Merge branch 'main' of github.com:SpikeInterface/probeinterface into add-regex-version-schema

Author: alejoe91

src/probeinterface/io.py

@@ -375,15 +375,6 @@ def write_BIDS_probe(folder: str | Path, probe_or_probegroup: Probe | ProbeGroup
         json.dump({"ProbeId": probes_dict}, f, indent=4)
 
     # Step 3: GENERATION OF CONTACTS.TSV
-    # ensure required contact identifiers are present
-    for probe in probes:
-        if probe.contact_ids is None:
-            raise ValueError(
-                "Contacts must have unique contact ids "
-                "and not None for export to BIDS probe format."
-                "Use `probegroup.auto_generate_contact_ids`."
-            )
-
     df = probegroup.to_dataframe()
     index = range(sum([p.get_contact_count() for p in probes]))
     df.rename(columns=tsv_label_map_to_BIDS, inplace=True)

src/probeinterface/probe.py

@@ -337,7 +337,10 @@ def set_contacts(
             Defines the two axes of the contact plane for each electrode.
             The third dimension corresponds to the probe `ndim` (2d or 3d).
         contact_ids: array[str] | None, default: None
-            Defines the contact ids for the contacts. If None, contact ids are not assigned.
+            Defines the contact ids for the contacts. If None, contact ids are
+            auto-generated as the zero-indexed strings ``["0", "1", ..., str(n - 1)]``
+            so a Probe always carries a stable, slice-invariant handle for each
+            contact. Pass an explicit array to override.
         shank_ids : array[str] | None, default: None
             Defines the shank ids for the contacts. If None, then
             these are assigned to a unique Shank.
@@ -379,8 +382,9 @@ def set_contacts(
         plane_axes = np.array(plane_axes)
         self._contact_plane_axes = plane_axes
 
-        if contact_ids is not None:
-            self.set_contact_ids(contact_ids)
+        if contact_ids is None:
+            contact_ids = np.arange(n).astype(str)
+        self.set_contact_ids(contact_ids)
 
         if shank_ids is None:
             # self._shank_ids = np.zeros(n, dtype=str)
@@ -567,8 +571,9 @@ def set_contact_ids(self, contact_ids: np.ndarray | list):
         """
         contact_ids = np.asarray(contact_ids)
         if np.all([c == "" for c in contact_ids]):
-            self._contact_ids = None
-            return
+            # Backward compat: previous versions serialized "unset" as empty
+            # strings. A Probe now always carries contact_ids, so regenerate.
+            contact_ids = np.arange(self.get_contact_count()).astype(str)
 
         if contact_ids.size != self.get_contact_count():
             raise ValueError(
@@ -1081,10 +1086,7 @@ def to_numpy(self, complete: bool = False) -> np.ndarray:
         if self._contact_sides is not None:
             arr["contact_sides"] = self.contact_sides
 
-        if self.contact_ids is None:
-            arr["contact_ids"] = [""] * self.get_contact_count()
-        else:
-            arr["contact_ids"] = self.contact_ids
+        arr["contact_ids"] = self.contact_ids
 
         if complete:
             arr["si_units"] = self.si_units

src/probeinterface/schema/probe.json.schema

@@ -120,7 +120,8 @@
           "annotations",
           "contact_positions",
           "contact_shapes",
-          "contact_shape_params"
+          "contact_shape_params",
+          "contact_ids"
         ],
         "additionalProperties": false
       }

tests/test_probe.py

@@ -141,6 +141,40 @@ def test_probe():
     # ~ plt.show()
 
 
+def test_set_contacts_auto_generates_contact_ids():
+    """When contact_ids is not supplied, Probe auto-generates ['0', ..., str(n-1)]."""
+    probe = Probe(ndim=2, si_units="um")
+    positions = np.array([[0, 0], [10, 0], [20, 0], [30, 0]])
+    probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
+
+    assert probe.contact_ids is not None
+    np.testing.assert_array_equal(probe.contact_ids, np.array(["0", "1", "2", "3"]))
+
+
+def test_set_contacts_respects_explicit_contact_ids():
+    """An explicit contact_ids argument is preserved verbatim."""
+    probe = Probe(ndim=2, si_units="um")
+    positions = np.array([[0, 0], [10, 0], [20, 0]])
+    probe.set_contacts(
+        positions=positions,
+        shapes="circle",
+        shape_params={"radius": 5},
+        contact_ids=["a", "b", "c"],
+    )
+
+    np.testing.assert_array_equal(probe.contact_ids, np.array(["a", "b", "c"]))
+
+
+def test_set_contact_ids_all_empty_strings_regenerates():
+    """Backward compat: older serialized probes used empty strings for 'unset'."""
+    probe = Probe(ndim=2, si_units="um")
+    positions = np.array([[0, 0], [10, 0], [20, 0]])
+    probe.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
+    probe.set_contact_ids(["", "", ""])
+
+    np.testing.assert_array_equal(probe.contact_ids, np.array(["0", "1", "2"]))
+
+
 def test_set_device_channel_indices_rejects_wrong_size():
     """Setting device_channel_indices with wrong count raises ValueError."""
     probe = Probe(ndim=2, si_units="um")