adding configurable CZYX chunk size (#154)

adding chunk_czyx to config to modify the chunksize.

mantis/analysis/AnalysisSettings.py

@@ -83,6 +83,7 @@ class ConcatenateSettings(MyBaseModel):
     X_slice: Union[list[int], Literal["all"]] = "all"
     Y_slice: Union[list[int], Literal["all"]] = "all"
     Z_slice: Union[list[int], Literal["all"]] = "all"
+    chunks_czyx: Union[Literal[None], list[int]] = None
 
     @validator("concat_data_paths")
     def check_concat_data_paths(cls, v):
@@ -106,6 +107,14 @@ def check_slices(cls, v):
             raise ValueError("Slices must be 'all' or lists of two non-negative integers.")
         return v
 
+    @validator("chunks_czyx")
+    def check_chunk_size(cls, v):
+        if v is not None and (
+            not isinstance(v, list) or len(v) != 4 or not all(isinstance(i, int) for i in v)
+        ):
+            raise ValueError("chunks_czyx must be a list of 4 integers (C, Z, Y, X)")
+        return v
+
 
 class StabilizationSettings(MyBaseModel):
     stabilization_estimation_channel: str

mantis/analysis/settings/example_concatenate_settings.yml

@@ -4,3 +4,4 @@ channel_names: [all,all]  # replace "all" with e.g. "[['Retardance', 'Orientatio
 X_slice: all  # replace "all" with e.g. "[0, 100]" for cropping
 Y_slice: all  # replace "all" with e.g. "[0, 100]" for cropping
 Z_slice: all  # replace "all" with e.g. "[0, 100]" for cropping
+chunks_czyx: null  # replace "null" with e.g. "[1, 100, 100, 100]" for desired chunking [C,Z,Y,X]

mantis/cli/concatenate.py

@@ -126,10 +126,16 @@ def concatenate(config_filepath: str, output_dirpath: str, num_processes: int):
     if cropped_shape_zyx[0] > Z or cropped_shape_zyx[1] > Y or cropped_shape_zyx[2] > X:
         raise ValueError("The cropped shape is larger than the original shape.")
 
+    # TODO: make assertion for chunk size?
+    if settings.chunks_czyx is not None:
+        chunk_size = [1] + list(settings.chunks_czyx)
+    else:
+        chunk_size = settings.chunks_czyx
+
     # Logic for creation of zarr and metadata
     output_metadata = {
         "shape": (len(time_indices), len(all_channel_names)) + tuple(cropped_shape_zyx),
-        "chunks": None,
+        "chunks": chunk_size,
         "scale": (1,) * 2 + tuple(output_voxel_size),
         "channel_names": all_channel_names,
         "dtype": np.float32,