Merge branch 'master' into add-zarrarray-as-mag

cluster_tools/Changelog.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/) `MAJOR.MIN
 For upgrade instructions, please check the respective *Breaking Changes* sections.
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.2...HEAD)
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.5...HEAD)
 
 ### Breaking Changes
 
@@ -18,6 +18,18 @@ For upgrade instructions, please check the respective *Breaking Changes* section
 ### Fixed
 
 
+## [0.15.5](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.5) - 2024-09-26
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.4...v0.15.5)
+
+
+## [0.15.4](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.4) - 2024-09-23
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.3...v0.15.4)
+
+
+## [0.15.3](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.3) - 2024-09-11
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.2...v0.15.3)
+
+
 ## [0.15.2](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.2) - 2024-09-05
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.1...v0.15.2)
 

docs/mkdocs.yml

@@ -100,6 +100,8 @@ nav:
               - webknossos-py/examples/zarr_and_dask.md
               - webknossos-py/examples/convert_4d_tiff.md
               - webknossos-py/examples/announce_dataset_upload.md
+              - webknossos-py/examples/accessing_metadata.md
+              - webknossos-py/examples/explore_and_add_remote.md
           - Annotation Examples:
               - webknossos-py/examples/apply_merger_mode.md
               - webknossos-py/examples/learned_segmenter.md
@@ -110,6 +112,7 @@ nav:
               - webknossos-py/examples/skeleton_path_length.md
               - webknossos-py/examples/upsample_skeleton.md
           - Administration Examples:
+              - webknossos-py/examples/teams_and_users.md
               - webknossos-py/examples/user_times.md
               - webknossos-py/examples/annotation_project_administration.md
       - API Reference:
@@ -125,6 +128,7 @@ nav:
               - Layer: api/webknossos/dataset/layer.md
               - MagView: api/webknossos/dataset/mag_view.md
               - View: api/webknossos/dataset/view.md
+              - RemoteFolder: api/webknossos/dataset/remote_folder.md
           - Annotation: api/webknossos/annotation/annotation.md
           - Skeleton:
               - Skeleton: api/webknossos/skeleton/skeleton.md

docs/src/webknossos-py/examples/accessing_metadata.md

@@ -0,0 +1,9 @@
+# Accessing Metadata
+
+This example show how to access and work with metadata in [remote datasets](../../api/webknossos/dataset/dataset.md#webknossos.dataset.dataset.RemoteDataset) and [remote folders](../../api/webknossos/dataset/remote_folder.md#webknossos.dataset.remote_folder.RemoteFolder).
+
+```python
+--8<--
+    webknossos/examples/accessing_metadata.py
+--8<--
+```

docs/src/webknossos-py/examples/explore_and_add_remote.md

@@ -0,0 +1,9 @@
+# Explore and add Remote Dataset
+
+This example shows how to create a [remote dataset](../../api/webknossos/dataset/dataset.md#webknossos.dataset.dataset.RemoteDataset) in webknossos from an existing Zarr dataset.
+
+```python
+--8<--
+webknossos/examples/explore_and_add_remote.py
+--8<--
+```

docs/src/webknossos-py/examples/teams_and_users.md

@@ -0,0 +1,9 @@
+# Teams and Users
+
+This example uses the [`User` class](../../api/webknossos/administration/user.md#webknossos.administration.user.User) and the [`Team` class](../../api/webknossos/administration/user.md#webknossos.administration.user.Team) to access information about the current user, all managed users and all teams this user is in. It also shows how to add a new team and assign a user as a team manager.
+
+```python
+--8<--
+webknossos/examples/teams_and_users.py
+--8<--
+```

webknossos/Changelog.md

@@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/) `MAJOR.MIN
 For upgrade instructions, please check the respective _Breaking Changes_ sections.
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.2...HEAD)
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.5...HEAD)
 
 ### Breaking Changes
 
@@ -22,6 +22,30 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Fixed
 
 
+## [0.15.5](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.5) - 2024-09-26
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.4...v0.15.5)
+
+### Added
+- Webknossos API functions were added: `Team.get_list()`, `Team.add("new_name")`, `User.assign_team_roles("teamName", isTeamManager: True)` and `RemoteDataset.explore_and_add_remote()` are available now. [#1196](https://github.com/scalableminds/webknossos-libs/pull/1196)
+
+
+## [0.15.4](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.4) - 2024-09-23
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.3...v0.15.4)
+
+### Added
+- Enable metadata access for remote datasets. [#1163](https://github.com/scalableminds/webknossos-libs/pull/1163)
+
+
+## [0.15.3](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.3) - 2024-09-11
+[Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.2...v0.15.3)
+
+### Breaking Changes
+- Conversion of images with 4 channels creates a dataset with four layers instead of a dataset with one RGB layer. [#1192](https://github.com/scalableminds/webknossos-libs/pull/1192)
+
+### Changed
+- Updated tifffile dependency to v2024.8.30. [#1190](https://github.com/scalableminds/webknossos-libs/pull/1190)
+
+
 ## [0.15.2](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.2) - 2024-09-05
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.1...v0.15.2)
 

webknossos/examples/accessing_metadata.py

@@ -0,0 +1,21 @@
+import webknossos as wk
+
+
+def main() -> None:
+    with wk.webknossos_context(url="https://webknossos.org/"):
+        l4_sample_dataset = wk.Dataset.open_remote("l4_sample")
+        # Access the metadata of the dataset
+        print(l4_sample_dataset.metadata)
+
+        # Edit the metadata of the dataset
+        l4_sample_dataset.metadata["new_key"] = "new_value"
+
+        # Access metadata of a folder
+        print(l4_sample_dataset.folder.metadata)
+
+        # Edit the metadata of the folder
+        l4_sample_dataset.folder.metadata["new_folder_key"] = "new_folder_value"
+
+
+if __name__ == "__main__":
+    main()

webknossos/examples/explore_and_add_remote.py

@@ -0,0 +1,14 @@
+import webknossos as wk
+
+
+def main() -> None:
+    # Explore a zarr dataset with webknossos by adding it as a remote dataset
+    wk.RemoteDataset.explore_and_add_remote(
+        "https://data-humerus.webknossos.org/data/zarr/b2275d664e4c2a96/HuaLab-CBA_Ca-mouse-unexposed-M1/color",
+        "Ca-mouse-unexposed-M1",
+        "/Datasets",
+    )
+
+
+if __name__ == "__main__":
+    main()

webknossos/examples/load_annotation_from_file.py

@@ -19,13 +19,16 @@ def load_annotation(annotation_file: Path) -> None:
         mag_view = segmentation_layer.get_finest_mag()
         segments = mag_view.read(absolute_bounding_box=BOUNDING_BOX)
 
+        # Drop channel dimension as it has depth 1
+        segments = segments[0]
+
         # Write segmentation IDs to an OME Tiff file
         imwrite(
             "segmentation.ome.tiff",
             segments.T,  # note, the tiff lib use different channel order
             ome=True,
             metadata={
-                "axes": "ZYXC",
+                "axes": "ZYX",
             },
         )
 

webknossos/examples/teams_and_users.py

@@ -0,0 +1,31 @@
+import webknossos as wk
+
+
+def main() -> None:
+    # Get the current user
+    current_user = wk.User.get_current_user()
+    print(
+        f"You are currently logged in as: {current_user.first_name} {current_user.last_name} ({current_user.email})."
+    )
+
+    # Get all users managed by the current user
+    all_my_users = wk.User.get_all_managed_users()
+    print("Managed users:")
+    for user in all_my_users:
+        print(f"\t{user.first_name} {user.last_name} ({user.email})")
+
+    # Get teams of current user
+    all_my_teams = wk.Team.get_list()
+    print("Teams:")
+    for team in all_my_teams:
+        print(f"\t{team.name} ({team.organization_id})")
+
+    # Add a new team
+    wk.Team.add("My new team")
+
+    # Set current user as team manager
+    current_user.assign_team_roles("My new team", is_team_manager=True)
+
+
+if __name__ == "__main__":
+    main()