Add preprocessing output as model input

Author: davidjurado

brats/preprocessing/project/mlcube.py

@@ -16,14 +16,11 @@ def run(
         data_path: str, parameters_file: str, output_path: str
     ) -> None:
 
-        env = os.environ.copy()
-        env.update({
-            'data_path': data_path,
-            'parameters_file': parameters_file,
-            'output_path': output_path
-        })
-
-        process = subprocess.Popen("./run.sh", cwd=".", env=env)
+        cmd = f"python3 preprocess.py --data_path={data_path} \
+            --parameters_file {parameters_file} --output_path {output_path}"
+        splitted_cmd = cmd.split()
+
+        process = subprocess.Popen(splitted_cmd, cwd=".")
         process.wait()
 
 class SanityCheckTask:

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
 
 
@@ -95,6 +96,9 @@ def main():
     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")
+    copyfile(input_file, output_file)
 
 if __name__ == "__main__":
     main()