Cleaned up RGB export work

extensions/chaeo/workflows.py

@@ -78,33 +78,19 @@ def export_patches_from_multichannel_zstack(
         )
         ti.click('export_3d_patches')
 
-    # if export_2d_patches:
-    #     files = export_patches_from_zstack(
-    #         Path(where_output) / '2d_patches',
-    #         stack.get_one_channel_data(patches_channel),
-    #         zmask_meta,
-    #         prefix=fstem,
-    #         draw_bounding_box=False,
-    #         rescale_clip=0.0,
-    #         make_3d=False,
-    #         focus_metric='max_sobel',
-    #     )
-    #     ti.click('export_2d_patches')
-
     if export_2d_patches:
         files = export_multichannel_patches_from_zstack(
-            Path(where_output) / '2d_patches_chlorophyl_contour',
+            Path(where_output) / '2d_patches',
             stack,
             zmask_meta,
             prefix=fstem,
-            draw_bounding_box=False,
             rescale_clip=0.0,
             make_3d=False,
             focus_metric='max_sobel',
             ch_white=4,
             ch_rgb_overlay=(3, None, None),
-            draw_contour=True,
-            contour_channel=1,
+            draw_bounding_box=True,
+            bounding_box_channel=1,
             overlay_gain=(0.1, 1.0, 1.0)
         )
         ti.click('export_2d_patches')