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Clean up watershed (again) #1693

Merged
merged 1 commit into from
Dec 16, 2019
Merged

Clean up watershed (again) #1693

merged 1 commit into from
Dec 16, 2019

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ttung
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@ttung ttung commented Dec 10, 2019

  • Get rid of the remaining naked numpy arrays and replace them with ImageStacks.
  • Use ImageStack.reduce rather than instantiating a Reduce Filter and applying it.

Depends on #1686
Test plan: ran iss notebook and found 69 cells.

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codecov-io commented Dec 10, 2019

Codecov Report

Merging #1693 into master will decrease coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1693      +/-   ##
==========================================
- Coverage   89.78%   89.78%   -0.01%     
==========================================
  Files         241      241              
  Lines        9076     9071       -5     
==========================================
- Hits         8149     8144       -5     
  Misses        927      927
Impacted Files Coverage Δ
starfish/core/image/Segment/watershed.py 95.61% <100%> (-0.19%) ⬇️

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@ttung ttung changed the base branch from tonytung-simplify-functionsource to master December 13, 2019 01:29
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So fresh and so clean!

- Get rid of the remaining naked numpy arrays and replace them with ImageStacks.
- Use ImageStack.reduce rather than instantiating a Reduce Filter and applying it.
- Get rid of self.nuclei_thresholded as it is not used.

Test plan: ran iss notebook and found 69 cells.
@ttung ttung merged commit 715b762 into master Dec 16, 2019
@ttung ttung deleted the tonytung-cleanup-watershed branch December 16, 2019 17:29
mattcai pushed a commit that referenced this pull request Dec 19, 2019
Remove starfish.core.image.Filter.util.bin_open as there are no more users of this method.

Depends on #1692, #1693, #1684, #1688
Test plan: ISS notebook still yields 96 cells.
ttung pushed a commit that referenced this pull request Jan 14, 2020
Remove starfish.core.image.Filter.util.bin_open as there are no more users of this method.

Depends on #1692, #1693, #1684, #1688
Test plan: ISS notebook still yields 96 cells.
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3 participants