SegmentationLayer attachments (#1312)

* wip attachments

* py3.10

* implement fixes for symlinks etc

* changelog

* add Dataset.get_segmentation_layer

* add test for upload

* add name to attachments

* pr feedback

* tests + docs

* add Dataset.fs_copy_dataset

* fixes for shallow_copy_dataset

* more work on shallow and remote copies

* threadpool for copytree

* resolved path

* add add_attachments

* types

* add test for add_attachments

* detect_legacy_attachments

* make dataset_path optional in Attachment.from_path_and_name

* imports

* alter the filenames based on the attachment name in add_copy_attachments and add_symlink_attachments

* variadic

Author: normanrz

webknossos/Changelog.md

@@ -15,6 +15,9 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- Added a feature to track attached files of a segmentation layer. Previously, these files were only auto-detected by WEBKNOSSOS based on the location in special folders. Attachments can be added, e.g. `dataset.get_segmentation_layer("segmentation").attachments.add_mesh('path/to/meshfile.hdf5')`. [#1312](https://github.com/scalableminds/webknossos-libs/pull/1312)
+- Added a `with_attachments` parameter to `Dataset.copy_dataset` to copy attachments. [#1312](https://github.com/scalableminds/webknossos-libs/pull/1312)
+- Added a `get_segmentation_layer` method to `Dataset` to get a correctly-typed segmentation layer by name. [#1312](https://github.com/scalableminds/webknossos-libs/pull/1312)
 
 ### Changed
 - When adding a layer, the used dtype is only valid if it is supported by webknossos. [#1316](https://github.com/scalableminds/webknossos-libs/pull/1316)

webknossos/examples/apply_merger_mode.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import cast
 
 import fastremap
 
@@ -26,7 +25,7 @@ def main() -> None:
         bbox=wk.BoundingBox((3457, 3323, 1204), (40, 10, 10)),
         path="testoutput/l4_sample",
     )
-    in_layer = cast(wk.SegmentationLayer, dataset.get_layer("segmentation"))
+    in_layer = dataset.get_segmentation_layer("segmentation")
     in_mag1 = in_layer.get_mag("1")
 
     ##############################

webknossos/examples/download_segments.py

@@ -4,6 +4,7 @@
 import webknossos as wk
 
 ANNOTATION_ID = "634e8fe1010000b4006f3cf4"
+SEGMENTATION_LAYER_NAME = "segmentation"
 SEGMENT_IDS = [32, 667325]
 MAG = wk.Mag("8-8-2")
 
@@ -12,7 +13,7 @@ def main() -> None:
     dataset = wk.Annotation.open_as_remote_dataset(
         ANNOTATION_ID, webknossos_url="https://webknossos.org"
     )
-    mag_view = dataset.get_segmentation_layers()[0].get_mag(MAG)
+    mag_view = dataset.get_segmentation_layer(SEGMENTATION_LAYER_NAME).get_mag(MAG)
 
     z = mag_view.bounding_box.topleft.z
     with mag_view.get_buffered_slice_reader() as reader: