Referencing fixes

ffrprep/ffrprep_cli.py

@@ -1561,8 +1561,10 @@ def get_parser():
         help=(
             "Reference channel(s) for re-referencing. Provide space-separated "
             "channel names (e.g. --ref_channels M1 M2). Use 'average' for "
-            "average reference. Comma-separated single-argument styles are "
-            "also accepted for backward compatibility (e.g. 'M1,M2')."
+            "average reference, or 'skip' if the data is already referenced "
+            "and should not be re-referenced. Comma-separated single-argument "
+            "styles are also accepted for backward compatibility (e.g. "
+            "'M1,M2')."
         ),
         nargs="+",
         type=str,
@@ -1813,6 +1815,10 @@ def parse_ref_channels(ref_str):
         # Already a sequence; ensure items are stripped and handle
         # comma-separated tokens inside any element for backward
         # compatibility (e.g. ['M1,M2'] -> ['M1','M2']).
+        if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "skip":
+            return []  # Data is already referenced; do not re-reference
+        if len(ref_str) == 1 and isinstance(ref_str[0], str) and ref_str[0].strip().lower() == "average":
+            return None  # Average reference
         out = []
         for item in ref_str:
             if isinstance(item, str) and "," in item:
@@ -1824,6 +1830,8 @@ def parse_ref_channels(ref_str):
     s = str(ref_str)
     if s.lower() == "average":
         return None  # Average reference
+    if s.lower() == "skip":
+        return []  # Data is already referenced; do not re-reference
     if "," in s:
         # Split and strip whitespace around channel names
         return [c.strip() for c in s.split(",") if c.strip()]

ffrprep/preproc.py

@@ -587,7 +587,8 @@ def reference_data(eeg_data=None, ref_channels=None):
         Channels to be used as reference. If more than one channel
         in list, the average of the channels in `ref_channels` will
         be used as the reference. If `None`, all channels will be
-        averaged as the reference.
+        averaged as the reference. If an empty list, the data is
+        marked as already referenced and is not modified.
         Default = None.
 
     Returns

ffrprep/tests/test_cli.py

@@ -220,6 +220,13 @@ def test_parse_ref_channels_average():
     assert parse_ref_channels("Average") is None
 
 
+def test_parse_ref_channels_average_from_argparse_list():
+    """--ref_channels uses nargs='+', so real CLI usage always passes a
+    list (e.g. ['average']) rather than a bare string."""
+    assert parse_ref_channels(["average"]) is None
+    assert parse_ref_channels(["AVERAGE"]) is None
+
+
 def test_parse_ref_channels_single():
     assert parse_ref_channels("Cz") == "Cz"
     assert parse_ref_channels("TP9") == "TP9"
@@ -235,6 +242,20 @@ def test_parse_ref_channels_empty_string():
     assert parse_ref_channels("") is None
 
 
+def test_parse_ref_channels_skip():
+    """'skip' normalizes to [] (data already referenced; do not modify)."""
+    assert parse_ref_channels("skip") == []
+    assert parse_ref_channels("SKIP") == []
+    assert parse_ref_channels("Skip") == []
+
+
+def test_parse_ref_channels_skip_from_argparse_list():
+    """--ref_channels uses nargs='+', so real CLI usage always passes a
+    list (e.g. ['skip']) rather than a bare string."""
+    assert parse_ref_channels(["skip"]) == []
+    assert parse_ref_channels(["SKIP"]) == []
+
+
 # ---------------------------------------------------------------------------
 # run_ffrprep — mocked end-to-end behavior
 # ---------------------------------------------------------------------------