nipreps / dmriprep

dMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse dMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

https://www.nipreps.org/dmriprep

Apache License 2.0

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Registration tools (arokem) #104

Open arokem opened 4 years ago

arokem commented 4 years ago

Continues the work started in #78

pull-assistant[bot] commented 4 years ago

Best reviewed: commit by commit

Optimal code review plan

[ENH] Add affine registration tools for EMC [ENH] Add coarse/precise affine/rigid templates Removes config files. To be reintroduced in the relevant context. Object-oriented interface, with fit and apply methods. Add nitransforms as a dependency.

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codecov[bot] commented 4 years ago

Codecov Report

Merging #104 into master will decrease coverage by 0.55%. The diff coverage is 35.55%.

@@            Coverage Diff             @@
##           master     #104      +/-   ##
==========================================
- Coverage   51.06%   50.51%   -0.56%     
==========================================
  Files          21       22       +1     
  Lines        1218     1263      +45     
  Branches      161      165       +4     
==========================================
+ Hits          622      638      +16     
- Misses        581      610      +29     
  Partials       15       15

Impacted Files	Coverage Δ
dmriprep/utils/register.py	`35.55% <35.55%> (ø)`

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pep8speaks commented 4 years ago

Hello @arokem, Thank you for updating!

In the file dmriprep/utils/register.py:

Line 79:5: F841 local variable 'transformed' is assigned to but never used Line 134:1: F811 redefinition of unused 'AffineRegistration' from line 10 Line 137:9: F841 local variable 'nbins' is assigned to but never used Line 138:9: F841 local variable 'sampling_prop' is assigned to but never used Line 139:9: F841 local variable 'metric' is assigned to but never used Line 140:9: F841 local variable 'level_iters' is assigned to but never used Line 141:9: F841 local variable 'sigmas' is assigned to but never used Line 142:9: F841 local variable 'factors' is assigned to but never used Line 143:9: F841 local variable 'pipeline' is assigned to but never used

To test for issues locally, pip install flake8 and then run flake8 dmriprep.

Comment last updated at 2020-09-29 15:30:40 UTC

oesteban commented 4 years ago

My plan is to rebase this on top of #78 after Derek updates that branch.