Add batch size to convert CLI. (#1158)

* Add batch size to convert CLI.

* Update changelog.

* Adapt option's help description.

Author: markbader

webknossos/Changelog.md

@@ -21,6 +21,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - 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)
 - The `from_images` method of the `Dataset` supports directories and single files as `input_path` now. [#1152](https://github.com/scalableminds/webknossos-libs/pull/1152)
+- Added option `--batch-size` to the convert command of the CLI. [#1158](https://github.com/scalableminds/webknossos-libs/pull/1158)
 
 ### 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/webknossos/cli/convert.py

@@ -102,6 +102,15 @@ def main(
     compress: Annotated[
         bool, typer.Option(help="Enable compression of the target dataset.")
     ] = False,
+    batch_size: Annotated[
+        Optional[int],
+        typer.Option(
+            help="Number of images to be processed in one batch (influences RAM consumption). "
+            "When creating a WKW dataset, batch-size must be a multiple of chunk-shape's z dimension. "
+            "When converting to Zarr, batch-size must be a multiple of the z dimension of the "
+            "shard shape (chunk-shape x chunks-per-shard).",
+        ),
+    ] = None,
     jobs: Annotated[
         int,
         typer.Option(
@@ -146,5 +155,6 @@ def main(
             executor=executor,
             compress=compress,
             layer_name=layer_name,
+            batch_size=batch_size,
             layer_category=category.value if category else None,
         )

webknossos/webknossos/dataset/dataset.py

@@ -1161,7 +1161,7 @@ def add_layer_from_images(
         * `channel`: may be used to select a single channel, if multiple are available
         * `timepoint`: for timeseries, select a timepoint to use by specifying it as an int, starting from 0
         * `czi_channel`: may be used to select a channel for .czi images, which differs from normal color-channels
-        * `batch_size`: size to process the images, must be a multiple of the chunk-size z-axis for uncompressed and the shard-size z-axis for compressed layers, default is the chunk-size or shard-size respectively
+        * `batch_size`: size to process the images (influences RAM consumption), must be a multiple of the chunk-size z-axis for uncompressed and the shard-size z-axis for compressed layers, default is the chunk-size or shard-size respectively
         * `allow_multiple_layers`: set to `True` if timepoints or channels may result in multiple layers being added (only the first is returned)
         * `max_layers`: only applies if `allow_multiple_layers=True`, limits the number of layers added via different channels or timepoints
         * `truncate_rgba_to_rgb`: only applies if `allow_multiple_layers=True`, set to `False` to write four channels into layers instead of an RGB channel