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Default sphere: From symmetric724 to repulsion724 #1894

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merged 8 commits into from Jul 26, 2019

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@skoudoro
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commented Jul 10, 2019

This PR should fix #590. We use repulsion724 as a default sphere instead of symmetric724

@skoudoro skoudoro added this to the 1.0 milestone Jul 10, 2019

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commented Jul 10, 2019

Hello @skoudoro, Thank you for updating !

Line 82:1: E402 module level import not at top of file
Line 192:81: E501 line too long (89 > 80 characters)

Line 92:1: E402 module level import not at top of file

Comment last updated at 2019-07-25 22:59:28 UTC
@arokem

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commented Jul 10, 2019

Hey @skoudoro : thanks for doing this. Maybe better to change everything to use default_sphere except in data/__init__.py?

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commented Jul 10, 2019

Yes, you are right, I hesitate to do it this way for no reason, I will update this PR this afternoon

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commented Jul 11, 2019

Thanks for having addressed this @skoudoro !

@@ -564,8 +565,9 @@ def test_csd_superres():
sh_order=16)
fit16 = model16.fit(S)

sphere = HemiSphere.from_sphere(get_sphere('symmetric724'))

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arokem Jul 11, 2019

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Why are we still using the symmetric sphere here?

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skoudoro Jul 11, 2019

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To avoid to update the whole tests 😄. It seems that when we use repulsion, there is 3 peaks instead of 2 and they do not line up with the sticks

@@ -74,8 +74,7 @@ def test_shore_metrics():

# compare the shore pdf with the ground truth multi_tensor pdf

sphere = get_sphere('symmetric724')
v = sphere.vertices
v = default_sphere.vertices

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arokem Jul 11, 2019

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I wonder if the change here caused the CI error on Python 3.5. I just restarted that build, to seehow intermittent that is.

@@ -567,7 +567,9 @@ def test_bootstap_peak_tracker():
seeds = [np.array([0., 1., 0.]), np.array([2., 4., 0.])]

tc = BinaryTissueClassifier((simple_image > 0).astype(float))
boot_dg = BootDirectionGetter.from_data(data, csd_model, 60)
sphere = HemiSphere.from_sphere(get_sphere('symmetric724'))

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arokem Jul 11, 2019

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Here as well: why are we still using symmetric?

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@skoudoro

skoudoro Jul 11, 2019

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almost the same comment as above. we can create an issue to spend more time on these 2 specifics tests and update them

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commented Jul 11, 2019

LGTM. Let's see how persistent that Travis failure is.

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commented Jul 11, 2019

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commented Jul 13, 2019

Looks like that failure is rather persistent. Seems like something about the SHORE metrics is sensitive to the choice of sphere.

@skoudoro skoudoro force-pushed the skoudoro:default_sphere branch from 3128383 to 4334f16 Jul 16, 2019

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commented Jul 16, 2019

Codecov Report

❗️ No coverage uploaded for pull request base (master@239c699). Click here to learn what that means.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff            @@
##             master    #1894   +/-   ##
=========================================
  Coverage          ?   85.39%           
=========================================
  Files             ?      118           
  Lines             ?    14240           
  Branches          ?     2235           
=========================================
  Hits              ?    12160           
  Misses            ?     1574           
  Partials          ?      506
Impacted Files Coverage Δ
dipy/reconst/dsi.py 79.67% <ø> (ø)
dipy/sims/voxel.py 90.45% <ø> (ø)
dipy/reconst/shore.py 85.15% <ø> (ø)
dipy/tracking/eudx.py 94.11% <ø> (ø)
dipy/reconst/mapmri.py 90.33% <ø> (ø)
dipy/viz/projections.py 20% <ø> (ø)
dipy/reconst/forecast.py 90.15% <100%> (ø)
dipy/tracking/life.py 97.75% <100%> (ø)
dipy/workflows/reconst.py 77.22% <100%> (ø)
dipy/data/__init__.py 81.45% <100%> (ø)
... and 1 more

@skoudoro skoudoro force-pushed the skoudoro:default_sphere branch 2 times, most recently from 1247d57 to a05b10f Jul 18, 2019

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commented Jul 25, 2019

The remaining CI error here seems to have been a glitch on Travis side. I just kicked off that build again. If that comes back green, should I go ahead and merge it? Are things all set on your side @skoudoro?

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commented Jul 25, 2019

Thank you for catching that. Everything good from my side. You can go ahead if it is good for you

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commented Jul 25, 2019

OK. Looks like the CI is all passing here.

Is this ready to go, or do you want to do anything more here, @skoudoro?

Anyone else have any additional comments?

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commented Jul 25, 2019

Nothing more, Ready to go

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commented Jul 25, 2019

Let's go!

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commented Jul 25, 2019

Oh no - looks like I can't merge this anymore. One more rebase, please?

@skoudoro skoudoro force-pushed the skoudoro:default_sphere branch from 7aba70a to 6f6f3a3 Jul 25, 2019

@Garyfallidis Garyfallidis merged commit 77c0686 into nipy:master Jul 26, 2019

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continuous-integration/appveyor/pr AppVeyor build failed
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Codacy/PR Quality Review Up to standards. A positive pull request.
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@skoudoro skoudoro deleted the skoudoro:default_sphere branch Jul 26, 2019

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