Fix duplicate probe_id field in ProbeGroup.to_numpy(complete=True)

doc/release_notes.rst

@@ -6,6 +6,7 @@ Release notes
 .. toctree::
    :maxdepth: 1
 
+   releases/0.4.2.rst
    releases/0.4.1.rst
    releases/0.4.0.rst
    releases/0.3.2.rst

doc/releases/0.4.2.rst

@@ -0,0 +1,9 @@
+probeinterface 0.4.2
+--------------------
+
+Oct, 16th 2026
+
+
+Bug fixes
+^^^^^^^^^
+* Fix duplicate ``probe_id`` field in ``ProbeGroup.to_numpy(complete=True)`` (#473)

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "probeinterface"
-version = "0.4.1"
+version = "0.4.2"
 authors = [
   { name="Samuel Garcia", email="sam.garcia.die@gmail.com" },
   { name="Alessio Buccino", email="alessiop.buccino@gmail.com" },

src/probeinterface/probegroup.py

@@ -144,12 +144,14 @@ def to_numpy(self, complete: bool = False) -> np.ndarray:
 
         # loop over probes to get all fields
         dtype = [("probe_index", "int64"), ("probe_id", "U100")]
+        # set by the probegroup: skip same-named contact annotations (e.g. from files saved with probeinterface<0.4)
+        group_fields = [name for name, _ in dtype]
         fields = []
         for probe_index, probe in enumerate(self.probes):
             arr = probe.to_numpy(complete=complete)
             probe_arr.append(arr)
             for k in arr.dtype.fields:
-                if k not in fields:
+                if k not in fields and k not in group_fields:
                     fields.append(k)
                     dtype += [(k, arr.dtype.fields[k][0])]
 

tests/test_probegroup.py

@@ -53,6 +53,22 @@ def test_probegroup_3d():
     assert probegroup.ndim == 3
 
 
+def test_to_numpy_with_probe_id_contact_annotation():
+    """A 'probe_id' contact annotation (e.g. from files saved with probeinterface<0.4) must not
+    duplicate the probegroup 'probe_id' field."""
+    probegroup = ProbeGroup()
+    for i in range(2):
+        probe = generate_dummy_probe()
+        probe.move([i * 100, 0])
+        probe.annotate_contacts(probe_id=["0"] * probe.get_contact_count())
+        probegroup.add_probe(probe)
+
+    arr = probegroup.to_numpy(complete=True)
+    assert list(arr.dtype.names).count("probe_id") == 1
+    assert np.array_equal(np.unique(arr["probe_id"]), ["0", "1"])
+    ProbeGroup.from_numpy(arr)
+
+
 def test_probegroup_allows_duplicate_positions_across_probes():
     """Test that ProbeGroup allows duplicate contact positions if they are in different probes."""
     from probeinterface import ProbeGroup, Probe