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Pipeline component and implementation for merging BinaryMaskCollections #1692

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merged 1 commit into from
Dec 16, 2019

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ttung
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@ttung ttung commented Dec 10, 2019

This does not handle the case where the pixel/physical ticks do not line up. This is for cases where we derive the data from the exact same set of images, and inherit their pixel/physical ticks from the same source.

Depends on #1690, #1691, #1696
Test plan: Added one positive test case, and tested the cases where the merge should fail.

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codecov-io commented Dec 10, 2019

Codecov Report

Merging #1692 into master will increase coverage by 0.18%.
The diff coverage is 97.4%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1692      +/-   ##
==========================================
+ Coverage   89.78%   89.96%   +0.18%     
==========================================
  Files         241      245       +4     
  Lines        9071     9148      +77     
==========================================
+ Hits         8144     8230      +86     
+ Misses        927      918       -9
Impacted Files Coverage Δ
starfish/morphology.py 0% <ø> (ø) ⬆️
starfish/core/morphology/Merge/simple.py 100% <100%> (ø)
starfish/core/morphology/Merge/__init__.py 100% <100%> (ø)
starfish/core/morphology/Merge/_base.py 87.5% <87.5%> (ø)
starfish/core/morphology/Merge/test/test_simple.py 97.77% <97.77%> (ø)
...fish/core/morphology/binary_mask/test/factories.py 100% <0%> (+11.36%) ⬆️
... and 1 more

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@ttung ttung changed the base branch from tonytung-merge-base to tonytung-fix-3d-factory December 11, 2019 18:41
@ttung ttung changed the base branch from tonytung-fix-3d-factory to tonytung-merge-base December 13, 2019 01:14
from .simple import SimpleMerge

# autodoc's automodule directive only captures the modules explicitly listed in __all__.
all_filters = {
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Suggested change
all_filters = {
all_methods = {

? are they all filters?

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You are correct. Will fix.

@ttung ttung force-pushed the tonytung-merge branch 2 times, most recently from 2c6fa67 to e120bda Compare December 13, 2019 18:16
@ttung ttung changed the base branch from tonytung-merge-base to master December 13, 2019 19:35
@ttung ttung force-pushed the tonytung-merge branch 2 times, most recently from 3aa90df to f8ebad0 Compare December 16, 2019 17:28
This does not handle the case where the pixel/physical ticks do not line up.  This is for cases where we derive the data from the exact same set of images, and inherit their pixel/physical ticks from the same source.

Test plan: Added one positive test case, and tested the cases where the merge should fail.
@ttung ttung merged commit 185faa6 into master Dec 16, 2019
@ttung ttung deleted the tonytung-merge branch December 16, 2019 18:45
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