Add chunk and shard shape to CLI convert command options. (#1150)

* Add chunk and shard shape to CLI convert command options.

* Update changelog.

* Add comment for regex in from_str method.

Author: markbader

webknossos/Changelog.md

@@ -19,6 +19,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 
 ### Changed
 - Added options `--layer-name` and `--mag` for compress command of the CLI. [#1141](https://github.com/scalableminds/webknossos-libs/pull/1141)
+- Added options `--chunk-shape` and `--chunks-per-shard` for convert command of the CLI. [#1150](https://github.com/scalableminds/webknossos-libs/pull/1150)
 
 ### Fixed
 - Fixed issue with webknossos URL and context URL being considered different when opening a remote dataset due to trailing slashes. [#1137](https://github.com/scalableminds/webknossos-libs/pull/1137)

webknossos/examples/upsample_skeleton.py

@@ -13,7 +13,7 @@ def main() -> None:
     """
     Scales a skeleton by a given factor. The factor is applied to the voxel size and the node positions.
 
-    This can be usefull when the skeletons are created in a downsampled version and need to be scaled back to the finest mag.
+    This can be useful when the skeletons are created in a downsampled version and need to be scaled back to the finest mag.
     """
     skeleton = wk.Skeleton.load(INPUT_PATH)
 

webknossos/webknossos/cli/convert.py

@@ -9,6 +9,7 @@
 
 from webknossos.dataset.length_unit import LengthUnit
 from webknossos.dataset.properties import DEFAULT_LENGTH_UNIT_STR, VoxelSize
+from webknossos.geometry.vec3_int import Vec3Int
 
 from ..dataset import DataFormat, Dataset
 from ..utils import get_executor_for_args
@@ -80,6 +81,24 @@ def main(
             "(if not provided, final component of target path is used)"
         ),
     ] = None,
+    chunk_shape: Annotated[
+        Optional[str],
+        typer.Option(
+            help="Chunk shape of the target dataset. Should be a comma separated string "
+            "(e.g. 64,64,64).",
+            parser=Vec3Int.from_str,
+            metavar="Vec3Int",
+        ),
+    ] = None,
+    chunks_per_shard: Annotated[
+        Optional[str],
+        typer.Option(
+            help="Shard shape of the target dataset. Should be a comma separated string "
+            "(e.g. 64,64,64).",
+            parser=Vec3Int.from_str,
+            metavar="Vec3Int",
+        ),
+    ] = None,
     compress: Annotated[
         bool, typer.Option(help="Enable compression of the target dataset.")
     ] = False,
@@ -121,6 +140,8 @@ def main(
             target,
             name=name,
             voxel_size_with_unit=voxel_size_with_unit,
+            chunk_shape=chunk_shape,  # type: ignore
+            chunks_per_shard=chunks_per_shard,  # type: ignore
             data_format=data_format,
             executor=executor,
             compress=compress,

webknossos/webknossos/geometry/vec3_int.py

@@ -110,8 +110,12 @@ def from_vec_or_int(vec_or_int: Union["Vec3IntLike", int]) -> "Vec3Int":
 
     @staticmethod
     def from_str(string: str) -> "Vec3Int":
-        if re.match(r"\(\d+,\d+,\d+\)", string):
+        if re.match(r"^\(\d+,\d+,\d+\)$", string):
+            # matches a string that consists of three comma-separated digits in parentheses
             return Vec3Int(tuple(map(int, re.findall(r"\d+", string))))
+        elif re.match(r"^\d+,\d+,\d+$", string):
+            # matches a string that consists of three digits separated by commas
+            return Vec3Int(tuple(map(int, string.split(","))))
 
         return Vec3Int.full(int(string))