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Fix localmaxpeakfinder spot_props filter #1839

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merged 6 commits into from
Jul 23, 2020

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mattcai
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@mattcai mattcai commented Mar 24, 2020

Fixed filtering of spot_props whose areas are too large or too small in image_to_spots of local_max_peak_finder. It can now handle 2D xarrays (i.e. is_volume=False) and can correctly set pixels to False (removing a spot_prop) for 3D xarrays.

In addition, added details for how to set local_max_peak_finder parameters in its tutorial.

@mattcai mattcai requested review from ttung and shanaxel42 March 24, 2020 23:19
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codecov-io commented Mar 24, 2020

Codecov Report

Merging #1839 into master will decrease coverage by 31.86%.
The diff coverage is 0.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           master    #1839       +/-   ##
===========================================
- Coverage   87.77%   55.91%   -31.87%     
===========================================
  Files         168      168               
  Lines        5785     5789        +4     
===========================================
- Hits         5078     3237     -1841     
- Misses        707     2552     +1845     
Impacted Files Coverage Δ
...fish/core/spots/FindSpots/local_max_peak_finder.py 28.68% <0.00%> (-67.93%) ⬇️
starfish/morphology.py 0.00% <0.00%> (-100.00%) ⬇️
...ish/core/imagestack/parser/tilefetcher/__init__.py 0.00% <0.00%> (-100.00%) ⬇️
...fish/core/imagestack/parser/tilefetcher/_parser.py 0.00% <0.00%> (-90.33%) ⬇️
starfish/test/full_pipelines/api/test_dartfish.py 19.67% <0.00%> (-80.33%) ⬇️
starfish/core/spots/DecodeSpots/util.py 20.40% <0.00%> (-79.60%) ⬇️
starfish/test/full_pipelines/api/test_iss_api.py 22.22% <0.00%> (-77.78%) ⬇️
...e/experiment/builder/test/factories/all_purpose.py 22.91% <0.00%> (-77.09%) ⬇️
starfish/core/starfish.py 0.00% <0.00%> (-76.93%) ⬇️
starfish/test/full_pipelines/api/test_merfish.py 23.80% <0.00%> (-76.20%) ⬇️
... and 86 more

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@mattcai mattcai requested a review from neuromusic March 24, 2020 23:37
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fixes #1836

@ttung
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ttung commented Jul 15, 2020

please remove the "expression" file before you commit, however.

@mattcai mattcai merged commit e42e071 into master Jul 23, 2020
@mattcai mattcai deleted the mcai-localmaxpeakfinder-2d-issue branch July 23, 2020 23:44
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4 participants