Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FIX: Collate fieldmap coefficients into list of lists #317

Merged
merged 2 commits into from
Dec 9, 2022

Conversation

effigies
Copy link
Member

@effigies effigies commented Dec 7, 2022

Currently the fieldmap coeffficients from each estimator are aggregated into a single list. When selected by downstream nodes, the first application node gets the first coefficient of the first estimator, the second application node gets the second coefficient of the first estimator, the third application node gets the first coefficient of the second estimator, and so on.

This has been obscured from using test datasets with only one estimator, so only the low frequency components are getting applied.

This PR simply prevents this list from being flattened. Will test with downstream to make sure a list of coefficients can be passed.

Node: single_subject_EB_wf (fmap_preproc_wf (out_merge_fmap_coeff (utility)
===========================================================================


 Hierarchy : fmriprep_0_0_wf.single_subject_EB_wf.fmap_preproc_wf.out_merge_fmap_coeff
 Exec ID : out_merge_fmap_coeff


Original Inputs
---------------


* axis : vstack
* in1 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00000/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00000/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* in2 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00001/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00001/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* in3 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00002/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00002/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* in4 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00003/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00003/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* no_flatten : False
* ravel_inputs : False


Execution Inputs
----------------


* axis : vstack
* in1 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00000/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00000/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* in2 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00001/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00001/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* in3 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00002/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00002/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* in4 : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00003/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00003/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']
* no_flatten : False
* ravel_inputs : False


Execution Outputs
-----------------


* out : ['/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00000/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00000/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00001/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00001/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00002/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00002/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00003/bs_filter/fmap_syn0Warp_Hz_trans_coeff000.nii.gz', '/scratch/fmriprep_0_0_wf/single_subject_EB_wf/fmap_preproc_wf/wf_auto_00003/bs_filter/fmap_syn0Warp_Hz_trans_coeff001.nii.gz']

@codecov-commenter
Copy link

codecov-commenter commented Dec 7, 2022

Codecov Report

Base: 83.92% // Head: 89.20% // Increases project coverage by +5.28% 🎉

Coverage data is based on head (16df78c) compared to base (b11551e).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##           master     #317      +/-   ##
==========================================
+ Coverage   83.92%   89.20%   +5.28%     
==========================================
  Files          25       25              
  Lines        2009     2011       +2     
  Branches      235      307      +72     
==========================================
+ Hits         1686     1794     +108     
+ Misses        281      178     -103     
+ Partials       42       39       -3     
Flag Coverage Δ
travis 83.93% <100.00%> (+0.01%) ⬆️
unittests 89.10% <100.00%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
sdcflows/workflows/base.py 100.00% <100.00%> (ø)
sdcflows/workflows/outputs.py 93.84% <0.00%> (+1.53%) ⬆️
sdcflows/interfaces/reportlets.py 89.83% <0.00%> (+1.69%) ⬆️
sdcflows/interfaces/bspline.py 85.00% <0.00%> (+8.33%) ⬆️
sdcflows/interfaces/fmap.py 87.35% <0.00%> (+14.94%) ⬆️
sdcflows/utils/tools.py 97.36% <0.00%> (+21.05%) ⬆️
sdcflows/workflows/fit/syn.py 69.82% <0.00%> (+21.30%) ⬆️
sdcflows/utils/phasemanip.py 94.02% <0.00%> (+28.35%) ⬆️

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

☔ View full report at Codecov.
📢 Do you have feedback about the report comment? Let us know in this issue.

@effigies effigies added this to the 2.2.0 milestone Dec 8, 2022
@effigies effigies added bug Something isn't working impact: high Estimated high impact task pipelines backport candidate labels Dec 8, 2022
@effigies effigies mentioned this pull request Dec 8, 2022
7 tasks
@effigies effigies merged commit 4b271a5 into nipreps:master Dec 9, 2022
@effigies effigies deleted the fix/collate_coeffs branch December 9, 2022 21:16
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
backport candidate bug Something isn't working impact: high Estimated high impact task pipelines
Projects
Status: Released
Development

Successfully merging this pull request may close these issues.

2 participants