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

extensions/chaeo/examples/batch_run_patches.py

-from pathlib import Path
-
-from model_server.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': True,
-        '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,
-        catch_and_continue=False,
-    )
-
-    print('Finished')
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