ENH: initial connectome workbench support #2594
Conversation
| def _format_arg(self, opt, spec, val): | ||
| if opt == "metric_out": | ||
| # ensure generated filename is assigned to trait | ||
| self.inputs.trait_set(metric_out=val) |
There was a problem hiding this comment.
bug? metric_out was displayed correctly in cmdline, but without this trait_set call, remained as Undefined in _list_outputs
|
You need to add |
| keep_extension=True, | ||
| argstr="%s", | ||
| position=4, | ||
| desc="The output metric") |
There was a problem hiding this comment.
Maybe rename this to out_file (or rename both here and outputs.out_file to metric_file)? In addition to resolving your trait weirdness, I think it'll be less confusing for people for the connected traits to have the same name.
| position=6, | ||
| argstr="%s", | ||
| desc=("A relevant anatomical surface with <current-sphere> mesh OR" | ||
| " a metric file with vertex areas for <current-sphere> mesh")) |
There was a problem hiding this comment.
Unimportant style point: I don't think parentheses are necessary for the line break and tabbing to be valid.
Codecov Report
@@ Coverage Diff @@
## master #2594 +/- ##
==========================================
- Coverage 67.62% 67.61% -0.01%
==========================================
Files 336 339 +3
Lines 42711 42782 +71
Branches 5278 5287 +9
==========================================
+ Hits 28883 28928 +45
- Misses 13151 13174 +23
- Partials 677 680 +3
Continue to review full report at Codecov.
|
| def _format_arg(self, opt, spec, val): | ||
| if opt == "out_file": | ||
| # ensure generated filename is assigned to trait | ||
| self.inputs.trait_set(out_file=val) |
There was a problem hiding this comment.
Sorry, I meant to say that I think this (and the _list_outputs entry) shouldn't be necessary if you make the input spec match the output spec.
| class MetricResample(WBCommand): | ||
| """ | ||
| Resample a metric file to a different mesh | ||
|
|
There was a problem hiding this comment.
I think it would help documentation to copy a bit more from their docs:
Resample a metric file to a different mesh
Resamples a metric file, given two spherical surfaces that are in
register. If ``ADAP_BARY_AREA`` is used, exactly one of -area-surfs or
``-area-metrics`` must be specified.
The ``ADAP_BARY_AREA`` method is recommended for ordinary metric data,
because it should use all data while downsampling, unlike ``BARYCENTRIC``.
The recommended areas option for most data is individual midthicknesses
for individual data, and averaged vertex area metrics from individual
midthicknesses for group average data.
The ``-current-roi`` option only masks the input, the output may be slightly
dilated in comparison, consider using ``-metric-mask`` on the output when
using ``-current-roi``.
The ``-largest option`` results in nearest vertex behavior when used with
``BARYCENTRIC``. When resampling a binary metric, consider thresholding at
0.5 after resampling rather than using ``-largest``.
There was a problem hiding this comment.
@oesteban Want to just push this change? It's after 5pm here.
Changes proposed in this pull request
wb_command -metric-resample)