switch from dorsal/ventral to superior/inferior

spec/ndx-anatomical-localization.extensions.yaml

@@ -16,15 +16,15 @@ groups:
         dtype: text
         required: true
       - name: x
-        doc: "One of: APLRDV, communicating the axis and direction of the x coordinate"
+        doc: "One of: APLRSI, communicating the axis and direction of the x coordinate. For dorsal/ventral use 'S/I' (superior/inferior)."
         dtype: text
         required: true
-      - name: y
-        doc: "One of: APLRDV, communicating the axis and direction of the y coordinate"
+      - name: "y"
+        doc: "One of: APLRSI, communicating the axis and direction of the y coordinate. For dorsal/ventral use 'S/I' (superior/inferior)."
         dtype: text
         required: true
       - name: z
-        doc: "One of: APLRDV, communicating the axis and direction of the z coordinate"
+        doc: "One of: APLRSI, communicating the axis and direction of the z coordinate. For dorsal/ventral use 'S/I' (superior/inferior)."
         dtype: text
         required: true
   - neurodata_type_def: AnatonicalCoordinatesTable
@@ -45,7 +45,7 @@ groups:
         neurodata_type_inc: VectorData
         doc: "The x coordinate"
         quantity: 1
-      - name: y
+      - name: "y"
         neurodata_type_inc: VectorData
         doc: "The y coordinate"
         quantity: 1

src/pynwb/ndx_anatomical_localization/__init__.py

@@ -27,31 +27,43 @@
 TempAnatonicalCoordinatesTable = get_class("AnatonicalCoordinatesTable", "ndx-anatomical-localization")
 
 
-
-
-
 @register_class("Space", "ndx-anatomical-localization")
 class Space(TempSpace):
     def __init__(self, name, space_name, origin, units, x, y, z):
-        valid_values = ["A", "P", "L", "R", "D", "V"]
-        assert x in valid_values, "x must be one of 'A', 'P', 'L', 'R', 'D', 'V'"
-        assert y in valid_values, "y must be one of 'A', 'P', 'L', 'R', 'D', 'V'"
-        assert z in valid_values, "z must be one of 'A', 'P', 'L', 'R', 'D', 'V'"
+        valid_values = ["A", "P", "L", "R", "S", "I"]
+        assert x in valid_values, "x must be one of 'A', 'P', 'L', 'R', 'S', 'I'"
+        assert y in valid_values, "y must be one of 'A', 'P', 'L', 'R', 'S', 'I'"
+        assert z in valid_values, "z must be one of 'A', 'P', 'L', 'R', 'S', 'I'"
 
-        map = dict(A="AP", P="AP", L="LR", R="LR", D="DV", V="DV")
-        new_var = [map[var] for var in (x,y,z)]
-        assert len(set(new_var)) == 3, "x, y, and z must be unique dimensions (AP, LR, DV)"
+        map = {"A": "AP", "P": "AP", "L": "LR", "R": "LR", "S": "SI", "I": "SI"}
+        new_var = [map[var] for var in (x, y, z)]
+        assert len(set(new_var)) == 3, "x, y, and z must be unique dimensions (AP, LR, SI)"
 
         super().__init__(name=name, space_name=space_name, origin=origin, units=units, x=x, y=y, z=z)
 
 
+    @classmethod
+    def get_predefined_space(cls, space_name):
+        if space_name == "CCFv3":
+            return Space(
+                name="space",
+                space_name="CCFv3",
+                origin="In the middle of the anterior commissure",
+                units="um",
+                x="R",
+                y="A",
+                z="S"
+            )
+
+
 @register_class("AnatonicalCoordinatesTable", "ndx-anatomical-localization")
 class AnatonicalCoordinatesTable(TempAnatonicalCoordinatesTable):
     def __init__(self, name, target, description, space, method):
         super().__init__(name=name, description=description, space=space, method=method)
         self.target_object.table = target
 
 
+
 # NOTE: `widgets/tetrode_series_widget.py` adds a "widget"
 # attribute to the TetrodeSeries class. This attribute is used by NWBWidgets.
 # Delete the `widgets` subpackage or the `tetrode_series_widget.py` module

src/pynwb/tests/test_anatomical_coordinates.py

@@ -19,7 +19,8 @@ def test_create_anatonical_coordinates_table():
 
 electrodes_table = mock_ElectrodeTable()
 
-space = Space(name="space", space_name="CCF", origin="origin", units="um", x="A", y="D", z="L")
+#space = Space(name="space", space_name="CCF", origin="origin", units="um", x="A", y="S", z="L")
+space = Space.get_predefined_space("CCFv3")
 
 table = AnatonicalCoordinatesTable(
     name="MyAnatonicalLocalization",