Merge pull request uncbiag#1 from PaulHax/cli

oai_analysis/pipeline_cli.py

@@ -0,0 +1,24 @@
+# Usage
+# python oai_analysis/pipeline_cli.py oai_analysis/data/test_data/colab_case/image_preprocessed.nii.gz OAI_results
+
+import argparse
+from pipeline import analysis_pipeline
+
+
+def main():
+    parser = argparse.ArgumentParser(description='OAI Analysis CLI')
+    parser.add_argument('input_path', type=str, help='Path to image file or directory containing DICOM series')
+    parser.add_argument('output_dir', type=str, help='Directory to make output files')
+    parser.add_argument(
+        '--no_intermediates',
+        action='store_true',
+        help='Do not write files representing intermediate steps to the output directory',
+    )
+
+    args = parser.parse_args()
+
+    analysis_pipeline(args.input_path, args.output_dir, not args.no_intermediates)
+
+
+if __name__ == '__main__':
+    main()