Add cli argument for coarsest mag. (#1203)

* Add cli argument for coarsest mag.

* Update changelog.

Author: markbader

webknossos/Changelog.md

@@ -15,6 +15,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 ### Breaking Changes
 
 ### Added
+- Added `--coarsest-mag` argument to the `webknossos downsample` command. [#1203](https://github.com/scalableminds/webknossos-libs/pull/1203)
 
 ### Changed
 

webknossos/webknossos/cli/downsample.py

@@ -8,8 +8,9 @@
 from typing_extensions import Annotated
 
 from ..dataset import Dataset, SamplingModes
+from ..geometry import Mag
 from ..utils import get_executor_for_args
-from ._utils import DistributionStrategy, SamplingMode, parse_path
+from ._utils import DistributionStrategy, SamplingMode, parse_mag, parse_path
 
 
 def main(
@@ -31,6 +32,14 @@ def main(
             help="Name of the layer to downsample (if not provided, all layers are downsampled)."
         ),
     ] = None,
+    coarsest_mag: Annotated[
+        Optional[Mag],
+        typer.Option(
+            help="Mag to stop downsampling at. \
+Should be number or minus separated string (e.g. 2 or 2-2-2).",
+            parser=parse_mag,
+        ),
+    ] = None,
     jobs: Annotated[
         int,
         typer.Option(
@@ -66,9 +75,14 @@ def main(
     with get_executor_for_args(args=executor_args) as executor:
         if layer_name is None:
             dataset.downsample(
+                coarsest_mag=coarsest_mag,
                 sampling_mode=SamplingModes.parse(sampling_mode.value),
                 executor=executor,
             )
         else:
             layer = dataset.get_layer(layer_name)
-            layer.downsample(executor=executor)
+            layer.downsample(
+                coarsest_mag=coarsest_mag,
+                sampling_mode=SamplingModes.parse(sampling_mode.value),
+                executor=executor,
+            )

webknossos/webknossos/dataset/dataset.py

@@ -1929,13 +1929,15 @@ def compress(
     def downsample(
         self,
         sampling_mode: SamplingModes = SamplingModes.ANISOTROPIC,
+        coarsest_mag: Optional[Mag] = None,
         executor: Optional[Executor] = None,
     ) -> None:
         """
         Downsamples all layers that are not yet downsampled.
         """
         for layer in self.layers.values():
             layer.downsample(
+                coarsest_mag=coarsest_mag,
                 sampling_mode=sampling_mode,
                 executor=executor,
             )