test and autopipe fixed

Former-commit-id: 9cc88b1
bhklab · Dec 9, 2021 · 2aca001 · 2aca001
1 parent a27dc3c
commit 2aca001
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/imgtools/autopipeline.py b/imgtools/autopipeline.py
@@ -14,6 +14,7 @@
 import datetime
 import numpy as np
 import json
+import shutil
 ###############################################################
 # Example usage:
 # python radcure_simple.py ./data/RADCURE/data ./RADCURE_output
@@ -190,8 +191,8 @@ def save_data(self):
             with open(file) as f:
                 metadata = json.load(f)
             self.output_df.loc[subject_id, list(metadata.keys())] = list(metadata.values())
-            os.remove(file)
         self.output_df.to_csv(self.output_df_path)
+        shutil.rmtree(os.path.join(self.output_directory,".temp"))
 
     def run(self):
         """Execute the pipeline, possibly in parallel.

diff --git a/tests/test_autopipe.py b/tests/test_autopipe.py
@@ -91,6 +91,6 @@ def test_pipeline(dataset_path,modalities):
         os.remove(crawl_path)
         os.remove(json_path)
         os.remove(edge_path)
-    # shutil.rmtree(output_path_mod)
+    shutil.rmtree(output_path_mod)