Fine-tuning export job

extensions/chaeo/examples/batch_run_patches.py

 from pathlib import Path
+import re
+from time import localtime, strftime
 
 import pandas as pd
 
@@ -10,9 +12,18 @@ if __name__ == '__main__':
     where_czi = Path(
         'z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0038/AutoMic/20230906-163415/Selection'
     )
+
+    where_output_root = Path(
+        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009'
+    )
+    yyyymmdd = strftime('%Y%m%d', localtime())
+    idx = 0
+    while Path(where_output_root / f'batch-output-{yyyymmdd}-{idx:04d}').exists():
+        idx += 1
     where_output = Path(
-        'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/batch_output'
+        where_output_root / f'batch-output-{yyyymmdd}-{idx:04d}'
     )
+
     csv_args = {'mode': 'w', 'header': True} # when creating file
     px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
     px_model = IlastikPixelClassifierModel(
@@ -20,9 +31,15 @@ if __name__ == '__main__':
     )
 
     for ff in where_czi.iterdir():
+        pattern = 'Selection--W([\d]+)--P([\d]+)-T([\d]+)'
+        ma = re.match(pattern, ff.stem)
+
         print(ff)
         if not ff.suffix.upper() == '.CZI':
             continue
+        if int(ma.groups()[1]) > 10: # skip second half of set
+            continue
+
 
         result = export_patches_from_multichannel_zstack(
             input_zstack_path=where_czi/ff,
@@ -33,8 +50,8 @@ if __name__ == '__main__':
             patches_channel=4,
             where_output=where_output,
             mask_type='boxes',
-            zmask_filters={'area': (1e3, 1e5)},
-            zmask_expand_box_by=(128, 3),
+            zmask_filters={'area': (1e3, 1e8)},
+            zmask_expand_box_by=(128, 0),
         )
 
         # parse and record results
@@ -49,4 +66,4 @@ if __name__ == '__main__':
             write_accessor_data_to_file(
                 where_output / k / (ff.stem + '.tif'),
                 InMemoryDataAccessor(result['interm'][k])
-                )
+                )
\ No newline at end of file

extensions/chaeo/workflows.py

@@ -66,6 +66,7 @@ def export_patches_from_multichannel_zstack(
         zmask_meta,
         prefix=fstem,
         draw_bounding_box=True,
+        rescale_clip=0.0,
     )
     ti.click('export_patches')