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feat: Add multiple otsu as threshold method with selection range of components #710

Merged
merged 13 commits into from
Oct 15, 2022
Merged

feat: Add multiple otsu as threshold method with selection range of components #710

merged 13 commits into from
Oct 15, 2022

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Czaki
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@Czaki Czaki commented Sep 12, 2022

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sourcery-ai bot commented Sep 12, 2022 •
edited
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Sourcery Code Quality Report

❌  Merging this PR will decrease code quality in the affected files by 0.10%.

Quality metrics Before After Change
Complexity 3.38 ⭐ 3.35 ⭐ -0.03 👍
Method Length 56.04 ⭐ 56.72 ⭐ 0.68 👎
Working memory 7.05 🙂 7.06 🙂 0.01 👎
Quality 72.26% 🙂 72.16% 🙂 -0.10% 👎
Other metrics Before After Change
Lines 2781 2892 111
Changed files Quality Before Quality After Quality Change
package/PartSegCore/analysis/measurement_calculation.py 71.07% 🙂 70.90% 🙂 -0.17% 👎
package/PartSegCore/segmentation/restartable_segmentation_algorithms.py 68.84% 🙂 69.15% 🙂 0.31% 👍
package/PartSegCore/segmentation/threshold.py 84.72% ⭐ 81.08% ⭐ -3.64% 👎
package/tests/test_PartSegCore/test_segmentation.py 72.91% 🙂 73.00% 🙂 0.09% 👍

Here are some functions in these files that still need a tune-up:

File Function Complexity Length Working Memory Quality Recommendation
package/PartSegCore/segmentation/restartable_segmentation_algorithms.py ThresholdBaseAlgorithm.calculation_run 24 😞 412 ⛔ 12 😞 26.72% 😞 Refactor to reduce nesting. Try splitting into smaller methods. Extract out complex expressions
package/PartSegCore/segmentation/restartable_segmentation_algorithms.py BaseMultiScaleOpening.calculation_run 15 🙂 399 ⛔ 15 😞 29.13% 😞 Try splitting into smaller methods. Extract out complex expressions
package/PartSegCore/analysis/measurement_calculation.py MeasurementProfile.calculate_yield 14 🙂 326 ⛔ 34.22% 😞 Try splitting into smaller methods
package/PartSegCore/analysis/measurement_calculation.py MeasurementResult.get_separated 15 🙂 196 😞 14 😞 38.04% 😞 Try splitting into smaller methods. Extract out complex expressions
package/PartSegCore/segmentation/restartable_segmentation_algorithms.py BaseThresholdFlowAlgorithm.calculation_run 8 ⭐ 263 ⛔ 15 😞 38.93% 😞 Try splitting into smaller methods. Extract out complex expressions

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  • 🙂 good
  • 😞 poor
  • ⛔ very poor

The 👍 and 👎 indicate whether the quality has improved or gotten worse with this pull request.

Please see our documentation here for details on how these metrics are calculated.

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@sourcery-ai sourcery-ai bot mentioned this pull request Sep 12, 2022
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deprecated-napari-hub-preview-bot bot commented Sep 12, 2022 •
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Preview page for your plugin is ready here:
https://preview.napari-hub.org/4DNucleome/PartSeg/710
Updated: 2022-10-15T23:06:51.603972

Czaki and others added 2 commits September 12, 2022 16:07
@Czaki
fix tests
db16c07
@sourcery-ai
feat: Add multiple otsu as threshold method with selection range of c…
8ad97b3 
…omponents (Sourcery refactored) (#711)

Co-authored-by: Sourcery AI <>
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codecov bot commented Sep 12, 2022 •
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Codecov Report

Base: 88.64% // Head: 88.66% // Increases project coverage by +0.01% 🎉

Coverage data is based on head (c53cefb) compared to base (54958d1).
Patch coverage: 98.70% of modified lines in pull request are covered.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop     #710      +/-   ##
===========================================
+ Coverage    88.64%   88.66%   +0.01%     
===========================================
  Files          190      190              
  Lines        29404    29450      +46     
===========================================
+ Hits         26066    26112      +46     
  Misses        3338     3338
Impacted Files Coverage Δ
package/PartSegCore/segmentation/threshold.py 98.12% <98.07%> (+0.42%) ⬆️
...ge/PartSegCore/analysis/measurement_calculation.py 97.07% <100.00%> (-0.04%) ⬇️
...egmentation/restartable_segmentation_algorithms.py 96.36% <100.00%> (+0.07%) ⬆️
...ackage/tests/test_PartSegCore/test_segmentation.py 100.00% <100.00%> (ø)

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@sourcery-ai sourcery-ai bot mentioned this pull request Sep 13, 2022
Merged
@Czaki Czaki merged commit cb16b0e into develop Oct 15, 2022
@Czaki Czaki deleted the feature/multipe_otsu_components branch October 15, 2022 23:36
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