🐛 Fix json_extract Construction
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #772 +/- ##
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Coverage 99.91% 99.91%
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Files 69 69
Lines 8518 8518
Branches 1637 1637
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Hits 8511 8511
Partials 7 7 ☔ View full report in Codecov by Sentry. |
shaneahmed
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json_extract Construction
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Jan 26, 2024
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Dec 12, 2024
## 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>
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shaneahmed
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## 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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Restructures the way the dsl builds the SQL expression to access JSON properties so that properties with a . in are correctly treated as a single key
Adds a test to check for correct behaviour when accessing a property containing a .
Addresses issue #771
Would like to check with John if removing json.dumps() is ok. I couldn't see a reason it was necessary and all tests pass/all the use-cases I tried worked fine, but maybe there is one I missed.