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ENH: Expand CIFTI2 constants to use a synonym recoder #1256

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Sep 22, 2023
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ENH: Expand CIFTI2 constants to use a synonym recoder #1256

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7071f00
ENH: Expand CIFTI2 constants to use a synonym recoder
effigies Sep 19, 2023
20bffc3
Update nibabel/cifti2/cifti2.py
effigies Sep 20, 2023
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93 changes: 59 additions & 34 deletions nibabel/cifti2/cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down Expand Up @@ -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):
"""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'),
)


Expand Down
8 changes: 4 additions & 4 deletions nibabel/cifti2/cifti2_axes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down Expand Up @@ -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

Expand Down