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Thresholded binarize conversion algorithm #1651

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merged 1 commit into from
Dec 5, 2019
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@ttung ttung commented Nov 14, 2019

BinarizeImage takes an ImageStack and binarizes it into a BinaryMaskCollection.

Depends on #1637
Test plan: add tests for simple binarizing, and to test the input requirements.

@ttung ttung requested review from shanaxel42 and removed request for shanaxel42 November 14, 2019 00:08
@ttung ttung force-pushed the tonytung-binarize branch from b81b682 to 7f145be Compare November 14, 2019 00:15
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codecov-io commented Nov 14, 2019

Codecov Report

Merging #1651 into master will increase coverage by 0.05%.
The diff coverage is 98.3%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1651      +/-   ##
==========================================
+ Coverage   90.13%   90.18%   +0.05%     
==========================================
  Files         233      237       +4     
  Lines        8870     8929      +59     
==========================================
+ Hits         7995     8053      +58     
- Misses        875      876       +1
Impacted Files Coverage Δ
starfish/core/morphology/Binarize/threshold.py 100% <100%> (ø)
...sh/core/morphology/Binarize/test/test_threshold.py 100% <100%> (ø)
starfish/core/morphology/Binarize/__init__.py 100% <100%> (ø)
starfish/core/morphology/Binarize/_base.py 87.5% <87.5%> (ø)

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@ttung ttung force-pushed the tonytung-binarize branch from 7f145be to 9f223c3 Compare November 14, 2019 05:23
@ttung ttung force-pushed the tonytung-additional-builders branch from de76069 to ac617af Compare November 15, 2019 23:45
@ttung ttung force-pushed the tonytung-binarize branch 2 times, most recently from 9fd1bef to dbfee13 Compare November 16, 2019 00:21
@ttung ttung force-pushed the tonytung-additional-builders branch from 5a456b5 to fa3f7de Compare November 17, 2019 22:11
@ttung ttung force-pushed the tonytung-binarize branch from dbfee13 to 03c71ba Compare November 17, 2019 22:11
@ttung ttung force-pushed the tonytung-additional-builders branch from fa3f7de to e512ca4 Compare November 18, 2019 06:08
@ttung ttung force-pushed the tonytung-binarize branch 5 times, most recently from 5f12820 to ecfc75a Compare November 18, 2019 20:55
@ttung ttung force-pushed the tonytung-additional-builders branch from 6276179 to d05355b Compare November 18, 2019 21:24
@ttung ttung force-pushed the tonytung-binarize branch 2 times, most recently from 9327c45 to d57ec01 Compare November 18, 2019 21:27
@ttung ttung force-pushed the tonytung-additional-builders branch from 4632f85 to ead1f9c Compare November 18, 2019 21:32
@ttung ttung force-pushed the tonytung-binarize branch 2 times, most recently from 535d281 to bb9ee75 Compare November 18, 2019 21:34
@ttung ttung force-pushed the tonytung-additional-builders branch from 45e7a41 to f66bca2 Compare November 18, 2019 21:40
@ttung ttung force-pushed the tonytung-binarize branch 2 times, most recently from eacace0 to 9a28a8a Compare November 18, 2019 21:42
@ttung ttung force-pushed the tonytung-additional-builders branch from 7ce3d9c to 7b732a9 Compare November 18, 2019 21:49
@ttung ttung force-pushed the tonytung-binarize branch 3 times, most recently from ef4557b to 3348ba1 Compare November 18, 2019 21:53
@ttung ttung changed the base branch from tonytung-additional-builders to master November 18, 2019 21:54
BinarizeImage takes an ImageStack and binarizes it into a BinaryMaskCollection.

Depends on #1637
Test plan: add tests for simple binarizing, and to test the input requirements.
@ttung ttung force-pushed the tonytung-binarize branch from 3c11ac0 to a4a3c27 Compare December 3, 2019 22:04
@ttung ttung merged commit 17abdbd into master Dec 5, 2019
@ttung ttung deleted the tonytung-binarize branch December 5, 2019 00:55
ttung pushed a commit that referenced this pull request Dec 6, 2019
…e. (#1671)

Refactor the existing watershed code to use the new binarizer and mask filtering (for binary opening).

Depends on #1670, #1651
Test plan: still see 69 cells in the iss notebook.
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3 participants