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Merged
merged 26 commits into from
Nov 22, 2021
Merged

NEW: Feature CLI For Nucleus Instance Segmentation #194

merged 26 commits into from
Nov 22, 2021

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@shaneahmed
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@shaneahmed shaneahmed commented Nov 18, 2021 •
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  • Add cli for nucleus instance segmentation
    • Add tests for cli and remove tests if cli is covering these.
  • Fix link for pretrained models in semantic segmentation
  • Rearrange add commands in cli
  • Replace get_wsireader with WSIReader.open as get_wsireader is being depreciated.
  • Update installation instructions for pygeos.
  • Fix OOM errors using garbage collection gc.collect().

@shaneahmed
DEV: Add nucleus_instance_segmentor to cli
4ce2b56 
- Add nucleus_instance_segmentor to cli
@shaneahmed
REF: Rename nucleus_instance_segmentor to nucleus_instance_segment
8b5ad98 
- Rename nucleus_instance_segmentor to nucleus_instance_segment
@shaneahmed
BUG: Add missing nucleus_instance_segment file
bc7a943 
- Add missing nucleus_instance_segment file
@shaneahmed
DEV: Add additional arguments to cli/nucleus_instance_segment
d488753 
- Add additional arguments to cli/nucleus_instance_segment
@shaneahmed
DOC: Fix link to pretrained models
08164a3 
- Fix link to pretrained models
@shaneahmed
TST: Add test for cli/nucleus_instance_segment
cfd519c 
- Add test for cli/nucleus_instance_segment.
@shaneahmed shaneahmed requested a review from vqdang November 18, 2021 17:45
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codecov bot commented Nov 18, 2021 •
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Codecov Report

Merging #194 (95334be) into develop (27280fa) will increase coverage by 0.03%.
The diff coverage is 100.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #194      +/-   ##
===========================================
+ Coverage    99.74%   99.77%   +0.03%     
===========================================
  Files           44       45       +1     
  Lines         3540     3572      +32     
  Branches       576      577       +1     
===========================================
+ Hits          3531     3564      +33     
+ Misses           3        2       -1     
  Partials         6        6
Impacted Files Coverage Δ
tiatoolbox/cli/semantic_segment.py 100.00% <ø> (ø)
tiatoolbox/models/dataset/abc.py 100.00% <ø> (+1.47%) ⬆️
...oolbox/models/engine/nucleus_instance_segmentor.py 98.41% <ø> (ø)
tiatoolbox/cli/__init__.py 100.00% <100.00%> (ø)
tiatoolbox/cli/nucleus_instance_segment.py 100.00% <100.00%> (ø)

Continue to review full report at Codecov.

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@shaneahmed
TST: Fix test for cli-nucleus-instance-segment
0715972 
- Fix test for cli-nucleus-instance-segment
@shaneahmed
BUG: Fix test check in cli-nucleus-instance-segment
8eb05b7 
- Fix test check in cli-nucleus-instance-segment
@shaneahmed
DOC: Update installation instructions for pygeos on Windows.
edc0df9 
- Update installation instructions for pygeos on Windows.
@shaneahmed
DOC: Update installation instructions for Windows
85ec77b 
- Update installation instructions for Windows
@shaneahmed
DOC: Fix indention issue
ec016f5 
- Fix indention issue on rst.
@shaneahmed
TST: Add ioconfig to cli test for nucleus segment
3a4b605 
- Add ioconfig to cli test for nucleus segment
@shaneahmed
TST: Break tests/models/test_nucleus_instance_segmentor into smaller …
78935fc 
…chunks

- Break tests/models/test_nucleus_instance_segmentor into smaller chunks
- Use pretrained_weights for nucleus_instance_segmentor
@shaneahmed
TST: Use smaller image in tests
3c9748d 
- Use smaller image in tests
@shaneahmed
TST: Update to smaller wsi for cli
d1fbb6b 
- Update to smaller wsi for cli
vqdang
vqdang approved these changes Nov 19, 2021
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Look ok. Thanks Shan.

@shaneahmed
TST: ON_Travis is True
69ce19a 
- ON_Travis is True
@shaneahmed
Merge remote-tracking branch 'origin/develop' into feature-cli-instan…
a4322c0 
…cesegment
@shaneahmed
TST: Add flag to ignore coverage
8010d59 
- Add flag to ignore coverage
@shaneahmed
BUG: Fix deepsource bug
a1bc5f0 
- Fix deepsource bug
@shaneahmed
TST: Add test without ioconfig
a00ac19 
- Add test without ioconfig
@shaneahmed
TST: Use smaller batch size for OOM errors on travis
86bf9e8 
- Use smaller batch size for OOM errors on travis
@shaneahmed
TST: Use smaller image for test
d9971c6 
- Use smaller image for test
@shaneahmed
TST: Use smaller image to avoid OOM on travis
4af1831 
- Use smaller image to avoid OOM on travis
@shaneahmed
TST: Use 512x512 image to avoid memory issues
3bbb799 
- Use 512x512 image to avoid memory issues
@John-P John-P changed the title NEW: Feature cli for nucleus instance segmentation NEW: Feature CLI For Nucleus Instance Segmentation Nov 21, 2021
@shaneahmed shaneahmed merged commit d98e091 into develop Nov 22, 2021
@shaneahmed shaneahmed deleted the feature-cli-instancesegment branch November 22, 2021 14:31
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@vqdang vqdang vqdang approved these changes

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@shaneahmed @vqdang