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* 🐛 Fix Writing MPP To NGFF v0.4 Zarr (#37) * 🐛 Change CoordinateTransform Order To YXC (#41) * 🐛 Fix Reading TIFF Resolution Tag * 🐛 Minor Bug Fixes (#40) * 🐛 Ensure cv2 Arg Is an int Tuple * ✨ Add TIFF Writer For CLI Based On Ext * 🐛 Add Missing **kwargs * 🚸 Change TIFFWriter OME Default To False * ✏️ Typo Fix transcribed -> transcoded * ♻️ Move CLI Tests To Seperate Module * 🐛 Fix Typo in Class For Transcoding From DICOM * ✅ Add CLI Tests * 🔧 Add release Branch To Workflows * 🔖 Bump version: 0.5.1 → 0.6.1 * 🔧 Set Tag To False In bump2version Config * ♻️ Rename Module To Avoid Shadowing * 📝 Update History * 📝 Reverse History Ordering * 🐛 Use A Zarr Intermediate For Writing JP2 (#44) Without this it was not possible to write a JP2 where the read tile size differs from the write tile size. * ♻️ Rename types Module To Avoid Shadowing (#45) Avoid shadowing the standard library types and typing modules. * 🐛 Use The Reader MPP When Writing JP2 (#46) * 🐛 Set Resolution Units (cm) With TIFFWriter (#47) * 🐛 Return None for MPP In JP2 With Not Boxes Shows a warning and returns None for MPP if no boxes are found in the JP2, e.g. for an invalid file. * ✨ Normalise TIFF Array Axes (#49) * 🐛 Return None for MPP In JP2 With Not Boxes Shows a warning and returns None for MPP if no boxes are found in the JP2, e.g. for an invalid file. * ✨ Normalise TIFF Array Axes Order * 🐛 Use Reader Tile Size For Transcode To TIFF (#51) * 🐛 Use Reader Tile Size For Transcode * 🚸 Validate Input * 🐛 Join Child Processes (#53) * 🐛 Join Child Processes * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * 🔧 Update pre-commit.ci Message Strings (#56) * 🐛 Fix Reading/Writing Resolution (#55) * 🐛 Fix Reading/Writing Resolution * ✏️ Typo Fix * 📝 Update History for v0.7.0 Release * 🔖 Bump version: 0.6.1 → 0.7.0 * ⬆️ Bump wheel from 0.37.1 to 0.38.4 (#60) * ⬆️ Bump wheel from 0.37.1 to 0.38.4 Bumps [wheel](https://github.com/pypa/wheel) from 0.37.1 to 0.38.4. - [Release notes](https://github.com/pypa/wheel/releases) - [Changelog](https://github.com/pypa/wheel/blob/main/docs/news.rst) - [Commits](pypa/wheel@0.37.1...0.38.4) --- updated-dependencies: - dependency-name: wheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> * 🐛 Remove Deprecated Numpy Type (np.float) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump black from 21.7b0 to 22.10.0 (#36) Bumps [black](https://github.com/psf/black) from 21.7b0 to 22.10.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/commits/22.10.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * 🐛 Fix MPP/AppMag Writing in SVSWriter (#58) * 🐛 Fix MPP/AppMag Writing in SVSWriter - `SVSWriter` reads "app_mag" from kwargs (default None). - Add `shaped=False` to TiffWriter context manager init (i.e. don't overwrite description with numpy style shape). - Add approximation of AppMap from MPP if only MPP given. - MPP SVS metadata is the mean of the reader mpp (falls back to SVSWriter init kwarg) or not written if None. - Set "outcolorspace" when writing SVS pages using tifffile. - Correctly filter out thumbnail warnings for `approx_ok`. - Change `subfiletype` to 0 (regular IFD) from 1 (reduced resolution). * 📝 Fix Notes List Formatting * 🐛 Remove Deprecated Numpy Type (np.float) * ⬆️ Bump zarr from 2.12.0 to 2.13.3 (#38) Bumps [zarr](https://github.com/zarr-developers/zarr-python) from 2.12.0 to 2.13.3. - [Release notes](https://github.com/zarr-developers/zarr-python/releases) - [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/docs/release.rst) - [Commits](zarr-developers/zarr-python@v2.12.0...v2.13.3) --- updated-dependencies: - dependency-name: zarr dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Update jinja2 requirement from <3.1.0 to <3.2.0 (#26) Updates the requirements on [jinja2](https://github.com/pallets/jinja) to permit the latest version. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@2.0rc1...3.1.2) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump tox from 3.14.0 to 3.26.0 (#31) Bumps [tox](https://github.com/tox-dev/tox) from 3.14.0 to 3.26.0. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/master/docs/changelog.rst) - [Commits](tox-dev/tox@3.14.0...3.26.0) --- updated-dependencies: - dependency-name: tox dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * 🤖 pre-commit autoupdate (#39) * 🤖 pre-commit autoupdate updates: - [github.com/executablebooks/mdformat: 0.7.14 → 0.7.16](hukkin/mdformat@0.7.14...0.7.16) - [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0](pre-commit/pre-commit-hooks@v4.3.0...v4.4.0) - [github.com/pycqa/isort: 5.10.1 → 5.11.4](PyCQA/isort@5.10.1...5.11.4) - [github.com/psf/black: 22.3.0 → 22.12.0](psf/black@22.3.0...22.12.0) - [github.com/PyCQA/flake8: 4.0.1 → 6.0.0](PyCQA/flake8@4.0.1...6.0.0) * 📌 Remove Bandit Version Pin * 🚨 Remove Manual Quotes Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ✨ Add DICOM VL WSI Writer (#79) * 🔧 Update Pre-Commit Config * 💩 Correct Tile Size From DICOM VL WSI Images * 🤖 pre-commit auto fixes [...] * 💩 Add MVP DICOM WSI Writer * 🔧 Update Manifest * 🚨 Add Warning stacklevel Args * 🔥 Remove Sample Tiles Generator * ⚰️ Remove Commented Out Code * ⚰️ Remove Commented Out Code * ✏️ Typo * 📝 Add Function Docstring * ⚰️ Remove Debugging Arg * 🥅 Catch StopIteration * 🎨 Remove Parens * 🎨 Remove Parens * 🐛 Fix Get Tile Shape For DICOM * 🐛 Fix Parse DICOM LossyImageCompressionMethod * 🐛 Fix Convert Test * ✅ Add Convert To DICOM Tests * ✅ Update Convert Scenario --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * ⬆️ Bump flake8 from 5.0.4 to 6.0.0 (#62) Bumps [flake8](https://github.com/pycqa/flake8) from 5.0.4 to 6.0.0. - [Release notes](https://github.com/pycqa/flake8/releases) - [Commits](PyCQA/flake8@5.0.4...6.0.0) --- updated-dependencies: - dependency-name: flake8 dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump watchdog from 2.1.9 to 2.3.1 (#76) Bumps [watchdog](https://github.com/gorakhargosh/watchdog) from 2.1.9 to 2.3.1. - [Release notes](https://github.com/gorakhargosh/watchdog/releases) - [Changelog](https://github.com/gorakhargosh/watchdog/blob/master/changelog.rst) - [Commits](gorakhargosh/watchdog@v2.1.9...v2.3.1) --- updated-dependencies: - dependency-name: watchdog dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump tox from 3.26.0 to 4.4.7 (#78) Bumps [tox](https://github.com/tox-dev/tox) from 3.26.0 to 4.4.7. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](tox-dev/tox@3.26.0...4.4.7) --- updated-dependencies: - dependency-name: tox dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump pytest from 7.1.3 to 7.2.2 (#77) Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.1.3 to 7.2.2. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](pytest-dev/pytest@7.1.3...7.2.2) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⚡ Avoid Decoding Entire TIFF Before Conversion (#48) * ♻️ Refactor thumbnail To Use get_tile * 💩 Fall Back To __getitem__ if get_tile Fails * 🚧 Swap To tifffile ZarrStore * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * 🐛 Handle `tifffile.aszarr` When Group Returned * ♻️ Mark Extra TIFFReader Attrs Private * ➕ Add dask For Axis Reordering * ♻️ Rename Public/Private Variables * ♻️ Refactor _can_transcode_from_reader * ➕ Add pytest-timeout For CI Debugging * 🏷️ Add Test Type Hints * ✅ Set Convert Test Timeout To 25s * 🔧 Add PyTest norecursedirs For Zarr * :poo: Fix TIFFReader Dask Array Read From Subprocess * ➕ Add Dask Distributed * 🔧 Increase PyTest Timeout + Add Duration Report * 🔧 Fix PyTest Opts * :poo: Use Xarray * ✅ Update Thumbnail Test * 🚨 Fix Linter Issues * 🚨 Remove Commented Out Code * 🚨 Add Linter Exception * ♻️ Refactor Tile Iterator + Add Dask Compatible Iterator * 🔥 Remove Unused Method * 🔧 Update Pre-Commit Config * ✅ Set Compression Level In Test * 🚨 Add Warning Stack Level --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * 🐛 Add Missing Enum Codec.from_tiff For DEFLATE (#84) * ✨ Add DICOM Transcode (#85) * ⬆️ Bump black from 22.10.0 to 23.1.0 (#80) Bumps [black](https://github.com/psf/black) from 22.10.0 to 23.1.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@22.10.0...23.1.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump pip from 22.2.2 to 23.0.1 (#82) Bumps [pip](https://github.com/pypa/pip) from 22.2.2 to 23.0.1. - [Release notes](https://github.com/pypa/pip/releases) - [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst) - [Commits](pypa/pip@22.2.2...23.0.1) --- updated-dependencies: - dependency-name: pip dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump wheel from 0.38.4 to 0.40.0 (#83) Bumps [wheel](https://github.com/pypa/wheel) from 0.38.4 to 0.40.0. - [Release notes](https://github.com/pypa/wheel/releases) - [Changelog](https://github.com/pypa/wheel/blob/main/docs/news.rst) - [Commits](pypa/wheel@0.38.4...0.40.0) --- updated-dependencies: - dependency-name: wheel dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * 🐛 Add Missing CLI Branch For DCM Convert (#86) * 🐛 Fix dtype Check In TIFFWriter (#87) * ⬆️ Bump zarr from 2.13.3 to 2.14.2 (#81) Bumps [zarr](https://github.com/zarr-developers/zarr-python) from 2.13.3 to 2.14.2. - [Release notes](https://github.com/zarr-developers/zarr-python/releases) - [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/docs/release.rst) - [Commits](zarr-developers/zarr-python@v2.13.3...v2.14.2) --- updated-dependencies: - dependency-name: zarr dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * 🚸 Add Unit Aliases In Conversion Functions (#88) * 🚸 Add Unit Aliases In Conversion Functions * ✅ Add Tests For microns_per_pixel Metadata * ✅ Ignore MPP Check For Zarr * ⬆️ Bump watchdog from 2.3.1 to 3.0.0 (#90) Bumps [watchdog](https://github.com/gorakhargosh/watchdog) from 2.3.1 to 3.0.0. - [Release notes](https://github.com/gorakhargosh/watchdog/releases) - [Changelog](https://github.com/gorakhargosh/watchdog/blob/master/changelog.rst) - [Commits](gorakhargosh/watchdog@v2.3.1...v3.0.0) --- updated-dependencies: - dependency-name: watchdog dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * ⬆️ Bump tox from 4.4.7 to 4.4.8 (#89) Bumps [tox](https://github.com/tox-dev/tox) from 4.4.7 to 4.4.8. - [Release notes](https://github.com/tox-dev/tox/releases) - [Changelog](https://github.com/tox-dev/tox/blob/main/docs/changelog.rst) - [Commits](tox-dev/tox@4.4.7...4.4.8) --- updated-dependencies: - dependency-name: tox dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> * 🔥 Remove OpenSlide Thumbnail Method (#92) Use base method instead which is more memory efficient. * ✨ Add Overwrite Option To Transcode CLI (#91) * ⬆️ Bump black from 23.1.0 to 23.3.0 (#93) Bumps [black](https://github.com/psf/black) from 23.1.0 to 23.3.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@23.1.0...23.3.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * 🚸 Prompt User To Make TILED_FULL DICOM Copy (#95) * 🚸 Prompt User To Make FULL_TILED DICOM Copy * ⬆️ Upgrade Minimum wsidicom Version * 🐛 Access To wsidicom Base Level * 🚸 Add Async Message When DICOM Init Is Slow * 🐛 Remove OpenSlide Thumbail Method (#97) This would break for images without reduced resolutions and the base implementation works well. * ⚡️ Use Persistent Workers To Get Tiles (#96) * 🚸 Raise From Previous Exception * ♻️ Refactoring * 🚸 Raise More Specific Exception * 🚸 Raise More Specific Exception * ♻️ Refactor Image Resizing Utils * 🧹 Tidying Up (#98) * 🎨 Print Level Counts From 1 In Progress Bar * ♻️ Minor Refactor * 🔧 Update Pre-Commit Config * 🚀 v0.8.0 Release (#99) * 📝 Update Release Notes * 🔖 Bump version: 0.7.0 → 0.8.0 * 🩹 Remove Unused Import --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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