Sisyphe.core.sisypheTransform

External packages/modules

• ANTs, image registration, http://stnava.github.io/ANTs/

• DIPY, MR diffusion image processing, https://www.dipy.org/

• NiBabel, Euler angle conversions, https://nipy.org/nibabel

• Numpy, scientific computing, https://numpy.org/

• PyQt5, Qt GUI, https://www.riverbankcomputing.com/software/pyqt/

• Scipy, scientific computing, https://docs.scipy.org/doc/scipy/index.html

• SimpleITK, medical image processing, https://simpleitk.org/

• vtk, visualization engine/3D rendering, https://vtk.org/

class Sisyphe.core.sisypheTransform.SisypheApplyTransform

Description

SisypheVolume resampling class.

Applies SisypheTransform geometric transformation to resample a moving image, ROI, mesh or streamlines into the space of a fixed image. Affine geometric transformation is in forward convention (apply inverse transformation to resample). Displacement field geometric transformation is in backward convention.

This class automatically updates the SisypheTransforms instances associated to the fixed, moving and resliced volumes.

Inheritance

object -> SisypheApplyTransform

Creation: 05/10/2021 Last revision: 11/02/2025

clearMesh() → None

Clear the moving mesh attribute of the current SisypheApplyTransform instance (set to none)

clearMoving() → None

Clear the moving volume attribute of the current SisypheApplyTransform instance (set to none)

clearMovingROI() → None

Clear the moving ROI attribute of the current SisypheApplyTransform instance (set to none)

clearMovingStreamlines() → None

Clear the moving streamlines attribute of the current SisypheApplyTransform instance (set to none)

execute(fixed: SisypheVolume | None = None, save: bool = True, dialog: bool = False, prefix: str | None = None, suffix: str | None = None, wait: DialogWait | None = None) → SisypheVolume | SisypheROI | SisypheMesh | SisypheStreamlines | None

Reslice the moving volume, ROI, mesh and streamlines attributes ith the geometric transformation attribute of the current SisypheApplyTransform instance.

Parameters

fixedSisyphe.core.sisypheVolume.SisypheVolume | None

fixed volume (default None)

savebool

save resliced moving volume if True (default)

dialogbool

• dialog to choice the resliced moving volume file name, if True

• addBundle suffix/prefix to the moving volume file name, if False (default)

prefixstr | None

file name prefix of the resliced moving volume (default None)

suffixstr | None

file name suffix of the resliced moving volume (default None)

waitSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

Sisyphe.core.sisypheVolume.SisypheVolume | Sisyphe.core.sisypheROI.SisypheROI | Sisyphe.core.sisypheMesh.SisypheMesh | Sisyphe.core.sisypheTracts.SisypheStreamlines

resliced moving attributes

getInterpolator() → str

Get the interpolator attribute of the current SisypheApplyTransform instance. This attribute defines the method of interpolation used to reslice the “moving” volume.

Returns

str

interpolation name. Methods of interpolation are : ‘nearest’, ‘linear’, ‘bspline’, ‘gaussian’, ‘hammingsinc’, ‘cosinesinc’, ‘welchsinc’, ‘lanczossinc’, ‘blackmansinc’

classmethod getInterpolatorCodeFromName(name: str) → int

Get SimpleITK’s interpolation int code from a name.

Parameters

namestr

interpolation name. Methods of interpolation are: ‘nearest’, ‘linear’, ‘bspline’, ‘gaussian’, ‘hammingsinc’, ‘cosinesinc’, ‘welchsinc’, ‘lanczossinc’, ‘blackmansinc’

Returns

int

SimpleITK’s interpolation int code

classmethod getInterpolatorNameFromCode(code: int) → str

Get interpolation name from a SimpleITK’s int code.

Parameters

codeint

SimpleITK’s interpolation int code

Returns

str

interpolation name. Methods of interpolation are : ‘nearest’, ‘linear’, ‘bspline’, ‘gaussian’, ‘hammingsinc’, ‘cosinesinc’, ‘welchsinc’, ‘lanczossinc’, ‘blackmansinc’

getInterpolatorSITKCode() → int

Get the interpolator attribute of the current SisypheApplyTransform instance. This attribute defines the method of interpolation used to reslice the “moving” volume.

Returns

int

SimpleITK’s interpolation int code

getMoving() → SisypheVolume

Get the moving volume attribute of the current SisypheApplyTransform instance.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

moving volume

getMovingMesh() → SisypheMesh

Get the moving mesh attribute of the current SisypheApplyTransform instance.

Returns

Sisyphe.core.sisypheMesh.SisypheMesh

moving mesh

getMovingROI() → SisypheROI

Get the moving ROI attribute of the current SisypheApplyTransform instance.

Returns

Sisyphe.core.sisypheROI.SisypheROI

moving roi

getMovingStreamlines() → SisypheStreamlines

Get the moving streamlines attribute of the current SisypheApplyTransform instance.

Returns

Sisyphe.core.sisypheTracts.SisypheStreamlines

moving streamlines

getResampleTransform() → SisypheTransform

Get the backward transform attribute of the current SisypheApplyTransform instance.

Returns

SisypheTransform

backward transform copy

getSITKResampleTransform() → Transform

Get backward transform attribute of the current SisypheApplyTransform instance as SimpleITK.Transform.

Returns

SimpleITK.Transform

SimpleITK backward transform copy

getSITKTransform() → AffineTransform | DisplacementFieldTransform

Get forward transform attribute of the current SisypheApplyTransform instance as SimpleITK.Transform.

Returns

SimpleITK.AffineTransform | SimpleITK.DisplacementFieldTransform

SimpleITK forward transform copy

getTransform() → SisypheTransform

Get the forward transform attribute of the current SisypheApplyTransform instance.

Returns

SisypheTransform

forward transfrom copy

hasAffineTransform() → bool

Check whether the transform attribute of the current SisypheApplyTransform instance is an affine geometric transformation.

Returns

bool

True if geometric transform is defined and is an affine transformation

hasDisplacementFieldTransform() → bool

Check whether the transform attribute of the current SisypheApplyTransform instance is a displacement field transformation.

Returns

bool

True if geometric transform is defined and is a displacement field transform

hasMoving() → bool

Check whether the moving volume attribute of the current SisypheApplyTransform instance is defined (not None).

Returns

bool

True if moving volume is defined

hasMovingMesh() → bool

Check whether the moving mesh attribute of the current SisypheApplyTransform instance is defined (not None).

Returns

bool

True if moving mes his defined

hasMovingROI() → bool

Check whether the moving ROI attribute of the current SisypheApplyTransform instance is defined (not None).

Returns

bool

True if moving roi is defined

hasMovingStreamlines() → bool

Check whether the moving streamlines attribute of the current SisypheApplyTransform instance is defined (not None).

Returns

bool

True if moving streamlines are defined

hasTransform() → bool

Check whether the transform attribute of the current SisypheApplyTransform instance is defined (not None).

Returns

bool

True if geometric transform is defined

resampleMesh(save: bool = True, dialog: bool = False, prefix: str | None = None, suffix: str | None = None, wait: DialogWait | None = None) → SisypheMesh | None

Reslice the moving mesh attribute with the geometric transformation attribute of the current SisypheApplyTransform instance.

Parameters

savebool

save resliced moving mesh if True (default)

dialogbool

• dialog to choice the resliced moving mesh file name, if True

• addBundle suffix/prefix to the moving mesh file name, if False (default)

prefixstr | None

file name prefix of the resliced moving mesh (default None)

suffixstr | None

file name suffix of the resliced moving mesh (default None)

waitSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

Sisyphe.core.sisypheMesh.SisypheMesh

resliced moving mesh

resampleMoving(fixed: SisypheVolume | None = None, save: bool = True, dialog: bool = False, prefix: str | None = None, suffix: str | None = None, wait: DialogWait | None = None) → SisypheVolume | None

Reslice the moving volume attribute with the geometric transformation attribute of the current SisypheApplyTransform instance.

Origin is not used during registration, origin must therefore be ignored at the resampling stage

Origin management:

• 1. moving volume origin is stored before resampling

• 2. set moving volume origin to (0.0, 0.0, 0.0)

• 3. moving volume resampling

• 4. moving volume origin is restored

• 5. copy moving volume attributes to resampled volume (identity, display, acquisition, acpc)

• 6. copy fixed volume ID to resampled volume (same brain space)

• 7. copy fixed volume origin to resampled volume

Parameters

fixedSisyphe.core.sisypheVolume.SisypheVolume | None

fixed volume (default None)

savebool

save resliced moving volume if True (default)

dialogbool

• dialog to choice the resliced moving volume file name, if True

• addBundle suffix/prefix to the moving volume file name, if False (default)

prefixstr | None

file name prefix of the resliced moving volume (default None)

suffixstr | None

file name suffix of the resliced moving volume (default None)

waitSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

resliced moving volume

resampleROI(save: bool = True, dialog: bool = False, prefix: str | None = None, suffix: str | None = None, wait: DialogWait | None = None) → SisypheROI | None

Reslice the moving ROI attribute with the geometric transformation attribute of the current SisypheApplyTransform instance.

Parameters

savebool

save resliced moving ROI if True (default)

dialogbool

• dialog to choice the resliced moving ROI file name, if True

• addBundle suffix/prefix to the moving ROI file name, if False (default)

prefixstr | None

file name prefix of the resliced moving ROI (default None)

suffixstr | None

file name suffix of the resliced moving ROI (default None)

waitSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

Sisyphe.core.sisypheROI.SisypheROI

resliced moving ROI

resampleStreamlines(save: bool = True, dialog: bool = False, prefix: str | None = None, suffix: str | None = None, wait: DialogWait | None = None) → SisypheStreamlines | None

Reslice the moving streamlines attribute with the geometric transformation attribute of the current SisypheApplyTransform instance.

Parameters

savebool

save resliced moving streamlines if True (default)

dialogbool

• dialog to choice the resliced moving streamlines file name, if True

• addBundle suffix/prefix to the moving streamlines file name, if False (default)

prefixstr | None

file name prefix of the resliced moving streamlines (default None)

suffixstr | None

file name suffix of the resliced moving streamlines (default None)

waitSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (default None)

Returns

Sisyphe.core.sisypheTracts.SisypheStreamlines

resliced moving streamlines

setFromTransforms(trfs: SisypheTransforms, ID: str | SisypheVolume) → None

Set the transform attribute of the current SisypheApplyTransform instance from a SisypheTransforms instance and an ID key.

Parameters

trfsSisypheTransforms

trasnform to copy

IDstr | Sisyphe.core.sisypheVolume.SisypheVolume

• ID key of the SisypheTransforms container, SisypheTransform = SisypheTransforms[ID] or

• ID key is the ID attribute of the SisypheVolume

setFromVolumes(fixed: SisypheVolume, moving: SisypheVolume) → None

Set attributes (size, spacing, moving volume and transform) of the current SisypheApplyTransform instance from fixed and moving SisypheVolume instances.

size and spacing: size and spacing attributes of the fixed SisypheVolume instance. transform: SisypheTransforms instance associated to the moving volume with ID attribute of the fixed volume as key.

Parameters

fixedSisyphe.core.sisypheVolume.SisypheVolume

fixed volume

movingSisyphe.core.sisypheVolume.SisypheVolume

moving volume

setInterpolator(v: int | str) → None

Set the interpolator attribute of the current SisypheApplyTransform instance. This attribute defines the method of interpolation used to reslice the “moving” volume.

Parameters

vint | str

SimpleITK’s interpolation int code or interpolation name. Methods of interpolation are : ‘nearest’, ‘linear’, ‘bspline’, ‘gaussian’,’hammingsinc’, ‘cosinesinc’, ‘welchsinc’, ‘lanczossinc’, ‘blackmansinc’

setMoving(img: SisypheVolume) → None

Set the moving volume attribute of the current SisypheApplyTransform instance.

Parameters

imgSisyphe.core.sisypheVolume.SisypheVolume

moving volume

setMovingMesh(mesh: SisypheMesh) → None

Set the moving mesh attribute of the current SisypheApplyTransform instance.

Parameters

meshSisyphe.core.sisypheMesh.SisypheMesh

moving mesh

setMovingROI(roi: SisypheROI) → None

Set the moving ROI attribute of the current SisypheApplyTransform instance.

Parameters

roiSisyphe.core.sisypheROI.SisypheROI

moving roi

setMovingStreamlines(sl: SisypheStreamlines) → None

Set the moving streamlines attribute of the current SisypheApplyTransform instance.

Parameters

slSisyphe.core.sisypheTracts.SisypheStreamlines

moving streamlines

setTransform(trf: SisypheTransform, center: bool = True) → None

Set the transform attribute of the current SisypheApplyTransform instance. This attribute defines the geometric transformation used to reslice the “moving” volume.

Parameters

trfSisypheTransform

transform to copy

centerbool

set center to 0.0, 0.0, 0.0 if False (default True)

updateTransforms(resampled: SisypheVolume, fixed: SisypheVolume | None) → None

Update the SisypheTransforms instance associated to fixed, moving and resliced volumes. Do not call this method, called by resampleMoving() method.

• Add forward transform (moving -> fixed/resampled) to moving volume SisypheTransforms (mtrfs)

• Add backward transform (resampled -> moving) to resampled volume SisypheTransforms (rtrfs)

• Add backward transform (fixed -> moving) to fixed volume SisypheTransforms (ftrfs)

• Update moving volume SisypheTransforms

  • Copy transforms from fixed volume to moving volume (mtrfs)

  • forward transform (moving -> fixed) pre multiplied by each fixed transforms

• Update fixed volume SisypheTransforms

  • Copy transforms from moving volume to fixed volume (ftrfs)

  • backward transform (fixed -> moving) pre multiplied by each moving transforms

• Update resampled volume SisypheTransforms

  • Copy transforms from fixed volume to resampled volume (rtrfs)

  • simple copy (fixed and resampled are registered and share same space)

Parameters

resampledSisyphe.core.sisypheVolume.SisypheVolume

resampled volume

fixedSisyphe.core.sisypheVolume.SisypheVolume | None

fixed volume (optional)

updateVolumeTransformsFromMoving(vol: SisypheVolume) → None

Copy the SisypheTransforms instance associated to the SisypheVolume moving volume to another SisypheVolume instance with the same ID (same space as moving volume)

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

volume SisypheTransforms is to be updated.

class Sisyphe.core.sisypheTransform.SisypheTransform(parent: SisypheVolume | None = None)

Description

PySisyphe geometric centered transformation class.

Uses forward convention, i.e. transformation of fixed to floating volume coordinates. To resample floating volume, apply the inverse i.e. backward transformation. Private attributes ID, spacing and size are those of the fixed image (resampling space)

Fixed and floating volumes are associated with instance attributes:

• Parent attribute = fixed volume.

• ID attribute = ID of the floating volume

Methods to copy to/from ANTs, SimpleITK and VTK geometric transformation classes. IO methods for common neuroimaging geometric transformation file formats.

Inheritance

object -> SisypheTransform

Creation: 05/10/2021 Last revision: 19/03/2025

addTranslations(t: list[float] | tuple[float, float, float]) → None

Add translations to the current SisypheTransform instance.

Parameters

ttuple[float, float, float] | list[float]

x-axis, y-axis and z-axis translations in mm

affineToDisplacementField(inverse: bool = True) → None

Convert the affine geometric transformation of the current SisypheTransform instance to a displacement field.

Parameters

inversebool

inverse affine geometric transformation if True (default)

applyInverseToPoint(coor: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float]

Apply the inverse geometric transformation of the current SisypheTransform instance to a point.

Parameters

coortuple[float, float, float] | list[float]

x-axis, y-axis and z-axis point coordinates

Returns

tuple[float, float, float] | list[float]

x-axis, y-axis and z-axis point coordinates

applyToPoint(coor: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float]

Apply the geometric transformation of the current SisypheTransform instance to a point.

Parameters

coortuple[float, float, float] | list[float]

x-axis, y-axis and z-axis point coordinates

Returns

tuple[float, float, float] | list[float]

x-axis, y-axis and z-axis point coordinates

composeRotations(r: list[float] | tuple[float, float, float], deg: bool = False) → None

Compose rotations to the current SisypheTransform instance.

Parameters

rtuple[float, float, float] | list[float]

rotations around x-axis, y-axis and z-axis

degbool

rotations in degrees if True, in radians otherwise (default False)

composeTransform(trf: SisypheTransform) → None

Compose a geometric transformation (SisypheTransform) to the current SisypheTransform instance.

Parameters

trfSisypheTransform

geometric transformation to compose

copy() → SisypheTransform

Copy the current SisypheTransform instance.

Returns

SisypheTransform

transform copy

copyAttributesFrom(t: SisypheTransform) → None

Copy attributes of a SisypheTransform instance to the current SisypheTransform instance.

Parameters

tSisypheTransform

copy attributes from this transform

copyAttributesTo(t: SisypheTransform) → None

Copy attributes of the current SisypheTransform instance to a SisypheTransform instance.

Parameters

tSisypheTransform

copy attributes to this transform

copyFrom(t: SisypheTransform) → None

Copy a SisypheTransform instance to the current SisypheTransform instance.

Parameters

tSisypheTransform

geometric transform

copyFromDisplacementFieldImage(img: SisypheImage | Image) → None

Copy a displacement field as SimpleITK.Image or Sisyphe.core.sisypheImage.SisypheImage instance to the current SisypheTransform instance.

Parameters

imgSisyphe.core.sisypheImage.SisypheImage | SimpleITK.Image

displacement field image

copyTo(t: SisypheTransform) → None

Copy the current SisypheTransform instance to a SisypheTransform instance.

Parameters

tSisypheTransform

transform copy

createXML(doc: Document, currentnode: Element) → None

Write the current SisypheTransform instance attributes to xml document instance. Use of this method is not recommended (called internally by saveAs method).

Parameters

docminidom.Document

xml document

currentnodeminidom.Element

xml root node

getANTSTransform() → ANTsTransform

Get an ants.core.ants_transform.ANTsTransform instance from the current SisypheTransform instance.

Returns

ants.core.ants_transform.ANTsTransform

ANTs transform copy

getAffineParametersFromMatrix(deg: bool = False) → tuple[list[float], list[float], list[float], list[float]]

Get affine parameters from the affine matrix attribute of the current SisypheTransform instance.

Parameters

degbool

rotations in degrees if True, in radians otherwise (default False)

Returns

tuple[list[float], list[float], list[float], list[float]]

• translations in x-axis, y-axis and z-axis

• rotations around x-axis, y-axis and z-axis

• zoom factors applied to x-axis, y-axis and z-axis

• shear factors for x-y, x-z, y-z axes

getAngleVector(deg: bool = False) → tuple[float, list[float]]

Get angle and vector of rotation axis from the rotations of the current SisypheTransform instance.

Parameters

degbool

angle in radians if False, in degrees otherwise

Returns

float, tuple[float, float, float] | list[float]

angle of rotation and vector of rotation axis

getCenter() → list[float]

Get the center of rotation of the current SisypheTransform instance.

Returns

list[float]

center of rotation coordinates

getDisplacementField() → SisypheVolume

Get the displacement field of the current SisypheTransform instance as SisypheVolume.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

displacement field image

getEquivalentTransformWithNewCenterOfRotation(c: list[float] | tuple[float, float, float]) → SisypheTransform

Calculate a geometric transformation equivalent to the current SisypheTransform instance, with a new center of rotation

1. Apply forward translation, old center to new center (translation = volume center - old center)

2. Apply rotation, after forward translation, center of rotation is new center

3. Apply backward translation, new center to old center

Parameters

ctuple[float, float, float] | list[float]

new center of rotation coordinates

Returns

SisypheTransform

classmethod getFileExt() → str

Get SisypheTransform file extension.

Returns

str

‘.xtrf’

classmethod getFilterExt() → str

Get SisypheTransform filter used by QFileDialog.getOpenFileName() and QFileDialog.getSaveFileName().

Returns

str

‘PySisyphe Geometric transformation (.xtrf)’

getFlattenMatrix(homogeneous: bool = False) → list[float]

Get the affine matrix of the current SisypheTransform instance as a list.

Parameters

homogeneousbool

homogeneous 4x4 affine matrix if True, 3x3 affine matrix otherwise

Returns

list[float]

16 elements (4x4 matrix) if homogeneous is True, 9 elements (3x3 matrix) otherwise

getID() → str

Get the ID attribute of the current SisypheTransform instance.

Returns

str

transform ID

getInverseSITKTransform() → AffineTransform

Get inverse of the current SisypheTransform instance as a SimpleITK.Transform instance.

Returns

SimpleITK.AffineTransform

inverse transform

getInverseTransform() → SisypheTransform

Get the inverse geometric transformation of the current SisypheTransform instance.

Returns

SisypheTransform

inverse geometric transformation

getInverseVTKTransform(center_correction: bool = False) → vtkTransform

Get the inverse affine matrix as vtk.vtkMatrix3x3 instance of the current SisypheTransform instance.

Parameters

center_correctionbool

if True, take into account center of rotation and replace translations by offset if center of rotation is not default (0.0,0.0,0.0),

Returns

vtk.vtkMatrix4x4

inverse transform as VTK homogeneous affine matrix

getMatrixColumn(c: int) → list[float] | tuple[float, float, float]

Get a column from the affine matrix of the current SisypheTransform instance.

Parameters

cint

column number (0 <= c < 3)

Returns

list[float]

column vector of affine matrix

getMatrixDiagonal() → list[float] | tuple[float, float, float]

Get the diagonal of the affine matrix of the current SisypheTransform instance.

Returns

list[float]

diagonal vector of affine matrix

getName() → str

Get the name attribute of the current SisypheTransform instance.

Returns

str

transform name

getNumpyArray(homogeneous: bool = False) → ndarray

Get the affine matrix as numpy.ndarray instance of the current SisypheTransform instance.

Parameters

homogeneousboolean

homogeneous 4x4 affine matrix if True, 3x3 affine matrix otherwise

Returns

numpy.ndarray

homogeneous affine matrix as numpy ndarray

getOffsets() → list[float]

Get offsets of the current SisypheTransform instance. if center of rotation is default (0.0, 0.0, 0.0), offsets are equal to translations. However, if center of rotation is not default, offsets are translations of an equivalent geometric transformation with a default center of rotation.

Returns

tuple[float, float, float] | list[float]

x-axis, y-axis and z-axis translations in mm

getParent() → SisypheVolume | None

Get the parent attribute of the current SisypheTransform instance.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

parent

getRotations(deg: bool = False) → list[float] | None

Get rotation attributes of the current SisypheTransform instance.

Parameters

deg : bool, rotations in degrees if True, in radians otherwise (default False)

Returns

list[float]

rotations around x-axis, y-axis and z-axis

getRotationsFromMatrix(deg: bool = False) → list[float]

Get rotations from the affine matrix attribute of the current SisypheTransform instance.

Parameters

degbool

rotations in degrees if True, in radians otherwise (default False)

Returns

list[float]

rotations around x-axis, y-axis and z-axis

getSITKDisplacementFieldSITKImage() → Image

Get a SimpleITK.Image instance from the displacement field of the current SisypheTransform instance.

Returns

SimpleITK.Image

displacement field image

getSITKDisplacementFieldTransform() → DisplacementFieldTransform

Get a SimpleITK.DisplacementFieldTransform instance from the current SisypheTransform instance.

Returns

SimpleITK.DisplacementFieldTransform

displacement field transform copy

getSITKTransform() → AffineTransform | DisplacementFieldTransform

Get a SimpleITK.Transform instance from the current SisypheTransform instance.

Returns

SimpleITK.AffineTransform | SimpleITK.DisplacementFieldTransform

transform copy

classmethod getSITKtoNumpy(trf: AffineTransform | Euler3DTransform) → ndarray

Convert SimpleITK.AffineTransform or SimpleITK.Euler3DTransform o a numpy.ndarray.

Parameters

trf : SimpleITK.AffineTransform | SimpleITK.Euler3DTransform

Returns

numpy.ndarray

homogeneous affine matrix

getSize() → list[int] | tuple[int, int, int]

Get the size attribute of the current SisypheTransform instance. Image size in the x, y and z axes of the floating volume (in voxels).

Returns

list[int]

image size in the x, y and z axes of the floating volume (in voxels)

getSpacing() → list[float] | tuple[float, float, float]

Get the spacing attribute of the current SisypheTransform instance. Voxel size in the x, y and z axes of the floating volume in mm.

Returns

list[float]

Voxel size in the x, y and z axes of the floating volume in mm

getTranslations() → list[float]

Get translation attributes of the current SisypheTransform instance.

Returns

tuple[float, float, float] | list[float]

x-axis, y-axis and z-axis translations in mm

getVTKMatrix3x3() → vtkMatrix3x3

Get the affine matrix as vtk.vtkMatrix3x3 instance of the current SisypheTransform instance.

Returns

vtk.vtkMatrix4x4

VTK affine matrix copy

getVTKMatrix4x4(center_correction: bool = False) → vtkMatrix4x4

Get the affine matrix as vtk.vtkMatrix4x4 instance of the current SisypheTransform instance.

Parameters

center_correctionbool

if True, replace translations by offset if center of rotation is not default (0.0,0.0,0.0),

Returns

vtk.vtkMatrix4x4

VTK homogeneous affine matrix copy

getVTKTransform(center_correction: bool = False) → vtkTransform

Get a vtk.vtkTransform instance from the current SisypheTransform instance.

Parameters

center_correctionbool

if True, replace translations by offset if center of rotation is not default (0.0,0.0,0.0),

Returns

vtk.vtkTransform

VTK transform copy

classmethod getVTKtoNumpy(trf: vtkMatrix4x4) → ndarray

Convert a vtk.vtkMatrix4x4 to a numpy.ndarray.

Parameters

trf : vtk.vtkMatrix4x4

Returns

numpy.ndarray

homogeneous affine matrix

getVersor() → list[float]

Get versor i.e. quaternion in w, x, y, z (real, then unit vector in 3D) from the rotation attributes of the current SisypheTransform instance.

Returns

tuple[float, float, float, float] | list[float]

versor

hasCenter() → bool

Check whether the center of rotation of the current SisypheTransform instance is defined (not 0.0, 0.0, 0.0).

Returns

bool

True if center is defined (not 0.0, 0.0, 0.0)

hasFixedVolumeAttributes() → bool

Check whether the attributes relating to fixed volume (size, spacing) of the current SisypheTransform instance are defined.

Returns

bool

True if ID, size and spacing attributes are defined

hasID() → bool

Check whether the ID attribute of the current SisypheTransform instance is defined (not ‘’)

Returns

bool

True if ID is defined

hasName() → bool

Check if the name attribute of the current SisypheTransform instance is defined (not ‘’).

Returns

bool

True if name attribute is defined

hasParent() → bool

Check if the parent attribute of the current SisypheTransform instance is defined (not None).

Returns

bool

True if parent attribute is defined

hasSameFixedVolumeAttributes(vol: SisypheVolume) → bool

Check whether the attributes of the current SisypheTransform instance relating to fixed volume (size, spacing) are those of a SisypheVolume instance.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

volume attributes to test

Returns

bool

True if the parameter volume has the same size and spacing attributes

hasSize() → bool

Check whether the size attribute of the current SisypheTransform instance is defined (not 0, 0, 0)

Returns

bool

True if size is defined

hasSpacing() → bool

Check whether the spacing attribute of the current SisypheTransform instance is defined (not 0.0, 0.0, 0.0)

Returns

bool

True if spacing is defined

isAffine() → bool

Check whether the current SisypheTransform instance is an affine geometric transformation.

Returns

bool

True if affine transform

isCenteredFromParent() → bool

Check whether the center of rotation of the current SisypheTransform instance is the center of the SisypheVolume parent attribute.

Returns

bool

True if center of rotation = parent volume center

isCenteredToSisypheVolume(vol: SisypheVolume) → bool

Check whether the center of rotation of the current SisypheTransform instance is the center of a SisypheVolume image.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

volume center used as center of rotation

Returns

bool

True if center of rotation = volume center

isDisplacementField() → bool

Check whether the current SisypheTransform instance is a displacement field geometric transformation.

Returns

bool

True if displacement field transform

isIdentity() → bool

Check if the current SisypheTransform instance is an identity geometric transformation.

Returns

bool

True if identity geometric transformation

isRigid() → bool

Check whether the current SisypheTransform instance is rigid geometric transformation. True if matrix is orthogonal i.e. M-1 Mt = I

Returns

bool

True if rigid transform

load(filename: str) → None

Load the current SisypheTransform instance from PySisyphe Transform (.xtrf) file.

Parameters

filenamestr

PySisyphe Transform file name

loadFromANTSTransform(filename: str) → None

Load the current SisypheTransform instance from a ANTs transform (.mat) file.

Parameters

filenamestr

ANTs transform file name

loadFromBrainVoyagerTransform(filename: str) → None

Load the current SisypheTransform instance from a BrainVoyager transform (.trf) file.

Parameters

filenamestr

BrainVoyager transform file name

loadFromMatfileTransform(filename: str) → None

Load the current SisypheTransform instance from a Matlab (.mat) file.

Parameters

filenamestr

Matlab file name

loadFromTfmTransform(filename: str) → None

Load the current SisypheTransform instance from a TFM (.tfm) file.

Parameters

filenamestr

TFM file name

loadFromTxtTransform(filename: str) → None

Load the current SisypheTransform instance from a text (.txt) file.

Parameters

filenamestr

text file name

loadFromXfmTransform(filename: str) → None

Load the current SisypheTransform instance from a XFM (.xfm) file.

Parameters

filenamestr

XFM file name

classmethod openTransform(filename: str) → SisypheTransform

create a SisypheTransform instance from PySisyphe geometric transformation file (.xtrf).

Parameters

filenamestr

geometric transformation file name

Returns

SisypheTransform

loaded geometric transform

parseXML(doc: Document) → None

Read the current SisypheTransform instance attributes from xml document instance. The use of this method is not recommended (called internally by load method).

Parameters

docminidom.Document

xml document

parseXMLNode(currentnode: Element) → None

Read the current SisypheTransform instance attributes from xml document instance. The use of this method is not recommended (called internally by parseXML method).

Parameters

currentnodeminidom.Element

xml document

postMultiply(trf: vtkTransform | vtkMatrix4x4 | SisypheTransform | AffineTransform | Euler3DTransform | ndarray, homogeneous: bool = False) → None

Compose a geometric transformation with the geometric transformation of the current SisypheTransform instance. Order of transformations 1. parameter 2. current (Post-multiply current by parameter)

Parameters

trfvtk.vtkTransform | vtk.vtkMatrix4x4 | SimpleITK.AffineTransform | SimpleITK.Euler3DTransform | ndarray | SisypheTransform

affine transform used to post-multiply

homogeneousbool

used for ndarray trf, 4x4 affine matrix if True, 3x3 affine matrix otherwise

preMultiply(trf: vtkTransform | vtkMatrix4x4 | SisypheTransform | AffineTransform | Euler3DTransform | ndarray, homogeneous: bool = False) → None

Compose a geometric transformation with the geometric transformation of the current SisypheTransform instance. Order of transformations 1. current 2. parameter (Pre-multiply current by parameter)

Parameters

trfvtk.vtkTransform | vtk.vtkMatrix4x4 | SimpleITK.AffineTransform | SimpleITK.Euler3DTransform | ndarray | SisypheTransform

affine transform used to pre-multiply

homogeneousbool

used for ndarray trf, 4x4 affine matrix if True, 3x3 affine matrix otherwise

removeCenter() → None

Set the center of rotation of the current SisypheTransform instance to [0.0, 0.0, 0.0]

removeDisplacementField() → None

Remove the displacement field of the current SisypheTransform instance.

saveAs(filename: str) → None

Save the current SisypheTransform instance to a PySisyphe Transform (.xtrf) file.

Parameters

filenamestr

PySisyphe Transform file name

saveDisplacementField(filename: str) → None

Save the displacement field of the current SisypheTransform instance as SisypheVolume. Adds ‘field_’ prefix to the filename parameter.

Parameters

filenamestr

displacement field file name

saveToANTSTransform(filename: str) → None

Save the current SisypheTransform instance to a ANTs transform (.mat) file.

Parameters

filenamestr

ANTs transform file name

saveToMatfileTransform(filename: str) → None

Save the current SisypheTransform instance to a Matlab (.mat) file.

Parameters

filenamestr

Matlab file name

saveToTfmTransform(filename: str) → None

Save the current SisypheTransform instance to a TFM (.tfm) file.

Parameters

filenamestr

TFM file name

saveToTxtTransform(filename: str) → None

Save the current SisypheTransform instance to a text (.txt) file.

Parameters

filenamestr

text file name

saveToXfmTransform(filename: str) → None

Save the current SisypheTransform instance to a XFM (.xfm) file.

Parameters

filenamestr

XFM file name

setANTSTransform(trf: ANTsTransform) → None

Copy an ants.core.ants_transform.ANTsTransform instance to the current SisypheTransform instance. The only ANTsTransform supported type is AffineTransform.

Parameters

trfants.core.ants_transform.ANTsTransform

ANTs transform to copy

setAffineParameters(t: list[float] | tuple[float, float, float] | None = None, r: list[float] | tuple[float, float, float] | None = None, z: list[float] | tuple[float, float, float] | None = None, s: list[float] | tuple[float, float, float] | None = None, deg: bool = False) → None

Set affine parameters i.e. translations, rotations, zooms and shears of the current SisypheTransform instance.

Parameters

ttuple[float, float, float] | list[float]

translations in x-axis, y-axis and z-axis

rtuple[float, float, float] | list[float]

rotations around x-axis, y-axis and z-axis

ztuple[float, float, float] | list[float]

zoom factors applied to x-axis, y-axis and z-axis

stuple[float, float, float] | list[float]

shear factors for x-y, x-z, y-z axes

degbool

angle in radians if False, in degrees otherwise

setAngleVector(a: float, v: list[float] | tuple[float, float, float], deg: bool = False) → None

Set rotation attributes of the current SisypheTransform instance from a vector of rotation axis and an angle. Rotation matrix is processed from the Rodrigues’ formula.

Parameters

afloat

angle of rotation

vtuple[float, float, float] | list[float]

vector of rotation axis

degbool

angle in radians if False, in degrees otherwise

setAttributesFromFixedVolume(vol: SisypheVolume) → None

Set the attributes relating to fixed volume (ID, size, spacing) of the current SisypheTransform instance from a SisypheVolume instance.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

copy ID, size and spacing attributes from this volume

setCenter(c: list[float] | tuple[float, float, float]) → None

Set the center of rotation of the current SisypheTransform instance.

Parameters

ctuple[float, float, float] | list[float]

center of rotation coordinates

setCenterFromParent() → None

Set the center of rotation of the current SisypheTransform instance to the center of the SisypheVolume parent attribute.

setCenterFromSisypheVolume(vol: SisypheVolume) → None

Set the center of rotation of the current SisypheTransform instance to the center of a SisypheVolume image.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

center of rotation = volume center

setFlattenMatrix(m: list[float], bycolumn: bool = False) → None

Set the affine matrix of the current SisypheTransform instance from a list.

Parameters

mlist[float]

9 (3x3 affine matrix) or 16 elements (4x4 homogeneous affine matrix)

bycolumnbool

elements in column order if True, row order otherwise

setID(ID: str | SisypheVolume) → None

Set the ID attribute of the current SisypheTransform instance.

Parameters

IDstr | Sisyphe.core.sisypheVolume.SisypheVolume

transform ID

setIdentity() → None

Clear the current SisypheTransform instance (set geometric transformation to identity).

setName(name: str) → None

Set the name attribute of the current SisypheTransform instance.

Parameters

namestr

transform name

setNumpyArray(np: ndarray) → None

Copy an affine matrix as numpy.ndarray instance to the current SisypheTransform instance.

Parameters

npnumpy.ndarray

homogeneous affine matrix

setParent(parent: SisypheVolume) → None

Set the parent attribute of the current SisypheTransform instance.

Parameters

parentSisyphe.core.sisypheVolume.SisypheVolume

parent volume

setRotations(r: list[float] | tuple[float, float, float], deg: bool = False) → None

Set rotation attributes of the current SisypheTransform instance. The order in which rotations are applied is x-axis, then y-axis and finally z-axis.

Parameters

rtuple[float, float, float] | list[float]

rotations around x-axis, y-axis and z-axis

degbool

rotations in degrees if True, in radians otherwise (default False)

setSITKDisplacementFieldImage(img: SisypheImage | Image) → None

Set a displacement field as SimpleITK.Image or Sisyphe.core.sisypheImage.SisypheImage instance to the current SisypheTransform instance.

Parameters

imgSisyphe.core.sisypheImage.SisypheImage | SimpleITK.Image

displacement field image

setSITKDisplacementFieldTransform(trf: DisplacementFieldTransform) → None

Set a SimpleITK.DisplacementFieldTransform instance to the current SisypheTransform instance.

Parameters

trfSimpleITK.DisplacementFieldTransform

displacement field transform

setSITKTransform(trf)

Copy a SimpleITK.Transform instance to the current SisypheTransform instance.

Parameters

trfSimpleITK.TranslationTransform | SimpleITK.VersorTransform | SimpleITK.ScaleTransform | SimpleITK.VersorRigid3DTransform | SimpleITK.Euler3DTransform | SimpleITK.Similarity3DTransform | SimpleITK.ScaleVersor3DTransform | SimpleITK.ScaleSkewVersor3DTransform | SimpleITK.AffineTransform | SimpleITK.DisplacementFieldTransform

SimpleITK geometric transform

setSize(size: list[int] | tuple[int, int, int])

Set the size attribute of the current SisypheTransform instance. Image size in the x, y and z axes of the floating volume (in voxels).

Parameters

sizelist[int]

image size in the x, y and z axes of the floating volume (in voxels)

setSpacing(spacing: list[float] | tuple[float, float, float]) → None

Set the spacing attribute of the current SisypheTransform instance. Voxel size in the x, y and z axes of the floating volume in mm.

Parameters

spacinglist[float]

Voxel size in the x, y and z axes of the floating volume in mm

setTranslations(t: list[float] | tuple[float, float, float]) → None

Set translation attributes of the current SisypheTransform instance.

Parameters

ttuple[float, float, float] | list[float]

x-axis, y-axis and z-axis translations in mm

setVTKMatrix3x3(mat: vtkMatrix3x3, center_reset: bool = False) → None

Copy an affine matrix as vtk.vtkMatrix3x3 instance to the current SisypheTransform instance.

Parameters

matvtk.vtkMatrix3x3

VTK affine matrix to copy

center_resetbool

set center of rotation to default (0.0, 0.0, 0.0) if True

setVTKMatrix4x4(mat: vtkMatrix4x4, center_reset: bool = False) → None

Copy an affine matrix as vtk.vtkMatrix4x4 instance to the current SisypheTransform instance. The center of rotation of the current SisypheTransform instance is set to default (0.0, 0.0, 0.0).

Parameters

matvtk.vtkMatrix4x4

VTK affine homogeneous affine matrix to copy

center_resetbool

set center of rotation to default (0.0, 0.0, 0.0) if True

setVTKTransform(trf: vtkTransform, center_reset: bool = False) → None

Copy a vtk.vtkTransform instance to the current SisypheTransform instance. The center of rotation of the current SisypheTransform instance is set to default (0.0, 0.0, 0.0).

Parameters

trfvtk.vtkTransform

VTK transform to copy

center_resetbool

set center of rotation to default (0.0, 0.0, 0.0) if True

setVersor(v: list[float] | tuple[float, float, float, float]) → None

Set rotation attributes of the current SisypheTransform instance from a versor i.e. quaternion in w, x, y, z (i.e. real, then unit vector in 3D).

Parameters

vtuple[float, float, float, float] | list[float]

versor

class Sisyphe.core.sisypheTransform.SisypheTransformCollection

Description

Named list container of SisypheTransform instances. Container key to address elements can be an int index, a transform ID str, a SisypheTransform instance (its ID attribute is used as str key) or a SisypheVolume instance (its ID attribute is used as str key).

Getter methods of the SisypheTransform class are added to the SisypheTransformCollection class, returning a list of values returned by each SisypheTransform element in the container.

Inheritance

object -> SisypheTransformCollection

Creation: 05/10/2021 Last revision: 18/04/05/2025

append(value: SisypheTransform, replace: bool = True) → None

Append a SisypheTransform element in the current SisypheTransformCollection instance container.

Parameters

valueSisypheTransform

geometric transformation to append

replace: bool

if value is already in the current container, replace it (default True)

clear() → None

Remove all elements from the current SisypheTransformCollection instance container (empty).

copy() → SisypheTransformCollection

Copy the current SisypheTransformCollection instance container (Shallow copy of elements).

Returns

SisypheTransformCollection

Shallow copy of container

copyToList() → list[SisypheTransform]

Copy the current SisypheTransformCollection instance container to a list (Shallow copy of elements).

Returns

list[SisypheTransform]

shallow copy to list of container elements

count() → int

Get the number of SisypheTransform elements in the current SisypheTransformCollection instance container.

Returns

int

number of SisypheTransform elements

getList() → list[SisypheTransform]

Get the list attribute of the current SisypheTransformCollection instance container (Shallow copy)

Returns

list[SisypheTransform]

shallow copy of container list

index(value: str | SisypheVolume | SisypheTransform) → int

Index of a SisypheTransform element in the current SisypheTransformCollection instance container.

Parameters

valuestr | SisypheTransform | Sisyphe.core.sisypheVolume.SisypheVolume

ID, SisypheTransform ID attribute or SisypheVolume ID attribute

Returns

int

index

insert(key: int | str | SisypheTransform | SisypheVolume, value: SisypheTransform) → None

Insert a SisypheTransform element at the position given by the key in the current SisypheTransformCollection instance container.

Parameters

keyint | str | SisypheTransform | Sisyphe.core.sisypheVolume.SisypheVolume | None

index, ID, SisypheTransform ID attribute or SisypheVolume ID attribute

valueSisypheTransform

geometric transformation to insert

isEmpty() → bool

Checks if SisypheTransformCollection instance container is empty.

Returns

bool

True if container is empty

keys() → list[str]

Get the list of keys in the current SisypheTransformCollection instance container.

Returns

list[str]

list of keys in the container

pop(key: int | str | SisypheTransform | SisypheVolume | None = None) → SisypheTransform

Remove a SisypheTransform element from the current SisypheTransformCollection instance container and return it. If key is None, removes and returns the last element.

Parameters

keyint | str | SisypheTransform | Sisyphe.core.sisypheVolume.SisypheVolume | None

• index, ID, SisypheTransform ID attribute or SisypheVolume ID attribute

• if None, remove the last element

Returns

SisypheTransform

element removed from the container

remove(value: int | str | SisypheTransform | SisypheVolume) → None

Remove a SisypheTransform element from the current SisypheTransformCollection instance container.

Parameters

valueint | str | SisypheTransform | Sisyphe.core.sisypheVolume.SisypheVolume

index, ID, SisypheTransform ID attribute or SisypheVolume ID attribute

reverse() → None

Reverses the order of the elements in the current SisypheTransformCollection instance container.

sort(reverse: bool = False) → None

Sort elements of the current SisypheTransformCollection instance container. Sorting is based on the ID attribute of the SisypheTransform elements, in the ascending order.

Parameters

reversebool

sorting in reverse order

class Sisyphe.core.sisypheTransform.SisypheTransforms(parent: SisypheVolume | None = None)

Description

Each SisypheVolume is associated with a SisypheTransforms instance, which stores all the geometric transformations calculated from co-registrations with other SisypheVolume instances.

This class works as a named list (key/value) container of SisypheTransform instances.

• Key: ID attribute of a SisypheVolume that is co-registered with the reference SisypheVolume.

• Value: the geometric transformation (SisypheTransform instance) used to co-register the SisypheVolume with the

reference SisypheVolume.

Inherits from SisypheTransformCollection class and adds

• ID attribute of the associated (or reference) SisypheVolume instance,

• IO methods.

Geometric transformations are in forward convention (apply inverse transformation to resample)

Inheritance

object -> SisypheTransformCollection -> SisypheTransforms

Creation: 05/10/2021 Last revision: 23/05/2024

appendIdentityTransformWithVolume(vol: SisypheVolume) → None

Add an identity geometric transformation with a SisypheVolume (parameter) in the current SisypheTransforms instance.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

volume (volume ID key) to associate with an identity tranform

copy() → SisypheTransforms

Copy the current SisypheTransforms instance container (Shallow copy of elements).

Returns

SisypheTransforms

container shallow copy

createXML(doc: Document) → None

Write the current SisypheTransforms instance attributes to xml document instance.

Parameters

docminidom.Document

xml document

classmethod getFileExt() → str

Get SisypheTransforms file extension.

Returns

str

‘.xtrfs’

getFilename() → str

Get the file name attribute of the current SisypheTransforms instance is defined.

Returns

str

file name attribute

classmethod getFilterExt() → str

Get SisypheTransforms filter used by QFileDialog.getOpenFileName() and QFileDialog.getSaveFileName().

Returns

str

‘PySisyphe Geometric transformation collection (.xtrfs)’

getReferenceID() → str

Get reference ID attribute of the current SisypheTransforms instance. The reference ID is the ID of the associated SisypheVolume.

Returns

str

reference ID

hasFilename() → bool

Check whether the file name attribute of the current SisypheTransforms instance is defined.

Returns

bool

True if file name attribute is defined

hasReferenceID() → bool

Check if the reference ID of the current SisypheTransforms instance is defined (not ‘’). The reference ID is the ID of the associated SisypheVolume.

Returns

bool

True if reference ID is defined

load(filename: str = '') → None

Load the current SisypheTransforms instance from a PySisyphe geometric transformation collection file (.xtrfs).

Parameters

filenamestr

• PySisyphe geometric transformation collection file name (optional)

• if filename is empty (‘’, default), the file name attribute of the current SisypheTransforms instance is used

classmethod openTransforms(filename) → SisypheTransforms

create a SisypheTransforms instance from PySisyphe geometric transformation collection file (.xtrfs).

Parameters

filenamestr

geometric transformation collection file name

Returns

SisypheTransforms

loaded geometric transformation collection

parseXML(doc: Document) → None

Read the current SisypheTransforms instance attributes from xml document instance.

Parameters

docminidom.Document

xml document

save(filename: str = '') → None

Save the current SisypheTransforms instance to a PySisyphe geometric transformation collection file (.xtrfs).

Parameters

filenamestr

PySisyphe geometric transformation collection file name (optional) if filename is empty (‘’, default), the file name attribute of the current SisypheTransforms instance is used

saveAs(filename: str) → None

Save the current SisypheTransforms instance to a PySisyphe geometric transformation collection file (.xtrfs).

Parameters

filenamestr

• PySisyphe geometric transformation collection file name

• The file name attribute of the current SisypheTransforms instance is replaced by this parameter

setFilenameFromVolume(img: SisypheVolume) → None

Copy the file name attribute of the current SisypheTransforms instance from the file name attribute of a SisypheVolume instance.

Parameters

imgSisyphe.core.sisypheVolume.SisypheVolume

volume filename to copy

setReferenceID(ID: str | SisypheVolume) → None

Set the reference ID attribute of the current SisypheTransforms instance. The reference ID is the ID of the associated SisypheVolume.

Parameters

IDstr | Sisyphe.core.sisypheVolume.SisypheVolume

ID or SisypheVolume’s ID attribute