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Some updates in Horizon fixing some issues for upcoming release #1924

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merged 55 commits into from Aug 5, 2019

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@Garyfallidis
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commented Jul 26, 2019

Images

  • Automatic contrast adjustment on load
  • 3D and 4D image support
  • Slider for seeing threshold
  • Provides access to colormaps
  • Picking voxels and showing underlying value
  • World or native coordinates supported

Streamlines

  • Uses distinguished_colormap to load multiple tractograms when --random_colors is set
  • Native coordinates disabled for now until this is updated with the StatefulTractogram
  • On the fly clustering with --cluster --cluster_thr 15 continues being supported
  • Slider for changing clustering threshold

Overall

  • Added global memory to communicate across actors and UI components.
  • Increase coverage
Garyfallidis added 30 commits May 23, 2019
BF: datasets with affines with negative values along the diagonal had…
… issues in giving the right data information. Should be now resolved. More tests needed concerning peaks
@codecov-io

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commented Jul 26, 2019

Codecov Report

Merging #1924 into master will decrease coverage by 0.11%.
The diff coverage is 44.66%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1924      +/-   ##
==========================================
- Coverage   83.89%   83.78%   -0.12%     
==========================================
  Files         118      118              
  Lines       14679    15016     +337     
  Branches     2326     2375      +49     
==========================================
+ Hits        12315    12581     +266     
- Misses       1814     1875      +61     
- Partials      550      560      +10
Impacted Files Coverage Δ
dipy/viz/gmem.py 100% <100%> (ø)
dipy/viz/app.py 44.44% <28.46%> (-7.51%) ⬇️
dipy/viz/panel.py 52.78% <46.12%> (-28.91%) ⬇️
dipy/workflows/viz.py 73.46% <53.84%> (-7.62%) ⬇️
dipy/workflows/io.py 72% <63.63%> (-2.47%) ⬇️
dipy/io/streamline.py 53.28% <0%> (-1.08%) ⬇️
dipy/tracking/streamline.py 92.3% <0%> (-0.66%) ⬇️
dipy/reconst/ivim.py 95.9% <0%> (-0.27%) ⬇️
dipy/data/fetcher.py 34.92% <0%> (-0.22%) ⬇️
dipy/reconst/fwdti.py 94.28% <0%> (ø) ⬆️
... and 24 more

@Garyfallidis Garyfallidis changed the title WIP: Some updates in Horizon fixing some issues for upcoming release Some updates in Horizon fixing some issues for upcoming release Aug 1, 2019

obj.VisibilityOff()
self.cea[ca]['expanded'] = 0

show_m.render()

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@skoudoro

skoudoro Aug 1, 2019

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missing a self here?

hz = Horizon(tractograms, images, cluster, cluster_thr, random_colors,
length_lt, length_gt, clusters_lt, clusters_gt,
world_coords, interactive, out_png)
hz = Horizon(tractograms, images, pams, cluster, cluster_thr, random_colors,

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skoudoro Aug 1, 2019

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pep8: random_colors too long

image_actor_z = actor.slicer(data, affine=np.eye(4))
affine = np.eye(4)

# renderer.add(actor.axes(scale=(50, 50, 50)))

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skoudoro Aug 1, 2019

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remove comment

line_slider_x = ui.LineSlider2D(min_value=0,
max_value=shape[0] - 1,
initial_value=shape[0] / 2,
text_template="{value:.0f}",
length=140)

_color_slider(line_slider_x)


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skoudoro Aug 1, 2019

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pep8: remove empty line

cluster_actors = []


HORIZON = GlobalHorizon()

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@skoudoro

skoudoro Aug 1, 2019

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HORIZON to HORIZONMEM

Garyfallidis added 4 commits Aug 2, 2019
Skipping tests that create Xserver error (xvfb)
With and only with xvfb and mesa XIO errors are created.
Needs more work to identify the reason.
Nonetheless application works successfully in all 3 major operating
systems. Automating the testing procedure for horizon using
recorded events still needs more work.
@Garyfallidis

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commented Aug 5, 2019

I suggest merging these fixes for now. More to come with 1.1 including increasing coverage for Horizon. I was planning to increase coverage here but there is an issue with xvfb which needs more investigation. Nonetheless, we have not seen any unexpected issues with the desktop version of this in all 3 operating systems (windows, linux and osx). So, I suggest to merge and write an issue to follow up.

@skoudoro skoudoro referenced this pull request Aug 5, 2019
1 of 3 tasks complete

@skoudoro skoudoro merged commit 9bdaf97 into nipy:master Aug 5, 2019

3 of 5 checks passed

codecov/patch 44.66% of diff hit (target 83.89%)
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codecov/project 83.78% (-0.12%) compared to 2ff8ace
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Codacy/PR Quality Review Up to standards. A positive pull request.
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continuous-integration/appveyor/pr AppVeyor build succeeded
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continuous-integration/travis-ci/pr The Travis CI build passed
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@skoudoro

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commented Aug 5, 2019

Thank you @Garyfallidis

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