Trying to run 2d kristineberg data through z-stack pipeline

extensions/chaeo/actual_runs/20230805_kristineberg_PA.py

+from pathlib import Path
+
+from extensions.chaeo.util import autonumber_new_directory, get_matching_files, loop_workflow
+from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+
+if __name__ == '__main__':
+    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_output = autonumber_new_directory(
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/output',
+        'batch-output'
+    )
+
+    px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+
+    params = {
+        'ilastik_project_file': px_ilp.__str__(),
+        'pxmap_threshold': 0.25,
+        'pixel_class': 0,
+        'zmask_channel': 0,
+        'patches_channel': 4,
+        'mask_type': 'boxes',
+        'zmask_filters': {'area': (1e3, 1e8)},
+        'zmask_expand_box_by': (128, 3),
+        'export_pixel_probabilities': True,
+        'export_2d_patches_for_training': True,
+        'export_2d_patches_for_annotation': True,
+        'export_3d_patches': False,
+        'export_annotated_zstack': True,
+        'export_patch_masks': True,
+    }
+
+    input_files = get_matching_files(where_czi, 'czi')
+
+    loop_workflow(
+        input_files,
+        where_output,
+        export_patches_from_multichannel_zstack,
+        params,
+        catch_and_continue=False,
+    )
+
+    print('Finished')
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extensions/chaeo/actual_runs/proj0004-exp0038-fixed.py

+from pathlib import Path
+
+from extensions.chaeo.util import autonumber_new_directory, get_matching_files, loop_workflow
+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_output = autonumber_new_directory(
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
+        'batch-output'
+    )
+
+    px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+
+    params = {
+        'ilastik_project_file': px_ilp.__str__(),
+        'pxmap_threshold': 0.25,
+        'pixel_class': 0,
+        'zmask_channel': 0,
+        'patches_channel': 4,
+        'mask_type': 'boxes',
+        'zmask_filters': {'area': (1e3, 1e8)},
+        'zmask_expand_box_by': (128, 3),
+        'export_pixel_probabilities': False,
+        'export_2d_patches_for_training': True,
+        'export_2d_patches_for_annotation': True,
+        'export_3d_patches': False,
+        'export_annotated_zstack': False,
+        'export_patch_masks': True,
+    }
+
+    input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (0, 10)}, )
+
+    loop_workflow(
+        input_files,
+        where_output,
+        export_patches_from_multichannel_zstack,
+        params,
+    )
+
+    print('Finished')
\ No newline at end of file

extensions/chaeo/examples/batch_run_patches.py

@@ -4,10 +4,11 @@ from extensions.chaeo.util import autonumber_new_directory, get_matching_files,
 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 = '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_output = autonumber_new_directory(
-        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
+        # 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output',
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/output',
         'batch-output'
     )
 
@@ -22,7 +23,7 @@ if __name__ == '__main__':
         'mask_type': 'boxes',
         'zmask_filters': {'area': (1e3, 1e8)},
         'zmask_expand_box_by': (128, 3),
-        'export_pixel_probabilities': False,
+        'export_pixel_probabilities': True,
         'export_2d_patches_for_training': True,
         'export_2d_patches_for_annotation': True,
         'export_3d_patches': False,
@@ -30,6 +31,7 @@ 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(

extensions/chaeo/workflows.py

@@ -38,7 +38,7 @@ def export_patches_from_multichannel_zstack(
     stack = generate_file_accessor(Path(input_zstack_path))
     fstem = Path(input_zstack_path).stem
     ti.click('file_input')
-    assert stack.nz > 1, 'Expecting z-stack'
+    # assert stack.nz > 1, 'Expecting z-stack'
 
     # MIP and classify pixels
     mip = InMemoryDataAccessor(