Update inference for changes in preprocessing.

mist/inference/main_inference.py

@@ -337,7 +337,7 @@ def test_time_inference(df,
                         no_preprocess=False,
                         output_std=False):
     config = read_json_file(config_file)
-    
+
     create_empty_dir(dest)
 
     # Set up rich progress bar
@@ -367,18 +367,15 @@ def test_time_inference(df,
                 og_ants_img = ants.image_read(image_list[0])
 
                 if no_preprocess:
-                    torch_img, _, fg_bbox, _ = convert_nifti_to_numpy(image_list, None)
+                    preprocessed_example = convert_nifti_to_numpy(image_list)
                 else:
-                    torch_img, _, fg_bbox, _ = preprocess_example(
-                        config, 
-                        image_list, 
-                        None, 
-                        False, 
-                        False, 
-                        None
+                    preprocessed_example = preprocess_example(
+                        config,
+                        image_list,
                     )
 
                 # Make image channels first and add batch dimension
+                torch_img = preprocessed_example["image"]
                 torch_img = np.transpose(torch_img, axes=(3, 0, 1, 2))
                 torch_img = np.expand_dims(torch_img, axis=0)
 
@@ -394,7 +391,7 @@ def test_time_inference(df,
                     blend_mode,
                     tta,
                     output_std,
-                    fg_bbox
+                    preprocessed_example["fg_bbox"]
                 )
 
                 # Apply postprocessing if required