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🐛 Fix Immutable Output from WSIReader #850

Merged
merged 1 commit into from
Aug 23, 2024
Merged

🐛 Fix Immutable Output from WSIReader #850

merged 1 commit into from
Aug 23, 2024

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mostafajahanifar
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@mostafajahanifar mostafajahanifar commented Aug 23, 2024 •
edited by shaneahmed
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The output of WSI readers (read_rect, read_region, etc) are immutable, i.e. Read-only. We assume that created Numpy arrays created from PIL images in the background_composite are mutable by default.
After Numpy v1.16.0, doing np.asarray(pil_image) will return an immutable Numpy array. Gladly, there is an easy fix for this, we should use np.array() instead of np.asarray.

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.86%. Comparing base (b0b1474) to head (ed40d71).
Report is 16 commits behind head on develop.

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop     #850   +/-   ##
========================================
  Coverage    99.86%   99.86%           
========================================
  Files           69       69           
  Lines         8656     8656           
  Branches      1653     1653           
========================================
  Hits          8644     8644           
  Misses           4        4           
  Partials         8        8

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@shaneahmed shaneahmed changed the title BUG: Fix immutable output from WSI readers 🐛 Fix Immutable Output from WSIReader Aug 23, 2024
@shaneahmed shaneahmed added bug Something isn't working enhancement New feature or request labels Aug 23, 2024
@shaneahmed shaneahmed linked an issue Aug 23, 2024 that may be closed by this pull request
Image reader read_region returns read-only np.ndarray #837
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@shaneahmed shaneahmed added this to the Release v1.5.2 milestone Aug 23, 2024
shaneahmed
shaneahmed approved these changes Aug 23, 2024
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Thanks @mostafajahanifar

@shaneahmed shaneahmed merged commit 70db186 into develop Aug 23, 2024
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@shaneahmed shaneahmed deleted the bug-fix-immutable-output branch August 23, 2024 13:46
@shaneahmed shaneahmed mentioned this pull request Dec 12, 2024
Merged
shaneahmed added a commit that referenced this pull request Dec 12, 2024
@shaneahmed @John-P
@pre-commit-ci @adamshephard @measty @mostafajahanifar @simongraham @Jiaqi-Lv @behnazelhaminia @GeorgeBatch @vqdang @Alon-Alexander
🔖 Release 1.6.0 (#895)
e14a4fc 
## TIAToolbox v1.6.0 (2024-12-12)

### Major Updates and Feature Improvements

- **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch)
  - Introduced `TimmBackbone` for running additional PyTorch Image Models.
  - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`.
  - Added an example notebook demonstrating feature extraction with foundation models.
  - `timm` added as a dependency.
- **Performance Enhancements with `torch.compile`** (#716)
  - Improved performance on newer GPUs using `torch.compile`.
- **Multichannel Input Support in `WSIReader`** (#742)
- **AnnotationStore Filtering for Patch Extraction** (#822)
- **Python 3.12 Support**
- **Deprecation of Python 3.8 Support**
- **CLI Response Time Improvements** (#795)

### API Changes

- **Device Specification Update** (#882)
  - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality.
- **Windows Compatibility Enhancement** (#769)
  - Replaced `POWER` with explicit multiplication.

### Bug Fixes and Other Changes

- **TIFFWSIReader Bound Reading Adjustment** (#777)
  - Fixed `read_bound` to use adjusted bounds.
  - Reduced code complexity in `WSIReader` (#814).
- **Annotation Rendering Fixes** (#813)
  - Corrected rendering of annotations with holes.
- **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch)
- **HoVer-Net Documentation Update** (#751)
  - Corrected class output information.
- **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander)
- **Bokeh Compatibility Updates**
  - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`.
  - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796).
- **JSON Extraction Fixes** (#772)
  - Restructured SQL expression construction for JSON properties with dots in keys.
- **VahadaneExtractor Warning** (#871)
  - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382).
- **PatchExtractor Error Message Refinement** (#883)
- **Immutable Output Fix in `WSIReader`** (#850)

### Development-Related Changes

- **Mypy Checks Added**
  - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`.
- **ReadTheDocs PDF Build Deprecation**
- **Formatter Update**
  - Replaced `black` with `ruff-format`.
- **Dependency Removal**
  - Removed `jinja2`.
- **Test Environment Update**
  - Updated to `Ubuntu 24.04`.
- **Conda Environment Workflow Update**
  - Implemented `micromamba` setup.
- **Codecov Reporting Fix** (#811)
  **Full Changelog:** v1.5.1...v1.6.0

---------

Co-authored-by: John Pocock <John-P@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Adam Shephard <39619155+adamshephard@users.noreply.github.com>
Co-authored-by: Mark Eastwood <20169086+measty@users.noreply.github.com>
Co-authored-by: Mostafa Jahanifar <74412979+mostafajahanifar@users.noreply.github.com>
Co-authored-by: Simon Graham <20071401+simongraham@users.noreply.github.com>
Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk>
Co-authored-by: Jiaqi-Lv <60471431+Jiaqi-Lv@users.noreply.github.com>
Co-authored-by: Dmitrii Blaginin <blaginin@mbp.lan>
Co-authored-by: behnazelhaminia <30952176+behnazelhaminia@users.noreply.github.com>
Co-authored-by: George Batchkala <46561186+GeorgeBatch@users.noreply.github.com>
Co-authored-by: vqdang <24943262+vqdang@users.noreply.github.com>
Co-authored-by: Jiaqi Lv <lvjiaqi9@gmail.com>
Co-authored-by: Alon Alexander <alon008@gmail.com>
@shaneahmed shaneahmed mentioned this pull request Dec 12, 2024
Merged
shaneahmed added a commit that referenced this pull request Dec 12, 2024
@shaneahmed
🔖 Release 1.6.0 (#898)
0ddd2b1 
## TIAToolbox v1.6.0 (2024-12-12)

### Major Updates and Feature Improvements

- **Foundation Models Support via `timm` API** (#856, contributed by @GeorgeBatch)
  - Introduced `TimmBackbone` for running additional PyTorch Image Models.
  - Tested models include `UNI`, `Prov-GigaPath`, and `H-optimus-0`.
  - Added an example notebook demonstrating feature extraction with foundation models.
  - `timm` added as a dependency.
- **Performance Enhancements with `torch.compile`** (#716)
  - Improved performance on newer GPUs using `torch.compile`.
- **Multichannel Input Support in `WSIReader`** (#742)
- **AnnotationStore Filtering for Patch Extraction** (#822)
- **Python 3.12 Support**
- **Deprecation of Python 3.8 Support**
- **CLI Response Time Improvements** (#795)

### API Changes

- **Device Specification Update** (#882)
  - Replaced `has_gpu` with `device` for specifying GPU or CPU usage, aligning with PyTorch's `Model.to()` functionality.
- **Windows Compatibility Enhancement** (#769)
  - Replaced `POWER` with explicit multiplication.

### Bug Fixes and Other Changes

- **TIFFWSIReader Bound Reading Adjustment** (#777)
  - Fixed `read_bound` to use adjusted bounds.
  - Reduced code complexity in `WSIReader` (#814).
- **Annotation Rendering Fixes** (#813)
  - Corrected rendering of annotations with holes.
- **Non-Tiled TIFF Support in `WSIReader`** (#807, contributed by @GeorgeBatch)
- **HoVer-Net Documentation Update** (#751)
  - Corrected class output information.
- **Citation File Fix for `cffconvert`** (#869, contributed by @Alon-Alexander)
- **Bokeh Compatibility Updates**
  - Updated `bokeh_app` for compatibility with `bokeh>=3.5.0`.
  - Switched from `size` to `radius` for `bokeh>3.4.0` compatibility (#796).
- **JSON Extraction Fixes** (#772)
  - Restructured SQL expression construction for JSON properties with dots in keys.
- **VahadaneExtractor Warning** (#871)
  - Added warning due to changes in `scikit-learn>0.23.0` dictionary learning (#382).
- **PatchExtractor Error Message Refinement** (#883)
- **Immutable Output Fix in `WSIReader`** (#850)

### Development-Related Changes

- **Mypy Checks Added**
  - Applied to `utils`, `tools`, `data`, `annotation`, and `cli/common`.
- **ReadTheDocs PDF Build Deprecation**
- **Formatter Update**
  - Replaced `black` with `ruff-format`.
- **Dependency Removal**
  - Removed `jinja2`.
- **Test Environment Update**
  - Updated to `Ubuntu 24.04`.
- **Conda Environment Workflow Update**
  - Implemented `micromamba` setup.
- **Codecov Reporting Fix** (#811)
  **Full Changelog:** v1.5.1...v1.6.0
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Image reader read_region returns read-only np.ndarray
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