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[REBASED] Apply Transform Workflow #1742

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merged 15 commits into from Mar 1, 2019

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@skoudoro
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commented Feb 15, 2019

The goal of this PR is to clean and rebase #1605. Look at #1605 for more information

parichit and others added 12 commits Jul 31, 2018
Crated a new branch with clean history for the affine registration wo…
…rkflow.

1) Committing to this branch all the code from the affine_registration branch (PR 1581)
2) New PR should be opened for this branch.
1) Fixed the PEP8 formatting issue in the dipy_align_affine and dipy_…
…apply_transform.

2) Changed the body of 'rigid()' function in align.py to call the center_of_mass function when the progressive flag is off.
1) Renamed the ApplyTransformFlow to ApplyAffineFlow to distinguish i…
…t from the Syn_Registration flow.

2) Made the changes in the command line wrapper to use the changed name for the workflow.
Changed the name of the function to test_apply_affine_transform() and…
… decreased the decimal precision to 1 decimal place for validating the travis tests.
@arokem
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LGTM. Just one small comment.

@@ -27,6 +27,16 @@ def save_nifti(fname, data, affine, hdr=None):
result_img.to_filename(fname)


def load_affine_matrix(fname):

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arokem Feb 15, 2019

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This is just a wrapper around np.loadtxt. Let's use that one.

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@skoudoro

skoudoro Feb 15, 2019

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thank you! addressed in d90ea0d

"""
return np.loadtxt(fname)


def save_affine_matrix(fname, affine):

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arokem Feb 15, 2019

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While we're here, could you please get rid of save_affine_matrix? That looks like a wrapper around np.savetxt.

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@skoudoro

skoudoro Feb 15, 2019

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ok, done in 4306c36

skoudoro added 2 commits Feb 15, 2019
@codecov-io

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commented Feb 17, 2019

Codecov Report

❗️ No coverage uploaded for pull request base (master@a115980). Click here to learn what that means.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master    #1742   +/-   ##
=========================================
  Coverage          ?   84.31%           
=========================================
  Files             ?      115           
  Lines             ?    13691           
  Branches          ?     2158           
=========================================
  Hits              ?    11543           
  Misses            ?     1647           
  Partials          ?      501
Impacted Files Coverage Δ
dipy/io/image.py 100% <ø> (ø)
dipy/workflows/align.py 91.59% <100%> (ø)
@arokem
arokem approved these changes Feb 19, 2019
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commented Feb 19, 2019

LGTM. Will merge in a couple of days, unless someone has something to add.

@skoudoro

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commented Mar 1, 2019

This PR is ready to go! Does anyone else want to take a look?

@arokem arokem merged commit b78df7a into nipy:master Mar 1, 2019

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@skoudoro skoudoro deleted the skoudoro:apply_transform branch Mar 4, 2019

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