Merge pull request #778 from fractal-analytics-platform/764-cellpose-task-output-roi-table-creation-performance-scaling

Fix wrong repeated overlap check for bounding-boxes in cellpose task

Author: tcompa

CHANGELOG.md

@@ -12,6 +12,7 @@
     * Refactor Cellpose Task inputs: Group advanced Cellpose parameters into the `CellposeModelParams` model that's provided via `advanced_cellpose_model_params` (\#738).
     * Refactor Cellpose Task inputs: Support independent normalization of 2 input channels in the Cellpose task (\#738).
     * Rename `task.cellpose_transforms` into `tasks.cellpose_utils` (\#738).
+    * Fix wrong repeated overlap checks for bounding-boxes in Cellpose task (\#778).
 * Development:
     * Switch to transitional pydantic.v1 imports, changes pydantic requirement to `==1.10.16` or `>=2.6.3` (\#760).
     * Support JSON-Schema generation for `Enum` task arguments (\#749).

fractal_tasks_core/tasks/cellpose_segmentation.py

@@ -541,13 +541,12 @@ def cellpose_segmentation(
 
             bbox_dataframe_list.append(bbox_df)
 
-            overlap_list = []
-            for df in bbox_dataframe_list:
-                overlap_list.extend(
-                    get_overlapping_pairs_3D(df, full_res_pxl_sizes_zyx)
-                )
+            overlap_list = get_overlapping_pairs_3D(
+                bbox_df, full_res_pxl_sizes_zyx
+            )
             if len(overlap_list) > 0:
                 logger.warning(
+                    f"ROI {indices} has "
                     f"{len(overlap_list)} bounding-box pairs overlap"
                 )