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CHANGELOG

v0.1.0 (2024-09-06)

Build

Chore

  • chore: 🔥 Remove CellMapSampler class and its dependencies. (5b4ee33)

  • chore: 🔥 Delete InferMasks class (e226bcc)

  • chore: 🙈 Remove GitHub actions temporarily. (bfaf6e6)

  • chore: update pre-commit (b76593f)

Ci

  • ci(dependabot): bump actions/setup-python from 3 to 5

Bumps actions/setup-python from 3 to 5.

updated-dependencies:

  • dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (4724aec)

  • ci(dependabot): bump actions/checkout from 3 to 4

Bumps actions/checkout from 3 to 4.

updated-dependencies:

  • dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (d4bb537)

  • ci(dependabot): bump pypa/gh-action-pypi-publish from 1.4.2 to 1.10.0

Bumps pypa/gh-action-pypi-publish from 1.4.2 to 1.10.0.

updated-dependencies:

  • dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-minor ...

Signed-off-by: dependabot[bot] <support@github.com> (d38e353)

  • ci(dependabot): bump peaceiris/actions-gh-pages from 3 to 4

Bumps peaceiris/actions-gh-pages from 3 to 4.

updated-dependencies:

  • dependency-name: peaceiris/actions-gh-pages dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (e878aaf)

  • ci(dependabot): bump actions/setup-python from 2 to 5

Bumps actions/setup-python from 2 to 5.

updated-dependencies:

  • dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (b0e1903)

  • ci(dependabot): bump actions/checkout from 2 to 4

Bumps actions/checkout from 2 to 4.

updated-dependencies:

  • dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (1b700eb)

  • ci: 👷 Add back GitHub actions (2b5d60d)

  • ci(dependabot): bump softprops/action-gh-release from 1 to 2

Bumps softprops/action-gh-release from 1 to 2.

updated-dependencies:

  • dependency-name: softprops/action-gh-release dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (b7707cb)

  • ci(dependabot): bump actions/checkout from 3 to 4

Bumps actions/checkout from 3 to 4.

updated-dependencies:

  • dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (b319c84)

  • ci(dependabot): bump codecov/codecov-action from 3 to 4

Bumps codecov/codecov-action from 3 to 4.

updated-dependencies:

  • dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (a1b0246)

  • ci(dependabot): bump actions/setup-python from 4 to 5

Bumps actions/setup-python from 4 to 5.

updated-dependencies:

  • dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ...

Signed-off-by: dependabot[bot] <support@github.com> (f8f0405)

Documentation

  • docs: 📝 Build docs (124b945)

  • docs: 📝 Update dataloader.py docs (fd53745)

  • docs: 📝 Update datasplit.py docs (a344fb3)

  • docs: 📝 Update multidataset.py docs (e54ae1b)

  • docs: 📝 Update dataset.py docs (69b0215)

  • docs: 📝 Update dataset.py docs.

Also remove separate "mask" production. (518da49)

  • docs: 📝 Update samplers/sampler.py docs. (ff2813e)

  • docs: 📝 Update transforms/augment/random_gamma.py docs. (0ce1723)

  • docs: 📝 Update transforms/augment/random_contrast.py docs. (628068c)

  • docs: 📝 Update transforms/augment/normalize.py docs. (c62611a)

  • docs: 📝 Update transforms/augment/nan_to_num.py docs. (251c673)

  • docs: 📝 Update transforms/augment/nan_to_num.py docs. (99ac373)

  • docs: 📝 Update transforms/augment/gaussian_noise.py docs. (193f4b2)

  • docs: 📝 Update transforms/targets/distance.py docs. (a6ef03a)

  • docs: 📝 Update transforms/targets/cellpose.py docs. (c0d051f)

  • docs: 📝 Update utils/dtype.py docs. (2ec8741)

  • docs: 📝 Update utils/figs.py docs. (4154900)

  • docs: 📝 Update image.py docs. (c7a2015)

  • docs: 📝 Correct type declaration. (d282773)

  • docs: 📝 Add example training call. (3246e1d)

Feature

  • feat: ✨ Add distance transform targets. (1d1265e)

  • feat: ✨ Make mostly HDF5 compatible. (517cefa)

  • feat: ✨ Arbitrary rotations implemented at dataset level. (ea1dae4)

  • feat: ✨ Add linear vs. nearest-neighbor interpolation for raw vs. masks. (412d34d)

  • feat: ✨ Arbitrary rotations implemented at image level. (2f789b3)

  • feat: 🚧 Arbitrary rotation mostly implemented. (92e7f61)

  • feat: ⚡️ Allow different padding betweek training and validation (075695f)

  • feat: ⚡️ Allow setting dataset arrays (dc8b118)

  • feat: ✨ Add image padding (d2e5261)

  • feat: 🚧 3D Rotations (badc110)

  • feat: 🚧 3D Rotations (495f686)

  • feat: 🚧 3D Rotations (45a552e)

  • feat: ⚡️ GPU distance transform for training targets (7029129)

  • feat: ✨ Allow for setting input/target arrays for train/validation datasets after datasplit creation. (a2f593a)

  • feat: ✨ Add get_image_dict util (e3aec3c)

  • feat: ✨ Add get_image_dict util (7f5e0b1)

  • feat: 🚧 class weights (6ff65a4)

  • feat: ✨ Allow setting spatial transforms after datasplit creation (b8aaa2c)

  • feat: ✨ True negatives available for training with nan_mask (33ac4ea)

  • feat: ⚡️ Fix masking and add inferred labels

Also bring in get_image_grid from cellmap_train (3d5bb21)

  • feat: ✨ Add target transform for inferring true-negatives by mutual exclusion. (bea7ace)

  • feat: ✨ Add augmentations brought from cellmap-train (fb3559d)

  • feat: ✨ Add loss masks (47118ff)

  • feat: ⚡️ Add get_class_weights to dataset and subdataset. (1f6674a)

  • feat: ✨ Add validation block sampling.

Also catch issues with overly small datasets given requested arrays. (73ffdf7)

  • feat: ✨ Add repr to dataset/split classes (1674993)

  • feat: ✨ Pretrain compatible

Refactor to allow targetless pretraining on large datasets. (1ae7b1b)

  • feat: ✨ Add Cellpose value transform. (ca76c7f)

  • feat: ✨ Dataloading works. Ready to train. (d83d1f3)

  • feat: ⚡️ Add weighted random sampling. (85fd727)

  • feat: ✨ Implement spatial transforms. (cf092c9)

  • feat: ⚡️ Add force_has_data (3929c35)

  • feat: 🔥 Complete retrieving image data.

Need to implement transforms. (d09b473)

  • feat: ⚡️ Implemented class counts. (12fcd33)

  • feat: 🔥 Add Tensorstore based data fetching (73185d2)

  • feat: ⚡️ Dataset looking ready. (a49ade1)

Fix

  • fix: 🐛 Bugs and docs (68c11d0)

  • fix: 🐛 Fix distance processing (3448556)

  • fix: 🐛 Fix colorbar issue in get_image_dict function (65c5f11)

  • fix: 🐛 Fix shuffling (2c6b193)

  • fix: 🐛 Fix refreshable sampler (2263b86)

  • fix: 🐛 Fix install bug? (c7a87c8)

  • fix: 🐛 Remove cellmap_train dependency. (b390bed)

  • fix: 🐛 Fix NaNtoNum and Normalize transforms (f34c9d5)

  • fix: 🐛 Remove uneccesary check in rotation augmentation (f5f0a1b)

  • fix: 🐛 Fix bug trying to get rotation angle for non-declared axes. (4860774)

  • fix: 🐛 Fix breaking change from fibsem-tools-7 (f4064ad)

  • fix: 🐛 Fix breaking change from fibsem-tools-7 (7148556)

  • fix: 🐛 Fix spatial transform control flow logic (98f8fa4)

  • fix: 🚀 Fix class weighting and sampling box size for padded datasets (988bd94)

  • fix: ⚡️ Bug fixes and small improvements. (7a700ae)

  • fix: 🚀 Change class weighting strategy (b5fab11)

  • fix: 🐛 Correct empty_store creation (d9ac8ea)

  • fix: 🐛 Fix 2D mask dataloading (056f11c)

  • fix: 🐛 Fix multidataset blockwise indexing. (6703814)

  • fix: 🐛 Fix multidataset indices (19fb422)

  • fix: 🚧 Subclass torch dataset Subset, hunting validation blocks bug (1c79c79)

  • fix: 🐛 Fix typing (712c595)

  • fix: 🐛 Fix spatial transform bug

introduced with transition to using torch rng (504eda9)

  • fix: 🐛 Corrected class weights for single class training.

Also removed masking unknown data with NaNs (needs debugging). (be10de8)

  • fix: 🩹 Catch out of bounds requests.

This is a hacky fix. The underlying issue needs to be found and corrected. (68e6f5e)

  • fix: 🐛 Debug validation_blocks (2bd5ec8)

  • fix: 🐛 Fix for validation Subsets. (7422143)

  • fix: 🐛 Fix bugs (5d9c21b)

  • fix: 🐛 Debug for many datasets (2a1134f)

  • fix: 🎨 Make datasplit from csv consistent with DaCapo convention (0b47770)

  • fix: 🎨 Make datasplit from csv consistent with DaCapo convention (6de372c)

  • fix: 🐛 Make 2D compatible (ad47e07)

  • fix: 🚧 WIP: Making 2D compatible (eeb4d18)

  • fix: 🚀 Works with Leibnetz and cellmap-train. (8dd846d)

  • fix: 🐛 Fix EmptyImage shape. (3054511)

  • fix: 🐛 Image and Dataset seem debugged. (2dbf137)

  • fix: 🚧 Debug CellMapImage and CellMapDataset. (68ec58f)

Performance

  • perf: ⚡️ Improve datasplit loading time. (bab1137)

  • perf: ⚡️ Improve datasplit loading time.

Also, remove fibsem-tools dependency (41e5268)

  • perf: ⚡️ Improve datasplit loading time.

Also, update xarray-tensorstore dependency, and add NaNtoNum transform. (371c39d)

  • perf: ⚡️ Put loss masks on cpu until calculation time. (4c8f553)

  • perf: ⚡️ Refactor to clean code and catch bugs.

Also begin working on sampler. (4b4589b)

  • perf: 🎨 Remove use of numpy random number generator. (4964e0a)

Refactor

  • refactor: ♻️ Switch from "if hasattr" to try/except (c4c07ca)

  • refactor: 🎨 Refactor calls (036fc49)

  • refactor: 🐛 Remove hidden property declarations (68bbdff)

  • refactor: 🐛 Remove hidden property declarations Also allow kwargs to dataloader (e2fd269)

  • refactor: 🐛 Remove hidden property declarations (001054e)

  • refactor: 🚚 Make get() functions into properties, and bug fix. (176d568)

  • refactor: ♻️ Add get_class_weights function (81666e6)

  • refactor: ♻️ Refactor transforms. (9a8b057)

  • refactor: 🚧 Add EmptyImage (c940cf3)

  • refactor: 🚧 Changes. (58e72a6)

  • refactor: 🚧 Switch to using ZarrDataset (26b9cdc)

  • refactor: 🚧 (861dddd)

Unknown

  • Remove Python 3.8 and 3.9 classifiers, add hatch package (23ce4bd)

  • Update python-publish.yml (ed0afa1)

  • Merge branch 'main' of github.com:janelia-cellmap/cellmap-data (cc72905)

  • Merge pull request #18 from janelia-cellmap/rhoadesScholar-patch-1

Update pyproject.toml (0674cb9)

  • Update tests.yml (aa6e0e8)

  • Update pyproject.toml (822d155)

  • Add black, twine, and build to optional dependencies in pyproject.toml (cd31206)

  • Merge pull request #15 from janelia-cellmap/dependabot/github_actions/actions/setup-python-5

ci(dependabot): bump actions/setup-python from 3 to 5 (d40c201)

  • Merge pull request #16 from janelia-cellmap/dependabot/github_actions/actions/checkout-4

ci(dependabot): bump actions/checkout from 3 to 4 (73d6985)

  • Merge pull request #17 from janelia-cellmap/dependabot/github_actions/pypa/gh-action-pypi-publish-1.10.0

ci(dependabot): bump pypa/gh-action-pypi-publish from 1.4.2 to 1.10.0 (0262bfd)

  • Merge branch 'main' of github.com:janelia-cellmap/cellmap-data (4121c10)

  • Update tests.yml (59523da)

  • mypy modifications (baffd73)

  • Add test for importing cellmap_data module (445962e)

  • Add badges for build status, license, and code coverage (d78764f)

  • Create tests.yml (357321d)

  • Create mypy.yml (a26cb28)

  • Create black.yml (c80162e)

  • Merge pull request #11 from janelia-cellmap/dependabot/github_actions/peaceiris/actions-gh-pages-4

ci(dependabot): bump peaceiris/actions-gh-pages from 3 to 4 (b40a221)

  • Merge pull request #10 from janelia-cellmap/dependabot/github_actions/actions/setup-python-5

ci(dependabot): bump actions/setup-python from 2 to 5 (3fd679a)

  • Merge pull request #12 from janelia-cellmap/dependabot/github_actions/actions/checkout-4

ci(dependabot): bump actions/checkout from 2 to 4 (c2a876b)

  • Create python-publish.yml (04c6ace)

  • Update docs.yml (2c32ed6)

  • Update docs.yml (a6b62b8)

  • Update docs.yml (d901062)

  • Update docs.yml (9b122bf)

  • Update docs.yml (818ca8a)

  • Create docs.yml (9c3750a)

  • Update dependabot.yml (18a415e)

  • Delete .github/workflows/jekyll-gh-pages.yml (d682cfc)

  • Update jekyll-gh-pages.yml (3d317c5)

  • Update jekyll-gh-pages.yml (1b527c2)

  • Update jekyll-gh-pages.yml (3ebc14a)

  • Update jekyll-gh-pages.yml (e1b8249)

  • Create jekyll-gh-pages.yml (2fe41a1)

  • Merge branch 'main' of github.com:janelia-cellmap/cellmap-data (6ea0f5f)

  • Update README.md (d49e42f)

  • Update README.md (411b286)

  • Update project name and references (c1a4e1c)

  • Merge pull request #8 from janelia-cellmap/fibsem-tools-7_compatible

fix: 🐛 Fix breaking change from fibsem-tools-7 (7a12cd9)

  • Update README.md (b954d23)

  • Merge pull request #7 from janelia-cellmap/loss_mask

Loss mask (b7d59e6)

  • Change default empty_value (6aac385)

  • Merge pull request #6 from janelia-cellmap/hot_fix_2D

Hot fix 2 d (2d3212a)

  • Change default empty_value (912e08d)

  • Update ci.yml

Don't test python 3.8 and 3.9 (c2a5be8)

  • Update README.md (5a55e84)

  • Add .gitignore entry for scratch directory and remove simple_train.py (39d3565)

  • Merge pull request #4 from janelia-cellmap/dependabot/github_actions/softprops/action-gh-release-2

ci(dependabot): bump softprops/action-gh-release from 1 to 2 (469a711)

  • Update README.md (b267e70)

  • Update repository URLs and badges (4dae1ae)

  • Update license link in README.md (0b6d698)

  • Merge pull request #2 from janelia-cellmap/dependabot/github_actions/actions/checkout-4

ci(dependabot): bump actions/checkout from 3 to 4 (5938aa2)

  • Merge pull request #1 from janelia-cellmap/dependabot/github_actions/codecov/codecov-action-4

ci(dependabot): bump codecov/codecov-action from 3 to 4 (cbe5c1b)

  • Merge pull request #3 from janelia-cellmap/dependabot/github_actions/actions/setup-python-5

ci(dependabot): bump actions/setup-python from 4 to 5 (2207747)

  • Add dependencies to pyproject.toml and set default version to 0.0.0 in init.py (22206e8)