❇️ Add Function to Save Engines Output in the `zarr` Format #724

AbishekRajVG · 2023-10-18T22:17:58Z

Updates to the tiatoolbox.utils.misc.py

Added functions to save the Tiatoolbox Engine outputs to Zarr and AnnotationStore files.

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measty

just left a couple of comments

tiatoolbox/utils/misc.py

codecov · 2023-10-18T22:40:01Z

Codecov Report

Merging #724 (277f0ee) into develop (9505af1) will increase coverage by 0.00%.
Report is 1 commits behind head on develop.
The diff coverage is 100.00%.

❗ Current head 277f0ee differs from pull request most recent head 3f9093e. Consider uploading reports for the commit 3f9093e to get more accurate results

@@           Coverage Diff            @@
##           develop     #724   +/-   ##
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  Coverage    99.85%   99.85%           
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  Files           65       65           
  Lines         7492     7506   +14     
  Branches      1459     1460    +1     
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+ Hits          7481     7495   +14     
  Misses           4        4           
  Partials         7        7

Files	Coverage Δ
tiatoolbox/utils/misc.py	`100.00% <100.00%> (ø)`

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tiatoolbox/utils/misc.py

…m/TissueImageAnalytics/tiatoolbox into dev-persist-patchpredictor-output

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…toolbox into dev-persist-patchpredictor-output

…m/TissueImageAnalytics/tiatoolbox into dev-persist-patchpredictor-output

AbishekRajVG · 2023-10-19T15:14:53Z

Thanks for your comments @shaneahmed and @measty. I've now updated the code accordingly and pushed my changes.

tests/test_utils.py

shaneahmed · 2023-10-19T15:26:48Z

Thanks for your comments @shaneahmed and @measty. I've now updated the code accordingly and pushed my changes.

@AbishekRajVG there is an error for docstring. Please can you address this? you can use ruff check . to test locally before pushing to Git.

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AbishekRajVG · 2023-10-19T17:41:36Z

Thanks for your comments @shaneahmed and @measty. I've now updated the code accordingly and pushed my changes.

@AbishekRajVG there is an error for docstring. Please can you address this? you can use ruff check . to test locally before pushing to Git.

Sorry about that, yes ruff check cleared and updates are pushed.

tiatoolbox/utils/misc.py

for more information, see https://pre-commit.ci

tests/test_utils.py

tiatoolbox/utils/misc.py

Co-authored-by: Shan E Ahmed Raza <[email protected]>

tiatoolbox/utils/misc.py

@TomastpPereira

## 1.5.0 (2023-12-15) ### Major Updates and Feature Improvements - Adds the bokeh visualization tool. #684 - The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines. - This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/. - Extends Annotation to Support Init from WKB #639 - Adds `IOConfig` for NuClick in `pretrained_model.yaml` #709 - Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724 - Adds Support for QuPath Annotation Imports #721 ### Changes to API - Adds `model.to(device)` and `model.load_model_from_file()` functionality to make it compatible with PyTorch API. #733 - Replaces `pretrained` with `weights` to make the engines compatible with the new PyTorch API. #621 - Adds support for high-level imports for various utility functions and classes such as `WSIReader`, `PatchPredictor` and `imread` #606, #607, - Adds `tiatoolbox.typing` for type hints. #619 - Fixes incorrect file size saved by `save_tiles`, issue with certain WSIs raised by @TomastpPereira - TissueMasker transform now returns mask instead of a list. #748 - Fixes #732 ### Bug Fixes and Other Changes - Fixes `pixman` incompability error on Colab #601 - Removes `shapely.speedups`. The module no longer has any affect in Shapely >=2.0. #622 - Fixes errors in the slidegraph example notebook #608 - Fixes bugs in WSI Registration #645, #670, #693 - Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712 - Fixes #710 - Fixes #738 raised by @xiachenrui ### Development related changes - Replaces `flake8` and `isort` with `ruff` #625, #666 - Adds `mypy` checks to `root` and `utils` package. This will be rolled out in phases to other modules. #723 - Adds a module to detect file types using magic number/signatures #616 - Uses `poetry` for version updates instead of `bump2version`. #638 - Removes `setup.cfg` and uses `pyproject.toml` for project configurations. - Reduces runtime for some unit tests e.g., #627, #630, #631, #629 - Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644 - Set up parallel tests locally #671 **Full Changelog:** v1.4.0...v1.5.0 --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mostafajahanifar <[email protected]> Co-authored-by: John Pocock <[email protected]> Co-authored-by: DavidBAEpstein <[email protected]> Co-authored-by: David Epstein <[email protected]> Co-authored-by: Ruqayya Awan <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: adamshephard <[email protected]> Co-authored-by: Abdol <[email protected]> Co-authored-by: Jiaqi-Lv <[email protected]> Co-authored-by: Abishek <[email protected]> Co-authored-by: Dmitrii Blaginin <[email protected]>

@TomastpPereira

## 1.5.0 (2023-12-15) ### Major Updates and Feature Improvements - Adds the bokeh visualization tool. #684 - The tool allows a user to launch a server on their machine to visualise whole slide images, overlay the results of deep learning algorithms or to select a patch from whole slide image and run TIAToolbox deep learning engines. - This tool powers the TIA demos server. For details please see https://tiademos.dcs.warwick.ac.uk/. - Extends Annotation to Support Init from WKB #639 - Adds `IOConfig` for NuClick in `pretrained_model.yaml` #709 - Adds functions to save the TIAToolbox Engine outputs to Zarr and AnnotationStore files. #724 - Adds Support for QuPath Annotation Imports #721 ### Changes to API - Adds `model.to(device)` and `model.load_model_from_file()` functionality to make it compatible with PyTorch API. #733 - Replaces `pretrained` with `weights` to make the engines compatible with the new PyTorch API. #621 - Adds support for high-level imports for various utility functions and classes such as `WSIReader`, `PatchPredictor` and `imread` #606, #607, - Adds `tiatoolbox.typing` for type hints. #619 - Fixes incorrect file size saved by `save_tiles`, issue with certain WSIs raised by @TomastpPereira - TissueMasker transform now returns mask instead of a list. #748 - Fixes #732 ### Bug Fixes and Other Changes - Fixes `pixman` incompability error on Colab #601 - Removes `shapely.speedups`. The module no longer has any affect in Shapely >=2.0. #622 - Fixes errors in the slidegraph example notebook #608 - Fixes bugs in WSI Registration #645, #670, #693 - Fixes the situation where PatchExtractor.get_coords() can return patch coords which lie fully outside the bounds of a slide. #712 - Fixes #710 - Fixes #738 raised by @xiachenrui ### Development related changes - Replaces `flake8` and `isort` with `ruff` #625, #666 - Adds `mypy` checks to `root` and `utils` package. This will be rolled out in phases to other modules. #723 - Adds a module to detect file types using magic number/signatures #616 - Uses `poetry` for version updates instead of `bump2version`. #638 - Removes `setup.cfg` and uses `pyproject.toml` for project configurations. - Reduces runtime for some unit tests e.g., #627, #630, #631, #629 - Reuses models and datasets in tests on GitHub actions by utilising cache #641, #644 - Set up parallel tests locally #671 **Full Changelog:** v1.4.0...v1.5.0

Added methods to persist patch predictor outputs to files

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AbishekRajVG added the dev tools Changes/Updates in Development tools label Oct 18, 2023

AbishekRajVG requested review from shaneahmed and measty October 18, 2023 22:17

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shaneahmed changed the title ~~Added methods to persist patch predictor outputs to files~~ ❇️ Add Function to Save Engines Output in the zarr Format Oct 19, 2023

shaneahmed added this to the Release v1.5.0 milestone Oct 19, 2023

AbishekRajVG and others added 6 commits October 19, 2023 16:04

Resolving review comments

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Merge branch 'dev-persist-patchpredictor-output' of https://github.co…

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shaneahmed modified the milestones: Release v1.5.0, Release v2.0.0 Oct 20, 2023

📝 Fix docstrings.

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🎨 New EngineABC Design for Patches #635

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Update tiatoolbox/utils/misc.py

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Co-authored-by: Shan E Ahmed Raza <[email protected]>

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[skip ci] Update docstring

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🔖 Release 1.5.0 #757

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🔖 Release 1.5.0 #761

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❇️ Add Function to Save Engines Output in the `zarr` Format #724

❇️ Add Function to Save Engines Output in the `zarr` Format #724

AbishekRajVG commented Oct 18, 2023 •

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AbishekRajVG commented Oct 19, 2023

❇️ Add Function to Save Engines Output in the zarr Format #724

❇️ Add Function to Save Engines Output in the zarr Format #724

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❇️ Add Function to Save Engines Output in the `zarr` Format #724

❇️ Add Function to Save Engines Output in the `zarr` Format #724

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