Move ProbeInsertion from ChannelsTable to Probe

spec/ndx-extracellular-channels.extensions.yaml

@@ -126,6 +126,11 @@ groups:
     dtype: text
     doc: Identifier of the probe, usually the serial number.
     required: false
+  groups:
+  - name: probe_insertion
+    neurodata_type_inc: ProbeInsertion
+    doc: Information about the insertion of a probe into the brain.
+    quantity: '?'
   links:
   - name: probe_model
     target_type: ProbeModel
@@ -287,11 +292,6 @@ groups:
     dtype: text
     doc: The brain area of the actual contact position, e.g., "CA1".
     quantity: '?'
-  groups:
-  - name: probe_insertion
-    neurodata_type_inc: ProbeInsertion
-    doc: Information about the insertion of a probe into the brain.
-    quantity: '?'
   links:
   - name: probe
     target_type: Probe

src/pynwb/tests/test_classes.py

@@ -201,6 +201,125 @@ def getContainer(self, nwbfile: NWBFile):
         return nwbfile.devices["Neuropixels 1.0 Probe Model"]
 
 
+class TestProbeInsertion(TestCase):
+    """Simple unit test for creating a ProbeInsertion."""
+
+    def test_constructor_minimal(self):
+        pi = ProbeInsertion()
+        assert pi.name == "probe_insertion"
+        assert pi.position_reference is None
+        assert pi.hemisphere is None
+        assert pi.depth_in_mm is None
+        assert pi.insertion_position_ap_in_mm is None
+        assert pi.insertion_position_ml_in_mm is None
+        assert pi.insertion_position_dv_in_mm is None
+        assert pi.insertion_angle_roll_in_deg is None
+        assert pi.insertion_angle_pitch_in_deg is None
+        assert pi.insertion_angle_yaw_in_deg is None
+
+    def test_constructor_with_depth(self):
+        pi = ProbeInsertion(
+            name="ProbeInsertion",  # test custom name
+            position_reference="Bregma at the cortical surface.",
+            hemisphere="left",
+            depth_in_mm=10.0,
+            insertion_position_ap_in_mm=2.0,
+            insertion_position_ml_in_mm=-4.0,
+            insertion_angle_roll_in_deg=-10.0,
+            insertion_angle_pitch_in_deg=0.0,
+            insertion_angle_yaw_in_deg=0.0,
+        )
+
+        assert pi.name == "ProbeInsertion"
+        assert pi.position_reference == "Bregma at the cortical surface."
+        assert pi.hemisphere == "left"
+        assert pi.depth_in_mm == 10.0
+        assert pi.insertion_position_ap_in_mm == 2.0
+        assert pi.insertion_position_ml_in_mm == -4.0
+        assert pi.insertion_position_dv_in_mm is None
+        assert pi.insertion_angle_roll_in_deg == -10.0
+        assert pi.insertion_angle_pitch_in_deg == 0.0
+        assert pi.insertion_angle_yaw_in_deg == 0.0
+
+    def test_constructor_with_dv(self):
+        """Test creating a ProbeInsertion with insertion_position_dv_in_mm instead of depth_in_mm"""
+        pi = ProbeInsertion(
+            name="ProbeInsertion",  # test custom name
+            position_reference="Bregma at the cortical surface.",
+            hemisphere="left",
+            insertion_position_ap_in_mm=2.0,
+            insertion_position_ml_in_mm=-4.0,
+            insertion_position_dv_in_mm=-10.0,
+            insertion_angle_roll_in_deg=-10.0,
+            insertion_angle_pitch_in_deg=0.0,
+            insertion_angle_yaw_in_deg=0.0,
+        )
+
+        assert pi.name == "ProbeInsertion"
+        assert pi.position_reference == "Bregma at the cortical surface."
+        assert pi.hemisphere == "left"
+        assert pi.depth_in_mm is None
+        assert pi.insertion_position_ap_in_mm == 2.0
+        assert pi.insertion_position_ml_in_mm == -4.0
+        assert pi.insertion_position_dv_in_mm == -10.0
+        assert pi.insertion_angle_roll_in_deg == -10.0
+        assert pi.insertion_angle_pitch_in_deg == 0.0
+        assert pi.insertion_angle_yaw_in_deg == 0.0
+
+
+class TestProbeInsertionDepthRoundTrip(NWBH5IOFlexMixin, TestCase):
+    """Simple roundtrip test for a ProbeInsertion."""
+
+    def getContainerType(self):
+        return "ProbeInsertion"
+
+    def addContainer(self):
+        pi = ProbeInsertion(
+            name="ProbeInsertion",  # test custom name
+            position_reference="Bregma at the cortical surface.",
+            hemisphere="left",
+            depth_in_mm=10.0,
+            insertion_position_ap_in_mm=2.0,
+            insertion_position_ml_in_mm=-4.0,
+            insertion_angle_roll_in_deg=-10.0,
+            insertion_angle_pitch_in_deg=0.0,
+            insertion_angle_yaw_in_deg=0.0,
+        )
+
+        # put this in nwbfile.scratch for testing
+        self.nwbfile.add_scratch(pi)
+
+    def getContainer(self, nwbfile: NWBFile):
+        return nwbfile.scratch["ProbeInsertion"]
+
+
+class TestProbeInsertionDVRoundTrip(NWBH5IOFlexMixin, TestCase):
+    """Simple roundtrip test for a ProbeInsertion with insertion_position_dv_in_mm instead of depth_in_mm."""
+
+    def getContainerType(self):
+        return "ProbeInsertion"
+
+    def addContainer(self):
+        pi = ProbeInsertion(
+            name="ProbeInsertion",  # test custom name
+            position_reference="Bregma at the cortical surface.",
+            hemisphere="left",
+            depth_in_mm=10.0,
+            insertion_position_ap_in_mm=2.0,
+            insertion_position_ml_in_mm=-4.0,
+            insertion_position_dv_in_mm=-10.0,
+            insertion_angle_roll_in_deg=-10.0,
+            insertion_angle_pitch_in_deg=0.0,
+            insertion_angle_yaw_in_deg=0.0,
+        )
+
+        # put this in nwbfile.scratch for testing
+        self.nwbfile.add_scratch(pi)
+
+    def getContainer(self, nwbfile: NWBFile):
+        return nwbfile.scratch["ProbeInsertion"]
+
+
 class TestProbe(TestCase):
     """Simple unit test for creating a Probe."""
 
@@ -230,9 +349,13 @@ def test_constructor_minimal(self):
         assert probe.name == "Neuropixels Probe 1"
         assert probe.identifier is None
         assert probe.probe_model is pm
+        assert probe.probe_insertion is None
 
     def test_constructor(self):
         """Test that the constructor for ProbeModel sets values as expected."""
+        # NOTE: ProbeInsertion must be named "probe_insertion" when used in Probe. this is the default.
+        pi = ProbeInsertion()
+
         ct = ContactsTable(
             description="Test contacts table",
         )
@@ -253,9 +376,12 @@ def test_constructor(self):
             name="Neuropixels Probe 1",
             identifier="28948291",
             probe_model=pm,
+            probe_insertion=pi,
         )
 
         assert probe.identifier == "28948291"
+        assert probe.probe_insertion is pi
+        assert probe.probe_model is pm
 
 
 class TestProbeRoundTrip(NWBH5IOFlexMixin, TestCase):
@@ -265,6 +391,9 @@ def getContainerType(self):
         return "Probe"
 
     def addContainer(self):
+        # NOTE: ProbeInsertion must be named "probe_insertion" when used in Probe. this is the default.
+        pi = ProbeInsertion()
+
         ct = ContactsTable(
             description="Test contacts table",
         )
@@ -290,6 +419,7 @@ def addContainer(self):
             name="Neuropixels Probe 1",
             identifier="28948291",
             probe_model=pm,
+            probe_insertion=pi,
         )
         self.nwbfile.add_device(probe)
 
@@ -331,123 +461,6 @@ def _create_test_probe():
     return probe
 
 
-class TestProbeInsertion(TestCase):
-    """Simple unit test for creating a ProbeInsertion."""
-
-    def test_constructor_minimal(self):
-        pi = ProbeInsertion()
-        assert pi.name == "probe_insertion"
-        assert pi.position_reference is None
-        assert pi.hemisphere is None
-        assert pi.depth_in_mm is None
-        assert pi.insertion_position_ap_in_mm is None
-        assert pi.insertion_position_ml_in_mm is None
-        assert pi.insertion_position_dv_in_mm is None
-        assert pi.insertion_angle_roll_in_deg is None
-        assert pi.insertion_angle_pitch_in_deg is None
-        assert pi.insertion_angle_yaw_in_deg is None
-
-    def test_constructor_with_depth(self):
-        pi = ProbeInsertion(
-            name="ProbeInsertion",  # test custom name
-            position_reference="Bregma at the cortical surface.",
-            hemisphere="left",
-            depth_in_mm=10.0,
-            insertion_position_ap_in_mm=2.0,
-            insertion_position_ml_in_mm=-4.0,
-            insertion_angle_roll_in_deg=-10.0,
-            insertion_angle_pitch_in_deg=0.0,
-            insertion_angle_yaw_in_deg=0.0,
-        )
-
-        assert pi.name == "ProbeInsertion"
-        assert pi.position_reference == "Bregma at the cortical surface."
-        assert pi.hemisphere == "left"
-        assert pi.depth_in_mm == 10.0
-        assert pi.insertion_position_ap_in_mm == 2.0
-        assert pi.insertion_position_ml_in_mm == -4.0
-        assert pi.insertion_position_dv_in_mm is None
-        assert pi.insertion_angle_roll_in_deg == -10.0
-        assert pi.insertion_angle_pitch_in_deg == 0.0
-        assert pi.insertion_angle_yaw_in_deg == 0.0
-
-    def test_constructor_with_dv(self):
-        pi = ProbeInsertion(
-            name="ProbeInsertion",  # test custom name
-            position_reference="Bregma at the cortical surface.",
-            hemisphere="left",
-            insertion_position_ap_in_mm=2.0,
-            insertion_position_ml_in_mm=-4.0,
-            insertion_position_dv_in_mm=-10.0,
-            insertion_angle_roll_in_deg=-10.0,
-            insertion_angle_pitch_in_deg=0.0,
-            insertion_angle_yaw_in_deg=0.0,
-        )
-
-        assert pi.name == "ProbeInsertion"
-        assert pi.position_reference == "Bregma at the cortical surface."
-        assert pi.hemisphere == "left"
-        assert pi.insertion_position_ap_in_mm == 2.0
-        assert pi.insertion_position_ml_in_mm == -4.0
-        assert pi.insertion_position_dv_in_mm == -10.0
-        assert pi.insertion_angle_roll_in_deg == -10.0
-        assert pi.insertion_angle_pitch_in_deg == 0.0
-        assert pi.insertion_angle_yaw_in_deg == 0.0
-
-
-class TestProbeInsertionDepthRoundTrip(NWBH5IOFlexMixin, TestCase):
-    """Simple roundtrip test for a ProbeInsertion."""
-
-    def getContainerType(self):
-        return "ProbeInsertion"
-
-    def addContainer(self):
-        pi = ProbeInsertion(
-            name="ProbeInsertion",  # test custom name
-            position_reference="Bregma at the cortical surface.",
-            hemisphere="left",
-            depth_in_mm=10.0,
-            insertion_position_ap_in_mm=2.0,
-            insertion_position_ml_in_mm=-4.0,
-            insertion_angle_roll_in_deg=-10.0,
-            insertion_angle_pitch_in_deg=0.0,
-            insertion_angle_yaw_in_deg=0.0,
-        )
-
-        # put this in nwbfile.scratch for testing
-        self.nwbfile.add_scratch(pi)
-
-    def getContainer(self, nwbfile: NWBFile):
-        return nwbfile.scratch["ProbeInsertion"]
-
-
-class TestProbeInsertionDVRoundTrip(NWBH5IOFlexMixin, TestCase):
-    """Simple roundtrip test for a ProbeInsertion."""
-
-    def getContainerType(self):
-        return "ProbeInsertion"
-
-    def addContainer(self):
-        pi = ProbeInsertion(
-            name="ProbeInsertion",  # test custom name
-            position_reference="Bregma at the cortical surface.",
-            hemisphere="left",
-            depth_in_mm=10.0,
-            insertion_position_ap_in_mm=2.0,
-            insertion_position_ml_in_mm=-4.0,
-            insertion_position_dv_in_mm=-10.0,
-            insertion_angle_roll_in_deg=-10.0,
-            insertion_angle_pitch_in_deg=0.0,
-            insertion_angle_yaw_in_deg=0.0,
-        )
-
-        # put this in nwbfile.scratch for testing
-        self.nwbfile.add_scratch(pi)
-
-    def getContainer(self, nwbfile: NWBFile):
-        return nwbfile.scratch["ProbeInsertion"]
-
-
 class TestChannelsTable(TestCase):
     """Simple unit test for creating a ChannelsTable."""
 
@@ -501,8 +514,6 @@ def test_constructor_add_row_with_reference(self):
     def test_constructor_add_row(self):
         """Test that the constructor for ChannelsTable sets values as expected."""
         probe = _create_test_probe()
-        # NOTE: ProbeInsertion must be named "probe_insertion" when used in ChannelsTable. this is the default.
-        pi = ProbeInsertion()
 
         ct = ChannelsTable(
             name="Neuropixels1ChannelsTable",  # test custom name
@@ -512,7 +523,6 @@ def test_constructor_add_row(self):
             position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
             position_confirmation_method="Histology",
             probe=probe,
-            probe_insertion=pi,
         )
 
         ct.add_row(
@@ -550,7 +560,6 @@ def test_constructor_add_row(self):
         assert ct.position_reference == "(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface."
         assert ct.position_confirmation_method == "Histology"
         assert ct.probe is probe
-        assert ct.probe_insertion is pi
         assert len(ct) == 2
         assert ct["contact"].data == [0, 1]
         assert ct["contact"].table is probe.probe_model.contacts_table
@@ -578,10 +587,6 @@ def addContainer(self):
         self.nwbfile.add_device(probe.probe_model)  # TODO change to add_device_model after integration in core
         self.nwbfile.add_device(probe)
 
-        pi = ProbeInsertion(
-            name="probe_insertion",
-        )
-
         ct = ChannelsTable(
             name="Neuropixels1ChannelsTable",  # test custom name
             description="Test channels table",
@@ -590,7 +595,6 @@ def addContainer(self):
             position_reference="(AP, ML, DV) = (0, 0, 0) corresponds to bregma at the cortical surface.",
             position_confirmation_method="Histology",
             probe=probe,
-            probe_insertion=pi,
         )
 
         ct.add_row(