Use brainglobe detaults

.gitignore

@@ -1,6 +1,9 @@
 # output NWB files
 *.nwb
 
+.idea
+.vscode
+
 # generated docs
 docs/source/_format_auto_docs
 

spec/ndx-anatomical-localization.extensions.yaml

@@ -12,30 +12,40 @@ groups:
         doc: "A space in which the coordinates are defined"
   - neurodata_type_def: Space
     neurodata_type_inc: NWBContainer
-    doc: "a space"
+    doc: >
+      This class defines a space in which coordinates are defined. It defines a reference image and the orientation
+      and origin of the axes. The default space is CCFv3 with BrainGlobe coordinates."
     attributes:
       - name: "space_name"
         doc: "name of the space"
         dtype: text
         required: true
       - name: origin
-        doc: "A description of where (0,0,0) is in the space. For example, 'bregma' is a common origin for mice."
+        doc: >
+          A description of where (0,0,0) is in the space. For example, 'bregma' is a common origin for mice.
+          If omitted, it is assumed to be the corner opposite to the orientation. e.g. if the orientation is 'PIL' 
+          (posterior, inferior, left; the default), the origin is assumed to be the anterior, superior, right corner.
+          For BrainGlobe, this value is not needed, but it is needed if you want to use, for example, IBL coordinates.
         dtype: text
-        required: true
+        required: false
       - name: units
         doc: "The units of measurement for the x,y,z coordinates. For example, 'mm' for millimeters."
         dtype: text
         required: true
       - name: orientation
-        doc: "A 3-letter string. One of A,P,L,R,S,I for each of x, y, and z. For example, the most common
-          orientation is 'RAS', which means x is right, y is anterior, and z is superior (a.k.a. dorsal).
-          For dorsal/ventral use 'S/I' (superior/inferior). In the AnatomicalCoordinatesTable, an orientation of
-          'RAS' corresponds to coordinates in the order of (ML (x), AP (y), DV (z))."
+        doc: >
+          A 3-letter string. One of A,P,L,R,S,I for each of x, y, and z. For example, default is 'PIL', which means
+          x is posterior, y is inferior (i.e. ventral), and z is left. For dorsal/ventral use 'S/I' (superior/inferior).
+          The default is 'PIL', which is the standard for BrainGlobe."
         dtype: text
         required: true
+        default_value: "PIL"
   - neurodata_type_def: AnatomicalCoordinatesTable
     neurodata_type_inc: DynamicTable
-    doc: "A table for storing anatomical coordinates for rows of another table determined using a single method"
+    doc: >
+      A table for storing anatomical localization of an object in a space. This is done by referencing rows of
+      another table. This allows for the same object to be localized in multiple spaces or using multiple different
+      methods.
     links:
       - target_type: Space
         quantity: 1
@@ -67,4 +77,4 @@ groups:
         neurodata_type_inc: VectorData
         doc: "The brain region associated with the localization"
         dtype: text
-        quantity: "?"
+        quantity: "?"

spec/ndx-anatomical-localization.namespace.yaml

@@ -10,4 +10,4 @@ namespaces:
   schema:
   - namespace: core
   - source: ndx-anatomical-localization.extensions.yaml
-  version: 0.1.0
+  version: 0.2.0

src/pynwb/ndx_anatomical_localization/ndx_anatomical_localization.py

@@ -24,24 +24,28 @@ class Space(TempSpace):
     @docval(
         {"name": "name", "type": str, "doc": "name of the NWB object"},
         {"name": "space_name", "type": str, "doc": "name of the space"},
-        {
-            "name": "origin",
-            "type": str,
-            "doc": "A description of where (0,0,0) is in the space. For example, 'bregma' is a common origin for mice.",
-        },
-        {
-            "name": "units",
-            "type": str,
-            "doc": "The units of measurement for the x,y,z coordinates. For example, 'mm' for millimeters.",
-        },
-        {
-            "name": "orientation",
-            "type": str,
-            "doc": """A 3-letter string. One of A,P,L,R,S,I for each of x, y, and z. For example, the most common
-          orientation is 'RAS', which means x is right, y is anterior, and z is superior (a.k.a. dorsal).
-          For dorsal/ventral use 'S/I' (superior/inferior). In the AnatomicalCoordinatesTable, an orientation of
-          'RAS' corresponds to coordinates in the order of (ML (x), AP (y), DV (z)).""",
-        },
+        dict(
+            name="origin",
+            type=str,
+            doc="""A description of where (0,0,0) is in the space. For example, 'bregma' is a common origin for mice.
+Another approach is to use a corner of the atlas bounding box. For example, BrainGlobe uses the anterior,
+superior, right corner as the origin for all of their atlases. In this case, you would specify this as 'ASR'.
+The orientation should then be the opposite for each letter: 'PIL'. We use this as the default here.""",
+            default="ASR",
+        ),
+        dict(
+            name="units",
+            type=str,
+            doc="The units of measurement for the x,y,z coordinates. For example, 'mm' for millimeters.",
+        ),
+        dict(
+            name="orientation",
+            type=str,
+            doc="""A 3-letter string. One of A,P,L,R,S,I for each of x, y, and z. For example, default is 'PIL', which means
+x is posterior, y is inferior (i.e. ventral), and z is left. For dorsal/ventral use 'S/I' (superior/inferior).
+The default is 'PIL', which is the standard for BrainGlobe.""",
+            default="PIL",
+        ),
         allow_positional=AllowPositional.ERROR,
     )
     def __init__(self, name, space_name, origin, units, orientation):
@@ -54,6 +58,11 @@ def __init__(self, name, space_name, origin, units, orientation):
         new_var = [map[var] for var in orientation]
         assert len(set(new_var)) == 3, "orientation must be unique dimensions (AP, LR, SI)"
 
+        opposites = {"A": "P", "P": "A", "L": "R", "R": "L", "S": "I", "I": "S"}
+        if len(origin) == 3 and [x in valid_values for x in origin]:
+            for x,y in zip(origin, orientation):
+                assert x != opposites[y], "origin and orientation must be in opposite directions"
+
         super().__init__(name=name, space_name=space_name, origin=origin, units=units, orientation=orientation)
 
     @classmethod