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[ENH] Include several operations to ANTs's ImageMath interface, including ReplicateImage and ReplicateDisplacement #3435

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merged 3 commits into from
Mar 21, 2022

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dmartindeblas
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@dmartindeblas dmartindeblas commented Mar 2, 2022

Summary

This PR addresses Issue #3434 . ReplicateImage and ReplicateDisplacement operations have been included in ANTs's ImageMath interface. Futhermore several other operations, that work well with the current structure of the interface, are included. Also, "args" trait has been overloaded so that its content is in the last position of the command line. Finally, for several of the included operations, copying the header of the input image does not make sense. A tuple called "_no_copy_header_operation" is defined to list such operations.

List of changes proposed in this PR (pull-request)

  • ReplicateImage and ReplicateDisplacement operations have been included
  • Several other operations included
  • "args" trait has been overloaded so that its content is in the last position of the command line
  • A tuple called "_no_copy_header_operation" is defined and used to set to False the trait "copy_header" and avoid that it is set to True
  • Documentation string modified so that mentions that there are more operations other than "PadImage" that so not allow for copy_header

Acknowledgment

  • (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

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codecov bot commented Mar 21, 2022

Codecov Report

Merging #3435 (f482310) into master (cd4c34d) will decrease coverage by 0.86%.
The diff coverage is 83.33%.

@@            Coverage Diff             @@
##           master    #3435      +/-   ##
==========================================
- Coverage   65.21%   64.34%   -0.87%     
==========================================
  Files         307      307              
  Lines       40478    40487       +9     
  Branches     5352     5353       +1     
==========================================
- Hits        26399    26053     -346     
- Misses      13008    13375     +367     
+ Partials     1071     1059      -12     
Flag Coverage Δ
unittests ?

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Impacted Files Coverage Δ
nipype/interfaces/ants/utils.py 89.04% <83.33%> (+0.10%) ⬆️
nipype/workflows/__init__.py 47.05% <0.00%> (-52.95%) ⬇️
nipype/utils/spm_docs.py 20.00% <0.00%> (-48.00%) ⬇️
nipype/interfaces/freesurfer/base.py 48.38% <0.00%> (-28.23%) ⬇️
nipype/utils/logger.py 56.92% <0.00%> (-27.70%) ⬇️
nipype/testing/fixtures.py 77.92% <0.00%> (-20.78%) ⬇️
nipype/interfaces/dcm2nii.py 50.92% <0.00%> (-14.36%) ⬇️
nipype/interfaces/ants/base.py 65.30% <0.00%> (-8.17%) ⬇️
nipype/interfaces/spm/base.py 60.06% <0.00%> (-7.60%) ⬇️
nipype/interfaces/io.py 48.09% <0.00%> (-7.15%) ⬇️
... and 15 more

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@effigies
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LGTM! Thanks!

@effigies effigies added this to the 1.7.1 milestone Mar 21, 2022
@effigies effigies merged commit 96c50f2 into nipy:master Mar 21, 2022
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2 participants