Merge pull request #352 from h-mayorquin/assertion_for_unique_positions

Check for unique positions within probe

Author: samuelgarcia

src/probeinterface/probe.py

@@ -8,6 +8,40 @@
 _possible_contact_shapes = ["circle", "square", "rect"]
 
 
+def _raise_non_unique_positions_error(positions):
+    """
+    Check for duplicate positions and raise ValueError with detailed information.
+
+    Parameters
+    ----------
+    positions : array
+        Array of positions to check for duplicates.
+
+    Raises
+    ------
+    ValueError
+        If duplicate positions are found, with detailed information about duplicates.
+    """
+    duplicates = {}
+    for index, pos in enumerate(positions):
+        pos_key = tuple(pos)
+        if pos_key in duplicates:
+            duplicates[pos_key].append(index)
+        else:
+            duplicates[pos_key] = [index]
+
+    duplicate_groups = {pos: indices for pos, indices in duplicates.items() if len(indices) > 1}
+    duplicate_info = []
+    for pos, indices in duplicate_groups.items():
+        pos_str = f"({', '.join(map(str, pos))})"
+        indices_str = f"[{', '.join(map(str, indices))}]"
+        duplicate_info.append(f"Position {pos_str} appears at indices {indices_str}")
+
+    raise ValueError(
+        f"Contact positions must be unique within a probe. Found {len(duplicate_groups)} duplicate(s): {'; '.join(duplicate_info)}"
+    )
+
+
 class Probe:
     """
     Class to handle the geometry of one probe.
@@ -279,6 +313,12 @@ def set_contacts(
         if positions.shape[1] != self.ndim:
             raise ValueError(f"positions.shape[1]: {positions.shape[1]} and ndim: {self.ndim} do not match!")
 
+        # Check for duplicate positions
+        unique_positions = np.unique(positions, axis=0)
+        positions_are_not_unique = unique_positions.shape[0] != positions.shape[0]
+        if positions_are_not_unique:
+            _raise_non_unique_positions_error(positions)
+
         self._contact_positions = positions
         n = positions.shape[0]
 

tests/test_probe.py

@@ -182,6 +182,21 @@ def test_save_to_zarr(tmp_path):
     assert probe == reloaded_probe, "Reloaded Probe object does not match the original"
 
 
+def test_position_uniqueness():
+    """Test that the error message matches the full expected string for three duplicates using pytest's match regex."""
+    import re
+
+    positions_with_dups = np.array([[0, 0], [10, 10], [0, 0], [20, 20], [0, 0], [10, 10]])
+    probe = Probe(ndim=2, si_units="um")
+    expected_error = (
+        "Contact positions must be unique within a probe. "
+        "Found 2 duplicate(s): Position (0, 0) appears at indices [0, 2, 4]; Position (10, 10) appears at indices [1, 5]"
+    )
+
+    with pytest.raises(ValueError, match=re.escape(expected_error)):
+        probe.set_contacts(positions=positions_with_dups, shapes="circle", shape_params={"radius": 5})
+
+
 if __name__ == "__main__":
     test_probe()
 

tests/test_probegroup.py

@@ -67,6 +67,31 @@ def test_probegroup_3d():
     assert probegroup.ndim == 3
 
 
+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
+    import numpy as np
+
+    # Probes have the same internal relative positions
+    positions = np.array([[0, 0], [10, 10]])
+    probe1 = Probe(ndim=2, si_units="um")
+    probe1.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
+    probe2 = Probe(ndim=2, si_units="um")
+    probe2.set_contacts(positions=positions, shapes="circle", shape_params={"radius": 5})
+
+    group = ProbeGroup()
+    group.add_probe(probe1)
+    group.add_probe(probe2)
+
+    # Should not raise any error
+    all_positions = np.vstack([p.contact_positions for p in group.probes])
+    # There are duplicates across probes, but this is allowed
+    assert (all_positions == [0, 0]).any()
+    assert (all_positions == [10, 10]).any()
+    # The group should have both probes
+    assert len(group.probes) == 2
+
+
 if __name__ == "__main__":
     test_probegroup()
     # ~ test_probegroup_3d()