refactor(clean-pixels): command 'clean-pixels' with --type dicom

Author: WillForan

deid/main/__init__.py

@@ -159,7 +159,7 @@ def get_parser():
         required=True,
     )
 
-    pixels = subparsers.add_parser("pixels", help="Clean dicom: scrub burn in pixels")
+    pixels = subparsers.add_parser("clean-pixels", help="Clean dicom: scrub burn in pixels")
     pixels.add_argument(
         "--input",
         dest="input",
@@ -174,6 +174,13 @@ def get_parser():
         type=str,
         default=None,
     )
+    pixels.add_argument(
+        "--type",
+        dest="type",
+        help="Input type. Currently only dicom supported.",
+        choices=['dicom'],
+        default="dicom",
+    )
 
     return parser
 
@@ -202,7 +209,7 @@ def main():
         from .identifiers import main
     elif args.command == "inspect":
         from .inspect import main
-    elif args.command == "pixels":
+    elif args.command == "clean-pixels":
         from .pixels import main
 
     else:

deid/tests/test_cli.py

@@ -53,7 +53,7 @@ def test_deidmain_write_identifiers(self):
 
     @patch(
         "sys.argv",
-        "deid --outfolder out/ pixels --deid deid.cfg --input ./".split(" "),
+        "deid --outfolder out/ clean-pixels --deid deid.cfg --input ./".split(" "),
     )
     def test_deidmain_clean_pixels(self):
         """