FIX: ANTs' tools maintenance overhaul #3180
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@@ Coverage Diff @@ ## master #3180 +/- ## ========================================== - Coverage 64.88% 64.18% -0.70% ========================================== Files 299 299 Lines 39506 39502 -4 Branches 5219 5219 ========================================== - Hits 25632 25355 -277 - Misses 12824 13110 +286 + Partials 1050 1037 -13
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oesteban force-pushed the enh/ants-utils-overhaul branch from df89399 to dffcb78 Compare 
satra reviewed Mar 2, 2020
satra reviewed Mar 2, 2020
| I was waiting on CI to pass to read through. I'll look tonight or tomorrow morning. |
effigies previously approved these changes Mar 3, 2020
effigies reviewed Mar 3, 2020
Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
oesteban force-pushed the enh/ants-utils-overhaul branch from 5acff55 to f88add4 Compare | Suggestions proposed on oesteban#10. |
RF: Move header copying to a mixin
| @satra - thumbs up after Chris' suggestions? |
| Having issues with Traceback (most recent call last): File "/home/oesteban/workspace/nipype/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/home/oesteban/workspace/nipype/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/home/oesteban/workspace/nipype/nipype/interfaces/base/core.py", line 398, in run runtime = self._post_run_hook(runtime) File "/home/oesteban/workspace/nipype/nipype/interfaces/mixins/fixheader.py", line 132, in _post_run_hook _copy_header(inputs[inp], outputs[out], keep_dtype=keep_dtype) KeyError: 'bias_image'it seems the mixin is not general enough? |
| Oh, I hadn't considered the output file might not exist. Yeah, I think a simple existence check makes sense. I think silent pass-through is fine for a mixin, as it's not responsible to make sure the file exists, only that if the file exists it has the right header. |
oesteban added a commit to oesteban/nipype that referenced this pull request Mar 14, 2020
In the last maintenance (nipy#3180) of the interface, we eliminated an important section of the ``_list_outputs``: nipy@6979cbd#diff-b6f33a19b0e06b91023416db5faf7323L544-L547 This PR addresses the problem: ``` Execution Outputs ----------------- * bias_image : <undefined> * output_image : /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0/sub-01_T1w_cor rected.nii.gz Runtime info ------------ * cmdline : N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /oak/stanford/groups/russpold/data/openfmri/ds000005/sub-01/anat/sub-01_T1w.nii.gz --convergence [ 50x 50x50x50x50, 1e-07 ] --output [ sub-01_T1w_corrected.nii.gz, sub-01_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/09_relabel_wm_maths_xform.nii.gz * duration : 15.334786 * hostname : dendrite * prev_wd : /home/oesteban/tmp/fmriprep-ds005 * working_dir : /home/oesteban/tmp/fmriprep-ds005/fprep-work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0 ``` (`bias_image` should be `'sub-01_T1w_bias.nii.gz'` given the `cmdline`)
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This PR:
Atropos(interfaces.ants.segmentation does not have options for PriorLabelImage arguments #3178)JointFusioninterface, for which there hasn't been any corresponding command line binary for very long time now.