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ENH: Read (and apply) ITK/ANTs' composite HDF5 transforms #79

Merged
merged 5 commits into from
Mar 26, 2020
Merged

ENH: Read (and apply) ITK/ANTs' composite HDF5 transforms #79

merged 5 commits into from
Mar 26, 2020

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oesteban
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Uses h5py to browse the transforms group, and concatenates them in a list
ready for nitransforms' wrapping into a TransformsChain.

The writer is not included in this PR.

The implementation takes into account the misspelling of "Tranforms" present
in transforms generated with older versions of ITK.

This implementation only accepts the composite transforms generated by ANTs.

Closes #4

@oesteban
feat(io.reader): draft implementation of ITK/ANTs' composite HDF5 tra…
a3372bc 
…nsforms

Uses ``h5py`` to browse the transforms group, and concatenates them in a list
ready for nitransforms' wrapping into a ``TransformsChain``.

The writer is not included in this PR.

The implementation takes into account the misspelling of "Tranforms" present
in transforms generated with older versions of ITK.

This implementation only accepts the composite transforms generated by ANTs.

Resolves: nipy#4
@oesteban oesteban added the enhancement New feature or request label Mar 25, 2020
@oesteban oesteban added this to the 20.0.0rc1 milestone Mar 25, 2020
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pull-assistant bot commented Mar 25, 2020 •
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Score: 0.95

Best reviewed: commit by commit

Optimal code review plan

     feat(io.reader): draft implementation of ITK/ANTs' composite HDF5 tran...

     feat: add test reading a real h5 generated by ANTs

     test: cover one more line of code with a test

     feat: split transform chains out from base and add a load function

     Update nitransforms/tests/test_manip.py

Powered by Pull Assistant. Last update a3372bc ... 3185b1d. Read the comment docs.

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codecov-io commented Mar 25, 2020 •
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Codecov Report

Merging #79 into master will increase coverage by 0.06%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #79      +/-   ##
==========================================
+ Coverage   98.89%   98.95%   +0.06%     
==========================================
  Files          11       12       +1     
  Lines         992     1050      +58     
  Branches      129      135       +6     
==========================================
+ Hits          981     1039      +58     
  Misses          6        6              
  Partials        5        5
Flag Coverage Δ
#unittests 98.95% <100.00%> (+0.06%) ⬆️
Impacted Files Coverage Δ
nitransforms/base.py 99.32% <100.00%> (-0.15%) ⬇️
nitransforms/io/itk.py 100.00% <100.00%> (ø)
nitransforms/manip.py 100.00% <100.00%> (ø)

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pep8speaks commented Mar 25, 2020 •
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Hello @oesteban! Thanks for updating this PR.

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2020-03-26 04:34:25 UTC

@oesteban
feat: split transform chains out from base and add a load function
26f9e80 
This was necessary to integrate one test equivalent to resampling with
``antsApplyTransforms``, but via nitransforms.
@oesteban oesteban marked this pull request as ready for review March 26, 2020 00:32
@oesteban oesteban changed the title ENH: draft implementation of ITK/ANTs' composite HDF5 transforms ENH: Read (and apply) ITK/ANTs' composite HDF5 transforms Mar 26, 2020
@oesteban oesteban requested a review from mgxd March 26, 2020 01:30
@oesteban oesteban mentioned this pull request Mar 26, 2020
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mgxd
mgxd approved these changes Mar 26, 2020
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lgtm, tiny comment

nitransforms/tests/test_manip.py Outdated Show resolved Hide resolved
@oesteban @mgxd
Update nitransforms/tests/test_manip.py
3185b1d 
Co-Authored-By: Mathias Goncalves <goncalves.mathias@gmail.com>
@oesteban oesteban merged commit 838d385 into nipy:master Mar 26, 2020
@oesteban oesteban deleted the enh/4-read-itk-h5 branch March 26, 2020 04:48
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Read in ITK's h5 transforms
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