Ran two more porto sets through pipeline

extensions/chaeo/batch_jobs/20231023_Porto_Live.py

+from pathlib import Path
+
+from model_server.util import autonumber_new_directory, get_matching_files, loop_workflow
+from extensions.chaeo.ecotaxa import write_ecotaxa_tsv
+from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+from extensions.ilastik.models import IlastikPixelClassifierModel
+
+
+if __name__ == '__main__':
+    sample_id = '20231023-porto-live'
+    root = Path('c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/')
+    where_czi = (root / 'TREC_STOP_26_Porto/231023_automic/20231023-182725_Live/LowZoom').__str__()
+    where_output = autonumber_new_directory(
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0021/output',
+        'batch-output'
+    )
+
+    px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__()
+
+    params = {
+        'pxmap_threshold': 0.25,
+        'pxmap_foreground_channel': 0,
+        'segmentation_channel': 0,
+        'zmask_zindex': None,
+        'patches_channel': 2,
+        'zmask_type': 'boxes',
+        'zmask_filters': {'area': (1e3, 1e8)},
+        'zmask_expand_box_by': (128, 3),
+        'export_pixel_probabilities': True,
+        'export_2d_patches_for_training': True,
+        'draw_bounding_box_on_2d_patch': True,
+        'export_2d_patches_for_annotation': True,
+        'export_3d_patches': False,
+        'export_annotated_zstack': True,
+        'export_patch_masks': True,
+        'zmask_clip': 0.01,
+        'rgb_overlay_channels': (1, None, None),
+        'rgb_overlay_weights': (0.2, 1.0, 1.0),
+        'draw_label_on_zstack': True,
+    }
+
+    input_files = get_matching_files(where_czi, 'czi', coord_filter={})
+
+    loop_workflow(
+        input_files,
+        where_output,
+        export_patches_from_multichannel_zstack,
+        [IlastikPixelClassifierModel(params={'project_file': Path(px_ilp)})],
+        params,
+        catch_and_continue=False,
+    )
+
+    csv_path = (Path(where_output) / 'workflow_data.csv').__str__()
+    write_ecotaxa_tsv(csv_path, where_output, sample_id=sample_id, scope_id='EMBL-MS-Zeiss-LSM900')
+
+    print('Finished')
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extensions/chaeo/batch_jobs/20231026_Porto.py

+from pathlib import Path
+
+from model_server.util import autonumber_new_directory, get_matching_files, loop_workflow
+from extensions.chaeo.ecotaxa import write_ecotaxa_tsv
+from extensions.chaeo.workflows import export_patches_from_multichannel_zstack
+from extensions.ilastik.models import IlastikPixelClassifierModel
+
+
+if __name__ == '__main__':
+    sample_id = '20231026-porto'
+    root = Path('c:/Users/rhodes/projects/proj0012-trec-handoff/owncloud-sync/TREC-HD/Images/')
+    where_czi = (root / 'TREC_STOP_26_Porto/231026_automic/20231026-152512_lowzoom_data/LowZoom').__str__()
+    where_output = autonumber_new_directory(
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0022/output',
+        'batch-output'
+    )
+
+    px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0017/pxAF405_dim8bit.ilp').__str__()
+
+    params = {
+        'pxmap_threshold': 0.25,
+        'pxmap_foreground_channel': 0,
+        'segmentation_channel': 0,
+        'zmask_zindex': None,
+        'patches_channel': 2,
+        'zmask_type': 'boxes',
+        'zmask_filters': {'area': (1e3, 1e8)},
+        'zmask_expand_box_by': (128, 3),
+        'export_pixel_probabilities': True,
+        'export_2d_patches_for_training': True,
+        'draw_bounding_box_on_2d_patch': True,
+        'export_2d_patches_for_annotation': True,
+        'export_3d_patches': False,
+        'export_annotated_zstack': True,
+        'export_patch_masks': True,
+        'zmask_clip': 0.01,
+        'rgb_overlay_channels': (1, None, None),
+        'rgb_overlay_weights': (0.2, 1.0, 1.0),
+        'draw_label_on_zstack': True,
+    }
+
+    input_files = get_matching_files(where_czi, 'czi', coord_filter={})
+
+    loop_workflow(
+        input_files,
+        where_output,
+        export_patches_from_multichannel_zstack,
+        [IlastikPixelClassifierModel(params={'project_file': Path(px_ilp)})],
+        params,
+        catch_and_continue=False,
+    )
+
+    csv_path = (Path(where_output) / 'workflow_data.csv').__str__()
+    write_ecotaxa_tsv(csv_path, where_output, sample_id=sample_id, scope_id='EMBL-MS-Zeiss-LSM900')
+
+    print('Finished')
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