Tuning parameters using boundary pixel classifier

extensions/chaeo/batch_jobs/20231023_Porto_4ch.py

@@ -23,8 +23,8 @@ if __name__ == '__main__':
     # write single-position TIF color stacks
     where_proc = Path(where_output) / 'proc'
 
-    for pos in range(0, cf.shape[cf.axes.index('S')]):
-    # for pos in [0, 50, 100, 150, 200]:
+    # for pos in range(0, cf.shape[cf.axes.index('S')]):
+    for pos in [0, 50, 100, 150, 200]:
         fname = f'{czi_filepath.stem}_p{pos:04d}.tif'
         write_accessor_data_to_file(
             where_proc / fname,
@@ -32,16 +32,16 @@ if __name__ == '__main__':
         )
         print(f'Wrote file {fname}')
 
-    px_ilp = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/ilastik/px_4ch_02.ilp').__str__()
+    px_ilp = Path('c:/Users/rhodes/projects/proj0017-ehcfm-analysis/exp0001/ilastik/px_TL_boundaries.ilp').__str__()
 
     params = {
-        'pxmap_threshold': 0.25,
+        'pxmap_threshold': 0.4,
         'pxmap_foreground_channel': 0,
-        'segmentation_channel': 0,
+        'segmentation_channel': 2,
         'zmask_zindex': None,
         'patches_channel': 2,
         'zmask_type': 'boxes',
-        'zmask_filters': {'area': (1e3, 1e8)},
+        'zmask_filters': {'area': (2e2, 1e8)},
         'zmask_expand_box_by': (128, 3),
         'export_pixel_probabilities': True,
         'export_2d_patches_for_training': True,
@@ -54,7 +54,7 @@ if __name__ == '__main__':
         'rgb_overlay_channels': (1, None, None),
         'rgb_overlay_weights': (0.2, 1.0, 1.0),
         'draw_label_on_zstack': True,
-        'pxmap_use_all_channels': True,
+        'pxmap_use_all_channels': False,
     }
 
     input_files = get_matching_files(where_proc, 'tif', coord_filter={})