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Csa and csd reconstruction workflow rebased #1241

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merged 8 commits into from Jun 9, 2017

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Garyfallidis commented May 13, 2017

This is a rebase of #1155
with some additional testing and using the new hdf5 format (.pam5) for saving PeaksAndMetrics.
@matthieudumont, @arokem and all give it a try.

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coveralls commented May 13, 2017

Coverage Status

Coverage increased (+0.04%) to 85.651% when pulling 751691a on Garyfallidis:csa_csd_workflow_rebased into ceed367 on nipy:master.

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coveralls commented May 13, 2017

Coverage Status

Coverage increased (+0.04%) to 85.651% when pulling 751691a on Garyfallidis:csa_csd_workflow_rebased into ceed367 on nipy:master.

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coveralls commented May 14, 2017

Coverage Status

Coverage increased (+0.05%) to 85.656% when pulling 84f073a on Garyfallidis:csa_csd_workflow_rebased into ceed367 on nipy:master.

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coveralls commented May 14, 2017

Coverage Status

Coverage increased (+0.05%) to 85.656% when pulling 84f073a on Garyfallidis:csa_csd_workflow_rebased into ceed367 on nipy:master.

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Garyfallidis commented May 14, 2017

Hi, this looks ready can you try it with your datasets? And tell me if it works for you?

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matthieudumont commented Jun 9, 2017

(sorry for long response time)
Looks good and works for me, merge it!

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Garyfallidis commented Jun 9, 2017

Perfeto! Thank you @matthieudumont. @arokem can you try it too and merge?

@@ -218,6 +218,8 @@ def main(**extra_args):
scripts = [pjoin('bin', 'dipy_reconst_dti'),
pjoin('bin', 'dipy_reconst_dti_restore'),
pjoin('bin', 'dipy_mask'),
pjoin('bin', 'dipy_reconst_csa'),
pjoin('bin', 'dipy_reconst_csd'),

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@arokem

arokem Jun 9, 2017

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This is still rather ad-hoc. We need to automate this.

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@arokem arokem merged commit 599af3e into nipy:master Jun 9, 2017

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coverage/coveralls Coverage increased (+0.05%) to 85.656%
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codecov-io commented Jun 9, 2017

Codecov Report

Merging #1241 into master will increase coverage by <.01%.
The diff coverage is 87.74%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1241      +/-   ##
==========================================
+ Coverage   87.04%   87.05%   +<.01%     
==========================================
  Files         225      226       +1     
  Lines       28109    28262     +153     
  Branches     3014     3026      +12     
==========================================
+ Hits        24468    24603     +135     
- Misses       2968     2976       +8     
- Partials      673      683      +10
Impacted Files Coverage Δ
dipy/io/tests/test_io_peaks.py 97.46% <100%> (+0.49%) ⬆️
dipy/io/peaks.py 92.45% <100%> (+0.56%) ⬆️
dipy/workflows/reconst.py 79.5% <77.33%> (-3.06%) ⬇️
dipy/workflows/tests/test_reconst_csa_csd.py 96.29% <96.29%> (ø)
dipy/direction/peaks.py 79.81% <0%> (+0.93%) ⬆️

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ShreyasFadnavis pushed a commit to ShreyasFadnavis/dipy that referenced this pull request Sep 20, 2018

Merge pull request nipy#1241 from Garyfallidis/csa_csd_workflow_rebased
Csa and csd reconstruction workflow rebased
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