Elevate patch annotations to workflow params

extensions/chaeo/actual_runs/20230805_kristineberg_PA.py

@@ -39,6 +39,7 @@ if __name__ == '__main__':
         '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,

extensions/chaeo/workflows.py

@@ -31,6 +31,9 @@ def export_patches_from_multichannel_zstack(
         export_pixel_probabilities=True,
         export_2d_patches_for_training=True,
         export_2d_patches_for_annotation=True,
+        draw_bounding_box_on_2d_patch=True,
+        draw_contour_on_2d_patch=False,
+        draw_mask_on_2d_patch=False,
         export_3d_patches=True,
         export_annotated_zstack=True,
         export_patch_masks=True,
@@ -85,7 +88,7 @@ def export_patches_from_multichannel_zstack(
             zmask_meta,
             prefix=fstem,
             draw_bounding_box=False,
-            rescale_clip=0.0,
+            rescale_clip=0.001,
             make_3d=True,
         )
         ti.click('export_3d_patches')
@@ -101,11 +104,11 @@ def export_patches_from_multichannel_zstack(
             focus_metric='max_sobel',
             ch_white=patches_channel,
             ch_rgb_overlay=rgb_overlay_channels,
-            draw_bounding_box=False,
+            draw_bounding_box=draw_bounding_box_on_2d_patch,
             bounding_box_channel=1,
             bounding_box_linewidth=2,
-            # draw_contour=True,
-            draw_mask=True,
+            draw_contour=draw_contour_on_2d_patch,
+            draw_mask=draw_mask_on_2d_patch,
             overlay_gain=rgb_overlay_weights,
         )
         df_patches = pd.DataFrame(files)