Exposed patch chlorophyl overlay parameters to workflow kwargs

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
 
 from model_server.accessors import CziImageFileAccessor, write_accessor_data_to_file, InMemoryDataAccessor
 from model_server.process import rescale
@@ -25,7 +26,7 @@ if __name__ == '__main__':
         'batch-output'
     )
 
-    px_ilp = Path.home() / 'model-server' / 'ilastik' / 'AF405-bodies_boundaries.ilp'
+    px_ilp = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0016/pxAF405_dim8bit.ilp')
 
     params = {
         'ilastik_project_file': px_ilp.__str__(),
@@ -42,23 +43,36 @@ if __name__ == '__main__':
         'export_3d_patches': False,
         'export_annotated_zstack': True,
         'export_patch_masks': True,
+        'rescale_zmask_clip': 0.01,
+        'rgb_overlay_channels': (3, None, None),
+        'rgb_overlay_weights': (0.5, 1.0, 1.0)
     }
 
-    input_files = get_matching_files(where_czi, 'czi')
+    # input_files = get_matching_files(where_czi, 'czi', coord_filter={'P': (5, 10)},)
+    input_files = get_matching_files(where_czi, 'czi', coord_filter={})
+
 
     tif_export_params = {
         'channel': 0,
         'rescale_zmask_clip': 0.01,
     }
 
+    # loop_workflow(
+    #     input_files,
+    #     where_output,
+    #     export_single_channel_tif_from_multichannel_czi,
+    #     tif_export_params,
+    #     catch_and_continue=False,
+    #     export_batch_csvs=False,
+    #     write_intermediate_products=False,
+    # )
+
     loop_workflow(
         input_files,
         where_output,
-        export_single_channel_tif_from_multichannel_czi,
-        tif_export_params,
+        export_patches_from_multichannel_zstack,
+        params,
         catch_and_continue=False,
-        export_batch_csvs=False,
-        write_intermediate_products=False,
     )
 
     print('Finished')
\ No newline at end of file

extensions/chaeo/workflows.py

@@ -35,6 +35,8 @@ def export_patches_from_multichannel_zstack(
         export_3d_patches=True,
         export_annotated_zstack=True,
         export_patch_masks=True,
+        rgb_overlay_channels=(None, None, None),
+        rgb_overlay_weights=(1.0, 1.0, 1.0),
 ) -> Dict:
     ti = Timer()
     stack = generate_file_accessor(Path(input_file_path))
@@ -99,13 +101,13 @@ def export_patches_from_multichannel_zstack(
             make_3d=False,
             focus_metric='max_sobel',
             ch_white=patches_channel,
-            ch_rgb_overlay=(3, None, None),
+            ch_rgb_overlay=rgb_overlay_channels,
             draw_bounding_box=False,
             bounding_box_channel=1,
             bounding_box_linewidth=2,
             # draw_contour=True,
             draw_mask=True,
-            overlay_gain=(0.1, 1.0, 1.0)
+            overlay_gain=rgb_overlay_weights,
         )
         df_patches = pd.DataFrame(files)
         ti.click('export_2d_patches')
@@ -117,7 +119,7 @@ def export_patches_from_multichannel_zstack(
     if export_2d_patches_for_training:
         files = export_multichannel_patches_from_zstack(
             Path(output_folder_path) / '2d_patches_training',
-            stack.get_one_channel_data(4),
+            stack.get_one_channel_data(patches_channel),
             zmask_meta,
             prefix=fstem,
             rescale_clip=0.001,
@@ -127,10 +129,9 @@ def export_patches_from_multichannel_zstack(
         df_patches = pd.DataFrame(files)
         ti.click('export_2d_patches')
         # associate 2d patches, dropping labeled objects that were not exported as patches
-        df = pd.merge(df, df_patches, left_index=True, right_on='df_index').drop(columns='df_index')
+        # df = pd.merge(df, df_patches, left_index=True, right_on='df_index').drop(columns='df_index')
         # prepopulate patch UUID
-        df['patch_id'] = df.apply(lambda _: uuid4(), axis=1)
-
+        # df['patch_id'] = df.apply(lambda _: uuid4(), axis=1)
 
     if export_patch_masks:
         files = export_patch_masks_from_zstack(