Modify ambiguous naming of well_size (ref #113)

Author: tcompa

fractal/tasks/create_zarr_structure.py

@@ -187,7 +187,8 @@ def create_zarr_structure(
                 mrf_path, mlf_path
             )
             # FIXME: hardcoded
-            well_size = {"x": 2560, "y": 2160, "z": 10}
+            image_size = {"x": 2560, "y": 2160}
+            well_size_z = 10
 
         # Extract pixel sizes
         pixel_size_z = site_metadata["pixel_size_z"][0]
@@ -347,7 +348,8 @@ def create_zarr_structure(
             # Prepare and write anndata table of FOV ROIs
             FOV_ROIs_table = prepare_FOV_ROI_table(
                 site_metadata.loc[f"{row+column}"],
-                well_size=well_size,
+                image_size=image_size,
+                well_size_z=well_size_z,
             )
             group_tables = group_FOV.create_group("tables/")  # noqa: F841
             write_elem(group_tables, "FOV_ROI_table", FOV_ROIs_table)

fractal/tasks/lib_regions_of_interest.py

@@ -10,20 +10,24 @@
 
 def prepare_FOV_ROI_table(
     df: pd.DataFrame,
-    well_size: Union[Dict, None] = None,
+    image_size: Union[Dict, None] = None,
+    well_size_z: int = None,
 ) -> ad.AnnData:
-    if well_size is None:
-        raise Exception("Missing well_size arg in prepare_ROIs_table")
+
+    if image_size is None:
+        raise Exception("Missing image_size arg in prepare_ROIs_table")
+    if well_size_z is None:
+        raise Exception("Missing well_size_z arg in prepare_ROIs_table")
 
     # Reset reference values for coordinates
     df["x_micrometer"] -= df["x_micrometer"].min()
     df["y_micrometer"] -= df["y_micrometer"].min()
     df["z_micrometer"] -= df["z_micrometer"].min()
 
     # Obtain box size in physical units
-    df["len_x_micrometer"] = well_size["x"] * df["pixel_size_x"]
-    df["len_y_micrometer"] = well_size["y"] * df["pixel_size_y"]
-    df["len_z_micrometer"] = well_size["z"] * df["pixel_size_z"]
+    df["len_x_micrometer"] = image_size["x"] * df["pixel_size_x"]
+    df["len_y_micrometer"] = image_size["y"] * df["pixel_size_y"]
+    df["len_z_micrometer"] = well_size_z * df["pixel_size_z"]
 
     # Remove unused column
     df.drop("bit_depth", inplace=True, axis=1)