add MagView.get_views_on_disk() (#621)

* add deprecation note

* add MagView.get_views_on_disk()

* add changelog entry

* Update webknossos/webknossos/skeleton/__init__.py

Co-authored-by: Philipp Otto <[email protected]>

Co-authored-by: Philipp Otto <[email protected]>

Author: jstriebel

webknossos/Changelog.md

@@ -34,6 +34,8 @@ For upgrade instructions, please check the respective *Breaking Changes* section
   * `Annotation`s can now be initialized from their attributes and an optional skeleton.
   * New methods on `Annotation`: `upload`, `add_volume_layer`, `delete_volume_layer`
   * `Annotation.load()` and `annoation.save()` also works with `.nml` files.
+- Added `MagView.get_views_on_disk()` as a shortcut to turning `get_bounding_boxes_on_disk` into views.
+  [#621](https://github.com/scalableminds/webknossos-libs/pull/621)
 
 ### Changed
 

webknossos/webknossos/annotation/annotation.py

@@ -571,8 +571,8 @@ def export_volume_layer_to_dataset(
 
         if largest_segment_id is None:
             max_value = max(
-                best_mag_view.read(absolute_bounding_box=bbox).max()
-                for bbox in best_mag_view.get_bounding_boxes_on_disk()
+                view.read().max()
+                for view in best_mag_view.get_views_on_disk(read_only=True)
             )
             layer.largest_segment_id = int(max_value)
         else:

webknossos/webknossos/dataset/mag_view.py

@@ -4,7 +4,7 @@
 import warnings
 from argparse import Namespace
 from pathlib import Path
-from typing import TYPE_CHECKING, Generator, Optional, Union
+from typing import TYPE_CHECKING, Iterator, Optional, Union
 from uuid import uuid4
 
 import numpy as np
@@ -227,7 +227,7 @@ def get_view(
 
     def get_bounding_boxes_on_disk(
         self,
-    ) -> Generator[BoundingBox, None, None]:
+    ) -> Iterator[BoundingBox]:
         """
         Returns a Mag(1) bounding box for each file on disk.
 
@@ -242,6 +242,18 @@ def get_bounding_boxes_on_disk(
 
             yield BoundingBox(cube_offset, cube_size).from_mag_to_mag1(self._mag)
 
+    def get_views_on_disk(
+        self,
+        read_only: Optional[bool] = None,
+    ) -> Iterator[View]:
+        """
+        Yields a view for each file on disk, which can be used for efficient parallelization.
+        """
+        for bbox in self.get_bounding_boxes_on_disk():
+            yield self.get_view(
+                absolute_offset=bbox.topleft, size=bbox.size, read_only=read_only
+            )
+
     def compress(
         self,
         target_path: Optional[Union[str, Path]] = None,

webknossos/webknossos/skeleton/__init__.py

@@ -9,6 +9,7 @@
 
 
 def open_nml(file_path: Union[PathLike, str]) -> Skeleton:
+    """open_nml is deprecated, please use Skeleton.load instead."""
     warnings.warn(
         "[DEPRECATION] open_nml is deprecated, please use Skeleton.load instead."
     )