fix reorder and do not accept it with auto_extract_entities

UNFmontreal · Jul 17, 2024 · 66c62cd · 66c62cd
1 parent 892f8aa
commit 66c62cd
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Showing 4 changed files with 14 additions and 5 deletions.
diff --git a/dcm2bids/cli/dcm2bids.py b/dcm2bids/cli/dcm2bids.py
@@ -47,17 +47,19 @@ def _build_arg_parser():
                    default=DEFAULT.output_dir,
                    help="Output BIDS directory. [%(default)s]")
 
-    p.add_argument("--auto_extract_entities",
+    g = p.add_mutually_exclusive_group()
+    g.add_argument("--auto_extract_entities",
                    action='store_true',
                    help="If set, it will automatically try to extract entity"
                    "information [task, dir, echo] based on the suffix and datatype."
                    " [%(default)s]")
 
-    p.add_argument("--do_not_reorder_entities",
+    g.add_argument("--do_not_reorder_entities",
                    action='store_true',
                    help="If set, it will not reorder entities according to the relative "
                         "ordering indicated in the BIDS specification and use the "
-                        "order defined in custom_entities by the user."
+                        "order defined in custom_entities by the user.\n"
+                        "Cannot be used with --auto_extract_entities. "
                         " [%(default)s]")
 
     p.add_argument("--bids_validate",

diff --git a/dcm2bids/dcm2bids_gen.py b/dcm2bids/dcm2bids_gen.py
@@ -62,6 +62,11 @@ def __init__(
         self.logLevel = log_level
         self.logger = logging.getLogger(__name__)
 
+        if self.auto_extract_entities and self.do_not_reorder_entities:
+            raise ValueError("Auto extract entities is set to True and "
+                              "do not reorder entities is set to True. "
+                              "Please choose only one option.")
+
     @property
     def dicom_dirs(self):
         """List of DICOMs directories"""

diff --git a/dcm2bids/sidecar.py b/dcm2bids/sidecar.py
@@ -460,7 +460,9 @@ def searchDcmTagEntity(self, sidecar, desc):
 
             # Keep entities asked in custom_entities
             # If dir found in custom_entities and concatenated_matches.keys we keep it
-            if "custom_entities" in desc.keys():
+            if "custom_entities" in desc.keys() and not self.auto_extract_entities:
+                entities = desc["custom_entities"]
+            elif "custom_entities" in desc.keys():
                 entities = set(concatenated_matches.keys()).intersection(set(descWithTask["custom_entities"]))
 
                 # custom_entities not a key for extractor or auto_extract_entities

diff --git a/tests/test_dcm2bids.py b/tests/test_dcm2bids.py
@@ -583,7 +583,7 @@ def test_dcm2bids_no_reorder_entities():
                       os.path.join(TEST_DATA_DIR, "config_test_no_reorder.json"),
                       bids_dir.name,
                       do_not_reorder_entities=True,
-                      auto_extract_entities=True)
+                      auto_extract_entities=False)
 
     app.run()