RF: Use a Recoder to handle forms of brain structure names

Author: effigies

nibabel/cifti2/cifti2.py

@@ -30,7 +30,9 @@
 from ..nifti2 import Nifti2Image, Nifti2Header
 from ..arrayproxy import reshape_dataobj
 from ..caret import CaretMetaData
-from ..volumeutils import make_dt_codes
+from ..volumeutils import make_dt_codes, Recoder
+from ..volumeutils import Recoder
+from warnings import warn
 
 
 def _float_01(val):
@@ -77,38 +79,62 @@ class Cifti2HeaderError(Exception):
                           'METER',
                           '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):
+    """ 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'))
 
 
 def _value_if_klass(val, klass):

nibabel/cifti2/cifti2_axes.py

@@ -502,7 +502,7 @@ 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]
@@ -536,7 +536,7 @@ 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')
         return proposed_name