From 8b43e471e7244490449c433b8d87d627ea563a44 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 2 Sep 2024 17:14:19 +0200 Subject: [PATCH] update changelog --- CHANGELOG.released.md | 60 ++++++++++++++++++++++++++++++++++++++++ CHANGELOG.unreleased.md | 51 +--------------------------------- MIGRATIONS.released.md | 9 ++++++ MIGRATIONS.unreleased.md | 6 +--- 4 files changed, 71 insertions(+), 55 deletions(-) diff --git a/CHANGELOG.released.md b/CHANGELOG.released.md index 6005c7c1a2a..0230187bb8d 100644 --- a/CHANGELOG.released.md +++ b/CHANGELOG.released.md @@ -7,6 +7,66 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`. For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md). +## [24.08.0](https://github.com/scalableminds/webknossos/releases/tag/24.08.0) - 2024-09-02 +[Commits](https://github.com/scalableminds/webknossos/compare/24.07.0...24.08.0) + +### Highlights +- The AI-based Quick Select can now be run on multiple sections at once. This can be configured in the tool settings. Also, the underlying model now uses Segment Anything 2. [#7965](https://github.com/scalableminds/webknossos/pull/7965) +- Metadata entries can now be added to datasets and folders. The metadata can be viewed and edited in the dashboard in the right details tab. [#7886](https://github.com/scalableminds/webknossos/pull/7886) +- The AI-based Quick Select can now be triggered with a single click. Drawing a rectangle is still supported. [#7993](https://github.com/scalableminds/webknossos/pull/7993) +- Added the option to resume an unfinished upload even after browser restarts. [#7981](https://github.com/scalableminds/webknossos/pull/7981) +- Added a feature to register all segments for a given bounding box at once via the context menu of the bounding box. [#7979](https://github.com/scalableminds/webknossos/pull/7979) + +### Added +- WEBKNOSSOS now automatically searches in subfolder / sub-collection identifiers for valid datasets in case a provided link to a remote dataset does not directly point to a dataset. [#7912](https://github.com/scalableminds/webknossos/pull/7912) +- Added the option to move a bounding box via dragging while pressing ctrl / meta. [#7892](https://github.com/scalableminds/webknossos/pull/7892) +- Added route `/import?url=` to automatically import and view remote datasets. [#7844](https://github.com/scalableminds/webknossos/pull/7844) +- Added that newly created, modified and clicked on bounding boxes are now highlighted and scrolled into view, while the bounding box tool is active. [#7935](https://github.com/scalableminds/webknossos/pull/7935) +- The configured unit in the dataset upload view is now passed to the convert_to_wkw worker job. [#7970](https://github.com/scalableminds/webknossos/pull/7970) +- Added option to expand or collapse all subgroups of a segment group in the segments tab. [#7911](https://github.com/scalableminds/webknossos/pull/7911) +- The context menu that is opened upon right-clicking a segment in the dataview port now contains the segment's name. [#7920](https://github.com/scalableminds/webknossos/pull/7920) +- Upgraded backend dependencies for improved performance and stability. [#7922](https://github.com/scalableminds/webknossos/pull/7922) +- Added Support for streaming datasets via Zarr version 3. [#7941](https://github.com/scalableminds/webknossos/pull/7941) +- It is now saved whether segment groups are collapsed or expanded, so this information doesn't get lost e.g. upon page reload. [#7928](https://github.com/scalableminds/webknossos/pull/7928/) +- It is now saved whether skeleton groups are collapsed or expanded. This information is also persisted to NML output. [#7939](https://github.com/scalableminds/webknossos/pull/7939) +- The context menu entry "Focus in Segment List" expands all necessary segment groups in the segments tab to show the highlighted segment. [#7950](https://github.com/scalableminds/webknossos/pull/7950) +- In the proofreading mode, you can enable/disable that only the active segment and the hovered segment are rendered. [#7654](https://github.com/scalableminds/webknossos/pull/7654) +- Upgraded s3 client for improved performance when loading remote datasets. [#7936](https://github.com/scalableminds/webknossos/pull/7936) +- The performance of the bounding box tab was improved. [#7974](https://github.com/scalableminds/webknossos/pull/7974) +- Added support for reading zstd-compressed zarr2 datasets [#7964](https://github.com/scalableminds/webknossos/pull/7964) +- The alignment job is in a separate tab of the "AI Tools" now. The "Align Sections" AI job now supports including manually created matches between adjacent section given as skeletons. [#7967](https://github.com/scalableminds/webknossos/pull/7967) +- Added `api.tracing.createNode(position, options)` to the front-end API. [#7998](https://github.com/scalableminds/webknossos/pull/7998) +- Added links in the workflow report for skipped tasks to the corresponding workflow view. [#8006](https://github.com/scalableminds/webknossos/pull/8006) +- Upgraded backend dependencies for improved performance and stability, including a memory leak fix for FossilDB. [#8014](https://github.com/scalableminds/webknossos/pull/8014) + +### Changed +- Replaced skeleton tab component with antd's ``component. Added support for selecting tree ranges with SHIFT. [#7819](https://github.com/scalableminds/webknossos/pull/7819) +- The warning about a mismatch between the scale of a pre-computed mesh and the dataset scale's factor now also considers all supported mags of the active segmentation layer. This reduces the false posive rate regarding this warning. [#7921](https://github.com/scalableminds/webknossos/pull/7921/) +- It is no longer allowed to edit annotations of other organizations, even if they are set to public and to others-may-edit. [#7923](https://github.com/scalableminds/webknossos/pull/7923) +- When proofreading segmentations, the user can now interact with super-voxels directly in the data viewports. Additionally, proofreading is significantly faster because the segmentation data doesn't have to be re-downloaded after each merge/split operation. [#7654](https://github.com/scalableminds/webknossos/pull/7654) +- Changed internal data model changing an organization's name to id and its displayName to name. The previously existing id was removed. [#7386](https://github.com/scalableminds/webknossos/pull/7386) +- Because of the way our models are trained, AI analysis and training is disabled for 2D and ND datasets, as well as for color layers with data type uInt24. [#7957](https://github.com/scalableminds/webknossos/pull/7957) +- The overall performance was improved (especially for the segments tab). [#7958](https://github.com/scalableminds/webknossos/pull/7958) +- The performance for the skeleton tab was improved. [#7989](https://github.com/scalableminds/webknossos/pull/7989) +- Upgraded ant icons to version 5.4. [#8007](https://github.com/scalableminds/webknossos/pull/8007) +- Increased maximum depth for ai-based quick select from 5 to 16. [#8021](https://github.com/scalableminds/webknossos/pull/8021) +- Zarr-streaming now uses the new unit-aware voxel size. This means that [wk-libs client v0.14.25 or newer](https://github.com/scalableminds/webknossos-libs/releases) is needed for dataset zarr streaming. [#8012](https://github.com/scalableminds/webknossos/pull/8012) +- Updated React to version 17. [#7765](https://github.com/scalableminds/webknossos/pull/7765) + +### Fixed +- Fixed a bug that allowed the default newly created bounding box to appear outside the dataset. In case the whole bounding box would be outside it is created regardless. [#7892](https://github.com/scalableminds/webknossos/pull/7892) +- Fixed a rare bug that could cause hanging dataset uploads. [#7932](https://github.com/scalableminds/webknossos/pull/7932) +- Fixed that comments of the active tree were not scrolled into view in some cases when switching to the comments tab. [8022](https://github.com/scalableminds/webknossos/pull/8022) +- Fixed that trashcan icons to remove layers during remote dataset upload were floating above the navbar. [#7954](https://github.com/scalableminds/webknossos/pull/7954) +- Fixed that the flood-filling action was available in the context menu although an editable mapping is active. Additionally volume related actions were removed from the context menu if only a skeleton layer is visible. [#7975](https://github.com/scalableminds/webknossos/pull/7975) +- Fixed that activating the skeleton tab would always change the active position to the active node. [#7958](https://github.com/scalableminds/webknossos/pull/7958) +- Made the newly added `filePaths` argument of the reserve upload route (see [#7981](https://github.com/scalableminds/webknossos/pull/7981)) optional to be backwards compatible with wklibs. [#8045](https://github.com/scalableminds/webknossos/pull/8045) +- Fixed that skeleton groups couldn't be collapsed or expanded in locked annotations. [#7988](https://github.com/scalableminds/webknossos/pull/7988) +- Fixed that the dashboard didn't notify the user about new datasets in the table. [#8025](https://github.com/scalableminds/webknossos/pull/8025) +- Fixed that registering segments for a bounding box did only work if the segmentation had mag 1. [#8009](https://github.com/scalableminds/webknossos/pull/8009) +- Fixed uploading datasets in neuroglancer precomputed and n5 data format. [#8008](https://github.com/scalableminds/webknossos/pull/8008) +- Various fixes for composing datasets with landmarks. Note that the interpretation of correspondence points was inverted for thin plate splines. [#7992](https://github.com/scalableminds/webknossos/pull/7992) + ## [24.07.0](https://github.com/scalableminds/webknossos/releases/tag/24.07.0) - 2024-07-05 [Commits](https://github.com/scalableminds/webknossos/compare/24.06.0...24.07.0) diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md index 49b483c4b20..6b0a7902fba 100644 --- a/CHANGELOG.unreleased.md +++ b/CHANGELOG.unreleased.md @@ -8,62 +8,13 @@ and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MIC For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md). ## Unreleased -[Commits](https://github.com/scalableminds/webknossos/compare/24.07.0...HEAD) +[Commits](https://github.com/scalableminds/webknossos/compare/24.08.0...HEAD) ### Added -- WEBKNOSSOS now automatically searches in subfolder / sub-collection identifiers for valid datasets in case a provided link to a remote dataset does not directly point to a dataset. [#7912](https://github.com/scalableminds/webknossos/pull/7912) -- Added the option to move a bounding box via dragging while pressing ctrl / meta. [#7892](https://github.com/scalableminds/webknossos/pull/7892) -- Added the option to add metadata entries to datasets and folders. The metadata can be viewed and edited in the dashboard in the right details tab.[#7886](https://github.com/scalableminds/webknossos/pull/7886) -- Added route `/import?url=` to automatically import and view remote datasets. [#7844](https://github.com/scalableminds/webknossos/pull/7844) -- Added that newly created, modified and clicked on bounding boxes are now highlighted and scrolled into view, while the bounding box tool is active. [#7935](https://github.com/scalableminds/webknossos/pull/7935) -- The configured unit in the dataset upload view is now passed to the convert_to_wkw worker job. [#7970](https://github.com/scalableminds/webknossos/pull/7970) -- Added option to expand or collapse all subgroups of a segment group in the segments tab. [#7911](https://github.com/scalableminds/webknossos/pull/7911) -- The context menu that is opened upon right-clicking a segment in the dataview port now contains the segment's name. [#7920](https://github.com/scalableminds/webknossos/pull/7920) -- Upgraded backend dependencies for improved performance and stability. [#7922](https://github.com/scalableminds/webknossos/pull/7922) -- Added Support for streaming datasets via Zarr version 3. [#7941](https://github.com/scalableminds/webknossos/pull/7941) -- It is now saved whether segment groups are collapsed or expanded, so this information doesn't get lost e.g. upon page reload. [#7928](https://github.com/scalableminds/webknossos/pull/7928/) -- It is now saved whether skeleton groups are collapsed or expanded. This information is also persisted to NML output. [#7939](https://github.com/scalableminds/webknossos/pull/7939) -- The context menu entry "Focus in Segment List" expands all necessary segment groups in the segments tab to show the highlighted segment. [#7950](https://github.com/scalableminds/webknossos/pull/7950) -- In the proofreading mode, you can enable/disable that only the active segment and the hovered segment are rendered. [#7654](https://github.com/scalableminds/webknossos/pull/7654) -- Upgraded s3 client for improved performance when loading remote datasets. [#7936](https://github.com/scalableminds/webknossos/pull/7936) -- The AI-based Quick Select can now be run on multiple sections at once. This can be configured in the tool settings. Also, the underlying model now uses Segment Anything 2. [#7965](https://github.com/scalableminds/webknossos/pull/7965) -- The AI-based Quick Select can now be triggered with a single click. Drawing a rectangle is still supported. [#7993](https://github.com/scalableminds/webknossos/pull/7993) -- To improve performance, only the visible bounding boxes are rendered in the bounding box tab (so-called virtualization). [#7974](https://github.com/scalableminds/webknossos/pull/7974) -- Added support for reading zstd-compressed zarr2 datasets [#7964](https://github.com/scalableminds/webknossos/pull/7964) -- Added the option to resume an unfinished upload event after browser restarts. [#7981](https://github.com/scalableminds/webknossos/pull/7981) -- The alignment job is in a separate tab of the "AI Tools" now. The "Align Sections" AI job now supports including manually created matches between adjacent section given as skeletons. [#7967](https://github.com/scalableminds/webknossos/pull/7967) -- Added `api.tracing.createNode(position, options)`` to the front-end API. [#7998](https://github.com/scalableminds/webknossos/pull/7998) -- Added a feature to register all segments for a given bounding box at once via the context menu of the bounding box. [#7979](https://github.com/scalableminds/webknossos/pull/7979) -- Added links in the workflow report for skipped tasks to the corresponding workflow view. [#8006](https://github.com/scalableminds/webknossos/pull/8006) -- Upgraded backend dependencies for improved performance and stability, including a memory leak fix for FossilDB. [#8014](https://github.com/scalableminds/webknossos/pull/8014) ### Changed -- Replaced skeleton tab component with antd's ``component. Added support for selecting tree ranges with SHIFT. [#7819](https://github.com/scalableminds/webknossos/pull/7819) -- The warning about a mismatch between the scale of a pre-computed mesh and the dataset scale's factor now also considers all supported mags of the active segmentation layer. This reduces the false posive rate regarding this warning. [#7921](https://github.com/scalableminds/webknossos/pull/7921/) -- It is no longer allowed to edit annotations of other organizations, even if they are set to public and to others-may-edit. [#7923](https://github.com/scalableminds/webknossos/pull/7923) -- When proofreading segmentations, the user can now interact with super-voxels directly in the data viewports. Additionally, proofreading is significantly faster because the segmentation data doesn't have to be re-downloaded after each merge/split operation. [#7654](https://github.com/scalableminds/webknossos/pull/7654) -- Changed internal data model changing an organization's name to id and its displayName to name. The previously existing id was removed. [#7386](https://github.com/scalableminds/webknossos/pull/7386) -- Because of the way our models are trained, AI analysis and training is disabled for 2D and ND datasets, as well as for color layers with data type uInt24. [#7957](https://github.com/scalableminds/webknossos/pull/7957) -- The overall performance was improved (especially for the segments tab). [#7958](https://github.com/scalableminds/webknossos/pull/7958) -- The performance for the skeleton tab was improved. [#7989](https://github.com/scalableminds/webknossos/pull/7989) -- Upgraded ant icons to version 5.4. [#8007](https://github.com/scalableminds/webknossos/pull/8007) -- Increased maximum depth for ai-based quick select from 5 to 16. [#8021](https://github.com/scalableminds/webknossos/pull/8021) -- Zarr-streaming now uses the new unit-aware voxel size. This means that [wk-libs client v0.14.25 or newer](https://github.com/scalableminds/webknossos-libs/releases) is needed for dataset zarr streaming. [#8012](https://github.com/scalableminds/webknossos/pull/8012) -- Updated React to version 17. [#7765](https://github.com/scalableminds/webknossos/pull/7765) ### Fixed -- Fixed a bug that allowed the default newly created bounding box to appear outside the dataset. In case the whole bounding box would be outside it is created regardless. [#7892](https://github.com/scalableminds/webknossos/pull/7892) -- Fixed a rare bug that could cause hanging dataset uploads. [#7932](https://github.com/scalableminds/webknossos/pull/7932) -- Fixed that comments of the active tree were not scrolled into view in some cases when switching to the comments tab. [8022](https://github.com/scalableminds/webknossos/pull/8022) -- Fixed that trashcan icons to remove layers during remote dataset upload were floating above the navbar. [#7954](https://github.com/scalableminds/webknossos/pull/7954) -- Fixed that the flood-filling action was available in the context menu although an editable mapping is active. Additionally volume related actions were removed from the context menu if only a skeleton layer is visible. [#7975](https://github.com/scalableminds/webknossos/pull/7975) -- Fixed that activating the skeleton tab would always change the active position to the active node. [#7958](https://github.com/scalableminds/webknossos/pull/7958) -- Made the newly added `filePaths` argument of the reserve upload route (see [#7981](https://github.com/scalableminds/webknossos/pull/7981)) optional to be backwards compatible with wklibs. [#8045](https://github.com/scalableminds/webknossos/pull/8045) -- Fixed that skeleton groups couldn't be collapsed or expanded in locked annotations. [#7988](https://github.com/scalableminds/webknossos/pull/7988) -- Fixed that the dashboard didn't notify the user about new datasets in the table. [#8025](https://github.com/scalableminds/webknossos/pull/8025) -- Fixed that registering segments for a bounding box did only work if the segmentation had mag 1. [#8009](https://github.com/scalableminds/webknossos/pull/8009) -- Fixed uploading datasets in neuroglancer precomputed and n5 data format. [#8008](https://github.com/scalableminds/webknossos/pull/8008) -- Various fixes for composing datasets with landmarks. Note that the interpretation of correspondence points was inverted for thin plate splines. [#7992](https://github.com/scalableminds/webknossos/pull/7992) ### Removed diff --git a/MIGRATIONS.released.md b/MIGRATIONS.released.md index c02fe8869e2..f5be3924160 100644 --- a/MIGRATIONS.released.md +++ b/MIGRATIONS.released.md @@ -6,6 +6,15 @@ See `MIGRATIONS.unreleased.md` for the changes which are not yet part of an offi This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`. User-facing changes are documented in the [changelog](CHANGELOG.released.md). +## [24.08.0](https://github.com/scalableminds/webknossos/releases/tag/24.08.0) - 2024-09-02 +[Commits](https://github.com/scalableminds/webknossos/compare/24.07.0...24.08.0) + +- If Segment Anything was already configured, it needs to be pointed to an endpoint that works with SAM 2. [#7965](https://github.com/scalableminds/webknossos/pull/7965) + +### Postgres Evolutions: +- [119-add-metadata-to-folders-and-datasets.sql](conf/evolutions/119-add-metadata-to-folders-and-datasets.sql) +- [120-remove-old-organization-id.sql](conf/evolutions/120-remove-old-organization-id.sql) + ## [24.07.0](https://github.com/scalableminds/webknossos/releases/tag/24.07.0) - 2024-07-05 [Commits](https://github.com/scalableminds/webknossos/compare/24.06.0...24.07.0) diff --git a/MIGRATIONS.unreleased.md b/MIGRATIONS.unreleased.md index 3278d5092bb..9b5dbe27a14 100644 --- a/MIGRATIONS.unreleased.md +++ b/MIGRATIONS.unreleased.md @@ -6,10 +6,6 @@ This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`. User-facing changes are documented in the [changelog](CHANGELOG.released.md). ## Unreleased -[Commits](https://github.com/scalableminds/webknossos/compare/24.07.0...HEAD) - -- If Segment Anything was already configured, it needs to be pointed to an endpoint that works with SAM 2. [#7965](https://github.com/scalableminds/webknossos/pull/7965) +[Commits](https://github.com/scalableminds/webknossos/compare/24.08.0...HEAD) ### Postgres Evolutions: -- [119-add-metadata-to-folders-and-datasets.sql](conf/evolutions/119-add-metadata-to-folders-and-datasets.sql) -- [120-remove-old-organization-id.sql](conf/evolutions/120-remove-old-organization-id.sql)