[FIX] fix afni.allineate interface #2502
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@@ Coverage Diff @@
## master #2502 +/- ##
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+ Coverage 66.87% 66.87% +<.01%
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Files 327 327
Lines 42448 42439 -9
Branches 5266 5263 -3
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- Hits 28387 28382 -5
- Misses 13362 13365 +3
+ Partials 699 692 -7
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Suggested changes to nipy#2502
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I'm tagging the changes I suggested in vanandrew#1 here.
I also made a couple other changes I saw while looking into this. This interface can be substantially reduced.
nipype/interfaces/afni/preprocess.py
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| @@ -219,6 +219,7 @@ class AllineateInputSpec(AFNICommandInputSpec): | |||
| desc='output file from 3dAllineate', | |||
| argstr='-prefix %s', | |||
| genfile=True, | |||
| hash_files=False, | |||
nipype/interfaces/afni/preprocess.py
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| @@ -219,6 +219,7 @@ class AllineateInputSpec(AFNICommandInputSpec): | |||
| desc='output file from 3dAllineate', | |||
| argstr='-prefix %s', | |||
| genfile=True, | |||
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We can replace genfile with the newer name_template.
- genfile=True,
+. name_template='%s_allineate',
+. name_source='in_file',In the PR I sent you, I've resolved the issue with it not respecting the xor tag.
nipype/interfaces/afni/preprocess.py
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| if self.inputs.out_weight_file: | ||
| if isdefined(self.inputs.out_weight_file): |
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Undefined evaluates to False, so this isn't necessary, here.
nipype/interfaces/afni/preprocess.py
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| @@ -519,7 +525,7 @@ def _list_outputs(self): | |||
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| def _gen_filename(self, name): | |||
| if name == 'out_file': | |||
| return self._list_outputs()[name] | |||
| return self._gen_outfilename() | |||
| return None | |||
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We should be able to remove this method entirely, if we're switching to name_template/name_source.
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Fast merge. 😃 |
| >>> allineate.inputs.reference = 'structural.nii' | ||
| >>> allineate.inputs.nwarp_fixmot = ['X', 'Y'] | ||
| >>> allineate.cmdline | ||
| '3dAllineate -source functional.nii -nwarp_fixmotX -nwarp_fixmotY -prefix functional_allineate -base structural.nii' |
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A question: Is -prefix functional_allineate the correct default, or should it be functional_allineate.nii?
If it should have the extension, we should add keep_extension=True to the out_file trait spec.
@tsalo @salma1601 You might also be good people to chime in here.
| # Do not generate filename when excluded by other inputs | ||
| if trait_spec.xor and any(isdefined(getattr(self.inputs, field)) | ||
| for field in trait_spec.xor): | ||
| return retval |
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Ah, right. I had it kind of backwards, but a similar fix to this should resolve #2506. I'll merge and propose a quick PR for that one.
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Ah, sorry. Forgot to |
Suggested changes to nipy/nipype#2502
Fixes #2499, #2216
Changes proposed in this pull request
-See linked issue #2499