FIX: ANTs' tools maintenance overhaul #3180
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ 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
Continue to review full report at Codecov.
|
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`)
1 task
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.