Segmentation error after closing and reopening scene is fixed

MedSAM/MedSAMLite/MedSAMLite.py

@@ -683,18 +683,25 @@ def showSegmentation(self, segmentation_mask):
         seg_sitk.CopyInformation(self.img_sitk)
         sitk.WriteImage(seg_sitk, segmentation_res_file) ########## Set your segmentation output here
         loaded_seg_file = slicer.util.loadSegmentation(segmentation_res_file)
-
+        
         segment_volume = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLLabelMapVolumeNode")
         slicer.modules.segmentations.logic().ExportAllSegmentsToLabelmapNode(loaded_seg_file, segment_volume, slicer.vtkSegmentation.EXTENT_REFERENCE_GEOMETRY)
-
+        
         current_seg_group = self.widget.editor.segmentationNode()
         if current_seg_group is None:
             if self.segment_res_group is None:
                 self.segment_res_group = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
                 self.segment_res_group.SetReferenceImageGeometryParameterFromVolumeNode(self.volume_node)
             current_seg_group = self.segment_res_group
 
-        slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(segment_volume, current_seg_group)
+        try:
+            check_if_node_is_removed = slicer.util.getNode(current_seg_group.GetID()) # if scene is closed and reopend, this line will raise an error
+            slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(segment_volume, current_seg_group)
+        except:
+            self.segment_res_group = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
+            self.segment_res_group.SetReferenceImageGeometryParameterFromVolumeNode(self.volume_node)
+            slicer.modules.segmentations.logic().ImportLabelmapToSegmentationNode(segment_volume, self.segment_res_group)
+
         slicer.mrmlScene.RemoveNode(segment_volume)
         slicer.mrmlScene.RemoveNode(loaded_seg_file)
 

server/server.py

@@ -223,7 +223,6 @@ def get_image(wmin: int, wmax: int):
             image = arr
             # H, W = arr.shape[1:]  # TODO: make sure h, w not filpped  #################### This line is causing problem
             H, W = arr.shape[1:]
-            print('Line 225, H, W:', H, W, file=sys.stderr)
 
     for slice_idx in range(image.shape[0]):
     # for slice_idx in tqdm(range(4)):
@@ -267,7 +266,6 @@ def get_bbox1024(mask_1024, bbox_shift=3):
     y_min, y_max = np.min(y_indices), np.max(y_indices)
     # add perturbation to bounding box coordinates
     H, W = mask_1024.shape
-    print('Line 269, H, W:', H, W, file=sys.stderr)
     x_min = max(0, x_min - bbox_shift)
     x_max = min(W, x_max + bbox_shift)
     y_min = max(0, y_min - bbox_shift)