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NEW: Add NuClick architecture#449

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shaneahmed merged 69 commits into
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feature-nuclick-architecture
Nov 14, 2022
Merged

NEW: Add NuClick architecture#449
shaneahmed merged 69 commits into
developfrom
feature-nuclick-architecture

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@mostafajahanifar mostafajahanifar commented Aug 26, 2022

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This PR adds NuClick architecture, as described in the paper below, to the toolbox.

Koohbanani, Navid Alemi, et al. "NuClick: a deep learning framework for interactive segmentation of microscopic images." Medical Image Analysis 65 (2020): 101771.

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Codecov Report

Merging #449 (1c678e9) into develop (a90b330) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##           develop     #449    +/-   ##
=========================================
  Coverage    99.63%   99.63%            
=========================================
  Files           61       62     +1     
  Lines         6240     6379   +139     
  Branches      1035     1043     +8     
=========================================
+ Hits          6217     6356   +139     
  Misses          10       10            
  Partials        13       13
Impacted Files Coverage Δ
tiatoolbox/models/architecture/idars.py 100.00% <100.00%> (ø)
tiatoolbox/models/architecture/mapde.py 100.00% <100.00%> (ø)
tiatoolbox/models/architecture/micronet.py 100.00% <100.00%> (ø)
tiatoolbox/models/architecture/nuclick.py 100.00% <100.00%> (ø)
tiatoolbox/models/architecture/sccnn.py 100.00% <100.00%> (ø)
tiatoolbox/models/architecture/unet.py 100.00% <100.00%> (ø)

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@shaneahmed shaneahmed added the enhancement New feature or request label Sep 1, 2022
shaneahmed and others added 15 commits September 2, 2022 11:38
@shaneahmed
Merge branch 'develop' into feature-nuclick-architecture
ba7c7af
@kesixu
Add files via upload
9b269eb
@shaneahmed
Merge branch 'develop' into feature-nuclick-architecture
1fe9005
@shaneahmed
Merge branch 'develop' into feature-nuclick-architecture
7db7a6f
@kesixu
TST: add nuclick test
4dcfae5
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[pre-commit.ci] auto fixes from pre-commit.com hooks
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for more information, see https://pre-commit.ci
@mostafajahanifar
Merge branch 'develop' of https://github.com/TIA-Lab/tiatoolbox into …
e96316f 
…feature-nuclick-architecture
@mostafajahanifar
Merge branch 'feature-nuclick-architecture' of https://github.com/TIA…
447d642 
…-Lab/tiatoolbox into feature-nuclick-architecture
@mostafajahanifar
MAIN: remove segmentation_to_detection function from arch
b2bb42e
@mostafajahanifar
MAINT: add typehints to ConvBNRelu
0c575e8
@kesixu @shaneahmed
Update tiatoolbox/models/architecture/nuclick.py
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Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Update tiatoolbox/models/architecture/nuclick.py
f8d759f 
Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Update tiatoolbox/models/architecture/nuclick.py
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Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Update tiatoolbox/models/architecture/nuclick.py
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Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Update tiatoolbox/models/architecture/nuclick.py
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Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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Thanks @mostafajahanifar and @kesixu. Please can you address some minor comments. We should be ready to merge it then.

mostafajahanifar and others added 12 commits November 2, 2022 12:30
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MAINT: Apply Shan suggestions from code review
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Merge branch 'develop' of https://github.com/TIA-Lab/tiatoolbox into …
6a635f4 
…feature-nuclick-architecture
@mostafajahanifar
MAIN: replace num_classes with num_output_channels for micronet
1cccb23
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Merge branch 'develop' of https://github.com/TIA-Lab/tiatoolbox into …
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…feature-nuclick-architecture
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MAIN: replace num_classes with num_output_channels for micronet
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Merge branch 'feature-nuclick-architecture' of https://github.com/TIA…
28a5baa 
…-Lab/tiatoolbox into feature-nuclick-architecture
@mostafajahanifar
MAIN: fix deepsource errors
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UPD: revert changes to preprocess function
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MAIN: fix PYL-W0221 with nuclick forward
f15e650
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MAIN: unify using preproc in all models
3a5c3d6
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MAIN: skip PYL-W0221
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@mostafajahanifar mostafajahanifar deleted the feature-nuclick-architecture branch November 9, 2022 17:24
@mostafajahanifar

mostafajahanifar commented Nov 9, 2022

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Dear @shaneahmed

I revised the code to make the input to all models consistent with num_output_channels argument. In particular, I changed MicroNet argument to num_output_channels but for MapDe changed it to num_classes because argument is actually referring to number of cell classes based on which number of output channels is generated ( num_output_channels=2*num_classes ).

I have also refactor all the models to use predefined (base class) preproc method instead of _tranform method. And made some other changes to avoid [PYL-W0221] pylint error.

@shaneahmed

shaneahmed commented Nov 10, 2022

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Dear @shaneahmed

I revised the code to make the input to all models consistent with num_output_channels argument. In particular, I changed MicroNet argument to num_output_channels but for MapDe changed it to num_classes because argument is actually referring to number of cell classes based on which number of output channels is generated ( num_output_channels=2*num_classes ).

I have also refactor all the models to use predefined (base class) preproc method instead of _tranform method. And made some other changes to avoid [PYL-W0221] pylint error.

Thanks @mostafajahanifar Please can you check the errors?

@shaneahmed shaneahmed merged commit 1f0c8ea into develop Nov 14, 2022
@shaneahmed shaneahmed mentioned this pull request Dec 20, 2022
Merged
shaneahmed added a commit that referenced this pull request Dec 20, 2022
@shaneahmed @John-P
@measty @ruqayya @mostafajahanifar @kesixu @DavidBAEpstein @adamshephard @simongraham @dependabot @pre-commit-ci @rogertrullo
🔖 REL: Release 1.3.0 (#523)
075c472 
# 1.3.1 (2022-12-20)

### Major Updates and Feature Improvements

- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449
- Adds Annotation Store Reader #476
- Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510

### Changes to API

- Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517

### Bug Fixes and Other Changes

- Simplifies example notebook for image reading for better readability
- Restricts Shapely version to \<2.0.0 for compatibility

### Development related changes

- Adds GitHub workflow for automatic generation of docker image
- Updates dependencies
- Updates bump2version config
- Enables flake8 E800 checks for commented codes.
- Fixes several errors generated by DeepSource.
- Prevent test dumping file to root
- Removes duplicate functions to generate parameterized test scenarios

Co-authored-by: John Pocock <John-P@users.noreply.github.com>
Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com>
Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>
Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com>
Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com>
Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com>
Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>
shaneahmed added a commit that referenced this pull request Dec 20, 2022
@shaneahmed @John-P
@measty @ruqayya @mostafajahanifar @kesixu @DavidBAEpstein @adamshephard @simongraham @dependabot @pre-commit-ci @rogertrullo
🔖 REL: Release 1.3.1 (#523)
79d26e9 
- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449
- Adds Annotation Store Reader #476
- Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510

- Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517

- Simplifies example notebook for image reading for better readability
- Restricts Shapely version to \<2.0.0 for compatibility

- Adds GitHub workflow for automatic generation of docker image
- Updates dependencies
- Updates bump2version config
- Enables flake8 E800 checks for commented codes.
- Fixes several errors generated by DeepSource.
- Prevent test dumping file to root
- Removes duplicate functions to generate parameterized test scenarios

Co-authored-by: John Pocock <John-P@users.noreply.github.com>
Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com>
Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>
Co-authored-by: kesixu <98600542+kesixu@users.noreply.github.com>
Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com>
Co-authored-by: adamshephard <39619155+adamshephard@users.noreply.github.com>
Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Roger Trullo <rogertrullo@hotmail.com>
@shaneahmed shaneahmed mentioned this pull request Dec 20, 2022
Merged
shaneahmed added a commit that referenced this pull request Dec 20, 2022
@shaneahmed @John-P
@mostafajahanifar @adamshephard @DavidBAEpstein @simongraham @measty @ruqayya
🔖 REL: REL: Release 1.3.1 (#524)
b5874b6 
# 1.3.1 (2022-12-20)

### Major Updates and Feature Improvements

- Adds [NuClick](https://arxiv.org/abs/2005.14511) architecture #449
- Adds Annotation Store Reader #476
- Adds [DFBR](https://arxiv.org/abs/2202.09971) method for registering pair of images #510

### Changes to API

- Adds a sample SVS loading function `tiatoolbox.data.small_svs()` to the data module #517

### Bug Fixes and Other Changes

- Simplifies example notebook for image reading for better readability
- Restricts Shapely version to \<2.0.0 for compatibility

### Development related changes

- Adds GitHub workflow for automatic generation of docker image
- Updates dependencies
- Updates bump2version config
- Enables flake8 E800 checks for commented codes.
- Fixes several errors generated by DeepSource.
- Prevent test dumping file to root
- Removes duplicate functions to generate parameterized test scenarios

Co-authored-by: John Pocock <John-P@users.noreply.github.com>
Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>
Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com>
Co-authored-by: David Epstein <22086916+DavidBAEpstein@users.noreply.github.com>
Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com>
Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
Co-authored-by: Ruqayya Awan <18444369+ruqayya@users.noreply.github.com>
Co-authored-by: Kesi Xu<98600542+kesixu@users.noreply.github.com>
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