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Cleaned PR for Apply Transform Workflow to quickly register a set of moving NIFTI images using a given affine matrix. #1605

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commented Jul 31, 2018

This work was done as part of the Google Summer of Code (GSOC-2018) DIPY project titled 'DIPY Workflow(s) and Quality Assurance'

This work pertains to extending the work done in PR 1604 by using the affine matrix generated by image registration for transforming a set of images without having to do the image registration again. Evidently, this workflow (ApplyAffineFlow) creates the registered images in a fraction of seconds when compared to the Image registration workflow.

Together the Image Registration Workflow and the Apply Affine Workflow provides the ability to registering a set of images and applying the generated transform to a set of moving images.

This is a clean and stable version of the PR 1598 that got mixed up due to code merge and rebase. The PR1598 must not be merged now. Instead, this PR should be merged with the codebase.

The link to the older PR (with all the conversations, commit history and improvements made based on community feedback can be seen below):
#1598

@parichit parichit changed the title Apply transform workflow to quickly register a set of moving NIFTI images using a given affine matrix. Clean PR for Apply transform workflow to quickly register a set of moving NIFTI images using a given affine matrix. Jul 31, 2018

@parichit parichit changed the title Clean PR for Apply transform workflow to quickly register a set of moving NIFTI images using a given affine matrix. Clean PR for Apply Transform Workflow to quickly register a set of moving NIFTI images using a given affine matrix. Jul 31, 2018

@parichit parichit changed the title Clean PR for Apply Transform Workflow to quickly register a set of moving NIFTI images using a given affine matrix. Cleaned PR for Apply Transform Workflow to quickly register a set of moving NIFTI images using a given affine matrix. Jul 31, 2018

@skoudoro skoudoro added the gsoc2018 label Aug 1, 2018

@parichit parichit force-pushed the parichit:apply_transform_clean branch from ca6c55e to eb44e4d Aug 7, 2018

parichit added 2 commits Aug 8, 2018
Decreased the decimal precision to 1 decimal places (in checking the …
…value of distance metric) to validate the tests by travis.
1) Updated the parameter documentation for optimal parameters and sim…
…ilarity metric in the optimize() function of the imaffine.py file.

2) Changed the parameter documentation in the run() method of the alignpy file for improved view on the command line.

@parichit parichit force-pushed the parichit:apply_transform_clean branch from 14d5ca8 to e0b046e Aug 13, 2018

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commented Aug 13, 2018

Codecov Report

Merging #1605 into master will increase coverage by 0.03%.
The diff coverage is 98.14%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1605      +/-   ##
==========================================
+ Coverage   87.34%   87.37%   +0.03%     
==========================================
  Files         246      246              
  Lines       31811    31985     +174     
  Branches     3451     3465      +14     
==========================================
+ Hits        27785    27948     +163     
- Misses       3204     3212       +8     
- Partials      822      825       +3
Impacted Files Coverage Δ
dipy/align/imaffine.py 91.84% <100%> (+0.04%) ⬆️
dipy/workflows/align.py 92.63% <100%> (-1.12%) ⬇️
dipy/io/image.py 100% <100%> (ø) ⬆️
dipy/workflows/tests/test_align.py 98.09% <97.77%> (+7.18%) ⬆️
dipy/core/graph.py 73.8% <0%> (-1.2%) ⬇️
dipy/reconst/mapmri.py 90.28% <0%> (-0.65%) ⬇️
dipy/workflows/multi_io.py 68% <0%> (+0.79%) ⬆️

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@skoudoro

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commented Feb 15, 2019

Closing in favor of the rebased version #1742. Thank you @parichit for this work.

@skoudoro skoudoro closed this Feb 15, 2019

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