Fix relative_position_in_mm should be in um

README.md

@@ -171,7 +171,7 @@ classDiagram
                 columns
                 --------------------------------------
                 id : VectorData[int]
-                relative_position_in_mm : List[Tuple[float, float], Tuple[float, float, float]]
+                relative_position_in_um : List[Tuple[float, float], Tuple[float, float, float]]
                 --> reference : str, optional
                 contact_id : VectorData[str], optional
                 shank_id : VectorData[str], optional

spec/ndx-extracellular-channels.extensions.yaml

@@ -5,7 +5,7 @@ groups:
   doc: Metadata about the contacts of a probe, compatible with the ProbeInterface
     specification.
   datasets:
-  - name: relative_position_in_mm
+  - name: relative_position_in_um
     neurodata_type_inc: VectorData
     dtype: float
     dims:
@@ -18,7 +18,7 @@ groups:
       - 2
     - - null
       - 3
-    doc: Relative position of the contact in millimeters, relative to `reference`.
+    doc: Relative position of the contact in micrometers, relative to `reference`.
     attributes:
     - name: reference
       dtype: text

src/pynwb/ndx_extracellular_channels/io.py

@@ -80,7 +80,7 @@ def to_probeinterface(ndx_probe: ndx_extracellular_channels.Probe) -> probeinter
     ndx_extracellular_channels.Probe.probe_model.manufacturer -> probeinterface.Probe.manufacturer
     ndx_extracellular_channels.Probe.probe_model.ndim -> probeinterface.Probe.ndim
     ndx_extracellular_channels.Probe.probe_model.planar_contour_in_um -> probeinterface.Probe.probe_planar_contour
-    ndx_extracellular_channels.Probe.probe_model.contacts_table["relative_position_in_mm"] ->
+    ndx_extracellular_channels.Probe.probe_model.contacts_table["relative_position_in_um"] ->
         probeinterface.Probe.contact_positions
     ndx_extracellular_channels.Probe.probe_model.contacts_table["shape"] -> probeinterface.Probe.contact_shapes
     ndx_extracellular_channels.Probe.probe_model.contacts_table["contact_id"] -> probeinterface.Probe.contact_ids
@@ -121,7 +121,7 @@ def to_probeinterface(ndx_probe: ndx_extracellular_channels.Probe) -> probeinter
     possible_shape_keys = ["radius_in_um", "width_in_um", "height_in_um"]
     contacts_table = ndx_probe.probe_model.contacts_table
 
-    positions.append(contacts_table["relative_position_in_mm"][:])
+    positions.append(contacts_table["relative_position_in_um"][:])
     shapes.append(contacts_table["shape"][:])
     if "contact_id" in contacts_table.colnames:
         if contact_ids is None:
@@ -198,7 +198,7 @@ def _single_probe_to_ndx_probe(
 
     for index in np.arange(probe.get_contact_count()):
         kwargs = dict(
-            relative_position_in_mm=probe.contact_positions[index],
+            relative_position_in_um=probe.contact_positions[index],
             plane_axes=probe.contact_plane_axes[index],
             shape=contacts_arr["contact_shapes"][index],
         )

src/pynwb/tests/test_classes.py

@@ -34,7 +34,7 @@ def test_constructor_add_row(self):
 
         # for testing, mix and match different shapes. np.nan means the radius/width/height does not apply
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
             contact_id="C1",
             shank_id="shank0",
@@ -45,7 +45,7 @@ def test_constructor_add_row(self):
         )
 
         ct.add_row(
-            relative_position_in_mm=[20.0, 10.0],
+            relative_position_in_um=[20.0, 10.0],
             shape="square",
             contact_id="C2",
             shank_id="shank0",
@@ -57,13 +57,13 @@ def test_constructor_add_row(self):
 
         # TODO might be nice to put this on the constructor of ContactsTable as relative_position__reference
         # without using a custom mapper
-        ct["relative_position_in_mm"].reference = "The bottom tip of the probe"
+        ct["relative_position_in_um"].reference = "The bottom tip of the probe"
 
         assert ct.name == "ContactsTable"
         assert ct.description == "Test contacts table"
-        assert ct["relative_position_in_mm"].reference == "The bottom tip of the probe"
+        assert ct["relative_position_in_um"].reference == "The bottom tip of the probe"
 
-        assert ct["relative_position_in_mm"].data == [[10.0, 10.0], [20.0, 10.0]]
+        assert ct["relative_position_in_um"].data == [[10.0, 10.0], [20.0, 10.0]]
         assert ct["shape"].data == ["circle", "square"]
         assert ct["contact_id"].data == ["C1", "C2"]
         assert ct["shank_id"].data == ["shank0", "shank0"]
@@ -89,7 +89,7 @@ def addContainer(self):
 
         # for testing, mix and match different shapes. np.nan means the radius/width/height does not apply
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
             contact_id="C1",
             shank_id="shank0",
@@ -100,7 +100,7 @@ def addContainer(self):
         )
 
         ct.add_row(
-            relative_position_in_mm=[20.0, 10.0],
+            relative_position_in_um=[20.0, 10.0],
             shape="square",
             contact_id="C2",
             shank_id="shank0",
@@ -128,7 +128,7 @@ def test_constructor(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
         )
 
@@ -155,7 +155,7 @@ def test_constructor_no_name(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
         )
 
@@ -181,7 +181,7 @@ def addContainer(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
         )
 
@@ -329,7 +329,7 @@ def test_constructor_minimal(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
         )
 
@@ -360,7 +360,7 @@ def test_constructor(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
         )
 
@@ -398,7 +398,7 @@ def addContainer(self):
             description="Test contacts table",
         )
         ct.add_row(
-            relative_position_in_mm=[10.0, 10.0],
+            relative_position_in_um=[10.0, 10.0],
             shape="circle",
         )
 
@@ -432,15 +432,15 @@ def _create_test_probe():
         description="Test contacts table",
     )
     ct.add_row(
-        relative_position_in_mm=[10.0, 10.0],
+        relative_position_in_um=[10.0, 10.0],
         shape="circle",
     )
     ct.add_row(
-        relative_position_in_mm=[10.0, 10.0],
+        relative_position_in_um=[10.0, 10.0],
         shape="circle",
     )
     ct.add_row(
-        relative_position_in_mm=[10.0, 10.0],
+        relative_position_in_um=[10.0, 10.0],
         shape="circle",
     )
 

src/pynwb/tests/test_example_usage_all.py

@@ -30,7 +30,7 @@ def test_all_classes():
     )
     # for demonstration, mix and match different shapes. np.nan means the radius/width/height does not apply
     contacts_table.add_row(
-        relative_position_in_mm=[10.0, 10.0],
+        relative_position_in_um=[10.0, 10.0],
         contact_id="C1",
         shank_id="shank0",
         plane_axes=[[1.0, 0.0], [0.0, 1.0]],
@@ -40,7 +40,7 @@ def test_all_classes():
         height_in_um=np.nan,
     )
     contacts_table.add_row(
-        relative_position_in_mm=[20.0, 10.0],
+        relative_position_in_um=[20.0, 10.0],
         contact_id="C2",
         shank_id="shank0",
         plane_axes=[[1 / np.sqrt(2), 1 / np.sqrt(2)], [-1 / np.sqrt(2), 1 / np.sqrt(2)]],
@@ -220,7 +220,7 @@ def test_all_classes():
 
         assert read_contacts_table.name == "contacts_table"
         assert read_contacts_table.description == "Test contacts table"
-        npt.assert_array_equal(read_contacts_table["relative_position_in_mm"].data[:], [[10.0, 10.0], [20.0, 10.0]])
+        npt.assert_array_equal(read_contacts_table["relative_position_in_um"].data[:], [[10.0, 10.0], [20.0, 10.0]])
         npt.assert_array_equal(read_contacts_table["shape"].data[:], ["circle", "square"])
         npt.assert_array_equal(read_contacts_table["contact_id"].data[:], ["C1", "C2"])
         npt.assert_array_equal(read_contacts_table["shank_id"].data[:], ["shank0", "shank0"])

src/pynwb/tests/test_example_usage_probeinterface.py

@@ -113,7 +113,7 @@ def test_from_probeinterface():
         assert nwbfile.devices["probe0"].probe_model.manufacturer == "Neuronexus"
         assert nwbfile.devices["probe0"].probe_model.ndim == 2
         npt.assert_array_equal(nwbfile.devices["probe0"].probe_model.planar_contour_in_um, polygon)
-        npt.assert_allclose(nwbfile.devices["probe0"].probe_model.contacts_table.relative_position_in_mm, positions)
+        npt.assert_allclose(nwbfile.devices["probe0"].probe_model.contacts_table.relative_position_in_um, positions)
         npt.assert_array_equal(nwbfile.devices["probe0"].probe_model.contacts_table["shape"].data[:], "circle")
         npt.assert_array_equal(nwbfile.devices["probe0"].probe_model.contacts_table["radius_in_um"].data[:], 5.0)
 
@@ -124,7 +124,7 @@ def test_from_probeinterface():
         assert nwbfile.devices["probe1"].probe_model.ndim == 2
         npt.assert_allclose(nwbfile.devices["probe1"].probe_model.planar_contour_in_um, probe1.probe_planar_contour)
         npt.assert_allclose(
-            nwbfile.devices["probe1"].probe_model.contacts_table.relative_position_in_mm, probe1.contact_positions
+            nwbfile.devices["probe1"].probe_model.contacts_table.relative_position_in_um, probe1.contact_positions
         )
         npt.assert_array_equal(nwbfile.devices["probe1"].probe_model.contacts_table["shape"].data[:], "circle")
         npt.assert_array_equal(
@@ -138,7 +138,7 @@ def test_from_probeinterface():
         assert nwbfile.devices["probe2"].probe_model.ndim == 2
         npt.assert_allclose(nwbfile.devices["probe2"].probe_model.planar_contour_in_um, probe2.probe_planar_contour)
         npt.assert_allclose(
-            nwbfile.devices["probe2"].probe_model.contacts_table.relative_position_in_mm, probe2.contact_positions
+            nwbfile.devices["probe2"].probe_model.contacts_table.relative_position_in_um, probe2.contact_positions
         )
         npt.assert_array_equal(nwbfile.devices["probe2"].probe_model.contacts_table["shape"].data[:], "square")
         npt.assert_array_equal(
@@ -154,7 +154,7 @@ def test_from_probeinterface():
             nwbfile.devices["renamed_probe3"].probe_model.planar_contour_in_um, probe3.probe_planar_contour
         )
         npt.assert_allclose(
-            nwbfile.devices["renamed_probe3"].probe_model.contacts_table.relative_position_in_mm,
+            nwbfile.devices["renamed_probe3"].probe_model.contacts_table.relative_position_in_um,
             probe3.contact_positions,
         )
         npt.assert_array_equal(nwbfile.devices["renamed_probe3"].probe_model.contacts_table["shape"].data[:], "circle")
@@ -184,8 +184,8 @@ def test_to_probeinterface():
             description="a table with electrode contacts",
             columns=[
                 pynwb.core.VectorData(
-                    name="relative_position_in_mm",
-                    description="the relative position of the contact in mm",
+                    name="relative_position_in_um",
+                    description="the relative position of the contact in micrometers",
                     data=[
                         (0.0, 0.0),
                         (0.0, 20.0),
@@ -241,7 +241,7 @@ def test_to_probeinterface():
     assert pi_probe0.serial_number == "0123"
     assert pi_probe0.model_name == "a1x32-edge-5mm-20-177_H32"
     assert pi_probe0.manufacturer == "Neuronexus"
-    npt.assert_array_equal(pi_probe0.contact_positions, probe_model0.contacts_table.relative_position_in_mm)
+    npt.assert_array_equal(pi_probe0.contact_positions, probe_model0.contacts_table.relative_position_in_um)
     npt.assert_array_equal(pi_probe0.contact_shapes, "circle")
     npt.assert_array_equal(pi_probe0.to_numpy()["radius"], 5.0)
 
@@ -251,7 +251,7 @@ def test_to_probeinterface():
 
     # for testing, mix and match different shapes. np.nan means the radius/width/height does not apply
     ct2.add_row(
-        relative_position_in_mm=[10.0, 10.0],
+        relative_position_in_um=[10.0, 10.0],
         shape="circle",
         contact_id="C1",
         shank_id="shank0",
@@ -261,7 +261,7 @@ def test_to_probeinterface():
         height_in_um=np.nan,
     )
     ct2.add_row(
-        relative_position_in_mm=[20.0, 10.0],
+        relative_position_in_um=[20.0, 10.0],
         shape="square",
         contact_id="C2",
         shank_id="shank0",
@@ -292,7 +292,7 @@ def test_to_probeinterface():
     assert pi_probe1.serial_number == "7890"
     assert pi_probe1.model_name == "Neuropixels 1.0"
     assert pi_probe1.manufacturer == "IMEC"
-    npt.assert_array_equal(pi_probe1.contact_positions, probe_model1.contacts_table.relative_position_in_mm)
+    npt.assert_array_equal(pi_probe1.contact_positions, probe_model1.contacts_table.relative_position_in_um)
     npt.assert_array_equal(pi_probe1.contact_shapes, ["circle", "square"])
     npt.assert_array_equal(
         pi_probe1.contact_plane_axes,
@@ -320,6 +320,6 @@ def test_to_probeinterface():
         assert pi_probe.serial_number == "0123"
         assert pi_probe.model_name == "a1x32-edge-5mm-20-177_H32"
         assert pi_probe.manufacturer == "Neuronexus"
-        npt.assert_array_equal(pi_probe.contact_positions, probe_model0.contacts_table.relative_position_in_mm)
+        npt.assert_array_equal(pi_probe.contact_positions, probe_model0.contacts_table.relative_position_in_um)
         npt.assert_array_equal(pi_probe.to_numpy()["radius"], 5.0)
         npt.assert_array_equal(pi_probe.contact_shapes, "circle")

src/spec/create_extension_spec.py

@@ -41,9 +41,9 @@ def main():
         default_name="contacts_table",
         datasets=[
             NWBDatasetSpec(
-                name="relative_position_in_mm",
+                name="relative_position_in_um",
                 neurodata_type_inc="VectorData",
-                doc="Relative position of the contact in millimeters, relative to `reference`.",
+                doc="Relative position of the contact in micrometers, relative to `reference`.",
                 dtype="float",
                 dims=[["num_contacts", "x, y"], ["num_contacts", "x, y, z"]],
                 shape=[[None, 2], [None, 3]],