Merge pull request #957 from fractal-analytics-platform/roi_table_index

Add safety check for masked loading of ROI tables to support ngio masked ROI tables

Author: jluethi

CHANGELOG.md

@@ -1,5 +1,9 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
+# 1.5.2
+* Library
+    * Update masked loading wrapper to support loading masking ROIs written by ngio (\#957).
+
 # 1.5.1
 * Tasks:
     * In `Convert Cellvoyager to OME-Zarr` & `Convert Cellvoyager Multiplexing to OME-Zarr` tasks, handle unset window start & end better (\#953).

fractal_tasks_core/masked_loading.py

@@ -105,10 +105,14 @@ def _preprocess_input(
 
     # Check that ROI_table.obs has the right column and extract label_value
     if column_name not in ROI_table.obs.columns:
-        raise ValueError(
-            'In _preprocess_input, "{column_name}" '
-            f" missing in {ROI_table.obs.columns=}"
-        )
+        if ROI_table.obs.index.name == column_name:
+            # Workaround for new ngio table
+            ROI_table.obs[column_name] = ROI_table.obs.index
+        else:
+            raise ValueError(
+                f"In _preprocess_input, {column_name=} "
+                f" missing in {ROI_table.obs.columns=}"
+            )
     label_value = int(
         float(ROI_table.obs[column_name].iloc[ROI_positional_index])
     )