diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..8c933ed --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,576 @@ +# CHANGELOG + +## v0.1.0 (2024-09-06) + +### Build + +* build: Initial Commit ([`cb4838f`](https://github.com/janelia-cellmap/cellmap-data/commit/cb4838fc155fe447e5245b37e317cf95bf2abcec)) + +### Chore + +* chore: 🔥 Remove CellMapSampler class and its dependencies. ([`5b4ee33`](https://github.com/janelia-cellmap/cellmap-data/commit/5b4ee33c9cf1160672fc5c934dd7a13aaef16eb6)) + +* chore: 🔥 Delete InferMasks class ([`e226bcc`](https://github.com/janelia-cellmap/cellmap-data/commit/e226bcc87b403e6e86d908e2f66e2fd51078e9fd)) + +* chore: 🙈 Remove GitHub actions temporarily. ([`bfaf6e6`](https://github.com/janelia-cellmap/cellmap-data/commit/bfaf6e6ec3df28fbcc82f604b688718070334e73)) + +* chore: update pre-commit ([`b76593f`](https://github.com/janelia-cellmap/cellmap-data/commit/b76593f6325e78c1c65d8f9953a7db4ceff1a5a9)) + +### Ci + +* ci(dependabot): bump actions/setup-python from 3 to 5 + +Bumps [actions/setup-python](https://github.com/actions/setup-python) from 3 to 5. +- [Release notes](https://github.com/actions/setup-python/releases) +- [Commits](https://github.com/actions/setup-python/compare/v3...v5) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/4724aec08fb8d3363959cff302d4ac212f656818)) + +* ci(dependabot): bump actions/checkout from 3 to 4 + +Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. +- [Release notes](https://github.com/actions/checkout/releases) +- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) +- [Commits](https://github.com/actions/checkout/compare/v3...v4) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/d4bb5377bcd3435bd981ed390baaa451a0ae9009)) + +* ci(dependabot): bump pypa/gh-action-pypi-publish from 1.4.2 to 1.10.0 + +Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.4.2 to 1.10.0. +- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) +- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/27b31702a0e7fc50959f5ad993c78deac1bdfc29...8a08d616893759ef8e1aa1f2785787c0b97e20d6) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/d38e35314dd06e0a7817d896212c56f48727f921)) + +* ci(dependabot): bump peaceiris/actions-gh-pages from 3 to 4 + +Bumps [peaceiris/actions-gh-pages](https://github.com/peaceiris/actions-gh-pages) from 3 to 4. +- [Release notes](https://github.com/peaceiris/actions-gh-pages/releases) +- [Changelog](https://github.com/peaceiris/actions-gh-pages/blob/main/CHANGELOG.md) +- [Commits](https://github.com/peaceiris/actions-gh-pages/compare/v3...v4) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/e878aaf620019e361e1a8e6510a4939b1f7d6581)) + +* ci(dependabot): bump actions/setup-python from 2 to 5 + +Bumps [actions/setup-python](https://github.com/actions/setup-python) from 2 to 5. +- [Release notes](https://github.com/actions/setup-python/releases) +- [Commits](https://github.com/actions/setup-python/compare/v2...v5) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/b0e1903bc9bffb3928cff6cc2a1818fd07f492a3)) + +* ci(dependabot): bump actions/checkout from 2 to 4 + +Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4. +- [Release notes](https://github.com/actions/checkout/releases) +- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) +- [Commits](https://github.com/actions/checkout/compare/v2...v4) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/1b700ebf94d8c8bd006f5bb0399bf03199260aca)) + +* ci: 👷 Add back GitHub actions ([`2b5d60d`](https://github.com/janelia-cellmap/cellmap-data/commit/2b5d60dab88b7631a351853fa5ff87a982b2b7ab)) + +* ci(dependabot): bump softprops/action-gh-release from 1 to 2 + +Bumps [softprops/action-gh-release](https://github.com/softprops/action-gh-release) from 1 to 2. +- [Release notes](https://github.com/softprops/action-gh-release/releases) +- [Changelog](https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md) +- [Commits](https://github.com/softprops/action-gh-release/compare/v1...v2) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/b7707cba3feef04c3cbaa992adf120135e75437b)) + +* ci(dependabot): bump actions/checkout from 3 to 4 + +Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. +- [Release notes](https://github.com/actions/checkout/releases) +- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) +- [Commits](https://github.com/actions/checkout/compare/v3...v4) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/b319c844dd79fa221e13be3749883c47476aab27)) + +* ci(dependabot): bump codecov/codecov-action from 3 to 4 + +Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. +- [Release notes](https://github.com/codecov/codecov-action/releases) +- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) +- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/a1b02466796d8a71a63f0059bef72e16e2542d69)) + +* ci(dependabot): bump actions/setup-python from 4 to 5 + +Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. +- [Release notes](https://github.com/actions/setup-python/releases) +- [Commits](https://github.com/actions/setup-python/compare/v4...v5) + +--- +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`](https://github.com/janelia-cellmap/cellmap-data/commit/f8f0405b5b4628c91451ec4478290d98216f8cb5)) + +### Documentation + +* docs: 📝 Build docs ([`124b945`](https://github.com/janelia-cellmap/cellmap-data/commit/124b945f3a60a4d2c419908a70ce95a78128f6a4)) + +* docs: 📝 Update dataloader.py docs ([`fd53745`](https://github.com/janelia-cellmap/cellmap-data/commit/fd537456f464b728eaa57d231286e7b81630dd58)) + +* docs: 📝 Update datasplit.py docs ([`a344fb3`](https://github.com/janelia-cellmap/cellmap-data/commit/a344fb3683f469bacdd8120f439e42a590e7518e)) + +* docs: 📝 Update multidataset.py docs ([`e54ae1b`](https://github.com/janelia-cellmap/cellmap-data/commit/e54ae1b801169a91edad54e27167f24885f181a1)) + +* docs: 📝 Update dataset.py docs ([`69b0215`](https://github.com/janelia-cellmap/cellmap-data/commit/69b02150207183970b550e2397b70b53494b34d7)) + +* docs: 📝 Update dataset.py docs. + +Also remove separate "mask" production. ([`518da49`](https://github.com/janelia-cellmap/cellmap-data/commit/518da4970eb7eb5765c4e5c97afa8d28f97151a5)) + +* docs: 📝 Update samplers/sampler.py docs. ([`ff2813e`](https://github.com/janelia-cellmap/cellmap-data/commit/ff2813e04c25e1b5ffba872ddaeee7f12bf3ebb0)) + +* docs: 📝 Update transforms/augment/random_gamma.py docs. ([`0ce1723`](https://github.com/janelia-cellmap/cellmap-data/commit/0ce1723242bde730d20af21a176e92a914bc0e30)) + +* docs: 📝 Update transforms/augment/random_contrast.py docs. ([`628068c`](https://github.com/janelia-cellmap/cellmap-data/commit/628068c811821484c91a47faee596324bb90a1a1)) + +* docs: 📝 Update transforms/augment/normalize.py docs. ([`c62611a`](https://github.com/janelia-cellmap/cellmap-data/commit/c62611affa056beeb1f2f3ee45f19a5c3ecbc24b)) + +* docs: 📝 Update transforms/augment/nan_to_num.py docs. ([`251c673`](https://github.com/janelia-cellmap/cellmap-data/commit/251c673e2d19da5a3e0f58ffefce0f379dfec211)) + +* docs: 📝 Update transforms/augment/nan_to_num.py docs. ([`99ac373`](https://github.com/janelia-cellmap/cellmap-data/commit/99ac373939282f57de0b52928b0b8619736810c8)) + +* docs: 📝 Update transforms/augment/gaussian_noise.py docs. ([`193f4b2`](https://github.com/janelia-cellmap/cellmap-data/commit/193f4b27041f7d262ddba08edf0bbcaccd31fba9)) + +* docs: 📝 Update transforms/targets/distance.py docs. ([`a6ef03a`](https://github.com/janelia-cellmap/cellmap-data/commit/a6ef03a9b2ea2deb1da3193275588bb4c1ec54d7)) + +* docs: 📝 Update transforms/targets/cellpose.py docs. ([`c0d051f`](https://github.com/janelia-cellmap/cellmap-data/commit/c0d051f80565b41bc195bc7cf7caaa6fce1e6a66)) + +* docs: 📝 Update utils/dtype.py docs. ([`2ec8741`](https://github.com/janelia-cellmap/cellmap-data/commit/2ec8741f219c21aaf3268e0c6dd7dac530f090ad)) + +* docs: 📝 Update utils/figs.py docs. ([`4154900`](https://github.com/janelia-cellmap/cellmap-data/commit/4154900d98bc27faf0824126871fdfa213cbfc90)) + +* docs: 📝 Update image.py docs. ([`c7a2015`](https://github.com/janelia-cellmap/cellmap-data/commit/c7a2015afdfee1acda629905a272150c45d79075)) + +* docs: 📝 Correct type declaration. ([`d282773`](https://github.com/janelia-cellmap/cellmap-data/commit/d2827731d093fe9ad0a25218a76e97493e93414b)) + +* docs: 📝 Add example training call. ([`3246e1d`](https://github.com/janelia-cellmap/cellmap-data/commit/3246e1df2ab46f35ed4a8b8b99fa4af16a7d7ce2)) + +### Feature + +* feat: ✨ Add distance transform targets. ([`1d1265e`](https://github.com/janelia-cellmap/cellmap-data/commit/1d1265ecaf6edd28a9846d9e1d8d082e48cc3eb5)) + +* feat: ✨ Make *mostly* HDF5 compatible. ([`517cefa`](https://github.com/janelia-cellmap/cellmap-data/commit/517cefa9c7e5883dc6e62a74af346ce56b734273)) + +* feat: ✨ Arbitrary rotations implemented at dataset level. ([`ea1dae4`](https://github.com/janelia-cellmap/cellmap-data/commit/ea1dae4cdf1fb37a4b1bcd652781131fee81b615)) + +* feat: ✨ Add linear vs. nearest-neighbor interpolation for raw vs. masks. ([`412d34d`](https://github.com/janelia-cellmap/cellmap-data/commit/412d34d2ed28275c23ab9b588258a080c8fe21f2)) + +* feat: ✨ Arbitrary rotations implemented at image level. ([`2f789b3`](https://github.com/janelia-cellmap/cellmap-data/commit/2f789b39d78b65a30489a889ddfd18f5249fee97)) + +* feat: 🚧 Arbitrary rotation mostly implemented. ([`92e7f61`](https://github.com/janelia-cellmap/cellmap-data/commit/92e7f61e2dc7fc568c1a9db4f35b3326735a34e0)) + +* feat: ⚡️ Allow different padding betweek training and validation ([`075695f`](https://github.com/janelia-cellmap/cellmap-data/commit/075695ffd979c895bba4d2d9cb4ff1a8f9110659)) + +* feat: ⚡️ Allow setting dataset arrays ([`dc8b118`](https://github.com/janelia-cellmap/cellmap-data/commit/dc8b1181e729f324ab905c8ec429f8a025553a6a)) + +* feat: ✨ Add image padding ([`d2e5261`](https://github.com/janelia-cellmap/cellmap-data/commit/d2e5261f7f52be41eb4337cc17264d86d05eeb8c)) + +* feat: 🚧 3D Rotations ([`badc110`](https://github.com/janelia-cellmap/cellmap-data/commit/badc1100482b377aecad838e888f5b2e1543593f)) + +* feat: 🚧 3D Rotations ([`495f686`](https://github.com/janelia-cellmap/cellmap-data/commit/495f686688d7427570a3f7d55e1124c14729ea61)) + +* feat: 🚧 3D Rotations ([`45a552e`](https://github.com/janelia-cellmap/cellmap-data/commit/45a552e51cb1d123c197159870982dea32385809)) + +* feat: ⚡️ GPU distance transform for training targets ([`7029129`](https://github.com/janelia-cellmap/cellmap-data/commit/70291292681dc11be18e937a7f9b9d7003c65f84)) + +* feat: ✨ Allow for setting input/target arrays for train/validation datasets after datasplit creation. ([`a2f593a`](https://github.com/janelia-cellmap/cellmap-data/commit/a2f593adeb64ec4e39068e7d413e5da767f53cf8)) + +* feat: ✨ Add get_image_dict util ([`e3aec3c`](https://github.com/janelia-cellmap/cellmap-data/commit/e3aec3c8c60904ad2cce9dddb94289aff6f9ba6a)) + +* feat: ✨ Add get_image_dict util ([`7f5e0b1`](https://github.com/janelia-cellmap/cellmap-data/commit/7f5e0b1c493558915bcd914b20b496fda810b590)) + +* feat: 🚧 class weights ([`6ff65a4`](https://github.com/janelia-cellmap/cellmap-data/commit/6ff65a465b29871d81462ff5ea739cad2e179009)) + +* feat: ✨ Allow setting spatial transforms after datasplit creation ([`b8aaa2c`](https://github.com/janelia-cellmap/cellmap-data/commit/b8aaa2cf7d03a5cec8ae115e46a28578afb32328)) + +* feat: ✨ True negatives available for training with nan_mask ([`33ac4ea`](https://github.com/janelia-cellmap/cellmap-data/commit/33ac4ea6eb59c62691d62124d5f7a23f9f726c62)) + +* feat: ⚡️ Fix masking and add inferred labels + +Also bring in get_image_grid from cellmap_train ([`3d5bb21`](https://github.com/janelia-cellmap/cellmap-data/commit/3d5bb210e51c973a6415d97100aa0846e90b52ee)) + +* feat: ✨ Add target transform for inferring true-negatives by mutual exclusion. ([`bea7ace`](https://github.com/janelia-cellmap/cellmap-data/commit/bea7ace3d1d95cc5808c27f570eb74cd923bdd0c)) + +* feat: ✨ Add augmentations brought from cellmap-train ([`fb3559d`](https://github.com/janelia-cellmap/cellmap-data/commit/fb3559df2f6b2a9722f7858f60c18baba48c5f2f)) + +* feat: ✨ Add loss masks ([`47118ff`](https://github.com/janelia-cellmap/cellmap-data/commit/47118fffb1b7048dad05af47ecbe2473fdbe8215)) + +* feat: ⚡️ Add get_class_weights to dataset and subdataset. ([`1f6674a`](https://github.com/janelia-cellmap/cellmap-data/commit/1f6674a7e7a9fff9fb2486c105c3f9c7bd4776d5)) + +* feat: ✨ Add validation block sampling. + +Also catch issues with overly small datasets given requested arrays. ([`73ffdf7`](https://github.com/janelia-cellmap/cellmap-data/commit/73ffdf740103dbb914f5b1bca1b6c02756e02368)) + +* feat: ✨ Add _repr_ to dataset/split classes ([`1674993`](https://github.com/janelia-cellmap/cellmap-data/commit/1674993935ccefd28dd144be0af46bbe0763d581)) + +* feat: ✨ Pretrain compatible + +Refactor to allow targetless pretraining on large datasets. ([`1ae7b1b`](https://github.com/janelia-cellmap/cellmap-data/commit/1ae7b1b30f04d5901e6e225cbf5087b7a3726f90)) + +* feat: ✨ Add Cellpose value transform. ([`ca76c7f`](https://github.com/janelia-cellmap/cellmap-data/commit/ca76c7f82723da5e776bf14639c5aa873c6f36de)) + +* feat: ✨ Dataloading works. Ready to train. ([`d83d1f3`](https://github.com/janelia-cellmap/cellmap-data/commit/d83d1f353c68d7aab76719f2324bb2b22a86dc04)) + +* feat: ⚡️ Add weighted random sampling. ([`85fd727`](https://github.com/janelia-cellmap/cellmap-data/commit/85fd727905fde71dd7f3cc8317d467d6d625a53a)) + +* feat: ✨ Implement spatial transforms. ([`cf092c9`](https://github.com/janelia-cellmap/cellmap-data/commit/cf092c9f5de3c1316a6208fc8ebb526a27bcea86)) + +* feat: ⚡️ Add force_has_data ([`3929c35`](https://github.com/janelia-cellmap/cellmap-data/commit/3929c35e8e741d1dfb1ea3c481558d789d71460d)) + +* feat: 🔥 Complete retrieving image data. + +Need to implement transforms. ([`d09b473`](https://github.com/janelia-cellmap/cellmap-data/commit/d09b473b47e94896bd806d19a1d660589c7ecf11)) + +* feat: ⚡️ Implemented class counts. ([`12fcd33`](https://github.com/janelia-cellmap/cellmap-data/commit/12fcd3380aa1892d14bb82433f10e8f01c38cbd3)) + +* feat: 🔥 Add Tensorstore based data fetching ([`73185d2`](https://github.com/janelia-cellmap/cellmap-data/commit/73185d28d0463b6d9d934718ba480da10867a700)) + +* feat: ⚡️ Dataset looking ready. ([`a49ade1`](https://github.com/janelia-cellmap/cellmap-data/commit/a49ade1d10050fc0cfdb33648b7914f5bd418452)) + +### Fix + +* fix: 🐛 Bugs and docs ([`68c11d0`](https://github.com/janelia-cellmap/cellmap-data/commit/68c11d099ebf404cffb6603bd885578c69868c76)) + +* fix: 🐛 Fix distance processing ([`3448556`](https://github.com/janelia-cellmap/cellmap-data/commit/3448556c6cbb9c65e8e23848e253fed49400dee5)) + +* fix: 🐛 Fix colorbar issue in get_image_dict function ([`65c5f11`](https://github.com/janelia-cellmap/cellmap-data/commit/65c5f11f4541fce30fb974aeeb5f8b66094e9b91)) + +* fix: 🐛 Fix shuffling ([`2c6b193`](https://github.com/janelia-cellmap/cellmap-data/commit/2c6b19394ff56c8b7a6f7fde43737882692ff206)) + +* fix: 🐛 Fix refreshable sampler ([`2263b86`](https://github.com/janelia-cellmap/cellmap-data/commit/2263b86f0136da087688164a72ea658e5941ad80)) + +* fix: 🐛 Fix install bug? ([`c7a87c8`](https://github.com/janelia-cellmap/cellmap-data/commit/c7a87c84573badf3ca7ad737407d0150b0d66fb0)) + +* fix: 🐛 Remove cellmap_train dependency. ([`b390bed`](https://github.com/janelia-cellmap/cellmap-data/commit/b390bedeb62e85eb9d23d33295f2ebbc7603c4a7)) + +* fix: 🐛 Fix NaNtoNum and Normalize transforms ([`f34c9d5`](https://github.com/janelia-cellmap/cellmap-data/commit/f34c9d5e2cf7c9e780298c522e37716f84abedf8)) + +* fix: 🐛 Remove uneccesary check in rotation augmentation ([`f5f0a1b`](https://github.com/janelia-cellmap/cellmap-data/commit/f5f0a1bbaada5bfd5524683b7b762d0f4595de2b)) + +* fix: 🐛 Fix bug trying to get rotation angle for non-declared axes. ([`4860774`](https://github.com/janelia-cellmap/cellmap-data/commit/4860774e7621cdf05bb423cedeed5ab2dd6bcc59)) + +* fix: 🐛 Fix breaking change from fibsem-tools-7 ([`f4064ad`](https://github.com/janelia-cellmap/cellmap-data/commit/f4064adf73fe76013136760feb0f692c265ccdcb)) + +* fix: 🐛 Fix breaking change from fibsem-tools-7 ([`7148556`](https://github.com/janelia-cellmap/cellmap-data/commit/71485564c18bee72720fb52a717e2f867df0783d)) + +* fix: 🐛 Fix spatial transform control flow logic ([`98f8fa4`](https://github.com/janelia-cellmap/cellmap-data/commit/98f8fa45dbcea68d70a3ca4c57c54958ed9f4693)) + +* fix: 🚀 Fix class weighting and sampling box size for padded datasets ([`988bd94`](https://github.com/janelia-cellmap/cellmap-data/commit/988bd9480a3949ec7b10bf82842cce44686d429a)) + +* fix: ⚡️ Bug fixes and small improvements. ([`7a700ae`](https://github.com/janelia-cellmap/cellmap-data/commit/7a700ae24c2f9a4eda99ca6b489803a9148cab3b)) + +* fix: 🚀 Change class weighting strategy ([`b5fab11`](https://github.com/janelia-cellmap/cellmap-data/commit/b5fab119ce318ba31741fcb36f585172c2d8ac5f)) + +* fix: 🐛 Correct empty_store creation ([`d9ac8ea`](https://github.com/janelia-cellmap/cellmap-data/commit/d9ac8ea7afa3b040f21ba6538ba70231a05e2bc1)) + +* fix: 🐛 Fix 2D mask dataloading ([`056f11c`](https://github.com/janelia-cellmap/cellmap-data/commit/056f11cb928df7d2f7ac729c0c5c37acfcc3b712)) + +* fix: 🐛 Fix multidataset blockwise indexing. ([`6703814`](https://github.com/janelia-cellmap/cellmap-data/commit/6703814ed582b02640bee6f30c3c6418399d25a1)) + +* fix: 🐛 Fix multidataset indices ([`19fb422`](https://github.com/janelia-cellmap/cellmap-data/commit/19fb422cd4cd281e35131218896c00d4442f6003)) + +* fix: 🚧 Subclass torch dataset Subset, hunting validation blocks bug ([`1c79c79`](https://github.com/janelia-cellmap/cellmap-data/commit/1c79c79d488cad4d55d91b9b632acdf8020089cf)) + +* fix: 🐛 Fix typing ([`712c595`](https://github.com/janelia-cellmap/cellmap-data/commit/712c5957f703e2bb5541b80251c0b572d3eeb18d)) + +* fix: 🐛 Fix spatial transform bug + +introduced with transition to using torch rng ([`504eda9`](https://github.com/janelia-cellmap/cellmap-data/commit/504eda9dc79e55e12ee30055c192680b9e763cc7)) + +* fix: 🐛 Corrected class weights for single class training. + +Also removed masking unknown data with NaNs (needs debugging). ([`be10de8`](https://github.com/janelia-cellmap/cellmap-data/commit/be10de8a333880bfb83976bd2ecfcb1a0bef5d81)) + +* fix: 🩹 Catch out of bounds requests. + +This is a hacky fix. The underlying issue needs to be found and corrected. ([`68e6f5e`](https://github.com/janelia-cellmap/cellmap-data/commit/68e6f5e07d845e0925f94c452753ab309f9b272e)) + +* fix: 🐛 Debug validation_blocks ([`2bd5ec8`](https://github.com/janelia-cellmap/cellmap-data/commit/2bd5ec8ca2ab0947f111baf6609626b53ac0813c)) + +* fix: 🐛 Fix for validation Subsets. ([`7422143`](https://github.com/janelia-cellmap/cellmap-data/commit/7422143218ac0c5239f0bb08c1d8c36dec5241be)) + +* fix: 🐛 Fix bugs ([`5d9c21b`](https://github.com/janelia-cellmap/cellmap-data/commit/5d9c21ba9bb3cf9d392c4c444230323c0cb471ea)) + +* fix: 🐛 Debug for many datasets ([`2a1134f`](https://github.com/janelia-cellmap/cellmap-data/commit/2a1134fd24d39f5948e88adf9e8c37c0750d4002)) + +* fix: 🎨 Make datasplit from csv consistent with DaCapo convention ([`0b47770`](https://github.com/janelia-cellmap/cellmap-data/commit/0b4777015c29d2a5b6bc5f31c14514904cc005d2)) + +* fix: 🎨 Make datasplit from csv consistent with DaCapo convention ([`6de372c`](https://github.com/janelia-cellmap/cellmap-data/commit/6de372c0ae6d2737fbd2799d35757446409300bb)) + +* fix: 🐛 Make 2D compatible ([`ad47e07`](https://github.com/janelia-cellmap/cellmap-data/commit/ad47e0777089a6044fb5e4c16b2e2b15603f6b00)) + +* fix: 🚧 WIP: Making 2D compatible ([`eeb4d18`](https://github.com/janelia-cellmap/cellmap-data/commit/eeb4d18b9ebf1415d2e915362db455d78106e83c)) + +* fix: 🚀 Works with Leibnetz and cellmap-train. ([`8dd846d`](https://github.com/janelia-cellmap/cellmap-data/commit/8dd846d8c522cd7f783ac94830fba0ec99579470)) + +* fix: 🐛 Fix EmptyImage shape. ([`3054511`](https://github.com/janelia-cellmap/cellmap-data/commit/3054511797b313df5e955aef8cb9bccf3e9e0e31)) + +* fix: 🐛 Image and Dataset seem debugged. ([`2dbf137`](https://github.com/janelia-cellmap/cellmap-data/commit/2dbf1372eef522b3abf859bca13cb427ae74bf09)) + +* fix: 🚧 Debug CellMapImage and CellMapDataset. ([`68ec58f`](https://github.com/janelia-cellmap/cellmap-data/commit/68ec58fee4dc741ce6b09760fe42540718085c6f)) + +### Performance + +* perf: ⚡️ Improve datasplit loading time. ([`bab1137`](https://github.com/janelia-cellmap/cellmap-data/commit/bab1137a3f519938117d4246a8982619d92bda32)) + +* perf: ⚡️ Improve datasplit loading time. + +Also, remove fibsem-tools dependency ([`41e5268`](https://github.com/janelia-cellmap/cellmap-data/commit/41e526839eaa140039bb9d21225ff1e62dc0f6a5)) + +* perf: ⚡️ Improve datasplit loading time. + +Also, update xarray-tensorstore dependency, and add NaNtoNum transform. ([`371c39d`](https://github.com/janelia-cellmap/cellmap-data/commit/371c39dc271fd86d162564686e0a4ce9cd28d0a7)) + +* perf: ⚡️ Put loss masks on cpu until calculation time. ([`4c8f553`](https://github.com/janelia-cellmap/cellmap-data/commit/4c8f553ddbe4de6f1cf70cf488e75c6bac9eab3c)) + +* perf: ⚡️ Refactor to clean code and catch bugs. + +Also begin working on sampler. ([`4b4589b`](https://github.com/janelia-cellmap/cellmap-data/commit/4b4589bf85ef891c54f2c8f0f28b8406c97c9c61)) + +* perf: 🎨 Remove use of numpy random number generator. ([`4964e0a`](https://github.com/janelia-cellmap/cellmap-data/commit/4964e0a198b6a793c9fca681e88e5f21050ea2b7)) + +### Refactor + +* refactor: ♻️ Switch from "if hasattr" to try/except ([`c4c07ca`](https://github.com/janelia-cellmap/cellmap-data/commit/c4c07caf757a012c77503a9e869e11cd68763474)) + +* refactor: 🎨 Refactor calls ([`036fc49`](https://github.com/janelia-cellmap/cellmap-data/commit/036fc49b2f213efa29b07d5de8b8ba1bc87d0e49)) + +* refactor: 🐛 Remove hidden property declarations ([`68bbdff`](https://github.com/janelia-cellmap/cellmap-data/commit/68bbdff60cb0271c2dee9bf4525aa6c6d97a4f4f)) + +* refactor: 🐛 Remove hidden property declarations +Also allow kwargs to dataloader ([`e2fd269`](https://github.com/janelia-cellmap/cellmap-data/commit/e2fd2692c12be44b720f2f9939b94f3617c9d047)) + +* refactor: 🐛 Remove hidden property declarations ([`001054e`](https://github.com/janelia-cellmap/cellmap-data/commit/001054e8d9dd846fe61996f06db6aa02c73f5f50)) + +* refactor: 🚚 Make get() functions into properties, and bug fix. ([`176d568`](https://github.com/janelia-cellmap/cellmap-data/commit/176d5683120367bab18a70f48e61fbed52a6883e)) + +* refactor: ♻️ Add get_class_weights function ([`81666e6`](https://github.com/janelia-cellmap/cellmap-data/commit/81666e697a2890708f45e65cd64474447629409c)) + +* refactor: ♻️ Refactor transforms. ([`9a8b057`](https://github.com/janelia-cellmap/cellmap-data/commit/9a8b057bad7ea764777e3f9b6929936e917871a8)) + +* refactor: 🚧 Add EmptyImage ([`c940cf3`](https://github.com/janelia-cellmap/cellmap-data/commit/c940cf3b5b54ddeb82d6bf666d96a70230f5e580)) + +* refactor: 🚧 Changes. ([`58e72a6`](https://github.com/janelia-cellmap/cellmap-data/commit/58e72a6d88768a6ab89495d187d515b69a74b9e5)) + +* refactor: 🚧 Switch to using ZarrDataset ([`26b9cdc`](https://github.com/janelia-cellmap/cellmap-data/commit/26b9cdc83bd4e38c77d3f5ab083970dbd1461de7)) + +* refactor: 🚧 ([`861dddd`](https://github.com/janelia-cellmap/cellmap-data/commit/861dddd0b6f6e21cd613bd74ca7e40ddfdbc964e)) + +### Unknown + +* Remove Python 3.8 and 3.9 classifiers, add hatch package ([`23ce4bd`](https://github.com/janelia-cellmap/cellmap-data/commit/23ce4bd2b5a5a0446feb01d7aae04b2c1f127dd5)) + +* Update python-publish.yml ([`ed0afa1`](https://github.com/janelia-cellmap/cellmap-data/commit/ed0afa1f012757d5b6ac566d5502a5ba7e73a345)) + +* Merge branch 'main' of github.com:janelia-cellmap/cellmap-data ([`cc72905`](https://github.com/janelia-cellmap/cellmap-data/commit/cc72905cbc3e6d0d293a0b3ef44a3a4cf7ed5a91)) + +* Merge pull request #18 from janelia-cellmap/rhoadesScholar-patch-1 + +Update pyproject.toml ([`0674cb9`](https://github.com/janelia-cellmap/cellmap-data/commit/0674cb9e1714c52fe8892e7d09c0cd61276b2e55)) + +* Update tests.yml ([`aa6e0e8`](https://github.com/janelia-cellmap/cellmap-data/commit/aa6e0e8330fa9b633ce0054194afa7e2954930da)) + +* Update pyproject.toml ([`822d155`](https://github.com/janelia-cellmap/cellmap-data/commit/822d1550a63c82f425c17c1ee64cb431a9830ba3)) + +* Add black, twine, and build to optional dependencies in pyproject.toml ([`cd31206`](https://github.com/janelia-cellmap/cellmap-data/commit/cd31206ea17e0f8816806099ca97f28ae1497516)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/d40c201b8ce0d020e48ffe4cf1ec21ada5dc6b5a)) + +* Merge pull request #16 from janelia-cellmap/dependabot/github_actions/actions/checkout-4 + +ci(dependabot): bump actions/checkout from 3 to 4 ([`73d6985`](https://github.com/janelia-cellmap/cellmap-data/commit/73d69856ecff5f2ce8d9a076fb77f251fb8eca63)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/0262bfdddaffcd38bcae80d90c466d9aa29198ae)) + +* Merge branch 'main' of github.com:janelia-cellmap/cellmap-data ([`4121c10`](https://github.com/janelia-cellmap/cellmap-data/commit/4121c10605b1f66c2376fb1e286b18e1a5cd60d3)) + +* Update tests.yml ([`59523da`](https://github.com/janelia-cellmap/cellmap-data/commit/59523da70f65fed595d22bf024752335b0fa7725)) + +* mypy modifications ([`baffd73`](https://github.com/janelia-cellmap/cellmap-data/commit/baffd73cbdf151fe6c72608f1ff282109d60ee7f)) + +* Add test for importing cellmap_data module ([`445962e`](https://github.com/janelia-cellmap/cellmap-data/commit/445962e6cf1b29f9169ba1c908c98bbfd2db426d)) + +* Add badges for build status, license, and code coverage ([`d78764f`](https://github.com/janelia-cellmap/cellmap-data/commit/d78764fdde06012bfc02930dd30b5c58152e803f)) + +* Create tests.yml ([`357321d`](https://github.com/janelia-cellmap/cellmap-data/commit/357321da421bf3932a4330226699f834380ec4d9)) + +* Create mypy.yml ([`a26cb28`](https://github.com/janelia-cellmap/cellmap-data/commit/a26cb28d8d13b5a75e5719558c55a8f3c94c3e19)) + +* Create black.yml ([`c80162e`](https://github.com/janelia-cellmap/cellmap-data/commit/c80162e785bd8f23c2f18cf873cb10dd6072dfa3)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/b40a2214e8fc854507f4fb5609a18cd8a5efd9c5)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/3fd679a7c8c0eac5d2565ce26daf95cbb6a5e2d8)) + +* Merge pull request #12 from janelia-cellmap/dependabot/github_actions/actions/checkout-4 + +ci(dependabot): bump actions/checkout from 2 to 4 ([`c2a876b`](https://github.com/janelia-cellmap/cellmap-data/commit/c2a876b02fd9bffa5a9fab77a4421c3f6db9e1ef)) + +* Create python-publish.yml ([`04c6ace`](https://github.com/janelia-cellmap/cellmap-data/commit/04c6ace77354c2e19de489a332a51edf069d9767)) + +* Update docs.yml ([`2c32ed6`](https://github.com/janelia-cellmap/cellmap-data/commit/2c32ed694ed8194d71b2b00c0b7f6d07d41eb8d4)) + +* Update docs.yml ([`a6b62b8`](https://github.com/janelia-cellmap/cellmap-data/commit/a6b62b8dd981dc10db1a7c9910ae443ed361dca2)) + +* Update docs.yml ([`d901062`](https://github.com/janelia-cellmap/cellmap-data/commit/d901062be963849e51f3d688bd36ec34d69b2536)) + +* Update docs.yml ([`9b122bf`](https://github.com/janelia-cellmap/cellmap-data/commit/9b122bfc8319b1da66d68d84127c906b707bb119)) + +* Update docs.yml ([`818ca8a`](https://github.com/janelia-cellmap/cellmap-data/commit/818ca8a5ebba9e6fb35b873a786f15eda8bb0f6c)) + +* Create docs.yml ([`9c3750a`](https://github.com/janelia-cellmap/cellmap-data/commit/9c3750a13a644d63a602dc1685f29cd172deaa89)) + +* Update dependabot.yml ([`18a415e`](https://github.com/janelia-cellmap/cellmap-data/commit/18a415e6da8104e64989911a79130a178fe5b603)) + +* Delete .github/workflows/jekyll-gh-pages.yml ([`d682cfc`](https://github.com/janelia-cellmap/cellmap-data/commit/d682cfc9e8bb5c847b29477376c329e7d093da51)) + +* Update jekyll-gh-pages.yml ([`3d317c5`](https://github.com/janelia-cellmap/cellmap-data/commit/3d317c535941e9591516cbb024e614f749ba18cf)) + +* Update jekyll-gh-pages.yml ([`1b527c2`](https://github.com/janelia-cellmap/cellmap-data/commit/1b527c2417f121739f02934c8f7c555ab2300321)) + +* Update jekyll-gh-pages.yml ([`3ebc14a`](https://github.com/janelia-cellmap/cellmap-data/commit/3ebc14a3d4e7d06fdbaabdd2e4a04690c7a035bc)) + +* Update jekyll-gh-pages.yml ([`e1b8249`](https://github.com/janelia-cellmap/cellmap-data/commit/e1b824986bfe162d75a30c1b7b4f6ca8a64436bb)) + +* Create jekyll-gh-pages.yml ([`2fe41a1`](https://github.com/janelia-cellmap/cellmap-data/commit/2fe41a1cc98fa57a0d4a10cd20ad9ea74275ecdf)) + +* Merge branch 'main' of github.com:janelia-cellmap/cellmap-data ([`6ea0f5f`](https://github.com/janelia-cellmap/cellmap-data/commit/6ea0f5f877f18fba511c3a153c239a1accd8f3e4)) + +* Update README.md ([`d49e42f`](https://github.com/janelia-cellmap/cellmap-data/commit/d49e42fc7c399f7b462b7b963a28ceecdfd5052f)) + +* Update README.md ([`411b286`](https://github.com/janelia-cellmap/cellmap-data/commit/411b2862dcfa9c1f661fb716cc7e7a09c45d26a7)) + +* Update project name and references ([`c1a4e1c`](https://github.com/janelia-cellmap/cellmap-data/commit/c1a4e1c196dc99547f5062dc02183bea594284e8)) + +* Merge pull request #8 from janelia-cellmap/fibsem-tools-7_compatible + +fix: 🐛 Fix breaking change from fibsem-tools-7 ([`7a12cd9`](https://github.com/janelia-cellmap/cellmap-data/commit/7a12cd92e0233ce4ac5750f58f0c3032aadae868)) + +* Update README.md ([`b954d23`](https://github.com/janelia-cellmap/cellmap-data/commit/b954d2394382de756a22b500e603ef9da3cedc9e)) + +* Merge pull request #7 from janelia-cellmap/loss_mask + +Loss mask ([`b7d59e6`](https://github.com/janelia-cellmap/cellmap-data/commit/b7d59e6eaf34accf37e010f94cbd3121561c60a5)) + +* Change default empty_value ([`6aac385`](https://github.com/janelia-cellmap/cellmap-data/commit/6aac385d87d72a1c9db264e671775810e5fc907d)) + +* Merge pull request #6 from janelia-cellmap/hot_fix_2D + +Hot fix 2 d ([`2d3212a`](https://github.com/janelia-cellmap/cellmap-data/commit/2d3212ad0d2886b5d66c9e6f622a876629fa5757)) + +* Change default empty_value ([`912e08d`](https://github.com/janelia-cellmap/cellmap-data/commit/912e08d36fa92c856a284da583ee63f7645c4068)) + +* Update ci.yml + +Don't test python 3.8 and 3.9 ([`c2a5be8`](https://github.com/janelia-cellmap/cellmap-data/commit/c2a5be88646031a98d3d35f716c0a1ad6e901114)) + +* Update README.md ([`5a55e84`](https://github.com/janelia-cellmap/cellmap-data/commit/5a55e840f0b3a697d17b6afa695e0d1808361d7f)) + +* Add .gitignore entry for scratch directory and remove simple_train.py ([`39d3565`](https://github.com/janelia-cellmap/cellmap-data/commit/39d356512cb548afbbd6907728f7c4f822141997)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/469a7114ec09c560f4b34eed9da84d3d7838b01e)) + +* Update README.md ([`b267e70`](https://github.com/janelia-cellmap/cellmap-data/commit/b267e70df6df4533da1160b09bd25ccca09388bd)) + +* Update repository URLs and badges ([`4dae1ae`](https://github.com/janelia-cellmap/cellmap-data/commit/4dae1ae1b64824d81206aeea464482b1d6b14d7c)) + +* Update license link in README.md ([`0b6d698`](https://github.com/janelia-cellmap/cellmap-data/commit/0b6d6985628fb00b1e05cfd1a9b3a80be5408cc1)) + +* Merge pull request #2 from janelia-cellmap/dependabot/github_actions/actions/checkout-4 + +ci(dependabot): bump actions/checkout from 3 to 4 ([`5938aa2`](https://github.com/janelia-cellmap/cellmap-data/commit/5938aa20a30f5b8db5ae784f3d73ff5a24e1e158)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/cbe5c1bcb8f159330a35512ab6f864efda1ca6ba)) + +* 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`](https://github.com/janelia-cellmap/cellmap-data/commit/220774702381dbecdb1fb0ff9dfd1dc95ec6a84e)) + +* Add dependencies to pyproject.toml and set default version to 0.0.0 in __init__.py ([`22206e8`](https://github.com/janelia-cellmap/cellmap-data/commit/22206e8d486eb57b0699a88163d3f83639b6658a))