Merge pull request #1256 from effigies/enh/cifti-constants

ENH: Expand CIFTI2 constants to use a synonym recoder
nipy · Sep 22, 2023 · 4e7ad07 · 4e7ad07
2 parents 590b226 + 20bffc3
commit 4e7ad07
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Showing 2 changed files with 63 additions and 38 deletions.
diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
@@ -30,7 +30,7 @@
 from ..filebasedimages import FileBasedHeader, SerializableImage
 from ..nifti1 import Nifti1Extensions
 from ..nifti2 import Nifti2Header, Nifti2Image
-from ..volumeutils import make_dt_codes
+from ..volumeutils import Recoder, make_dt_codes
 
 
 def _float_01(val):
@@ -80,39 +80,64 @@ class Cifti2HeaderError(Exception):
     'RADIAN',
 )
 
-CIFTI_BRAIN_STRUCTURES = (
-    'CIFTI_STRUCTURE_ACCUMBENS_LEFT',
-    'CIFTI_STRUCTURE_ACCUMBENS_RIGHT',
-    'CIFTI_STRUCTURE_ALL_WHITE_MATTER',
-    'CIFTI_STRUCTURE_ALL_GREY_MATTER',
-    'CIFTI_STRUCTURE_AMYGDALA_LEFT',
-    'CIFTI_STRUCTURE_AMYGDALA_RIGHT',
-    'CIFTI_STRUCTURE_BRAIN_STEM',
-    'CIFTI_STRUCTURE_CAUDATE_LEFT',
-    'CIFTI_STRUCTURE_CAUDATE_RIGHT',
-    'CIFTI_STRUCTURE_CEREBELLAR_WHITE_MATTER_LEFT',
-    'CIFTI_STRUCTURE_CEREBELLAR_WHITE_MATTER_RIGHT',
-    'CIFTI_STRUCTURE_CEREBELLUM',
-    'CIFTI_STRUCTURE_CEREBELLUM_LEFT',
-    'CIFTI_STRUCTURE_CEREBELLUM_RIGHT',
-    'CIFTI_STRUCTURE_CEREBRAL_WHITE_MATTER_LEFT',
-    'CIFTI_STRUCTURE_CEREBRAL_WHITE_MATTER_RIGHT',
-    'CIFTI_STRUCTURE_CORTEX',
-    'CIFTI_STRUCTURE_CORTEX_LEFT',
-    'CIFTI_STRUCTURE_CORTEX_RIGHT',
-    'CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_LEFT',
-    'CIFTI_STRUCTURE_DIENCEPHALON_VENTRAL_RIGHT',
-    'CIFTI_STRUCTURE_HIPPOCAMPUS_LEFT',
-    'CIFTI_STRUCTURE_HIPPOCAMPUS_RIGHT',
-    'CIFTI_STRUCTURE_OTHER',
-    'CIFTI_STRUCTURE_OTHER_GREY_MATTER',
-    'CIFTI_STRUCTURE_OTHER_WHITE_MATTER',
-    'CIFTI_STRUCTURE_PALLIDUM_LEFT',
-    'CIFTI_STRUCTURE_PALLIDUM_RIGHT',
-    'CIFTI_STRUCTURE_PUTAMEN_LEFT',
-    'CIFTI_STRUCTURE_PUTAMEN_RIGHT',
-    'CIFTI_STRUCTURE_THALAMUS_LEFT',
-    'CIFTI_STRUCTURE_THALAMUS_RIGHT',
+
+def _full_structure(struct: str):
+    """Expands STRUCT_NAME into:
+
+    STRUCT_NAME, CIFTI_STRUCTURE_STRUCT_NAME, StructName
+    """
+    return (
+        struct,
+        f'CIFTI_STRUCTURE_{struct}',
+        ''.join(word.capitalize() for word in struct.split('_')),
+    )
+
+
+CIFTI_BRAIN_STRUCTURES = Recoder(
+    (
+        # For simplicity of comparison, use the ordering from:
+        # https://github.com/Washington-University/workbench/blob/b985f5d/src/Common/StructureEnum.cxx
+        # (name,          ciftiname,                     guiname)
+        # ('CORTEX_LEFT', 'CIFTI_STRUCTURE_CORTEX_LEFT', 'CortexLeft')
+        _full_structure('CORTEX_LEFT'),
+        _full_structure('CORTEX_RIGHT'),
+        _full_structure('CEREBELLUM'),
+        _full_structure('ACCUMBENS_LEFT'),
+        _full_structure('ACCUMBENS_RIGHT'),
+        _full_structure('ALL'),
+        _full_structure('ALL_GREY_MATTER'),
+        _full_structure('ALL_WHITE_MATTER'),
+        _full_structure('AMYGDALA_LEFT'),
+        _full_structure('AMYGDALA_RIGHT'),
+        _full_structure('BRAIN_STEM'),
+        _full_structure('CAUDATE_LEFT'),
+        _full_structure('CAUDATE_RIGHT'),
+        _full_structure('CEREBELLAR_WHITE_MATTER_LEFT'),
+        _full_structure('CEREBELLAR_WHITE_MATTER_RIGHT'),
+        _full_structure('CEREBELLUM_LEFT'),
+        _full_structure('CEREBELLUM_RIGHT'),
+        _full_structure('CEREBRAL_WHITE_MATTER_LEFT'),
+        _full_structure('CEREBRAL_WHITE_MATTER_RIGHT'),
+        _full_structure('CORTEX'),
+        _full_structure('DIENCEPHALON_VENTRAL_LEFT'),
+        _full_structure('DIENCEPHALON_VENTRAL_RIGHT'),
+        _full_structure('HIPPOCAMPUS_LEFT'),
+        _full_structure('HIPPOCAMPUS_RIGHT'),
+        _full_structure('INVALID'),
+        _full_structure('OTHER'),
+        _full_structure('OTHER_GREY_MATTER'),
+        _full_structure('OTHER_WHITE_MATTER'),
+        _full_structure('PALLIDUM_LEFT'),
+        _full_structure('PALLIDUM_RIGHT'),
+        _full_structure('PUTAMEN_LEFT'),
+        _full_structure('PUTAMEN_RIGHT'),
+        ## Also commented out in connectome_wb; unclear if deprecated, planned, or what
+        # _full_structure("SUBCORTICAL_WHITE_MATTER_LEFT")
+        # _full_structure("SUBCORTICAL_WHITE_MATTER_RIGHT")
+        _full_structure('THALAMUS_LEFT'),
+        _full_structure('THALAMUS_RIGHT'),
+    ),
+    fields=('name', 'ciftiname', 'guiname'),
 )
 
 

diff --git a/nibabel/cifti2/cifti2_axes.py b/nibabel/cifti2/cifti2_axes.py
@@ -520,7 +520,7 @@ def to_cifti_brain_structure_name(name):
         ValueError: raised if the input name does not match a known anatomical structure in CIFTI-2
         """
         if name in cifti2.CIFTI_BRAIN_STRUCTURES:
-            return name
+            return cifti2.CIFTI_BRAIN_STRUCTURES.ciftiname[name]
         if not isinstance(name, str):
             if len(name) == 1:
                 structure = name[0]
@@ -554,10 +554,10 @@ def to_cifti_brain_structure_name(name):
             proposed_name = f'CIFTI_STRUCTURE_{structure.upper()}'
         else:
             proposed_name = f'CIFTI_STRUCTURE_{structure.upper()}_{orientation.upper()}'
-        if proposed_name not in cifti2.CIFTI_BRAIN_STRUCTURES:
+        if proposed_name not in cifti2.CIFTI_BRAIN_STRUCTURES.ciftiname:
             raise ValueError(
-                f'{name} was interpreted as {proposed_name}, which is not '
-                'a valid CIFTI brain structure'
+                f'{name} was interpreted as {proposed_name}, '
+                'which is not a valid CIFTI brain structure'
             )
         return proposed_name