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Spot Refactor: LocalSearchBlobDetector #1577

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merged 1 commit into from
Sep 27, 2019

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shanaxel42
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Both STARmap and current Seqfish currently use LocalSearchBlobDetector. This refactor eliminates the need for a separate LocalSearchBlobDetector class and instead both assays now use the regular BlobDetector and the PerRoundMaxChannel with a trace building strategy of 'nearest neighbors'. A lot of the changes here are mostly just moving code that already existed in LocalSearchBlobDetector and a few changes to make BlobDetector work for both ISS and STARmap.

@shanaxel42 shanaxel42 force-pushed the saxelrod-starMap-refactor branch from 81bebcb to 6806a8c Compare September 25, 2019 21:43
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codecov-io commented Sep 25, 2019

Codecov Report

Merging #1577 into saxelrod-remove-old-blob will increase coverage by 0.16%.
The diff coverage is 100%.

Impacted file tree graph

@@                     Coverage Diff                      @@
##           saxelrod-remove-old-blob    #1577      +/-   ##
============================================================
+ Coverage                     88.06%   88.22%   +0.16%     
============================================================
  Files                           148      149       +1     
  Lines                          5169     5240      +71     
============================================================
+ Hits                           4552     4623      +71     
  Misses                          617      617
Impacted Files Coverage Δ
starfish/types.py 100% <ø> (ø) ⬆️
starfish/core/types/__init__.py 100% <ø> (ø) ⬆️
starfish/core/spots/DecodeSpots/trace_builders.py 100% <100%> (ø) ⬆️
starfish/core/types/_constants.py 98.21% <100%> (+0.1%) ⬆️
...re/spots/DetectSpots/local_search_blob_detector.py 95.23% <100%> (+0.04%) ⬆️
starfish/core/types/_spot_finding_results.py 93.93% <100%> (+0.39%) ⬆️
...spots/DecodeSpots/per_round_max_channel_decoder.py 100% <100%> (ø) ⬆️
starfish/core/spots/DecodeSpots/util.py 100% <100%> (ø)
starfish/core/spots/FindSpots/blob.py 95.91% <100%> (+0.36%) ⬆️

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@shanaxel42 shanaxel42 force-pushed the saxelrod-starMap-refactor branch 2 times, most recently from 2f2b3bb to fe9436e Compare September 26, 2019 18:37
@shanaxel42 shanaxel42 force-pushed the saxelrod-remove-old-blob branch from 5eed9c3 to c3e2771 Compare September 26, 2019 21:40
@shanaxel42 shanaxel42 force-pushed the saxelrod-starMap-refactor branch from fe9436e to b467f58 Compare September 26, 2019 21:40
@shanaxel42 shanaxel42 force-pushed the saxelrod-remove-old-blob branch from c3e2771 to 89a13f2 Compare September 26, 2019 23:09
@shanaxel42 shanaxel42 force-pushed the saxelrod-starMap-refactor branch from b467f58 to 6bc46d5 Compare September 26, 2019 23:09
@shanaxel42 shanaxel42 mentioned this pull request Sep 26, 2019
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@shanaxel42 shanaxel42 changed the title Spot Refactor: STARmap and current SeqFish Spot Refactor: LocalSearchBlobDetector Sep 27, 2019
@shanaxel42 shanaxel42 force-pushed the saxelrod-starMap-refactor branch from 6bc46d5 to f2148b4 Compare September 27, 2019 17:49
@shanaxel42 shanaxel42 merged commit f2148b4 into saxelrod-remove-old-blob Sep 27, 2019
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2 participants