brainhops.datamodel.enums

Enumerations shared across the data model, such as interpolation orders and boundary conditions.

Classes

SimplifyPolicy

Bases: StrEnum

How hard a transformation may be looked at, and therefore how far it may be simplified.

none -- declared type only: nothing is inspected, nothing is rewritten.
analytic -- structure only: None parameters, array shapes, axis lists and wrapper contents are read; no value is read and no lazy inverse is materialized. Invertibility, injectivity and surjectivity of a matrix transformation are assumed from its shape at this level (a square matrix is presumed invertible, a wide one surjective, a tall one injective).
numeric -- values too: zero tests, diagonality, orthogonality, rank; a typed inverse may be materialized when a leaf is downcast. Rank replaces the analytic shape assumption, so a square singular matrix is not invertible here.

BoundaryCondition

Bases: StrEnum

Boundary conditions for interpolation and resampling.

The following boundary conditions are supported:

Value	Aliases	Description
`nearest`	`edge`, `border`	`(a a a a \| a b c d \| d d d d)`
`reflect`	`symmetric`, `dct2`	`(d c b a \| a b c d \| d c b a)`
`mirror`	`dct1`	`(d c b \| a b c d \| c b a)`
`grid-wrap`	`circular`, `circulant`, `dft`	`(a b c d \| a b c d \| a b c d)`
`wrap`		`(d b c d \| a b c d \| b c a b)`
`constant`	`zero`, `zeros`	`(0 0 0 0 \| a b c d \| 0 0 0 0)`

InterpolationOrder

Bases: IntEnum

Interpolation order for interpolation and resampling.

The following interpolation orders are supported:

Name	Aliases	Value	Description
`zeroth`	`nearest`	0	Nearest neighbor interpolation.
`first`	`linear`	1	Linear interpolation.
`second`	`quadratic`	2	Quadratic interpolation.
`third`	`cubic`	3	Cubic interpolation.
`fourth`		4	Fourth-order interpolation.
`fifth`		5	Fifth-order interpolation.
`barycentric`		-1	Barycentric interpolation.
`fourier`		-2	Fourier interpolation.

OrientationType

Bases: StrEnum

Orientation types for coordinate systems and transformations.

Currently, only the "anatomical" orientation is supported.

Name	Value	Description
`anatomical`	`"anatomical"`	Anatomical orientation.

AnatomicalOrientationValue

Bases: StrEnum

Anatomical orientation values for coordinate systems and transformations.

The following values are supported:

Name	Value	Description
`left_to_right`	`"left-to-right"`
`right_to_left`	`"right-to-left"`
`proximal_to_distal`	`"proximal-to-distal"`
`distal_to_proximal`	`"distal-to-proximal"`
`anterior_to_posterior`	`"anterior-to-posterior"`	front-to-back
`posterior_to_anterior`	`"posterior-to-anterior"`	back-to-front
`inferior_to_superior`	`"inferior-to-superior"`	feet-to-head
`superior_to_inferior`	`"superior-to-inferior"`	head-to-feet
`dorsal_to_palmar`	`"dorsal-to-palmar"`	back of hand to palm
`palmar_to_dorsal`	`"palmar-to-dorsal"`	palm to back of hand
`dorsal_to_plantar`	`"dorsal-to-plantar"`	top of foot to sole
`plantar_to_dorsal`	`"plantar-to-dorsal"`	sole to top of foot
`rostral_to_caudal`	`"rostral-to-caudal"`	nose/beak-to-tail, especially for nervous system
`caudal_to_rostral`	`"caudal-to-rostral"`	tail-to-nose/beak, especially for nervous system
`cranial_to_caudal`	`"cranial-to-caudal"`	head-to-tail
`caudal_to_cranial`	`"caudal-to-cranial"`	tail-to-head
`dorsal_to_ventral`	`"dorsal-to-ventral"`	back/top-to-belly/bottom
`ventral_to_dorsal`	`"ventral-to-dorsal"`	belly/bottom-to-back/top
`superficial_to_deep`	`"superficial-to-deep"`	outer surface to inner depth, e.g. skin, gut, cortex
`deep_to_superficial`	`"deep-to-superficial"`	inner depth to outer surface
`apical_to_basal`	`"apical-to-basal"`	apical to basal surface, e.g. epithelial layers, polarized cells
`basal_to_apical`	`"basal-to-apical"`	basal to apical surface
`apex_to_base`	`"apex-to-base"`	tip to broad base, e.g. heart, lungs
`base_to_apex`	`"base-to-apex"`	broad base to tip

SpaceEnum

Bases: StrEnum

The known labels of a world space, used by the space, input_space and output_space metadata fields.

The first five members are the names that NIfTI gives to its sform_code and qform_code values. They are followed by the BIDS template identifiers, which BIDS uses for SpatialReference and for the space- entity of a file name, and by the spaces that BIDS defines without a template. A label that is not listed here is kept as a plain string.

Member	Value	Meaning
`scanner`	`"scanner"`	NIfTI xform code 1: scanner-based anatomical coordinates
`aligned`	`"aligned"`	NIfTI xform code 2: aligned to another file
`talairach`	`"talairach"`	NIfTI xform code 3: Talairach-Tournoux atlas
`mni`	`"mni"`	NIfTI xform code 4: MNI 152
`template`	`"template"`	NIfTI xform code 5: another template
`ICBM452AirSpace`	`"ICBM452AirSpace"`	BIDS standard template (volume)
`ICBM452Warp5Space`	`"ICBM452Warp5Space"`	BIDS standard template (volume)
`IXI549Space`	`"IXI549Space"`	BIDS standard template (volume)
`MNI152Lin`	`"MNI152Lin"`	BIDS standard template (volume)
`MNI152NLin2009aAsym`	`"MNI152NLin2009aAsym"`	BIDS standard template (volume)
`MNI152NLin2009aSym`	`"MNI152NLin2009aSym"`	BIDS standard template (volume)
`MNI152NLin2009bAsym`	`"MNI152NLin2009bAsym"`	BIDS standard template (volume)
`MNI152NLin2009bSym`	`"MNI152NLin2009bSym"`	BIDS standard template (volume)
`MNI152NLin2009cAsym`	`"MNI152NLin2009cAsym"`	BIDS standard template (volume)
`MNI152NLin2009cSym`	`"MNI152NLin2009cSym"`	BIDS standard template (volume)
`MNI152NLin6Asym`	`"MNI152NLin6Asym"`	BIDS standard template (volume)
`MNI152NLin6Sym`	`"MNI152NLin6Sym"`	BIDS standard template (volume)
`MNI305`	`"MNI305"`	BIDS standard template (volume)
`MNIColin27`	`"MNIColin27"`	BIDS standard template (volume)
`MNIInfant`	`"MNIInfant"`	BIDS standard template (volume)
`MNIPediatricAsym`	`"MNIPediatricAsym"`	BIDS standard template (volume)
`NMT31Sym`	`"NMT31Sym"`	BIDS standard template (volume)
`OASIS30AntsOASISAnts`	`"OASIS30AntsOASISAnts"`	BIDS standard template (volume)
`OASIS30Atropos`	`"OASIS30Atropos"`	BIDS standard template (volume)
`Talairach`	`"Talairach"`	BIDS standard template (volume)
`UNCInfant`	`"UNCInfant"`	BIDS standard template (volume)
`fsaverage`	`"fsaverage"`	BIDS standard template (surface)
`fsaverage3`	`"fsaverage3"`	BIDS standard template (surface)
`fsaverage4`	`"fsaverage4"`	BIDS standard template (surface)
`fsaverage5`	`"fsaverage5"`	BIDS standard template (surface)
`fsaverage6`	`"fsaverage6"`	BIDS standard template (surface)
`fsaveragesym`	`"fsaveragesym"`	BIDS standard template (surface)
`fsLR`	`"fsLR"`	BIDS standard template (surface)
`fsnative`	`"fsnative"`	BIDS standard template (surface)
`orig`	`"orig"`	BIDS non-standard space
`anat`	`"anat"`	BIDS non-standard space
`T1w`	`"T1w"`	BIDS non-standard space
`T2w`	`"T2w"`	BIDS non-standard space
`individual`	`"individual"`	BIDS non-standard space
`study`	`"study"`	BIDS non-standard space

IntentEnum

Bases: StrEnum

The known values of the intent metadata field, which says what the values of an image represent.

The members are the NIfTI intent names, spelled as nibabel spells them, with their NIfTI intent codes. Codes 2 to 24 name statistical distributions, codes 1001 to 2005 name other kinds of values, and the codes from 2006 onwards are FSL's own. An intent that is not listed here is kept as a plain string.

Member	Value	NIfTI code
`correlation`	`"correlation"`	2
`t_test`	`"t test"`	3
`f_test`	`"f test"`	4
`z_score`	`"z score"`	5
`chi2`	`"chi2"`	6
`beta`	`"beta"`	7
`binomial`	`"binomial"`	8
`gamma`	`"gamma"`	9
`poisson`	`"poisson"`	10
`normal`	`"normal"`	11
`non_central_f_test`	`"non central f test"`	12
`non_central_chi2`	`"non central chi2"`	13
`logistic`	`"logistic"`	14
`laplace`	`"laplace"`	15
`uniform`	`"uniform"`	16
`non_central_t_test`	`"non central t test"`	17
`weibull`	`"weibull"`	18
`chi`	`"chi"`	19
`inverse_gaussian`	`"inverse gaussian"`	20
`extreme_value_1`	`"extreme value 1"`	21
`p_value`	`"p value"`	22
`log_p_value`	`"log p value"`	23
`log10_p_value`	`"log10 p value"`	24
`estimate`	`"estimate"`	1001
`label`	`"label"`	1002
`neuroname`	`"neuroname"`	1003
`general_matrix`	`"general matrix"`	1004
`symmetric_matrix`	`"symmetric matrix"`	1005
`displacement_vector`	`"displacement vector"`	1006
`vector`	`"vector"`	1007
`pointset`	`"pointset"`	1008
`triangle`	`"triangle"`	1009
`quaternion`	`"quaternion"`	1010
`dimensionless`	`"dimensionless"`	1011
`time_series`	`"time series"`	2001
`node_index`	`"node index"`	2002
`rgb_vector`	`"rgb vector"`	2003
`rgba_vector`	`"rgba vector"`	2004
`shape`	`"shape"`	2005
`fnirt_disp_field`	`"fnirt disp field"`	2006
`fnirt_cubic_spline_coef`	`"fnirt cubic spline coef"`	2007
`fnirt_dct_coef`	`"fnirt dct coef"`	2008
`fnirt_quad_spline_coef`	`"fnirt quad spline coef"`	2009
`topup_field`	`"topup field"`	2018

Manufacturer

Bases: StrEnum

The known values of the manufacturer metadata field (BIDS Manufacturer), spelled as converters such as dcm2niix normalise the DICOM Manufacturer tag. Any other manufacturer is kept as a plain string.

Member	Value
`Siemens`	`"Siemens"`
`GE`	`"GE"`
`Philips`	`"Philips"`
`Canon`	`"Canon"`
`Toshiba`	`"Toshiba"`
`Hitachi`	`"Hitachi"`
`Bruker`	`"Bruker"`
`UIH`	`"UIH"`
`MRSolutions`	`"MRSolutions"`

IlluminationType

Bases: StrEnum

The known values of the illumination_type metadata field, which are the members of the OME Channel.IlluminationType enumeration. Any other value is kept as a plain string.

Member	Value
`Transmitted`	`"Transmitted"`
`Epifluorescence`	`"Epifluorescence"`
`Oblique`	`"Oblique"`
`NonLinear`	`"NonLinear"`
`Other`	`"Other"`

ContrastMethod

Bases: StrEnum

The known values of the contrast_method metadata field, which are the members of the OME Channel.ContrastMethod enumeration. Any other value is kept as a plain string.

Member	Value
`Brightfield`	`"Brightfield"`
`Phase`	`"Phase"`
`DIC`	`"DIC"`
`HoffmanModulation`	`"HoffmanModulation"`
`ObliqueIllumination`	`"ObliqueIllumination"`
`PolarizedLight`	`"PolarizedLight"`
`Darkfield`	`"Darkfield"`
`Fluorescence`	`"Fluorescence"`
`Other`	`"Other"`