Restored batch example to a working state, confirmed batch jobs run

extensions/chaeo/examples/batch_run_patches.py

@@ -4,11 +4,9 @@ from model_server.util import autonumber_new_directory, get_matching_files, loop
 from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
 
 if __name__ == '__main__':
-    # where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
-    where_czi = 'c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/TREC_STOP_15_Kristineberg/230805_automic_AI_PA/20230805-122525_AI_PA_successfulrun_recognitiononPLL405cilindionas/Selection'
+    where_czi = 'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
     where_output = autonumber_new_directory(
-        # 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
-        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/output',
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
         'batch-output'
     )
 
@@ -31,7 +29,6 @@ if __name__ == '__main__':
         'export_patch_masks': True,
     }
 
-    # input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
     input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
 
     loop_workflow(
@@ -39,6 +36,7 @@ if __name__ == '__main__':
         where_output,
         export_patches_from_multichannel_zstack,
         params,
+        catch_and_continue=False,
     )
 
     print('Finished')
\ No newline at end of file

extensions/chaeo/workflows.py

@@ -23,8 +23,8 @@ def export_patches_from_multichannel_zstack(
         pxmap_threshold: float,
         pixel_class: int,
         zmask_channel: int,
-        zmask_zindex: None,  # None for MIP,
         patches_channel: int,
+        zmask_zindex: int = None,  # None for MIP,
         rescale_zmask_clip: int = None,
         mask_type: str = 'boxes',
         zmask_filters: Dict = None,