4.) refactoring allen smFish with new spot finding #1593

shanaxel42 · 2019-10-01T14:43:36Z

This PR:

adds a version of TrackpyLocalMaxPeakFinder to the new FindSpots module that process SpotFindingResults
Adds a new trace building strategy to use in decoding called SEQUENTIAL that builds spot traces without merging across channels and imaging rounds. Used for sequential methods like smFIsh.
refactors smFish to use FindSpots.TrackpyLocalMaxPeakFinder DecodeSpots.PerRoundMaxChannel with the trace building strategy SEQUENTIAL

codecov-io · 2019-10-01T14:56:44Z

Codecov Report

Merging #1593 into master will decrease coverage by 1.96%.
The diff coverage is 28.64%.

@@            Coverage Diff             @@
##           master    #1593      +/-   ##
==========================================
- Coverage   88.18%   86.22%   -1.97%     
==========================================
  Files         152      155       +3     
  Lines        5241     5516     +275     
==========================================
+ Hits         4622     4756     +134     
- Misses        619      760     +141

Impacted Files	Coverage Δ
...spots/DetectSpots/trackpy_local_max_peak_finder.py	`90.69% <0%> (-2.16%)`	⬇️
starfish/data.py	`50% <0%> (-3.34%)`	⬇️
starfish/core/spots/FindSpots/__init__.py	`100% <100%> (ø)`	⬆️
starfish/core/types/_constants.py	`98.24% <100%> (+0.03%)`	⬆️
starfish/core/spots/DecodeSpots/__init__.py	`100% <100%> (ø)`	⬆️
...fish/core/spots/FindSpots/local_max_peak_finder.py	`22.54% <22.54%> (ø)`
starfish/core/spots/DecodeSpots/trace_builders.py	`68.96% <25%> (-31.04%)`	⬇️
...e/spots/FindSpots/trackpy_local_max_peak_finder.py	`30% <30%> (ø)`
...rfish/test/full_pipelines/api/test_allen_smFISH.py	`33.33% <37.5%> (ø)`	⬆️
starfish/core/spots/DecodeSpots/metric_decoder.py	`45% <45%> (ø)`
... and 7 more

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ttung · 2019-10-08T21:47:22Z

notebooks/py/smFISH.py

@@ -123,6 +125,11 @@ def processing_pipeline(
    print("Loading images...")
    images = enumerate(experiment[fov_name].get_images(FieldOfView.PRIMARY_IMAGES))

+    decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(


following the other components of this pipeline, this should be above (search for "define")

I wanted to put it above but there's no access to the experiment.codebook at that point

Ahh, I see.

ttung · 2019-10-08T21:47:48Z

notebooks/py/smFISH.py

-        spot_attributes = tlmpf.run(primary_image)
-        all_intensities.append(spot_attributes)
+        spots = tlmpf.run(primary_image)
+        decoded_intensities = decoder.run(spots)


should add print("Decoding spots...")

ttung · 2019-10-08T21:49:07Z

starfish/core/spots/DecodeSpots/trace_builders.py

@@ -66,5 +103,6 @@ def build_traces_nearest_neighbors(spot_results: SpotFindingResults, anchor_roun

 trace_builders: Mapping[TraceBuildingStrategies, Callable] = {
    TraceBuildingStrategies.EXACT_MATCH: build_spot_traces_exact_match,
-    TraceBuildingStrategies.NEAREST_NEIGHBOR: build_traces_nearest_neighbors
+    TraceBuildingStrategies.NEAREST_NEIGHBOR: build_traces_nearest_neighbors,
+    TraceBuildingStrategies.SEQUENTIAL: build_traces_sequential


Suggested change

TraceBuildingStrategies.SEQUENTIAL: build_traces_sequential

TraceBuildingStrategies.SEQUENTIAL: build_traces_sequential,

ttung · 2019-10-08T22:00:15Z

starfish/core/spots/FindSpots/trackpy_local_max_peak_finder.py

+    Parameters
+    ----------
+
+    spot_diameter : odd integer or tuple of odd integers.


params are not actually typed to match what is in the description.

the params' types in the documentation does not follow the standard style we use (which is whatever is the typing in the actual function declaration).

the styling for defaults does not match the styling for defaults in earlier PRs.

some defaults are missing.

ttung · 2019-10-08T22:01:22Z

starfish/test/full_pipelines/api/test_allen_smFISH.py



-@pytest.mark.skip('issues with checksums prevent this data from working properly')
+@pytest.mark.skip('This test runs but takes forever')


hahahahaha

For what it's worth, there are a few allen smfish FOVs that have relatively few spots and run relatively quickly (2-3 minutes?)

Do you know which ones?

fov_004 has very few spots.

ttung · 2019-10-11T04:25:21Z

notebooks/py/smFISH.py

@@ -123,6 +125,11 @@ def processing_pipeline(
    print("Loading images...")
    images = enumerate(experiment[fov_name].get_images(FieldOfView.PRIMARY_IMAGES))

+    decoder = starfish.spots.DecodeSpots.PerRoundMaxChannel(


Ahh, I see.

ttung · 2019-10-11T04:32:50Z

starfish/test/full_pipelines/api/test_allen_smFISH.py



-@pytest.mark.skip('issues with checksums prevent this data from working properly')
+@pytest.mark.skip('This test runs but takes forever')


fov_004 has very few spots.

* refactoring localMaxPeakFinder * adding MetricDecoder to DecodeSpots (#1596)

shanaxel42 force-pushed the saxelrod-starMap-refactor branch from e0d8464 to cffb21c Compare October 1, 2019 15:14

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shanaxel42 force-pushed the fix-branch branch from 0eaec71 to 3ad1a4e Compare October 1, 2019 15:32

shanaxel42 mentioned this pull request Oct 1, 2019

5.) refactoring localMaxPeakFinder/osmFIsh #1594

Merged

shanaxel42 requested a review from ttung October 1, 2019 15:47

shanaxel42 mentioned this pull request Oct 1, 2019

6.)adding MetricDecoder to DecodeSpots #1596

Merged

shanaxel42 force-pushed the saxelrod-starMap-refactor branch from 5996a09 to 8dd6a0b Compare October 3, 2019 17:42

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ttung requested changes Oct 8, 2019

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shanaxel42 changed the base branch from saxelrod-starMap-refactor to master October 10, 2019 19:42

shanaxel42 requested a review from ttung October 10, 2019 20:39

ttung approved these changes Oct 11, 2019

View reviewed changes

refactoring allen smFish with new spot finding

e116567

shanaxel42 force-pushed the fix-branch branch from 02bce4a to e116567 Compare October 11, 2019 16:55

5.) refactoring localMaxPeakFinder/osmFIsh (#1594)

1623205

* refactoring localMaxPeakFinder * adding MetricDecoder to DecodeSpots (#1596)

shanaxel42 merged commit 70f53cc into master Oct 15, 2019

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4.) refactoring allen smFish with new spot finding #1593

4.) refactoring allen smFish with new spot finding #1593

shanaxel42 commented Oct 1, 2019 •

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	TraceBuildingStrategies.SEQUENTIAL: build_traces_sequential
	TraceBuildingStrategies.SEQUENTIAL: build_traces_sequential,



		@pytest.mark.skip('issues with checksums prevent this data from working properly')
		@pytest.mark.skip('This test runs but takes forever')

4.) refactoring allen smFish with new spot finding #1593

4.) refactoring allen smFish with new spot finding #1593

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shanaxel42 commented Oct 1, 2019 •

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codecov-io commented Oct 1, 2019 •

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