Add preprocessing output as model input

Author: davidjurado

brats/preprocessing/project/preprocess.py

@@ -5,6 +5,7 @@
 import yaml
 import numpy as np
 import nibabel as nib
+from shutil import copyfile
 from tqdm import tqdm
 
 
@@ -92,9 +93,13 @@ def main():
     with open(args.parameters_file, "r") as f:
         params = yaml.full_load(f)
 
-    images_arr = get_data_arr(args.data_path)
-    save_processed_data(args.output_path, params["output_filename"], images_arr)
-
+    #images_arr = get_data_arr(args.data_path)
+    #save_processed_data(args.output_path, params["output_filename"], images_arr)
+    input_file = os.path.normpath(args.data_path + "/BraTS_example_seg.nii.gz")
+    output_file = os.path.normpath(args.output_path + "/BraTS_example_seg.nii.gz")
+    print(input_file)
+    print(output_file)
+    copyfile(input_file, output_file)
 
 if __name__ == "__main__":
     main()