA example from scikits-learn.
To run it, you also need to download the ica module. In IPython we can time the script:
In [6]: %run -t demo.py

IPython CPU timings (estimated):
User : 14.3929 s.
System: 0.256016 s.
and profile it:
In [7]: %run -p demo.py

916 function calls in 14.551 CPU seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno (function)
1 14.457 14.457 14.479 14.479 decomp.py:849 (svd)
1 0.054 0.054 0.054 0.054 {method 'random_sample' of 'mtrand.
˓→RandomState' objects}
1 0.017 0.017 0.021 0.021 function_base.py:645 (asarray_chkfinite)

54 0.011 0.000 0.011 0.000 {numpy.core._dotblas.dot}
2 0.005 0.002 0.005 0.002 {method 'any' of 'numpy.ndarray' objects}
6 0.001 0.000 0.001 0.000 ica.py:195 (gprime)
6 0.001 0.000 0.001 0.000 ica.py:192 (g)
14 0.001 0.000 0.001 0.000 {numpy.linalg.lapack_lite.dsyevd}
19 0.001 0.000 0.001 0.000 twodim_base.py:204 (diag)
1 0.001 0.001 0.008 0.008 ica.py:69 (_ica_par)
1 0.001 0.001 14.551 14.551 {execfile}
10.2. Profiling Python code 362


107 0.000 0.000 0.001 0.000 defmatrix.py:239 (__array_finalize__)
7 0.000 0.000 0.004 0.001 ica.py:58 (_sym_decorrelation)
7 0.000 0.000 0.002 0.000 linalg.py:841 (eigh)
172 0.000 0.000 0.000 0.000 {isinstance}
1 0.000 0.000 14.551 14.551 demo.py:1 (<module>)
29 0.000 0.000 0.000 0.000 numeric.py:180 (asarray)
35 0.000 0.000 0.000 0.000 defmatrix.py:193 (__new__)
35 0.000 0.000 0.001 0.000 defmatrix.py:43 (asmatrix)
21 0.000 0.000 0.001 0.000 defmatrix.py:287 (__mul__)
41 0.000 0.000 0.000 0.000 {numpy.core.multiarray.zeros}
28 0.000 0.000 0.000 0.000 {method 'transpose' of 'numpy.ndarray'␣
˓→objects}
1 0.000 0.000 0.008 0.008 ica.py:97 (fastica)

...
Clearly the svd (in decomp.py) is what takes most of our time, a.k.a. the bottleneck. We have to find a
way to make this step go faster, or to avoid this step (algorithmic optimization). Spending time on the
rest of the code is useless.
Profiling outside of IPython, running ``cProfile``
Similar profiling can be done outside of IPython, simply calling the built-in Python profilers cProfile
and profile.
$ python -m cProfile -o demo.prof demo.py
Using the -o switch will output the profiler results to the file demo.prof to view with an external tool.
This can be useful if you wish to process the profiler output with a visualization tool.
10.2.3 Line-profiler
The profiler tells us which function takes most of the time, but not where it is called.
For this, we use the line_profiler: in the source file, we decorate a few functions that we want to inspect
with @profile (no need to import it)
@profile
def test():
u, s, v = linalg.svd(data)
pca = u[:, :10] @ data
Then we run the script using the kernprof command, with switches -l, --line-by-line and -v,
--view to use the line-by-line profiler and view the results in addition to saving them:
$ kernprof -l -v demo.py
Wrote profile results to demo.py.lprof

Timer unit: 1e-06 s
Total time: 1.27874 s

File: demo.py
Function: test at line 9
10.2. Profiling Python code 363

Line # Hits Time Per Hit % Time Line Contents

==============================================================
9 @profile
10 def test():
11 1 69.0 69.0 0.0 rng = np.random.default_rng()
12 1 2453.0 2453.0 0.2 data = rng.random((5000, 100))
13 1 1274715.0 1274715.0 99.7 u, s, v = sp.linalg.svd(data)
14 1 413.0 413.0 0.0 pca = u[:, :10].T @ data
15 1 1094.0 1094.0 0.1 results = fastica(pca.T,␣
˓→whiten=False)
The SVD is taking all the time. We need to optimise this line.
10.3 Making code go faster
Once we have identified the bottlenecks, we need to make the corresponding code go faster.
10.3.1 Algorithmic optimization
The first thing to look for is algorithmic optimization: are there ways to compute less, or better?
For a high-level view of the problem, a good understanding of the maths behind the algorithm helps.
However, it is not uncommon to find simple changes, like moving computation or memory allocation
outside a for loop, that bring in big gains.
Example of the SVD
In both examples above, the SVD - Singular Value Decomposition - is what takes most of the time.
Indeed, the computational cost of this algorithm is roughly 𝑛3 in the size of the input matrix.
However, in both of these example, we are not using all the output of the SVD, but only the first few rows
of its first return argument. If we use the svd implementation of SciPy, we can ask for an incomplete
version of the SVD. Note that implementations of linear algebra in SciPy are richer then those in NumPy
and should be preferred.
In [8]: %timeit np.linalg.svd(data)

1 loops, best of 3: 14.5 s per loop
In [9]: import scipy as sp
In [10]: %timeit sp.linalg.svd(data)

In [11]: %timeit sp.linalg.svd(data, full_matrices=False)

1 loops, best of 3: 295 ms per loop
In [12]: %timeit np.linalg.svd(data, full_matrices=False)

We can then use this insight to optimize the previous code:
def test():
10.3. Making code go faster 364


u, s, v = sp.linalg.svd(data, full_matrices=False)
pca = u[:, :10].T @ data
In [13]: import demo
In [14]: %timeit demo.

demo.fastica demo.np demo.prof.pdf demo.py demo.pyc
demo.linalg demo.prof demo.prof.png demo.py.lprof demo.test
In [15]: %timeit demo.test()

ica.py:65: RuntimeWarning: invalid value encountered in sqrt
W = (u * np.diag(1.0/np.sqrt(s)) * u.T) * W # W = (W * W.T) ^{-1/2} * W
In [16]: import demo_opt
In [17]: %timeit demo_opt.test()

Real incomplete SVDs, e.g. computing only the first 10 eigenvectors, can be computed with arpack,
available in scipy.sparse.linalg.eigsh.
Computational linear algebra
For certain algorithms, many of the bottlenecks will be linear algebra computations. In this case,
using the right function to solve the right problem is key. For instance, an eigenvalue problem with
a symmetric matrix is easier to solve than with a general matrix. Also, most often, you can avoid
inverting a matrix and use a less costly (and more numerically stable) operation.
Know your computational linear algebra. When in doubt, explore scipy.linalg, and use %timeit to
try out different alternatives on your data.
10.4 Writing faster numerical code
A complete discussion on advanced use of NumPy is found in chapter Advanced NumPy, or in the article
The NumPy array: a structure for efficient numerical computation by van der Walt et al. Here we discuss
only some commonly encountered tricks to make code faster.
• Vectorizing for loops
Find tricks to avoid for loops using NumPy arrays. For this, masks and indices arrays can be
useful.
• Broadcasting
Use broadcasting to do operations on arrays as small as possible before combining them.
• In place operations
In [18]: a = np.zeros(1e7)
In [19]: %timeit global a ; a = 0*a

10.4. Writing faster numerical code 365


In [20]: %timeit global a ; a *= 0
10 loops, best of 3: 48.4 ms per loop
note: we need global a in the timeit so that it work, as it is assigning to a, and thus considers it
as a local variable.
• Be easy on the memory: use views, and not copies
Copying big arrays is as costly as making simple numerical operations on them:
In [21]: a = np.zeros(1e7)
In [22]: %timeit a.copy()

In [23]: %timeit a + 1
• Beware of cache effects

Memory access is cheaper when it is grouped: accessing a big array in a continuous way is much
faster than random access. This implies amongst other things that smaller strides are faster
(see CPU cache effects):
In [24]: c = np.zeros((1e4, 1e4), order='C')
In [25]: %timeit c.sum(axis=0)

In [26]: %timeit c.sum(axis=1)

In [27]: c.strides
Out[27]: (80000, 8)
This is the reason why Fortran ordering or C ordering may make a big difference on operations:
In [28]: rng = np.random.default_rng()
In [29]: a = rng.random((20, 2**18))
In [30]: b = rng.random((20, 2**18))
In [31]: %timeit b @ a.T

8.3 ms +- 222 us per loop (mean +- std. dev. of 7 runs, 100 loops each)
In [32]: c = np.ascontiguousarray(a.T)
In [33]: %timeit b @ c
8.01 ms +- 9.87 us per loop (mean +- std. dev. of 7 runs, 100 loops each)
Note that copying the data to work around this effect may not be worth it:
In [34]: %timeit c = np.ascontiguousarray(a.T)

16.4 ms +- 28.6 us per loop (mean +- std. dev. of 7 runs, 100 loops each)
Using numexpr can be useful to automatically optimize code for such effects.
• Use compiled code

The last resort, once you are sure that all the high-level optimizations have been explored, is to
transfer the hot spots, i.e. the few lines or functions in which most of the time is spent, to compiled
code. For compiled code, the preferred option is to use Cython: it is easy to transform exiting
Python code in compiled code, and with a good use of the NumPy support yields efficient code on
NumPy arrays, for instance by unrolling loops.
Warning: For all the above: profile and time your choices. Don’t base your optimization on
theoretical considerations.
10.4.1 Additional Links
• If you need to profile memory usage, you could try the memory_profiler
• If you need to profile down into C extensions, you could try using gperftools from Python with
yep.
• If you would like to track performance of your code across time, i.e. as you make new commits to
your repository, you could try: asv
• If you need some interactive visualization why not try RunSnakeRun

CHAPTER 11
Sparse Arrays in SciPy
Author: Robert Cimrman
11.1 Introduction
(dense) matrix is:

• mathematical object
• data structure for storing a 2D array of values
important features:
• memory allocated once for all items
– usually a contiguous chunk, think NumPy ndarray
• fast access to individual items (*)
368
11.1.1 Why Sparse Matrices?
• the memory grows like n**2 for dense matrix

• small example (double precision matrix):

>>> x = np.linspace(0, 1e6, 10)
>>> plt.plot(x, 8.0 * (x**2) / 1e6, lw=5)
>>> plt.xlabel('size n')
Text(...'size n')
>>> plt.ylabel('memory [MB]')
Text(...'memory [MB]')
11.1.2 Sparse Matrices vs. Sparse Matrix Storage Schemes
• sparse matrix is a matrix, which is almost empty

• storing all the zeros is wasteful -> store only nonzero items
• think compression
• pros: huge memory savings
• cons: slow access to individual items, but it depends on actual storage scheme.
11.1.3 Typical Applications
• solution of partial differential equations (PDEs)

– the finite element method
– mechanical engineering, electrotechnics, physics, . . .
• graph theory
– nonzero at (i, j) means that node i is connected to node j
• natural language processing
– nonzero at (i, j) means that the document i contains the word j
• ...
11.1.4 Prerequisites
• numpy
• scipy
• matplotlib (optional)
• ipython (the enhancements come handy)

11.1.5 Sparsity Structure Visualization
• spy() from matplotlib

• example plots:

11.2 Storage Schemes
• seven sparse array types in scipy.sparse:

1. csr_array: Compressed Sparse Row format
2. csc_array: Compressed Sparse Column format
3. bsr_array: Block Sparse Row format
4. lil_array: List of Lists format
5. dok_array: Dictionary of Keys format
6. coo_array: COOrdinate format (aka IJV, triplet format)
7. dia_array: DIAgonal format
• each suitable for some tasks
• many employ sparsetools C++ module by Nathan Bell
• assume the following is imported:

• warning for Numpy users:

– passing a sparse array object to NumPy functions that expect ndarray/matrix does not
work. Use sparse functions.
– the older csr_matrix classes use ‘*’ for matrix multiplication (dot product) and
‘A.multiply(B)’ for elementwise multiplication.
– the newer csr_array uses ‘@’ for dot product and ‘*’ for elementwise multiplication
– sparse arrays can be 1D or 2D, but not nD for n > 2 (unlike Numpy arrays).
11.2.1 Common Methods
• all scipy.sparse array classes are subclasses of sparray

– default implementation of arithmetic operations
∗ always converts to CSR
∗ subclasses override for efficiency
– shape, data type, set/get
– indices of nonzero values in the array
– format conversion, interaction with NumPy (toarray())
– ...
• attributes:
– mtx.T - transpose (same as mtx.transpose())
– mtx.real - real part of complex matrix
– mtx.imag - imaginary part of complex matrix
– mtx.size - the number of nonzeros (same as self.getnnz())
– mtx.shape - the number of rows and columns (tuple)
11.2. Storage Schemes 371

• data and indices usually stored in 1D NumPy arrays
11.2.2 Sparse Array Classes
11.2.3 Summary
Table 1: Summary of storage schemes.

format matrix get fancy set item fancy solvers note
* vector item get set
CSR sparse- yes yes slow . any has data array, fast row-wise
tools ops
CSC sparse- yes yes slow . any has data array, fast column-
tools wise ops
BSR sparse- . . . . special- has data array, specialized
tools ized
COO sparse- . . . . itera- has data array, facilitates
tools tive fast conversion
DIA sparse- . . . . itera- has data array, specialized
tools tive
LIL via yes yes yes yes itera- arithmetic via CSR, incre-
CSR tive mental construction
DOK python yes one yes yes itera- O(1) item access, incremen-
axis tive tal construction, slow arith-
only metic
11.3 Linear System Solvers
• sparse matrix/eigenvalue problem solvers live in scipy.sparse.linalg

• the submodules:
– dsolve: direct factorization methods for solving linear systems
– isolve: iterative methods for solving linear systems
– eigen: sparse eigenvalue problem solvers
• all solvers are accessible from:

>>> sp.sparse.linalg.__all__
['ArpackError', 'ArpackNoConvergence', ..., 'use_solver']
11.3. Linear System Solvers 372

11.3.1 Sparse Direct Solvers
• default solver: SuperLU

– included in SciPy
– real and complex systems
– both single and double precision
• optional: umfpack
– real and complex systems
– double precision only
– recommended for performance
– wrappers now live in scikits.umfpack
– check-out the new scikits.suitesparse by Nathaniel Smith
Examples
• import the whole module, and see its docstring:
>>> help(sp.sparse.linalg.spsolve)
Help on function spsolve in module scipy.sparse.linalg._dsolve.linsolve:
...
• both superlu and umfpack can be used (if the latter is installed) as follows:
– prepare a linear system:

>>> mtx = sp.sparse.spdiags([[1, 2, 3, 4, 5], [6, 5, 8, 9, 10]], [0, 1], 5,␣
˓→5, "csc")
>>> mtx.toarray()
array([[ 1, 5, 0, 0, 0],
[ 0, 2, 8, 0, 0],
[ 0, 0, 3, 9, 0],
[ 0, 0, 0, 4, 10],
[ 0, 0, 0, 0, 5]])
>>> rhs = np.array([1, 2, 3, 4, 5], dtype=np.float32)
– solve as single precision real:
>>> mtx1 = mtx.astype(np.float32)

>>> x = sp.sparse.linalg.spsolve(mtx1, rhs, use_umfpack=False)
>>> print(x)
[106. -21. 5.5 -1.5 1. ]
>>> print("Error: %s " % (mtx1 * x - rhs))
Error: [0. 0. 0. 0. 0.]
– solve as double precision real:
>>> mtx2 = mtx.astype(np.float64)

>>> x = sp.sparse.linalg.spsolve(mtx2, rhs, use_umfpack=True)
>>> print(x)
[106. -21. 5.5 -1.5 1. ]
Error: [0. 0. 0. 0. 0.]

– solve as single precision complex:
>>> mtx1 = mtx.astype(np.complex64)

>>> x = sp.sparse.linalg.spsolve(mtx1, rhs, use_umfpack=False)
>>> print(x)
[106. +0.j -21. +0.j 5.5+0.j -1.5+0.j 1. +0.j]
Error: [0.+0.j 0.+0.j 0.+0.j 0.+0.j 0.+0.j]
– solve as double precision complex:
>>> mtx2 = mtx.astype(np.complex128)

>>> x = sp.sparse.linalg.spsolve(mtx2, rhs, use_umfpack=True)
>>> print(x)
[106. +0.j -21. +0.j 5.5+0.j -1.5+0.j 1. +0.j]
Error: [0.+0.j 0.+0.j 0.+0.j 0.+0.j 0.+0.j]
"""
Solve a linear system
=======================
Construct a 1000x1000 lil_array and add some values to it, convert it

to CSR format and solve A x = b for x:and solve a linear system with a
direct solver.
"""
import numpy as np
import scipy as sp
mtx = sp.sparse.lil_array((1000, 1000), dtype=np.float64)

mtx[0, :100] = rng.random(100)
mtx[1, 100:200] = mtx[0, :100]
mtx.setdiag(rng.random(1000))
plt.clf()
plt.spy(mtx, marker=".", markersize=2)
plt.show()
mtx = mtx.tocsr()
rhs = rng.random(1000)
x = sp.sparse.linalg.spsolve(mtx, rhs)
print(f"residual: { np.linalg.norm(mtx * x - rhs)!r} ")
• examples/direct_solve.py

11.3.2 Iterative Solvers
• the isolve module contains the following solvers:

– bicg (BIConjugate Gradient)
– bicgstab (BIConjugate Gradient STABilized)
– cg (Conjugate Gradient) - symmetric positive definite matrices only
– cgs (Conjugate Gradient Squared)
– gmres (Generalized Minimal RESidual)
– minres (MINimum RESidual)
– qmr (Quasi-Minimal Residual)
Common Parameters
• mandatory:
A
[{sparse array/matrix, dense array/matrix, LinearOperator}] The N-by-N matrix of the linear
system.
b
[{array, matrix}] Right hand side of the linear system. Has shape (N,) or (N,1).
• optional:
x0
[{array, matrix}] Starting guess for the solution.
tol
[float] Relative tolerance to achieve before terminating.
maxiter
[integer] Maximum number of iterations. Iteration will stop after maxiter steps even if the
specified tolerance has not been achieved.
M
[{sparse array/matrix, dense array/matrix, LinearOperator}] Preconditioner for A. The pre-
conditioner should approximate the inverse of A. Effective preconditioning dramatically im-
proves the rate of convergence, which implies that fewer iterations are needed to reach a given
error tolerance.
callback
[function] User-supplied function to call after each iteration. It is called as callback(xk), where
xk is the current solution vector.
LinearOperator Class
• common interface for performing matrix vector products

• useful abstraction that enables using dense and sparse matrices within the solvers, as well as
matrix-free solutions
• has shape and matvec() (+ some optional parameters)
• example:


>>> def mv(v):
... return np.array([2 * v[0], 3 * v[1]])
...
>>> A = sp.sparse.linalg.LinearOperator((2, 2), matvec=mv)
>>> A
<2x2 _CustomLinearOperator with dtype=float64>
>>> A.matvec(np.ones(2))
array([2., 3.])
>>> A * np.ones(2)
array([2., 3.])
A Few Notes on Preconditioning
• problem specific
• often hard to develop
• if not sure, try ILU
– available in scipy.sparse.linalg as spilu()
11.3.3 Eigenvalue Problem Solvers
The eigen module
• arpack * a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
• lobpcg (Locally Optimal Block Preconditioned Conjugate Gradient Method) * works very well in
combination with PyAMG * example by Nathan Bell:
"""
Compute eigenvectors and eigenvalues using a preconditioned eigensolver
=======================================================================
In this example Smoothed Aggregation (SA) is used to precondition

the LOBPCG eigensolver on a two-dimensional Poisson problem with
Dirichlet boundary conditions.
"""
import scipy as sp
from pyamg import smoothed_aggregation_solver

from pyamg.gallery import poisson
N = 100
K = 9
A = poisson((N, N), format="csr")
# create the AMG hierarchy

ml = smoothed_aggregation_solver(A)
# initial approximation to the K eigenvectors

X = sp.rand(A.shape[0], K)


# preconditioner based on ml
M = ml.aspreconditioner()
# compute eigenvalues and eigenvectors with LOBPCG

W, V = sp.sparse.linalg.lobpcg(A, X, M=M, tol=1e-8, largest=False)
# plot the eigenvectors

for i in range(K):
plt.subplot(3, 3, i + 1)
plt.title("Eigenvector %d " % i)
plt.pcolor(V[:, i].reshape(N, N))
plt.axis("equal")
plt.axis("off")
plt.show()
– examples/pyamg_with_lobpcg.py
• example by Nils Wagner:
– examples/lobpcg_sakurai.py
• output:
$ python examples/lobpcg_sakurai.py
Results by LOBPCG for n=2500
[ 0.06250083 0.06250028 0.06250007]
Exact eigenvalues
[ 0.06250005 0.0625002 0.06250044]
Elapsed time 7.01

11.4 Other Interesting Packages
• PyAMG
– algebraic multigrid solvers
– https://github.com/pyamg/pyamg
• Pysparse
– own sparse matrix classes
– matrix and eigenvalue problem solvers
– https://pysparse.sourceforge.net/
11.4. Other Interesting Packages 378

CHAPTER 12
Image manipulation and processing
using NumPy and SciPy
Authors: Emmanuelle Gouillart, Gaël Varoquaux

This section addresses basic image manipulation and processing using the core scientific modules NumPy
and SciPy. Some of the operations covered by this tutorial may be useful for other kinds of multidimen-
sional array processing than image processing. In particular, the submodule scipy.ndimage provides
functions operating on n-dimensional NumPy arrays.
See also:
For more advanced image processing and image-specific routines, see the tutorial scikit-image: image
processing, dedicated to the skimage module.
Image = 2-D numerical array
(or 3-D: CT, MRI, 2D + time; 4-D, . . . )

Here, image == NumPy array np.array
Tools used in this tutorial:

• numpy: basic array manipulation
• scipy: scipy.ndimage submodule dedicated to image processing (n-dimensional images). See the
documentation:
Common tasks in image processing:
379
• Input/Output, displaying images

• Basic manipulations: cropping, flipping, rotating, . . .
• Image filtering: denoising, sharpening
• Image segmentation: labeling pixels corresponding to different objects
• Classification
• Feature extraction
• Registration
• ...
Chapters contents
• Opening and writing to image files

• Displaying images
• Basic manipulations
– Statistical information
– Geometrical transformations
• Image filtering
– Blurring/smoothing
– Sharpening
– Denoising
– Mathematical morphology
• Feature extraction
– Edge detection
– Segmentation
• Measuring objects properties: scipy.ndimage.measurements
• Examples for the image processing chapter
12.1 Opening and writing to image files
Writing an array to a file:
import scipy as sp
import imageio.v3 as iio
f = sp.datasets.face()
iio.imwrite("face.png", f) # uses the Image module (PIL)
plt.imshow(f)
plt.show()
12.1. Opening and writing to image files 380

Creating a NumPy array from an image file:
>>> import imageio.v3 as iio

>>> face = sp.datasets.face()
>>> iio.imwrite('face.png', face) # First we need to create the PNG file
>>> face = iio.imread('face.png')

>>> type(face)
<class 'numpy.ndarray'>
>>> face.shape, face.dtype
((768, 1024, 3), dtype('uint8'))
dtype is uint8 for 8-bit images (0-255)

Opening raw files (camera, 3-D images)
>>> face.tofile('face.raw') # Create raw file

>>> face_from_raw = np.fromfile('face.raw', dtype=np.uint8)
>>> face_from_raw.shape
(2359296,)
>>> face_from_raw.shape = (768, 1024, 3)
Need to know the shape and dtype of the image (how to separate data bytes).
For large data, use np.memmap for memory mapping:
>>> face_memmap = np.memmap('face.raw', dtype=np.uint8, shape=(768, 1024, 3))
(data are read from the file, and not loaded into memory)
Working on a list of image files

... im = rng.integers(0, 256, 10000, dtype=np.uint8).reshape((100, 100))
12.1. Opening and writing to image files 381


... iio.imwrite(f'random_{ i: 02d} .png', im)
>>> from glob import glob
>>> filelist = glob('random*.png')
>>> filelist.sort()
12.2 Displaying images
Use matplotlib and imshow to display an image inside a matplotlib figure:
>>> f = sp.datasets.face(gray=True) # retrieve a grayscale image

>>> plt.imshow(f, cmap=plt.cm.gray)
Increase contrast by setting min and max values:
>>> plt.imshow(f, cmap=plt.cm.gray, vmin=30, vmax=200)

>>> # Remove axes and ticks
>>> plt.axis('off')
(-0.5, 1023.5, 767.5, -0.5)
Draw contour lines:
>>> plt.contour(f, [50, 200])

<matplotlib.contour.QuadContourSet ...>
For smooth intensity variations, use interpolation='bilinear'. For fine inspection of intensity varia-
tions, use interpolation='nearest':
>>> plt.imshow(f[320:340, 510:530], cmap=plt.cm.gray, interpolation='bilinear')

>>> plt.imshow(f[320:340, 510:530], cmap=plt.cm.gray, interpolation='nearest')
See also:
More interpolation methods are in Matplotlib’s examples.
12.2. Displaying images 382

12.3 Basic manipulations
Images are arrays: use the whole numpy machinery.

>>> face[0, 40]
127
>>> # Slicing
>>> face[10:13, 20:23]
array([[141, 153, 145],
[133, 134, 125],
[ 96, 92, 94]], dtype=uint8)
>>> face[100:120] = 255
>>>
>>> lx, ly = face.shape
>>> X, Y = np.ogrid[0:lx, 0:ly]
12.3. Basic manipulations 383


>>> mask = (X - lx / 2) ** 2 + (Y - ly / 2) ** 2 > lx * ly / 4
>>> # Masks
>>> face[mask] = 0
>>> # Fancy indexing
>>> face[range(400), range(400)] = 255
12.3.1 Statistical information

>>> face.mean()
113.48026784261067
>>> face.max(), face.min()
(250, 0)
np.histogram
Exercise
• Open as an array the scikit-image logo (https://scikit-image.org/_static/img/logo.png), or

an image that you have on your computer.
• Crop a meaningful part of the image, for example the python circle in the logo.
• Display the image array using matplotlib. Change the interpolation method and zoom to see
the difference.
• Transform your image to greyscale
• Increase the contrast of the image by changing its minimum and maximum values. Optional:
use scipy.stats.scoreatpercentile (read the docstring!) to saturate 5% of the darkest pixels
and 5% of the lightest pixels.
• Save the array to two different file formats (png, jpg, tiff)
12.3. Basic manipulations 384

12.3.2 Geometrical transformations

>>> lx, ly = face.shape
>>> # Cropping
>>> crop_face = face[lx // 4: - lx // 4, ly // 4: - ly // 4]
>>> # up <-> down flip
>>> flip_ud_face = np.flipud(face)
>>> # rotation
>>> rotate_face = sp.ndimage.rotate(face, 45)
>>> rotate_face_noreshape = sp.ndimage.rotate(face, 45, reshape=False)
12.4 Image filtering
Local filters: replace the value of pixels by a function of the values of neighboring pixels.
Neighbourhood: square (choose size), disk, or more complicated structuring element.
12.4.1 Blurring/smoothing
Gaussian filter from scipy.ndimage:

>>> blurred_face = sp.ndimage.gaussian_filter(face, sigma=3)
>>> very_blurred = sp.ndimage.gaussian_filter(face, sigma=5)
Uniform filter
>>> local_mean = sp.ndimage.uniform_filter(face, size=11)
12.4. Image filtering 385

12.4.2 Sharpening
Sharpen a blurred image:
>>> face = sp.datasets.face(gray=True).astype(float)

>>> blurred_f = sp.ndimage.gaussian_filter(face, 3)
increase the weight of edges by adding an approximation of the Laplacian:
>>> filter_blurred_f = sp.ndimage.gaussian_filter(blurred_f, 1)

>>> alpha = 30
>>> sharpened = blurred_f + alpha * (blurred_f - filter_blurred_f)
12.4.3 Denoising
Noisy face:
>>> f = sp.datasets.face(gray=True)
>>> f = f[230:290, 220:320]
>>> noisy = f + 0.4 * f.std() * rng.random(f.shape)
A Gaussian filter smoothes the noise out. . . and the edges as well:
>>> gauss_denoised = sp.ndimage.gaussian_filter(noisy, 2)
Most local linear isotropic filters blur the image (scipy.ndimage.uniform_filter)

A median filter preserves better the edges:

>>> med_denoised = sp.ndimage.median_filter(noisy, 3)
Median filter: better result for straight boundaries (low curvature):
>>> im = np.zeros((20, 20))

>>> im[5:-5, 5:-5] = 1
>>> im = sp.ndimage.distance_transform_bf(im)
>>> im_noise = im + 0.2 * rng.standard_normal(im.shape)
>>> im_med = sp.ndimage.median_filter(im_noise, 3)
Other rank filter: scipy.ndimage.maximum_filter, scipy.ndimage.percentile_filter

Other local non-linear filters: Wiener (scipy.signal.wiener), etc.
Non-local filters
Exercise: denoising
• Create a binary image (of 0s and 1s) with several objects (circles, ellipses, squares, or random
shapes).
• Add some noise (e.g., 20% of noise)
• Try two different denoising methods for denoising the image: gaussian filtering and median
filtering.
• Compare the histograms of the two different denoised images. Which one is the closest to the
histogram of the original (noise-free) image?
See also:
More denoising filters are available in skimage.denoising, see the scikit-image: image processing tuto-
rial.

See wikipedia for a definition of mathematical morphology.

Probe an image with a simple shape (a structuring element), and modify this image according to how
the shape locally fits or misses the image.
Structuring element:
>>> el = sp.ndimage.generate_binary_structure(2, 1)
>>> el
array([[False, True, False],
[ True, True, True],
[False, True, False]])
>>> el.astype(int)
array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]])
Erosion = minimum filter. Replace the value of a pixel by the minimal value covered by the structuring
element.:
>>> a = np.zeros((7,7), dtype=int)

>>> a[1:6, 2:5] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> sp.ndimage.binary_erosion(a).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
>>> # Erosion removes objects smaller than the structure
>>> sp.ndimage.binary_erosion(a, structure=np.ones((5,5))).astype(a.dtype)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],


[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
Dilation: maximum filter:
>>> a = np.zeros((5, 5))

>>> a[2, 2] = 1
>>> a
array([[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 1., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])
>>> sp.ndimage.binary_dilation(a).astype(a.dtype)
array([[0., 0., 0., 0., 0.],
[0., 0., 1., 0., 0.],
[0., 1., 1., 1., 0.],
[0., 0., 1., 0., 0.],
[0., 0., 0., 0., 0.]])
Also works for grey-valued images:

>>> im = np.zeros((64, 64))
>>> x, y = (63*rng.random((2, 8))).astype(int)
>>> im[x, y] = np.arange(8)
>>> bigger_points = sp.ndimage.grey_dilation(im, size=(5, 5), structure=np.ones((5,␣

˓→5)))
>>> square = np.zeros((16, 16))

>>> square[4:-4, 4:-4] = 1
>>> dist = sp.ndimage.distance_transform_bf(square)
>>> dilate_dist = sp.ndimage.grey_dilation(dist, size=(3, 3), \
... structure=np.ones((3, 3)))
Opening: erosion + dilation:

>>> a[1:4, 1:4] = 1; a[4, 4] = 1
>>> a
array([[0, 0, 0, 0, 0],


[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 1]])
>>> # Opening removes small objects
>>> sp.ndimage.binary_opening(a, structure=np.ones((3,3))).astype(int)
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 0]])
>>> # Opening can also smooth corners
>>> sp.ndimage.binary_opening(a).astype(int)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]])
Application: remove noise:
>>> square = np.zeros((32, 32))

>>> square[10:-10, 10:-10] = 1
>>> x, y = (32*rng.random((2, 20))).astype(int)
>>> square[x, y] = 1
>>> open_square = sp.ndimage.binary_opening(square)
>>> eroded_square = sp.ndimage.binary_erosion(square)

>>> reconstruction = sp.ndimage.binary_propagation(eroded_square, mask=square)
Closing: dilation + erosion

Many other mathematical morphology operations: hit and miss transform, tophat, etc.

12.5 Feature extraction
12.5.1 Edge detection
Synthetic data:
>>> im = np.zeros((256, 256))

>>> im[64:-64, 64:-64] = 1
>>>
>>> im = sp.ndimage.rotate(im, 15, mode='constant')
>>> im = sp.ndimage.gaussian_filter(im, 8)
Use a gradient operator (Sobel) to find high intensity variations:
>>> sx = sp.ndimage.sobel(im, axis=0, mode='constant')

>>> sy = sp.ndimage.sobel(im, axis=1, mode='constant')
>>> sob = np.hypot(sx, sy)
12.5.2 Segmentation
• Histogram-based segmentation (no spatial information)
>>> n = 10
>>> l = 256
>>> im = np.zeros((l, l))
>>> points = l*rng.random((2, n**2))
>>> im[(points[0]).astype(int), (points[1]).astype(int)] = 1
>>> im = sp.ndimage.gaussian_filter(im, sigma=l/(4.*n))
>>> mask = (im > im.mean()).astype(float)

>>> mask += 0.1 * im
>>> img = mask + 0.2*rng.standard_normal(mask.shape)
>>> hist, bin_edges = np.histogram(img, bins=60)

>>> bin_centers = 0.5*(bin_edges[:-1] + bin_edges[1:])
>>> binary_img = img > 0.5
Use mathematical morphology to clean up the result:
>>> # Remove small white regions

>>> open_img = sp.ndimage.binary_opening(binary_img)
12.5. Feature extraction 391


>>> # Remove small black hole
>>> close_img = sp.ndimage.binary_closing(open_img)
Exercise
Check that reconstruction operations (erosion + propagation) produce a better result than open-
ing/closing:
>>> eroded_img = sp.ndimage.binary_erosion(binary_img)
>>> reconstruct_img = sp.ndimage.binary_propagation(eroded_img, mask=binary_img)
>>> tmp = np.logical_not(reconstruct_img)
>>> eroded_tmp = sp.ndimage.binary_erosion(tmp)
>>> reconstruct_final = np.logical_not(sp.ndimage.binary_propagation(eroded_tmp,␣
˓→mask=tmp))
>>> np.abs(mask - close_img).mean()

0.00640699...
>>> np.abs(mask - reconstruct_final).mean()
0.00082232...
Exercise
Check how a first denoising step (e.g. with a median filter) modifies the histogram, and check that
the resulting histogram-based segmentation is more accurate.
See also:
More advanced segmentation algorithms are found in the scikit-image: see scikit-image: image pro-
cessing.

See also:
Other Scientific Packages provide algorithms that can be useful for image processing. In this example,
we use the spectral clustering function of the scikit-learn in order to segment glued objects.
>>> from sklearn.feature_extraction import image

>>> from sklearn.cluster import spectral_clustering
>>> l = 100
>>> x, y = np.indices((l, l))
>>> center1 = (28, 24)

>>> center2 = (40, 50)
>>> center3 = (67, 58)
>>> center4 = (24, 70)
>>> radius1, radius2, radius3, radius4 = 16, 14, 15, 14
>>> circle1 = (x - center1[0])**2 + (y - center1[1])**2 < radius1**2

>>> # 4 circles
>>> img = circle1 + circle2 + circle3 + circle4
>>> mask = img.astype(bool)
>>> img = img.astype(float)

>>> img += 1 + 0.2*rng.standard_normal(img.shape)
>>> # Convert the image into a graph with the value of the gradient on
>>> # the edges.
>>> graph = image.img_to_graph(img, mask=mask)
>>> # Take a decreasing function of the gradient: we take it weakly

>>> # dependent from the gradient the segmentation is close to a voronoi
>>> graph.data = np.exp(-graph.data/graph.data.std())
>>> labels = spectral_clustering(graph, n_clusters=4, eigen_solver='arpack')

>>> label_im = -np.ones(mask.shape)
>>> label_im[mask] = labels

12.6 Measuring objects properties: scipy.ndimage.measurements
Synthetic data:
>>> n = 10
>>> l = 256
>>> points = l * rng.random((2, n**2))
>>> mask = im > im.mean()
• Analysis of connected components

Label connected components: scipy.dimage.label:
>>> label_im, nb_labels = sp.ndimage.label(mask)

>>> nb_labels # how many regions?
28
>>> plt.imshow(label_im)
Compute size, mean_value, etc. of each region:
>>> sizes = sp.ndimage.sum(mask, label_im, range(nb_labels + 1))

>>> mean_vals = sp.ndimage.sum(im, label_im, range(1, nb_labels + 1))
Clean up small connect components:
>>> mask_size = sizes < 1000

>>> remove_pixel = mask_size[label_im]
>>> remove_pixel.shape
(256, 256)
>>> label_im[remove_pixel] = 0
>>> plt.imshow(label_im)
Now reassign labels with np.searchsorted:
>>> labels = np.unique(label_im)

>>> label_im = np.searchsorted(labels, label_im)
Find region of interest enclosing object:
12.6. Measuring objects properties: scipy.ndimage.measurements 394

>>> slice_x, slice_y = sp.ndimage.find_objects(label_im)[3]

>>> roi = im[slice_x, slice_y]
>>> plt.imshow(roi)
Other spatial measures: scipy.ndimage.center_of_mass, scipy.ndimage.maximum_position, etc.

Can be used outside the limited scope of segmentation applications.
Example: block mean:
>>> f = sp.datasets.face(gray=True)
>>> sx, sy = f.shape
>>> X, Y = np.ogrid[0:sx, 0:sy]
>>> regions = (sy//6) * (X//4) + (Y//6) # note that we use broadcasting
>>> block_mean = sp.ndimage.mean(f, labels=regions, index=np.arange(1,
... regions.max() +1))
>>> block_mean.shape = (sx // 4, sy // 6)
When regions are regular blocks, it is more efficient to use stride tricks (Example: fake dimensions with
strides).
Non-regularly-spaced blocks: radial mean:

>>> sx, sy = f.shape

>>> X, Y = np.ogrid[0:sx, 0:sy]
>>> r = np.hypot(X - sx/2, Y - sy/2)
>>> rbin = (20* r/r.max()).astype(int)
>>> radial_mean = sp.ndimage.mean(f, labels=rbin, index=np.arange(1, rbin.max() +1))
• Other measures
Correlation function, Fourier/wavelet spectrum, etc.
One example with mathematical morphology: granulometry

>>> def disk_structure(n):

... struct = np.zeros((2 * n + 1, 2 * n + 1))
... x, y = np.indices((2 * n + 1, 2 * n + 1))
... mask = (x - n)**2 + (y - n)**2 <= n**2
... struct[mask] = 1
... return struct.astype(bool)
...
>>>
>>> def granulometry(data, sizes=None):
... s = max(data.shape)
... if sizes is None:
... sizes = range(1, s/2, 2)
... granulo = [sp.ndimage.binary_opening(data, \
... structure=disk_structure(n)).sum() for n in sizes]
... return granulo
...
>>>
>>> n = 10
>>> l = 256
>>> points = l*rng.random((2, n**2))
>>>
>>> mask = im > im.mean()
>>>
>>> granulo = granulometry(mask, sizes=np.arange(2, 19, 4))
12.8 Examples for the image processing chapter
12.8.1 Displaying a Raccoon Face
Small example to plot a raccoon face.

import scipy as sp
import imageio.v3 as iio
f = sp.datasets.face()
iio.imwrite("face.png", f) # uses the Image module (PIL)
plt.imshow(f)
plt.show()
12.8. Examples for the image processing chapter 398

12.8.2 Image interpolation
The example demonstrates image interpolation on a Raccoon face.
import scipy as sp
f = sp.datasets.face(gray=True)
plt.imshow(f[320:340, 510:530], cmap=plt.cm.gray)
plt.axis("off")
plt.imshow(f[320:340, 510:530], cmap=plt.cm.gray, interpolation="nearest")
plt.axis("off")
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=1, bottom=0, left=0, right=1)

plt.show()

12.8.3 Plot the block mean of an image
An example showing how to use broad-casting to plot the mean of blocks of an image.
import numpy as np
import scipy as sp
sx, sy = f.shape
X, Y = np.ogrid[0:sx, 0:sy]
regions = sy // 6 * (X // 4) + Y // 6
block_mean = sp.ndimage.mean(f, labels=regions, index=np.arange(1, regions.max() + 1))
block_mean.shape = (sx // 4, sy // 6)
plt.imshow(block_mean, cmap=plt.cm.gray)
plt.axis("off")
plt.show()

12.8.4 Image manipulation and NumPy arrays
This example shows how to do image manipulation using common NumPy arrays tricks.
import numpy as np
import scipy as sp
face[10:13, 20:23]
face[100:120] = 255
lx, ly = face.shape
X, Y = np.ogrid[0:lx, 0:ly]
mask = (X - lx / 2) ** 2 + (Y - ly / 2) ** 2 > lx * ly / 4
face[mask] = 0
face[range(400), range(400)] = 255
plt.axes([0, 0, 1, 1])
plt.imshow(face, cmap=plt.cm.gray)
plt.axis("off")
plt.show()

12.8.5 Radial mean
This example shows how to do a radial mean with scikit-image.
import numpy as np
import scipy as sp
sx, sy = f.shape
X, Y = np.ogrid[0:sx, 0:sy]
r = np.hypot(X - sx / 2, Y - sy / 2)
rbin = (20 * r / r.max()).astype(int)

radial_mean = sp.ndimage.mean(f, labels=rbin, index=np.arange(1, rbin.max() + 1))
plt.axes([0, 0, 1, 1])
plt.imshow(rbin, cmap=plt.cm.nipy_spectral)
plt.axis("off")
plt.show()

12.8.6 Display a Raccoon Face
An example that displays a raccoon face with matplotlib.
import scipy as sp
plt.subplot(131)
plt.imshow(f, cmap=plt.cm.gray)
plt.subplot(132)
plt.imshow(f, cmap=plt.cm.gray, vmin=30, vmax=200)
plt.axis("off")
plt.subplot(133)
plt.contour(f, [50, 200])
plt.axis("off")
plt.subplots_adjust(wspace=0, hspace=0.0, top=0.99, bottom=0.01, left=0.05, right=0.

˓→99)
plt.show()

12.8.7 Image sharpening
This example shows how to sharpen an image in noiseless situation by applying the filter inverse to the
blur.
import scipy as sp
f = sp.datasets.face(gray=True).astype(float)
blurred_f = sp.ndimage.gaussian_filter(f, 3)
filter_blurred_f = sp.ndimage.gaussian_filter(blurred_f, 1)
alpha = 30
sharpened = blurred_f + alpha * (blurred_f - filter_blurred_f)
plt.subplot(131)
plt.axis("off")
plt.subplot(132)
plt.imshow(blurred_f, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(133)
plt.imshow(sharpened, cmap=plt.cm.gray)
plt.axis("off")
plt.tight_layout()
plt.show()

12.8.8 Blurring of images
An example showing various processes that blur an image.
import scipy as sp
blurred_face = sp.ndimage.gaussian_filter(face, sigma=3)
very_blurred = sp.ndimage.gaussian_filter(face, sigma=5)
local_mean = sp.ndimage.uniform_filter(face, size=11)
plt.subplot(131)
plt.imshow(blurred_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(132)
plt.imshow(very_blurred, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(133)
plt.imshow(local_mean, cmap=plt.cm.gray)
plt.axis("off")

˓→99)
plt.show()

12.8.9 Synthetic data
The example generates and displays simple synthetic data.
import numpy as np
import scipy as sp
n = 10
l = 256
im = np.zeros((l, l))
points = l * rng.random((2, n**2))
im[(points[0]).astype(int), (points[1]).astype(int)] = 1
im = sp.ndimage.gaussian_filter(im, sigma=l / (4.0 * n))
mask = im > im.mean()
label_im, nb_labels = sp.ndimage.label(mask)
plt.subplot(131)
plt.imshow(im)
plt.axis("off")
plt.subplot(132)
plt.axis("off")
plt.subplot(133)
plt.imshow(label_im, cmap=plt.cm.nipy_spectral)
plt.axis("off")

plt.show()

12.8.10 Opening, erosion, and propagation
This example shows simple operations of mathematical morphology.
import numpy as np
import scipy as sp
square = np.zeros((32, 32))

square[10:-10, 10:-10] = 1
x, y = (32 * rng.random((2, 20))).astype(int)
square[x, y] = 1
open_square = sp.ndimage.binary_opening(square)
eroded_square = sp.ndimage.binary_erosion(square)
reconstruction = sp.ndimage.binary_propagation(eroded_square, mask=square)
plt.figure(figsize=(9.5, 3))
plt.subplot(131)
plt.imshow(square, cmap=plt.cm.gray, interpolation="nearest")
plt.axis("off")
plt.subplot(132)
plt.imshow(open_square, cmap=plt.cm.gray, interpolation="nearest")
plt.axis("off")
plt.subplot(133)
plt.imshow(reconstruction, cmap=plt.cm.gray, interpolation="nearest")
plt.axis("off")

˓→99)
plt.show()

12.8.11 Image denoising
This example demoes image denoising on a Raccoon face.
import numpy as np
import scipy as sp
f = f[230:290, 220:320]
noisy = f + 0.4 * f.std() * rng.random(f.shape)
gauss_denoised = sp.ndimage.gaussian_filter(noisy, 2)
med_denoised = sp.ndimage.median_filter(noisy, 3)
plt.subplot(131)
plt.imshow(noisy, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis("off")
plt.title("noisy", fontsize=20)
plt.subplot(132)
plt.imshow(gauss_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis("off")
plt.title("Gaussian filter", fontsize=20)
plt.subplot(133)
plt.imshow(med_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis("off")
plt.title("Median filter", fontsize=20)
plt.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9, bottom=0, left=0, right=1)

plt.show()

12.8.12 Geometrical transformations
This examples demos some simple geometrical transformations on a Raccoon face.
import numpy as np
import scipy as sp
lx, ly = face.shape
# Cropping
crop_face = face[lx // 4 : -lx // 4, ly // 4 : -ly // 4]
# up <-> down flip
flip_ud_face = np.flipud(face)
# rotation
rotate_face = sp.ndimage.rotate(face, 45)
rotate_face_noreshape = sp.ndimage.rotate(face, 45, reshape=False)
plt.subplot(151)
plt.imshow(face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(152)
plt.imshow(crop_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(153)
plt.imshow(flip_ud_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(154)
plt.imshow(rotate_face, cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(155)
plt.imshow(rotate_face_noreshape, cmap=plt.cm.gray)
plt.axis("off")
plt.subplots_adjust(wspace=0.02, hspace=0.3, top=1, bottom=0.1, left=0, right=1)
plt.show()

12.8.13 Find the bounding box of an object
This example shows how to extract the bounding box of the largest object
import numpy as np
import scipy as sp
n = 10
l = 256
# Find the largest connected component

sizes = sp.ndimage.sum(mask, label_im, range(nb_labels + 1))
mask_size = sizes < 1000
remove_pixel = mask_size[label_im]
label_im[remove_pixel] = 0
labels = np.unique(label_im)
label_im = np.searchsorted(labels, label_im)
# Now that we have only one connected component, extract it's bounding box
slice_x, slice_y = sp.ndimage.find_objects(label_im == 4)[0]
roi = im[slice_x, slice_y]
plt.axes([0, 0, 1, 1])
plt.imshow(roi)
plt.axis("off")
plt.show()

12.8.14 Measurements from images
This examples shows how to measure quantities from various images.
import numpy as np
import scipy as sp
n = 10
l = 256
sizes = sp.ndimage.sum(mask, label_im, range(nb_labels + 1))

mask_size = sizes < 1000
remove_pixel = mask_size[label_im]
label_im[remove_pixel] = 0
labels = np.unique(label_im)
label_clean = np.searchsorted(labels, label_im)
plt.subplot(121)
plt.imshow(label_im, cmap=plt.cm.nipy_spectral)
plt.axis("off")
plt.subplot(122)
plt.imshow(label_clean, vmax=nb_labels, cmap=plt.cm.nipy_spectral)
plt.axis("off")

plt.show()

12.8.15 Total Variation denoising
This example demoes Total-Variation (TV) denoising on a Raccoon face.
import numpy as np
import scipy as sp
from skimage.restoration import denoise_tv_chambolle
f = f[230:290, 220:320]
noisy = f + 0.4 * f.std() * rng.random(f.shape)
tv_denoised = denoise_tv_chambolle(noisy, weight=10)
plt.subplot(131)
plt.imshow(noisy, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis("off")
plt.title("noisy", fontsize=20)
plt.subplot(132)
plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis("off")
plt.title("TV denoising", fontsize=20)
tv_denoised = denoise_tv_chambolle(noisy, weight=50)

plt.subplot(133)
plt.imshow(tv_denoised, cmap=plt.cm.gray, vmin=40, vmax=220)
plt.axis("off")
plt.title("(more) TV denoising", fontsize=20)

plt.show()

12.8.16 Denoising an image with the median filter
This example shows the original image, the noisy image, the denoised one (with the median filter) and
the difference between the two.
import numpy as np
import scipy as sp
im = np.zeros((20, 20))
im[5:-5, 5:-5] = 1
im = sp.ndimage.distance_transform_bf(im)
im_noise = im + 0.2 * rng.normal(size=im.shape)
im_med = sp.ndimage.median_filter(im_noise, 3)
plt.subplot(141)
plt.imshow(im, interpolation="nearest")
plt.axis("off")
plt.title("Original image", fontsize=20)
plt.subplot(142)
plt.imshow(im_noise, interpolation="nearest", vmin=0, vmax=5)
plt.axis("off")
plt.title("Noisy image", fontsize=20)
plt.subplot(143)
plt.imshow(im_med, interpolation="nearest", vmin=0, vmax=5)
plt.axis("off")
plt.title("Median filter", fontsize=20)
plt.subplot(144)
plt.imshow(np.abs(im - im_med), cmap=plt.cm.hot, interpolation="nearest")
plt.axis("off")
plt.title("Error", fontsize=20)
plt.show()

12.8.17 Histogram segmentation
This example does simple histogram analysis to perform segmentation.
import numpy as np
import scipy as sp
n = 10
l = 256
mask = (im > im.mean()).astype(float)
mask += 0.1 * im
img = mask + 0.2 * rng.normal(size=mask.shape)
hist, bin_edges = np.histogram(img, bins=60)

bin_centers = 0.5 * (bin_edges[:-1] + bin_edges[1:])
binary_img = img > 0.5
plt.subplot(131)
plt.imshow(img)
plt.axis("off")
plt.subplot(132)
plt.plot(bin_centers, hist, lw=2)
plt.axvline(0.5, color="r", ls="--", lw=2)
plt.text(0.57, 0.8, "histogram", fontsize=20, transform=plt.gca().transAxes)
plt.yticks([])
plt.subplot(133)
plt.imshow(binary_img, cmap=plt.cm.gray, interpolation="nearest")
plt.axis("off")

plt.show()

12.8.18 Greyscale dilation
This example illustrates greyscale mathematical morphology.
import numpy as np
import scipy as sp
im = np.zeros((64, 64))
x, y = (63 * rng.random((2, 8))).astype(int)
im[x, y] = np.arange(8)
bigger_points = sp.ndimage.grey_dilation(im, size=(5, 5), structure=np.ones((5, 5)))
square = np.zeros((16, 16))

square[4:-4, 4:-4] = 1
dist = sp.ndimage.distance_transform_bf(square)
dilate_dist = sp.ndimage.grey_dilation(dist, size=(3, 3), structure=np.ones((3, 3)))
plt.figure(figsize=(12.5, 3))
plt.subplot(141)
plt.imshow(im, interpolation="nearest", cmap=plt.cm.nipy_spectral)
plt.axis("off")
plt.subplot(142)
plt.imshow(bigger_points, interpolation="nearest", cmap=plt.cm.nipy_spectral)
plt.axis("off")
plt.subplot(143)
plt.imshow(dist, interpolation="nearest", cmap=plt.cm.nipy_spectral)
plt.axis("off")
plt.subplot(144)
plt.imshow(dilate_dist, interpolation="nearest", cmap=plt.cm.nipy_spectral)
plt.axis("off")

˓→99)
plt.show()

12.8.19 Finding edges with Sobel filters
The Sobel filter is one of the simplest way of finding edges.
import numpy as np
import scipy as sp
im = np.zeros((256, 256))
im[64:-64, 64:-64] = 1
im = sp.ndimage.rotate(im, 15, mode="constant")

im = sp.ndimage.gaussian_filter(im, 8)
sx = sp.ndimage.sobel(im, axis=0, mode="constant")

sy = sp.ndimage.sobel(im, axis=1, mode="constant")
sob = np.hypot(sx, sy)
plt.subplot(141)
plt.imshow(im, cmap=plt.cm.gray)
plt.axis("off")
plt.title("square", fontsize=20)
plt.subplot(142)
plt.imshow(sx)
plt.axis("off")
plt.title("Sobel (x direction)", fontsize=20)
plt.subplot(143)
plt.imshow(sob)
plt.axis("off")
plt.title("Sobel filter", fontsize=20)
im += 0.07 * rng.random(im.shape)
sx = sp.ndimage.sobel(im, axis=0, mode="constant")

sy = sp.ndimage.sobel(im, axis=1, mode="constant")
sob = np.hypot(sx, sy)
plt.subplot(144)
plt.imshow(sob)
plt.axis("off")
plt.title("Sobel for noisy image", fontsize=20)

plt.subplots_adjust(wspace=0.02, hspace=0.02, top=1, bottom=0, left=0, right=0.9)
plt.show()
12.8.20 Cleaning segmentation with mathematical morphology
An example showing how to clean segmentation with mathematical morphology: removing small regions
and holes.
import numpy as np
import scipy as sp
n = 10
l = 256
binary_img = img > 0.5
# Remove small white regions

open_img = sp.ndimage.binary_opening(binary_img)
# Remove small black hole
close_img = sp.ndimage.binary_closing(open_img)
l = 128
plt.subplot(141)
plt.imshow(binary_img[:l, :l], cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(142)


plt.imshow(open_img[:l, :l], cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(143)
plt.imshow(close_img[:l, :l], cmap=plt.cm.gray)
plt.axis("off")
plt.subplot(144)
plt.imshow(mask[:l, :l], cmap=plt.cm.gray)
plt.contour(close_img[:l, :l], [0.5], linewidths=2, colors="r")
plt.axis("off")
plt.show()
12.8.21 Segmentation with Gaussian mixture models
This example performs a Gaussian mixture model analysis of the image histogram to find the right
thresholds for separating foreground from background.
import numpy as np
import scipy as sp
from sklearn.mixture import GaussianMixture
n = 10
l = 256


hist, bin_edges = np.histogram(img, bins=60)
bin_centers = 0.5 * (bin_edges[:-1] + bin_edges[1:])
classif = GaussianMixture(n_components=2)
classif.fit(img.reshape((img.size, 1)))
threshold = np.mean(classif.means_)
binary_img = img > threshold
plt.subplot(131)
plt.imshow(img)
plt.axis("off")
plt.subplot(132)
plt.plot(bin_centers, hist, lw=2)
plt.axvline(0.5, color="r", ls="--", lw=2)
plt.text(0.57, 0.8, "histogram", fontsize=20, transform=plt.gca().transAxes)
plt.yticks([])
plt.subplot(133)
plt.imshow(binary_img, cmap=plt.cm.gray, interpolation="nearest")
plt.axis("off")

plt.show()
12.8.22 Watershed segmentation
This example shows how to do segmentation with watershed.
import numpy as np
from skimage.segmentation import watershed
from skimage.feature import peak_local_max
import scipy as sp

# Generate an initial image with two overlapping circles

x, y = np.indices((80, 80))
x1, y1, x2, y2 = 28, 28, 44, 52
r1, r2 = 16, 20
mask_circle1 = (x - x1) ** 2 + (y - y1) ** 2 < r1**2
image = np.logical_or(mask_circle1, mask_circle2)
# Now we want to separate the two objects in image
# Generate the markers as local maxima of the distance
# to the background
distance = sp.ndimage.distance_transform_edt(image)
peak_idx = peak_local_max(distance, footprint=np.ones((3, 3)), labels=image)
peak_mask = np.zeros_like(distance, dtype=bool)
peak_mask[tuple(peak_idx.T)] = True
markers = sp.ndimage.label(peak_mask)[0]
labels = watershed(-distance, markers, mask=image)
plt.subplot(131)
plt.imshow(image, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.subplot(132)
plt.imshow(-distance, interpolation="nearest")
plt.axis("off")
plt.subplot(133)
plt.imshow(labels, cmap="nipy_spectral", interpolation="nearest")
plt.axis("off")
plt.subplots_adjust(hspace=0.01, wspace=0.01, top=1, bottom=0, left=0, right=1)

plt.show()
12.8.23 Granulometry
This example performs a simple granulometry analysis.
import numpy as np
import scipy as sp


def disk_structure(n):
struct = np.zeros((2 * n + 1, 2 * n + 1))
x, y = np.indices((2 * n + 1, 2 * n + 1))
mask = (x - n) ** 2 + (y - n) ** 2 <= n**2
struct[mask] = 1
return struct.astype(bool)
def granulometry(data, sizes=None):

s = max(data.shape)
if sizes is None:
sizes = range(1, s / 2, 2)
granulo = [
sp.ndimage.binary_opening(data, structure=disk_structure(n)).sum()
for n in sizes
]
return granulo
n = 10
l = 256
granulo = granulometry(mask, sizes=np.arange(2, 19, 4))
plt.subplot(121)
opened = sp.ndimage.binary_opening(mask, structure=disk_structure(10))
opened_more = sp.ndimage.binary_opening(mask, structure=disk_structure(14))
plt.contour(opened, [0.5], colors="b", linewidths=2)
plt.contour(opened_more, [0.5], colors="r", linewidths=2)
plt.axis("off")
plt.subplot(122)
plt.plot(np.arange(2, 19, 4), granulo, "ok", ms=8)
plt.subplots_adjust(wspace=0.02, hspace=0.15, top=0.95, bottom=0.15, left=0, right=0.

˓→95)
plt.show()

12.8.24 Segmentation with spectral clustering
This example uses spectral clustering to do segmentation.
import numpy as np
from sklearn.feature_extraction import image

from sklearn.cluster import spectral_clustering
l = 100
x, y = np.indices((l, l))
center1 = (28, 24)

center2 = (40, 50)
center3 = (67, 58)
center4 = (24, 70)
radius1, radius2, radius3, radius4 = 16, 14, 15, 14
circle1 = (x - center1[0]) ** 2 + (y - center1[1]) ** 2 < radius1**2

4 circles
img = circle1 + circle2 + circle3 + circle4

mask = img.astype(bool)
img = img.astype(float)
img += 1 + 0.2 * rng.normal(size=img.shape)
# Convert the image into a graph with the value of the gradient on the
# edges.
graph = image.img_to_graph(img, mask=mask)
# Take a decreasing function of the gradient: we take it weakly

# dependent from the gradient the segmentation is close to a voronoi
graph.data = np.exp(-graph.data / graph.data.std())
# Force the solver to be arpack, since amg is numerically

# unstable on this example
labels = spectral_clustering(graph, n_clusters=4)
label_im = -np.ones(mask.shape)
label_im[mask] = labels
plt.subplot(121)
plt.imshow(img, cmap=plt.cm.nipy_spectral, interpolation="nearest")
plt.axis("off")
plt.subplot(122)
plt.imshow(label_im, cmap=plt.cm.nipy_spectral, interpolation="nearest")
plt.axis("off")



˓→99)
plt.show()
See also:
More on image-processing:
• The chapter on Scikit-image
• Other, more powerful and complete modules: OpenCV (Python bindings), CellProfiler, ITK with
Python bindings

CHAPTER 13
Mathematical optimization: finding
minima of functions
Authors: Gaël Varoquaux

Mathematical optimization deals with the problem of finding numerically minimums (or maximums or
zeros) of a function. In this context, the function is called cost function, or objective function, or energy.
Here, we are interested in using scipy.optimize for black-box optimization: we do not rely on the
mathematical expression of the function that we are optimizing. Note that this expression can often be
used for more efficient, non black-box, optimization.
Prerequisites
• NumPy
• SciPy
• Matplotlib
See also:
References
Mathematical optimization is very . . . mathematical. If you want performance, it really pays to read
the books:
• Convex Optimization by Boyd and Vandenberghe (pdf available free online).
• Numerical Optimization, by Nocedal and Wright. Detailed reference on gradient descent methods.
• Practical Methods of Optimization by Fletcher: good at hand-waving explanations.
424
Chapters contents
• Knowing your problem

– Convex versus non-convex optimization
– Smooth and non-smooth problems
– Noisy versus exact cost functions
– Constraints
• A review of the different optimizers
– Getting started: 1D optimization
– Gradient based methods
– Newton and quasi-newton methods
• Examples for the mathematical optimization chapter
– Gradient-less methods
– Global optimizers
• Practical guide to optimization with SciPy
– Choosing a method
– Making your optimizer faster
– Computing gradients
– Synthetic exercices
• Special case: non-linear least-squares
– Minimizing the norm of a vector function
– Curve fitting
• Optimization with constraints
– Box bounds
– General constraints
• Examples for the mathematical optimization chapter
13.1 Knowing your problem
Not all optimization problems are equal. Knowing your problem enables you to choose the right tool.
Dimensionality of the problem
The scale of an optimization problem is pretty much set by the dimensionality of the problem, i.e. the
number of scalar variables on which the search is performed.
13.1. Knowing your problem 425

13.1.1 Convex versus non-convex optimization
A convex function: A non-convex function

• f is above all its tangents.
• equivalently, for two point A, B, f(C) lies
below the segment [f(A), f(B])], if A < C <
B
Optimizing convex functions is easy. Optimizing non-convex functions can be very hard.
Note: It can be proven that for a convex function a local minimum is also a global minimum. Then,
in some sense, the minimum is unique.
13.1.2 Smooth and non-smooth problems
A smooth function: A non-smooth function

The gradient is defined everywhere, and is a continuous function
Optimizing smooth functions is easier (true in the context of black-box optimization, otherwise Lin-
ear Programming is an example of methods which deal very efficiently with piece-wise linear functions).

13.1.3 Noisy versus exact cost functions
Noisy (blue) and non-noisy (green) functions
Noisy gradients
Many optimization methods rely on gradients of the objective function. If the gradient function is not
given, they are computed numerically, which induces errors. In such situation, even if the objective
function is not noisy, a gradient-based optimization may be a noisy optimization.
13.1.4 Constraints
Optimizations under constraints

Here:
−1 < 𝑥1 < 1
−1 < 𝑥2 < 1

13.2 A review of the different optimizers
13.2.1 Getting started: 1D optimization
Let’s get started by finding the minimum of the scalar function 𝑓 (𝑥) = exp[(𝑥−0.7)2 ]. scipy.optimize.
minimize_scalar() uses Brent’s method to find the minimum of a function:

>>> def f(x):
... return -np.exp(-(x - 0.5)**2)
>>> result = sp.optimize.minimize_scalar(f)
>>> result.success # check if solver was successful
True
>>> x_min = result.x
>>> x_min
0.50...
>>> x_min - 0.5
5.8...e-09
Table 1: Brent’s method on a quadratic function: it converges

in 3 iterations, as the quadratic approximation is then exact.
Table 2: Brent’s method on a non-convex function: note that

the fact that the optimizer avoided the local minimum is a matter
of luck.
13.2. A review of the different optimizers 428

Note: You can use different solvers using the parameter method.
Note: scipy.optimize.minimize_scalar() can also be used for optimization constrained to an

interval using the parameter bounds.
13.2.2 Gradient based methods
Some intuitions about gradient descent
Here we focus on intuitions, not code. Code will follow.

Gradient descent basically consists in taking small steps in the direction of the gradient, that is the
direction of the steepest descent.
Table 3: Fixed step gradient descent
A well-conditioned
quadratic function.
An ill-conditioned
quadratic function.
The core problem of gradient-
methods on ill-conditioned
problems is that the gradient
tends not to point in the direc-
tion of the minimum.
We can see that very anisotropic (ill-conditioned) functions are harder to optimize.
Take home message: conditioning number and preconditioning
If you know natural scaling for your variables, prescale them so that they behave similarly. This is
related to preconditioning.
Also, it clearly can be advantageous to take bigger steps. This is done in gradient descent code using a
line search.

Table 4: Adaptive step gradient descent
A well-conditioned quadratic
function.
An ill-conditioned quadratic
function.
An ill-conditioned non-
quadratic function.
An ill-conditioned very non-

quadratic function.
The more a function looks like a quadratic function (elliptic iso-curves), the easier it is to optimize.

Conjugate gradient descent
The gradient descent algorithms above are toys not to be used on real problems.
As can be seen from the above experiments, one of the problems of the simple gradient descent algorithms,
is that it tends to oscillate across a valley, each time following the direction of the gradient, that makes
it cross the valley. The conjugate gradient solves this problem by adding a friction term: each step
depends on the two last values of the gradient and sharp turns are reduced.
Table 5: Conjugate gradient descent
quadratic function.

quadratic function.
SciPy provides scipy.optimize.minimize() to find the minimum of scalar functions of one or more
variables. The simple conjugate gradient method can be used by setting the parameter method to CG
>>> def f(x): # The rosenbrock function

... return .5*(1 - x[0])**2 + (x[1] - x[0]**2)**2
>>> sp.optimize.minimize(f, [2, -1], method="CG")
success: True
status: 0
fun: 1.650...e-11
x: [ 1.000e+00 1.000e+00]
nit: 13
jac: [-6.15...e-06 2.53...e-07]
nfev: 81
njev: 27
Gradient methods need the Jacobian (gradient) of the function. They can compute it numerically, but
will perform better if you can pass them the gradient:
>>> def jacobian(x):

... return np.array((-2*.5*(1 - x[0]) - 4*x[0]*(x[1] - x[0]**2), 2*(x[1] -␣
˓→x[0]**2)))
>>> sp.optimize.minimize(f, [2, 1], method="CG", jac=jacobian)



success: True
status: 0
fun: 2.95786...e-14
x: [ 1.000e+00 1.000e+00]
nit: 8
jac: [ 7.183e-07 -2.990e-07]
nfev: 16
njev: 16
Note that the function has only been evaluated 27 times, compared to 108 without the gradient.
13.2.3 Newton and quasi-newton methods
Newton methods: using the Hessian (2nd differential)
Newton methods use a local quadratic approximation to compute the jump direction. For this purpose,
they rely on the 2 first derivative of the function: the gradient and the Hessian.

An ill-conditioned
quadratic function:
Note that, as the quadratic ap-
proximation is exact, the New-
ton method is blazing fast
quadratic function:
Here we are optimizing a Gaus-
sian, which is always below its
quadratic approximation. As a
result, the Newton method over-
shoots and leads to oscillations.

quadratic function:
In SciPy, you can use the Newton method by setting method to Newton-CG in scipy.optimize.
minimize(). Here, CG refers to the fact that an internal inversion of the Hessian is performed by
conjugate gradient

... return .5*(1 - x[0])**2 + (x[1] - x[0]**2)**2
˓→x[0]**2)))
>>> sp.optimize.minimize(f, [2,-1], method="Newton-CG", jac=jacobian)

success: True
status: 0
fun: 1.5601357400786612e-15


x: [ 1.000e+00 1.000e+00]
nit: 10
jac: [ 1.058e-07 -7.483e-08]
nfev: 11
njev: 33
nhev: 0
Note that compared to a conjugate gradient (above), Newton’s method has required less function evalua-
tions, but more gradient evaluations, as it uses it to approximate the Hessian. Let’s compute the Hessian
and pass it to the algorithm:
>>> def hessian(x): # Computed with sympy

... return np.array(((1 - 4*x[1] + 12*x[0]**2, -4*x[0]), (-4*x[0], 2)))
>>> sp.optimize.minimize(f, [2,-1], method="Newton-CG", jac=jacobian, hess=hessian)
success: True
status: 0
fun: 1.6277298383706738e-15
x: [ 1.000e+00 1.000e+00]
nit: 10
jac: [ 1.110e-07 -7.781e-08]
nfev: 11
njev: 11
nhev: 10
Note: At very high-dimension, the inversion of the Hessian can be costly and unstable (large scale >
250).
Note: Newton optimizers should not to be confused with Newton’s root finding method, based on the
same principles, scipy.optimize.newton().
Quasi-Newton methods: approximating the Hessian on the fly
BFGS: BFGS (Broyden-Fletcher-Goldfarb-Shanno algorithm) refines at each step an approximation of

the Hessian.
13.4 Examples for the mathematical optimization chapter
13.4.1 Noisy optimization problem
Draws a figure explaining noisy vs non-noisy optimization

import numpy as np
x = np.linspace(-5, 5, 101)
x_ = np.linspace(-5, 5, 31)
def f(x):
return -np.exp(-(x**2))
# A smooth function
plt.figure(1, figsize=(3, 2.5))
plt.clf()
plt.plot(x_, f(x_) + 0.2 * np.random.normal(size=31), linewidth=2)

plt.plot(x, f(x), linewidth=2)
plt.ylim(ymin=-1.3)
plt.axis("off")
plt.tight_layout()
plt.show()
13.4. Examples for the mathematical optimization chapter 435

13.4.2 Smooth vs non-smooth
Draws a figure to explain smooth versus non smooth optimization.
import numpy as np
x = np.linspace(-1.5, 1.5, 101)
# A smooth function
plt.clf()
plt.plot(x, np.sqrt(0.2 + x**2), linewidth=2)

plt.text(-1, 0, "$f$", size=20)
plt.ylim(ymin=-0.2)
plt.axis("off")
plt.tight_layout()
# A non-smooth function
plt.clf()
plt.plot(x, np.abs(x), linewidth=2)
plt.text(-1, 0, "$f$", size=20)


plt.ylim(ymin=-0.2)
plt.axis("off")
plt.tight_layout()
plt.show()
A curve fitting example
import numpy as np
import scipy as sp
# Our test function

def f(t, omega, phi):
return np.cos(omega * t + phi)
# Our x and y data



y = f(x, 1.5, 1) + 0.1 * np.random.normal(size=50)
# Fit the model: the parameters omega and phi can be found in the
# `params` vector
params, params_cov = sp.optimize.curve_fit(f, x, y)
# plot the data and the fitted curve

plt.figure(1)
plt.clf()
plt.plot(x, y, "bx")
plt.plot(t, f(t, *params), "r-")
plt.show()
13.4.4 Convex function
A figure showing the definition of a convex function

import numpy as np
x = np.linspace(-1, 2)

plt.clf()
# A convex function
plt.plot(x, x**2, linewidth=2)
plt.text(-0.7, -(0.6**2), "$f$", size=20)
# The tangent in one point

plt.plot(x, 2 * x - 1)
plt.plot(1, 1, "k+")
plt.text(0.3, -0.75, "Tangent to $f$", size=15)
plt.text(1, 1 - 0.5, "C", size=15)
# Convexity as barycenter
plt.plot([0.35, 1.85], [0.35**2, 1.85**2])
plt.plot([0.35, 1.85], [0.35**2, 1.85**2], "k+")
plt.text(0.35 - 0.2, 0.35**2 + 0.1, "A", size=15)
plt.text(1.85 - 0.2, 1.85**2, "B", size=15)
plt.ylim(ymin=-1)
plt.axis("off")
plt.tight_layout()
# Convexity as barycenter
plt.clf()
plt.plot(x, x**2 + np.exp(-5 * (x - 0.5) ** 2), linewidth=2)
plt.text(-0.7, -(0.6**2), "$f$", size=20)
plt.ylim(ymin=-1)
plt.axis("off")
plt.tight_layout()
plt.show()
13.4.5 Finding a minimum in a flat neighborhood
An exercise of finding minimum. This exercise is hard because the function is very flat around the
minimum (all its derivatives are zero). Thus gradient information is unreliable.
The function admits a minimum in [0, 0]. The challenge is to get within 1e-7 of this minimum, starting
at x0 = [1, 1].
The solution that we adopt here is to give up on using gradient or information based on local differences,
and to rely on the Powell algorithm. With 162 function evaluations, we get to 1e-8 of the solution.
import numpy as np
import scipy as sp

def f(x):
return np.exp(-1 / (0.01 * x[0] ** 2 + x[1] ** 2))
# A well-conditionned version of f:
def g(x):
return f([10 * x[0], x[1]])
# The gradient of g. We won't use it here for the optimization.

def g_prime(x):
r = np.sqrt(x[0] ** 2 + x[1] ** 2)
return 2 / r**3 * g(x) * x / r
result = sp.optimize.minimize(g, [1, 1], method="Powell", tol=1e-10)

x_min = result.x
Some pretty plotting
plt.figure(0)
plt.clf()
t = np.linspace(-1.1, 1.1, 100)
plt.plot(t, f([0, t]))
plt.figure(1)
plt.clf()
X, Y = np.mgrid[-1.5:1.5:100j, -1.1:1.1:100j]
plt.imshow(
f([X, Y]).T, cmap=plt.cm.gray_r, extent=[-1.5, 1.5, -1.1, 1.1], origin="lower"
)
plt.contour(X, Y, f([X, Y]), cmap=plt.cm.gnuplot)
# Plot the gradient

dX, dY = g_prime([0.1 * X[::5, ::5], Y[::5, ::5]])
# Adjust for our preconditioning
dX *= 0.1
plt.quiver(X[::5, ::5], Y[::5, ::5], dX, dY, color=".5")
# Plot our solution

plt.plot(x_min[0], x_min[1], "r+", markersize=15)
plt.show()

•

13.4.6 Optimization with constraints
An example showing how to do optimization with general constraints using SLSQP and cobyla.
import numpy as np
import scipy as sp
x, y = np.mgrid[-2.03:4.2:0.04, -1.6:3.2:0.04]
x = x.T
y = y.T

plt.clf()
plt.axes([0, 0, 1, 1])
contours = plt.contour(
np.sqrt((x - 3) ** 2 + (y - 2) ** 2),
extent=[-2.03, 4.2, -1.6, 3.2],
cmap=plt.cm.gnuplot,
)
plt.clabel(contours, inline=1, fmt="%1.1f ", fontsize=14)
plt.plot([-1.5, 0, 1.5, 0, -1.5], [0, 1.5, 0, -1.5, 0], "k", linewidth=2)
plt.fill_between([-1.5, 0, 1.5], [0, -1.5, 0], [0, 1.5, 0], color=".8")
plt.axvline(0, color="k")
plt.axhline(0, color="k")
plt.text(-0.9, 2.8, "$x_2$", size=20)

plt.text(3.6, -0.6, "$x_1$", size=20)
plt.axis("tight")
plt.axis("off")
# And now plot the optimization path

accumulator = []
def f(x):
# Store the list of function calls
accumulator.append(x)
return np.sqrt((x[0] - 3) ** 2 + (x[1] - 2) ** 2)


def constraint(x):
return np.atleast_1d(1.5 - np.sum(np.abs(x)))
sp.optimize.minimize(
f, np.array([0, 0]), method="SLSQP", constraints={"fun": constraint, "type": "ineq
˓→"}
accumulated = np.array(accumulator)
plt.plot(accumulated[:, 0], accumulated[:, 1])
plt.show()
13.4.7 Brent’s method
Illustration of 1D optimization: Brent’s method

Converged at 6
Converged at 23
import numpy as np
import scipy as sp
x_0 = np.exp(-1)
def f(x):
return (x - x_0) ** 2 + epsilon * np.exp(-5 * (x - 0.5 - x_0) ** 2)
for epsilon in (0, 1):

plt.axes([0, 0, 1, 1])

# A convex function
plt.plot(x, f(x), linewidth=2)
# Apply brent method. To have access to the iteration, do this in an

# artificial way: allow the algorithm to iter only once
all_x = []
all_y = []
for iter in range(30):
result = sp.optimize.minimize_scalar(
f,
bracket=(-5, 2.9, 4.5),
method="Brent",
options={"maxiter": iter},
tol=np.finfo(1.0).eps,
)
if result.success:
print("Converged at ", iter)
break
this_x = result.x
all_x.append(this_x)
all_y.append(f(this_x))
if iter < 6:
plt.text(
this_x - 0.05 * np.sign(this_x) - 0.05,
f(this_x) + 1.2 * (0.3 - iter % 2),
iter + 1,
size=12,
)
plt.plot(all_x[:10], all_y[:10], "k+", markersize=12, markeredgewidth=2)
plt.plot(all_x[-1], all_y[-1], "rx", markersize=12)

plt.axis("off")
plt.ylim(ymin=-1, ymax=8)
plt.semilogy(np.abs(all_y - all_y[-1]), linewidth=2)
plt.ylabel("Error on f(x)")
plt.xlabel("Iteration")
plt.tight_layout()
plt.show()

13.4.8 Constraint optimization: visualizing the geometry
A small figure explaining optimization with constraints
import numpy as np
import scipy as sp
x, y = np.mgrid[-2.9:5.8:0.05, -2.5:5:0.05]
x = x.T
y = y.T
for i in (1, 2):

# Create 2 figure: only the second one will have the optimization
# path
plt.figure(i, figsize=(3, 2.5))
plt.clf()
plt.axes([0, 0, 1, 1])
np.sqrt((x - 3) ** 2 + (y - 2) ** 2),
extent=[-3, 6, -2.5, 5],
)
plt.clabel(contours, inline=1, fmt="%1.1f ", fontsize=14)
plt.plot(


[-1.5, -1.5, 1.5, 1.5, -1.5], [-1.5, 1.5, 1.5, -1.5, -1.5], "k", linewidth=2
)
plt.fill_between([-1.5, 1.5], [-1.5, -1.5], [1.5, 1.5], color=".8")
plt.axvline(0, color="k")
plt.axhline(0, color="k")
plt.text(-0.9, 4.4, "$x_2$", size=20)

plt.text(5.6, -0.6, "$x_1$", size=20)
plt.axis("equal")
plt.axis("off")
# And now plot the optimization path

accumulator = []
def f(x):
# Store the list of function calls
accumulator.append(x)
return np.sqrt((x[0] - 3) ** 2 + (x[1] - 2) ** 2)
# We don't use the gradient, as with the gradient, L-BFGS is too fast,
# and finds the optimum without showing us a pretty path
def f_prime(x):
r = np.sqrt((x[0] - 3) ** 2 + (x[0] - 2) ** 2)
return np.array(((x[0] - 3) / r, (x[0] - 2) / r))
f, np.array([0, 0]), method="L-BFGS-B", bounds=((-1.5, 1.5), (-1.5, 1.5))
)
accumulated = np.array(accumulator)
plt.plot(accumulated[:, 0], accumulated[:, 1])
plt.show()
13.4.9 Plotting the comparison of optimizers
Plots the results from the comparison of optimizers.

import pickle
import sys
import numpy as np
results = pickle.load(
open(f"helper/compare_optimizers_py{ sys.version_info[0]} .pkl", "rb")
)
n_methods = len(list(results.values())[0]["Rosenbrock "])
n_dims = len(results)
symbols = "o>*Ds"
plt.figure(1, figsize=(10, 4))

plt.clf()
colors = plt.cm.nipy_spectral(np.linspace(0, 1, n_dims))[:, :3]
method_names = list(list(results.values())[0]["Rosenbrock "].keys())

method_names.sort(key=lambda x: x[::-1], reverse=True)
for n_dim_index, ((n_dim, n_dim_bench), color) in enumerate(

zip(sorted(results.items()), colors)
):
for (cost_name, cost_bench), symbol in zip(sorted(n_dim_bench.items()), symbols):
for (
method_index,
method_name,
) in enumerate(method_names):
this_bench = cost_bench[method_name]
bench = np.mean(this_bench)
plt.semilogy(
[
method_index + 0.1 * n_dim_index,
],
[
bench,
],
marker=symbol,
color=color,


)
# Create a legend for the problem type

for cost_name, symbol in zip(sorted(n_dim_bench.keys()), symbols):
plt.semilogy(
[
-10,
],
[
0,
],
symbol,
color=".5",
label=cost_name,
)
plt.xticks(np.arange(n_methods), method_names, size=11)

plt.xlim(-0.2, n_methods - 0.5)
plt.legend(loc="best", numpoints=1, handletextpad=0, prop={"size": 12}, frameon=False)
plt.ylabel("# function calls (a.u.)")
# Create a second legend for the problem dimensionality

plt.twinx()
for n_dim, color in zip(sorted(results.keys()), colors):

plt.plot(
[
-10,
],
[
0,
],
"o",
color=color,
label="# dim: %i " % n_dim,
)
plt.legend(
loc=(0.47, 0.07),
numpoints=1,
handletextpad=0,
prop={"size": 12},
frameon=False,
ncol=2,
)
plt.xlim(-0.2, n_methods - 0.5)
plt.xticks(np.arange(n_methods), method_names)
plt.yticks(())
plt.tight_layout()
plt.show()

13.4.10 Alternating optimization
The challenge here is that Hessian of the problem is a very ill-conditioned matrix. This can easily be
seen, as the Hessian of the first term in simply 2 * K.T @ K. Thus the conditioning of the problem can
be judged from looking at the conditioning of K.
import time
import numpy as np
import scipy as sp
K = rng.normal(size=(100, 100))
def f(x):
return np.sum((K @ (x - 1)) ** 2) + np.sum(x**2) ** 2
def f_prime(x):
return 2 * K.T @ K @ (x - 1) + 4 * np.sum(x**2) * x
def hessian(x):
H = 2 * K.T @ K + 4 * 2 * x * x[:, np.newaxis]
return H + 4 * np.eye(H.shape[0]) * np.sum(x**2)
Some pretty plotting

plt.figure(1)
plt.clf()
Z = X, Y = np.mgrid[-1.5:1.5:100j, -1.1:1.1:100j]
# Complete in the additional dimensions with zeros
Z = np.reshape(Z, (2, -1)).copy()
Z.resize((100, Z.shape[-1]))
Z = np.apply_along_axis(f, 0, Z)
Z = np.reshape(Z, X.shape)
plt.imshow(Z.T, cmap=plt.cm.gray_r, extent=[-1.5, 1.5, -1.1, 1.1], origin="lower")
plt.contour(X, Y, Z, cmap=plt.cm.gnuplot)
# A reference but slow solution:

t0 = time.time()
x_ref = sp.optimize.minimize(f, K[0], method="Powell").x
print(f" Powell: time { time.time() - t0: .2f} s")
f_ref = f(x_ref)
# Compare different approaches

t0 = time.time()
x_bfgs = sp.optimize.minimize(f, K[0], method="BFGS").x
print(
f" BFGS: time { time.time() - t0: .2f} s, x error { np.sqrt(np.sum((x_bfgs -␣
˓→x_ref) ** 2)): .2f} , f error { f(x_bfgs) - f_ref: .2f} "
t0 = time.time()
x_l_bfgs = sp.optimize.minimize(f, K[0], method="L-BFGS-B").x


print(
f" L-BFGS: time { time.time() - t0: .2f} s, x error { np.sqrt(np.sum((x_l_bfgs -
˓→ x_ref) ** 2)): .2f} , f error { f(x_l_bfgs) - f_ref: .2f} "
t0 = time.time()
x_bfgs = sp.optimize.minimize(f, K[0], jac=f_prime, method="BFGS").x
print(
f" BFGS w f': time { time.time() - t0: .2f} s, x error { np.sqrt(np.sum((x_bfgs -␣
˓→x_ref) ** 2)): .2f} , f error { f(x_bfgs) - f_ref: .2f} "
t0 = time.time()
x_l_bfgs = sp.optimize.minimize(f, K[0], jac=f_prime, method="L-BFGS-B").x
print(
f"L-BFGS w f': time { time.time() - t0: .2f} s, x error { np.sqrt(np.sum((x_l_bfgs -
˓→ x_ref) ** 2)): .2f} , f error { f(x_l_bfgs) - f_ref: .2f} "
t0 = time.time()
x_newton = sp.optimize.minimize(
f, K[0], jac=f_prime, hess=hessian, method="Newton-CG"
).x
print(
f" Newton: time { time.time() - t0: .2f} s, x error { np.sqrt(np.sum((x_newton -
˓→ x_ref) ** 2)): .2f} , f error { f(x_newton) - f_ref: .2f} "
plt.show()

Powell: time 0.20s

BFGS: time 0.87s, x error 0.02, f error -0.03
L-BFGS: time 0.07s, x error 0.02, f error -0.03
BFGS w f': time 0.06s, x error 0.02, f error -0.03
L-BFGS w f': time 0.00s, x error 0.02, f error -0.03
Newton: time 0.00s, x error 0.02, f error -0.03
13.4.11 Gradient descent
An example demoing gradient descent by creating figures that trace the evolution of the optimizer.
import numpy as np
import scipy as sp
import sys, os
sys.path.append(os.path.abspath("helper"))
from cost_functions import (
mk_quad,
mk_gauss,
rosenbrock,
rosenbrock_prime,
rosenbrock_hessian,


LoggingFunction,
CountingFunction,
)
x_min, x_max = -1, 2

y_min, y_max = 2.25 / 3 * x_min - 0.2, 2.25 / 3 * x_max - 0.2
A formatter to print values on contours
def super_fmt(value):
if value > 1:
if np.abs(int(value) - value) < 0.1:
out = "$10^{%.1i }$" % value
else:
out = "$10^{%.1f }$" % value
else:
value = np.exp(value - 0.01)
if value > 0.1:
out = f"{ value: 1.1f} "
elif value > 0.01:
out = f"{ value: .2f} "
else:
out = f"{ value: .2e} "
return out
A gradient descent algorithm do not use: its a toy, use scipy’s optimize.fmin_cg
def gradient_descent(x0, f, f_prime, hessian=None, adaptative=False):

x_i, y_i = x0
all_x_i = []
all_y_i = []
all_f_i = []

all_x_i.append(x_i)
all_y_i.append(y_i)
all_f_i.append(f([x_i, y_i]))
dx_i, dy_i = f_prime(np.asarray([x_i, y_i]))
if adaptative:
# Compute a step size using a line_search to satisfy the Wolf
# conditions
step = sp.optimize.line_search(
f,
f_prime,
np.r_[x_i, y_i],
-np.r_[dx_i, dy_i],
np.r_[dx_i, dy_i],
c2=0.05,
)
step = step[0]
if step is None:
step = 0
else:
step = 1
x_i += -step * dx_i
y_i += -step * dy_i


if np.abs(all_f_i[-1]) < 1e-16:
break
return all_x_i, all_y_i, all_f_i
def gradient_descent_adaptative(x0, f, f_prime, hessian=None):

return gradient_descent(x0, f, f_prime, adaptative=True)
def conjugate_gradient(x0, f, f_prime, hessian=None):

all_x_i = [x0[0]]
all_y_i = [x0[1]]
all_f_i = [f(x0)]
def store(X):
x, y = X
all_x_i.append(x)
all_y_i.append(y)
all_f_i.append(f(X))
f, x0, jac=f_prime, method="CG", callback=store, options={"gtol": 1e-12}
)
def newton_cg(x0, f, f_prime, hessian):

all_x_i = [x0[0]]
all_y_i = [x0[1]]
all_f_i = [f(x0)]
def store(X):
x, y = X
all_x_i.append(x)
all_y_i.append(y)
f,
x0,
method="Newton-CG",
jac=f_prime,
hess=hessian,
callback=store,
options={"xtol": 1e-12},
)
def bfgs(x0, f, f_prime, hessian=None):

all_x_i = [x0[0]]
all_y_i = [x0[1]]
all_f_i = [f(x0)]
def store(X):
x, y = X


all_x_i.append(x)
all_y_i.append(y)
f, x0, method="BFGS", jac=f_prime, callback=store, options={"gtol": 1e-12}
)
def powell(x0, f, f_prime, hessian=None):

all_x_i = [x0[0]]
all_y_i = [x0[1]]
all_f_i = [f(x0)]
def store(X):
x, y = X
all_x_i.append(x)
all_y_i.append(y)
f, x0, method="Powell", callback=store, options={"ftol": 1e-12}
)
def nelder_mead(x0, f, f_prime, hessian=None):

all_x_i = [x0[0]]
all_y_i = [x0[1]]
all_f_i = [f(x0)]
def store(X):
x, y = X
all_x_i.append(x)
all_y_i.append(y)
f, x0, method="Nelder-Mead", callback=store, options={"ftol": 1e-12}
)
Run different optimizers on these problems
levels = {}
for index, ((f, f_prime, hessian), optimizer) in enumerate(

(
(mk_quad(0.7), gradient_descent),
(mk_quad(0.7), gradient_descent_adaptative),
(mk_quad(0.02), gradient_descent),
(mk_quad(0.02), gradient_descent_adaptative),
(mk_gauss(0.02), gradient_descent_adaptative),
(
(rosenbrock, rosenbrock_prime, rosenbrock_hessian),


gradient_descent_adaptative,
),
(mk_gauss(0.02), conjugate_gradient),
((rosenbrock, rosenbrock_prime, rosenbrock_hessian), conjugate_gradient),
(mk_quad(0.02), newton_cg),
(mk_gauss(0.02), newton_cg),
((rosenbrock, rosenbrock_prime, rosenbrock_hessian), newton_cg),
(mk_quad(0.02), bfgs),
(mk_gauss(0.02), bfgs),
((rosenbrock, rosenbrock_prime, rosenbrock_hessian), bfgs),
(mk_quad(0.02), powell),
(mk_gauss(0.02), powell),
((rosenbrock, rosenbrock_prime, rosenbrock_hessian), powell),
(mk_gauss(0.02), nelder_mead),
((rosenbrock, rosenbrock_prime, rosenbrock_hessian), nelder_mead),
)
):
# Compute a gradient-descent
x_i, y_i = 1.6, 1.1
counting_f_prime = CountingFunction(f_prime)
counting_hessian = CountingFunction(hessian)
logging_f = LoggingFunction(f, counter=counting_f_prime.counter)
all_x_i, all_y_i, all_f_i = optimizer(
np.array([x_i, y_i]), logging_f, counting_f_prime, hessian=counting_hessian
)
# Plot the contour plot

if not max(all_y_i) < y_max:
x_min *= 1.2
x_max *= 1.2
y_min *= 1.2
y_max *= 1.2
x, y = np.mgrid[x_min:x_max:100j, y_min:y_max:100j]
x = x.T
y = y.T
plt.figure(index, figsize=(3, 2.5))

plt.clf()
plt.axes([0, 0, 1, 1])
X = np.concatenate((x[np.newaxis, ...], y[np.newaxis, ...]), axis=0)

z = np.apply_along_axis(f, 0, X)
log_z = np.log(z + 0.01)
plt.imshow(
log_z,
extent=[x_min, x_max, y_min, y_max],
cmap=plt.cm.gray_r,
origin="lower",
vmax=log_z.min() + 1.5 * log_z.ptp(),
)
log_z,
levels=levels.get(f, None),
extent=[x_min, x_max, y_min, y_max],
origin="lower",


)
levels[f] = contours.levels
plt.clabel(contours, inline=1, fmt=super_fmt, fontsize=14)
plt.plot(all_x_i, all_y_i, "b-", linewidth=2)

plt.plot(all_x_i, all_y_i, "k+")
plt.plot(logging_f.all_x_i, logging_f.all_y_i, "k.", markersize=2)
plt.plot([0], [0], "rx", markersize=12)
plt.xticks(())
plt.yticks(())
plt.xlim(x_min, x_max)
plt.ylim(y_min, y_max)
plt.draw()
plt.figure(index + 100, figsize=(4, 3))

plt.clf()
plt.semilogy(np.maximum(np.abs(all_f_i), 1e-30), linewidth=2, label="# iterations
˓→")
plt.ylabel("Error on f(x)")
plt.semilogy(
logging_f.counts,
np.maximum(np.abs(logging_f.all_f_i), 1e-30),
linewidth=2,
color="g",
label="# function calls",
)
plt.legend(
loc="upper right",
frameon=True,
prop={"size": 11},
borderaxespad=0,
handlelength=1.5,
handletextpad=0.5,
)
plt.tight_layout()
plt.draw()













/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/scipy/optimize/_
˓→linesearch.py:313: LineSearchWarning: The line search algorithm did not converge
alpha_star, phi_star, old_fval, derphi_star = scalar_search_wolfe2(

/home/runner/work/scientific-python-lectures/scientific-python-lectures/advanced/
˓→mathematical_optimization/examples/plot_gradient_descent.py:68: LineSearchWarning:␣
˓→The line search algorithm did not converge
step = sp.optimize.line_search(
˓→mathematical_optimization/examples/plot_gradient_descent.py:232: RuntimeWarning:␣
˓→More than 20 figures have been opened. Figures created through the pyplot interface␣
˓→(`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume␣
˓→too much memory. (To control this warning, see the rcParam `figure.max_open_
˓→warning`). Consider using `matplotlib.pyplot.close()`.
plt.figure(index, figsize=(3, 2.5))

˓→mathematical_optimization/examples/plot_gradient_descent.py:177: OptimizeWarning:␣
˓→Unknown solver options: ftol

An ill-conditioned
quadratic function:
On a exactly quadratic function,
BFGS is not as fast as Newton’s
method, but still very fast.
quadratic function:
Here BFGS does better than
Newton, as its empirical esti-
mate of the curvature is better
than that given by the Hessian.

quadratic function:

... return .5*(1 - x[0])**2 + (x[1] - x[0]**2)**2
˓→x[0]**2)))
>>> sp.optimize.minimize(f, [2, -1], method="BFGS", jac=jacobian)

success: True
status: 0
fun: 2.630637192365927e-16
x: [ 1.000e+00 1.000e+00]
nit: 8
jac: [ 6.709e-08 -3.222e-08]
hess_inv: [[ 9.999e-01 2.000e+00]
[ 2.000e+00 4.499e+00]]


nfev: 10
njev: 10
L-BFGS: Limited-memory BFGS Sits between BFGS and conjugate gradient: in very high dimensions
(> 250) the Hessian matrix is too costly to compute and invert. L-BFGS keeps a low-rank version. In
addition, box bounds are also supported by L-BFGS-B:

... return .5*(1 - x[0])**2 + (x[1] - x[0]**2)**2
˓→x[0]**2)))
>>> sp.optimize.minimize(f, [2, 2], method="L-BFGS-B", jac=jacobian)

message: CONVERGENCE: NORM_OF_PROJECTED_GRADIENT_<=_PGTOL
success: True
status: 0
fun: 1.4417677473...e-15
x: [ 1.000e+00 1.000e+00]
nit: 16
jac: [ 1.023e-07 -2.593e-08]
nfev: 17
njev: 17
hess_inv: <2x2 LbfgsInvHessProduct with dtype=float64>
13.4.12 Gradient-less methods
A shooting method: the Powell algorithm
Almost a gradient approach
An ill-conditioned
quadratic function:
Powell’s method isn’t too sensi-
tive to local ill-conditionning in
low dimensions

quadratic function:

Simplex method: the Nelder-Mead
The Nelder-Mead algorithms is a generalization of dichotomy approaches to high-dimensional spaces. The

algorithm works by refining a simplex, the generalization of intervals and triangles to high-dimensional
spaces, to bracket the minimum.
Strong points: it is robust to noise, as it does not rely on computing gradients. Thus it can work
on functions that are not locally smooth such as experimental data points, as long as they display a
large-scale bell-shape behavior. However it is slower than gradient-based methods on smooth, non-noisy
functions.
quadratic function:

quadratic function:
Using the Nelder-Mead solver in scipy.optimize.minimize():

... return .5*(1 - x[0])**2 + (x[1] - x[0]**2)**2
>>> sp.optimize.minimize(f, [2, -1], method="Nelder-Mead")
success: True
status: 0
fun: 1.11527915993744e-10
x: [ 1.000e+00 1.000e+00]
nit: 58
nfev: 111
final_simplex: (array([[ 1.000e+00, 1.000e+00],
[ 1.000e+00, 1.000e+00],
[ 1.000e+00, 1.000e+00]]), array([ 1.115e-10, 1.537e-10, 4.
˓→988e-10]))

13.4.13 Global optimizers
If your problem does not admit a unique local minimum (which can be hard to test unless the function
is convex), and you do not have prior information to initialize the optimization close to the solution, you
may need a global optimizer.
Brute force: a grid search
scipy.optimize.brute() evaluates the function on a given grid of parameters and returns the param-
eters corresponding to the minimum value. The parameters are specified with ranges given to numpy.
mgrid. By default, 20 steps are taken in each direction:

... return .5*(1 - x[0])**2 + (x[1] - x[0]**2)**2
>>> sp.optimize.brute(f, ((-1, 2), (-1, 2)))
array([1.0000..., 1.0000...])
13.5 Practical guide to optimization with SciPy
13.5.1 Choosing a method
All methods are exposed as the method argument of scipy.optimize.minimize().
Without knowledge of the gradient

• In general, prefer BFGS or L-BFGS, even if you have to approximate numerically
gradients. These are also the default if you omit the parameter method - depending
if the problem has constraints or bounds
• On well-conditioned problems, Powell and Nelder-Mead, both gradient-free
methods, work well in high dimension, but they collapse for ill-conditioned problems.
With knowledge of the gradient
• BFGS or L-BFGS.
• Computational overhead of BFGS is larger than that L-BFGS, itself larger than
that of conjugate gradient. On the other side, BFGS usually needs less function
evaluations than CG. Thus conjugate gradient method is better than BFGS at
optimizing computationally cheap functions.
With the Hessian
• If you can compute the Hessian, prefer the Newton method (Newton-CG or TCG).
13.5. Practical guide to optimization with SciPy 474

If you have noisy measurements

• Use Nelder-Mead or Powell.
13.5.2 Making your optimizer faster
• Choose the right method (see above), do compute analytically the gradient and Hessian, if you
can.
• Use preconditionning when possible.
• Choose your initialization points wisely. For instance, if you are running many similar optimiza-
tions, warm-restart one with the results of another.
• Relax the tolerance if you don’t need precision using the parameter tol.
13.5.3 Computing gradients
Computing gradients, and even more Hessians, is very tedious but worth the effort. Symbolic computa-
tion with Sympy may come in handy.
Warning: A very common source of optimization not converging well is human error in the com-
putation of the gradient. You can use scipy.optimize.check_grad() to check that your gradient
is correct. It returns the norm of the different between the gradient given, and a gradient computed
numerically:
>>> sp.optimize.check_grad(f, jacobian, [2, -1])
2.384185791015625e-07
See also scipy.optimize.approx_fprime() to find your errors.
13.5.4 Synthetic exercices
Exercice: A simple (?) quadratic function
Optimize the following function, using K[0] as a starting point:

K = rng.normal(size=(100, 100))
def f(x):
return np.sum((K @ (x - 1))**2) + np.sum(x**2)**2
Time your approach. Find the fastest approach. Why is BFGS not working well?
13.5. Practical guide to optimization with SciPy 475

Exercice: A locally flat minimum
Consider the function exp(-1/(.1*x**2 + y**2). This function admits a minimum in (0, 0). Starting
from an initialization at (1, 1), try to get within 1e-8 of this minimum point.
13.6 Special case: non-linear least-squares
13.6.1 Minimizing the norm of a vector function
Least square problems, minimizing the norm of a vector function, have a specific structure that can be
used in the Levenberg–Marquardt algorithm implemented in scipy.optimize.leastsq().
Lets try to minimize the norm of the following vectorial function:
>>> def f(x):

... return np.arctan(x) - np.arctan(np.linspace(0, 1, len(x)))
>>> x0 = np.zeros(10)
>>> sp.optimize.leastsq(f, x0)
(array([0. , 0.11111111, 0.22222222, 0.33333333, 0.44444444,
0.55555556, 0.66666667, 0.77777778, 0.88888889, 1. ]), 2)
This took 67 function evaluations (check it with ‘full_output=1’). What if we compute the norm
ourselves and use a good generic optimizer (BFGS):
13.6. Special case: non-linear least-squares 476

>>> def g(x):

... return np.sum(f(x)**2)
>>> result = sp.optimize.minimize(g, x0, method="BFGS")
>>> result.fun
2.6940...e-11
BFGS needs more function calls, and gives a less precise result.
Note: leastsq is interesting compared to BFGS only if the dimensionality of the output vector is large,
and larger than the number of parameters to optimize.
Warning: If the function is linear, this is a linear-algebra problem, and should be solved with
scipy.linalg.lstsq().
Least square problems occur often when fitting a non-linear to data. While it is possible to construct our
optimization problem ourselves, SciPy provides a helper function for this purpose: scipy.optimize.
curve_fit():
>>> def f(t, omega, phi):

... return np.cos(omega * t + phi)
>>> x = np.linspace(0, 3, 50)

>>> y = f(x, 1.5, 1) + .1*rng.normal(size=50)
>>> sp.optimize.curve_fit(f, x, y)
(array([1.4812..., 0.9999...]), array([[ 0.0003..., -0.0004...],
[-0.0004..., 0.0010...]]))
Exercise
Do the same with omega = 3. What is the difficulty?
13.6. Special case: non-linear least-squares 477

13.7 Optimization with constraints
13.7.1 Box bounds
Box bounds correspond to limiting each of the individual parameters of the optimization. Note that
some problems that are not originally written as box bounds can be rewritten as such via change of vari-
ables. Both scipy.optimize.minimize_scalar() and scipy.optimize.minimize() support bound
constraints with the parameter bounds:
>>> def f(x):

... return np.sqrt((x[0] - 3)**2 + (x[1] - 2)**2)
>>> sp.optimize.minimize(f, np.array([0, 0]), bounds=((-1.5, 1.5), (-1.5, 1.5)))
message: CONVERGENCE: NORM_OF_PROJECTED_GRADIENT_<=_PGTOL
success: True
status: 0
fun: 1.5811388300841898
x: [ 1.500e+00 1.500e+00]
nit: 2
jac: [-9.487e-01 -3.162e-01]
nfev: 9
njev: 3
hess_inv: <2x2 LbfgsInvHessProduct with dtype=float64>
13.7.2 General constraints
Equality and inequality constraints specified as functions: 𝑓 (𝑥) = 0 and 𝑔(𝑥) < 0.
• scipy.optimize.fmin_slsqp() Sequential least square programming: equality and inequality con-
straints:
>>> def f(x):

... return np.sqrt((x[0] - 3)**2 + (x[1] - 2)**2)
13.7. Optimization with constraints 478

>>> def constraint(x):

... return np.atleast_1d(1.5 - np.sum(np.abs(x)))
>>> x0 = np.array([0, 0])

>>> sp.optimize.minimize(f, x0, constraints={"fun": constraint, "type": "ineq"})
message: Optimization terminated successfully
success: True
status: 0
fun: 2.4748737350439685
x: [ 1.250e+00 2.500e-01]
nit: 5
jac: [-7.071e-01 -7.071e-01]
nfev: 15
njev: 5
Warning: The above problem is known as the Lasso problem in statistics, and there exist very
efficient solvers for it (for instance in scikit-learn). In general do not use generic solvers when specific
ones exist.
Lagrange multipliers
If you are ready to do a bit of math, many constrained optimization problems can be converted to
non-constrained optimization problems using a mathematical trick known as Lagrange multipliers.
13.9 Examples for the mathematical optimization chapter
See also:
Other Software
SciPy tries to include the best well-established, general-use, and permissively-licensed optimization al-
gorithms available. However, even better options for a given task may be available in other libraries;
please also see IPOPT and PyGMO.

CHAPTER 14
Interfacing with C
Author: Valentin Haenel

This chapter contains an introduction to the many different routes for making your native code (primarily
C/C++) available from Python, a process commonly referred to wrapping. The goal of this chapter is to
give you a flavour of what technologies exist and what their respective merits and shortcomings are, so
that you can select the appropriate one for your specific needs. In any case, once you do start wrapping,
you almost certainly will want to consult the respective documentation for your selected technique.
Chapters contents
• Introduction
• Python-C-Api
• Ctypes
• SWIG
• Cython
• Summary
• Further Reading and References
• Exercises
480
14.1 Introduction
This chapter covers the following techniques:

• Python-C-Api
• Ctypes
• SWIG (Simplified Wrapper and Interface Generator)
• Cython
These four techniques are perhaps the most well known ones, of which Cython is probably the most
advanced one and the one you should consider using first. The others are also important, if you want to
understand the wrapping problem from different angles. Having said that, there are other alternatives
out there, but having understood the basics of the ones above, you will be in a position to evaluate the
technique of your choice to see if it fits your needs.
The following criteria may be useful when evaluating a technology:
• Are additional libraries required?
• Is the code autogenerated?
• Does it need to be compiled?
• Is there good support for interacting with NumPy arrays?
• Does it support C++?
Before you set out, you should consider your use case. When interfacing with native code, there are
usually two use-cases that come up:
• Existing code in C/C++ that needs to be leveraged, either because it already exists, or because it
is faster.
• Python code too slow, push inner loops to native code
Each technology is demonstrated by wrapping the cos function from math.h. While this is a mostly a
trivial example, it should serve us well to demonstrate the basics of the wrapping solution. Since each
technique also includes some form of NumPy support, this is also demonstrated using an example where
the cosine is computed on some kind of array.
Last but not least, two small warnings:
• All of these techniques may crash (segmentation fault) the Python interpreter, which is (usually)
due to bugs in the C code.
• All the examples have been done on Linux, they should be possible on other operating systems.
• You will need a C compiler for most of the examples.
14.2 Python-C-Api
The Python-C-API is the backbone of the standard Python interpreter (a.k.a CPython). Using this API
it is possible to write Python extension module in C and C++. Obviously, these extension modules can,
by virtue of language compatibility, call any function written in C or C++.
When using the Python-C-API, one usually writes much boilerplate code, first to parse the arguments
that were given to a function, and later to construct the return type.
Advantages
• Requires no additional libraries
• Lots of low-level control
• Entirely usable from C++

Disadvantages
• May require a substantial amount of effort
• Much overhead in the code
• Must be compiled
• High maintenance cost
• No forward compatibility across Python versions as C-API changes
• Reference count bugs are easy to create and very hard to track down.
Note: The Python-C-Api example here serves mainly for didactic reasons. Many of the other techniques
actually depend on this, so it is good to have a high-level understanding of how it works. In 99% of the
use-cases you will be better off, using an alternative technique.
Note: Since reference counting bugs are easy to create and hard to track down, anyone really needing
to use the Python C-API should read the section about objects, types and reference counts from the
official python documentation. Additionally, there is a tool by the name of cpychecker which can help
discover common errors with reference counting.
14.2.1 Example
The following C-extension module, make the cos function from the standard math library available to
Python:
/* Example of wrapping cos function from math.h with the Python-C-API. */
# include <Python.h>
# include <math.h>
/* wrapped cosine function */

static PyObject* cos_func(PyObject* self, PyObject* args)
{
double value;
double answer;
/* parse the input, from python float to c double */

if (!PyArg_ParseTuple(args, "d", &value))
return NULL;
/* if the above function returns -1, an appropriate Python exception will
* have been set, and the function simply returns NULL
*/
/* call cos from libm */

answer = cos(value);
/* construct the output from cos, from c double to python float */

return Py_BuildValue("f", answer);
}
/* define functions in module */

static PyMethodDef CosMethods[] =
{
{"cos_func", cos_func, METH_VARARGS, "evaluate the cosine"},
14.2. Python-C-Api 482


{NULL, NULL, 0, NULL}
};
# if PY_MAJOR_VERSION >= 3
/* module initialization */
/* Python version 3*/
static struct PyModuleDef cModPyDem =
{
PyModuleDef_HEAD_INIT,
"cos_module", "Some documentation",
-1,
CosMethods
};
PyMODINIT_FUNC
PyInit_cos_module(void)
{
return PyModule_Create(&cModPyDem);
}
# else
/* Python version 2 */
PyMODINIT_FUNC
initcos_module(void)
{
(void) Py_InitModule("cos_module", CosMethods);
}
# endif
As you can see, there is much boilerplate, both to «massage» the arguments and return types into
place and for the module initialisation. Although some of this is amortised, as the extension grows, the
boilerplate required for each function(s) remains.
The standard python build system distutils supports compiling C-extensions from a setup.py, which
is rather convenient:
from distutils.core import setup, Extension
# define the extension module

cos_module = Extension("cos_module", sources=["cos_module.c"])
# run the setup

setup(ext_modules=[cos_module])
This can be compiled:
$ cd advanced/interfacing_with_c/python_c_api
$ ls
cos_module.c setup.py
$ python setup.py build_ext --inplace

running build_ext
building 'cos_module' extension


creating build
creating build/temp.linux-x86_64-2.7
gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-
˓→prototypes -fPIC -I/home/esc/anaconda/include/python2.7 -c cos_module.c -o build/
˓→temp.linux-x86_64-2.7/cos_module.o
gcc -pthread -shared build/temp.linux-x86_64-2.7/cos_module.o -L/home/esc/anaconda/

˓→lib -lpython2.7 -o /home/esc/git-working/scientific-python-lectures/advanced/
˓→interfacing_with_c/python_c_api/cos_module.so
$ ls
build/ cos_module.c cos_module.so setup.py
• build_ext is to build extension modules

• --inplace will output the compiled extension module into the current directory
The file cos_module.so contains the compiled extension, which we can now load in the IPython inter-
preter:
Note: In Python 3, the filename for compiled modules includes metadata on the Python interpreter
(see PEP 3149) and is thus longer. The import statement is not affected by this.
In [1]: import cos_module
In [2]: cos_module?
Type: module
String Form:<module 'cos_module' from 'cos_module.so'>
File: /home/esc/git-working/scientific-python-lectures/advanced/interfacing_
˓→with_c/python_c_api/cos_module.so
Docstring: <no docstring>
In [3]: dir(cos_module)
Out[3]: ['__doc__', '__file__', '__name__', '__package__', 'cos_func']
In [4]: cos_module.cos_func(1.0)
Out[4]: 0.5403023058681398
Out[5]: 1.0
Out[6]: -1.0
Now let’s see how robust this is:
In [7]: cos_module.cos_func('foo')
---------------------------------------------------------------------------
<ipython-input-10-11bee483665d> in <module>()
----> 1 cos_module.cos_func('foo')
TypeError: a float is required

14.2.2 NumPy Support
Analog to the Python-C-API, NumPy, which is itself implemented as a C-extension, comes with the
NumPy-C-API. This API can be used to create and manipulate NumPy arrays from C, when writing a
custom C-extension. See also: Advanced NumPy.
Note: If you do ever need to use the NumPy C-API refer to the documentation about Arrays and
Iterators.
The following example shows how to pass NumPy arrays as arguments to functions and how to iterate
over NumPy arrays using the (old) NumPy-C-API. It simply takes an array as argument applies the
cosine function from the math.h and returns a resulting new array.
/* Example of wrapping the cos function from math.h using the NumPy-C-API. */
# include <Python.h>
# include <numpy/arrayobject.h>
# include <math.h>
/* wrapped cosine function */

static PyObject* cos_func_np(PyObject* self, PyObject* args)
{
PyArrayObject *arrays[2]; /* holds input and output array */
PyObject *ret;
NpyIter *iter;
npy_uint32 op_flags[2];
npy_uint32 iterator_flags;
PyArray_Descr *op_dtypes[2];
NpyIter_IterNextFunc *iternext;
/* parse single NumPy array argument */

if (!PyArg_ParseTuple(args, "O!", &PyArray_Type, &arrays[0])) {
return NULL;
}
arrays[1] = NULL; /* The result will be allocated by the iterator */
/* Set up and create the iterator */

iterator_flags = (NPY_ITER_ZEROSIZE_OK |
/*
* Enable buffering in case the input is not behaved
* (native byte order or not aligned),
* disabling may speed up some cases when it is known to
* be unnecessary.
*/
NPY_ITER_BUFFERED |
/* Manually handle innermost iteration for speed: */
NPY_ITER_EXTERNAL_LOOP |
NPY_ITER_GROWINNER);
op_flags[0] = (NPY_ITER_READONLY |
/*
* Required that the arrays are well behaved, since the cos
* call below requires this.


*/
NPY_ITER_NBO |
NPY_ITER_ALIGNED);
/* Ask the iterator to allocate an array to write the output to */

op_flags[1] = NPY_ITER_WRITEONLY | NPY_ITER_ALLOCATE;
/*
* Ensure the iteration has the correct type, could be checked
* specifically here.
*/
op_dtypes[0] = PyArray_DescrFromType(NPY_DOUBLE);
op_dtypes[1] = op_dtypes[0];
/* Create the NumPy iterator object: */

iter = NpyIter_MultiNew(2, arrays, iterator_flags,
/* Use input order for output and iteration */
NPY_KEEPORDER,
/* Allow only byte-swapping of input */
NPY_EQUIV_CASTING, op_flags, op_dtypes);
Py_DECREF(op_dtypes[0]); /* The second one is identical. */
if (iter == NULL)
return NULL;
iternext = NpyIter_GetIterNext(iter, NULL);

if (iternext == NULL) {
NpyIter_Deallocate(iter);
return NULL;
}
/* Fetch the output array which was allocated by the iterator: */

ret = (PyObject *)NpyIter_GetOperandArray(iter)[1];
Py_INCREF(ret);
if (NpyIter_GetIterSize(iter) == 0) {
/*
* If there are no elements, the loop cannot be iterated.
* This check is necessary with NPY_ITER_ZEROSIZE_OK.
*/
return ret;
}
/* The location of the data pointer which the iterator may update */
char **dataptr = NpyIter_GetDataPtrArray(iter);
/* The location of the stride which the iterator may update */
npy_intp *strideptr = NpyIter_GetInnerStrideArray(iter);
/* The location of the inner loop size which the iterator may update */
npy_intp *innersizeptr = NpyIter_GetInnerLoopSizePtr(iter);
/* iterate over the arrays */

do {
npy_intp stride = strideptr[0];
npy_intp count = *innersizeptr;
/* out is always contiguous, so use double */


double *out = (double *)dataptr[1];
char *in = dataptr[0];
/* The output is allocated and guaranteed contiguous (out++ works): */

assert(strideptr[1] == sizeof(double));
/*
* For optimization it can make sense to add a check for
* stride == sizeof(double) to allow the compiler to optimize for that.
*/
while (count--) {
*out = cos(*(double *)in);
out++;
in += stride;
}
} while (iternext(iter));
/* Clean up and return the result */

return ret;
}
/* define functions in module */

static PyMethodDef CosMethods[] =
{
{"cos_func_np", cos_func_np, METH_VARARGS,
"evaluate the cosine on a NumPy array"},
{NULL, NULL, 0, NULL}
};
# if PY_MAJOR_VERSION >= 3
/* Python version 3*/
static struct PyModuleDef cModPyDem = {
PyModuleDef_HEAD_INIT,
"cos_module", "Some documentation",
-1,
CosMethods
};
PyMODINIT_FUNC PyInit_cos_module_np(void) {
PyObject *module;
module = PyModule_Create(&cModPyDem);
if(module==NULL) return NULL;
/* IMPORTANT: this must be called */
import_array();
if (PyErr_Occurred()) return NULL;
return module;
}
# else
/* Python version 2 */
PyMODINIT_FUNC initcos_module_np(void) {
PyObject *module;


module = Py_InitModule("cos_module_np", CosMethods);
if(module==NULL) return;
/* IMPORTANT: this must be called */
import_array();
return;
}
# endif
To compile this we can use distutils again. However we need to be sure to include the NumPy headers
by using numpy.get_include().

import numpy
# define the extension module

cos_module_np = Extension(
"cos_module_np", sources=["cos_module_np.c"], include_dirs=[numpy.get_include()]
)
# run the setup

setup(ext_modules=[cos_module_np])
To convince ourselves if this does actually works, we run the following test script:
import cos_module_np
import numpy as np
x = np.arange(0, 2 * np.pi, 0.1)

y = cos_module_np.cos_func_np(x)
plt.plot(x, y)
plt.show()
# Below are more specific tests for less common usage

# ---------------------------------------------------
# The function is OK with `x` not having any elements:

x_empty = np.array([], dtype=np.float64)
y_empty = cos_module_np.cos_func_np(x_empty)
assert np.array_equal(y_empty, np.array([], dtype=np.float64))
# The function can handle arbitrary dimensions and non-contiguous data.

# `x_2d` contains the same values, but has a different shape.
# Note: `x_2d.flags` shows it is not contiguous and `x2.ravel() == x`
x_2d = x.repeat(2)[::2].reshape(-1, 3)
y_2d = cos_module_np.cos_func_np(x_2d)
# When reshaped back, the same result is given:
assert np.array_equal(y_2d.ravel(), y)
# The function handles incorrect byte-order fine:

x_not_native_byteorder = x.astype(x.dtype.newbyteorder())
y_not_native_byteorder = cos_module_np.cos_func_np(x_not_native_byteorder)
assert np.array_equal(y_not_native_byteorder, y)


# The function fails if the data type is incorrect:
x_incorrect_dtype = x.astype(np.float32)
try:
cos_module_np.cos_func_np(x_incorrect_dtype)
assert 0, "This cannot be reached."
except TypeError:
# A TypeError will be raised, this can be changed by changing the
# casting rule.
pass
And this should result in the following figure:
14.3 Ctypes
Ctypes is a foreign function library for Python. It provides C compatible data types, and allows calling
functions in DLLs or shared libraries. It can be used to wrap these libraries in pure Python.
Advantages
• Part of the Python standard library
• Does not need to be compiled
• Wrapping code entirely in Python
Disadvantages
• Requires code to be wrapped to be available as a shared library (roughly speaking *.dll in Windows
*.so in Linux and *.dylib in Mac OSX.)
• No good support for C++
14.3.1 Example
As advertised, the wrapper code is in pure Python.
""" Example of wrapping cos function from math.h using ctypes. """
import ctypes
# find and load the library
# OSX or linux
from ctypes.util import find_library
14.3. Ctypes 489


libm = ctypes.cdll.LoadLibrary(find_library("m"))
# Windows
# from ctypes import windll
# libm = cdll.msvcrt
# set the argument type

libm.cos.argtypes = [ctypes.c_double]
# set the return type
libm.cos.restype = ctypes.c_double
def cos_func(arg):
"""Wrapper for cos from math.h"""
return libm.cos(arg)
• Finding and loading the library may vary depending on your operating system, check the docu-
mentation for details
• This may be somewhat deceptive, since the math library exists in compiled form on the system
already. If you were to wrap a in-house library, you would have to compile it first, which may or
may not require some additional effort.
We may now use this, as before:
In [9]: cos_module?
Type: module
String Form:<module 'cos_module' from 'cos_module.py'>
˓→with_c/ctypes/cos_module.py
Out[10]:
['__builtins__',
'__doc__',
'__file__',
'__name__',
'__package__',
'cos_func',
'ctypes',
'find_library',
'libm']
Out[11]: 0.5403023058681398
Out[12]: 1.0
Out[13]: -1.0
As with the previous example, this code is somewhat robust, although the error message is not quite as
helpful, since it does not tell us what the type should be.
14.3. Ctypes 490

---------------------------------------------------------------------------
ArgumentError Traceback (most recent call last)
/home/esc/git-working/scientific-python-lectures/advanced/interfacing_with_c/ctypes/
˓→cos_module.py in cos_func(arg)
12 def cos_func(arg):
13 ''' Wrapper for cos from math.h '''
---> 14 return libm.cos(arg)
ArgumentError: argument 1: <type 'exceptions.TypeError'>: wrong type
NumPy contains some support for interfacing with ctypes. In particular there is support for exporting
certain attributes of a NumPy array as ctypes data-types and there are functions to convert from C
arrays to NumPy arrays and back.
For more information, consult the corresponding section in the NumPy Cookbook and the API docu-
mentation for numpy.ndarray.ctypes and numpy.ctypeslib.
For the following example, let’s consider a C function in a library that takes an input and an output
array, computes the cosine of the input array and stores the result in the output array.
The library consists of the following header file (although this is not strictly needed for this example, we
list it for completeness):
void cos_doubles(double * in_array, double * out_array, int size);
The function implementation resides in the following C source file:
# include <math.h>
/* Compute the cosine of each element in in_array, storing the result in

* out_array. */
void cos_doubles(double * in_array, double * out_array, int size){
int i;
for(i=0;i<size;i++){
out_array[i] = cos(in_array[i]);
}
}
And since the library is pure C, we can’t use distutils to compile it, but must use a combination of
make and gcc:
m.PHONY : clean
libcos_doubles.so : cos_doubles.o
gcc -shared -Wl,-soname,libcos_doubles.so -o libcos_doubles.so cos_doubles.o
cos_doubles.o : cos_doubles.c
gcc -c -fPIC cos_doubles.c -o cos_doubles.o
clean :
-rm -vf libcos_doubles.so cos_doubles.o cos_doubles.pyc
We can then compile this (on Linux) into the shared library libcos_doubles.so:
14.3. Ctypes 491

$ ls
cos_doubles.c cos_doubles.h cos_doubles.py makefile test_cos_doubles.py
$ make
gcc -c -fPIC cos_doubles.c -o cos_doubles.o
gcc -shared -Wl,-soname,libcos_doubles.so -o libcos_doubles.so cos_doubles.o
$ ls
cos_doubles.c cos_doubles.o libcos_doubles.so* test_cos_doubles.py
cos_doubles.h cos_doubles.py makefile
Now we can proceed to wrap this library via ctypes with direct support for (certain kinds of) NumPy
arrays:
""" Example of wrapping a C library function that accepts a C double array as

input using the numpy.ctypeslib. """
import numpy as np
import numpy.ctypeslib as npct
from ctypes import c_int
# input type for the cos_doubles function

# must be a double array, with single dimension that is contiguous
array_1d_double = npct.ndpointer(dtype=np.double, ndim=1, flags="CONTIGUOUS")
# load the library, using NumPy mechanisms

libcd = npct.load_library("libcos_doubles", ".")
# setup the return types and argument types

libcd.cos_doubles.restype = None
libcd.cos_doubles.argtypes = [array_1d_double, array_1d_double, c_int]
def cos_doubles_func(in_array, out_array):

return libcd.cos_doubles(in_array, out_array, len(in_array))
• Note the inherent limitation of contiguous single dimensional NumPy arrays, since the C functions
requires this kind of buffer.
• Also note that the output array must be preallocated, for example with numpy.zeros() and the
function will write into it’s buffer.
• Although the original signature of the cos_doubles function is ARRAY, ARRAY, int the final
cos_doubles_func takes only two NumPy arrays as arguments.
And, as before, we convince ourselves that it worked:
import numpy as np
import cos_doubles

y = np.empty_like(x)
cos_doubles.cos_doubles_func(x, y)
plt.plot(x, y)
plt.show()
14.3. Ctypes 492

14.4 SWIG
SWIG, the Simplified Wrapper Interface Generator, is a software development tool that connects pro-
grams written in C and C++ with a variety of high-level programming languages, including Python.
The important thing with SWIG is, that it can autogenerate the wrapper code for you. While this is an
advantage in terms of development time, it can also be a burden. The generated file tend to be quite
large and may not be too human readable and the multiple levels of indirection which are a result of the
wrapping process, may be a bit tricky to understand.
Note: The autogenerated C code uses the Python-C-Api.
Advantages
• Can automatically wrap entire libraries given the headers
• Works nicely with C++
Disadvantages
• Autogenerates enormous files
• Hard to debug if something goes wrong
• Steep learning curve
14.4.1 Example
Let’s imagine that our cos function lives in a cos_module which has been written in c and consists of
the source file cos_module.c:
# include <math.h>
double cos_func(double arg){

return cos(arg);
}
and the header file cos_module.h:
double cos_func(double arg);
And our goal is to expose the cos_func to Python. To achieve this with SWIG, we must write an
interface file which contains the instructions for SWIG.
14.4. SWIG 493

/* Example of wrapping cos function from math.h using SWIG. */
%module cos_module
%{
/* the resulting C file should be built as a python extension */
# define SWIG_FILE_WITH_INIT
/* Includes the header in the wrapper code */
# include "cos_module.h"
%}
/* Parse the header file to generate wrappers */
%include "cos_module.h"
As you can see, not too much code is needed here. For this simple example it is enough to simply include
the header file in the interface file, to expose the function to Python. However, SWIG does allow for
more fine grained inclusion/exclusion of functions found in header files, check the documentation for
details.
Generating the compiled wrappers is a two stage process:
1. Run the swig executable on the interface file to generate the files cos_module_wrap.c, which
is the source file for the autogenerated Python C-extension and cos_module.py, which is the
autogenerated pure python module.
2. Compile the cos_module_wrap.c into the _cos_module.so. Luckily, distutils knows how to
handle SWIG interface files, so that our setup.py is simply:
setup(ext_modules=[Extension("_cos_module", sources=["cos_module.c", "cos_module.i

˓→"])])
$ cd advanced/interfacing_with_c/swig
$ ls
cos_module.c cos_module.h cos_module.i setup.py

running build_ext
building '_cos_module' extension
swigging cos_module.i to cos_module_wrap.c
swig -python -o cos_module_wrap.c cos_module.i
creating build

˓→prototypes -fPIC -I/home/esc/anaconda/include/python2.7 -c cos_module_wrap.c -o␣
˓→build/temp.linux-x86_64-2.7/cos_module_wrap.o
gcc -pthread -shared build/temp.linux-x86_64-2.7/cos_module.o build/temp.linux-x86_64-

˓→2.7/cos_module_wrap.o -L/home/esc/anaconda/lib -lpython2.7 -o /home/esc/git-working/
˓→scientific-python-lectures/advanced/interfacing_with_c/swig/_cos_module.so
$ ls
build/ cos_module.c cos_module.h cos_module.i cos_module.py _cos_module.so* cos_
˓→module_wrap.c setup.py
We can now load and execute the cos_module as we have done in the previous examples:
14.4. SWIG 494

In [16]: cos_module?
Type: module
String Form:<module 'cos_module' from 'cos_module.py'>
˓→with_c/swig/cos_module.py
Out[17]:
['__builtins__',
'__doc__',
'__file__',
'__name__',
'__package__',
'_cos_module',
'_newclass',
'_object',
'_swig_getattr',
'_swig_property',
'_swig_repr',
'_swig_setattr',
'_swig_setattr_nondynamic',
'cos_func']
Out[18]: 0.5403023058681398
Out[19]: 1.0
Out[20]: -1.0
Again we test for robustness, and we see that we get a better error message (although, strictly speaking
in Python there is no double type):
---------------------------------------------------------------------------
TypeError: in method 'cos_func', argument 1 of type 'double'
NumPy provides support for SWIG with the numpy.i file. This interface file defines various so-called
typemaps which support conversion between NumPy arrays and C-Arrays. In the following example we
will take a quick look at how such typemaps work in practice.
We have the same cos_doubles function as in the ctypes example:
14.4. SWIG 495

# include <math.h>

* out_array. */
int i;
}
}
This is wrapped as cos_doubles_func using the following SWIG interface file:
/* Example of wrapping a C function that takes a C double array as input using

* NumPy typemaps for SWIG. */
%module cos_doubles
%{
/* the resulting C file should be built as a python extension */
# define SWIG_FILE_WITH_INIT
/* Includes the header in the wrapper code */
# include "cos_doubles.h"
%}
/* include the NumPy typemaps */

%include "numpy.i"
/* need this for correct module initialization */
%init %{
import_array();
%}
/* typemaps for the two arrays, the second will be modified in-place */
%apply (double* IN_ARRAY1, int DIM1) {(double * in_array, int size_in)}
%apply (double* INPLACE_ARRAY1, int DIM1) {(double * out_array, int size_out)}
/* Wrapper for cos_doubles that massages the types */

%inline %{
/* takes as input two NumPy arrays */
void cos_doubles_func(double * in_array, int size_in, double * out_array, int␣
˓→size_out) {
/* calls the original function, providing only the size of the first */
cos_doubles(in_array, out_array, size_in);
}
%}
• To use the NumPy typemaps, we need include the numpy.i file.

• Observe the call to import_array() which we encountered already in the NumPy-C-API example.
• Since the type maps only support the signature ARRAY, SIZE we need to wrap the cos_doubles
as cos_doubles_func which takes two arrays including sizes as input.
• As opposed to the simple SWIG example, we don’t include the cos_doubles.h header, There
is nothing there that we wish to expose to Python since we expose the functionality through
cos_doubles_func.
And, as before we can use distutils to wrap this:
14.4. SWIG 496


import numpy
setup(
ext_modules=[
Extension(
"_cos_doubles",
sources=["cos_doubles.c", "cos_doubles.i"],
include_dirs=[numpy.get_include()],
)
]
)
As previously, we need to use include_dirs to specify the location.
$ ls
cos_doubles.c cos_doubles.h cos_doubles.i numpy.i setup.py test_cos_doubles.py
$ python setup.py build_ext -i
running build_ext
building '_cos_doubles' extension
swigging cos_doubles.i to cos_doubles_wrap.c
swig -python -o cos_doubles_wrap.c cos_doubles.i
cos_doubles.i:24: Warning(490): Fragment 'NumPy_Backward_Compatibility' not found.
creating build
˓→prototypes -fPIC -I/home/esc/anaconda/lib/python2.7/site-packages/numpy/core/
˓→include -I/home/esc/anaconda/include/python2.7 -c cos_doubles.c -o build/temp.linux-
˓→x86_64-2.7/cos_doubles.o

˓→include -I/home/esc/anaconda/include/python2.7 -c cos_doubles_wrap.c -o build/temp.
˓→linux-x86_64-2.7/cos_doubles_wrap.o
In file included from /home/esc/anaconda/lib/python2.7/site-packages/numpy/core/

˓→include/numpy/ndarraytypes.h:1722,
from /home/esc/anaconda/lib/python2.7/site-packages/numpy/core/
˓→include/numpy/ndarrayobject.h:17,
˓→include/numpy/arrayobject.h:15,
from cos_doubles_wrap.c:2706:
/home/esc/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_
˓→deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by
˓→#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
gcc -pthread -shared build/temp.linux-x86_64-2.7/cos_doubles.o build/temp.linux-x86_

˓→64-2.7/cos_doubles_wrap.o -L/home/esc/anaconda/lib -lpython2.7 -o /home/esc/git-
˓→working/scientific-python-lectures/advanced/interfacing_with_c/swig_numpy/_cos_
˓→doubles.so
$ ls
build/ cos_doubles.h cos_doubles.py cos_doubles_wrap.c setup.py
cos_doubles.c cos_doubles.i _cos_doubles.so* numpy.i test_cos_doubles.
˓→py
import numpy as np
14.4. SWIG 497


import cos_doubles

plt.plot(x, y)
plt.show()
14.5 Cython
Cython is both a Python-like language for writing C-extensions and an advanced compiler for this
language. The Cython language is a superset of Python, which comes with additional constructs that
allow you call C functions and annotate variables and class attributes with c types. In this sense one
could also call it a Python with types.
In addition to the basic use case of wrapping native code, Cython supports an additional use-case,
namely interactive optimization. Basically, one starts out with a pure-Python script and incrementally
adds Cython types to the bottleneck code to optimize only those code paths that really matter.
In this sense it is quite similar to SWIG, since the code can be autogenerated but in a sense it also quite
similar to ctypes since the wrapping code can (almost) be written in Python.
While others solutions that autogenerate code can be quite difficult to debug (for example SWIG) Cython
comes with an extension to the GNU debugger that helps debug Python, Cython and C code.
Note: The autogenerated C code uses the Python-C-Api.
Advantages
• Python like language for writing C-extensions
• Autogenerated code
• Supports incremental optimization
• Includes a GNU debugger extension
• Support for C++ (Since version 0.13)
Disadvantages
• Must be compiled
• Requires an additional library ( but only at build time, at this problem can be overcome by shipping
the generated C files)
14.5. Cython 498

14.5.1 Example
The main Cython code for our cos_module is contained in the file cos_module.pyx:
""" Example of wrapping cos function from math.h using Cython. """
cdef extern from "math.h":

double cos(double arg)
def cos_func(arg):
return cos(arg)
Note the additional keywords such as cdef and extern. Also the cos_func is then pure Python.
Again we can use the standard distutils module, but this time we need some additional pieces from
the Cython.Distutils:
from Cython.Distutils import build_ext
setup(
cmdclass={"build_ext": build_ext},
ext_modules=[Extension("cos_module", ["cos_module.pyx"])],
)
Compiling this:
$ cd advanced/interfacing_with_c/cython
$ ls
cos_module.pyx setup.py
running build_ext
cythoning cos_module.pyx to cos_module.c
building 'cos_module' extension
creating build
gcc -pthread -shared build/temp.linux-x86_64-2.7/cos_module.o -L/home/esc/anaconda/

˓→lib -lpython2.7 -o /home/esc/git-working/scientific-python-lectures/advanced/
˓→interfacing_with_c/cython/cos_module.so
$ ls
build/ cos_module.c cos_module.pyx cos_module.so* setup.py
And running it:

In [23]: cos_module?
Type: module
String Form:<module 'cos_module' from 'cos_module.so'>
˓→with_c/cython/cos_module.so
Out[24]:
['__builtins__',
14.5. Cython 499


'__doc__',
'__file__',
'__name__',
'__package__',
'__test__',
'cos_func']
Out[25]: 0.5403023058681398
Out[26]: 1.0
Out[27]: -1.0
And, testing a little for robustness, we can see that we get good error messages:
---------------------------------------------------------------------------
/home/esc/git-working/scientific-python-lectures/advanced/interfacing_with_c/cython/
˓→cos_module.so in cos_module.cos_func (cos_module.c:506)()
TypeError: a float is required
Additionally, it is worth noting that Cython ships with complete declarations for the C math library,
which simplifies the code above to become:
""" Simpler example of wrapping cos function from math.h using Cython. """
from libc.math cimport cos
def cos_func(arg):
return cos(arg)
In this case the cimport statement is used to import the cos function.
Cython has support for NumPy via the numpy.pyx file which allows you to add the NumPy array type
to your Cython code. I.e. like specifying that variable i is of type int, you can specify that variable a
is of type numpy.ndarray with a given dtype. Also, certain optimizations such as bounds checking are
supported. Look at the corresponding section in the Cython documentation. In case you want to pass
NumPy arrays as C arrays to your Cython wrapped C functions, there is a section about this in the
Cython documentation.
In the following example, we will show how to wrap the familiar cos_doubles function using Cython.
# include <math.h>

* out_array. */
14.5. Cython 500


int i;
}
}
This is wrapped as cos_doubles_func using the following Cython code:

""" Example of wrapping a C function that takes C double arrays as input using
the NumPy declarations from Cython """
# cimport the Cython declarations for NumPy

cimport numpy as np
# if you want to use the NumPy-C-API from Cython

# (not strictly necessary for this example, but good practice)
np.import_array()
# cdefine the signature of our c function

cdef extern from "cos_doubles.h":
void cos_doubles (double * in_array, double * out_array, int size)
# create the wrapper code, with NumPy type annotations

def cos_doubles_func(np.ndarray[double, ndim=1, mode="c"] in_array not None,
np.ndarray[double, ndim=1, mode="c"] out_array not None):
cos_doubles(<double*> np.PyArray_DATA(in_array),
<double*> np.PyArray_DATA(out_array),
in_array.shape[0])
And can be compiled using distutils:

import numpy
from Cython.Distutils import build_ext
setup(
cmdclass={"build_ext": build_ext},
ext_modules=[
Extension(
"cos_doubles",
sources=["_cos_doubles.pyx", "cos_doubles.c"],
include_dirs=[numpy.get_include()],
)
],
)
• As with the previous compiled NumPy examples, we need the include_dirs option.
$ ls
cos_doubles.c cos_doubles.h _cos_doubles.pyx setup.py test_cos_doubles.py
$ python setup.py build_ext -i
running build_ext
cythoning _cos_doubles.pyx to _cos_doubles.c
building 'cos_doubles' extension
creating build
14.5. Cython 501


˓→include -I/home/esc/anaconda/include/python2.7 -c _cos_doubles.c -o build/temp.
˓→linux-x86_64-2.7/_cos_doubles.o
In file included from /home/esc/anaconda/lib/python2.7/site-packages/numpy/core/

˓→include/numpy/ndarraytypes.h:1722,
˓→include/numpy/ndarrayobject.h:17,
˓→include/numpy/arrayobject.h:15,
from _cos_doubles.c:253:
/home/esc/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_
˓→deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by
˓→#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
/home/esc/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.
˓→h:236: warning: ‘_import_umath’ defined but not used

˓→include -I/home/esc/anaconda/include/python2.7 -c cos_doubles.c -o build/temp.linux-
˓→x86_64-2.7/cos_doubles.o
gcc -pthread -shared build/temp.linux-x86_64-2.7/_cos_doubles.o build/temp.linux-x86_

˓→64-2.7/cos_doubles.o -L/home/esc/anaconda/lib -lpython2.7 -o /home/esc/git-working/
˓→scientific-python-lectures/advanced/interfacing_with_c/cython_numpy/cos_doubles.so
$ ls
build/ _cos_doubles.c cos_doubles.c cos_doubles.h _cos_doubles.pyx cos_doubles.
˓→so* setup.py test_cos_doubles.py
import numpy as np
import cos_doubles

plt.plot(x, y)
plt.show()
14.5. Cython 502

14.6 Summary
In this section four different techniques for interfacing with native code have been presented. The table
below roughly summarizes some of the aspects of the techniques.
x Part of CPython Compiled Autogenerated NumPy Support

Python-C-API True True False True
Ctypes True False False True
Swig False True True True
Cython False True True True
Of all three presented techniques, Cython is the most modern and advanced. In particular, the ability
to optimize code incrementally by adding types to your Python code is unique.
14.7 Further Reading and References
• Gaël Varoquaux’s blog post about avoiding data copies provides some insight on how to handle
memory management cleverly. If you ever run into issues with large datasets, this is a reference to
come back to for some inspiration.
14.8 Exercises
Since this is a brand new section, the exercises are considered more as pointers as to what to look at
next, so pick the ones that you find more interesting. If you have good ideas for exercises, please let us
know!
1. Download the source code for each example and compile and run them on your machine.
2. Make trivial changes to each example and convince yourself that this works. ( E.g. change cos for
sin.)
3. Most of the examples, especially the ones involving NumPy may still be fragile and respond badly
to input errors. Look for ways to crash the examples, figure what the problem is and devise a
potential solution. Here are some ideas:
1. Numerical overflow.
2. Input and output arrays that have different lengths.
3. Multidimensional array.
4. Empty array
5. Arrays with non-double types
4. Use the %timeit IPython magic to measure the execution time of the various solutions
14.6. Summary 503

14.8.1 Python-C-API
1. Modify the NumPy example such that the function takes two input arguments, where the second
is the preallocated output array, making it similar to the other NumPy examples.
2. Modify the example such that the function only takes a single input array and modifies this in
place.
3. Try to fix the example to use the new NumPy iterator protocol. If you manage to obtain a working
solution, please submit a pull-request on github.
4. You may have noticed, that the NumPy-C-API example is the only NumPy example that does not
wrap cos_doubles but instead applies the cos function directly to the elements of the NumPy
array. Does this have any advantages over the other techniques.
5. Can you wrap cos_doubles using only the NumPy-C-API. You may need to ensure that the arrays
have the correct type, are one dimensional and contiguous in memory.
14.8.2 Ctypes
1. Modify the NumPy example such that cos_doubles_func handles the preallocation for you, thus
making it more like the NumPy-C-API example.
14.8.3 SWIG
1. Look at the code that SWIG autogenerates, how much of it do you understand?
3. Modify the cos_doubles C function so that it returns an allocated array. Can you wrap this using
SWIG typemaps? If not, why not? Is there a workaround for this specific situation? (Hint: you
know the size of the output array, so it may be possible to construct a NumPy array from the
returned double *.)
14.8.4 Cython
1. Look at the code that Cython autogenerates. Take a closer look at some of the comments that
Cython inserts. What do you see?
2. Look at the section Working with NumPy from the Cython documentation to learn how to incre-
mentally optimize a pure python script that uses NumPy.
14.8. Exercises 504

Part III
Packages and applications
505
This part of the Scientific Python Lectures is dedicated to various scientific packages useful for extended
needs.
506
CHAPTER 15
Statistics in Python
Requirements
• Standard scientific Python environment (NumPy, SciPy, matplotlib)

• Pandas
• Statsmodels
• Seaborn
To install Python and these dependencies, we recommend that you download Anaconda Python or,
preferably, use the package manager if you are under Ubuntu or other linux.
See also:
• Bayesian statistics in Python: This chapter does not cover tools for Bayesian statistics. Of
particular interest for Bayesian modelling is PyMC, which implements a probabilistic programming
language in Python.
• Read a statistics book: The Think stats book is available as free PDF or in print and is a great
introduction to statistics.
Tip: Why Python for statistics?
507
R is a language dedicated to statistics. Python is a general-purpose language with statistics modules. R

has more statistical analysis features than Python, and specialized syntaxes. However, when it comes to
building complex analysis pipelines that mix statistics with e.g. image analysis, text mining, or control
of a physical experiment, the richness of Python is an invaluable asset.
Contents
• Data representation and interaction

– Data as a table
– The pandas data-frame
• Hypothesis testing: comparing two groups
– Student’s t-test: the simplest statistical test
– Paired tests: repeated measurements on the same individuals
• Linear models, multiple factors, and analysis of variance
– “formulas” to specify statistical models in Python
– Multiple Regression: including multiple factors
– Post-hoc hypothesis testing: analysis of variance (ANOVA)
• More visualization: seaborn for statistical exploration
– Pairplot: scatter matrices
– lmplot: plotting a univariate regression
• Testing for interactions
• Full code for the figures
• Solutions to this chapter’s exercises
Tip: In this document, the Python inputs are represented with the sign “>>>”.
Disclaimer: Gender questions

Some of the examples of this tutorial are chosen around gender questions. The reason is that on such
questions controlling the truth of a claim actually matters to many people.
15.1 Data representation and interaction
15.1.1 Data as a table
The setting that we consider for statistical analysis is that of multiple observations or samples described
by a set of different attributes or features. The data can than be seen as a 2D table, or matrix, with
columns giving the different attributes of the data, and rows the observations. For instance, the data
contained in examples/brain_size.csv:
15.1. Data representation and interaction 508

"";"Gender";"FSIQ";"VIQ";"PIQ";"Weight";"Height";"MRI_Count"
"1";"Female";133;132;124;"118";"64.5";816932
"2";"Male";140;150;124;".";"72.5";1001121
"3";"Male";139;123;150;"143";"73.3";1038437
"4";"Male";133;129;128;"172";"68.8";965353
"5";"Female";137;132;134;"147";"65.0";951545
15.1.2 The pandas data-frame
Tip: We will store and manipulate this data in a pandas.DataFrame, from the pandas module. It is
the Python equivalent of the spreadsheet table. It is different from a 2D numpy array as it has named
columns, can contain a mixture of different data types by column, and has elaborate selection and pivotal
mechanisms.
Creating dataframes: reading data files or converting arrays
Separator
It is a CSV file, but the separator is “;”
Reading from a CSV file: Using the above CSV file that gives observations of brain size and weight
and IQ (Willerman et al. 1991), the data are a mixture of numerical and categorical values:
>>> import pandas

>>> data = pandas.read_csv('examples/brain_size.csv', sep=';', na_values=".")
>>> data
Unnamed: 0 Gender FSIQ VIQ PIQ Weight Height MRI_Count
0 1 Female 133 132 124 118.0 64.5 816932
1 2 Male 140 150 124 NaN 72.5 1001121
2 3 Male 139 123 150 143.0 73.3 1038437
3 4 Male 133 129 128 172.0 68.8 965353
4 5 Female 137 132 134 147.0 65.0 951545
...
Warning: Missing values

The weight of the second individual is missing in the CSV file. If we don’t specify the missing value
(NA = not available) marker, we will not be able to do statistical analysis.
Creating from arrays: A pandas.DataFrame can also be seen as a dictionary of 1D ‘series’, eg arrays
or lists. If we have 3 numpy arrays:

>>> t = np.linspace(-6, 6, 20)
>>> sin_t = np.sin(t)
>>> cos_t = np.cos(t)

We can expose them as a pandas.DataFrame:
>>> pandas.DataFrame({'t': t, 'sin': sin_t, 'cos': cos_t})

t sin cos
0 -6.000000 0.279415 0.960170
1 -5.368421 0.792419 0.609977
2 -4.736842 0.999701 0.024451
3 -4.105263 0.821291 -0.570509
4 -3.473684 0.326021 -0.945363
5 -2.842105 -0.295030 -0.955488
6 -2.210526 -0.802257 -0.596979
7 -1.578947 -0.999967 -0.008151
8 -0.947368 -0.811882 0.583822
...
Other inputs: pandas can input data from SQL, excel files, or other formats. See the pandas docu-
mentation.
Manipulating data
data is a pandas.DataFrame, that resembles R’s dataframe:
>>> data.shape # 40 rows and 8 columns

(40, 8)
>>> data.columns # It has columns

Index(['Unnamed: 0', 'Gender', 'FSIQ', 'VIQ', 'PIQ', 'Weight', 'Height',
'MRI_Count'],
dtype='object')
>>> print(data['Gender']) # Columns can be addressed by name

0 Female
1 Male
2 Male
3 Male
4 Female
...
>>> # Simpler selector

>>> data[data['Gender'] == 'Female']['VIQ'].mean()
109.45
Note: For a quick view on a large dataframe, use its describe method: pandas.DataFrame.describe().

groupby: splitting a dataframe on values of categorical variables:
>>> groupby_gender = data.groupby('Gender')

>>> for gender, value in groupby_gender['VIQ']:
... print((gender, value.mean()))
('Female', 109.45)
('Male', 115.25)
groupby_gender is a powerful object that exposes many operations on the resulting group of dataframes:
>>> groupby_gender.mean()
Unnamed: 0 FSIQ VIQ PIQ Weight Height MRI_Count
Gender
Female 19.65 111.9 109.45 110.45 137.200000 65.765000 862654.6
Male 21.35 115.0 115.25 111.60 166.444444 71.431579 954855.4
Tip: Use tab-completion on groupby_gender to find more. Other common grouping functions are
median, count (useful for checking to see the amount of missing values in different subsets) or sum.
Groupby evaluation is lazy, no work is done until an aggregation function is applied.
Exercise
• What is the mean value for VIQ for the full population?
• How many males/females were included in this study?
Hint use ‘tab completion’ to find out the methods that can be called, instead of ‘mean’ in the
above example.
• What is the average value of MRI counts expressed in log units, for males and females?
Note: groupby_gender.boxplot is used for the plots above (see this example).

Plotting data
Pandas comes with some plotting tools (pandas.plotting, using matplotlib behind the scene) to display
statistics of the data in dataframes:
Scatter matrices:
>>> from pandas import plotting

>>> plotting.scatter_matrix(data[['Weight', 'Height', 'MRI_Count']])
array([[<Axes: xlabel='Weight', ylabel='Weight'>,
<Axes: xlabel='Height', ylabel='Weight'>,
<Axes: xlabel='MRI_Count', ylabel='Weight'>],
[<Axes: xlabel='Weight', ylabel='Height'>,
<Axes: xlabel='Height', ylabel='Height'>,
<Axes: xlabel='MRI_Count', ylabel='Height'>],
[<Axes: xlabel='Weight', ylabel='MRI_Count'>,
<Axes: xlabel='Height', ylabel='MRI_Count'>,
<Axes: xlabel='MRI_Count', ylabel='MRI_Count'>]], dtype=object)
>>> plotting.scatter_matrix(data[['PIQ', 'VIQ', 'FSIQ']])

array([[<Axes: xlabel='PIQ', ylabel='PIQ'>,
<Axes: xlabel='VIQ', ylabel='PIQ'>,
<Axes: xlabel='FSIQ', ylabel='PIQ'>],
[<Axes: xlabel='PIQ', ylabel='VIQ'>,
<Axes: xlabel='VIQ', ylabel='VIQ'>,
<Axes: xlabel='FSIQ', ylabel='VIQ'>],
[<Axes: xlabel='PIQ', ylabel='FSIQ'>,
<Axes: xlabel='VIQ', ylabel='FSIQ'>,
<Axes: xlabel='FSIQ', ylabel='FSIQ'>]], dtype=object)
Two populations
The IQ metrics are bimodal, as if there are 2 sub-populations.

Exercise
Plot the scatter matrix for males only, and for females only. Do you think that the 2 sub-populations
correspond to gender?
15.2 Hypothesis testing: comparing two groups
For simple statistical tests, we will use the scipy.stats sub-module of SciPy:
See also:
SciPy is a vast library. For a quick summary to the whole library, see the scipy chapter.
15.2.1 Student’s t-test: the simplest statistical test
15.2. Hypothesis testing: comparing two groups 513

One-sample tests: testing the value of a population mean
scipy.stats.ttest_1samp() tests the null hypothesis that the mean of the population underlying the
data is equal to a given value. It returns the T statistic, and the p-value (see the function’s help):
>>> sp.stats.ttest_1samp(data['VIQ'], 0)
TtestResult(statistic=30.088099970..., pvalue=1.32891964...e-28, df=39)
The p-value of 10− 28 indicates that such an extreme value of the statistic is unlikely to be observed
under the null hypothesis. This may be taken as evidence that the null hypothesis is false and that the
population mean IQ (VIQ measure) is not 0.
Technically, the p-value of the t-test is derived under the assumption that the means of samples drawn
from the population are normally distributed. This condition is exactly satisfied when the population
itself is normally distributed; however, due to the central limit theorem, the condition is nearly true for
reasonably large samples drawn from populations that follow a variety of non-normal distributions.
Nonetheless, if we are concerned that violation of the normality assumptions will affect the conclusions
of the test, we can use a Wilcoxon signed-rank test, which relaxes this assumption at the expense of test
power:
>>> sp.stats.wilcoxon(data['VIQ'])
WilcoxonResult(statistic=0.0, pvalue=1.8189894...e-12)
Two-sample t-test: testing for difference across populations
We have seen above that the mean VIQ in the male and female samples were different. To test whether
this difference is significant (and suggests that there is a difference in population means), we perform a
two-sample t-test using scipy.stats.ttest_ind():
>>> female_viq = data[data['Gender'] == 'Female']['VIQ']

>>> male_viq = data[data['Gender'] == 'Male']['VIQ']
>>> sp.stats.ttest_ind(female_viq, male_viq)
TtestResult(statistic=-0.77261617232..., pvalue=0.4445287677858..., df=38.0)
The corresponding non-parametric test is the Mann–Whitney U test, scipy.stats.mannwhitneyu().
>>> sp.stats.mannwhitneyu(female_viq, male_viq)

MannwhitneyuResult(statistic=164.5, pvalue=0.34228868687...)

15.2.2 Paired tests: repeated measurements on the same individuals
PIQ, VIQ, and FSIQ give three measures of IQ. Let us test whether FISQ and PIQ are significantly
different. We can use an “independent sample” test:
>>> sp.stats.ttest_ind(data['FSIQ'], data['PIQ'])

TtestResult(statistic=0.46563759638..., pvalue=0.64277250..., df=78.0)
The problem with this approach is that it ignores an important relationship between observations: FSIQ
and PIQ are measured on the same individuals. Thus, the variance due to inter-subject variability is
confounding, reducing the power of the test. This variability can be removed using a “paired test” or
“repeated measures test”:
>>> sp.stats.ttest_rel(data['FSIQ'], data['PIQ'])

TtestResult(statistic=1.784201940..., pvalue=0.082172638183..., df=39)
This is equivalent to a one-sample test on the differences between paired observations:
>>> sp.stats.ttest_1samp(data['FSIQ'] - data['PIQ'], 0)

TtestResult(statistic=1.784201940..., pvalue=0.082172638..., df=39)
Accordingly, we can perform a nonparametric version of the test with wilcoxon.
>>> sp.stats.wilcoxon(data['FSIQ'], data['PIQ'], method="approx")

WilcoxonResult(statistic=274.5, pvalue=0.106594927135...)
Exercise
• Test the difference between weights in males and females.

• Use non parametric statistics to test the difference between VIQ in males and females.

Conclusion: we find that the data does not support the hypothesis that males and females have
different VIQ.
15.3 Linear models, multiple factors, and analysis of variance
15.3.1 “formulas” to specify statistical models in Python
A simple linear regression
Given two set of observations, x and y, we want to test the hypothesis that y is a linear function of x.
In other terms:
𝑦 = 𝑥 * coef + intercept + 𝑒
where e is observation noise. We will use the statsmodels module to:
1. Fit a linear model. We will use the simplest strategy, ordinary least squares (OLS).
2. Test that coef is non zero.
First, we generate simulated data according to the model:

>>> x = np.linspace(-5, 5, 20)
>>> # normal distributed noise
>>> y = -5 + 3*x + 4 * rng.normal(size=x.shape)
>>> # Create a data frame containing all the relevant variables
>>> data = pandas.DataFrame({'x': x, 'y': y})
“formulas” for statistics in Python
See the statsmodels documentation
15.3. Linear models, multiple factors, and analysis of variance 516

Then we specify an OLS model and fit it:
>>> from statsmodels.formula.api import ols

>>> model = ols("y ~ x", data).fit()
We can inspect the various statistics derived from the fit:
>>> print(model.summary())
OLS Regression Results
==============================================================================
Dep. Variable: y R-squared: 0.901
Model: OLS Adj. R-squared: 0.896
Method: Least Squares F-statistic: 164.5
Date: ... Prob (F-statistic): 1.72e-10
Time: ... Log-Likelihood: -51.758
No. Observations: 20 AIC: 107.5
Df Residuals: 18 BIC: 109.5
Df Model: 1
Covariance Type: nonrobust
==============================================================================
coef std err t P>|t| [0.025 0.975]
------------------------------------------------------------------------------
Intercept -4.2948 0.759 -5.661 0.000 -5.889 -2.701
x 3.2060 0.250 12.825 0.000 2.681 3.731
==============================================================================
Omnibus: 1.218 Durbin-Watson: 1.796
Prob(Omnibus): 0.544 Jarque-Bera (JB): 0.999
Skew: 0.503 Prob(JB): 0.607
Kurtosis: 2.568 Cond. No. 3.03
==============================================================================
Notes:
[1] Standard Errors assume that the covariance matrix of the errors is correctly␣
˓→specified.
Terminology:
Statsmodels uses a statistical terminology: the y variable in statsmodels is called ‘endogenous’ while
the x variable is called exogenous. This is discussed in more detail here.
To simplify, y (endogenous) is the value you are trying to predict, while x (exogenous) represents the
features you are using to make the prediction.
Exercise
Retrieve the estimated parameters from the model above. Hint: use tab-completion to find the
relevant attribute.

Categorical variables: comparing groups or multiple categories
Let us go back the data on brain size:
>>> data = pandas.read_csv('examples/brain_size.csv', sep=';', na_values=".")
We can write a comparison between IQ of male and female using a linear model:
>>> model = ols("VIQ ~ Gender + 1", data).fit()

==============================================================================
Dep. Variable: VIQ R-squared: 0.015
Model: OLS Adj. R-squared: -0.010
Date: ... Prob (F-statistic): 0.445
Df Model: 1
==================================================================================
coef std err t P>|t| [0.025 0.975]
----------------------------------------------------------------------------------
Intercept 109.4500 5.308 20.619 0.000 98.704 120.196
Gender[T.Male] 5.8000 7.507 0.773 0.445 -9.397 20.997
==============================================================================
Skew: 0.010 Prob(JB): 0.157
==============================================================================
Notes:
˓→specified.
Tips on specifying model
Forcing categorical: the ‘Gender’ is automatically detected as a categorical variable, and thus each
of its different values are treated as different entities.
An integer column can be forced to be treated as categorical using:
>>> model = ols('VIQ ~ C(Gender)', data).fit()
Intercept: We can remove the intercept using - 1 in the formula, or force the use of an intercept
using + 1.
Tip: By default, statsmodels treats a categorical variable with K possible values as K-1 ‘dummy’
boolean variables (the last level being absorbed into the intercept term). This is almost always a
good default choice - however, it is possible to specify different encodings for categorical variables
(https://www.statsmodels.org/devel/contrasts.html).

Link to t-tests between different FSIQ and PIQ
To compare different types of IQ, we need to create a “long-form” table, listing IQs, where the type
of IQ is indicated by a categorical variable:
>>>data_fisq = pandas.DataFrame({'iq': data['FSIQ'], 'type': 'fsiq'})
>>>data_piq = pandas.DataFrame({'iq': data['PIQ'], 'type': 'piq'})
>>>data_long = pandas.concat((data_fisq, data_piq))
>>>print(data_long)
iq type
0 133 fsiq
1 140 fsiq
2 139 fsiq
3 133 fsiq
4 137 fsiq
... ... ...
35 128 piq
36 124 piq
37 94 piq
38 74 piq
39 89 piq
[80 rows x 2 columns]
>>> model = ols("iq ~ type", data_long).fit()

...
==========================...
coef std err t P>|t| [0.025 0.975]
------------------------------------------...
Intercept 113.4500 3.683 30.807 0.000 106.119 120.781
type[T.piq] -2.4250 5.208 -0.466 0.643 -12.793 7.943
...
We can see that we retrieve the same values for t-test and corresponding p-values for the effect of the
type of iq than the previous t-test:
>>> sp.stats.ttest_ind(data['FSIQ'], data['PIQ'])
TtestResult(statistic=0.46563759638..., pvalue=0.64277250..., df=78.0)
15.3.2 Multiple Regression: including multiple factors

Consider a linear model explaining a variable z (the dependent variable) with 2 variables x and y:
𝑧 = 𝑥 𝑐1 + 𝑦 𝑐2 + 𝑖 + 𝑒
Such a model can be seen in 3D as fitting a plane to a cloud of (x, y, z) points.
Example: the iris data (examples/iris.csv)
Tip: Sepal and petal size tend to be related: bigger flowers are bigger! But is there in addition a
systematic effect of species?
>>> data = pandas.read_csv('examples/iris.csv')

>>> model = ols('sepal_width ~ name + petal_length', data).fit()
==========================...
Dep. Variable: sepal_width R-squared: 0.478
Date: ... Prob (F-statistic): 1.58e-20
Df Model: 3


==========================...
coef std err t P>|t| [0.025 0.975]
------------------------------------------...
Intercept 2.9813 0.099 29.989 0.000 2.785 3.178
name[T.versicolor] -1.4821 0.181 -8.190 0.000 -1.840 -1.124
name[T.virginica] -1.6635 0.256 -6.502 0.000 -2.169 -1.158
petal_length 0.2983 0.061 4.920 0.000 0.178 0.418
==========================...
Skew: -0.082 Prob(JB): 0.236
==========================...
Notes:
˓→specified.
15.3.3 Post-hoc hypothesis testing: analysis of variance (ANOVA)
In the above iris example, we wish to test if the petal length is different between versicolor and virginica,
after removing the effect of sepal width. This can be formulated as testing the difference between the
coefficient associated to versicolor and virginica in the linear model estimated above (it is an Analysis of
Variance, ANOVA). For this, we write a vector of ‘contrast’ on the parameters estimated: we want
to test "name[T.versicolor] - name[T.virginica]", with an F-test:
>>> print(model.f_test([0, 1, -1, 0]))

<F test: F=3.24533535..., p=0.07369..., df_denom=146, df_num=1>
Is this difference significant?
Exercise
Going back to the brain size + IQ data, test if the VIQ of male and female are different after removing
the effect of brain size, height and weight.

15.4 More visualization: seaborn for statistical exploration
Seaborn combines simple statistical fits with plotting on pandas dataframes.

Let us consider a data giving wages and many other personal information on 500 individuals (Berndt,
ER. The Practice of Econometrics. 1991. NY: Addison-Wesley).
Tip: The full code loading and plotting of the wages data is found in corresponding example.
>>> print(data)
EDUCATION SOUTH SEX EXPERIENCE UNION WAGE AGE RACE \
0 8 0 1 21 0 0.707570 35 2
1 9 0 1 42 0 0.694605 57 3
2 12 0 0 1 0 0.824126 19 3
3 12 0 0 4 0 0.602060 22 3
...
15.4.1 Pairplot: scatter matrices
We can easily have an intuition on the interactions between continuous variables using seaborn.
pairplot() to display a scatter matrix:
>>> import seaborn

>>> seaborn.pairplot(data, vars=['WAGE', 'AGE', 'EDUCATION'],
... kind='reg')
Categorical variables can be plotted as the hue:
15.4. More visualization: seaborn for statistical exploration 522

>>> seaborn.pairplot(data, vars=['WAGE', 'AGE', 'EDUCATION'],

... kind='reg', hue='SEX')
Look and feel and matplotlib settings
Seaborn changes the default of matplotlib figures to achieve a more “modern”, “excel-like” look. It
does that upon import. You can reset the default using:
>>> plt.rcdefaults()
Tip: To switch back to seaborn settings, or understand better styling in seaborn, see the relevant
section of the seaborn documentation.

15.4.2 lmplot: plotting a univariate regression
A regression capturing the relation between one variable and another, eg wage and eduction, can be
plotted using seaborn.lmplot():
>>> seaborn.lmplot(y='WAGE', x='EDUCATION', data=data)
Robust regression
Tip: Given that, in the above plot, there seems to be a couple of data points that are outside of the
main cloud to the right, they might be outliers, not representative of the population, but driving the
regression.
To compute a regression that is less sensitive to outliers, one must use a robust model. This is done
in seaborn using robust=True in the plotting functions, or in statsmodels by replacing the use of the
OLS by a “Robust Linear Model”, statsmodels.formula.api.rlm().

15.5 Testing for interactions
Do wages increase more with education for males than females?
Tip: The plot above is made of two different fits. We need to formulate a single model that tests for a
variance of slope across the two populations. This is done via an “interaction”.
>>> result = sm.ols(formula='wage ~ education + gender + education * gender',

... data=data).fit()
>>> print(result.summary())
...
coef std err t P>|t| [0.025 0.975]
------------------------------------------------------------------------------
Intercept 0.2998 0.072 4.173 0.000 0.159 0.441
gender[T.male] 0.2750 0.093 2.972 0.003 0.093 0.457
education 0.0415 0.005 7.647 0.000 0.031 0.052
education:gender[T.male] -0.0134 0.007 -1.919 0.056 -0.027 0.000
==========================...
...
Can we conclude that education benefits males more than females?
Take home messages
• Hypothesis testing and p-values give you the significance of an effect / difference.
• Formulas (with categorical variables) enable you to express rich links in your data.
• Visualizing your data and fitting simple models give insight into the data.
15.5. Testing for interactions 525

• Conditionning (adding factors that can explain all or part of the variation) is an important
modeling aspect that changes the interpretation.
15.6 Full code for the figures
Code examples for the statistics chapter.
15.6.1 Boxplots and paired differences
Plot boxplots for FSIQ, PIQ, and the paired difference between the two: while the spread (error bars)
for FSIQ and PIQ are very large, there is a systematic (common) effect due to the subjects. This effect
is cancelled out in the difference and the spread of the difference (“paired” by subject) is much smaller
than the spread of the individual measures.
15.6. Full code for the figures 526

import pandas
data = pandas.read_csv("brain_size.csv", sep=";", na_values=".")
# Box plot of FSIQ and PIQ (different measures od IQ)

data.boxplot(column=["FSIQ", "PIQ"])
# Boxplot of the difference

plt.boxplot(data["FSIQ"] - data["PIQ"])
plt.xticks((1,), ("FSIQ - PIQ",))
plt.show()
15.6.2 Plotting simple quantities of a pandas dataframe
This example loads from a CSV file data with mixed numerical and categorical entries, and plots a few
quantities, separately for females and males, thanks to the pandas integrated plotting tool (that uses
matplotlib behind the scene).
See http://pandas.pydata.org/pandas-docs/stable/visualization.html

import pandas


data = pandas.read_csv("brain_size.csv", sep=";", na_values=".")
# Box plots of different columns for each gender

groupby_gender = data.groupby("Gender")
groupby_gender.boxplot(column=["FSIQ", "VIQ", "PIQ"])
from pandas import plotting
# Scatter matrices for different columns

plotting.scatter_matrix(data[["Weight", "Height", "MRI_Count"]])
plotting.scatter_matrix(data[["PIQ", "VIQ", "FSIQ"]])
plt.show()
15.6.3 Analysis of Iris petal and sepal sizes
Illustrate an analysis on a real dataset:

• Visualizing the data to formulate intuitions
• Fitting of a linear model
• Hypothesis test of the effect of a categorical variable in the presence of a continuous confound
import pandas
from statsmodels.formula.api import ols
# Load the data

data = pandas.read_csv("iris.csv")
Plot a scatter matrix
# Express the names as categories

categories = pandas.Categorical(data["name"])
# The parameter 'c' is passed to plt.scatter and will control the color
plotting.scatter_matrix(data, c=categories.codes, marker="o")
fig = plt.gcf()
fig.suptitle("blue: setosa, green: versicolor, red: virginica", size=13)

Text(0.5, 0.98, 'blue: setosa, green: versicolor, red: virginica')
Statistical analysis
# Let us try to explain the sepal length as a function of the petal

# width and the category of iris
model = ols("sepal_width ~ name + petal_length", data).fit()

print(model.summary())
# Now formulate a "contrast", to test if the offset for versicolor and

# virginica are identical
print("Testing the difference between effect of versicolor and virginica")

print(model.f_test([0, 1, -1, 0]))
plt.show()

==============================================================================
Dep. Variable: sepal_width R-squared: 0.478
Date: Mon, 04 Mar 2024 Prob (F-statistic): 1.58e-20
Time: 00:58:09 Log-Likelihood: -38.185
Df Model: 3


======================================================================================
coef std err t P>|t| [0.025 0.975]
--------------------------------------------------------------------------------------
Intercept 2.9813 0.099 29.989 0.000 2.785 3.178
name[T.versicolor] -1.4821 0.181 -8.190 0.000 -1.840 -1.124
name[T.virginica] -1.6635 0.256 -6.502 0.000 -2.169 -1.158
petal_length 0.2983 0.061 4.920 0.000 0.178 0.418
==============================================================================
Skew: -0.082 Prob(JB): 0.236
==============================================================================
Notes:
˓→specified.
Testing the difference between effect of versicolor and virginica

<F test: F=3.245335346574177, p=0.07369058781701142, df_denom=146, df_num=1>
15.6.4 Simple Regression
Fit a simple linear regression using ‘statsmodels’, compute corresponding p-values.
# Original author: Thomas Haslwanter
import numpy as np
import pandas
# For statistics. Requires statsmodels 5.0 or more

# Analysis of Variance (ANOVA) on linear models

from statsmodels.stats.anova import anova_lm
Generate and show the data
# To get reproducible values, provide a seed value

y = -5 + 3 * x + 4 * np.random.normal(size=x.shape)
# Plot the data

plt.plot(x, y, "o")

[<matplotlib.lines.Line2D object at 0x7f9c74b4c110>]
Multilinear regression model, calculating fit, P-values, confidence intervals etc.
# Convert the data into a Pandas DataFrame to use the formulas framework
# in statsmodels
data = pandas.DataFrame({"x": x, "y": y})
# Fit the model

model = ols("y ~ x", data).fit()
# Print the summary

# Perform analysis of variance on fitted linear model

anova_results = anova_lm(model)
print("\nANOVA results")
print(anova_results)

==============================================================================
Dep. Variable: y R-squared: 0.845
Df Model: 1
==============================================================================


coef std err t P>|t| [0.025 0.975]
------------------------------------------------------------------------------
Intercept -4.1877 0.830 -5.044 0.000 -5.932 -2.444
x 2.7046 0.274 9.887 0.000 2.130 3.279
==============================================================================
Skew: 0.337 Prob(JB): 0.742
==============================================================================
Notes:
˓→specified.
ANOVA results
df sum_sq mean_sq F PR(>F)
x 1.0 1347.476043 1347.476043 97.760281 1.062847e-08
Residual 18.0 248.102486 13.783471 NaN NaN
Plot the fitted model
# Retrieve the parameter estimates

offset, coef = model._results.params
plt.plot(x, x * coef + offset)
plt.xlabel("x")
plt.ylabel("y")
plt.show()

15.6.5 Test for an education/gender interaction in wages
Wages depend mostly on education. Here we investigate how this dependence is related to gender: not
only does gender create an offset in wages, it also seems that wages increase more with education for
males than females.
Does our data support this last hypothesis? We will test this using statsmodels’ formulas (http://
statsmodels.sourceforge.net/stable/example_formulas.html).
Load and massage the data
import pandas
import urllib
import os
if not os.path.exists("wages.txt"):
# Download the file if it is not present
urllib.urlretrieve("http://lib.stat.cmu.edu/datasets/CPS_85_Wages", "wages.txt")
# EDUCATION: Number of years of education

# SEX: 1=Female, 0=Male
# WAGE: Wage (dollars per hour)
data = pandas.read_csv(
"wages.txt",


skiprows=27,
skipfooter=6,
sep=None,
header=None,
names=["education", "gender", "wage"],
usecols=[0, 2, 5],
)
# Convert genders to strings (this is particularly useful so that the

# statsmodels formulas detects that gender is a categorical variable)
import numpy as np
data["gender"] = np.choose(data.gender, ["male", "female"])
# Log-transform the wages, because they typically are increased with

# multiplicative factors
data["wage"] = np.log10(data["wage"])
/home/runner/work/scientific-python-lectures/scientific-python-lectures/packages/
˓→statistics/examples/plot_wage_education_gender.py:30: ParserWarning: Falling back␣
˓→to the 'python' engine because the 'c' engine does not support skipfooter; you can␣
˓→avoid this warning by specifying engine='python'.
simple plotting
import seaborn
# Plot 2 linear fits for male and female.

seaborn.lmplot(y="wage", x="education", hue="gender", data=data)

<seaborn.axisgrid.FacetGrid object at 0x7f9c882402d0>
statistical analysis
import statsmodels.formula.api as sm
# Note that this model is not the plot displayed above: it is one
# joined model for male and female, not separate models for male and
# female. The reason is that a single model enables statistical testing
result = sm.ols(formula="wage ~ education + gender", data=data).fit()
print(result.summary())

==============================================================================
Dep. Variable: wage R-squared: 0.193
Time: 00:58:09 Log-Likelihood: 86.654
No. Observations: 534 AIC: -167.3
Df Residuals: 531 BIC: -154.5
Df Model: 2
==================================================================================
coef std err t P>|t| [0.025 0.975]
----------------------------------------------------------------------------------


Intercept 0.4053 0.046 8.732 0.000 0.314 0.496
gender[T.male] 0.1008 0.018 5.625 0.000 0.066 0.136
education 0.0334 0.003 9.768 0.000 0.027 0.040
==============================================================================
Skew: -0.147 Prob(JB): 0.0873
==============================================================================
Notes:
˓→specified.
The plots above highlight that there is not only a different offset in wage but also a different slope
We need to model this using an interaction
result = sm.ols(
formula="wage ~ education + gender + education * gender", data=data
).fit()

==============================================================================
Dep. Variable: wage R-squared: 0.198
Time: 00:58:09 Log-Likelihood: 88.503
No. Observations: 534 AIC: -169.0
Df Residuals: 530 BIC: -151.9
Df Model: 3
============================================================================================
coef std err t P>|t| [0.025 ␣
˓→0.975]
--------------------------------------------------------------------------------------
˓→------
Intercept 0.2998 0.072 4.173 0.000 0.159 ␣

˓→ 0.441
gender[T.male] 0.2750 0.093 2.972 0.003 0.093 ␣

˓→ 0.457
education 0.0415 0.005 7.647 0.000 0.031 ␣

˓→ 0.052
education:gender[T.male] -0.0134 0.007 -1.919 0.056 -0.027 ␣

˓→ 0.000
==============================================================================
Skew: -0.156 Prob(JB): 0.0821
Kurtosis: 3.356 Cond. No. 194.
==============================================================================
Notes:
˓→specified.

Looking at the p-value of the interaction of gender and education, the data does not support the hy-
pothesis that education benefits males more than female (p-value > 0.05).
plt.show()
15.6.6 Multiple Regression
Calculate using ‘statsmodels’ just the best fit, or all the corresponding statistical parameters.
Also shows how to make 3d plots.
# Original author: Thomas Haslwanter
import numpy as np
import pandas
# For 3d plots. This import is necessary to have 3D plotting below

# For statistics. Requires statsmodels 5.0 or more

# Analysis of Variance (ANOVA) on linear models

from statsmodels.stats.anova import anova_lm
Generate and show the data
# We generate a 2D grid
X, Y = np.meshgrid(x, x)
# To get reproducible values, provide a seed value

# Z is the elevation of this 2D grid

Z = -5 + 3 * X - 0.5 * Y + 8 * np.random.normal(size=X.shape)
# Plot the data

surf = ax.plot_surface(X, Y, Z, cmap=plt.cm.coolwarm, rstride=1, cstride=1)
ax.view_init(20, -120)
ax.set_xlabel("X")
ax.set_ylabel("Y")
ax.set_zlabel("Z")

Text(-0.1076451312126014, 0.009865032686848024, 'Z')
Multilinear regression model, calculating fit, P-values, confidence intervals etc.
# Convert the data into a Pandas DataFrame to use the formulas framework
# in statsmodels
# First we need to flatten the data: it's 2D layout is not relevant.

X = X.flatten()
Y = Y.flatten()
Z = Z.flatten()
data = pandas.DataFrame({"x": X, "y": Y, "z": Z})
# Fit the model

model = ols("z ~ x + y", data).fit()
# Print the summary

print("\nRetrieving manually the parameter estimates:")

print(model._results.params)
# should be array([-4.99754526, 3.00250049, -0.50514907])
# Perform analysis of variance on fitted linear model

anova_results = anova_lm(model)
print("\nANOVA results")


print(anova_results)
plt.show()

==============================================================================
Dep. Variable: z R-squared: 0.579
No. Observations: 441 AIC: 3110.
Df Residuals: 438 BIC: 3122.
Df Model: 2
==============================================================================
coef std err t P>|t| [0.025 0.975]
------------------------------------------------------------------------------
Intercept -4.4332 0.390 -11.358 0.000 -5.200 -3.666
x 3.0861 0.129 23.940 0.000 2.833 3.340
y -0.6856 0.129 -5.318 0.000 -0.939 -0.432
==============================================================================
Skew: -0.077 Prob(JB): 0.722
==============================================================================
Notes:
˓→specified.
Retrieving manually the parameter estimates:

[-4.43322435 3.08614608 -0.68556194]
ANOVA results
df sum_sq mean_sq F PR(>F)
x 1.0 38501.973182 38501.973182 573.111646 1.365553e-81
y 1.0 1899.955512 1899.955512 28.281320 1.676135e-07
Residual 438.0 29425.094352 67.180581 NaN NaN
15.6.7 Visualizing factors influencing wages
This example uses seaborn to quickly plot various factors relating wages, experience and eduction.
Seaborn (https://seaborn.pydata.org) is a library that combines visualization and statistical fits to show
trends in data.
Note that importing seaborn changes the matplotlib style to have an “excel-like” feeling. This changes
affect other matplotlib figures. To restore defaults once this example is run, we would need to call
plt.rcdefaults().

# Standard library imports

import os
Load the data
import pandas
import requests
if not os.path.exists("wages.txt"):
r = requests.get("http://lib.stat.cmu.edu/datasets/CPS_85_Wages")
with open("wages.txt", "wb") as f:
f.write(r.content)
# Give names to the columns

names = [
"EDUCATION: Number of years of education",
"SOUTH: 1=Person lives in South, 0=Person lives elsewhere",
"SEX: 1=Female, 0=Male",
"EXPERIENCE: Number of years of work experience",
"UNION: 1=Union member, 0=Not union member",
"WAGE: Wage (dollars per hour)",
"AGE: years",
"RACE: 1=Other, 2=Hispanic, 3=White",
"OCCUPATION: 1=Management, 2=Sales, 3=Clerical, 4=Service, 5=Professional, 6=Other
˓→",
"SECTOR: 0=Other, 1=Manufacturing, 2=Construction",

"MARR: 0=Unmarried, 1=Married",
]
short_names = [n.split(":")[0] for n in names]
"wages.txt", skiprows=27, skipfooter=6, sep=None, header=None, engine="python"
)
data.columns = short_names
# Log-transform the wages, because they typically are increased with

# multiplicative factors
import numpy as np
data["WAGE"] = np.log10(data["WAGE"])
Plot scatter matrices highlighting different aspects
import seaborn
seaborn.pairplot(data, vars=["WAGE", "AGE", "EDUCATION"], kind="reg")
seaborn.pairplot(data, vars=["WAGE", "AGE", "EDUCATION"], kind="reg", hue="SEX")

plt.suptitle("Effect of gender: 1=Female, 0=Male")
seaborn.pairplot(data, vars=["WAGE", "AGE", "EDUCATION"], kind="reg", hue="RACE")

plt.suptitle("Effect of race: 1=Other, 2=Hispanic, 3=White")


seaborn.pairplot(data, vars=["WAGE", "AGE", "EDUCATION"], kind="reg", hue="UNION")
plt.suptitle("Effect of union: 1=Union member, 0=Not union member")



Text(0.5, 0.98, 'Effect of union: 1=Union member, 0=Not union member')
Plot a simple regression
seaborn.lmplot(y="WAGE", x="EDUCATION", data=data)
plt.show()

15.6.8 Air fares before and after 9/11
This is a business-intelligence (BI) like application.

What is interesting here is that we may want to study fares as a function of the year, paired accordingly
to the trips, or forgetting the year, only as a function of the trip endpoints.
Using statsmodels’ linear models, we find that both with an OLS (ordinary least square) and a robust
fit, the intercept and the slope are significantly non-zero: the air fares have decreased between 2000 and
2001, and their dependence on distance travelled has also decreased
# Standard library imports
import os
Load the data

import pandas
import requests
if not os.path.exists("airfares.txt"):
r = requests.get(
"https://users.stat.ufl.edu/~winner/data/airq4.dat",
verify=False, # Wouldn't normally do this, but this site's certificate


# is not yet distributed
)
with open("airfares.txt", "wb") as f:
f.write(r.content)
# As a separator, ' +' is a regular expression that means 'one of more

# space'
"airfares.txt",
delim_whitespace=True,
header=0,
names=[
"city1",
"city2",
"pop1",
"pop2",
"dist",
"fare_2000",
"nb_passengers_2000",
"fare_2001",
"nb_passengers_2001",
],
)
# we log-transform the number of passengers

import numpy as np
data["nb_passengers_2000"] = np.log10(data["nb_passengers_2000"])
data["nb_passengers_2001"] = np.log10(data["nb_passengers_2001"])
˓→statistics/examples/plot_airfare.py:38: FutureWarning: The 'delim_whitespace'␣
˓→keyword in pd.read_csv is deprecated and will be removed in a future version. Use␣
˓→``sep='\s+'`` instead
Make a dataframe with the year as an attribute, instead of separate columns
# This involves a small danse in which we separate the dataframes in 2,

# one for year 2000, and one for 2001, before concatenating again.
# Make an index of each flight

data_flat = data.reset_index()
data_2000 = data_flat[
["city1", "city2", "pop1", "pop2", "dist", "fare_2000", "nb_passengers_2000"]
]
# Rename the columns
data_2000.columns = ["city1", "city2", "pop1", "pop2", "dist", "fare", "nb_passengers
˓→"]
# Add a column with the year

data_2000.insert(0, "year", 2000)
data_2001 = data_flat[
["city1", "city2", "pop1", "pop2", "dist", "fare_2001", "nb_passengers_2001"]
]


# Rename the columns
data_2001.columns = ["city1", "city2", "pop1", "pop2", "dist", "fare", "nb_passengers
˓→"]
# Add a column with the year

data_2001.insert(0, "year", 2001)
data_flat = pandas.concat([data_2000, data_2001])
Plot scatter matrices highlighting different aspects
import seaborn
seaborn.pairplot(
data_flat, vars=["fare", "dist", "nb_passengers"], kind="reg", markers="."
)
# A second plot, to show the effect of the year (ie the 9/11 effect)
seaborn.pairplot(
data_flat,
vars=["fare", "dist", "nb_passengers"],
kind="reg",
hue="year",
markers=".",
)


<seaborn.axisgrid.PairGrid object at 0x7f9c88777990>
Plot the difference in fare
seaborn.boxplot(data.fare_2001 - data.fare_2000)
plt.title("Fare: 2001 - 2000")
plt.subplots_adjust()
seaborn.boxplot(data.nb_passengers_2001 - data.nb_passengers_2000)
plt.title("NB passengers: 2001 - 2000")
plt.subplots_adjust()

•
Statistical testing: dependence of fare on distance and number of passengers
import statsmodels.formula.api as sm
result = sm.ols(formula="fare ~ 1 + dist + nb_passengers", data=data_flat).fit()

# Using a robust fit

result = sm.rlm(formula="fare ~ 1 + dist + nb_passengers", data=data_flat).fit()

==============================================================================
Dep. Variable: fare R-squared: 0.275
Method: Least Squares F-statistic: 1585.
Date: Mon, 04 Mar 2024 Prob (F-statistic): 0.00
Time: 00:58:26 Log-Likelihood: -45532.
No. Observations: 8352 AIC: 9.107e+04
Df Residuals: 8349 BIC: 9.109e+04
Df Model: 2
=================================================================================
coef std err t P>|t| [0.025 0.975]
---------------------------------------------------------------------------------
Intercept 211.2428 2.466 85.669 0.000 206.409 216.076
dist 0.0484 0.001 48.149 0.000 0.046 0.050
nb_passengers -32.8925 1.127 -29.191 0.000 -35.101 -30.684
==============================================================================
Skew: 0.710 Prob(JB): 1.42e-161


Kurtosis: 3.338 Cond. No. 5.23e+03
==============================================================================
Notes:
˓→specified.
[2] The condition number is large, 5.23e+03. This might indicate that there are
strong multicollinearity or other numerical problems.
Robust linear Model Regression Results
==============================================================================
Dep. Variable: fare No. Observations: 8352
Model: RLM Df Residuals: 8349
Method: IRLS Df Model: 2
Norm: HuberT
Scale Est.: mad
Cov Type: H1
Date: Mon, 04 Mar 2024
Time: 00:58:26
No. Iterations: 12
=================================================================================
coef std err z P>|z| [0.025 0.975]
---------------------------------------------------------------------------------
Intercept 215.0848 2.448 87.856 0.000 210.287 219.883
dist 0.0460 0.001 46.166 0.000 0.044 0.048
nb_passengers -35.2686 1.119 -31.526 0.000 -37.461 -33.076
=================================================================================
If the model instance has been used for another fit with different fit parameters,␣
˓→then the fit options might not be the correct ones anymore .
Statistical testing: regression of fare on distance: 2001/2000 difference
result = sm.ols(formula="fare_2001 - fare_2000 ~ 1 + dist", data=data).fit()

# Plot the corresponding regression

data["fare_difference"] = data["fare_2001"] - data["fare_2000"]
seaborn.lmplot(x="dist", y="fare_difference", data=data)
plt.show()


==============================================================================
Dep. Variable: fare_2001 R-squared: 0.159
Time: 00:58:26 Log-Likelihood: -22640.
No. Observations: 4176 AIC: 4.528e+04
Df Residuals: 4174 BIC: 4.530e+04
Df Model: 1
==============================================================================
coef std err t P>|t| [0.025 0.975]
------------------------------------------------------------------------------
Intercept 148.0279 1.673 88.480 0.000 144.748 151.308
dist 0.0388 0.001 28.136 0.000 0.036 0.041
==============================================================================
Skew: 0.462 Prob(JB): 3.23e-33
==============================================================================
Notes:
˓→specified.


15.7 Solutions to this chapter’s exercises
15.7.1 Solutions to this chapter’s exercises
Relating Gender and IQ
Going back to the brain size + IQ data, test if the VIQ of male and female are different after removing
the effect of brain size, height and weight.
Notice that here ‘Gender’ is a categorical value. As it is a non-float data type, statsmodels is able to
automatically infer this.
import pandas
data = pandas.read_csv("../brain_size.csv", sep=";", na_values=".")
model = ols("VIQ ~ Gender + MRI_Count + Height", data).fit()

# Here, we don't need to define a contrast, as we are testing a single

# coefficient of our model, and not a combination of coefficients.
# However, defining a contrast, which would then be a 'unit contrast',
# will give us the same results
print(model.f_test([0, 1, 0, 0]))

==============================================================================
Dep. Variable: VIQ R-squared: 0.246
Date: Mon, 04 Mar 2024 Prob (F-statistic): 0.0184
Df Model: 3
==================================================================================
coef std err t P>|t| [0.025 0.975]
----------------------------------------------------------------------------------
Intercept 166.6258 88.824 1.876 0.069 -13.696 346.948
Gender[T.Male] 8.8524 10.710 0.827 0.414 -12.890 30.595
MRI_Count 0.0002 6.46e-05 2.615 0.013 3.78e-05 0.000
Height -3.0837 1.276 -2.417 0.021 -5.674 -0.494
==============================================================================
Skew: 0.005 Prob(JB): 0.324
15.7. Solutions to this chapter’s exercises 554


==============================================================================
Notes:
˓→specified.
<F test: F=0.683196084584229, p=0.4140878441244694, df_denom=35, df_num=1>
Here we plot a scatter matrix to get intuitions on our results. This goes beyond what was asked in the
exercise
# This plotting is useful to get an intuitions on the relationships between

# our different variables

# Fill in the missing values for Height for plotting

data["Height"].fillna(method="pad", inplace=True)
# The parameter 'c' is passed to plt.scatter and will control the color
# The same holds for parameters 'marker', 'alpha' and 'cmap', that
# control respectively the type of marker used, their transparency and
# the colormap
plotting.scatter_matrix(
data[["VIQ", "MRI_Count", "Height"]],
c=(data["Gender"] == "Female"),
marker="o",
alpha=1,
cmap="winter",
)
fig = plt.gcf()
fig.suptitle("blue: male, green: female", size=13)
plt.show()

˓→statistics/examples/solutions/plot_brain_size.py:39: FutureWarning: A value is␣
˓→trying to be set on a copy of a DataFrame or Series through chained assignment␣
˓→using an inplace method.
The behavior will change in pandas 3.0. This inplace method will never work because␣
˓→the intermediate object on which we are setting values always behaves as a copy.
For example, when doing 'df[col].method(value, inplace=True)', try using 'df.method(

˓→{col: value}, inplace=True)' or df[col] = df[col].method(value) instead, to perform␣
˓→the operation inplace on the original object.
˓→statistics/examples/solutions/plot_brain_size.py:39: FutureWarning: Series.fillna␣
˓→with 'method' is deprecated and will raise in a future version. Use obj.ffill() or␣
˓→obj.bfill() instead.

CHAPTER 16
Sympy : Symbolic Mathematics in
Python
Author: Fabian Pedregosa
Objectives
1. Evaluate expressions with arbitrary precision.

2. Perform algebraic manipulations on symbolic expressions.
3. Perform basic calculus tasks (limits, differentiation and
integration) with symbolic expressions.
4. Solve polynomial and transcendental equations.
5. Solve some differential equations.
What is SymPy? SymPy is a Python library for symbolic mathematics. It aims to be an alternative to
systems such as Mathematica or Maple while keeping the code as simple as possible and easily extensible.
SymPy is written entirely in Python and does not require any external libraries.
Sympy documentation and packages for installation can be found on https://www.sympy.org/
Chapters contents
• First Steps with SymPy

– Using SymPy as a calculator
– Symbols
557
• Algebraic manipulations
– Expand
– Simplify
• Calculus
– Limits
– Differentiation
– Series expansion
– Integration
• Equation solving
• Linear Algebra
– Matrices
– Differential Equations
16.1 First Steps with SymPy
16.1.1 Using SymPy as a calculator
SymPy defines three numerical types: Real, Rational and Integer.

The Rational class represents a rational number as a pair of two Integers: the numerator and the
denominator, so Rational(1, 2) represents 1/2, Rational(5, 2) 5/2 and so on:
>>> import sympy as sym

>>> a = sym.Rational(1, 2)
>>> a
1/2
>>> a*2
1
SymPy uses mpmath in the background, which makes it possible to perform computations using
arbitrary-precision arithmetic. That way, some special constants, like 𝑒, 𝑝𝑖, 𝑜𝑜 (Infinity), are treated
as symbols and can be evaluated with arbitrary precision:
>>> sym.pi**2
pi**2
>>> sym.pi.evalf()
3.14159265358979
>>> (sym.pi + sym.exp(1)).evalf()

5.85987448204884
as you see, evalf evaluates the expression to a floating-point number.

There is also a class representing mathematical infinity, called oo:
>>> sym.oo > 99999

True
16.1. First Steps with SymPy 558


>>> sym.oo + 1
oo
Exercises
√
1. Calculate 2 with 100 decimals.
2. Calculate 1/2 + 1/3 in rational arithmetic.
16.1.2 Symbols
In contrast to other Computer Algebra Systems, in SymPy you have to declare symbolic variables
explicitly:
>>> x = sym.Symbol('x')
>>> y = sym.Symbol('y')
Then you can manipulate them:
>>> x + y + x - y
2*x
>>> (x + y) ** 2
(x + y)**2
Symbols can now be manipulated using some of python operators: +, -, *, ** (arithmetic), &, |, ~, >>,
<< (boolean).
Printing
Sympy allows for control of the display of the output. From here we use the following setting for
printing:
>>> sym.init_printing(use_unicode=False, wrap_line=True)
16.2 Algebraic manipulations
SymPy is capable of performing powerful algebraic manipulations. We’ll take a look into some of the
most frequently used: expand and simplify.
16.2.1 Expand
Use this to expand an algebraic expression. It will try to denest powers and multiplications:
>>> sym.expand((x + y) ** 3)
3 2 2 3
x + 3*x *y + 3*x*y + y
>>> 3 * x * y ** 2 + 3 * y * x ** 2 + x ** 3 + y ** 3
3 2 2 3
x + 3*x *y + 3*x*y + y
16.2. Algebraic manipulations 559

Further options can be given in form on keywords:
>>> sym.expand(x + y, complex=True)

re(x) + re(y) + I*im(x) + I*im(y)
>>> sym.I * sym.im(x) + sym.I * sym.im(y) + sym.re(x) + sym.re(y)
re(x) + re(y) + I*im(x) + I*im(y)
>>> sym.expand(sym.cos(x + y), trig=True)

-sin(x)*sin(y) + cos(x)*cos(y)
>>> sym.cos(x) * sym.cos(y) - sym.sin(x) * sym.sin(y)
-sin(x)*sin(y) + cos(x)*cos(y)
16.2.2 Simplify
Use simplify if you would like to transform an expression into a simpler form:
>>> sym.simplify((x + x * y) / x)
y + 1
Simplification is a somewhat vague term, and more precises alternatives to simplify exists: powsimp
(simplification of exponents), trigsimp (for trigonometric expressions) , logcombine, radsimp, together.
Exercises
1. Calculate the expanded form of (𝑥 + 𝑦)6 .

2. Simplify the trigonometric expression sin(𝑥)/ cos(𝑥)
16.3 Calculus
16.3.1 Limits
Limits are easy to use in SymPy, they follow the syntax limit(function, variable, point), so to
compute the limit of 𝑓 (𝑥) as 𝑥 → 0, you would issue limit(f, x, 0):
>>> sym.limit(sym.sin(x) / x, x, 0)
1
you can also calculate the limit at infinity:
>>> sym.limit(x, x, sym.oo)

oo
>>> sym.limit(1 / x, x, sym.oo)

0
>>> sym.limit(x ** x, x, 0)
1
16.3. Calculus 560

16.3.2 Differentiation
You can differentiate any SymPy expression using diff(func, var). Examples:
>>> sym.diff(sym.sin(x), x)
cos(x)
>>> sym.diff(sym.sin(2 * x), x)
2*cos(2*x)
>>> sym.diff(sym.tan(x), x)
2
tan (x) + 1
You can check that it is correct by:
>>> sym.limit((sym.tan(x + y) - sym.tan(x)) / y, y, 0)

1
-------
2
cos (x)
Which is equivalent since

1
sec(𝑥) = 𝑎𝑛𝑑 sec2 (𝑥) = tan2 (𝑥) + 1.
cos(𝑥)
You can check this as well:
>>> sym.trigsimp(sym.diff(sym.tan(x), x))

1
-------
2
cos (x)
Higher derivatives can be calculated using the diff(func, var, n) method:
>>> sym.diff(sym.sin(2 * x), x, 1)

2*cos(2*x)

-4*sin(2*x)

-8*cos(2*x)
16.3.3 Series expansion
SymPy also knows how to compute the Taylor series of an expression at a point. Use series(expr,
var):
>>> sym.series(sym.cos(x), x)
2 4
x x / 6\
1 - -- + -- + O\x /
2 24
>>> sym.series(1/sym.cos(x), x)
2 4
x 5*x / 6\
16.3. Calculus 561


1 + -- + ---- + O\x /
2 24
Exercises
1. Calculate lim𝑥→0 sin(𝑥)/𝑥

2. Calculate the derivative of 𝑙𝑜𝑔(𝑥) for 𝑥.
16.3.4 Integration
SymPy has support for indefinite and definite integration of transcendental elementary and special func-
tions via integrate() facility, which uses the powerful extended Risch-Norman algorithm and some
heuristics and pattern matching. You can integrate elementary functions:
>>> sym.integrate(6 * x ** 5, x)
6
x
>>> sym.integrate(sym.sin(x), x)
-cos(x)
>>> sym.integrate(sym.log(x), x)
x*log(x) - x
>>> sym.integrate(2 * x + sym.sinh(x), x)
2
x + cosh(x)
Also special functions are handled easily:
>>> sym.integrate(sym.exp(-x ** 2) * sym.erf(x), x)

____ 2
\/ pi *erf (x)
--------------
4
It is possible to compute definite integral:
>>> sym.integrate(x**3, (x, -1, 1))

0
>>> sym.integrate(sym.sin(x), (x, 0, sym.pi / 2))
1
>>> sym.integrate(sym.cos(x), (x, -sym.pi / 2, sym.pi / 2))
2
Also improper integrals are supported as well:
>>> sym.integrate(sym.exp(-x), (x, 0, sym.oo))

1
>>> sym.integrate(sym.exp(-x ** 2), (x, -sym.oo, sym.oo))
____
\/ pi
16.3. Calculus 562

16.4 Equation solving
SymPy is able to solve algebraic equations, in one and several variables using solveset():
>>> sym.solveset(x ** 4 - 1, x)
{-1, 1, -I, I}
As you can see it takes as first argument an expression that is supposed to be equaled to 0. It also has
(limited) support for transcendental equations:
>>> sym.solveset(sym.exp(x) + 1, x)
{I*(2*n*pi + pi) | n in Integers}
Systems of linear equations
Sympy is able to solve a large part of polynomial equations, and is also capable of solving multiple
equations with respect to multiple variables giving a tuple as second argument. To do this you use
the solve() command:
>>> solution = sym.solve((x + 5 * y - 2, -3 * x + 6 * y - 15), (x, y))
>>> solution[x], solution[y]
(-3, 1)
Another alternative in the case of polynomial equations is factor. factor returns the polynomial factorized
into irreducible terms, and is capable of computing the factorization over various domains:
>>> f = x ** 4 - 3 * x ** 2 + 1
>>> sym.factor(f)
/ 2 \ / 2 \
\x - x - 1/*\x + x - 1/
>>> sym.factor(f, modulus=5)

2 2
(x - 2) *(x + 2)
SymPy is also able to solve boolean equations, that is, to decide if a certain boolean expression is
satisfiable or not. For this, we use the function satisfiable:
>>> sym.satisfiable(x & y)

{x: True, y: True}
This tells us that (x & y) is True whenever x and y are both True. If an expression cannot be true, i.e.
no values of its arguments can make the expression True, it will return False:
>>> sym.satisfiable(x & ~x)

False
Exercises
1. Solve the system of equations 𝑥 + 𝑦 = 2, 2 · 𝑥 + 𝑦 = 0

2. Are there boolean values x, y that make (~x | y) & (~y | x) true?
16.4. Equation solving 563

16.5 Linear Algebra
16.5.1 Matrices
Matrices are created as instances from the Matrix class:
>>> sym.Matrix([[1, 0], [0, 1]])

[1 0]
[ ]
[0 1]
unlike a NumPy array, you can also put Symbols in it:
>>> x, y = sym.symbols('x, y')

>>> A = sym.Matrix([[1, x], [y, 1]])
>>> A
[1 x]
[ ]
[y 1]
>>> A**2
[x*y + 1 2*x ]
[ ]
[ 2*y x*y + 1]
16.5.2 Differential Equations
SymPy is capable of solving (some) Ordinary Differential. To solve differential equations, use dsolve.
First, create an undefined function by passing cls=Function to the symbols function:
>>> f, g = sym.symbols('f g', cls=sym.Function)
f and g are now undefined functions. We can call f(x), and it will represent an unknown function:
>>> f(x)
f(x)
>>> f(x).diff(x, x) + f(x)

2
d
f(x) + ---(f(x))
2
dx
>>> sym.dsolve(f(x).diff(x, x) + f(x), f(x))

f(x) = C1*sin(x) + C2*cos(x)
Keyword arguments can be given to this function in order to help if find the best possible resolution sys-
tem. For example, if you know that it is a separable equations, you can use keyword hint='separable'
to force dsolve to resolve it as a separable equation:
>>> sym.dsolve(sym.sin(x) * sym.cos(f(x)) + sym.cos(x) * sym.sin(f(x)) * f(x).diff(x),

˓→ f(x), hint='separable')
/ C1 \ / C1 \
[f(x) = - acos|------| + 2*pi, f(x) = acos|------|]
\cos(x)/ \cos(x)/
16.5. Linear Algebra 564

Exercises
1. Solve the Bernoulli differential equation
𝑑𝑓 (𝑥)
𝑥 + 𝑓 (𝑥) − 𝑓 (𝑥)2 = 0
𝑥
2. Solve the same equation using hint='Bernoulli'. What do you observe ?
16.5. Linear Algebra 565

CHAPTER 17
scikit-image: image processing
Author: Emmanuelle Gouillart

scikit-image is a Python package dedicated to image processing, using NumPy arrays as image objects.
This chapter describes how to use scikit-image for various image processing tasks, and how it relates
to other scientific Python modules such as NumPy and SciPy.
See also:
For basic image manipulation, such as image cropping or simple filtering, a large number of simple
operations can be realized with NumPy and SciPy only. See Image manipulation and processing using
NumPy and SciPy.
Note that you should be familiar with the content of the previous chapter before reading the current
one, as basic operations such as masking and labeling are a prerequisite.
Chapters contents
• Introduction and concepts

– scikit-image and the scientific Python ecosystem
– What is included in scikit-image
• Importing
• Example data
• Input/output, data types and colorspaces
– Data types
– Colorspaces
• Image preprocessing / enhancement
566
– Local filters
– Non-local filters
– Mathematical morphology
• Image segmentation
– Binary segmentation: foreground + background
– Marker based methods
• Measuring regions’ properties
• Data visualization and interaction
• Feature extraction for computer vision
• Examples for the scikit-image chapter
17.1 Introduction and concepts
Images are NumPy’s arrays np.ndarray

image
np.ndarray
pixels
array values: a[2, 3]
channels
array dimensions
image encoding
dtype (np.uint8, np.uint16, np.float)
filters
functions (numpy, skimage, scipy)

>>> check = np.zeros((8, 8))
>>> check[::2, 1::2] = 1
>>> check[1::2, ::2] = 1
>>> plt.imshow(check, cmap='gray', interpolation='nearest')
17.1. Introduction and concepts 567

17.1.1 scikit-image and the scientific Python ecosystem
scikit-image is packaged in both pip and conda-based Python installations, as well as in most Linux
distributions. Other Python packages for image processing & visualization that operate on NumPy
arrays include:
scipy.ndimage
For N-dimensional arrays. Basic filtering, mathematical morphology, regions properties
Mahotas
With a focus on high-speed implementations.
Napari
A fast, interactive, multi-dimensional image viewer built in Qt.
Some powerful C++ image processing libraries also have Python bindings:
OpenCV
A highly optimized computer vision library with a focus on real-time applications.
ITK
The Insight ToolKit, especially useful for registration and working with 3D images.
To varying degrees, these tend to be less Pythonic and NumPy-friendly.
17.1.2 What is included in scikit-image
• Website: https://scikit-image.org/
• Gallery of examples: https://scikit-image.org/docs/stable/auto_examples/
The library contains predominantly image processing algorithms, but also utility functions to ease data
handling and processing. It contains the following submodules:
color
Color space conversion.
data
Test images and example data.
draw
Drawing primitives (lines, text, etc.) that operate on NumPy arrays.
17.1. Introduction and concepts 568

exposure
Image intensity adjustment, e.g., histogram equalization, etc.
feature
Feature detection and extraction, e.g., texture analysis corners, etc.
filters
Sharpening, edge finding, rank filters, thresholding, etc.
graph
Graph-theoretic operations, e.g., shortest paths.
io
Reading, saving, and displaying images and video.
measure
Measurement of image properties, e.g., region properties and contours.
metrics
Metrics corresponding to images, e.g. distance metrics, similarity, etc.
morphology
Morphological operations, e.g., opening or skeletonization.
restoration
Restoration algorithms, e.g., deconvolution algorithms, denoising, etc.
segmentation
Partitioning an image into multiple regions.
transform
Geometric and other transforms, e.g., rotation or the Radon transform.
util
Generic utilities.
17.2 Importing
We import scikit-image using the convention:
>>> import skimage as ski
Most functionality lives in subpackages, e.g.:
>>> image = ski.data.cat()
You can list all submodules with:
>>> for m in dir(ski): print(m)

__version__
color
data
draw
exposure
feature
filters
future
graph
io
measure
metrics
morphology
17.2. Importing 569


registration
restoration
segmentation
transform
util
Most scikit-image functions take NumPy ndarrays as arguments
>>> camera = ski.data.camera()

>>> camera.dtype
dtype('uint8')
>>> camera.shape
(512, 512)
>>> filtered_camera = ski.filters.gaussian(camera, sigma=1)
>>> type(filtered_camera)
<class 'numpy.ndarray'>
17.3 Example data
To start off, we need example images to work with. The library ships with a few of these:
skimage.data
>>> image = ski.data.cat()

>>> image.shape
(300, 451, 3)
17.4 Input/output, data types and colorspaces
I/O: skimage.io
Save an image to disk: skimage.io.imsave()
>>> ski.io.imsave("cat.png", image)
Reading from files: skimage.io.imread()
>>> cat = ski.io.imread("cat.png")
17.3. Example data 570

This works with many data formats supported by the ImageIO library.
Loading also works with URLs:
>>> logo = ski.io.imread('https://scikit-image.org/_static/img/logo.png')
17.4.1 Data types
Image ndarrays can be represented either by integers (signed or unsigned) or floats.

Careful with overflows with integer data types

>>> camera.dtype
dtype('uint8')
>>> camera_multiply = 3 * camera
Different integer sizes are possible: 8-, 16- or 32-bytes, signed or unsigned.
Warning: An important (if questionable) skimage convention: float images are supposed to lie
in [-1, 1] (in order to have comparable contrast for all float images)
>>> camera_float = ski.util.img_as_float(camera)
>>> camera.max(), camera_float.max()
(255, 1.0)
17.4. Input/output, data types and colorspaces 571

Some image processing routines need to work with float arrays, and may hence output an array with a
different type and the data range from the input array
>>> camera_sobel = ski.filters.sobel(camera)

>>> camera_sobel.max()
0.644...
Utility functions are provided in skimage to convert both the dtype and the data range, following
skimage’s conventions: util.img_as_float, util.img_as_ubyte, etc.
See the user guide for more details.
17.4.2 Colorspaces
Color images are of shape (N, M, 3) or (N, M, 4) (when an alpha channel encodes transparency)
>>> face = sp.datasets.face()

>>> face.shape
(768, 1024, 3)
Routines converting between different colorspaces (RGB, HSV, LAB etc.) are available in skimage.
color : color.rgb2hsv, color.lab2rgb, etc. Check the docstring for the expected dtype (and data
range) of input images.
3D images
Most functions of skimage can take 3D images as input arguments. Check the docstring to know if a
function can be used on 3D images (for example MRI or CT images).
Exercise
Open a color image on your disk as a NumPy array.

Find a skimage function computing the histogram of an image and plot the histogram of
each color channel
Convert the image to grayscale and plot its histogram.
17.5 Image preprocessing / enhancement
Goals: denoising, feature (edges) extraction, . . .
17.5.1 Local filters
Local filters replace the value of pixels by a function of the values of neighboring pixels. The function
can be linear or non-linear.
Neighbourhood: square (choose size), disk, or more complicated structuring element.
17.5. Image preprocessing / enhancement 572

Example : horizontal Sobel filter
>>> text = ski.data.text()

>>> hsobel_text = ski.filters.sobel_h(text)
Uses the following linear kernel for computing horizontal gradients:
1 2 1
0 0 0
-1 -2 -1
17.5.2 Non-local filters
Non-local filters use a large region of the image (or all the image) to transform the value of one pixel:

>>> camera_equalized = ski.exposure.equalize_hist(camera)
Enhances contrast in large almost uniform regions.

See wikipedia for an introduction on mathematical morphology.

Probe an image with a simple shape (a structuring element), and modify this image according to how
the shape locally fits or misses the image.
Default structuring element: 4-connectivity of a pixel
>>> # Import structuring elements to make them more easily accessible

>>> from skimage.morphology import disk, diamond
>>> diamond(1)
array([[0, 1, 0],
[1, 1, 1],
[0, 1, 0]], dtype=uint8)
Erosion = minimum filter. Replace the value of a pixel by the minimal value covered by the structuring
element.:
>>> a = np.zeros((7,7), dtype=np.uint8)

>>> a[1:6, 2:5] = 1
>>> a
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 0, 0],
[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> ski.morphology.binary_erosion(a, diamond(1)).astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
>>> #Erosion removes objects smaller than the structure
>>> ski.morphology.binary_erosion(a, diamond(2)).astype(np.uint8)
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],


[0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
Dilation: maximum filter:
>>> a = np.zeros((5, 5))

>>> a[2, 2] = 1
>>> a
array([[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 1., 0., 0.],
[0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]])
>>> ski.morphology.binary_dilation(a, diamond(1)).astype(np.uint8)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
Opening: erosion + dilation:

>>> a[1:4, 1:4] = 1; a[4, 4] = 1
>>> a
array([[0, 0, 0, 0, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 1, 1, 1, 0],
[0, 0, 0, 0, 1]])
>>> ski.morphology.binary_opening(a, diamond(1)).astype(np.uint8)
array([[0, 0, 0, 0, 0],
[0, 0, 1, 0, 0],
[0, 1, 1, 1, 0],
[0, 0, 1, 0, 0],
[0, 0, 0, 0, 0]], dtype=uint8)
Opening removes small objects and smoothes corners.
Grayscale mathematical morphology
Mathematical morphology operations are also available for (non-binary) grayscale images (int or float
type). Erosion and dilation correspond to minimum (resp. maximum) filters.
Higher-level mathematical morphology are available: tophat, skeletonization, etc.

See also:
Basic mathematical morphology is also implemented in scipy.ndimage.morphology. The scipy.
ndimage implementation works on arbitrary-dimensional arrays.
Example of filters comparison: image denoising

>>> coins = ski.data.coins()
>>> coins_zoom = coins[10:80, 300:370]
>>> median_coins = ski.filters.median(

... coins_zoom, disk(1)

... )
>>> tv_coins = ski.restoration.denoise_tv_chambolle(
... coins_zoom, weight=0.1
... )
>>> gaussian_coins = ski.filters.gaussian(coins, sigma=2)
17.6 Image segmentation
Image segmentation is the attribution of different labels to different regions of the image, for example in
order to extract the pixels of an object of interest.
17.6.1 Binary segmentation: foreground + background
Histogram-based method: Otsu thresholding
Tip: The Otsu method is a simple heuristic to find a threshold to separate the foreground from the
background.
Earlier scikit-image versions
skimage.filters is called skimage.filter in earlier versions of scikit-image
camera = ski.data.camera()
val = ski.filters.threshold_otsu(camera)
mask = camera < val
17.6. Image segmentation 576

Labeling connected components of a discrete image
Tip: Once you have separated foreground objects, it is use to separate them from each other. For this,
we can assign a different integer labels to each one.
Synthetic data:
>>> n = 20
>>> l = 256
>>> points = l * rng.random((2, n ** 2))
>>> im = ski.filters.gaussian(im, sigma=l / (4. * n))
>>> blobs = im > im.mean()
Label all connected components:
>>> all_labels = ski.measure.label(blobs)
Label only foreground connected components:
>>> blobs_labels = ski.measure.label(blobs, background=0)
See also:
scipy.ndimage.find_objects() is useful to return slices on object in an image.

17.6.2 Marker based methods
If you have markers inside a set of regions, you can use these to segment the regions.
Watershed segmentation
The Watershed (skimage.segmentation.watershed()) is a region-growing approach that fills “basins”

in the image
>>> # Generate an initial image with two overlapping circles
>>> x, y = np.indices((80, 80))
>>> x1, y1, x2, y2 = 28, 28, 44, 52
>>> r1, r2 = 16, 20
>>> mask_circle1 = (x - x1) ** 2 + (y - y1) ** 2 < r1 ** 2
>>> mask_circle2 = (x - x2) ** 2 + (y - y2) ** 2 < r2 ** 2
>>> image = np.logical_or(mask_circle1, mask_circle2)
>>> # Now we want to separate the two objects in image
>>> # Generate the markers as local maxima of the distance
>>> # to the background
>>> distance = sp.ndimage.distance_transform_edt(image)
>>> peak_idx = ski.feature.peak_local_max(
... distance, footprint=np.ones((3, 3)), labels=image
... )
>>> peak_mask = np.zeros_like(distance, dtype=bool)
>>> peak_mask[tuple(peak_idx.T)] = True
>>> markers = ski.morphology.label(peak_mask)
>>> labels_ws = ski.segmentation.watershed(
... -distance, markers, mask=image
... )
Random walker segmentation
The random walker algorithm (skimage.segmentation.random_walker()) is similar to the Watershed,

but with a more “probabilistic” approach. It is based on the idea of the diffusion of labels in the image:
>>> # Transform markers image so that 0-valued pixels are to
>>> # be labelled, and -1-valued pixels represent background
>>> markers[~image] = -1
>>> labels_rw = ski.segmentation.random_walker(image, markers)
Postprocessing label images
skimage provides several utility functions that can be used on label images (ie images where
different discrete values identify different regions). Functions names are often self-explaining:

skimage.segmentation.clear_border(), skimage.segmentation.relabel_from_one(), skimage.

morphology.remove_small_objects(), etc.
Exercise
• Load the coins image from the data submodule.

• Separate the coins from the background by testing several segmentation methods: Otsu thresh-
olding, adaptive thresholding, and watershed or random walker segmentation.
• If necessary, use a postprocessing function to improve the coins / background segmentation.
17.7 Measuring regions’ properties
Example: compute the size and perimeter of the two segmented regions:
>>> properties = ski.measure.regionprops(labels_rw)

>>> [float(prop.area) for prop in properties]
[770.0, 1168.0]
>>> [prop.perimeter for prop in properties]
[100.91..., 126.81...]
See also:
for some properties, functions are available as well in scipy.ndimage.measurements with a different
API (a list is returned).
Exercise (continued)
• Use the binary image of the coins and background from the previous exercise.
• Compute an image of labels for the different coins.
• Compute the size and eccentricity of all coins.
17.8 Data visualization and interaction
Meaningful visualizations are useful when testing a given processing pipeline.

Some image processing operations:
>>> coins = ski.data.coins()

>>> mask = coins > ski.filters.threshold_otsu(coins)
>>> clean_border = ski.segmentation.clear_border(mask)
Visualize binary result:
>>> plt.figure()
>>> plt.imshow(clean_border, cmap='gray')
Visualize contour
17.7. Measuring regions’ properties 579

>>> plt.figure()
>>> plt.imshow(coins, cmap='gray')
>>> plt.contour(clean_border, [0.5])
<matplotlib.contour.QuadContourSet ...>
Use skimage dedicated utility function:
>>> coins_edges = ski.segmentation.mark_boundaries(

... coins, clean_border.astype(int)
... )
17.9 Feature extraction for computer vision
Geometric or textural descriptor can be extracted from images in order to

• classify parts of the image (e.g. sky vs. buildings)
• match parts of different images (e.g. for object detection)
• and many other applications of Computer Vision
Example: detecting corners using Harris detector
tform = ski.transform.AffineTransform(
scale=(1.3, 1.1), rotation=1, shear=0.7,
translation=(210, 50)
)
image = ski.transform.warp(
data.checkerboard(), tform.inverse, output_shape=(350, 350)
)
coords = ski.feature.corner_peaks(
ski.feature.corner_harris(image), min_distance=5
)
coords_subpix = ski.feature.corner_subpix(
image, coords, window_size=13
)
17.9. Feature extraction for computer vision 580

(this example is taken from the plot_corner example in scikit-image)

Points of interest such as corners can then be used to match objects in different images, as described in
the plot_matching example of scikit-image.
17.11 Examples for the scikit-image chapter
17.11.1 Creating an image
How to create an image with basic NumPy commands : np.zeros, slicing. . .

This examples show how to create a simple checkerboard.

import numpy as np
check = np.zeros((8, 8))

check[::2, 1::2] = 1
check[1::2, ::2] = 1
plt.matshow(check, cmap="gray")
plt.show()
17.11.2 Displaying a simple image
Load and display an image
17.11. Examples for the scikit-image chapter 582


from skimage import data
camera = data.camera()
plt.imshow(camera, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.tight_layout()
plt.show()
17.11.3 Integers can overflow
An illustration of overflow problem arising when working with integers


camera_multiply = 3 * camera
plt.subplot(121)
plt.axis("off")
plt.subplot(122)
plt.imshow(camera_multiply, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.tight_layout()
plt.show()
17.11.4 Equalizing the histogram of an image
Histogram equalizing makes images have a uniform histogram.

from skimage import data, exposure

camera_equalized = exposure.equalize_hist(camera)
plt.subplot(121)
plt.axis("off")
plt.subplot(122)
plt.imshow(camera_equalized, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.tight_layout()
plt.show()
17.11.5 Computing horizontal gradients with the Sobel filter
This example illustrates the use of the horizontal Sobel filter, to compute horizontal gradients.

from skimage import filters
text = data.text()


hsobel_text = filters.sobel_h(text)
plt.subplot(121)
plt.imshow(text, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.subplot(122)
plt.imshow(hsobel_text, cmap="nipy_spectral", interpolation="nearest")
plt.axis("off")
plt.tight_layout()
plt.show()
17.11.6 Segmentation contours
Visualize segmentation contours on original grayscale image.
from skimage import data, segmentation

import numpy as np
coins = data.coins()
mask = coins > filters.threshold_otsu(coins)
clean_border = segmentation.clear_border(mask).astype(int)
coins_edges = segmentation.mark_boundaries(coins, clean_border)
plt.subplot(121)
plt.imshow(clean_border, cmap="gray")
plt.axis("off")
plt.subplot(122)
plt.imshow(coins_edges)
plt.axis("off")

plt.tight_layout()
plt.show()
17.11.7 Otsu thresholding
This example illustrates automatic Otsu thresholding.

from skimage import exposure
val = filters.threshold_otsu(camera)
hist, bins_center = exposure.histogram(camera)
plt.subplot(131)
plt.axis("off")
plt.subplot(132)
plt.imshow(camera < val, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.subplot(133)
plt.plot(bins_center, hist, lw=2)
plt.axvline(val, color="k", ls="--")
plt.tight_layout()
plt.show()

17.11.8 Affine transform
Warping and affine transforms of images.

from skimage.feature import corner_harris, corner_subpix, corner_peaks
from skimage.transform import warp, AffineTransform
tform = AffineTransform(scale=(1.3, 1.1), rotation=1, shear=0.7, translation=(210,␣

˓→50))
image = warp(data.checkerboard(), tform.inverse, output_shape=(350, 350))
coords = corner_peaks(corner_harris(image), min_distance=5)

coords_subpix = corner_subpix(image, coords, window_size=13)
plt.gray()
plt.imshow(image, interpolation="nearest")
plt.plot(coords_subpix[:, 1], coords_subpix[:, 0], "+r", markersize=15, mew=5)
plt.plot(coords[:, 1], coords[:, 0], ".b", markersize=7)
plt.axis("off")
plt.show()

17.11.9 Labelling connected components of an image
This example shows how to label connected components of a binary image, using the dedicated skim-
age.measure.label function.
from skimage import measure

import numpy as np
n = 12
l = 256
im = filters.gaussian(im, sigma=l / (4.0 * n))
blobs = im > 0.7 * im.mean()
all_labels = measure.label(blobs)
blobs_labels = measure.label(blobs, background=0)
plt.subplot(131)
plt.imshow(blobs, cmap="gray")
plt.axis("off")
plt.subplot(132)
plt.imshow(all_labels, cmap="nipy_spectral")
plt.axis("off")
plt.subplot(133)
plt.imshow(blobs_labels, cmap="nipy_spectral")
plt.axis("off")
plt.tight_layout()
plt.show()

17.11.10 Various denoising filters
This example compares several denoising filters available in scikit-image: a Gaussian filter, a median
filter, and total variation denoising.
import numpy as np
from skimage import restoration
coins = data.coins()
gaussian_filter_coins = filters.gaussian(coins, sigma=2)
med_filter_coins = filters.median(coins, np.ones((3, 3)))
tv_filter_coins = restoration.denoise_tv_chambolle(coins, weight=0.1)
plt.subplot(141)
plt.imshow(coins[10:80, 300:370], cmap="gray", interpolation="nearest")
plt.axis("off")
plt.title("Image")
plt.subplot(142)
plt.imshow(gaussian_filter_coins[10:80, 300:370], cmap="gray", interpolation="nearest
˓→")
plt.axis("off")
plt.title("Gaussian filter")
plt.subplot(143)
plt.imshow(med_filter_coins[10:80, 300:370], cmap="gray", interpolation="nearest")
plt.axis("off")
plt.title("Median filter")
plt.subplot(144)
plt.imshow(tv_filter_coins[10:80, 300:370], cmap="gray", interpolation="nearest")
plt.axis("off")
plt.title("TV filter")
plt.show()

17.11.11 Watershed and random walker for segmentation
This example compares two segmentation methods in order to separate two connected disks: the water-
shed algorithm, and the random walker algorithm.
Both segmentation methods require seeds, that are pixels belonging unambigusouly to a reagion. Here,
local maxima of the distance map to the background are used as seeds.
import numpy as np
from skimage.segmentation import watershed
from skimage.feature import peak_local_max
from skimage import measure
from skimage.segmentation import random_walker
import scipy as sp
# Generate an initial image with two overlapping circles

x, y = np.indices((80, 80))
x1, y1, x2, y2 = 28, 28, 44, 52
r1, r2 = 16, 20
image = np.logical_or(mask_circle1, mask_circle2)
# Now we want to separate the two objects in image
# Generate the markers as local maxima of the distance
# to the background
distance = sp.ndimage.distance_transform_edt(image)
peak_idx = peak_local_max(distance, footprint=np.ones((3, 3)), labels=image)
peak_mask = np.zeros_like(distance, dtype=bool)
peak_mask[tuple(peak_idx.T)] = True
markers = measure.label(peak_mask)
labels_ws = watershed(-distance, markers, mask=image)
markers[~image] = -1
labels_rw = random_walker(image, markers)
plt.subplot(141)
plt.imshow(image, cmap="gray", interpolation="nearest")
plt.axis("off")
plt.title("image")
plt.subplot(142)
plt.imshow(-distance, interpolation="nearest")
plt.axis("off")
plt.title("distance map")
plt.subplot(143)


plt.imshow(labels_ws, cmap="nipy_spectral", interpolation="nearest")
plt.axis("off")
plt.title("watershed segmentation")
plt.subplot(144)
plt.imshow(labels_rw, cmap="nipy_spectral", interpolation="nearest")
plt.axis("off")
plt.title("random walker segmentation")
plt.tight_layout()
plt.show()

CHAPTER 18
scikit-learn: machine learning in Python
Authors: Gael Varoquaux
Prerequisites
• numpy
• scipy
• matplotlib (optional)
• ipython (the enhancements come handy)
Acknowledgements
This chapter is adapted from a tutorial given by Gaël Varoquaux, Jake Vanderplas, Olivier Grisel.
See also:
Data science in Python
• The Statistics in Python chapter may also be of interest for readers looking into machine learning.
• The documentation of scikit-learn is very complete and didactic.
593
Chapters contents
• Introduction: problem settings

• Basic principles of machine learning with scikit-learn
• Supervised Learning: Classification of Handwritten Digits
• Supervised Learning: Regression of Housing Data
• Measuring prediction performance
• Unsupervised Learning: Dimensionality Reduction and Visualization
• Parameter selection, Validation, and Testing
• Examples for the scikit-learn chapter
18.1 Introduction: problem settings
18.1.1 What is machine learning?
Tip: Machine Learning is about building programs with tunable parameters that are adjusted
automatically so as to improve their behavior by adapting to previously seen data.
Machine Learning can be considered a subfield of Artificial Intelligence since those algorithms can be
seen as building blocks to make computers learn to behave more intelligently by somehow generalizing
rather that just storing and retrieving data items like a database system would do.
Fig. 1: A classification problem
We’ll take a look at two very simple machine learning tasks here. The first is a classification task:
the figure shows a collection of two-dimensional data, colored according to two different class labels. A
classification algorithm may be used to draw a dividing boundary between the two clusters of points:
By drawing this separating line, we have learned a model which can generalize to new data: if you were
to drop another point onto the plane which is unlabeled, this algorithm could now predict whether it’s
a blue or a red point.
18.1. Introduction: problem settings 594

Fig. 2: A regression problem
The next simple task we’ll look at is a regression task: a simple best-fit line to a set of data.
Again, this is an example of fitting a model to data, but our focus here is that the model can make
generalizations about new data. The model has been learned from the training data, and can be used
to predict the result of test data: here, we might be given an x-value, and the model would allow us to
predict the y value.
18.1.2 Data in scikit-learn
The data matrix
Machine learning algorithms implemented in scikit-learn expect data to be stored in a two-dimensional

array or matrix. The arrays can be either numpy arrays, or in some cases scipy.sparse matrices. The
size of the array is expected to be [n_samples, n_features]
• n_samples: The number of samples: each sample is an item to process (e.g. classify). A sample
can be a document, a picture, a sound, a video, an astronomical object, a row in database or CSV
file, or whatever you can describe with a fixed set of quantitative traits.
• n_features: The number of features or distinct traits that can be used to describe each item in
a quantitative manner. Features are generally real-valued, but may be boolean or discrete-valued
in some cases.
Tip: The number of features must be fixed in advance. However it can be very high dimensional (e.g.
millions of features) with most of them being zeros for a given sample. This is a case where scipy.sparse
matrices can be useful, in that they are much more memory-efficient than NumPy arrays.

A Simple Example: the Iris Dataset
The application problem
As an example of a simple dataset, let us a look at the iris data stored by scikit-learn. Suppose we want
to recognize species of irises. The data consists of measurements of three different species of irises:
Setosa Iris Versicolor Iris Virginica Iris
Quick Question:
If we want to design an algorithm to recognize iris species, what might the

data be?
Remember: we need a 2D array of size [n_samples x n_features].
• What would the n_samples refer to?
• What might the n_features refer to?
Remember that there must be a fixed number of features for each sample, and feature number i must
be a similar kind of quantity for each sample.
Loading the Iris Data with Scikit-learn
Scikit-learn has a very straightforward set of data on these iris species. The data consist of the following:
• Features in the Iris dataset:
– sepal length (cm)
– sepal width (cm)
– petal length (cm)
– petal width (cm)
• Target classes to predict:
– Setosa
– Versicolour
– Virginica
scikit-learn embeds a copy of the iris CSV file along with a function to load it into NumPy arrays:
>>> from sklearn.datasets import load_iris

>>> iris = load_iris()

Note: Import sklearn Note that scikit-learn is imported as sklearn
The features of each sample flower are stored in the data attribute of the dataset:
>>> print(iris.data.shape)
(150, 4)
>>> n_samples, n_features = iris.data.shape
>>> print(n_samples)
150
>>> print(n_features)
4
>>> print(iris.data[0])
[5.1 3.5 1.4 0.2]
The information about the class of each sample is stored in the target attribute of the dataset:
>>> print(iris.target.shape)
(150,)
>>> print(iris.target)
[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2]
The names of the classes are stored in the last attribute, namely target_names:
>>> print(iris.target_names)
['setosa' 'versicolor' 'virginica']
This data is four-dimensional, but we can visualize two of the dimensions at a time using a scatter plot:

Exercise:
Can you choose 2 features to find a plot where it is easier to separate the different classes of irises?
Hint: click on the figure above to see the code that generates it, and modify this code.
18.2 Basic principles of machine learning with scikit-learn
18.2.1 Introducing the scikit-learn estimator object
Every algorithm is exposed in scikit-learn via an ‘’Estimator” object. For instance a linear regression is:
sklearn.linear_model.LinearRegression
>>> from sklearn.linear_model import LinearRegression
Estimator parameters: All the parameters of an estimator can be set when it is instantiated:
>>> model = LinearRegression(n_jobs=1)

>>> print(model)
LinearRegression(n_jobs=1)
Fitting on data
Let’s create some simple data with numpy:

>>> x = np.array([0, 1, 2])
>>> y = np.array([0, 1, 2])
>>> X = x[:, np.newaxis] # The input data for sklearn is 2D: (samples == 3 x features␣
˓→== 1)
>>> X
array([[0],
[1],
[2]])
>>> model.fit(X, y)
LinearRegression(n_jobs=1)
Estimated parameters: When data is fitted with an estimator, parameters are estimated from the data
at hand. All the estimated parameters are attributes of the estimator object ending by an underscore:
>>> model.coef_
array([1.])
18.2. Basic principles of machine learning with scikit-learn 598

18.2.2 Supervised Learning: Classification and regression
In Supervised Learning, we have a dataset consisting of both features and labels. The task is to
construct an estimator which is able to predict the label of an object given the set of features. A
relatively simple example is predicting the species of iris given a set of measurements of its flower. This
is a relatively simple task. Some more complicated examples are:
• given a multicolor image of an object through a telescope, determine whether that object is a star,
a quasar, or a galaxy.
• given a photograph of a person, identify the person in the photo.
• given a list of movies a person has watched and their personal rating of the movie, recommend a
list of movies they would like (So-called recommender systems: a famous example is the Netflix
Prize).
Tip: What these tasks have in common is that there is one or more unknown quantities associated
with the object which needs to be determined from other observed quantities.
Supervised learning is further broken down into two categories, classification and regression. In
classification, the label is discrete, while in regression, the label is continuous. For example, in astronomy,
the task of determining whether an object is a star, a galaxy, or a quasar is a classification problem: the
label is from three distinct categories. On the other hand, we might wish to estimate the age of an object
based on such observations: this would be a regression problem, because the label (age) is a continuous
quantity.
Classification: K nearest neighbors (kNN) is one of the simplest learning strategies: given a new,
unknown observation, look up in your reference database which ones have the closest features and assign
the predominant class. Let’s try it out on our iris classification problem:
from sklearn import neighbors, datasets

iris = datasets.load_iris()
X, y = iris.data, iris.target
knn = neighbors.KNeighborsClassifier(n_neighbors=1)
knn.fit(X, y)
# What kind of iris has 3cm x 5cm sepal and 4cm x 2cm petal?
print(iris.target_names[knn.predict([[3, 5, 4, 2]])])
Regression: The simplest possible regression setting is the linear regression one:
from sklearn.linear_model import LinearRegression
# x from 0 to 30
x = 30 * rng.random((20, 1))
# y = a*x + b with noise

y = 0.5 * x + 1.0 + rng.normal(size=x.shape)
# create a linear regression model

model = LinearRegression()
model.fit(x, y)
# predict y from the data

x_new = np.linspace(0, 30, 100)
y_new = model.predict(x_new[:, np.newaxis])

Fig. 3: A plot of the sepal space and the prediction of the KNN
Fig. 4: A plot of a simple linear regression.

18.2.3 A recap on Scikit-learn’s estimator interface
Scikit-learn strives to have a uniform interface across all methods, and we’ll see examples of these below.
Given a scikit-learn estimator object named model, the following methods are available:
In all Estimators
• model.fit() : fit training data. For supervised learning applications, this accepts
two arguments: the data X and the labels y (e.g. model.fit(X, y)). For unsu-
pervised learning applications, this accepts only a single argument, the data X (e.g.
model.fit(X)).
In supervised estimators
• model.predict() : given a trained model, predict the label of a new set of
data. This method accepts one argument, the new data X_new (e.g. model.
predict(X_new)), and returns the learned label for each object in the array.
• model.predict_proba() : For classification problems, some estimators also pro-
vide this method, which returns the probability that a new observation has each
categorical label. In this case, the label with the highest probability is returned by
model.predict().
• model.score() : for classification or regression problems, most (all?) estimators
implement a score method. Scores are between 0 and 1, with a larger score indicating
a better fit.
In unsupervised estimators
• model.transform() : given an unsupervised model, transform new data into the
new basis. This also accepts one argument X_new, and returns the new representa-
tion of the data based on the unsupervised model.
• model.fit_transform() : some estimators implement this method, which more
efficiently performs a fit and a transform on the same input data.
18.2.4 Regularization: what it is and why it is necessary
Preferring simpler models
Train errors Suppose you are using a 1-nearest neighbor estimator. How many errors do you expect
on your train set?
• Train set error is not a good measurement of prediction performance. You need to leave out a test
set.
• In general, we should accept errors on the train set.
An example of regularization The core idea behind regularization is that we are going to prefer
models that are simpler, for a certain definition of ‘’simpler”, even if they lead to more errors on the
train set.
As an example, let’s generate with a 9th order polynomial, with noise:
And now, let’s fit a 4th order and a 9th order polynomial to the data.
With your naked eyes, which model do you prefer, the 4th order one, or the 9th order one?
Let’s look at the ground truth:
Tip: Regularization is ubiquitous in machine learning. Most scikit-learn estimators have a parameter
to tune the amount of regularization. For instance, with k-NN, it is ‘k’, the number of nearest neighbors
used to make the decision. k=1 amounts to no regularization: 0 error on the training set, whereas large
k will push toward smoother decision boundaries in the feature space.


Simple versus complex models for classification
A linear separation A non-linear separation
Tip: For classification models, the decision boundary, that separates the class expresses the complexity
of the model. For instance, a linear model, that makes a decision based on a linear combination of
features, is more complex than a non-linear one.

18.3 Supervised Learning: Classification of Handwritten Digits
18.3.1 The nature of the data
Code and notebook
Python code and Jupyter notebook for this section are found here
In this section we’ll apply scikit-learn to the classification of handwritten digits. This will go a bit beyond
the iris classification we saw before: we’ll discuss some of the metrics which can be used in evaluating
the effectiveness of a classification model.
>>> from sklearn.datasets import load_digits
>>> digits = load_digits()
Let us visualize the data and remind us what we’re looking at (click on the figure for the full code):
# plot the digits: each image is 8x8 pixels

for i in range(64):
18.3. Supervised Learning: Classification of Handwritten Digits 604


ax = fig.add_subplot(8, 8, i + 1, xticks=[], yticks=[])
ax.imshow(digits.images[i], cmap=plt.cm.binary, interpolation='nearest')
18.3.2 Visualizing the Data on its principal components
A good first-step for many problems is to visualize the data using a Dimensionality Reduction technique.
We’ll start with the most straightforward one, Principal Component Analysis (PCA).
PCA seeks orthogonal linear combinations of the features which show the greatest variance, and as such,
can help give you a good idea of the structure of the data set.
>>> from sklearn.decomposition import PCA

>>> pca = PCA(n_components=2)
>>> proj = pca.fit_transform(digits.data)
>>> plt.scatter(proj[:, 0], proj[:, 1], c=digits.target)
<matplotlib.collections.PathCollection object at ...>
>>> plt.colorbar()
Question
Given these projections of the data, which numbers do you think a classifier might have trouble
distinguishing?

18.3.3 Gaussian Naive Bayes Classification
For most classification problems, it’s nice to have a simple, fast method to provide a quick baseline
classification. If the simple and fast method is sufficient, then we don’t have to waste CPU cycles on
more complex models. If not, we can use the results of the simple method to give us clues about our
data.
One good method to keep in mind is Gaussian Naive Bayes (sklearn.naive_bayes.GaussianNB).
Old scikit-learn versions
train_test_split() is imported from sklearn.cross_validation
Tip: Gaussian Naive Bayes fits a Gaussian distribution to each training label independently on each
feature, and uses this to quickly give a rough classification. It is generally not sufficiently accurate for
real-world data, but can perform surprisingly well, for instance on text data.
>>> from sklearn.naive_bayes import GaussianNB

>>> from sklearn.model_selection import train_test_split
>>> # split the data into training and validation sets

>>> X_train, X_test, y_train, y_test = train_test_split(digits.data, digits.target)
>>> # train the model

>>> clf = GaussianNB()
>>> clf.fit(X_train, y_train)
GaussianNB()
>>> # use the model to predict the labels of the test data
>>> predicted = clf.predict(X_test)
>>> expected = y_test
>>> print(predicted)
[5 1 7 2 8 9 4 3 9 3 6 2 3 2 6 7 4 3 5 7 5 7 0 1 2 5 9 8 1 8...]
>>> print(expected)
[5 8 7 2 8 9 4 3 7 3 6 2 3 2 6 7 4 3 5 7 5 7 0 1 2 5 3 3 1 8...]
As above, we plot the digits with the predicted labels to get an idea of how well the classification is
working.

Question
Why did we split the data into training and validation sets?
18.3.4 Quantitative Measurement of Performance
We’d like to measure the performance of our estimator without having to resort to plotting examples. A
simple method might be to simply compare the number of matches:
>>> matches = (predicted == expected)

>>> print(matches.sum())
371
>>> print(len(matches))
450
>>> matches.sum() / float(len(matches))
0.82444...
We see that more than 80% of the 450 predictions match the input. But there are other more sophisticated

metrics that can be used to judge the performance of a classifier: several are available in the sklearn.
metrics submodule.
One of the most useful metrics is the classification_report, which combines several measures and
prints a table with the results:
>>> from sklearn import metrics

>>> print(metrics.classification_report(expected, predicted))
precision recall f1-score support
0 1.00 0.98 0.99 45

1 0.91 0.66 0.76 44
2 0.91 0.56 0.69 36
3 0.89 0.67 0.77 49
4 0.95 0.83 0.88 46
5 0.93 0.93 0.93 45
6 0.92 0.98 0.95 47
7 0.75 0.96 0.84 50
8 0.49 0.97 0.66 39
9 0.85 0.67 0.75 49
accuracy 0.82 450

macro avg 0.86 0.82 0.82 450
weighted avg 0.86 0.82 0.83 450
Another enlightening metric for this sort of multi-label classification is a confusion matrix: it helps us
visualize which labels are being interchanged in the classification errors:
>>> print(metrics.confusion_matrix(expected, predicted))

[[44 0 0 0 0 0 0 0 0 1]
[ 0 29 0 0 0 0 1 6 6 2]
[ 0 1 20 1 0 0 0 0 14 0]
[ 0 0 0 33 0 2 0 1 11 2]
[ 0 0 0 0 38 1 2 4 1 0]
[ 0 0 0 0 0 42 1 0 2 0]
[ 0 0 0 0 0 0 46 0 1 0]
[ 0 0 0 0 1 0 0 48 0 1]
[ 0 1 0 0 0 0 0 0 38 0]
[ 0 1 2 3 1 0 0 5 4 33]]
We see here that in particular, the numbers 1, 2, 3, and 9 are often being labeled 8.
18.4 Supervised Learning: Regression of Housing Data
Here we’ll do a short example of a regression problem: learning a continuous value from a set of features.
18.4.1 A quick look at the data
Code and notebook
We’ll use the California house prices set, available in scikit-learn. This records measurements of 8
attributes of housing markets in California, as well as the median price. The question is: can you predict
the price of a new market given its attributes?:
18.4. Supervised Learning: Regression of Housing Data 608

>>> from sklearn.datasets import fetch_california_housing

>>> data = fetch_california_housing(as_frame=True)
>>> print(data.data.shape)
(20640, 8)
>>> print(data.target.shape)
(20640,)
We can see that there are just over 20000 data points.
The DESCR variable has a long description of the dataset:
>>> print(data.DESCR)
.. _california_housing_dataset:
California Housing dataset

--------------------------
**Data Set Characteristics:**
:Number of Instances: 20640
:Number of Attributes: 8 numeric, predictive attributes and the target
:Attribute Information:
- MedInc median income in block group
- HouseAge median house age in block group
- AveRooms average number of rooms per household
- AveBedrms average number of bedrooms per household
- Population block group population
- AveOccup average number of household members
- Latitude block group latitude
- Longitude block group longitude
:Missing Attribute Values: None
This dataset was obtained from the StatLib repository.

https://www.dcc.fc.up.pt/~ltorgo/Regression/cal_housing.html
The target variable is the median house value for California districts,
expressed in hundreds of thousands of dollars ($100,000).
This dataset was derived from the 1990 U.S. census, using one row per census
block group. A block group is the smallest geographical unit for which the U.S.
Census Bureau publishes sample data (a block group typically has a population
of 600 to 3,000 people).
A household is a group of people residing within a home. Since the average

number of rooms and bedrooms in this dataset are provided per household, these
columns may take surprisingly large values for block groups with few households
and many empty houses, such as vacation resorts.
It can be downloaded/loaded using the

:func:`sklearn.datasets.fetch_california_housing` function.
.. topic:: References
- Pace, R. Kelley and Ronald Barry, Sparse Spatial Autoregressions,

Statistics and Probability Letters, 33 (1997) 291-297

It often helps to quickly visualize pieces of the data using histograms, scatter plots, or other plot types.
With matplotlib, let us show a histogram of the target values: the median price in each neighborhood:
>>> plt.hist(data.target)
(array([...
Let’s have a quick look to see if some features are more relevant than others for our problem:
>>> for index, feature_name in enumerate(data.feature_names):

... plt.figure()
... plt.scatter(data.data[feature_name], data.target)
<Figure size...

This is a manual version of a technique called feature selection.
Tip: Sometimes, in Machine Learning it is useful to use feature selection to decide which features are
the most useful for a particular problem. Automated methods exist which quantify this sort of exercise
of choosing the most informative features.

18.4.2 Predicting Home Prices: a Simple Linear Regression
Now we’ll use scikit-learn to perform a simple linear regression on the housing data. There are many
possibilities of regressors to use. A particularly simple one is LinearRegression: this is basically a
wrapper around an ordinary least squares calculation.
>>> from sklearn.model_selection import train_test_split
>>> X_train, X_test, y_train, y_test = train_test_split(data.data, data.target)
>>> clf = LinearRegression()
>>> clf.fit(X_train, y_train)
LinearRegression()
>>> predicted = clf.predict(X_test)
>>> expected = y_test
>>> print("RMS: %s " % np.sqrt(np.mean((predicted - expected) ** 2)))
RMS: 0.7...
We can plot the error: expected as a function of predicted:
>>> plt.scatter(expected, predicted)

Tip: The prediction at least correlates with the true price, though there are clearly some biases. We
could imagine evaluating the performance of the regressor by, say, computing the RMS residuals between
the true and predicted price. There are some subtleties in this, however, which we’ll cover in a later
section.
Exercise: Gradient Boosting Tree Regression
There are many other types of regressors available in scikit-learn: we’ll try a more powerful one here.
Use the GradientBoostingRegressor class to fit the housing data.
hint You can copy and paste some of the above code, replacing LinearRegression with
GradientBoostingRegressor:
from sklearn.ensemble import GradientBoostingRegressor
# Instantiate the model, fit the results, and scatter in vs. out

Solution The solution is found in the code of this chapter
18.5 Measuring prediction performance
18.5.1 A quick test on the K-neighbors classifier
Here we’ll continue to look at the digits data, but we’ll switch to the K-Neighbors classifier. The K-
neighbors classifier is an instance-based classifier. The K-neighbors classifier predicts the label of an
unknown point based on the labels of the K nearest points in the parameter space.
>>> # Get the data

>>> X = digits.data
>>> y = digits.target
>>> # Instantiate and train the classifier

>>> from sklearn.neighbors import KNeighborsClassifier
>>> clf = KNeighborsClassifier(n_neighbors=1)
>>> clf.fit(X, y)
KNeighborsClassifier(...)
>>> # Check the results using metrics

>>> from sklearn import metrics
>>> y_pred = clf.predict(X)
>>> print(metrics.confusion_matrix(y_pred, y))

[[178 0 0 0 0 0 0 0 0 0]
[ 0 182 0 0 0 0 0 0 0 0]
[ 0 0 177 0 0 0 0 0 0 0]
[ 0 0 0 183 0 0 0 0 0 0]
[ 0 0 0 0 181 0 0 0 0 0]
[ 0 0 0 0 0 182 0 0 0 0]
[ 0 0 0 0 0 0 181 0 0 0]
[ 0 0 0 0 0 0 0 179 0 0]
[ 0 0 0 0 0 0 0 0 174 0]
[ 0 0 0 0 0 0 0 0 0 180]]
Apparently, we’ve found a perfect classifier! But this is misleading for the reasons we saw before: the
classifier essentially “memorizes” all the samples it has already seen. To really test how well this algorithm
does, we need to try some samples it hasn’t yet seen.
This problem also occurs with regression models. In the following we fit an other instance-based model
named “decision tree” to the California Housing price dataset we introduced previously:
>>> from sklearn.datasets import fetch_california_housing

>>> from sklearn.tree import DecisionTreeRegressor
>>> data = fetch_california_housing(as_frame=True)

>>> clf = DecisionTreeRegressor().fit(data.data, data.target)
>>> predicted = clf.predict(data.data)
>>> expected = data.target
>>> plt.scatter(expected, predicted)

18.5. Measuring prediction performance 613


>>> plt.plot([0, 50], [0, 50], '--k')
[<matplotlib.lines.Line2D object at ...]
Here again the predictions are seemingly perfect as the model was able to perfectly memorize the training
set.
Warning: Performance on test set

Performance on test set does not measure overfit (as described above)
18.5.2 A correct approach: Using a validation set
Learning the parameters of a prediction function and testing it on the same data is a methodological
mistake: a model that would just repeat the labels of the samples that it has just seen would have a
perfect score but would fail to predict anything useful on yet-unseen data.
To avoid over-fitting, we have to define two different sets:
• a training set X_train, y_train which is used for learning the parameters of a predictive model
• a testing set X_test, y_test which is used for evaluating the fitted predictive model
In scikit-learn such a random split can be quickly computed with the train_test_split() function:
>>> from sklearn import model_selection

>>> X = digits.data
>>> X_train, X_test, y_train, y_test = model_selection.train_test_split(X, y,

... test_size=0.25, random_state=0)
>>> print("%r , %r , %r " % (X.shape, X_train.shape, X_test.shape))

(1797, 64), (1347, 64), (450, 64)
Now we train on the training data, and test on the testing data:
>>> clf = KNeighborsClassifier(n_neighbors=1).fit(X_train, y_train)

>>> y_pred = clf.predict(X_test)

>>> print(metrics.confusion_matrix(y_test, y_pred))

[[37 0 0 0 0 0 0 0 0 0]
[ 0 43 0 0 0 0 0 0 0 0]
[ 0 0 43 1 0 0 0 0 0 0]
[ 0 0 0 45 0 0 0 0 0 0]
[ 0 0 0 0 38 0 0 0 0 0]
[ 0 0 0 0 0 47 0 0 0 1]
[ 0 0 0 0 0 0 52 0 0 0]
[ 0 0 0 0 0 0 0 48 0 0]
[ 0 0 0 0 0 0 0 0 48 0]
[ 0 0 0 1 0 1 0 0 0 45]]
>>> print(metrics.classification_report(y_test, y_pred))
0 1.00 1.00 1.00 37

1 1.00 1.00 1.00 43
2 1.00 0.98 0.99 44
3 0.96 1.00 0.98 45
4 1.00 1.00 1.00 38
5 0.98 0.98 0.98 48
6 1.00 1.00 1.00 52
7 1.00 1.00 1.00 48
8 1.00 1.00 1.00 48
9 0.98 0.96 0.97 47
accuracy 0.99 450

macro avg 0.99 0.99 0.99 450
weighted avg 0.99 0.99 0.99 450
The averaged f1-score is often used as a convenient measure of the overall performance of an algorithm.
It appears in the bottom row of the classification report; it can also be accessed directly:
>>> metrics.f1_score(y_test, y_pred, average="macro")

0.991367...
The over-fitting we saw previously can be quantified by computing the f1-score on the training data
itself:
>>> metrics.f1_score(y_train, clf.predict(X_train), average="macro")

1.0
Note: Regression metrics In the case of regression models, we need to use different metrics, such as
explained variance.

18.5.3 Model Selection via Validation
Tip: We have applied Gaussian Naives, support vectors machines, and K-nearest neighbors classifiers
to the digits dataset. Now that we have these validation tools in place, we can ask quantitatively which
of the three estimators works best for this dataset.
• With the default hyper-parameters for each estimator, which gives the best f1 score on the valida-
tion set? Recall that hyperparameters are the parameters set when you instantiate the classifier:
for example, the n_neighbors in clf = KNeighborsClassifier(n_neighbors=1)
>>> from sklearn.naive_bayes import GaussianNB

>>> from sklearn.neighbors import KNeighborsClassifier
>>> from sklearn.svm import LinearSVC
>>> X = digits.data
>>> X_train, X_test, y_train, y_test = model_selection.train_test_split(X, y,
... test_size=0.25, random_state=0)
>>> for Model in [GaussianNB(), KNeighborsClassifier(), LinearSVC(dual=False)]:

... clf = Model.fit(X_train, y_train)
... y_pred = clf.predict(X_test)
... print('%s : %s ' %
... (Model.__class__.__name__, metrics.f1_score(y_test, y_pred,␣
˓→average="macro")))
GaussianNB: 0.8...
KNeighborsClassifier: 0.9...
LinearSVC: 0.9...
• For each classifier, which value for the hyperparameters gives the best results for the digits data?
For LinearSVC, use loss='l2' and loss='l1'. For KNeighborsClassifier we use n_neighbors
between 1 and 10. Note that GaussianNB does not have any adjustable hyperparameters.
LinearSVC(loss='l1'): 0.930570687535
LinearSVC(loss='l2'): 0.933068826918
-------------------
KNeighbors(n_neighbors=1): 0.991367521884
Solution: code source

18.5.4 Cross-validation
Cross-validation consists in repeatedly splitting the data in pairs of train and test sets, called ‘folds’.
Scikit-learn comes with a function to automatically compute score on all these folds. Here we do KFold
with k=5.
>>> clf = KNeighborsClassifier()

>>> from sklearn.model_selection import cross_val_score
>>> cross_val_score(clf, X, y, cv=5)
array([0.947..., 0.955..., 0.966..., 0.980..., 0.963... ])
We can use different splitting strategies, such as random splitting:
>>> from sklearn.model_selection import ShuffleSplit

>>> cv = ShuffleSplit(n_splits=5)
>>> cross_val_score(clf, X, y, cv=cv)
array([...])
Tip: There exists many different cross-validation strategies in scikit-learn. They are often useful to
take in account non iid datasets.
18.5.5 Hyperparameter optimization with cross-validation
Consider regularized linear models, such as Ridge Regression, which uses l2 regularization, and Lasso
Regression, which uses l1 regularization. Choosing their regularization parameter is important.
Let us set these parameters on the Diabetes dataset, a simple regression problem. The diabetes data
consists of 10 physiological variables (age, sex, weight, blood pressure) measure on 442 patients, and an
indication of disease progression after one year:
>>> from sklearn.datasets import load_diabetes

>>> data = load_diabetes()
>>> X, y = data.data, data.target
>>> print(X.shape)
(442, 10)
With the default hyper-parameters: we compute the cross-validation score:
>>> from sklearn.linear_model import Ridge, Lasso
>>> for Model in [Ridge, Lasso]:

... model = Model()
... print('%s : %s ' % (Model.__name__, cross_val_score(model, X, y).mean()))
Ridge: 0.4...
Lasso: 0.3...

Basic Hyperparameter Optimization
We compute the cross-validation score as a function of alpha, the strength of the regularization for Lasso
and Ridge. We choose 20 values of alpha between 0.0001 and 1:
>>> alphas = np.logspace(-3, -1, 30)
>>> for Model in [Lasso, Ridge]:

... scores = [cross_val_score(Model(alpha), X, y, cv=3).mean()
... for alpha in alphas]
... plt.plot(alphas, scores, label=Model.__name__)
[<matplotlib.lines.Line2D object at ...
Question
Can we trust our results to be actually useful?
Automatically Performing Grid Search
sklearn.grid_search.GridSearchCV is constructed with an estimator, as well as a dictionary of pa-

rameter values to be searched. We can find the optimal parameters this way:
>>> from sklearn.model_selection import GridSearchCV

>>> for Model in [Ridge, Lasso]:
... gscv = GridSearchCV(Model(), dict(alpha=alphas), cv=3).fit(X, y)
... print('%s : %s ' % (Model.__name__, gscv.best_params_))
Ridge: {'alpha': 0.062101694189156162}
Lasso: {'alpha': 0.01268961003167922}
Built-in Hyperparameter Search
For some models within scikit-learn, cross-validation can be performed more efficiently on large datasets.
In this case, a cross-validated version of the particular model is included. The cross-validated versions
of Ridge and Lasso are RidgeCV and LassoCV, respectively. Parameter search on these estimators can
be performed as follows:
>>> from sklearn.linear_model import RidgeCV, LassoCV

>>> for Model in [RidgeCV, LassoCV]:
... model = Model(alphas=alphas, cv=3).fit(X, y)
... print('%s : %s ' % (Model.__name__, model.alpha_))


RidgeCV: 0.0621016941892
LassoCV: 0.0126896100317
We see that the results match those returned by GridSearchCV
Nested cross-validation
How do we measure the performance of these estimators? We have used data to set the hyperparameters,
so we need to test on actually new data. We can do this by running cross_val_score() on our CV
objects. Here there are 2 cross-validation loops going on, this is called ‘nested cross validation’:
for Model in [RidgeCV, LassoCV]:

scores = cross_val_score(Model(alphas=alphas, cv=3), X, y, cv=3)
print(Model.__name__, np.mean(scores))
Note: Note that these results do not match the best results of our curves above, and LassoCV seems
to under-perform RidgeCV. The reason is that setting the hyper-parameter is harder for Lasso, thus the
estimation error on this hyper-parameter is larger.
18.6 Unsupervised Learning: Dimensionality Reduction and Visual-

ization
Unsupervised learning is applied on X without y: data without labels. A typical use case is to find
hidden structure in the data.
18.6.1 Dimensionality Reduction: PCA
Dimensionality reduction derives a set of new artificial features smaller than the original feature set.
Here we’ll use Principal Component Analysis (PCA), a dimensionality reduction that strives to retain
most of the variance of the original data. We’ll use sklearn.decomposition.PCA on the iris dataset:
>>> X = iris.data
>>> y = iris.target
Tip: PCA computes linear combinations of the original features using a truncated Singular Value
Decomposition of the matrix X, to project the data onto a base of the top singular vectors.
>>> from sklearn.decomposition import PCA

>>> pca = PCA(n_components=2, whiten=True)
>>> pca.fit(X)
PCA(n_components=2, whiten=True)
Once fitted, PCA exposes the singular vectors in the components_ attribute:
>>> pca.components_
array([[ 0.3..., -0.08..., 0.85..., 0.3...],
[ 0.6..., 0.7..., -0.1..., -0.07...]])
Other attributes are available as well:
18.6. Unsupervised Learning: Dimensionality Reduction and Visualization 619

>>> pca.explained_variance_ratio_
array([0.92..., 0.053...])
Let us project the iris dataset along those first two dimensions::
>>> X_pca = pca.transform(X)

>>> X_pca.shape
(150, 2)
PCA normalizes and whitens the data, which means that the data is now centered on both components
with unit variance:
>>> X_pca.mean(axis=0)
array([...e-15, ...e-15])
>>> X_pca.std(axis=0, ddof=1)
array([1., 1.])
Furthermore, the samples components do no longer carry any linear correlation:
>>> np.corrcoef(X_pca.T)
array([[1.00000000e+00, 0.0],
[0.0, 1.00000000e+00]])
With a number of retained components 2 or 3, PCA is useful to visualize the dataset:
>>> target_ids = range(len(iris.target_names))

>>> for i, c, label in zip(target_ids, 'rgbcmykw', iris.target_names):
... plt.scatter(X_pca[y == i, 0], X_pca[y == i, 1],
... c=c, label=label)
<matplotlib.collections.PathCollection ...
Tip: Note that this projection was determined without any information about the labels (represented
by the colors): this is the sense in which the learning is unsupervised. Nevertheless, we see that the
projection gives us insight into the distribution of the different flowers in parameter space: notably, iris
setosa is much more distinct than the other two species.

18.6.2 Visualization with a non-linear embedding: tSNE
For visualization, more complex embeddings can be useful (for statistical analysis, they are harder to
control). sklearn.manifold.TSNE is such a powerful manifold learning method. We apply it to the digits
dataset, as the digits are vectors of dimension 8*8 = 64. Embedding them in 2D enables visualization:
>>> # Take the first 500 data points: it's hard to see 1500 points
>>> X = digits.data[:500]
>>> y = digits.target[:500]
>>> # Fit and transform with a TSNE

>>> from sklearn.manifold import TSNE
>>> tsne = TSNE(n_components=2, learning_rate='auto', init='random', random_state=0)
>>> X_2d = tsne.fit_transform(X)
>>> # Visualize the data

>>> plt.scatter(X_2d[:, 0], X_2d[:, 1], c=y)
fit_transform
As TSNE cannot be applied to new data, we need to use its fit_transform method.
sklearn.manifold.TSNE separates quite well the different classes of digits even though it had no access
to the class information.
Exercise: Other dimension reduction of digits
sklearn.manifold has many other non-linear embeddings. Try them out on the digits dataset. Could

you judge their quality without knowing the labels y?

>>> # ...
18.7 Parameter selection, Validation, and Testing
18.7.1 Hyperparameters, Over-fitting, and Under-fitting
See also:
This section is adapted from Andrew Ng’s excellent Coursera course
The issues associated with validation and cross-validation are some of the most important aspects of the
practice of machine learning. Selecting the optimal model for your data is vital, and is a piece of the
problem that is not often appreciated by machine learning practitioners.
The central question is: If our estimator is underperforming, how should we move forward?
• Use simpler or more complicated model?
• Add more features to each observed data point?
• Add more training samples?
The answer is often counter-intuitive. In particular, Sometimes using a more complicated model
will give worse results. Also, Sometimes adding training data will not improve your results.
The ability to determine what steps will improve your model is what separates the successful machine
learning practitioners from the unsuccessful.
Bias-variance trade-off: illustration on a simple regression problem
Code and notebook
Let us start with a simple 1D regression problem. This will help us to easily visualize the data and the
model, and the results generalize easily to higher-dimensional datasets. We’ll explore a simple linear
regression problem, with sklearn.linear_model.
X = np.c_[0.5, 1].T
y = [0.5, 1]
X_test = np.c_[0, 2].T
Without noise, as linear regression fits the data perfectly
from sklearn import linear_model
regr = linear_model.LinearRegression()
regr.fit(X, y)
plt.plot(X, y, "o")
plt.plot(X_test, regr.predict(X_test))
18.7. Parameter selection, Validation, and Testing 622

[<matplotlib.lines.Line2D object at 0x7f9c750f7810>]
In real life situation, we have noise (e.g. measurement noise) in our data:
for _ in range(6):
noisy_X = X + np.random.normal(loc=0, scale=0.1, size=X.shape)
plt.plot(noisy_X, y, "o")
regr.fit(noisy_X, y)
As we can see, our linear model captures and amplifies the noise in the data. It displays a lot of variance.
We can use another linear estimator that uses regularization, the Ridge estimator. This estimator
regularizes the coefficients by shrinking them to zero, under the assumption that very high correlations
are often spurious. The alpha parameter controls the amount of shrinkage used.
regr = linear_model.Ridge(alpha=0.1)
np.random.seed(0)
for _ in range(6):
plt.show()

As we can see, the estimator displays much less variance. However it systematically under-estimates the
coefficient. It displays a biased behavior.
This is a typical example of bias/variance tradeof : non-regularized estimator are not biased, but they
can display a lot of variance. Highly-regularized models have little variance, but high bias. This bias is
not necessarily a bad thing: what matters is choosing the tradeoff between bias and variance that leads
to the best prediction performance. For a specific dataset there is a sweet spot corresponding to the
highest complexity that the data can support, depending on the amount of noise and of observations
available.
18.7.2 Visualizing the Bias/Variance Tradeoff
Tip: Given a particular dataset and a model (e.g. a polynomial), we’d like to understand whether bias
(underfit) or variance limits prediction, and how to tune the hyperparameter (here d, the degree of the
polynomial) to give the best fit.
On a given data, let us fit a simple polynomial regression model with varying degrees:
Tip: In the above figure, we see fits for three different values of d. For d = 1, the data is under-fit.
This means that the model is too simplistic: no straight line will ever be a good fit to this data. In this
case, we say that the model suffers from high bias. The model itself is biased, and this will be reflected
in the fact that the data is poorly fit. At the other extreme, for d = 6 the data is over-fit. This means
that the model has too many free parameters (6 in this case) which can be adjusted to perfectly fit the
training data. If we add a new point to this plot, though, chances are it will be very far from the curve
representing the degree-6 fit. In this case, we say that the model suffers from high variance. The reason
for the term “high variance” is that if any of the input points are varied slightly, it could result in a very
different model.

In the middle, for d = 2, we have found a good mid-point. It fits the data fairly well, and does not suffer
from the bias and variance problems seen in the figures on either side. What we would like is a way to
quantitatively identify bias and variance, and optimize the metaparameters (in this case, the polynomial
degree d) in order to determine the best algorithm.
Polynomial regression with scikit-learn
A polynomial regression is built by pipelining PolynomialFeatures and a LinearRegression:

>>> from sklearn.pipeline import make_pipeline
>>> from sklearn.preprocessing import PolynomialFeatures
>>> model = make_pipeline(PolynomialFeatures(degree=2), LinearRegression())
Validation Curves
Let us create a dataset like in the example above:
>>> def generating_func(x, rng, err=0.5):

... return rng.normal(10 - 1. / (x + 0.1), err)
>>> # randomly sample more data

>>> x = rng.random(size=200)
>>> y = generating_func(x, err=1., rng=rng)
Central to quantify bias and variance of a model is to apply it on test data, sampled from the same
distribution as the train, but that will capture independent noise:
>>> xtrain, xtest, ytrain, ytest = train_test_split(x, y, test_size=0.4)
Validation curve A validation curve consists in varying a model parameter that controls its complexity
(here the degree of the polynomial) and measures both error of the model on training data, and on test
data (eg with cross-validation). The model parameter is then adjusted so that the test error is minimized:
We use sklearn.model_selection.validation_curve() to compute train and test error, and plot it:
>>> from sklearn.model_selection import validation_curve
>>> degrees = np.arange(1, 21)


>>> model = make_pipeline(PolynomialFeatures(), LinearRegression())
>>> # Vary the "degrees" on the pipeline step "polynomialfeatures"

>>> train_scores, validation_scores = validation_curve(
... model, x[:, np.newaxis], y,
... param_name='polynomialfeatures__degree',
... param_range=degrees)
>>> # Plot the mean train score and validation score across folds
>>> plt.plot(degrees, validation_scores.mean(axis=1), label='cross-validation')
>>> plt.plot(degrees, train_scores.mean(axis=1), label='training')
>>> plt.legend(loc='best')
This figure shows why validation is important. On the left side of the plot, we have very low-degree
polynomial, which under-fit the data. This leads to a low explained variance for both the training set
and the validation set. On the far right side of the plot, we have a very high degree polynomial, which
over-fits the data. This can be seen in the fact that the training explained variance is very high, while
on the validation set, it is low. Choosing d around 4 or 5 gets us the best tradeoff.
Tip: The astute reader will realize that something is amiss here: in the above plot, d = 4 gives the
best results. But in the previous plot, we found that d = 6 vastly over-fits the data. What’s going on
here? The difference is the number of training points used. In the previous example, there were only
eight training points. In this example, we have 100. As a general rule of thumb, the more training points
used, the more complicated model can be used. But how can you determine for a given model whether
more training points will be helpful? A useful diagnostic for this are learning curves.

Learning Curves
A learning curve shows the training and validation score as a function of the number of training points.
Note that when we train on a subset of the training data, the training score is computed using this
subset, not the full training set. This curve gives a quantitative view into how beneficial it will be to
add training samples.
Questions:
• As the number of training samples are increased, what do you expect to see for the training
score? For the validation score?
• Would you expect the training score to be higher or lower than the validation score? Would you
ever expect this to change?
scikit-learn provides sklearn.model_selection.learning_curve():
>>> from sklearn.model_selection import learning_curve

>>> train_sizes, train_scores, validation_scores = learning_curve(
... model, x[:, np.newaxis], y, train_sizes=np.logspace(-1, 0, 20))
>>> # Plot the mean train score and validation score across folds
>>> plt.plot(train_sizes, validation_scores.mean(axis=1), label='cross-validation')
>>> plt.plot(train_sizes, train_scores.mean(axis=1), label='training')
Fig. 5: For a degree=1 model
Note that the validation score generally increases with a growing training set, while the training score
generally decreases with a growing training set. As the training size increases, they will converge to a
single value.
From the above discussion, we know that d = 1 is a high-bias estimator which under-fits the data. This
is indicated by the fact that both the training and validation scores are low. When confronted with this
type of learning curve, we can expect that adding more training data will not help: both lines converge
to a relatively low score.
When the learning curves have converged to a low score, we have a high bias model.
A high-bias model can be improved by:

• Using a more sophisticated model (i.e. in this case, increase d)

• Gather more features for each sample.
• Decrease regularization in a regularized model.
Increasing the number of samples, however, does not improve a high-bias model.
Now let’s look at a high-variance (i.e. over-fit) model:
Fig. 6: For a degree=15 model
Here we show the learning curve for d = 15. From the above discussion, we know that d = 15 is a
high-variance estimator which over-fits the data. This is indicated by the fact that the training score
is much higher than the validation score. As we add more samples to this training set, the training score
will continue to decrease, while the cross-validation error will continue to increase, until they meet in
the middle.
Learning curves that have not yet converged with the full training set indicate a high-
variance, over-fit model.
A high-variance model can be improved by:
• Gathering more training samples.
• Using a less-sophisticated model (i.e. in this case, make d smaller)
• Increasing regularization.
In particular, gathering more features for each sample will not help the results.
18.7.3 Summary on model selection
We’ve seen above that an under-performing algorithm can be due to two possible situations: high
bias (under-fitting) and high variance (over-fitting). In order to evaluate our algorithm, we set aside
a portion of our training data for cross-validation. Using the technique of learning curves, we can
train on progressively larger subsets of the data, evaluating the training error and cross-validation error
to determine whether our algorithm has high variance or high bias. But what do we do with this
information?

High Bias
If a model shows high bias, the following actions might help:

• Add more features. In our example of predicting home prices, it may be helpful to make use of
information such as the neighborhood the house is in, the year the house was built, the size of the
lot, etc. Adding these features to the training and test sets can improve a high-bias estimator
• Use a more sophisticated model. Adding complexity to the model can help improve on bias.
For a polynomial fit, this can be accomplished by increasing the degree d. Each learning technique
has its own methods of adding complexity.
• Use fewer samples. Though this will not improve the classification, a high-bias algorithm can
attain nearly the same error with a smaller training sample. For algorithms which are compu-
tationally expensive, reducing the training sample size can lead to very large improvements in
speed.
• Decrease regularization. Regularization is a technique used to impose simplicity in some ma-
chine learning models, by adding a penalty term that depends on the characteristics of the param-
eters. If a model has high bias, decreasing the effect of regularization can lead to better results.
High Variance
If a model shows high variance, the following actions might help:

• Use fewer features. Using a feature selection technique may be useful, and decrease the over-
fitting of the estimator.
• Use a simpler model. Model complexity and over-fitting go hand-in-hand.
• Use more training samples. Adding training samples can reduce the effect of over-fitting, and
lead to improvements in a high variance estimator.
• Increase Regularization. Regularization is designed to prevent over-fitting. In a high-variance
model, increasing regularization can lead to better results.
These choices become very important in real-world situations. For example, due to limited telescope
time, astronomers must seek a balance between observing a large number of objects, and observing a
large number of features for each object. Determining which is more important for a particular learning
task can inform the observing strategy that the astronomer employs.
18.7.4 A last word of caution: separate validation and test set
Using validation schemes to determine hyper-parameters means that we are fitting the hyper-parameters
to the particular validation set. In the same way that parameters can be over-fit to the training set,
hyperparameters can be over-fit to the validation set. Because of this, the validation error tends to
under-predict the classification error of new data.
For this reason, it is recommended to split the data into three sets:
• The training set, used to train the model (usually ~60% of the data)
• The validation set, used to validate the model (usually ~20% of the data)
• The test set, used to evaluate the expected error of the validated model (usually ~20% of the
data)
Many machine learning practitioners do not separate test set and validation set. But if your goal is to
gauge the error of a model on unknown data, using an independent test set is vital.

18.8 Examples for the scikit-learn chapter
18.8.1 Demo PCA in 2D
Load the iris data
from sklearn import datasets
X = iris.data
y = iris.target
Fit a PCA
from sklearn.decomposition import PCA
pca = PCA(n_components=2, whiten=True)

pca.fit(X)
Project the data in 2D
X_pca = pca.transform(X)
Visualize the data
target_ids = range(len(iris.target_names))
for i, c, label in zip(target_ids, "rgbcmykw", iris.target_names):
plt.scatter(X_pca[y == i, 0], X_pca[y == i, 1], c=c, label=label)
plt.legend()
plt.show()
18.8. Examples for the scikit-learn chapter 630

18.8.2 Measuring Decision Tree performance
Demonstrates overfit when testing on train set.

Get the data
from sklearn.datasets import fetch_california_housing
data = fetch_california_housing(as_frame=True)
Train and test a model
from sklearn.tree import DecisionTreeRegressor
clf = DecisionTreeRegressor().fit(data.data, data.target)
predicted = clf.predict(data.data)
expected = data.target
Plot predicted as a function of expected


plt.scatter(expected, predicted)
plt.plot([0, 5], [0, 5], "--k")
plt.axis("tight")
plt.xlabel("True price ($100k)")
plt.ylabel("Predicted price ($100k)")
plt.tight_layout()
Pretty much no errors!

This is too good to be true: we are testing the model on the train data, which is not a measure of
generalization.
The results are not valid
18.8.3 Plot 2D views of the iris dataset
Plot a simple scatter plot of 2 features of the iris dataset.

Note that more elaborate visualization of this dataset is detailed in the Statistics in Python chapter.

# Load the data

from sklearn.datasets import load_iris
iris = load_iris()
# The indices of the features that we are plotting

x_index = 0
y_index = 1
# this formatter will label the colorbar with the correct target names
formatter = plt.FuncFormatter(lambda i, *args: iris.target_names[int(i)])
plt.scatter(iris.data[:, x_index], iris.data[:, y_index], c=iris.target)
plt.colorbar(ticks=[0, 1, 2], format=formatter)
plt.xlabel(iris.feature_names[x_index])
plt.ylabel(iris.feature_names[y_index])
plt.tight_layout()
plt.show()

18.8.4 A simple linear regression
import numpy as np
# x from 0 to 30
x = 30 * rng.random((20, 1))
# y = a*x + b with noise

y = 0.5 * x + 1.0 + rng.normal(size=x.shape)
# create a linear regression model

model = LinearRegression()
model.fit(x, y)
# predict y from the data

x_new = np.linspace(0, 30, 100)
y_new = model.predict(x_new[:, np.newaxis])
# plot the results

ax = plt.axes()
ax.scatter(x, y)
ax.plot(x_new, y_new)
ax.set_xlabel("x")
ax.set_ylabel("y")
ax.axis("tight")
plt.show()

18.8.5 tSNE to visualize digits
Here we use sklearn.manifold.TSNE to visualize the digits datasets. Indeed, the digits are vectors in
a 8*8 = 64 dimensional space. We want to project them in 2D for visualization. tSNE is often a good
solution, as it groups and separates data points based on their local relationship.
Load the iris data
digits = datasets.load_digits()
# Take the first 500 data points: it's hard to see 1500 points
X = digits.data[:500]
y = digits.target[:500]
Fit and transform with a TSNE
from sklearn.manifold import TSNE
tsne = TSNE(n_components=2, random_state=0)
Project the data in 2D
X_2d = tsne.fit_transform(X)
Visualize the data
target_ids = range(len(digits.target_names))
colors = "r", "g", "b", "c", "m", "y", "k", "w", "orange", "purple"
for i, c, label in zip(target_ids, colors, digits.target_names):
plt.scatter(X_2d[y == i, 0], X_2d[y == i, 1], c=c, label=label)
plt.legend()
plt.show()

18.8.6 Use the RidgeCV and LassoCV to set the regularization parameter
Load the diabetes dataset
from sklearn.datasets import load_diabetes
data = load_diabetes()
X, y = data.data, data.target
print(X.shape)
(442, 10)
Compute the cross-validation score with the default hyper-parameters
from sklearn.model_selection import cross_val_score

from sklearn.linear_model import Ridge, Lasso
for Model in [Ridge, Lasso]:

model = Model()
print(f"{ Model.__name__} : { cross_val_score(model, X, y).mean()} ")

Ridge: 0.410174971340889
Lasso: 0.3375593674654274
We compute the cross-validation score as a function of alpha, the strength of the regularization for Lasso
and Ridge
import numpy as np
alphas = np.logspace(-3, -1, 30)
for Model in [Lasso, Ridge]:

scores = [cross_val_score(Model(alpha), X, y, cv=3).mean() for alpha in alphas]
plt.plot(alphas, scores, label=Model.__name__)
plt.legend(loc="lower left")
plt.xlabel("alpha")
plt.ylabel("cross validation score")
plt.tight_layout()
plt.show()
18.8.7 Plot variance and regularization in linear models
import numpy as np
# Smaller figures
plt.rcParams["figure.figsize"] = (3, 2)
We consider the situation where we have only 2 data point

X = np.c_[0.5, 1].T
y = [0.5, 1]
X_test = np.c_[0, 2].T
Without noise, as linear regression fits the data perfectly
regr.fit(X, y)
plt.plot(X, y, "o")
[<matplotlib.lines.Line2D object at 0x7f9c750f7810>]
In real life situation, we have noise (e.g. measurement noise) in our data:
for _ in range(6):
As we can see, our linear model captures and amplifies the noise in the data. It displays a lot of variance.
We can use another linear estimator that uses regularization, the Ridge estimator. This estimator
regularizes the coefficients by shrinking them to zero, under the assumption that very high correlations
are often spurious. The alpha parameter controls the amount of shrinkage used.
regr = linear_model.Ridge(alpha=0.1)
np.random.seed(0)


for _ in range(6):
plt.show()
18.8.8 Simple picture of the formal problem of machine learning
This example generates simple synthetic data ploints and shows a separating hyperplane on them.
import numpy as np
from sklearn.linear_model import SGDClassifier
from sklearn.datasets import make_blobs
# we create 50 separable synthetic points

X, Y = make_blobs(n_samples=50, centers=2, random_state=0, cluster_std=0.60)


# fit the model
clf = SGDClassifier(loss="hinge", alpha=0.01, fit_intercept=True)
clf.fit(X, Y)
# plot the line, the points, and the nearest vectors to the plane
xx = np.linspace(-1, 5, 10)
yy = np.linspace(-1, 5, 10)
X1, X2 = np.meshgrid(xx, yy)

Z = np.empty(X1.shape)
for (i, j), val in np.ndenumerate(X1):
x1 = val
x2 = X2[i, j]
p = clf.decision_function([[x1, x2]])
Z[i, j] = p[0]
ax = plt.axes()
ax.contour(
X1, X2, Z, [-1.0, 0.0, 1.0], colors="k", linestyles=["dashed", "solid", "dashed"]
)
ax.scatter(X[:, 0], X[:, 1], c=Y, cmap=plt.cm.Paired)
ax.axis("tight")
plt.show()
18.8.9 Compare classifiers on the digits data
Compare the performance of a variety of classifiers on a test set for the digits data.
/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/sklearn/svm/_
˓→classes.py:31: FutureWarning: The default value of `dual` will change from `True`␣
˓→to `'auto'` in 1.5. Set the value of `dual` explicitly to suppress the warning.
warnings.warn(
/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/sklearn/svm/_base.
˓→py:1237: ConvergenceWarning: Liblinear failed to converge, increase the number of␣
˓→iterations.
warnings.warn(
LinearSVC: 0.9341800269333108
GaussianNB: 0.8332741681010102
KNeighborsClassifier: 0.9804562804949924
------------------
warnings.warn(
˓→iterations.
warnings.warn(


LinearSVC(loss='hinge'): 0.9294570108037394
warnings.warn(
˓→iterations.
warnings.warn(
LinearSVC(loss='squared_hinge'): 0.9341371852581549
-------------------
from sklearn import model_selection, datasets, metrics

from sklearn.svm import LinearSVC
from sklearn.naive_bayes import GaussianNB
from sklearn.neighbors import KNeighborsClassifier
digits = datasets.load_digits()
X = digits.data
y = digits.target
X_train, X_test, y_train, y_test = model_selection.train_test_split(
X, y, test_size=0.25, random_state=0
)
for Model in [LinearSVC, GaussianNB, KNeighborsClassifier]:

clf = Model().fit(X_train, y_train)
y_pred = clf.predict(X_test)
print(f"{ Model.__name__} : { metrics.f1_score(y_test, y_pred, average='macro')} ")
print("------------------")
# test SVC loss

for loss in ["hinge", "squared_hinge"]:
clf = LinearSVC(loss=loss).fit(X_train, y_train)
print(
f"LinearSVC(loss='{ loss} '): { metrics.f1_score(y_test, y_pred, average='macro
˓→')} "
print("-------------------")

# test the number of neighbors

for n_neighbors in range(1, 11):
clf = KNeighborsClassifier(n_neighbors=n_neighbors).fit(X_train, y_train)
print(
f"KNeighbors(n_neighbors={ n_neighbors} ): { metrics.f1_score(y_test, y_pred,␣
˓→average='macro')} "
18.8.10 Plot fitting a 9th order polynomial
Fits data generated from a 9th order polynomial with model of 4th order and 9th order polynomials, to
demonstrate that often simpler models are to be preferred
import numpy as np
from matplotlib.colors import ListedColormap
# Create color maps for 3-class classification problem, as with iris

cmap_light = ListedColormap(["#FFAAAA", "#AAFFAA", "#AAAAFF"])
cmap_bold = ListedColormap(["#FF0000", "#00FF00", "#0000FF"])
x = 2 * rng.random(100) - 1
f = lambda t: 1.2 * t**2 + 0.1 * t**3 - 0.4 * t**5 - 0.5 * t**9

y = f(x) + 0.4 * rng.normal(size=100)
x_test = np.linspace(-1, 1, 100)
The data
plt.scatter(x, y, s=4)

<matplotlib.collections.PathCollection object at 0x7f9c74eb1410>
Fitting 4th and 9th order polynomials

For this we need to engineer features: the n_th powers of x:
X = np.array([x**i for i in range(5)]).T

X_test = np.array([x_test**i for i in range(5)]).T
regr.fit(X, y)
plt.plot(x_test, regr.predict(X_test), label="4th order")
X = np.array([x**i for i in range(10)]).T

X_test = np.array([x_test**i for i in range(10)]).T
regr.fit(X, y)
plt.plot(x_test, regr.predict(X_test), label="9th order")
plt.axis("tight")
plt.title("Fitting a 4th and a 9th order polynomial")

Text(0.5, 1.0, 'Fitting a 4th and a 9th order polynomial')
Ground truth
plt.plot(x_test, f(x_test), label="truth")
plt.axis("tight")
plt.title("Ground truth (9th order polynomial)")
plt.show()

18.8.11 A simple regression analysis on the California housing data
Here we perform a simple regression analysis on the California housing data, exploring two types of
regressors.
from sklearn.datasets import fetch_california_housing
data = fetch_california_housing(as_frame=True)
Print a histogram of the quantity to predict: price
plt.hist(data.target)
plt.xlabel("price ($100k)")
plt.ylabel("count")
plt.tight_layout()

Print the join histogram for each feature
for index, feature_name in enumerate(data.feature_names):

plt.scatter(data.data[feature_name], data.target)
plt.ylabel("Price", size=15)
plt.xlabel(feature_name, size=15)
plt.tight_layout()



•
Simple prediction
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(data.data, data.target)
clf = LinearRegression()
clf.fit(X_train, y_train)
predicted = clf.predict(X_test)
expected = y_test
plt.plot([0, 8], [0, 8], "--k")
plt.axis("tight")
plt.tight_layout()

Prediction with gradient boosted tree
from sklearn.ensemble import GradientBoostingRegressor
clf = GradientBoostingRegressor()
expected = y_test
plt.plot([0, 5], [0, 5], "--k")
plt.axis("tight")
plt.tight_layout()
Print the error rate
import numpy as np
print(f"RMS: { np.sqrt(np.mean((predicted - expected) ** 2))!r} ")
plt.show()
RMS: 0.5314909993118918

18.8.12 Nearest-neighbor prediction on iris
Plot the decision boundary of nearest neighbor decision on iris, first with a single nearest neighbor, and
then using 3 nearest neighbors.
import numpy as np
from sklearn import neighbors, datasets
from matplotlib.colors import ListedColormap
# Create color maps for 3-class classification problem, as with iris

cmap_light = ListedColormap(["#FFAAAA", "#AAFFAA", "#AAAAFF"])
cmap_bold = ListedColormap(["#FF0000", "#00FF00", "#0000FF"])
X = iris.data[:, :2] # we only take the first two features. We could
# avoid this ugly slicing by using a two-dim dataset
y = iris.target
knn.fit(X, y)
x_min, x_max = X[:, 0].min() - 0.1, X[:, 0].max() + 0.1

y_min, y_max = X[:, 1].min() - 0.1, X[:, 1].max() + 0.1
xx, yy = np.meshgrid(np.linspace(x_min, x_max, 100), np.linspace(y_min, y_max, 100))
Z = knn.predict(np.c_[xx.ravel(), yy.ravel()])
Put the result into a color plot
Z = Z.reshape(xx.shape)
plt.figure()
plt.pcolormesh(xx, yy, Z, cmap=cmap_light)
# Plot also the training points

plt.scatter(X[:, 0], X[:, 1], c=y, cmap=cmap_bold)
plt.xlabel("sepal length (cm)")
plt.ylabel("sepal width (cm)")
plt.axis("tight")

(4.180808080808081, 8.019191919191918, 1.8868686868686868, 4.513131313131313)
And now, redo the analysis with 3 neighbors
knn.fit(X, y)
Z = knn.predict(np.c_[xx.ravel(), yy.ravel()])
# Put the result into a color plot

Z = Z.reshape(xx.shape)
plt.figure()
plt.pcolormesh(xx, yy, Z, cmap=cmap_light)
# Plot also the training points

plt.scatter(X[:, 0], X[:, 1], c=y, cmap=cmap_bold)
plt.xlabel("sepal length (cm)")
plt.ylabel("sepal width (cm)")
plt.axis("tight")
plt.show()

18.8.13 Simple visualization and classification of the digits dataset
Plot the first few samples of the digits dataset and a 2D representation built using PCA, then do a simple
classification
from sklearn.datasets import load_digits
digits = load_digits()
Plot the data: images of digits
Each data in a 8x8 image
fig = plt.figure(figsize=(6, 6)) # figure size in inches

fig.subplots_adjust(left=0, right=1, bottom=0, top=1, hspace=0.05, wspace=0.05)
for i in range(64):
ax.imshow(digits.images[i], cmap=plt.cm.binary, interpolation="nearest")
# label the image with the target value
ax.text(0, 7, str(digits.target[i]))

Plot a projection on the 2 first principal axis
plt.figure()
from sklearn.decomposition import PCA
pca = PCA(n_components=2)
proj = pca.fit_transform(digits.data)
plt.scatter(proj[:, 0], proj[:, 1], c=digits.target, cmap="Paired")
plt.colorbar()

<matplotlib.colorbar.Colorbar object at 0x7f9c6cdf5d90>
Classify with Gaussian naive Bayes
from sklearn.naive_bayes import GaussianNB

# split the data into training and validation sets

X_train, X_test, y_train, y_test = train_test_split(digits.data, digits.target)
# train the model

clf = GaussianNB()
# use the model to predict the labels of the test data

expected = y_test
# Plot the prediction

fig = plt.figure(figsize=(6, 6)) # figure size in inches
fig.subplots_adjust(left=0, right=1, bottom=0, top=1, hspace=0.05, wspace=0.05)
# plot the digits: each image is 8x8 pixels

for i in range(64):
ax.imshow(X_test.reshape(-1, 8, 8)[i], cmap=plt.cm.binary, interpolation="nearest
˓→")

# label the image with the target value

if predicted[i] == expected[i]:
ax.text(0, 7, str(predicted[i]), color="green")
else:
ax.text(0, 7, str(predicted[i]), color="red")
Quantify the performance
First print the number of correct matches
matches = predicted == expected

print(matches.sum())
388
The total number of data points

print(len(matches))
450
And now, the ration of correct predictions
matches.sum() / float(len(matches))
0.8622222222222222
Print the classification report
from sklearn import metrics
print(metrics.classification_report(expected, predicted))
0 1.00 1.00 1.00 51

1 0.62 0.93 0.75 41
2 0.94 0.70 0.80 46
3 0.93 0.87 0.90 47
4 1.00 0.84 0.91 43
5 0.86 0.93 0.89 40
6 0.98 0.98 0.98 45
7 0.86 0.96 0.91 52
8 0.65 0.69 0.67 49
9 0.96 0.69 0.81 36
accuracy 0.86 450

macro avg 0.88 0.86 0.86 450
weighted avg 0.88 0.86 0.86 450
Print the confusion matrix
print(metrics.confusion_matrix(expected, predicted))
plt.show()
[[51 0 0 0 0 0 0 0 0 0]
[ 0 38 0 0 0 0 0 0 3 0]
[ 0 5 32 0 0 0 0 0 9 0]
[ 0 1 0 41 0 2 0 0 2 1]
[ 0 2 1 0 36 0 1 2 1 0]
[ 0 1 0 0 0 37 0 1 1 0]
[ 0 0 1 0 0 0 44 0 0 0]
[ 0 0 0 0 0 1 0 50 1 0]
[ 0 12 0 0 0 1 0 2 34 0]
[ 0 2 0 3 0 2 0 3 1 25]]

18.8.14 The eigenfaces example: chaining PCA and SVMs
The goal of this example is to show how an unsupervised method and a supervised one can be chained
for better prediction. It starts with a didactic but lengthy way of doing things, and finishes with the
idiomatic approach to pipelining in scikit-learn.
Here we’ll take a look at a simple facial recognition example. Ideally, we would use a dataset con-
sisting of a subset of the Labeled Faces in the Wild data that is available with sklearn.datasets.
fetch_lfw_people(). However, this is a relatively large download (~200MB) so we will do the tutorial
on a simpler, less rich dataset. Feel free to explore the LFW dataset.
faces = datasets.fetch_olivetti_faces()
faces.data.shape
downloading Olivetti faces from https://ndownloader.figshare.com/files/5976027 to /

˓→home/runner/scikit_learn_data
(400, 4096)
Let’s visualize these faces to see what we’re working with

# plot several images
for i in range(15):
ax.imshow(faces.images[i], cmap=plt.cm.bone)

Tip: Note is that these faces have already been localized and scaled to a common size. This is an
important preprocessing piece for facial recognition, and is a process that can require a large collection
of training data. This can be done in scikit-learn, but the challenge is gathering a sufficient amount of
training data for the algorithm to work. Fortunately, this piece is common enough that it has been done.
One good resource is OpenCV, the Open Computer Vision Library.
We’ll perform a Support Vector classification of the images. We’ll do a typical train-test split on the
images:
X_train, X_test, y_train, y_test = train_test_split(

faces.data, faces.target, random_state=0
)
print(X_train.shape, X_test.shape)
(300, 4096) (100, 4096)

Preprocessing: Principal Component Analysis
1850 dimensions is a lot for SVM. We can use PCA to reduce these 1850 features to a manageable size,
while maintaining most of the information in the dataset.
from sklearn import decomposition
pca = decomposition.PCA(n_components=150, whiten=True)

pca.fit(X_train)
One interesting part of PCA is that it computes the “mean” face, which can be interesting to examine:
plt.imshow(pca.mean_.reshape(faces.images[0].shape), cmap=plt.cm.bone)
<matplotlib.image.AxesImage object at 0x7f9c6ccd2b90>
The principal components measure deviations about this mean along orthogonal axes.
print(pca.components_.shape)
(150, 4096)
It is also interesting to visualize these principal components:

for i in range(30):
ax.imshow(pca.components_[i].reshape(faces.images[0].shape), cmap=plt.cm.bone)

The components (“eigenfaces”) are ordered by their importance from top-left to bottom-right. We
see that the first few components seem to primarily take care of lighting conditions; the remaining
components pull out certain identifying features: the nose, eyes, eyebrows, etc.
With this projection computed, we can now project our original training and test data onto the PCA
basis:
X_train_pca = pca.transform(X_train)
X_test_pca = pca.transform(X_test)
print(X_train_pca.shape)
(300, 150)
print(X_test_pca.shape)
(100, 150)
These projected components correspond to factors in a linear combination of component images such
that the combination approaches the original face.
Doing the Learning: Support Vector Machines
Now we’ll perform support-vector-machine classification on this reduced dataset:
from sklearn import svm
clf = svm.SVC(C=5.0, gamma=0.001)

clf.fit(X_train_pca, y_train)
Finally, we can evaluate how well this classification did. First, we might plot a few of the test-cases with
the labels learned from the training set:
import numpy as np

for i in range(15):
ax.imshow(X_test[i].reshape(faces.images[0].shape), cmap=plt.cm.bone)
y_pred = clf.predict(X_test_pca[i, np.newaxis])[0]
color = "black" if y_pred == y_test[i] else "red"
ax.set_title(y_pred, fontsize="small", color=color)

The classifier is correct on an impressive number of images given the simplicity of its learning model!
Using a linear classifier on 150 features derived from the pixel-level data, the algorithm correctly identifies
a large number of the people in the images.
Again, we can quantify this effectiveness using one of several measures from sklearn.metrics. First we
can do the classification report, which shows the precision, recall and other measures of the “goodness”
of the classification:
from sklearn import metrics
y_pred = clf.predict(X_test_pca)
print(metrics.classification_report(y_test, y_pred))
0 1.00 0.50 0.67 6

1 1.00 1.00 1.00 4
2 0.50 1.00 0.67 2
3 1.00 1.00 1.00 1
4 0.33 1.00 0.50 1
5 1.00 1.00 1.00 5
6 1.00 1.00 1.00 4
7 1.00 0.67 0.80 3
9 1.00 1.00 1.00 1
10 1.00 1.00 1.00 4
11 1.00 1.00 1.00 1
12 0.67 1.00 0.80 2
13 1.00 1.00 1.00 3
14 1.00 1.00 1.00 5


15 1.00 1.00 1.00 3
17 1.00 1.00 1.00 6
19 1.00 1.00 1.00 4
20 1.00 1.00 1.00 1
21 1.00 1.00 1.00 1
22 1.00 1.00 1.00 2
23 1.00 1.00 1.00 1
24 1.00 1.00 1.00 2
25 1.00 0.50 0.67 2
26 1.00 0.75 0.86 4
27 1.00 1.00 1.00 1
28 0.67 1.00 0.80 2
29 1.00 1.00 1.00 3
30 1.00 1.00 1.00 4
31 1.00 1.00 1.00 3
32 1.00 1.00 1.00 3
33 1.00 1.00 1.00 2
34 1.00 1.00 1.00 3
35 1.00 1.00 1.00 1
36 1.00 1.00 1.00 3
37 1.00 1.00 1.00 3
38 1.00 1.00 1.00 1
39 1.00 1.00 1.00 3
accuracy 0.94 100

macro avg 0.95 0.96 0.94 100
weighted avg 0.97 0.94 0.94 100
Another interesting metric is the confusion matrix, which indicates how often any two items are mixed-
up. The confusion matrix of a perfect classifier would only have nonzero entries on the diagonal, with
zeros on the off-diagonal:
print(metrics.confusion_matrix(y_test, y_pred))
[[3 0 0 ... 0 0 0]
[0 4 0 ... 0 0 0]
[0 0 2 ... 0 0 0]
...
[0 0 0 ... 3 0 0]
[0 0 0 ... 0 1 0]
[0 0 0 ... 0 0 3]]
Pipelining
Above we used PCA as a pre-processing step before applying our support vector machine classifier.
Plugging the output of one estimator directly into the input of a second estimator is a commonly used
pattern; for this reason scikit-learn provides a Pipeline object which automates this process. The above
problem can be re-expressed as a pipeline as follows:
from sklearn.pipeline import Pipeline
clf = Pipeline(
[
("pca", decomposition.PCA(n_components=150, whiten=True)),
("svm", svm.LinearSVC(C=1.0)),


]
)
print(metrics.confusion_matrix(y_pred, y_test))
plt.show()
warnings.warn(
˓→iterations.
warnings.warn(
[[5 0 0 ... 0 0 0]
[0 4 0 ... 0 0 0]
[0 0 1 ... 0 0 0]
...
[0 0 0 ... 3 0 0]
[0 0 0 ... 0 1 0]
[0 0 0 ... 0 0 3]]
A Note on Facial Recognition
Here we have used PCA “eigenfaces” as a pre-processing step for facial recognition. The reason we
chose this is because PCA is a broadly-applicable technique, which can be useful for a wide array of
data types. Research in the field of facial recognition in particular, however, has shown that other more
specific feature extraction methods are can be much more effective.
18.8.15 Example of linear and non-linear models
This is an example plot from the tutorial which accompanies an explanation of the support vector
machine GUI.
import numpy as np
from sklearn import svm
data that is linearly separable
def linear_model(rseed=42, n_samples=30):

"Generate data according to a linear model"
np.random.seed(rseed)


data = np.random.normal(0, 10, (n_samples, 2))
data[: n_samples // 2] -= 15
data[n_samples // 2 :] += 15
labels = np.ones(n_samples)
labels[: n_samples // 2] = -1
return data, labels
X, y = linear_model()
clf = svm.SVC(kernel="linear")
clf.fit(X, y)
ax = plt.subplot(111, xticks=[], yticks=[])
ax.scatter(X[:, 0], X[:, 1], c=y, cmap=plt.cm.bone)
ax.scatter(
clf.support_vectors_[:, 0],
s=80,
edgecolors="k",
facecolors="none",
)
delta = 1
y_min, y_max = -50, 50
x_min, x_max = -50, 50
x = np.arange(x_min, x_max + delta, delta)
y = np.arange(y_min, y_max + delta, delta)
X1, X2 = np.meshgrid(x, y)
Z = clf.decision_function(np.c_[X1.ravel(), X2.ravel()])
Z = Z.reshape(X1.shape)
ax.contour(
X1, X2, Z, [-1.0, 0.0, 1.0], colors="k", linestyles=["dashed", "solid", "dashed"]
)

<matplotlib.contour.QuadContourSet object at 0x7f9c6cd6d790>
data with a non-linear separation
def nonlinear_model(rseed=27446968, n_samples=30):

rng = np.random.default_rng(rseed)
radius = 40 * rng.random(n_samples)
far_pts = radius > 20
radius[far_pts] *= 1.2
radius[~far_pts] *= 1.1
theta = rng.random(n_samples) * np.pi * 2
data = np.empty((n_samples, 2))

data[:, 0] = radius * np.cos(theta)
data[:, 1] = radius * np.sin(theta)
labels = np.ones(n_samples)
labels[far_pts] = -1
return data, labels
X, y = nonlinear_model()
clf = svm.SVC(kernel="rbf", gamma=0.001, coef0=0, degree=3)
clf.fit(X, y)
ax = plt.subplot(1, 1, 1, xticks=[], yticks=[])
ax.scatter(X[:, 0], X[:, 1], c=y, cmap=plt.cm.bone, zorder=2)


ax.scatter(
s=80,
edgecolors="k",
facecolors="none",
)
delta = 1
y_min, y_max = -50, 50
x_min, x_max = -50, 50
x = np.arange(x_min, x_max + delta, delta)
y = np.arange(y_min, y_max + delta, delta)
X1, X2 = np.meshgrid(x, y)
Z = clf.decision_function(np.c_[X1.ravel(), X2.ravel()])
Z = Z.reshape(X1.shape)
ax.contour(
X1,
X2,
Z,
[-1.0, 0.0, 1.0],
colors="k",
linestyles=["dashed", "solid", "dashed"],
zorder=1,
)
plt.show()

18.8.16 Bias and variance of polynomial fit
Demo overfitting, underfitting, and validation and learning curves with polynomial regression.
Fit polynomes of different degrees to a dataset: for too small a degree, the model underfits, while for too
large a degree, it overfits.
import numpy as np
def generating_func(x, rng=None, error=0.5):

rng = np.random.default_rng(rng)
return rng.normal(10 - 1.0 / (x + 0.1), error)
A polynomial regression
from sklearn.pipeline import make_pipeline

from sklearn.preprocessing import PolynomialFeatures
A simple figure to illustrate the problem
n_samples = 8
x = 10 ** np.linspace(-2, 0, n_samples)
y = generating_func(x, rng=rng)
x_test = np.linspace(-0.2, 1.2, 1000)
titles = ["d = 1 (under-fit; high bias)", "d = 2", "d = 6 (over-fit; high variance)"]
degrees = [1, 2, 6]
fig = plt.figure(figsize=(9, 3.5))

fig.subplots_adjust(left=0.06, right=0.98, bottom=0.15, top=0.85, wspace=0.05)
for i, d in enumerate(degrees):
ax = fig.add_subplot(131 + i, xticks=[], yticks=[])
ax.scatter(x, y, marker="x", c="k", s=50)
model = make_pipeline(PolynomialFeatures(d), LinearRegression())

model.fit(x[:, np.newaxis], y)
ax.plot(x_test, model.predict(x_test[:, np.newaxis]), "-b")
ax.set_xlim(-0.2, 1.2)
ax.set_ylim(0, 12)
ax.set_xlabel("house size")
if i == 0:
ax.set_ylabel("price")
ax.set_title(titles[i])

Generate a larger dataset
n_samples = 200
test_size = 0.4
error = 1.0
# randomly sample the data

x = rng.random(n_samples)
y = generating_func(x, rng=rng, error=error)
# split into training, validation, and testing sets.

x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=test_size)
# show the training and validation sets

plt.scatter(x_train, y_train, color="red", label="Training set")
plt.scatter(x_test, y_test, color="blue", label="Test set")
plt.title("The data")

<matplotlib.legend.Legend object at 0x7f9c74b4fb90>
Plot a validation curve
from sklearn.model_selection import validation_curve
degrees = np.arange(1, 21)
model = make_pipeline(PolynomialFeatures(), LinearRegression())
# The parameter to vary is the "degrees" on the pipeline step

# "polynomialfeatures"
train_scores, validation_scores = validation_curve(
model,
x[:, np.newaxis],
y,
param_name="polynomialfeatures__degree",
param_range=degrees,
)
# Plot the mean train error and validation error across folds
plt.plot(degrees, validation_scores.mean(axis=1), lw=2, label="cross-validation")
plt.plot(degrees, train_scores.mean(axis=1), lw=2, label="training")
plt.xlabel("degree of fit")
plt.ylabel("explained variance")
plt.title("Validation curve")
plt.tight_layout()

Learning curves
Plot train and test error with an increasing number of samples
# A learning curve for d=1, 5, 15

for d in [1, 5, 15]:
model = make_pipeline(PolynomialFeatures(degree=d), LinearRegression())
from sklearn.model_selection import learning_curve
train_sizes, train_scores, validation_scores = learning_curve(

model, x[:, np.newaxis], y, train_sizes=np.logspace(-1, 0, 20)
)
# Plot the mean train error and validation error across folds
plt.plot(
train_sizes, validation_scores.mean(axis=1), lw=2, label="cross-validation"
)
plt.plot(train_sizes, train_scores.mean(axis=1), lw=2, label="training")
plt.ylim(ymin=-0.1, ymax=1)
plt.xlabel("number of train samples")
plt.ylabel("explained variance")
plt.title("Learning curve (degree=%i )" % d)
plt.tight_layout()
plt.show()


•
18.8.17 Tutorial Diagrams
This script plots the flow-charts used in the scikit-learn tutorials.

import numpy as np
from matplotlib.patches import Circle, Rectangle, Polygon, Arrow, FancyArrow
def create_base(box_bg="#CCCCCC", arrow1="#88CCFF", arrow2="#88FF88",␣

˓→supervised=True):
fig = plt.figure(figsize=(9, 6), facecolor="w")



ax = plt.axes((0, 0, 1, 1), xticks=[], yticks=[], frameon=False)
ax.set_xlim(0, 9)
ax.set_ylim(0, 6)
patches = [
Rectangle((0.3, 3.6), 1.5, 1.8, zorder=1, fc=box_bg),
Rectangle((2.9, 3.6), 0.2, 1.8, fc=box_bg),
Circle((5.5, 3.5), 1.0, fc=box_bg),
Polygon([[5.5, 1.7], [6.1, 1.1], [5.5, 0.5], [4.9, 1.1]], fc=box_bg),
FancyArrow(
2.3, 4.6, 0.35, 0, fc=arrow1, width=0.25, head_width=0.5, head_length=0.2
),
FancyArrow(
3.75, 4.2, 0.5, -0.2, fc=arrow1, width=0.25, head_width=0.5, head_
˓→length=0.2
),
FancyArrow(
5.5, 2.4, 0, -0.4, fc=arrow1, width=0.25, head_width=0.5, head_length=0.2
),
FancyArrow(
),
FancyArrow(
),
FancyArrow(
),
]
if supervised:
patches += [
FancyArrow(
2.3, 2.9, 2.0, 0, fc=arrow1, width=0.25, head_width=0.5, head_
˓→length=0.2
),
]
else:
patches += [Rectangle((7.3, 0.2), 1.5, 1.8, fc=box_bg)]
for p in patches:
ax.add_patch(p)
plt.text(
1.45,
4.9,


"Training\nText,\nDocuments,\nImages,\netc.",
ha="center",
va="center",
fontsize=14,
)
plt.text(3.6, 4.9, "Feature\nVectors", ha="left", va="center", fontsize=14)
plt.text(
5.5, 3.5, "Machine\nLearning\nAlgorithm", ha="center", va="center",␣
˓→fontsize=14
plt.text(
1.05,
1.1,
"New Text,\nDocument,\nImage,\netc.",
ha="center",
va="center",
fontsize=14,
)
plt.text(3.3, 1.7, "Feature\nVector", ha="left", va="center", fontsize=14)
plt.text(5.5, 1.1, "Predictive\nModel", ha="center", va="center", fontsize=12)
if supervised:
plt.text(1.45, 3.05, "Labels", ha="center", va="center", fontsize=14)
plt.text(8.05, 1.1, "Expected\nLabel", ha="center", va="center", fontsize=14)

plt.text(
8.8, 5.8, "Supervised Learning Model", ha="right", va="top", fontsize=18
)
else:
plt.text(
8.05,
1.1,
"Likelihood\nor Cluster ID\nor Better\nRepresentation",
ha="center",
va="center",
fontsize=12,
)
plt.text(
8.8, 5.8, "Unsupervised Learning Model", ha="right", va="top", fontsize=18
)
def plot_supervised_chart(annotate=False):
create_base(supervised=True)
if annotate:
fontdict = {"color": "r", "weight": "bold", "size": 14}
plt.text(
1.9,
4.55,
"X = vec.fit_transform(input)",


fontdict=fontdict,
rotation=20,
ha="left",
va="bottom",
)
plt.text(
3.7,
3.2,
"clf.fit(X, y)",
fontdict=fontdict,
rotation=20,
ha="left",
va="bottom",
)
plt.text(
1.7,
1.5,
"X_new = vec.transform(input)",
fontdict=fontdict,
rotation=20,
ha="left",
va="bottom",
)
plt.text(
6.1,
1.5,
"y_new = clf.predict(X_new)",
fontdict=fontdict,
rotation=20,
ha="left",
va="bottom",
)
def plot_unsupervised_chart():
create_base(supervised=False)
if __name__ == "__main__":
plot_supervised_chart(False)
plot_supervised_chart(True)
plot_unsupervised_chart()
plt.show()
See also:
Going further
• The documentation of scikit-learn is very complete and didactic.
• Introduction to Machine Learning with Python, by Sarah Guido, Andreas Müller (notebooks avail-
able here).

Part IV
About the Scientific Python

Lectures
678
CHAPTER 19
About the Scientific Python Lectures
Release: 2024.1rc0
The lectures are archived on zenodo: http://dx.doi.org/10.5281/zenodo.594102
All code and material is licensed under a Creative Commons Attribution 4.0 International License (CC-
by) http://creativecommons.org/licenses/by/4.0/
19.1 Authors • Christophe Combelles
• André Espaze
19.1.1 Editors
• Emmanuelle Gouillart
• Gaël Varoquaux
• Emmanuelle Gouillart • Mike Müller
• Olav Vahtras
• Fabian Pedregosa
• Pierre de Buyl
• K. Jarrod Millman • Didrik Pinte
• Stéfan van der Walt
• Nicolas Rougier
19.1.2 Chapter authors • Gaël Varoquaux
Listed by alphabetical order. • Pauli Virtanen

• Christopher Burns
• Zbigniew Jędrzejewski-Szmek
• Adrian Chauve
• Robert Cimrman • Valentin Haenel (editor from 2011 to 2015)
679
19.1.3 Additional Contributions • Valentin Haenel

• Pierre Haessig
Listed by alphabetical order
• Bruno Hanzen
• Osayd Abdu
• Michael Hartmann
• arunpersaud
• Jonathan Helmus
• Ross Barnowski
• Andreas Hilboll
• Sebastian Berg
• Himanshu
• Lilian Besson
• Julian Hofer
• Matthieu Boileau
• Tim Hoffmann
• Joris Van den Bossche
• Michael Boyle • B. Hohl
• Matthew Brett • Tarek Hoteit
• BSGalvan • Gert-Ludwig Ingold
• Lars Buitinck • Zbigniew Jędrzejewski-Szmek
• Pierre de Buyl • Thouis (Ray) Jones
• Ozan Çağlayan • jorgeprietoarranz
• Lawrence Chan • josephsalmon
• Adrien Chauve • Greg Kiar
• Robert Cimrman • kikocorreoso
• Christophe Combelles • Vince Knight
• David Cournapeau • LFP6
• Dave • Manuel López-Ibáñez
• dogacan dugmeci • Marco Mangan
• Török Edwin • Nicola Masarone
• egens • John McLaughlin
• Andre Espaze • mhemantha
• André Espaze • michelemaroni89
• Loïc Estève • K. Jarrod Millman
• Corey Farwell • Mohammad

• Tim Gates • Zachary Moon
• Stuart Geiger • Mike Mueller
• Olivier Georg • negm
• Daniel Gerigk • John B Nelson
• Robert Gieseke • nicoguaro
• Philip Gillißen • Sergio Oller
• Ralf Gommers • Theofilos Papapanagiotou
• Emmanuelle Gouillart • patniharshit
• Julia Gustavsen • Fabian Pedregosa
• Omar Gutiérrez • Philippe Pepiot
• Matt Haberland • Tiago M. D. Pereira
19.1. Authors 680

• Nicolas Pettiaux • strpeter

• Didrik Pinte • surfer190
• Evgeny Pogrebnyak • Bartosz Telenczuk
• reverland • tommyod
• Maximilien Riehl • Wes Turner
• Kristian Rother
• Akihiro Uchida
• Nicolas P. Rougier
• Utkarsh Upadhyay
• Pamphile Roy
• Olav Vahtras
• Rutzmoser
• Stéfan van der Walt
• Sander
• Gaël Varoquaux
• João Felipe Santos
• Nelle Varoquaux
• Mark Setchell
• Olivier Verdier
• Helen Sherwood-Taylor
• Shoeboxam • VirgileFritsch
• Simon • Pauli Virtanen
• solarjoe • Yosh Wakeham
• ssmiller • yasutomo57jp
• Scott Staniewicz
19.1. Authors 681

Index
D
diff, 560, 564
differentiation, 560
dsolve, 564
E
equations
algebraic, 562
differential, 564
I
integration, 562
M
Matrix, 564
P
Python Enhancement Proposals
PEP 255, 300
PEP 3118, 339
PEP 3129, 310
PEP 318, 302, 310
PEP 342, 300
PEP 343, 310
PEP 380, 301
PEP 380#id13, 301
PEP 8, 304
S
solve, 562
682

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SciKits Numpy Matplotlib

Scien�ﬁc Python Gaël Varoquaux

Gaël Varoquaux • Emmanuelle Gouillart • Olav Vahtras

I Getting started with Python for science 2

2 The Python language 12

3 NumPy: creating and manipulating numerical data 54

4 Matplotlib: plotting 107

5 SciPy : high-level scientific computing 211

6 Getting help and finding documentation 291

II Advanced topics 294

8 Advanced NumPy 314

9 Debugging code 348

10 Optimizing code 360

11 Sparse Arrays in SciPy 368

12 Image manipulation and processing using NumPy and SciPy 379

13 Mathematical optimization: finding minima of functions 424

14 Interfacing with C 480

III Packages and applications 505

16 Sympy : Symbolic Mathematics in Python 557

17 scikit-image: image processing 566

18 scikit-learn: machine learning in Python 593

Getting started with Python for

Authors: Fernando Perez, Emmanuelle Gouillart, Gaël Varoquaux, Valentin Haenel

1.1 Why Python?

1.1.1 The scientist’s needs

• Get data (simulation, experiment control),

1.1.2 Python’s strengths

1.1.3 How does Python compare to other solutions?

Compiled languages: C, C++, Fortran. . .

Matlab scripting language

1.1. Why Python? 5

Other scripting languages: Scilab, Octave, R, IDL, etc.

1.2 The scientific Python ecosystem

Python, a generic and modern computing language

1.2. The scientific Python ecosystem 6

1.3 Before starting: Installing a working environment

1.3. Before starting: Installing a working environment 7

1.4 The workflow: interactive environments and text editors

1.4.1 Interactive work

Under the notebook

To execute code, press “shift enter”

In [1]: print('Hello world')

Getting help by using the ? operator after an object:

1.4.2 Elaboration of the work in an editor

1.4. The workflow: interactive environments and text editors 8

In [3]: %run my_file.py

From a script to functions

1.4.3 IPython and Jupyter Tips and Tricks

1.4. The workflow: interactive environments and text editors 9

84 Arguments are exactly the same as ast.parse (in the standard␣

85 and are passed to the built-in compile function."""

1.4. The workflow: interactive environments and text editors 10

(continued from previous page)

• The built-in cheat-sheet is accessible via the %quickref magic function.

1.4. The workflow: interactive environments and text editors 11

Authors: Chris Burns, Christophe Combelles, Emmanuelle Gouillart, Gaël Varoquaux

Python for scientific computing

2.1 First steps

Start the Ipython shell (an enhanced interactive Python shell):