Minor fixes, still can't tell if the slurm cluster is actually being …

…used...

cluster/slurm.py

@@ -25,4 +25,5 @@ def build_slurm_cluster(config: dict):
     )
 
     cluster.adapt(minimum=0, maximum=jobs)
+    #cluster.scale(jobs)
     return Client(cluster)

image/formats.py

@@ -3,7 +3,7 @@
 
 import dask.array as da
 import zarr
-from imagecodecs.numcodecs import Blosc
+from numcodecs import Blosc
 
 from skimage.io import imread
 
@@ -18,6 +18,8 @@ def validate_or_enforce_zarr(source: str, save_path: str = None, chunk_formats:
 
     :return: the zarr file as a dask array, the actual pixel sizes of the chunks
     """
+    print(os.listdir("."))
+
     if not os.path.isfile(source):
         raise ValueError("The source provided was not a valid path.")
 
@@ -32,14 +34,16 @@ def validate_or_enforce_zarr(source: str, save_path: str = None, chunk_formats:
 
         # Optional chunk size
         if not chunk_formats:
-            chunk_formats = (100, 100, 1)
+            if len(image_size) == 2:
+                chunk_formats = (100, 100)
+            else:
+                chunk_formats = (100, 100, 1)
         else:
             image_size = image.shape
             if len(image_size) == 2:
                 chunk_formats = (
                     math.ceil(image_size[0] / chunk_formats[0]),
                     math.ceil(image_size[1] / chunk_formats[1]),
-                    1
                 )
             else:
                 chunk_formats = (
@@ -63,7 +67,6 @@ def validate_or_enforce_zarr(source: str, save_path: str = None, chunk_formats:
                 chunk_formats = (
                     math.ceil(image_size[0] / chunk_formats[0]),
                     math.ceil(image_size[1] / chunk_formats[1]),
-                    1
                 )
             else:
                 chunk_formats = (

workflow/workflows.py

@@ -49,4 +49,4 @@ def run_workflow(data_path, data, directives, tile_settings, save_intermediates=
 
     # Final output
     # TODO: Better name chaining
-    output_zarr_to_directory(data, "workflow_output.zarr", data)
+    output_zarr_to_directory(data_path, "workflow_output.zarr", data)