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vectorize labeling spot lookups #1215

Merged
merged 2 commits into from
Apr 19, 2019
Merged

vectorize labeling spot lookups #1215

merged 2 commits into from
Apr 19, 2019

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ambrosejcarr
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Trying to knock some seconds off of starfish. Here's part 2!

  • adds vectorization to spot lookups over label images

before:

image

after:

image

@ambrosejcarr ambrosejcarr requested a review from kne42 April 18, 2019 05:14
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codecov-io commented Apr 18, 2019

Codecov Report

Merging #1215 into master will increase coverage by <.01%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #1215      +/-   ##
==========================================
+ Coverage   88.52%   88.52%   +<.01%     
==========================================
  Files         133      133              
  Lines        4976     4968       -8     
==========================================
- Hits         4405     4398       -7     
+ Misses        571      570       -1
Impacted Files Coverage Δ
starfish/spots/_target_assignment/label.py 96.42% <100%> (+1.98%) ⬆️

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cool, looks fancy

ambrosejcarr and others added 2 commits April 19, 2019 13:51
* replace xarray groupby with pandas groupby command to expedite
processing time of combine_adjacent_features.
@ambrosejcarr ambrosejcarr merged commit f772c3b into master Apr 19, 2019
@ambrosejcarr ambrosejcarr deleted the ajc-vectorize-label branch April 19, 2019 17:52
& (intensities.y <= y_max)
& (intensities.x >= x_min)
& (intensities.x <= x_max),
drop=True
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would it make sense to add: intensities.cell_id != nan?

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4 participants