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6.)adding MetricDecoder to DecodeSpots #1596

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merged 1 commit into from
Oct 15, 2019
Merged

6.)adding MetricDecoder to DecodeSpots #1596

merged 1 commit into from
Oct 15, 2019

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shanaxel42
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@shanaxel42 shanaxel42 commented Oct 1, 2019 •
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Add version of MetricDistance decoder to new DecodeSpots module

depends on: #1594 #1593 #1592 #1518 #1517

@shanaxel42 shanaxel42 changed the title adding MetricDecoder to DecodeSpots 6.)adding MetricDecoder to DecodeSpots Oct 1, 2019
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codecov-io commented Oct 1, 2019 •
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Codecov Report

❗ No coverage uploaded for pull request base (saxelrod-osm-fish-new@c25bbee). Click here to learn what that means.
The diff coverage is 28.64%.

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@@                   Coverage Diff                    @@
##             saxelrod-osm-fish-new    #1596   +/-   ##
========================================================
  Coverage                         ?   48.07%           
========================================================
  Files                            ?      222           
  Lines                            ?     8369           
  Branches                         ?        0           
========================================================
  Hits                             ?     4023           
  Misses                           ?     4346           
  Partials                         ?        0
Impacted Files Coverage Δ
starfish/types.py 100% <ø> (ø)
starfish/core/types/__init__.py 100% <ø> (ø)
...re/spots/DetectSpots/local_search_blob_detector.py 24.76% <0%> (ø)
...spots/DetectSpots/trackpy_local_max_peak_finder.py 62.79% <0%> (ø)
starfish/core/spots/FindSpots/__init__.py 100% <100%> (ø)
starfish/core/spots/FindSpots/blob.py 89.79% <100%> (ø)
starfish/core/types/_constants.py 98.24% <100%> (ø)
starfish/core/spots/DecodeSpots/__init__.py 100% <100%> (ø)
...spots/DecodeSpots/per_round_max_channel_decoder.py 100% <100%> (ø)
...eSpots/test/test_nearest_neighbor_trace_builder.py 15.46% <15.46%> (ø)
... and 7 more

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@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from b89c389 to 3d96b11 Compare October 3, 2019 17:42
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch 3 times, most recently from baea8aa to ff4d042 Compare October 7, 2019 16:33
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from 27698d6 to 5b09a36 Compare October 7, 2019 19:19
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from ff4d042 to 014a97d Compare October 7, 2019 19:19
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from 5b09a36 to fac9141 Compare October 8, 2019 17:31
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from 014a97d to 4b334b9 Compare October 8, 2019 17:31
@shanaxel42 shanaxel42 requested a review from ttung October 8, 2019 21:34
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from fac9141 to f46d2ca Compare October 8, 2019 22:48
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from 4b334b9 to 8498865 Compare October 8, 2019 22:48
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from f46d2ca to 64ea392 Compare October 8, 2019 22:56
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch 2 times, most recently from 3a4515e to cc83e34 Compare October 9, 2019 15:24
ttung
ttung requested changes Oct 9, 2019
View reviewed changes
starfish/core/spots/DecodeSpots/metric_decoder.py Outdated
Comment on lines 40 to 42
anchor_round: int = 1,
search_radius: int = 3,
trace_building_strategy: TraceBuildingStrategies = TraceBuildingStrategies.EXACT_MATCH
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these are not documented.

starfish/core/spots/DecodeSpots/metric_decoder.py Outdated
self.min_intensity = min_intensity
self.norm_order = norm_order
self.metric = metric
self.trace_builder = trace_builders[trace_building_strategy]
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nit: this should be in the same order as the params generally.

@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch 2 times, most recently from c734e65 to dee4210 Compare October 9, 2019 17:50
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from 9c44352 to 879f771 Compare October 9, 2019 17:50
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from dee4210 to cd52ba5 Compare October 9, 2019 17:57
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from 5ff0e1c to facfd14 Compare October 9, 2019 18:24
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch 2 times, most recently from 1e124de to 98ea4f2 Compare October 9, 2019 21:46
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from 1d254d9 to ff7d5f7 Compare October 9, 2019 21:55
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from 98ea4f2 to 4917520 Compare October 9, 2019 21:55
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from ff7d5f7 to ba6d3be Compare October 9, 2019 22:03
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch 2 times, most recently from 51c8b5d to e92cf06 Compare October 9, 2019 22:36
@shanaxel42 shanaxel42 requested a review from ttung October 9, 2019 22:44
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from e92cf06 to 86eb514 Compare October 9, 2019 23:25
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from 86eb514 to e79dd49 Compare October 10, 2019 15:15
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from 402245d to b4eb1b5 Compare October 10, 2019 19:42
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from e79dd49 to 0edeb9a Compare October 10, 2019 19:42
@shanaxel42 shanaxel42 force-pushed the saxelrod-osm-fish-new branch from b4eb1b5 to c25bbee Compare October 11, 2019 16:55
@shanaxel42 shanaxel42 force-pushed the saxelrod-metric-distance branch from 0edeb9a to 40f7e16 Compare October 11, 2019 16:55
@shanaxel42 shanaxel42 merged commit 83059fc into saxelrod-osm-fish-new Oct 15, 2019
shanaxel42 pushed a commit that referenced this pull request Oct 15, 2019
5.) refactoring localMaxPeakFinder/osmFIsh (#1594)
1623205 
* refactoring localMaxPeakFinder

* adding MetricDecoder to DecodeSpots (#1596)
shanaxel42 pushed a commit that referenced this pull request Oct 15, 2019
4.) refactoring allen smFish with new spot finding (#1593)
70f53cc 
* refactoring allen smFish with new spot finding

* 5.) refactoring localMaxPeakFinder/osmFIsh (#1594)

* refactoring localMaxPeakFinder

* adding MetricDecoder to DecodeSpots (#1596)
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@shanaxel42 @codecov-io @ttung