From de78b97231b955bea7daf6707d9abf0fce4ee091 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Wed, 24 Jun 2026 14:12:21 -0600
Subject: [PATCH] channel deduplication

---
 neo/rawio/baserawio.py               | 26 ++++++++++++++++++++++----
 neo/test/rawiotest/test_axonrawio.py | 11 +++++++++++
 2 files changed, 33 insertions(+), 4 deletions(-)

diff --git a/neo/rawio/baserawio.py b/neo/rawio/baserawio.py
index 4207f3c03..2bb25f5c2 100644
--- a/neo/rawio/baserawio.py
+++ b/neo/rawio/baserawio.py
@@ -709,10 +709,28 @@ def _check_stream_signal_channel_characteristics(self):
                     f"do not have the same {_common_sig_characteristics} {unique_characteristics}"
                 )
 
-            # also check that channel_id is unique inside a stream
-            channel_ids = signal_channels[mask]["id"]
-            if np.unique(channel_ids).size != channel_ids.size:
-                raise ValueError(f"signal_channels do not have unique ids for stream {stream_index}")
+            # Channel ids must be unique inside a stream so a channel can be addressed by id
+            # (see channel_id_to_index). Some files, e.g. re-saved exports, store duplicate ids.
+            # Rather than refuse an otherwise-readable file, make the duplicates unique by
+            # suffixing them and warn, so the data stays readable and id-based selection works.
+            channel_indexes = np.flatnonzero(mask)
+            channel_ids = list(signal_channels["id"][channel_indexes])
+            if len(set(channel_ids)) != len(channel_ids):
+                used_ids = set()
+                deduplicated_ids = []
+                for channel_id in channel_ids:
+                    new_id = channel_id
+                    suffix = 0
+                    while new_id in used_ids:
+                        suffix += 1
+                        new_id = f"{channel_id}-{suffix}"
+                    used_ids.add(new_id)
+                    deduplicated_ids.append(new_id)
+                signal_channels["id"][channel_indexes] = deduplicated_ids
+                self.logger.warning(
+                    f"signal_channels in stream {stream_index} have non-unique ids; duplicates were "
+                    "made unique by suffixing so channels remain addressable by id."
+                )
 
         self._several_channel_groups = signal_streams.size > 1
 
diff --git a/neo/test/rawiotest/test_axonrawio.py b/neo/test/rawiotest/test_axonrawio.py
index a1cb7dd2b..d602d76ce 100644
--- a/neo/test/rawiotest/test_axonrawio.py
+++ b/neo/test/rawiotest/test_axonrawio.py
@@ -28,6 +28,17 @@ def test_read_raw_protocol(self):
 
         reader.read_raw_protocol()
 
+    def test_non_unique_channel_ids_are_deduplicated(self):
+        # Some ABF files (e.g. re-saved exports) store duplicate signal_channel ids. Rather than
+        # refuse an otherwise-readable file, neo makes the ids unique and warns, so the data stays
+        # readable and channels remain addressable by id.
+        path = self.get_local_path("axon/intracellular_data/files_with_errors/non_unique_channel_ids.abf")
+        reader = AxonRawIO(filename=path)
+        with self.assertLogs(reader.logger, level="WARNING"):
+            reader.parse_header()
+        channel_ids = list(reader.header["signal_channels"]["id"])
+        self.assertEqual(len(channel_ids), len(set(channel_ids)))
+
 
 if __name__ == "__main__":
     unittest.main()