Update app.py

app.py

@@ -13,9 +13,13 @@ def run_segmentation(uploaded_file, modality):
     input_filename = f"input_{job_id}.nii.gz"
     output_folder = f"segmentations_{job_id}"
     
-
-    with open(input_filename, "wb") as f:
-        f.write(uploaded_file.read())
+    if isinstance(uploaded_file, str):
+        shutil.copy(uploaded_file, input_filename)
+    elif hasattr(uploaded_file, "read"):
+        with open(input_filename, "wb") as f:
+            f.write(uploaded_file.read())
+    else:
+        return "Invalid file input", None
     
     command = ["TotalSegmentator", "-i", input_filename, "-o", output_folder]
     if modality == "MR":
@@ -34,7 +38,6 @@ def run_segmentation(uploaded_file, modality):
                 arcname = os.path.relpath(file_path, output_folder)
                 zipf.write(file_path, arcname)
     
-
     seg_files = [os.path.join(output_folder, f) for f in os.listdir(output_folder) if f.endswith('.nii.gz')]
     if seg_files:
         seg_file = seg_files[0]
@@ -55,7 +58,6 @@ def run_segmentation(uploaded_file, modality):
     else:
         image_filename = None
 
-
     os.remove(input_filename)
     shutil.rmtree(output_folder)