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README.md

@@ -12,4 +12,4 @@ limitations under the License.
 -->
 
 # MONAI VISTA Repository
-This is the repository for VISTA3D and VISTA2D For the older VISTA2.5d code, please checkout the vista2.5d branch
+This is the repository for VISTA3D and VISTA2D For the older VISTA2.5d code, please checkout the vista2.5d branch

vista3d/README.md

@@ -128,7 +128,7 @@ Ask and answer questions on [MONAI VISTA's GitHub discussions tab](https://githu
 
 ## License
 
-The codebase is under Apache 2.0 Licence. The model weight is under special NVIDIA license. 
+The codebase is under Apache 2.0 Licence. The model weight is under special NVIDIA license.
 
 ## Reference
 

vista3d/data/README.md

@@ -81,7 +81,7 @@ The output of this step is multiple JSON files, each file corresponds
 to one dataset.
 
 ##### 2. Add label_dict.json and label_mapping.json
-Add new class indexes to `label_dict.json` and the local to global mapping to `label_mapping.json`. 
+Add new class indexes to `label_dict.json` and the local to global mapping to `label_mapping.json`.
 
 ## SupverVoxel Generation
 1. Download the segment anything repo and download the ViT-H weights

vista3d/scripts/debugger.py

@@ -123,16 +123,20 @@ def on_button_click(event, ax=ax):
             print("-- segmenting ---")
             self.generate_mask()
             print("-- done ---")
-            print("-- Note: Point only prompts will only do 128 cubic segmentation, a cropping artefact will be observed. ---")
-            print("-- Note: Point without class will be treated as supported class, which has worse zero-shot ability. Try class > 132 to perform better zeroshot. ---")
+            print(
+                "-- Note: Point only prompts will only do 128 cubic segmentation, a cropping artefact will be observed. ---"
+            )
+            print(
+                "-- Note: Point without class will be treated as supported class, which has worse zero-shot ability. Try class > 132 to perform better zeroshot. ---"
+            )
             print("-- Note: CTRL + Right Click will be adding negative points. ---")
             print(
                 "-- Note: Click points on different foreground class will cause segmentation conflicts. Clear first. ---"
             )
             print(
                 "-- Note: Click points not matching class prompts will also cause confusion. ---"
             )
-            
+
             self.update_slice(ax)
             # self.point_start = len(self.clicked_points)
 

vista3d/scripts/train.py

@@ -27,6 +27,12 @@
 import torch
 import torch.distributed as dist
 import yaml
+from data.datasets import (
+    compute_dataset_weights,
+    get_class_names,
+    get_datalist_with_dataset_name,
+    get_datalist_with_dataset_name_and_transform,
+)
 from monai import transforms
 from monai.apps.auto3dseg.auto_runner import logger
 from monai.apps.utils import DEFAULT_FMT
@@ -41,12 +47,6 @@
 from torch.utils.tensorboard import SummaryWriter
 from tqdm import tqdm
 
-from data.datasets import (
-    compute_dataset_weights,
-    get_class_names,
-    get_datalist_with_dataset_name,
-    get_datalist_with_dataset_name_and_transform,
-)
 from vista3d import vista_model_registry
 
 from .sliding_window import sliding_window_inference

vista3d/scripts/validation/build_vista3d_eval_only.py

@@ -16,7 +16,6 @@
 import numpy as np
 import torch
 from monai.metrics import compute_dice
-
 from vista3d.modeling import (
     VISTA3D2,
     Class_Mapping_Classify,

vista3d/vista3d/modeling/vista3d.py

@@ -16,7 +16,6 @@
 import torch
 import torch.nn as nn
 from monai.utils import optional_import
-
 from scripts.utils.trans_utils import convert_points_to_disc
 from scripts.utils.trans_utils import get_largest_connected_component_mask as lcc
 from scripts.utils.workflow_utils import sample_points_patch_val