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Refactor watershed mask creation using new API #1694

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merged 1 commit into from
Jan 14, 2020

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@ttung ttung commented Dec 10, 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.

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codecov-io commented Dec 10, 2019

Codecov Report

Merging #1694 into master will increase coverage by 0.01%.
The diff coverage is 90.47%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1694      +/-   ##
==========================================
+ Coverage   90.16%   90.17%   +0.01%     
==========================================
  Files         246      246              
  Lines        9159     9153       -6     
==========================================
- Hits         8258     8254       -4     
+ Misses        901      899       -2
Impacted Files Coverage Δ
starfish/core/image/Filter/util.py 89.28% <ø> (+7.46%) ⬆️
starfish/core/image/Segment/watershed.py 93.75% <90.47%> (-1.1%) ⬇️

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@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 4513d58 to 76f2263 Compare December 11, 2019 05:15
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from 46501cd to 62c41a2 Compare December 11, 2019 18:38
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch 2 times, most recently from 3b4e4a8 to c764a73 Compare December 11, 2019 18:42
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from 78850ef to f07f681 Compare December 11, 2019 19:09
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from c764a73 to 23118e9 Compare December 11, 2019 19:09
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from f07f681 to 994f91c Compare December 13, 2019 01:13
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 23118e9 to 522e03e Compare December 13, 2019 01:13
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from 994f91c to ef47769 Compare December 13, 2019 01:28
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 522e03e to 242f2cd Compare December 13, 2019 01:28
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 242f2cd to f1dc79b Compare December 13, 2019 18:12
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from 5261a09 to edaec92 Compare December 13, 2019 18:14
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch 2 times, most recently from 65e87e2 to 6fb7277 Compare December 13, 2019 18:16
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from 44e98ac to f5c5a7c Compare December 13, 2019 19:33
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch 2 times, most recently from e40027f to ca78705 Compare December 13, 2019 19:43
@ttung ttung force-pushed the tonytung-refactor-mask-creation-base branch from 04472fc to d21d75d Compare December 14, 2019 02:19
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from ca78705 to c3a2da5 Compare December 14, 2019 02:19
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from c3a2da5 to db18e28 Compare December 16, 2019 17:28
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from db18e28 to f6370c1 Compare December 16, 2019 17:45
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from af75643 to 31a67d5 Compare December 16, 2019 18:58
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 31a67d5 to 9afcb3c Compare December 16, 2019 19:00
@ttung ttung changed the base branch from tonytung-refactor-mask-creation-base to tonytung-refactor-label December 16, 2019 19:01
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 9afcb3c to 8d1f3ed Compare December 16, 2019 19:18
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 8d1f3ed to d3de7fd Compare December 16, 2019 21:37
ttung pushed a commit that referenced this pull request Dec 16, 2019
… watershed

Use the component from #1700 to replace the remaining procedural code in the existing watershed component.

Depends on #1700, #1699, #1694
Test plan: visually the ISS notebook looks the same.
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch 3 times, most recently from d09f5b1 to a2c85c5 Compare December 20, 2019 23:23
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from a2c85c5 to 76b8f16 Compare January 6, 2020 21:08
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from 76b8f16 to 6651456 Compare January 6, 2020 21:21
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch 5 times, most recently from f348591 to cab1c86 Compare January 13, 2020 22:06
@ttung ttung changed the base branch from tonytung-refactor-label to master January 13, 2020 22:07
@ttung ttung force-pushed the tonytung-refactor-mask-creation branch from cab1c86 to a002338 Compare January 13, 2020 22:08
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 ttung force-pushed the tonytung-refactor-mask-creation branch from a002338 to 0090920 Compare January 13, 2020 23:23
@ttung ttung merged commit e666d82 into master Jan 14, 2020
@ttung ttung deleted the tonytung-refactor-mask-creation branch January 14, 2020 06:37
ttung pushed a commit that referenced this pull request Jan 15, 2020
… watershed (#1701)

Use the component from #1700 to replace the remaining procedural code in the existing watershed component.

Depends on #1700, #1699, #1694
Test plan: visually the ISS notebook looks the same.
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3 participants