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Cleaned PR for Affine Registration Workflow with Supporting Quality Metrics #1604

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parichit 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 developing and testing the Affine registration workflow for overlaying bio-medical images in different modes (center of mass, translation, rigid body and affine registration). The modes of registration can be controlled easily via the command line parameters and the relative impact on the results can be assessed quantitatively via the generated output metrics. More information in the metrics can be seen in the code documentation as well as by trying the '-h' or help of the workflow.

This PR contains the stable and clean code for affine registration workflow. This should be merged in place of PR 1581. PR 1581 must not be merged now.

The original PR 1581 with the conversation history, all the original commits, commits for improvement based on community feedback can be seen below:
#1581

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pep8speaks commented Jul 31, 2018

Hello @parichit, Thank you for updating !

Line 146:9: E303 too many blank lines (2)

Comment last updated on August 14, 2018 at 06:00 Hours UTC

@skoudoro skoudoro added the gsoc2018 label Aug 1, 2018

@parichit parichit force-pushed the parichit:affine_registration_clean branch from e951e87 to d55dfb2 Aug 7, 2018

Decreased the decimal precision to 1 decimal places (in checking the …
…value of distance metric) to validate the tests by travis.
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codecov-io commented Aug 8, 2018

Codecov Report

Merging #1604 into master will increase coverage by 0.02%.
The diff coverage is 97.5%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1604      +/-   ##
==========================================
+ Coverage   87.34%   87.37%   +0.02%     
==========================================
  Files         246      246              
  Lines       31811    31943     +132     
  Branches     3451     3462      +11     
==========================================
+ Hits        27785    27909     +124     
- Misses       3204     3207       +3     
- Partials      822      827       +5
Impacted Files Coverage Δ
dipy/align/imaffine.py 91.84% <100%> (+0.04%) ⬆️
dipy/workflows/align.py 90.12% <100%> (-3.63%) ⬇️
dipy/io/image.py 100% <100%> (ø) ⬆️
dipy/workflows/tests/test_align.py 97.46% <96.87%> (+6.55%) ⬆️
dipy/core/graph.py 73.8% <0%> (-1.2%) ⬇️

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logging.info("Similarity metric:"+str(xopt))
logging.info("Distance measure:"+str(fopt))

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Garyfallidis Aug 8, 2018

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Optimal parameters
Similarity metric

parichit added some commits Aug 13, 2018

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.
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skoudoro commented Feb 7, 2019

Closing in favor of #1735. Thanks @parichit for this work.

@skoudoro skoudoro closed this Feb 7, 2019

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