Add back ProbeModel.model, remove 1D contour case

spec/ndx-extracellular-channels.extensions.yaml

@@ -89,18 +89,17 @@ groups:
     default_value: 2
     doc: dimension of the probe
     required: false
+  - name: model
+    dtype: text
+    doc: Name of the model of the probe, e.g., 'Neuropixels 1.0'.
   - name: planar_contour_in_um
     dtype: float
     dims:
-    - - num_points
-      - x
     - - num_points
       - x, y
     - - num_points
       - x, y, z
     shape:
-    - - null
-      - 1
     - - null
       - 2
     - - null

src/pynwb/ndx_extracellular_channels/io.py

@@ -203,6 +203,7 @@ def _single_probe_to_ndx_probe(
     probe_model = ndx_extracellular_channels.ProbeModel(
         name=model_name,
         manufacturer=probe.manufacturer,
+        model=model_name,
         ndim=probe.ndim,
         planar_contour_in_um=probe.probe_planar_contour * conversion_factor,
         contacts_table=contacts_table,

src/pynwb/tests/test_classes.py

@@ -137,6 +137,7 @@ def test_constructor(self):
         pm = ProbeModel(
             name="Neuropixels 1.0",
             description="A neuropixels probe",
+            model="Neuropixels 1.0",
             manufacturer="IMEC",
             # TODO make planar_contour_in_um optional
             planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
@@ -169,6 +170,7 @@ def addContainer(self):
         pm = ProbeModel(
             name="Neuropixels 1.0",
             description="A neuropixels probe",
+            model="Neuropixels 1.0",
             manufacturer="IMEC",
             planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
             contacts_table=ct,
@@ -197,6 +199,7 @@ def test_constructor_minimal(self):
         pm = ProbeModel(
             name="Neuropixels 1.0",
             description="A neuropixels probe",
+            model="Neuropixels 1.0",
             manufacturer="IMEC",
             planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
             contacts_table=ct,
@@ -224,6 +227,7 @@ def test_constructor(self):
         pm = ProbeModel(
             name="Neuropixels 1.0",
             description="A neuropixels probe",
+            model="Neuropixels 1.0",
             manufacturer="IMEC",
             planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
             contacts_table=ct,
@@ -256,6 +260,7 @@ def addContainer(self):
         pm = ProbeModel(
             name="Neuropixels 1.0",
             description="A neuropixels probe",
+            model="Neuropixels 1.0",
             manufacturer="IMEC",
             planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
             contacts_table=ct,
@@ -297,6 +302,7 @@ def _create_test_probe():
     pm = ProbeModel(
         name="Neuropixels 1.0",
         description="A neuropixels probe",
+        model="Neuropixels 1.0",
         manufacturer="IMEC",
         planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
         contacts_table=ct,

src/pynwb/tests/test_example_usage_all.py

@@ -55,6 +55,7 @@
 pm = ProbeModel(
     name="Neuropixels 1.0",
     description="A neuropixels probe",
+    model="neuropixels 1.0",
     manufacturer="IMEC",
     planar_contour_in_um=[[-10.0, -10.0], [10.0, -10.0], [10.0, 10.0], [-10.0, 10.0]],
     contacts_table=contacts_table,

src/spec/create_extension_spec.py

@@ -167,6 +167,14 @@ def main():
         attributes=[
             # inherits name, description, manufacturer from Device
             NWBAttributeSpec(name="ndim", doc="dimension of the probe", dtype="int", default_value=2),
+            NWBAttributeSpec(
+                # although the ProbeModel also has a name attribute, the name must be unique across all
+                # devices in the NWB file, and users may decide to use a more descriptive name than just
+                # the model name
+                name="model",
+                doc="Name of the model of the probe, e.g., 'Neuropixels 1.0'.",
+                dtype="text",
+            ),
             NWBAttributeSpec(
                 name="planar_contour_in_um",  # TODO should this just be "contour"?
                 doc=("The coordinates of the nodes of the polygon that describe the shape (contour) of the probe, "
@@ -175,8 +183,8 @@ def main():
                      "See 'probe_planar_contour' in "
                      "https://probeinterface.readthedocs.io/en/main/format_spec.html for more details."),
                 dtype="float",
-                dims=[["num_points", "x"], ["num_points", "x, y"], ["num_points", "x, y, z"]],
-                shape=[[None, 1], [None, 2], [None, 3]],
+                dims=[["num_points", "x, y"], ["num_points", "x, y, z"]],
+                shape=[[None, 2], [None, 3]],
             ),
         ],
     )