Sisyphe.core.sisypheVolume

External packages/modules

• Cython, static compiler, https://cython.org/

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

• ITK, medical image processing, https://itk.org/

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

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

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

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

class Sisyphe.core.sisypheVolume.SisypheVolume(image: str | Image | ndarray | vtkImageData | ANTsImage | SisypheVolume | None = None, **kargs)

Description

PySisyphe volume class.

SisypheVolume is in RAS+ world coordinates convention (as MNI, Nibabel, NIFTI…) with origin to corner of the voxel

• x, direction[1.0, 0.0, 0.0]: left(-) to right(+)

• y, direction[0.0, 1.0, 0.0]: posterior(-) to anterior(+)

• z: direction[0.0, 0.0, 1.0]: inferior(-) to superior(+)

SimpleITK, ITK, DICOM is in LPS+ world coordinates convention

• x: right(-) to left(+) -> apply flipx for RAS+ conversion

• y: anterior(-) to posterior(+) -> apply flipy for RAS+ conversion

• z: inferior(-) to superior(+)

This class provides access to internal SimpleITK, ITK, VTK and numpy image classes, which share the same image buffer (behaviour inherited from the ancestor class SisypheImage).

Supported properties:

• Array ID: ID number calculated from scalar values (md5 algorithm)

• ID: space ID, can be shared between several volumes (i.e. image of the same subject with same field of view)

• identity: lastname, firstname, birthdate, gender

• acquisition: modality, sequence, date of scan, stereotactic frame, signal unit, labels for label map modality,

degrees of freedom and autocorrelations for statistical maps - display: look-up table colormap, range and window values, slope/intercept - acpc: AC coordinates, PC coordinates, geometric transformation to geometric reference with axes aligned on the AC-PC line with origin to the AC coordinates - transforms: list of geometric transformations to all co-registered volumes - dicom: access to Dicom fields of the related XmlDicom file (created during Dicom conversion)

Overloaded operators which work with int, float, SisypheVolume, SisypheImage, SimpleITK Image, and numpy array instances.

• Arithmetic +, -, /, //, *

• Logic & (and), | (or), ^ (xor), ~ (not)

• Relational >, >=, <, <=, ==, !=

Getter and Setter access to scalar values with slicing ability.

• Getter: v = instance_name[x, y, z]

• Setter: instance_name[x, y, z] = v

• x, y, z are int or pythonic slicing (i.e. python slice object, syntax first:last:step)

Deep copy methods to and from SimpleITK, ITK, VTK, ANTs, NiBabel and numpy image instances. IO methods for the most common neuroimaging file formats (BrainVoyager, FreeSurfer, Nifti, Nrrd, Minc, VTK).

Inheritance

object -> SisypheImage -> SisypheVolume

Creation: 04/02/2021 Last revisions: 18/04/2025

property acpc: SisypheACPC

Set the acp instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheACPC attributes are: (AC) and posterior (PC) commissure coordinates, rigid geometric transformation i.e. geometric transformation to reference with axes aligned on the AC-PC line, with midACPC point as center of rotation.

Returns

Sisyphe.core.sisypheImageAttributes.SisypheACPC

acpc attribute

property acquisition: SisypheAcquisition

Get the acquisition instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheAcquisition attributes are: modality, sequence, date of scan, frame, units of scalar values, labels for LB modality, degrees of freedom and autocorrelation for statistical map sequences.

Returns

Sisyphe.core.sisypheImageAttributes.SisypheAcquisition

acquisition attribute

cast(datatype: str) → SisypheVolume

SisypheVolume copy of the current SisypheVolume instance with a new datatype.

Parameters

datatypestr

numpy datatype

Returns

SisypheVolume

cast volume

clearXmlDicom() → None

Clear the XmlDicom instance of the current SisypheVolume instance (set to None).

componentsToSisypheVolumeCollection() → SisypheVolumeCollection

Copy each component of the current SisypheVolume instance to a SisypheVolumeCollection.

Returns

SisypheVolumeCollection

collection of components

copy() → SisypheVolume

SisypheVolume copy of the current SisypheVolume instance.

Returns

SisypheVolume

image copy

copyAttributesFrom(img: SisypheVolume, id: bool = True, identity: bool = True, acquisition: bool = True, display: bool = True, acpc: bool = True, transform: bool = True, slope: bool = True) → None

Copy the properties and attributes of a SisypheVolume instance to the current SisypheVolume instance.

Parameters

imgSisypheVolume

copy from this instance

idbool

copy ID attribute if True (default)

identitybool

copy identity property if True (default)

acquisitionbool

copy acquisition property if True (default)

displaybool

copy display property if True (default)

acpcbool

copy acpc property if True (default)

transformbool

copy transform property if True (default)

slopebool

copy slope/intercept attributes if True (default)

copyAttributesTo(img: SisypheVolume, id: bool = True, identity: bool = True, acquisition: bool = True, display: bool = True, acpc: bool = True, transform: bool = True, slope: bool = True) → None

Copy the properties and attributes of the current SisypheVolume instance to a SisypheVolume instance.

Parameters

imgSisypheVolume

copy to this instance

idbool

copy ID attribute if True (default)

identitybool

copy identity property if True (default)

acquisitionbool

copy acquisition property if True (default)

displaybool

copy display property if True (default)

acpcbool

copy acpc property if True (default)

transformbool

copy transform property if True (default)

slopebool

copy slope/intercept attributes if True (default)

copyComponent(c: int = 0) → SisypheVolume

Copy a component of the current SisypheVolume instance.

Parameters

cint

component index (default 0)

Returns

SisypheVolume

single-component volume

copyFilenameFrom(vol: SisypheVolume) → None

Copy the file name attribute of a SisypheVolume instance to the current SisypheVolume instance

Parameters

volSisypheVolume

copy from this volume

copyFilenameTo(vol: SisypheVolume) → None

Copy the file name attribute of the current SisypheVolume instance to a SisypheVolume instance.

Parameters

volSisypheVolume

copy to this volume

copyFromANTSImage(img: ANTsImage) → None

Copy an ANTsImage buffer to the current SisypheVolume instance. Image buffer is not shared between ANTsImage and SisypheVolume instances.

Parameters

imgants.core.ANTsImage

image to copy

copyFromITKImage(img: <itkTemplate itk::Image>) → None

Copy an ITKImage buffer to the current SisypheVolume instance. Image buffer is not shared between ITKImage and SisypheVolume instances.

Parameters

imgitk.Image

image to copy

copyFromNumpyArray(img: ndarray, spacing: list[float] | tuple[float, float, float] = (1.0, 1.0, 1.0), origin: list[float] | tuple[float, float, float] = (0, 0, 0), direction: tuple | list = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0), defaultshape: bool = True) → None

Copy a Numpy array buffer to the current SisypheVolume instance. Image buffer is not shared between numpy array and SisypheVolume instances.

Parameters

imgnumpy.ndarray

image to copy

spacinglist[float, float, float] | tuple[float, float, float]

voxel sizes in mm (default 1.0, 1.0, 1.0)

originlist[float, float, float] | tuple[float, float, float]

origin coordinates (default 0.0, 0.0, 0.0)

directionlist[float]

axes directions

defaultshapebool

if True (default), numpy shape order is reversed (i.e. z, y, x)

copyFromSITKImage(img: Image) → None

Copy a SimpleITK image buffer to the current SisypheVolume instance. Image buffer is not shared between SimpleITK image and SisypheVolume instances.

Parameters

imgSimpleITK.Image

image to copy

copyFromVTKImage(img: vtkImageData) → None

Copy a VTKImageData buffer to the current SisypheVolume instance. Image buffer is not shared between VTKImageData and SisypheVolume instances.

Parameters

imgvtk.vtkImageData

image to copy

copyPropertiesFrom(img: SisypheVolume, identity: bool = True, acquisition: bool = True, display: bool = True, acpc: bool = True, slope: bool = True) → None

Copy the properties of a SisypheVolume instance to the current SisypheVolume instance.

Parameters

imgSisypheVolume

copy from this instance

identitybool

copy identity property if True (default)

acquisitionbool

copy acquisition property if True (default)

displaybool

copy display property if True (default)

acpcbool

copy acpc property if True (default)

slopebool

copy slope/intercept attributes if True (default)

copyPropertiesTo(img: SisypheVolume, identity: bool = True, acquisition: bool = True, display: bool = True, acpc: bool = True, slope: bool = True) → None

Copy the properties of the current SisypheVolume instance to a SisypheVolume instance.

Parameters

imgSisypheVolume

copy to this instance

identitybool

copy identity property if True (default)

acquisitionbool

copy acquisition property if True (default)

displaybool

copy display property if True (default)

acpcbool

copy acpc property if True (default)

slopebool

copy slope/intercept attributes if True (default)

createXML(doc: Document, single: bool = True) → None

Write the current SisypheVolume instance attributes to xml instance. This method is called by save() and saveAs() methods, it is not recommended for use.

Parameters

docminidom.Document

xml document

singlebool

• if True, saved in a single file (xml part + binary part)

• if False, The xml part is saved in .xvol file and the binary part in .raw file

property dicom: XmlDicom | None

Get the XmlDicom instance of the current SisypheVolume instance. XmlDicom file stores DICOM fields in a key/value XML file. Each SisypheVolume converted from Dicom files is associated with an XmlDicom file (same file name with .xdcm extension).

Returns

Sisyphe.core.sisypheDicom.XmlDicom

XmlDicom attribute

property display: SisypheDisplay

Get the display instance of the current SisypheVolume instance.

Returns

Sisyphe.core.sisypheImageAttributes.SisypheDisplay

display attribute

getACPC() → SisypheACPC

Set the acp instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheACPC attributes are: (AC) and posterior (PC) commissure coordinates, rigid geometric transformation i.e. geometric transformation to reference with axes aligned on the AC-PC line, with midACPC point as center of rotation.

Returns

Sisyphe.core.sisypheImageAttributes.SisypheACPC

acpc attribute

getAcquisition() → SisypheAcquisition

Get the acquisition instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheAcquisition attributes are: modality, sequence, date of scan, frame, units of scalar values, labels for LB modality, degrees of freedom and autocorrelation for statistical map sequences.

Returns

Sisyphe.core.sisypheImageAttributes.SisypheAcquisition

acquisition attribute

getArrayID() → str

Get the Array ID attribute of the current SisypheVolume instance.

There are two types of identifier (i.e. ID):

• Array ID: unique, calculated from scalar values (md5 algorithm). This cannot be edited.

• ID: this is a space ID, it is not unique, all volumes sharing a common space have the same ID. This

attribute is used as key in the Sisyphe.core.sisypheTransform.SisypheTransforms instances.

Returns

str

Array ID

getBasename() → str

Get the base name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Returns

str

base name (base part of the file name)

getBitmapCapture(index: int, zoom: float = 1.0, orient: str = 'a') → QImage

Get a bitmap capture of the current SisypheVolume instance.

Parameters

indexint

slice index

zoomfloat

zoom factor (default 1.0, no zoom)

orientint

slice orientation (‘a’ axial, ‘c’ coronal or ‘s’ sagittal)

Returns

PyQt5.QtGui.QImage

Bitmap Qt image

getComponentAllZero(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get vectors whose values are all zero in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

single-component volume

getComponentArgmax() → SisypheVolume

Get the index of the highest scalar value of each vector in a multicomponent image.

Returns

SisypheVolume

single-component volume

getComponentArgmin(nonzero: bool = False) → SisypheVolume

Get the index of the lowest scalar value of each vector in a multicomponent image.

Parameters

nonzerobool

exclude zero values if True

Returns

SisypheVolume

single-component volume

getComponentKurtosis(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get kurtosis of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component kurtosis volume

getComponentMax(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get maximum of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component max volume

getComponentMean(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get mean of each vector in a multicomponent image. Process all components or a subset selected by indices.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed

Returns

SisypheVolume

component mean volume

getComponentMedian(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get median of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component median volume

getComponentMin(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get minimum of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component min volume

getComponentNumberOfNonZero(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get the number of non-zero values for each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

single-component volume

getComponentPercentile(perc: int = 25, c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get percentile of each vector in a multicomponent image.

Parameters

percint

percentile (default 25, first quartile)

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component percentile volume

getComponentRange(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get range (max - min) of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component range volume

getComponentSkewness(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get skewness of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component skewness volume

getComponentStd(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Get standard deviation of each vector in a multicomponent image.

Parameters

cint | list[int] | tuple[int, …] | slice | None

component indices

• list[int]: list of component indices

• tuple[int, …]: tuple of component indices

• slice: slice of component indices (start:end:step)

• None: no selection, all components are processed (default)

Returns

SisypheVolume

component std volume

getCompression() → bool

Get the compression attribute of the current SisypheVolume instance. PySisyphe volume format (.xvol) can be optionally gzipped.

Returns

bool

True, if compression is enabled

getCrop(c: tuple | list | ndarray) → SisypheVolume

Get a cropped volume of the current SisypheVolume instance.

Parameters

ctuple | list

xmin, xmax, ymin, ymax, zmin, zmax

Returns

SisypheVolume

cropped volume

getCroppedProjection(slc: int, d: str = 'left', thickness: float = 0.0, func: str = 'max', output: str = 'native', emask: SisypheVolume | None = None) → Image | ndarray | QImage | SisypheVolume

Get a 2D projection of the current SisypheVolume instance. The projection is processed to a depth expressed in mm from the head surface (default 0.0, whole brain, no thickness). Operators applied to voxels on a projection line: maximum, mean, median, standard deviation, sum. The volume can be cut out to a specified depth (slice index) in the direction of projection.

Parameters

slcint

cutting plan (orientation is given by d parameter, see below)

dstr

direction of the projection: ‘left’, ‘right’, ‘ant’, ‘post’, ‘top’, ‘bottom’

thickness: float

projection by a given thickness in mm (default 0.0, whole brain, no thickness)

funcstr

• ‘max’, ‘mean’, ‘median’, ‘std’, ‘sum’, ‘label’

• if ‘label’: threshold > 0 instead of automatic to process mask, and then uses ‘max’ operator

outputstr

output format: ‘numpy’ numpy.ndarray, ‘sitk’ SimpleITK.Image, ‘qimage’ PyQt5.gui.QImage, ‘native’ SisypheVolume

emaskSisypheVolume

if mask is None (default), mask is processed from the current SisypheImage instance (automatic thresholding with Huang algorithm for grayscale images, or non-zero voxels for label images). If an explicit mask is given, array size must match the current SisypheImage instance.

Returns

SimpleITK.Image | numpy.ndarray | PyQt5.QtGui.QPixmap | SisypheVolume

• SimpleITK.Image if output = ‘sitk’,

• numpy.ndarray if output = ‘numpy’,

• PyQt5.QtGui.QImage if output = ‘qimage’,

• SisypheVolume if output = ‘native’

getDirname() → str

Get the path name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Returns

str

path name (path part of the file name)

getDisplay() → SisypheDisplay

Get the display instance of the current SisypheVolume instance.

Returns

Sisyphe.core.sisypheImageAttributes.SisypheDisplay

display attribute

classmethod getFileExt() → str

Get SisypheVolume file extension.

Returns

str

‘.xvol’

getFilename() → str

Get the file name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Returns

str

file name

getFilenamePrefix(sep: str = '_') → str

Get prefix (if any) from the file name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Parameters

sepstr

char between prefix and base name (default ‘_’)

Returns

str

prefix

getFilenameSuffix(sep: str = '_') → str

Get suffix (if any) from the file name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Parameters

sepstr

char between prefix and base name (default ‘_’)

Returns

str

suffix

classmethod getFilterExt() → str

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

Returns

str

‘PySisyphe Volume (.xvol)’

getFlip(axis: list[bool]) → SisypheVolume

Get a flipped copy of the current SisypheVolume instance.

Parameters

axislist[bool, bool, bool]

flip axis if True, axis order x, y, z.

Returns

SisypheVolume

flipped volume

getICBMTransform() → SisypheTransform | None

Get the geometric transformation to the ICBM152 template space (if any) in the transforms attribute of the current SisypheVolume instance.

Returns

Sisyphe.core.sisypheTransform.SisypheTransform | None

geometric transform to ICBM152 template space

getICBMfromWorld(p: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float] | None

Convert world coordinates to ICBM coordinates. Returns None if the transforms attribute of the current SisypheVolume instance does not contain the ‘ICBM152’ ID.

Parameters

plist[float, float, float] | tuple[float, float, float]

World coordinates

Returns

tuple[float, float, float] | None

ICBM coordinates

getID() → str

Get the ID attribute of the current SisypheVolume instance.

There are two types of identifier (i.e. ID):

• Array ID: unique, calculated from scalar values (md5 algorithm). This cannot be edited.

• ID: this is a space ID, it is not unique, all volumes sharing a common space have the same ID. This

attribute is used as key in the Sisyphe.core.sisypheTransform.SisypheTransforms instances.

Returns

str

ID

getIdentity() → SisypheIdentity

Get the identity instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheIdentity attributes are: lastname, firstname, gender, birthdate

Returns

Sisyphe.core.sisypheImageAttributes.SisypheIdentity

identity attribute

getIntercept() → float

Set the intercept attribute of the current SisypheVolume instance. The slope and intercept attributes are used to apply a linear transformation of the scalar values: value = slope * scalar value + intercept.

Returns

float

intercept value

getLEKSELLTransform() → SisypheTransform | None

Get the geometric transformation to the LEKSELL space (if any) in the transforms attribute of the current SisypheVolume instance.

Returns

Sisyphe.core.sisypheTransform.SisypheTransform

geometric transform to LEKSELL space

getLEKSELLfromWorld(p: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float] | None

Convert world coordinates to LEKSELL coordinates Returns None if the transforms attribute of the current SisypheVolume instance does not contain the ‘LEKSELL’ ID.

Parameters

plist[float, float, float] | tuple[float, float, float]

World coordinates

Returns

tuple[float, float, float] | None

LEKSELL coordinates

getMask(algo: str = 'huang', morpho: str = '', niter: int = 1, kernel: int = 0, fill: str = '', c: int | None = 0) → SisypheVolume

Calc SisypheVolume mask of the head.

Parameters

algostr

Automatic thresholding algorithm used for background segmentation: ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’ or ‘moments’

morphostr

binary morphology operator, ‘dilate’, ‘erode’, ‘open’, ‘close’ or ‘’ (default, no morphology)

niterint

number of binary morphology iterations (default 1)

kernelint

structuring element size (default 0, no morphology)

fillstr

• ‘2d’, fill holes slice by slice

• ‘3d’, fill holes in 3D

• ‘’, no filling (default)

cint | None

• parameter only used for multi-component image

• int index of the component to process (default 0, first component)

• None, processing is performed on the mean image

Returns

SisypheVolume

mask

getMask2(algo: str = 'huang', morphoiter: int = 1, kernel: int = 0, c: int | None = 0) → SisypheVolume

Calc SisypheVolume mask of the head.

Parameters

algostr

Automatic thresholding algorithm used for background segmentation: ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’ or ‘moments’

morphoiterint

number of binary morphology iterations (default 2)

kernelint

structuring element size, 0 automatic value (kernel=2 if spacing < 1.5 mm, kernel=1 otherwise)

cint | None

• parameter only used for multi-component image

• int index of the component to process (default 0, first component)

• None, processing is performed on the mean image

Returns

SisypheVolume

mask

getMaskROI(name: str = 'Mask', algo: str = 'huang', morpho: str = '', niter: int = 1, kernel: int = 0, fill: str = '', c: int | None = 0) → SisypheROI

Calc Sisyphe.core.sisypheROI.SisypheROI mask of the head.

Parameters

namestr

roi name

algostr

Automatic thresholding algorithm used for background segmentation: ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’ or ‘moments’

morphostr

binary morphology operator, ‘dilate’, ‘erode’, ‘open’, ‘close’ or ‘’ (default, no morphology)

niterint

number of binary morphology iterations (default 1)

kernelint

structuring element size (default 0, no morphology)

fillstr

• ‘2d’, fill holes slice by slice

• ‘3d’, fill holes in 3D

• ‘’, no filling (default)

cint | None

• parameter only used for multi-component image

• int index of the component to process (default 0, first component)

• None, processing is performed on the mean image

Returns

Sisyphe.core.sisypheROI.SisypheROI

mask roi

getMaskROI2(name: str = 'Mask', algo: str = 'huang', morphoiter: int = 1, kernel: int = 0, c: int | None = 0) → SisypheROI

Calc Sisyphe.core.sisypheROI.SisypheROI mask of the head.

Parameters

namestr

roi name

algostr

Automatic thresholding algorithm used for background segmentation: ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’ or ‘moments’

morphoiterint

number of binary morphology iterations (default 2)

kernelint

structuring element size, 0 automatic value (kernel=2 if spacing < 1.5 mm, kernel=1 otherwise)

cint | None

• parameter only used for multi-component image

• int index of the component to process (default 0, first component)

• None, processing is performed on the mean image

Returns

Sisyphe.core.sisypheROI.SisypheROI

mask roi

getName() → str

Get the name attribute of the current SisypheVolume instance. This is the base part of the file name, without extension.

Returns

str

name (base part of the file name, without extension)

getNonZeroMask(c: int | None = 0) → SisypheVolume

Calc SisypheImage mask of non-zero voxels of the current SisypheImage instance.

Parameters

cint | None

• parameter only used for multi-component image

• int index of the component to process (default 0, first component)

• None, processing is performed on the mean image

Returns

SisypheVolume

non-zero mask

getOrientation() → int

Get the orientation attribute of the current SisypheVolume instance as int code.

Returns

int

1 ‘axial’, 2 ‘coronal’, 3 ‘sagittal’ or 0 ‘unspecified’

getOrientationAsString() → str

Get the orientation attribute of the current SisypheVolume instance as str.

Returns

str

‘axial’, ‘coronal’, ‘sagittal’ or ‘unspecified’

getProjection(d: str = 'left', thickness: float = 0.0, func: str = 'max', output: str = 'native', emask: SisypheVolume | None = None) → Image | ndarray | QImage | SisypheVolume

Get a 2D projection of the current SisypheVolume instance. The projection is processed to a depth expressed in mm from the head surface (default 0.0, whole brain, no thickness). Operators applied to voxels on a projection line: maximum, mean, median, standard deviation, sum.

Parameters

dstr

direction of the projection: ‘left’, ‘right’, ‘ant’, ‘post’, ‘top’, ‘bottom’

thickness: float

projection by a given thickness in mm (default 0.0, whole brain, no thickness)

funcstr

• ‘max’, ‘mean’, ‘median’, ‘std’, ‘sum’, ‘label’

• if ‘label’: threshold > 0 instead of automatic to process mask, and then uses ‘max’ operator

outputstr

output format: ‘numpy’ numpy.ndarray, ‘sitk’ SimpleITK.Image, ‘qimage’ PyQt5.gui.QImage, ‘native’ SisypheVolume

emaskSisypheVolume

if mask is None (default), mask is processed from the current SisypheImage instance (automatic thresholding with Huang algorithm for grayscale images, or non-zero voxels for label images). If an explicit mask is given, array size must match the current SisypheImage instance.

Returns

SimpleITK.Image | numpy.ndarray | PyQt5.QtGui.QPixmap | SisypheVolume

• SimpleITK.Image if output = ‘sitk’,

• numpy.ndarray if output = ‘numpy’,

• PyQt5.QtGui.QImage if output = ‘qimage’,

• SisypheVolume if output = ‘native’

getROI(threshold: float = 0.5, op: str = '>', c: int | None = 0) → SisypheROI

Converting current SisypheVolume instance to Sisyphe.core.sisypheROI.SisypheROI.

Parameters

thresholdfloat

threshold for binarization (default 0.5)

opstr

comparison operator: ‘>’ (default), ‘>=’, ‘<’, ‘<=’, ‘==’, ‘!=’

cint | None

parameter only used for multi-component image - int index of the component to process (default 0, first component) - None, processing is performed on the mean image

Returns

Sisyphe.core.sisypheROI.SisypheROI

getSlope() → float

Get the slope attribute of the current SisypheVolume instance. The slope and intercept attributes are used to apply a linear transformation of the scalar values: value = slope * scalar value + intercept.

Returns

float

slope value

getStandardizeIntensity(method: str = 'norm') → SisypheVolume

Get an intensity normalized copy of the current SisypheImage instance.

Parameters

methodstr

• ‘norm’, standardize the intensity as zscore (i.e. zero mean, [-std, +std] mapped to [0, 1]

• ‘rescale’, standardize the intensity values to the range [0, 1]

Returns

SisypheVolume

standardized volume

getTransformFromID(ID: str | SisypheVolume) → SisypheTransform | None

Get the geometric transformation corresponding to a given ID in the transforms attribute of the current SisypheVolume instance.

Parameters

IDstr | SisypheVolume

ID or SisypheVolume ID attribute

Returns

Sisyphe.core.sisypheTransform.SisypheTransform | None

geometric transform

getTransformFromIndex(index: int) → SisypheTransform

Get the geometric transformation corresponding to a given index in the transforms attribute of the current SisypheVolume instance.

Parameters

indexint

index in geometric transform collection

Returns

Sisyphe.core.sisypheTransform.SisypheTransform

geometric transform

getTransforms() → SisypheTransforms

Set the transforms attribute of the current SisypheVolume attribute. Each SisypheVolume is associated with a SisypheTransforms instance, which stores all the geometric transformations calculated from co-registrations with other SisypheVolume instances. This transforms attribute is saved the same file name with .xtrfs extension.

Returns

SisypheTransforms

geometric transform collection

getTruncateIntensity(centile: int = 1, outputrange: tuple[float, float] | None = None) → SisypheVolume

Get intensity truncated copy of the current SisypheImage instance. Truncate threshold is expressed in percentile (min threshold = centile, max threshold = 100 - centile). The max and min values of the output image are given in the output range parameter. If output range is None, max and min values of the output image are the max and min truncate thresholds.

Parameters

centileint

truncate threshold expressed in percentile

outputrangetuple[float, float] | None

max and min values of the output image

Returns

SisypheVolume

truncated volume

classmethod getVolumeAttribute(filename: str, attr: str) → str | int | float | tuple | list

Get an attribute of a PySisyphe Volume file (.xvol).

Parameters

filenamestr

PySisyphe Volume file name

attrstr

attribute name: ID, size, spacing, FOV, number of componentes, datatype, origin, directions, orientation, modality, sequence, date of scan, stereotactic frame, scalar unit, range, window, slope, intercept, lastname, firstname, gender, date of birthday

Returns

str | int | float | tuple | list

attribute value

classmethod getVolumeAttributes(filename: str) → dict

Get attributes of a PySisyphe Volume file (.xvol).

Parameters

filenamestr

PySisyphe Volume file name

Returns

dict

attribute keys: ID, size, spacing, FOV, number of componentes, datatype, origin, directions, orientation, modality, sequence, date of scan, stereotactic frame, scalar unit, range, window, slope, intercept, lastname, firstname, gender, date of birthday

getWorldfromICBM(p: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float] | None

Convert ICBM coordinates to world coordinates Returns None if the transforms attribute of the current SisypheVolume instance does not contain the ‘ICBM152’ ID.

Parameters

plist[float, float, float] | tuple[float, float, float]

ICBM coordinates

Returns

tuple[float, float, float] | None

world coordinates

getWorldfromLEKSELL(p: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float] | None

Convert LEKSELL coordinates to world coordinates Returns None if the transforms attribute of the current SisypheVolume instance does not contain the ‘LEKSELL’ ID.

Parameters

plist[float, float, float] | tuple[float, float, float]

LEKSELL coordinates

Returns

tuple[float, float, float] | None

world coordinates

getWorldfromTransform(ID: str | SisypheVolume, p: list[float] | tuple[float, float, float]) → list[float] | tuple[float, float, float]

Extract the geometric transformation corresponding to an ID key from the SisypheTransforms attribute of the current SisypheVolume instance. Then apply this geometric transformation to a given point.

Parameters

IDstr | SisypheVolume

ID or SisypheVolume ID attribute

plist[float, float, float] | tuple[float, float, float]

point coordinates

Returns

tuple[float, float, float]

point coordinates, returns the same point coordinates if the ID is not in the SisypheTransforms attribute

getXmlDicom() → XmlDicom | None

Get the XmlDicom instance of the current SisypheVolume instance. XmlDicom file stores DICOM fields in a key/value XML file. Each SisypheVolume converted from Dicom files is associated with an XmlDicom file (same file name with .xdcm extension).

Returns

Sisyphe.core.sisypheDicom.XmlDicom

XmlDicom attribute

classmethod getXmlVolume(filename: str) → XmlVolume

Get a XmlVolume instance of a PySisyphe Volume file (.xvol).

Parameters

filenamestr

PySisyphe Volume file name

Returns

Sisyphe.core.sisypheXml.XmlVolume

XmlVolume

hasFilename() → bool

Check whether the filename attribute of the current SisypheVolume instance is defined (i.e. not ‘’)

Returns

bool

True if filename attribute is defined

hasICBMTransform() → bool

Check whether the transforms attribute of the current SisypheVolume instance contains a geometric transformation to the ICBM152 template space (contains ID == ‘ICBM152’).

Returns

bool

True if an ICBM152 transform is in collection

hasLEKSELLTransform() → bool

Check whether the transforms attribute of the current SisypheVolume instance contains a geometric transformation to the LEKSELL space (contains ID == ‘LEKSELL’).

Returns

bool

True if a LEKSELL transform is in collection

hasSameID(ID: str | SisypheVolume | SisypheROI | SisypheMesh) → bool

Check if an ID is identical to the ID of the current SisypheVolume instance.

Parameters

IDstr | SisypheVolume | Sisyphe.core.sisypheROI.SisypheROI | Sisyphe.core.sisypheMesh.SisypheMesh

ID, SisypheVolume ID attribute, SisypheROI ID attribute or SisypheMesh ID attribute

Returns

bool

hasTransform(ID: str | SisypheVolume) → bool

Check whether the transforms attribute of the current SisypheVolume attribute contains a given ID.

Parameters

IDstr | SisypheVolume

ID or SisypheVolume ID attribute

Returns

bool

True if geometric transform is in collection

hasXmlDicom() → bool

Check whether the XmlDicom instance of the current SisypheVolume instance is defined (not None). XmlDicom file stores DICOM fields in a key/value XML file. Each SisypheVolume converted from Dicom files is associated with an XmlDicom file (same file name with .xdcm extension).

Returns

Sisyphe.core.sisypheDicom.XmlDicom

XmlDicom attribute

property identity: SisypheIdentity

Get the identity instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheIdentity attributes are: lastname, firstname, gender, birthdate

Returns

Sisyphe.core.sisypheImageAttributes.SisypheIdentity

identity attribute

isAxial() → bool

Check whether the orientation attribute of the current SisypheVolume instance is axial.

Returns

bool

True if axial orientation

isCoronal() → bool

Check whether the orientation attribute of the current SisypheVolume instance is coronal.

Returns

bool

True if coronal orientation

isIdentityTransform(ID: str | SisypheVolume) → bool

Check whether the geometric transformation corresponding to a given ID in the transforms attribute of the current SisypheVolume instance, is an identity transformation.

Parameters

IDstr | SisypheVolume

ID or SisypheVolume ID attribute

Returns

bool

True if identity geometric transform

isSagittal() → bool

Check whether the orientation attribute of the current SisypheVolume instance is sagittal.

Returns

bool

True if sagittal orientation

labelToROI(label: int = 0) → SisypheROI

Converting a label of the current SisypheVolume instance to Sisyphe.core.sisypheROI.SisypheROI. The modality of the current SisypheVolume instance must be LB (Label).

Parameters

labelint

label index (default 0)

Returns

Sisyphe.core.sisypheROI.SisypheROI

roi converted from label volume

load(filename: str = '', binary: bool = True) → None

Load the current SisypheVolume instance from a PySisyphe Volume (.xvol) file.

Parameters

filenamestr

PySisyphe Volume file name (optional). If filename is empty (‘’, default), the file name attribute of the current SisypheVolume instance is used

binarybool

if False, load only xml part (attributes), not binary part (array), default is True (load xml and binary parts)

loadFromBrainVoyagerVMR(filename: str) → None

Load the current SisypheVolume instance from a BrainVoyager (.vmr) file.

Parameters

filenamestr

BrainVoyager file name

loadFromFreeSurferMGH(filename: str) → None

Load the current SisypheVolume instance from a FreeSurfer (.mgh, .mgz) file.

Parameters

filenamestr

FreeSurfer file name

loadFromMINC(filename: str) → None

Load the current SisypheVolume instance from a Minc (.minc) file.

Parameters

filenamestr

Minc file name

loadFromNIFTI(filename: str, reorient: bool = True) → None

Load the current SisypheVolume instance from a Nifti (.nii) file.

Parameters

filenamestr

Nifti file name

reorientbool

conversion to RAS+ world coordinates convention if True (default)

loadFromNRRD(filename: str) → None

Load the current SisypheVolume instance from a Nrrd (.nrrd) file.

Parameters

filenamestr

Nrrd file name

loadFromNumpy(filename: str) → None

Load the current SisypheVolume instance from a numpy (.npy) file.

Parameters

filenamestr

numpy file name

loadFromSisyphe(filename: str) → None

Load the current SisypheVolume instance from an old Sisyphe Volume (.vol) file.

Parameters

filenamestr

old Sisyphe Volume file name

loadFromVTK(filename: str) → None

Load the current SisypheVolume instance from a VTK (.vtk) file.

Parameters

filenamestr

VTK file name

loadTransforms() → None

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

loadXmlDicom() → None

Load the XmlDicom instance associated to the current SisypheVolume instance. XmlDicom file stores DICOM fields in a key/value XML file. Each SisypheVolume converted from Dicom files is associated with an XmlDicom file (same file name with .xdcm extension).

classmethod openVolume(filename: str) → SisypheVolume | None

create a SisypheVolume instance from PySisyphe Volume file (.xvol).

Parameters

filenamestr

volume file name

Returns

SisypheVolume

loaded volume

parseXML(doc: Document) → dict

Read the current SisypheVolume instance attributes from xml instance. This method is called by load() method, it is not recommended for use.

Parameters

docminidom.Document

xml document

Returns

dict[str]

Key / Value

• ‘size’: list[int, int, int], image size in each axis

• ‘components’: int, number of components

• ‘spacing’: list[float, float, float], voxel size in each axis

• ‘origin’: list[float, float, float], origin coordinates

• ‘datatype’: str, numpy datatype

• ‘directions’: list[float], direction vectors

• ‘array’: bytes, array image

removeAllPrefixes(sep: str = '_') → None

Remove all prefixes from the file name attribute of the current SisypheVolume instance.

Parameters

sepstr

char between prefix(es) (default ‘_’)

removeAllSuffixes(sep: str = '_') → None

Remove all prefixes from the file name attribute of the current SisypheVolume instance.

Parameters

sepstr

char between prefix(es) (default ‘_’)

removeDisplay() → None

Clear the display attribute of the current SisypheVolume instance. Default display values: gray level colormap, no windowing.

removeNeckSlices(f: float = 1.8) → SisypheVolume

Get a new SisypheVolume instance, cropped in z. Most sagittal MRI scans have extensive and useless inferior coverage. This function crop MR volume in z direction, removing empty slices and lower slices of neck below foramen magnum.

Parameters

ffloat

multiplicative factor to adjust the neck slice. Lower values remove more slices, higher values keep more slices (between 1.5 and 2.0, default 1.8 close to the foramen magnum for most MR images)

Returns

SisypheVolume

cropped volume

removeSuffixNumber() → None

Remove a suffix number (if any) from the file name attribute of the current SisypheVolume instance.

save(filename: str = '', single: bool = True) → None

Save the current SisypheVolume instance to a PySisyphe Volume (.xvol) file.

Parameters

filenamestr

PySisyphe Volume file name (optional). if filename is empty (‘’, default), the file name attribute of the current SisypheVolume instance is used

singlebool

• if True, saved in a single file (xml part + binary part)

• if False, The xml part is saved in .xvol file and the binary part in .raw file

saveAs(filename: str, single: bool = True) → None

Save the current SisypheVolume instance to a PySisyphe Volume (.xvol) file.

Parameters

filenamestr

PySisyphe Volume file name

singlebool

• if True, saved in a single file (xml part + binary part)

• if False, The xml part is saved in .xvol file and the binary part in .raw file

saveBitmapCapture(filename: str, index: int, zoom: float = 1.0, orient: str = 'a') → None

Save a bitmap capture of the current SisypheVolume instance.

Parameters

filename : str index : int

slice index

zoomfloat

zoom factor (default 1.0, no zoom)

orientint

slice orientation (‘a’ axial, ‘c’ coronal or ‘s’ sagittal)

Returns

PyQt5.QtGui.QPixmap

Bitmap Qt pixmap

saveToMINC(filename: str = '') → None

Save the current SisypheVolume instance to a Minc (.minc) file.

Parameters

filenamestr

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

saveToNIFTI(filename: str = '', compress: bool = False) → None

Save the current SisypheVolume instance to a Nifti (.nii) file.

Parameters

filenamestr

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

compressbool

gzip compression if True (default False)

saveToNRRD(filename: str = '') → None

Save the current SisypheVolume instance to a Nrrd (.nrrd) file.

Parameters

filenamestr

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

saveToNumpy(filename: str = '') → None

Save the current SisypheVolume instance to a numpy (.npy) file.

Parameters

filenamestr

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

saveToVTK(filename: str = '') → None

Save the current SisypheVolume instance to a VTK (.vtk) file.

Parameters

filenamestr

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

saveTransforms() → None

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

setACPC(acpc: SisypheACPC) → None

Set the acp instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheACPC attributes are: (AC) and posterior (PC) commissure coordinates, rigid geometric transformation i.e. geometric transformation to reference with axes aligned on the AC-PC line, with midACPC point as center of rotation.

Parameters

acpcSisyphe.core.sisypheImageAttributes.SisypheACPC

acpc attribute

setAcquisition(acquisition: SisypheAcquisition) → None

Set the acquisition instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheAcquisition attributes are: modality, sequence, date of scan, frame, units of scalar values, labels for LB modality, degrees of freedom and autocorrelation for statistical map sequences.

Parameters

acquisitionSisyphe.core.sisypheImageAttributes.SisypheAcquisition

acquisition attribute

setCompression(v: bool) → None

Set the compression attribute of the current SisypheVolume instance. ySisyphe volume format (.xvol) can be optionally gzipped.

Parameters

vbool

compression is enabled if True

setCompressionOff() → None

Disables gzip file compression of the current SisypheVolume instance. PySisyphe volume format (.xroi) can be optionally gzipped.

setCompressionOn() → None

Enables gzip file compression of the current SisypheVolume instance. PySisyphe volume format (.xroi) can be optionally gzipped.

setDefaultDirections() → None

Set vectors of image axes to default in RAS+ coordinates system. PySisyphe uses RAS+ world coordinates system convention (as MNI, Nibabel, Dipy…) with origin to corner of the voxel

• x, direction [1.0, 0.0, 0.0]: left(-) to right(+)

• y, direction [0.0, 1.0, 0.0]: posterior(-) to anterior(+)

• z, direction [0.0, 0.0, 1.0]: inferior(-) to superior(+)

Directions is a list of 9 float, 3 vectors of 3 floats

• First vector, x image axis direction, [1.0, 0.0, 0.0] (RAS+ default)

• Second vector, y image axis direction, [0.0, 1.0, 0.0] (RAS+ default)

• Third vector, y image axis direction, [0.0, 0.0, 1.0] (RAS+ default)

setDirections(direction: tuple = (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0)) → None

Set vectors of image axes in RAS+ coordinates system. PySisyphe uses RAS+ world coordinates system convention (as MNI, Nibabel, Dipy…) with origin to corner of the voxel.

• x, direction [1.0, 0.0, 0.0]: left(-) to right(+)

• y, direction [0.0, 1.0, 0.0]: posterior(-) to anterior(+)

• z, direction [0.0, 0.0, 1.0]: inferior(-) to superior(+)

Directions is a list of 9 float, 3 vectors of 3 floats

• First vector, x image axis direction, [1.0, 0.0, 0.0] (RAS+ default)

• Second vector, y image axis direction, [0.0, 1.0, 0.0] (RAS+ default)

• Third vector, y image axis direction, [0.0, 0.0, 1.0] (RAS+ default)

Parameters

directionlist[float]

vectors of image axes

setDirname(path: str) → None

Set the path name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Parameters

pathstr

path name (path part of the file name)

setDisplay(display: SisypheDisplay) → None

Set the display instance of the current SisypheVolume instance.

Parameters

displaySisyphe.core.sisypheImageAttributes.SisypheDisplay

display attribute

setFilename(filename: str) → None

Set the file name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Parameters

filenamestr

file name

setFilenamePrefix(prefix: str, sep: str = '_') → None

Set a prefix to the file name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Parameters

prefixstr

prefix to add

sepstr

char between prefix and base name (default ‘_’)

setFilenameSuffix(suffix: str, sep: str = '_') → None

Set a suffix to the file name attribute of the current SisypheVolume instance. The file name attribute is used to save the current SisypheVolume instance.

Parameters

suffixstr

suffix to add

sepstr

char between base name and suffix (default ‘_’)

setID(ID: str | SisypheVolume) → None

Set the ID attribute of the current SisypheVolume instance.

There are two ID types:

• ID is a space ID, it is not unique, all volumes sharing a common space have the same ID. This attribute is

used as key in the Sisyphe.core.sisypheTransform.SisypheTransforms instances - Array ID, unique, calculated from scalar values (md5 algorithm). This cannot be edited.

Parameters

IDstr | SisypheVolume

ID or SisypheVolume ID attribute

setIDtoATROPOS() → None

Set the ID attribute of the current SisypheVolume instance to ATROPOS.

setIDtoICBM152() → None

Set the ID attribute of the current SisypheVolume instance to ICBM152.

setIDtoICBM452() → None

Set the ID attribute of the current SisypheVolume instance to ICBM452.

setIDtoSRI24() → None

Set the ID attribute of the current SisypheVolume instance to SRI24.

setIdentity(identity: SisypheIdentity) → None

Set the identity instance of the current SisypheVolume instance. Sisyphe.core.sisypheImageAttributes.SisypheIdentity attributes are: lastname, firstname, gender, birthdate

Parameters

identitySisyphe.core.sisypheImageAttributes.SisypheIdentity

identity attribute

setIntercept(intercept: float = 0.0) → None

Set the intercept attribute of the current SisypheVolume instance. The slope and intercept attributes are used to apply a linear transformation of the scalar values: value = slope * scalar value + intercept.

Parameters

interceptfloat

intercept value

setOrientation(orient: str = 'axial') → None

Set the orientation attribute of the current SisypheVolume instance.

Parameters

orientstr

‘axial’, ‘coronal’, ‘sagittal’ or ‘unspecified’

setOrientationToAxial() → None

Set the orientation attribute of the current SisypheVolume instance to axial.

setOrientationToCoronal() → None

Set the orientation attribute of the current SisypheVolume instance to coronal.

setOrientationToSagittal() → None

Set the orientation attribute of the current SisypheVolume instance to sagittal.

setSITKImage(img: Image) → None

Shallow copy of a SimpleITK Image to the SimpleITK Image attribute of the current SisypheVolume instance. Image buffer is shared between SimpleITK image and current SisypheVolume instances.

Parameters

imgSimpleITK.Image

image to copy

setSlope(slope: float = 1.0) → None

Set the slope attribute of the current SisypheVolume instance. The slope and intercept attributes are used to apply a linear transformation of the scalar values: value = slope * scalar value + intercept.

Parameters

slopefloat

slope value

setTransforms(transforms: SisypheTransforms, force: bool = False) → None

Set the transforms attribute of the current SisypheVolume attribute. Each SisypheVolume is associated with a SisypheTransforms instance which stores all the geometric transformations calculated from co-registrations with other SisypheVolume instances. This transforms attribute is saved the same file name with .xtrfs extension.

Parameters

transformsSisypheTransforms

geometric transform collection to copy

forcebool

if True, ignores reference ID (default False)

property transforms: SisypheTransforms

Set the transforms attribute of the current SisypheVolume attribute. Each SisypheVolume is associated with a SisypheTransforms instance, which stores all the geometric transformations calculated from co-registrations with other SisypheVolume instances. This transforms attribute is saved the same file name with .xtrfs extension.

Returns

SisypheTransforms

geometric transform collection

updateArrayID() → None

Re-calculate the array ID attribute from the scalar values of the current SisypheVolume instance.

class Sisyphe.core.sisypheVolume.SisypheVolumeCollection

Description

Named list container of SisypheVolume instances. Container key to address elements can be int index, ID str or SisypheVolume (uses ID attribute as str key).

Getter methods of the SisypheVolume class are added to the SisypheVolumeCollection class, returning a list of values sent by each SisypheVolume element in the container.

Inheritance

object -> SisypheVolumeCollection

Creation: 04/02/2021 Last revision: 20/12/2024

append(value: SisypheVolume) → None

Append a SisypheVolume element in the current SisypheVolumeCollection instance container.

Parameters

valueSisypheVolume

volume to append

clear() → None

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

copy() → SisypheVolumeCollection

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

Returns

SisypheVolumeCollection

Shallow copy of collection elements

copyFromList(vols: list[SisypheVolume]) → None

Copy a list of SisypheVolume to the current SisypheVolumeCollection instance container (Shallow copy of image array)

Parameters

volslist[SisypheVolume]

list of volumes to copy in collection

copyToList() → list[SisypheVolume]

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

Returns

list[SisypheVolume]

shallow copy of collection elements

copyToMultiComponentSisypheVolume() → SisypheVolume

Copy the current SisypheVolumeCollection instance to a multi-component SisypheVolume instance

Returns

SisypheVolume

multi-component volume

copyToNumpyArray(defaultshape: bool = True) → ndarray

Copy the current SisypheVolumeCollection instance to a numpy.ndarray.

Returns

numpy.ndarray

multi-component numpy array

count() → int

Get the number of SisypheVolume elements in the current SisypheVolumeCollection instance container.

Returns

int

number of SisypheVolume elements

getArgmaxVolume() → SisypheVolume

Calculate argmax image of the SisypheVolume images in the current SisypheVolumeCollection instance. argmax returns the image index of the minimum value in the SisypheVolumeCollection instance.

Returns

SisypheVolume

argmax volume

getArgminVolume() → SisypheVolume

Calculate argmin image of the SisypheVolume images in the current SisypheVolumeCollection instance. argmin returns the image index of the minimum value in the SisypheVolumeCollection instance.

Returns

SisypheVolume

argmin volume

getList() → list[SisypheVolume]

Get the list attribute of the current SisypheVolumeCollection instance container (Shallow copy of the elements).

Returns

list[SisypheVolume]

shallow copy of collection

getMaxVolume(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Calculate maximum image of the SisypheVolume images in the current SisypheVolumeCollection instance. Process all volumes or a subset selected by indices.

Parameters

cint | list[int] | tuple[int, …] | slice | None

volume indices

• list[int]: list of indices

• tuple[int, …]: tuple of indices

• slice: slice of indices (start:end:step)

• None: no selection, all volumes are processed

Returns

SisypheVolume

max volume

getMeanVolume(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Calculate mean image of the SisypheVolume images in the current SisypheVolumeCollection instance. Process all volumes or a subset selected by indices.

Parameters

cint | list[int] | tuple[int, …] | slice | None

volume indices

• list[int]: list of indices

• tuple[int, …]: tuple of indices

• slice: slice of indices (start:end:step)

• None: no selection, all volumes are processed

Returns

SisypheVolume

mean volume

getMedianVolume(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Calculate median image of the SisypheVolume images in the current SisypheVolumeCollection instance. Process all volumes or a subset selected by indices.

Parameters

cint | list[int] | tuple[int, …] | slice | None

volume indices

• list[int]: list of indices

• tuple[int, …]: tuple of indices

• slice: slice of indices (start:end:step)

• None: no selection, all volumes are processed

Returns

SisypheVolume

median volume

getMinVolume(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Calculate minimum image of the SisypheVolume images in the current SisypheVolumeCollection instance. Process all volumes or a subset selected by indices.

Parameters

cint | list[int] | tuple[int, …] | slice | None

volume indices

• list[int]: list of indices

• tuple[int, …]: tuple of indices

• slice: slice of indices (start:end:step)

• None: no selection, all volumes are processed

Returns

SisypheVolume

min volume

getPercentileVolume(perc: int = 25, c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Calculate percentile image of the SisypheVolume images in the current SisypheVolumeCollection instance. Process all volumes or a subset selected by indices.

Parameters

percint

percentile value (default 25, first quartile)

cint | list[int] | tuple[int, …] | slice | None

volume indices

• list[int]: list of indices

• tuple[int, …]: tuple of indices

• slice: slice of indices (start:end:step)

• None: no selection, all volumes are processed

Returns

SisypheVolume

percentile volume

getStdVolume(c: list[int] | tuple[int, ...] | slice | None = None) → SisypheVolume

Calculate standard deviation image of the SisypheVolume images in the current SisypheVolumeCollection instance. Process all volumes or a subset selected by indices.

Parameters

cint | list[int] | tuple[int, …] | slice | None

volume indices

• list[int]: list of indices

• tuple[int, …]: tuple of indices

• slice: slice of indices (start:end:step)

• None: no selection, all volumes are processed

Returns

SisypheVolume

std volume

getValuesAt(x: int, y: int, z: int, asnumpy: bool = False) → list[float] | ndarray

Get scalar values in a voxel of the SisypheVolume images in the current SisypheVolumeCollection instance. The current SisypheVolumeCollection instance must be homogeneous (see isHomogeneous() method)

Parameters

xint

x-axis voxel coordinate

yint

y-axis voxel coordinate

zint

z-axis voxel coordinate

asnumpybool

returns numpy.ndarray if True, list[float] otherwise (default False)

Returns

numpy.ndarray | list[float]

volues at voxel (x, y, z)

getValuesInsideMask(mask: SisypheImage) → list[ndarray]

Get scalar values inside a mask of the SisypheVolume images in the current SisypheVolumeCollection instance. The current SisypheVolumeCollection instance must be homogeneous (see isHomogeneous() method)

Parameters

mask : Sisyphe.core.sisypheImage.SisypheImage

Returns

numpy.ndarray | list[float]

values inside mask

getVector(x: int, y: int, z: int, asnumpy: bool = False) → list[float] | ndarray

Get scalar values in a voxel of the SisypheVolume images in the current SisypheVolumeCollection instance. The current SisypheVolumeCollection instance must be homogeneous (see isHomogeneous() method)

Parameters

xint

x-axis voxel coordinate

yint

y-axis voxel coordinate

zint

z-axis voxel coordinate

asnumpybool

returns numpy.ndarray if True, list[float] otherwise (default False)

Returns

numpy.ndarray | list[float]

volues at voxel (x, y, z)

index(value: str | SisypheVolume) → int

Index of a SisypheVolume element in the current SisypheVolumeCollection instance container.

Parameters

valuestr | SisypheVolume

ID, SisypheVolume ID attribute

Returns

int

index

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

Insert a SisypheVolume element at the position given by the key in the current SisypheVolumeCollection instance container.

Parameters

keyint | str | SisypheVolume

index, ID, SisypheVolume ID attribute

valueSisypheVolume

volume to insert

isEmpty() → bool

Check if SisypheVolumeCollection instance container is empty.

Returns

bool

True if container is empty

isHomogeneous() → bool

Check whether SisypheVolume instances is the current SisypheVolumeCollection are homogeneous (i.e. same field of view and datatype)

Returns

bool

True if container is homogeneous

keys() → list[str]

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

Returns

list[str]

list of keys in the container

labelSTAPLECombination() → SisypheVolume

Performs a pixelwise combination of Labels, where each of them represents a segmentation of the same image. The labelings are weighted relative to each other based on their “performance” as estimated by an expectation-maximization algorithm. In the process, a ground truth segmentation is estimated, and the estimated performances of the individual segmentations are relative to this estimated ground truth.

The algorithm is based on the binary STAPLE algorithm by Warfield et al. : S. Warfield, K. Zou, W. Wells, “Validation of image segmentation and expert quality with an expectation-maximization algorithm” in MICCAI 2002: Fifth International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer-Verlag, Heidelberg, Germany, 2002, pp. 298-306

Returns

SisypheVolume

combined volume

labelVotingCombination() → SisypheVolume

Performs a pixelwise combination of Labels, where each of them represents a segmentation of the same image. Label voting is a simple method of classifier combination applied to image segmentation. Typically, the accuracy of the combined segmentation exceeds the accuracy of the input segmentations. Voting is therefore commonly used as a way of boosting segmentation performance.

The use of label voting for combination of multiple segmentations is described in T. Rohlfing and C. R. Maurer, Jr., “Multi-classifier framework for atlas-based image segmentation,” Pattern Recognition Letters, 2005.

Returns

SisypheVolume

combined volume

load(filenames: str | list[str]) → None

Load SisypheVolume elements in the current SisypheVolumeCollection instance container from a list of PySisyphe volume (.xvol) file names.

Parameters

filenamesstr | list[str]

list of PySisyphe Volume (.xvol) file names

loadFromMINC(filenames: str | list[str]) → None

Load SisypheVolume elements in the current SisypheVolumeCollection instance container from a list of Minc file names.

Parameters

filenamesstr | list[str]

list of Minc file names

loadFromNIFTI(filenames: str | list[str]) → None

Load SisypheVolume elements in the current SisypheVolumeCollection instance container from a list of Nifti file names.

Parameters

filenamesstr | list[str]

list of Nifti file names

loadFromNRRD(filenames: str | list[str]) → None

Load SisypheVolume elements in the current SisypheVolumeCollection instance container from a list of Nrrd file names.

Parameters

filenamesstr | list[str]

list of Nrrd file names

loadFromSisyphe(filenames: str | list[str]) → None

Load SisypheVolume elements in the current SisypheVolumeCollection instance container from a list of old Sisyphe volume (.vol) file names.

Parameters

filenamesstr | list[str]

list of old Sisyphe Volume (.vol) file names

loadFromVTK(filenames: str | list[str]) → None

Load SisypheVolume elements in the current SisypheVolumeCollection instance container from a list of VTK file names.

Parameters

filenamesstr | list[str]

list of VTK file names

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

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

Parameters

keyint | str | SisypheVolume

• index, ID, SisypheVolume ID attribute

• if None, remove the last element

Returns

SisypheVolume

element removed from the container

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

Remove a SisypheVolume element from the current SisypheVolumeCollection instance container.

Parameters

valueint | str | SisypheVolume

index, ID, SisypheVolume ID attribute

resample(trf: SisypheTransform, save: bool = True, dialog: bool = False, prefix: str | None = None, suffix: str | None = None, wait: DialogWait | None = None) → SisypheVolumeCollection

Resample all the SisypheVolume images in the current SisypheVolumeCollection instance. The current SisypheVolumeCollection instance must be homogeneous (see isHomogeneous() method)

Parameters

trfSisyphe.core.sisypheTransform.SisypheTransform

geometric transformation to apply

savebool

save resampled images if True (default)

dialogbool

• dialog to choice the resampled image file names, if True

• addBundle suffix/prefix to the image file names, if False (default)

prefixstr | None

file name prefix of the resampled images (default None)

suffixstr | None

file name suffix of the resampled images (default None)

waitSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheVolumeCollection

resampled images

reverse() → None

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

save() → None

Iteratively save SisypheVolume elements in the current SisypheVolumeCollection instance container.

saveToMulticomponentVolume(filename: str, copyattr: bool | dict[slice(<class 'str'>, <class 'bool'>, None)] = False) → None

Save SisypheVolume elements of the current SisypheVolumeCollection instance container to a multi-component SisypheVolume.

Parameters

filenamestr

file name

copyattrbool | dict[str: bool]

• bool: copy all attributes if True (default False)

• or dict, keys

  • ‘ID’: bool, copy ID attribute if True

  • ‘identity’: bool, copy identity attribute if True

  • ‘acquisition’: bool, copy acquisition attribute if True

  • ‘display’: bool, copy display attribute if True

  • ‘acpc’: bool, copy acpc attribute if True

  • ‘transform’: bool, copy transform attribute if True

  • ‘slope’: bool, copy slope/intercept attributes if True

setList(vols: list[SisypheVolume])

Copy a list of SisypheVolume to the current SisypheVolumeCollection instance container (Shallow copy of list).

Parameters

volslist[SisypheVolume]

list of volumes to copy in collection

sort(reverse: bool = False) → None

Sort elements of the current SisypheVolumeCollection instance container. Sorting is based on the name attribute of the SisypheVolume elements, in the ascending order.

Parameters

reversebool

sorting in reverse order

toLabelVolume(threshold: float = 0.5) → SisypheVolume

Copy the current SisypheVolumeCollection instance to a SisypheVolume label instance. Each image of the current SisypheVolumeCollection instance is thresholded to get a binary image, this image is multiplied by its index in the container to get a label image.

Parameters

thresholdfloat

threshold applied to each image of the current SisypheVolumeCollection instance to get a binary image (default 0.5)

Returns

SisypheVolume

label volume

Sisyphe.core.sisypheVolume.multiComponentSisypheVolumeFromList(vols: list[SisypheVolume] | SisypheVolumeCollection) → SisypheVolume

Create a multicomponent SisypheVolume from a list of single-component SisypheVolume or a SisypheVolumeCollection.

Parameters

volslist[SisypheVolume] | SisypheVolumeCollection

list of single-component volumes

Returns

SisypheVolume

multi-component volume