Cleanup after conversion and also do not copy source image metadata. …

…Dtype breaks masks.
NL-BioImaging · Apr 4, 2024 · d1eb12c · d1eb12c
1 parent 1786982
commit d1eb12c
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/data/SLURM_Get_Results.py b/data/SLURM_Get_Results.py
@@ -254,7 +254,7 @@ def saveImagesToOmeroAsDataset(conn, folder, client, dataset_id, new_dataset=Tru
                     source_image_id = images[0].getId()
                 except IndexError:
                     source_image_id = None
-                logger.debug(img_data.shape, dataset_id, source_image_id)
+                logger.debug(f"{img_data.shape}, {dataset_id}, {source_image_id}, {img_data.dtype}")
                 logger.debug(
                     f"B4 turning to yxzct -- Number of unique values: {np.unique(img_data)} | shape: {img_data.shape}")
 
@@ -269,12 +269,12 @@ def saveImagesToOmeroAsDataset(conn, folder, client, dataset_id, new_dataset=Tru
                     renamed = name
 
                 logger.debug(
-                    f"B4 posting to Omero -- Number of unique values: {np.unique(img_data)} | shape: {img_data.shape}")
+                    f"B4 posting to Omero -- Number of unique values: {np.unique(img_data)} | shape: {img_data.shape} | dtype: {img_data.dtype}")
                 img_id = ezomero.post_image(conn, img_data,
                                             renamed,
                                             dataset_id=dataset_id,
                                             dim_order="yxzct",
-                                            source_image_id=source_image_id,
+                                            # source_image_id=source_image_id,
                                             description=f"Result from job {job_id} | analysis {folder}")
 
                 del img_data

diff --git a/workflows/SLURM_Run_Workflow.py b/workflows/SLURM_Run_Workflow.py
@@ -284,6 +284,8 @@ def runScript():
                         slurmJob.wait_for_completion(slurmClient, conn)
                         if not slurmJob.completed():
                             raise Exception(f"Conversion is not completed: {slurmJob}")
+                        else:
+                            slurmJob.cleanup(slurmClient)
                     except Exception as e:
                         UI_messages += f" ERROR WITH CONVERTING DATA: {e}"
                         raise e