add create option

Author: mzouink

cellmap_flow/blockwise/blockwise_processor.py

@@ -55,6 +55,13 @@ def __init__(self, yaml_config: str, create=True):
         if self.workers <= 1:
             logger.error("Workers should be greater than 1.")
             return
+        if "create" in self.config:
+            create = self.config["create"]
+            if isinstance(create, str):
+                logger.warning(
+                    f"Type config[create] is str = {create}, better set a bool"
+                )
+                create = create.lower() == "true"
 
         task_name = self.config["task_name"]
 
@@ -124,7 +131,9 @@ def __init__(self, yaml_config: str, create=True):
                         offset=(0, 0, 0),
                     )
                 except Exception as e:
-                    raise Exception(f"Failed to prepare {self.output_path/channel/'s0'} \n try deleting it manually and run again ! {e}")
+                    raise Exception(
+                        f"Failed to prepare {self.output_path/channel/'s0'} \n try deleting it manually and run again ! {e}"
+                    )
             else:
                 try:
                     array = open_ds(
@@ -147,8 +156,8 @@ def process_fn(self, block):
 
         chunk_data = chunk_data.astype(self.dtype)
 
-        # if self.output_arrays[0][block.write_roi].any():
-        #     return
+        if self.output_arrays[0][block.write_roi].any():
+            return
 
         for i, array in enumerate(self.output_arrays):
 

cellmap_flow/globals.py

@@ -48,7 +48,7 @@ def __repr__(self):
     def __str__(self):
         return f"Flow({self.__dict__})"
 
-    def get_output_dtype(self,model_output_dtype=None):
+    def get_output_dtype(self, model_output_dtype=None):
         dtype = np.float32
 
         if model_output_dtype is not None:

cellmap_flow/tmp.py

@@ -0,0 +1,7 @@
+# %%
+dataset_name = (
+    "/Users/zouinkhim/Desktop/cellmap/cellmap-flow/tests/script_test/dummy.zarr/raw"
+)
+from cellmap_flow.image_data_interface import ImageDataInterface
+
+x = ImageDataInterface(dataset_name)