Sisyphe.core.sisypheTracts

External packages/modules

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

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

• pandas, data structures and data analysis tools, https://pandas.pydata.org/

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

• scipy, scientific computing, https://scipy.org/

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

class Sisyphe.core.sisypheTracts.SisypheBundle(s: int | list[int] | tuple[int, int, int] | None = None)

Description

Container of tracts (streamlines) indices in an associated SisypheStreamlines instance belonging to a bundle. The SisypheBundle instance is an attribute of the associated SisypheStreamlines instance.

Scope of methods:

• set operators between SisypheBundle instances (union, intersection, difference, symmetric difference)

• logic operators between SisypheBundle instances (and, or, xor)

• addBundle and sub arithmetic operators between SisypheBundle instances

• Color representation

  • RGB mode, colors derived from unit vector directed to next point of the tract

  • CMAP mode, colors derived from scalar values associated with points using the look-up table colormap

  attribute - COLOR mode, solid color given by the color attribute

• Color, used in COLOR mode

• Look-up table colormap, used in CMAP mode

• Line width

• Visibility

• Opacity

Inheritance

object -> SisypheBundle

Creation: 26/10/2023 Last revision: 10/04/2025

appendTracts(tracts: int | list[int] | tuple[int]) → None

Append element(s) (i.e. index of a tract (streamline) in the associated SisypheStreamlines instance) to the current SisypheBundle instance.

Parameters

tractsint | list[int] | tuple[int, ]

tract indices in the associated SisypheStreamlines instance

clear() → None

Remove all the tract indices from the current SisypheBundle instance.

copy() → SisypheBundle

Copy the current SisypheBundle instance.

Returns

SisypheBundle

bundle copy

copyToList() → list[int]

Copy the current SisypheBundle instance to a list.

Returns

list[int]

list copy of bundle

count() → int

Get the number of tracts (streamlines) in the current SisypheBundle instance.

Returns

int

number of tracts (streamlines)

difference(other: SisypheBundle) → None

Difference between the current SisypheBundle instance and a SisypheBundle instance given as parameter. The result replaces the current SisypheBundle instance.

Parameters

otherSisypheBundle

second operand bundle for subtraction

getColorRepresentation() → int

Get the color representation attribute of the current SisypheBundle instance.

Returns

int

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis component in

red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - 2, COLOR mode, solid color given by the color attribute of the current instance.

getColorRepresentationAsString() → str

Get the color representation attribute of the current SisypheBundle instance from a str.

Returns

str

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current instance.

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

Get the color attribute of the current SisypheBundle instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Returns

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

bundle color red, green, blue (each component between 0.0 and 1.0)

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

Get the color attribute of the current SisypheBundle instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Returns

tuple[int, int, int] | list[int, int, int]

bundle color red, green, blue (each component between 0 and 255)

getLineWidth() → float

Get the line width attribute of the current SisypheBundle instance in mm.

Returns

float

line width in mm

getList() → list[int]

Get the list attribute of the current SisypheBundle instance container.

Returns

list[int]

list copy of bundle

getLut() → SisypheLut

Get the look-up table colormap attribute of the current SisypheBundle instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Returns

Sisyphe.core.sisypheLUT.SisypheLut

bundle lut

getName() → str

Get the name attribute of the current SisypheBundle instance.

Returns

str

bundle name

getOpacity() → float

Get the opacity attribute of the current SisypheBundle instance.

Returns

float

bundle opacity, between 0.0 (transparent) and 1.0 (opaque)

getQColor() → QColor

Get the color attribute of the current SisypheBundle instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Returns

PyQt5.QtGui.QColor

bundle color

hasName() → bool

Check whether the name attribute of the current SisypheBundle instance is defined (not empty).

Returns

bool

True if name attribute is defined

intersection(other: SisypheBundle) → None

Intersection between the current SisypheBundle instance and a SisypheBundle instance given as parameter. The result replaces the current SisypheBundle instance.

Parameters

otherSisypheBundle

bundle used for intersection

isColorRepresentation() → bool

Check whether the color representation of the current bundle is in COLOR mode. The tracts have a solid color given by the color attribute.

Returns

bool

True if color representation

isEmpty() → bool

Check whether the current SisypheBundle instance is empty (no tract).

Returns

bool

True if bundle is empty

isRGBRepresentation() → bool

Check whether the color representation of the current bundle is in RGB mode. Colors are derived from unit vector directed to next point of the tract (x-axis component in red, y-axis component in green and z-axis component in blue).

Returns

bool

True if RGB representation

isScalarsRepresentation() → bool

Check whether the color representation of the current bundle is in SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute.

Returns

bool

True if scalars representation

removeTracts(tracts: int | list[int] | tuple[int]) → None

Remove element(s) (i.e. index of a tract (streamline) in the associated SisypheStreamlines instance) to the current SisypheBundle instance.

Parameters

tractsint | list[int] | tuple[int, ]

tract indices in the associated SisypheStreamlines instance

sameName(name: str | SisypheBundle) → bool

Check whether the current SisypheBundle instance has the same name as the parameter.

Parameters

name : str | SisypheBundle

Returns

bool

True if same name

setColorRepresentation(v: int) → None

Set the color representation attribute of the current SisypheBundle instance.

Parameters

vint

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis component in

red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - 2, COLOR mode, solid color given by the color attribute of the current instance.

setColorRepresentationAsString(v: str) → None

Set the color representation attribute of the current SisypheBundle instance from a str.

Parameters

vstr

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current instance.

setColorRepresentationToColor() → None

Set the color representation attribute of the current SisypheBundle instance to COLOR mode. The tracts have a solid color given by the color attribute.

setColorRepresentationToRGB() → None

Set the color representation attribute of the current SisypheBundle instance to RGB mode. Colors are derived from unit vector directed to next point of the tract (x-axis component in red, y-axis component in green and z-axis component in blue).

setColorRepresentationToScalars() → None

Set the color representation attribute of the current SisypheBundle instance to SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute.

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

Set the color attribute of the current SisypheBundle instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

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

bundle color red, green, blue (each component between 0.0 and 1.0)

setIntColor(c: list[int] | tuple[int, int, int]) → None

Set the color attribute of the current SisypheBundle instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

ctuple[int, int, int] | list[int, int, int]

bundle color red, green, blue (each component between 0 and 255)

setLineWidth(v: float) → None

Set the line width attribute of the current SisypheBundle instance in mm.

Parameters

vfloat

line width in mm

setLut(lut: str | SisypheLut) → None

Set the look-up table colormap attribute the current SisypheBundle instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Parameters

lutstr | Sisyphe.core.SisypheLUT.SisypheLut

bundle lut

setName(name: str) → None

Set the name attribute of the current SisypheBundle instance.

Parameters

namestr

bundle name

setOpacity(v: float) → None

Set the opacity attribute of the current SisypheBundle instance.

Parameters

vfloat

bundle opacity, between 0.0 (transparent) and 1.0 (opaque)

setQColor(c: QColor) → None

Set the color attribute of the current SisypheBundle instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

c : PyQt5.QtGui.QColor

symDifference(other: SisypheBundle) → None

Symmetric difference between the current SisypheBundle instance and a SisypheBundle instance given as parameter. The result replaces the current SisypheBundle instance.

Parameters

otherSisypheBundle

second operand bundle for Symmetric difference

union(other: SisypheBundle) → None

Union between the current SisypheBundle instance and a SisypheBundle instance given as parameter. The result replaces the current SisypheBundle instance.

Parameters

otherSisypheBundle

bundle used for union

class Sisyphe.core.sisypheTracts.SisypheBundleCollection

Description

Named list container of SisypheBundle instances with int index or str name key for addressing container elements.

Scope of methods:

• container methods

• set operator methods between SisypheBundle elements of the container (union, intersection, difference,

symmetric difference)

Inheritance

object -> SisypheBundleCollection

Creation: 26/10/2023 Last revision: 06/12/2023

append(value: SisypheBundle) → None

Append a SisypheBundle element in the current SisypheBundleCollection instance container.

Parameters

valueSisypheBundle

bundle to append in the container

clear() → None

Remove all the SisypheBundle elements from the current SisypheBundleCollection instance.

copy() → SisypheBundleCollection

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

Returns

SisypheBundleCollection

shallow copy of bundle

copyToList() → list[SisypheBundle]

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

Returns

list[SisypheBundle]

shallow copy of bundle to list

count() → int

Get the number of SisypheBundle elements in the current SisypheBundleCollection instance.

Returns

int

number of SisypheBundle elements

difference(names: list[str], newname: str) → None

Difference of SisypheBundle elements of the current SisypheBundleCollection. Bundles are selected by their name attributes. The resulting SisyphusBundle is appended to the container.

Parameters

nameslist[str, ]

list of bundle names

newname :

name of the new bundle (difference result)

getList() → list[SisypheBundle]

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

Returns

list[SisypheBundle]

shallow copy of bundle to list

index(value: str | SisypheBundle) → int

Index of a SisypheBundle element in the current SisypheBundleCollection instance container.

Parameters

valuestr | SisypheBundle

bundle name or SisypheBundle

Returns

int

index of bundle in the container

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

Insert a SisypheBundle element at the position given by the key in the current SisypheBundleCollection instance container.

Parameters

keyint | str | SisypheBundle | None

index or bundle name or SisypheBundle

valueSisypheBundle

bundle to insert in the container

intersection(names: list[str], newname: str) → None

Intersection of SisypheBundle elements of the current SisypheBundleCollection. Bundles are selected by their name attributes. The resulting SisyphusBundle is appended to the container.

Parameters

nameslist[str, ]

list of bundle names

newname :

name of the new bundle (intersection result)

isEmpty() → bool

Check whether the current SisypheBundleCollection instance is empty (no bundle).

Returns

bool

True if container is empty

keys() → list[str]

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

Returns

list[str]

list of keys in the container

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

Remove a SisypheBundle elements from the current SisypheBundleCollection instance and return it. If key is None, removes and returns the last element.

Parameters

keyint | str | SisypheBundle | None

index or bundle name or SisypheBundle to remove

Returns

SisypheBundle

bundle removed from the container

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

Remove a SisypheBundle element from the current SisypheBundleCollection instance.

Parameters

valueint | str | SisypheBundle

index or bundle name or SisypheBundle instance to remove

rename(old: str, new: str) → None

Rename a bundle of the current SisypheBundleCollection instance container.

Parameters

oldstr

Old bundle name

newstr

New bundle name

reverse() → None

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

symDifference(names: list[str], newname: str) → None

Symmetric difference of SisypheBundle elements of the current SisypheBundleCollection. Bundles are selected by their name attributes. The resulting SisyphusBundle is appended to the container.

Parameters

nameslist[str, ]

list of bundle names

newname :

name of the new bundle (symmetric difference result)

union(names: list[str], newname: str) → None

Union of SisypheBundle elements of the current SisypheBundleCollection. Bundles are selected by their name attributes. The resulting SisypheBundle is appended to the container.

Parameters

nameslist[str, ]

list of bundle names

newname :

name of the new bundle (union result)

class Sisyphe.core.sisypheTracts.SisypheDKIModel(algfit: str = 'WLS')

Description

Class to manage diffusion kurtosis model.

Methods to calculate diffusion derived maps (mean diffusivity, fractional anisotropy…).

Inheritance

object -> SisypheDiffusionModel -> SisypheDkIDModel

Creation: 29/10/2023 Last revision: 21/03/2024

computeFitting(algfit: str = '', wait: DialogWait | None = None) → None

Estimate the diffusion model of the current SisypheDKIModel instance.

Parameters

algfitstr

fitting algorithm:

• ‘WLS’ weighted least squares

• ‘OLS’ ordinary least squares

• ‘CLS’ constrained ordinary least squares

• ‘CWLS’ constrained weighted least squares

• if is empty, uses fitting algorithm attribute

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getAxialDiffusivity() → SisypheVolume

Calculate Axial Diffusivity (AD) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

AD map

getFA() → SisypheVolume

Calculate Fractional Anisotropy (FA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

FA map

getFitAlgorithm() → str

Get the fitting algorithm attribute of the current SisypheDKIModel instance.

Returns

str

fitting algorithm:

• ‘WLS’ weighted least squares

• ‘OLS’ ordinary least squares

• ‘CLS’ constrained ordinary least squares

• ‘CWLS’ constrained weighted least squares

getGA() → SisypheVolume

Calculate Geodesic Anisotropy (GA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GA map

getMD() → SisypheVolume

Calculate Mean Diffusivity (MD) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

MD map

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.dki.DiffusionKurtosisModel

dipy DKI model

getRadialDiffusivity() → SisypheVolume

Calculate Radial Diffusivity (RD) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

RD map

getTrace() → SisypheVolume

Calculate Tensor Trace map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

trace map

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheDKIModel

Create a SisypheDKIModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheDKIModel

loaded DKI model

parseXML(doc: Document) → dict

Read the current SisypheDKIModel 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

keys(str), values:

• ‘model’, str, ‘DKI’

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

setFitAlgorithm(algfit: str = 'WLS') → None

Set the fitting algorithm attribute of the current SisypheDKIModel instance.

Parameters

algfitstr

fitting algorithm:

• ‘WLS’ weighted least squares

• ‘OLS’ ordinary least squares

• ‘CLS’ constrained ordinary least squares

• ‘CWLS’ constrained weighted least squares

class Sisyphe.core.sisypheTracts.SisypheDSIDModel

Description

Class to manage diffusion spectrum imaging deconvolution model

Inheritance

object -> SisypheDiffusionModel -> SisypheDSIDModel

Creation: 29/10/2023 Last revision: 21/03/2024

computeFitting(wait: DialogWait | None = None) → None

Estimate the diffusion model of the current SisypheDSIDModel instance.

Parameters

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getGFA() → SisypheVolume

Calculate Generalized Fractional Anisotropy (GFA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GFA map

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.dsi.DiffusionSpectrumDeconvModel

dipy DSID model

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheDSIDModel

Create a SisypheDSIDModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheDSIModel

loaded DSID model

parseXML(doc: Document) → dict

Read the current SisypheDSIDModel 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

keys(str), values:

• ‘model’, str, ‘DSID’

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

class Sisyphe.core.sisypheTracts.SisypheDSIModel

Description

Class to manage diffusion spectrum imaging model

Inheritance

object -> SisypheDiffusionModel -> SisypheDSIModel

Creation: 29/10/2023 Last revision: 21/03/2024

computeFitting(wait: DialogWait | None = None) → None

Estimate the diffusion model of the current SisypheDSIModel instance.

Parameters

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getGFA() → SisypheVolume

Calculate Generalized Fractional Anisotropy (GFA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GFA map

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.dsi.DiffusionSpectrumModel

dipy DSI model

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheDSIModel

Create a SisypheDSIModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheDSIModel

loaded DSI model

parseXML(doc: Document) → dict

Read the current SisypheDSIModel 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

keys(str), values:

• ‘model’, str, ‘DSI’

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

class Sisyphe.core.sisypheTracts.SisypheDTIModel(algfit: str = 'WLS')

Description

Class to manage diffusion tensor imaging model.

Methods to calculate diffusion derived maps (mean diffusivity, fractional anisotropy…).

Inheritance

object -> SisypheDiffusionModel -> SisypheDTIModel

Creation: 27/10/2023 Last revision: 21/03/2024

computeFitting(algfit: str = '', wait: DialogWait | None = None) → None

Estimate the diffusion model of the current SisypheDTIModel instance.

Parameters

algfitstr

fitting algorithm:

• ‘WLS’ weighted least squares

• ‘OLS’ ordinary least squares

• ‘NLLS’ non-linear least squares

• ‘RT’ restore robust tensor

• if is empty, uses fitting algorithm attribute

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getAxialDiffusivity() → SisypheVolume

Calculate Axial Diffusivity (AD) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

AD map

getDeviatropic() → ndarray

Calculate Deviatropic Diffusivity.

Returns

numpy.ndarray

deviatropic Diffusivity

getEigenValues() → ndarray

Get tensor eigen values.

Returns

numpy.ndarray

eigen values

getEigenVectors() → ndarray

Get tensor eigen vectors.

Returns

numpy.ndarray

eigen vectors

getFA() → SisypheVolume

Calculate Fractional Anisotropy (FA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

FA map

getFitAlgorithm() → str

Get the fitting algorithm attribute of the current SisypheDTIModel instance.

Returns

str

fitting algorithm:

• ‘WLS’ weighted least squares

• ‘OLS’ ordinary least squares

• ‘NLLS’ non-linear least squares

• ‘RT’ restore robust tensor

getGA() → SisypheVolume

Calculate Geodesic Anisotropy (GA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GA map

getIsotropic() → ndarray

Calculate Isotropic Diffusivity.

Returns

numpy.ndarray

isotropic Diffusivity

getMD() → SisypheVolume

Calculate Mean Diffusivity (MD) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

MD map

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.dti.TensorModel

dipy DTI model

getRadialDiffusivity() → SisypheVolume

Calculate Radial Diffusivity (RD) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

RD map

getTensor() → ndarray

Get tensors.

Returns

numpy.ndarray

tensors

getTrace() → SisypheVolume

Calculate Tensor Trace map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

Trace map

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheDTIModel

Create a SisypheDTIModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheDiffusionModel

loaded diffusion model

parseXML(doc: Document) → dict

Read the current SisypheDTIModel 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

keys(str), values:

• ‘model’, str, ‘DTI’

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

setFitAlgorithm(algfit: str = 'WLS') → None

Set the fitting algorithm attribute of the current SisypheDTIModel instance.

Parameters

algfitstr

fitting algorithm:

• ‘WLS’ weighted least squares

• ‘OLS’ ordinary least squares

• ‘NLLS’ non-linear least squares

• ‘RT’ restore robust tensor

class Sisyphe.core.sisypheTracts.SisypheDiffusionModel

Description

Abstract class for diffusion models.

Scope of methods:

• gradient values and vectors management

• diffusion weighted images management

• IO methods

Inheritance

object -> SisypheDiffusionModel

Creation: 27/10/2023 Last revisions: 08/04/2025

calcMask(algo: str = 'huang', niter: int = 2, kernel: int = 1)

Calculate brain mask of the current SisypheDiffusionModel instance.

Parameters

algostr

brain mask parameter, algorithm used to estimate background threshold (default huang): ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’

niterint

brain mask parameter, number of binary morphology iterations (default 2). No brain mask if 0.

kernelint

brain mask parameter, kernel size of binary morphology operator (default 1). No brain mask if 0.

clear() → None

Clear attributes of the current SisypheDiffusionModel instance.

computeFitting(wait: DialogWait | None = None) → None

Abstract method, must be implemented in the derived classes. Estimating the diffusion model.

count() → int

Number of diffusion weighted images (diffusion values/vectors) in the current SisypheDiffusionModel instance.

Returns

int

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getDWI() → ndarray

Get diffusion weighted images from the current SisypheDiffusionModel instance.

Returns

numpy.ndarray

diffusion weighted images

getDWIMean()

Get diffusion-weighted mean image from the current SisypheDiffusionModel instance.

Returns

numpy.ndarray

diffusion weighted mean image

getFOV(decimals: int | None = None) → tuple[float, float, float]

Get the field of view (FOV) of the current SisypheDiffusionModel instance.

Parameters

decimalsint | None

number of decimals used to round values, if None no round

Returns

tuple[float, float, float]

field of view of diffusion-weighted images (mm)

classmethod getFileExt() → str

Get SisypheDiffusionModel file extension.

Returns

str

‘.xdmodel’

classmethod getFilterExt() → str

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

Returns

str

‘PySisyphe Diffusion model (.xdmodel)’

getFittedModel()

Get the estimated model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.dti.TensorFit | dipy.reconst.dki.DiffusionKurtosisFit | dipy.reconst.shm.SphHarmFit | dipy.reconst.dsiDiffusionSpectrumFit | dipy.reconst.dsiDiffusionSpectrumDeconvFit

dipy estimated diffusion model

getGradientTable() → GradientTable

Get the gradient table attribute of the current SisypheDiffusion instance.

Returns

dipy.core.gradients.GradientTable

gradient table

getGradients() → tuple[ndarray, ndarray]

Get gradient values/vectors attributes of the current SisypheDiffusionModel instance.

Returns

tuple[ndarray, ndarray]

• gradients b values numpy.ndarray, shape(n, 1)

• gradient direction vectors numpy.ndarray, shape(n, 3)

getMask() → ndarray

Get the brain mask attribute of the current SisypheDiffusionModel instance.

Returns

numpy.ndarray

brain mask

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.dti.TensorModel | dipy.reconst.dki.DiffusionKurtosisModel | dipy.reconst.shm.CsaOdfModel | dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel | dipy.reconst.dsi.DiffusionSpectrumModel | dipy.reconst.dsi.DiffusionSpectrumDeconvModel

dipy diffusion model

getReferenceID()

Get reference ID attribute of the current SisypheDiffusionModel instance. By default, this ID is the array ID of the mean B0, which is calculated when diffusion-weighted images are added to the model using the loadDWI() or setDWI() method.

Returns

str

reference ID

getShape() → tuple[int, int, int]

Get the diffusion weighted image shape of the current SisypheDiffusionModel instance.

Returns

tuple[int, int, int]

diffusion weighted image shape

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

Get the diffusion weighted images spacing of the current SisypheDiffusionModel instance.

Returns

tuple[float, float, float]

diffusion weighted images spacing i.e. voxel size (mm) in each dimension

hasDWI() → bool

Check whether diffusion-weighted images are defined in the current SisypheDiffusionModel instance.

Returns

bool

True if diffusion-weighted images are defined

hasGradients() → bool

Check whether gradient attributes of the current SisypheDiffusionModel instance are defined (not None).

Returns

bool

True if gradients are defined

hasReferenceID()

Check whether reference ID attribute of the current SisypheDiffusionModel instance is defined (not ‘’).

Returns

bool

True if reference ID is defined

isFitted() → bool

Check whether the diffusion of the current SisypheDiffusionModel instance is estimated (fitted)

Returns

bool

True if diffusion model is estimated

loadDWI(filenames: list[str]) → None

Load diffusion weighted images (Sisyphe.core.sisypheVolume.SisypheVolume) to the current SisypheDiffusionModel instance.

Parameters

filenameslist[str]

list of PySisyphe Volumes (.xvol) file names

loadGradients(bvalsfile: str, bvecsfile: str, lpstoras: bool = False) → None

Load gradient values/vectors attributes of the current SisypheDiffusionModel instance from text or xml files.

Parameters

bvalsfilestr

gradients b values file name

bvecsfilestr

gradient direction vectors file name

lpstorasbool

gradient reorientation if True, LPS+ (DICOM) to RAS+ conversion (flip x and y)

loadMask(filename: str) → None

Load brain mask to the current SisypheDiffusionModel instance.

Parameters

filenamestr

brain mask file name

loadModel(filename: str, binary: bool = True, wait: DialogWait | None = None) → None

Load the current SisypheDiffusionModel instance from a PySisyphe diffusion model (.xdmodel) file.

Parameters

filenamestr

PySisyphe diffusion model file name

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheDiffusionModel

Create a SisypheDiffusionModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheDiffusionModel

loaded diffusion model

parseXML(doc: Document) → dict

Read the current SisypheDiffusionModel 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

keys(str), values:

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

reorientGradients(trf: SisypheTransform) → None

Apply a geometric transformation to gradient attributes of the current SisypheDiffusionModel instance.

Parameters

trfSisyphe.core.sisypheTransform.SisypheTransform

geometric transformation

saveModel(filename: str, wait: DialogWait | None = None) → None

Save the current SisypheDiffusionModel instance to a PySisyphe diffusion model (.xdmodel) file.

Parameters

filenamestr

PySisyphe diffusion model file name

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

setDWI(vols: SisypheVolumeCollection) → None

Set diffusion-weighted images to the current SisypheDiffusionModel instance.

Parameters

volsSisypheVolumeCollection

diffusion weighted images container

setDWIFromNumpy(dwi: ndarray, spacing: list[float] | tuple[float, float, float] | None = None) → None

Set diffusion weighted images to the current SisypheDiffusionModel instance.

Parameters

dwinumpy.ndarray

diffusion weighted images container

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

voxel size (mm) in each dimension

setGradients(bvals: ndarray, bvecs: ndarray, lpstoras: bool = False) → None

Set gradient values/vectors attributes of the current SisypheDiffusionModel instance from numpy.ndarray.

Parameters

bvalsnumpy.ndarray

gradients b values numpy.ndarray, shape(n, 1)

bvecsnumpy.ndarray

gradient direction vectors numpy.ndarray, shape(n, 3)

lpstorasbool

gradient reorientation if True, LPS+ (DICOM) to RAS+ orientation convention (flip x and y)

setMask(mask: ndarray | SisypheROI | SisypheVolume) → None

Set the brain mask attribute of the current SisypheDiffusionModel instance.

Parameters

numpy.ndarray | Sisyphe.core.SisypheROI | Sisyphe.core.SisypheVolume

brain mask

class Sisyphe.core.sisypheTracts.SisypheSHCSAModel(order: int = 6)

Description

Class to manage spherical harmonic model with constant solid angle reconstruction

Inheritance

object -> SisypheDiffusionModel -> SisypheSHCSAModel

Creation: 29/10/2023 Last revision: 21/03/2024

computeFitting(order: int = 6, wait: DialogWait | None = None) → None

Estimate the diffusion model of the current SisypheSHCSAModel instance.

Parameters

orderint

spherical harmonic order of the model (default 6)

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getGFA() → SisypheVolume

Calculate Generalized Fractional Anisotropy (GFA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GFA map

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.shm.CsaOdfModel

dipy SHCSA model

getOrder() → int

Set the spherical harmonic order attribute of the current SisypheSHCSAModel instance.

Returns

int

spherical harmonic order of the model (default 6)

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheSHCSAModel

Create a SisypheSHCSAModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheSHCSAModel

loaded SHCSA model

parseXML(doc: Document) → dict

Read the current SisypheSHCSAModel 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

keys(str), values:

• ‘model’, str, ‘SHCSA’

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

setOrder(order: int = 6) → None

Set the spherical harmonic order attribute of the current SisypheSHCSAModel instance.

Parameters

orderint

spherical harmonic order of the model (default 6)

class Sisyphe.core.sisypheTracts.SisypheSHCSDModel(order: int = 6)

Description

Class to manage constrained spherical harmonic deconvolution model

Inheritance

object -> SisypheDiffusionModel -> SisypheSHCSDModel

Creation: 29/10/2023 Last revision: 21/03/2024

computeFitting(order: int = 0, wait: DialogWait | None = None) → None

Estimate the diffusion model of the current SisypheSHCSDModel instance.

Parameters

orderint

spherical harmonic order of the model (default 6)

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (default None)

createXML(doc: Document) → None

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

Parameters

docminidom.Document

xml document

getFA() → SisypheVolume

Calculate Generalized Fractional Anisotropy (GFA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GFA map

getGFA() → SisypheVolume

Calculate Generalized Fractional Anisotropy (GFA) map.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

GFA map

getModel()

Get the model attribute of the current SisypheDiffusion instance.

Returns

dipy.reconst.csdeconv.ConstrainedSphericalDeconvModel

dipy SHCSD model

getOrder() → int

Set the spherical harmonic order attribute of the current SisypheSHCSDModel instance.

Returns

int

spherical harmonic order of the model (default 6)

classmethod openModel(filename: str, fit: bool = False, binary: bool = True, wait: DialogWait | None = None) → SisypheSHCSDModel

Create a SisypheSHCSDModel instance from a PySisyphe Diffusion model (.xdmodel) file.

Parameters

filenamestr

Diffusion model file name

fitbool

compute model fitting (default False)

binarybool

• if True, binary part (DWI images, mask image, mean DWI image) is loaded (default True)

• if False, only xml part is loaded

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheSHCSDModel

loaded SHCSD model

parseXML(doc: Document) → dict

Read the current SisypheSHCSDModel 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

keys(str), values:

• ‘model’, str, ‘SHCSD’

• ‘dtype’, str, diffusion weighted images datatype

• ‘shape’, list[int, int, int], diffusion weighted images shape (image size in each dimension)

setOrder(order: int = 6) → None

Set the spherical harmonic order attribute of the current SisypheSHCSDModel instance.

Parameters

orderint

spherical harmonic order of the model (default 6)

class Sisyphe.core.sisypheTracts.SisypheStreamlines(sl: ArraySequence | ndarray | None = None, compress=False)

Description

Class to manage a list of streamlines. A streamline is represented as a numpy ndarray of size (n×3) where each row of the array represent a 3D point of the streamline. A set of streamlines is represented with a list of numpy ndarray of size (Ni×3) for i=1:M where M is the number of streamlines in the set.

This class has a SisypheBundleCollection private attribute to classify the streamlines in bundles. It is used by all methods that process bundles.

Attributes:

• reference ID, space ID of the diffusion weighted images used for the tracking process

• shape and spacing of the diffusion-weighted images used for the tracking process

• file name, file name used to save the current instance

• display attributes (color representation mode, color, look-up table colormap, line width, opacity)

Scope of methods:

• container-like methods

• tract feature methods (length, curvature, center of mass, principal direction, distances…)

• bundle feature methods

• bundle selection and clustering methods (virtual dissection)

• bundle conversion to ROI and Mesh

• maps processing (density, path length, connectivity)

• IO methods to and from Tck, Trk, Vtk, Vtp, Fib, Dpy and numpy formats

Inheritance

object -> SisypheStreamlines

Creation: 26/10/2023 Last Revision: 14/04/2025

addBundleToSisypheTractCollection(tracts: SisypheTractCollection, bundle: str = 'all')

Add streamlines of a bundle in the current SisypheStreamlines instance to a SisypheTractCollection instance.

Parameters

tractsSisypheTractCollection

tracts to add to bundle

bundlestr

bundle name or ‘all’ for all streamlines

append(sl: ndarray | ArraySequence, bundlename: str = '') → None

Append streamlines to the current SisypheStreamlines instance.

Parameters

slnumpy.ndarray | dipy.tracking.Streamlines

streamline(s) to append

bundlenamestr

Create a new bundle with appended streamlines

applyAtlasTransformToStreamlines(inplace: bool = False) → SisypheStreamlines | None

Resampling of streamlines from the current SisypheStreamlines instance into atlas space.

Parameters

inplacebool

if True, replace streamlines of the current SisypheStreamlines instance with resampled ones

Returns

SisypheStreamlines | None

resampled streamlines

applyTransformToStreamlines(trf: SisypheTransform, inplace: bool = False) → SisypheStreamlines | None

Apply a geometric transformations to the streamlines of the current SisypheStreamlines instance.

Parameters

trfSisyphe.core.sisypheTransform.SisypheTransform

geometric transformation

inplacebool

if True, replace streamlines of the current SisypheStreamlines instance with resampled ones

Returns

SisypheStreamlines | None

resampled streamlines

atlasRegistration()

Calculate affine transformation between whole-brain atlas tractogram and tractogram of the current instance. This transformation is stored in affine attribute (affine transformation from HCP ICBM152 space to current space).

bundleCentersOfMass(bundle: str = 'all') → list[list[float] | tuple[float, float, float]]

Get the streamlines centers of mass in a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

list[list[float, float, float]

streamline centers of mass

bundleCentroidDistanceSelection(centroid: ndarray, subsample: int = 12, dist: str = 'mam', threshold: float = 10.0, bundle: str = 'all') → SisypheBundle

Create a new bundle with streamlines of a bundle selected by a distance to centroid threshold.

Parameters

centroidndarray

centroid streamline used as reference to select streamlines

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time, each streamline is subsampled (default 12 points)

diststr

• ‘mam’ mean average minimum distance

• ‘mdf’ average pointwise euclidean distance

thresholdfloat

dist parameter threshold (default 10.0 mm)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

SisypheBundle

bundle with indices of streamlines selected

bundleClusterConfidence(mdf: int = 5, power: int = 1, subsample: int = 12, bundle: str = 'all') → ndarray

Computes the cluster confidence index (cci), which is an estimation of the support a set of streamlines gives to a particular pathway. The cci provides a voting system where by each streamline (within a set tolerance) gets to vote on how much support it lends to. Outlier pathways score relatively low on cci, since they do not have many streamlines voting for them. These outliers can be removed by thresholding on the cci metric.

Parameters

mdfint

maximum MDF distance (mm) that will be considered a ‘supporting’ streamline and included in cci calculation (default 5 mm)

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time, each streamline is subsampled (default 12 points)

powerint

power to which the MDF distance for each streamline will be raised to determine how much it contributes to the cci. High values of power make the contribution value degrade much faster. e.g., a streamline with 5 mm MDF similarity contributes 1/5 to the cci if power is 1, but only contributes 1/5^2 = 1/25 if power is 2 (default 1).

bundlestr

bundle name or ‘all’ for all streamlines

Returns

numpy.ndarray

cci

bundleClusterConfidenceFiltering(mdf: int = 5, subsample: int = 12, power: int = 1, ccithreshold: float = 1.0, bundle: str = 'all') → tuple[SisypheBundle, ndarray]

Create a new bundle with streamlines of a bundle selected by a clustering confidence algorithm. Computes the cluster confidence index (cci), which is an estimation of the support a set of streamlines gives to a particular pathway. The cci provides a voting system where by each streamline (within a set tolerance) gets to vote on how much support it lends to. Outlier pathways score relatively low on cci, since they do not have many streamlines voting for them. These outliers can be removed by thresholding on the cci metric.

Parameters

mdfint

maximum MDF distance (mm) that will be considered a ‘supporting’ streamline and included in cci calculation (default 5 mm)

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time, each streamline is subsampled (default 12 points)

powerint

power to which the MDF distance for each streamline will be raised to determine how much it contributes to the cci. High values of power make the contribution value degrade much faster. e.g., a streamline with 5 mm MDF similarity contributes 1/5 to the cci if power is 1, but only contributes 1/5^2 = 1/25 if power is 2 (default 1).

ccithresholdfloat

cci threshold used to select streamlines

bundlestr

bundle name or ‘all’ for all streamlines

Returns

tuple[SisypheBundle, ndarray]

• SisypheBundle, indices of streamlines with cci >= ccithreshold

• ndarray, cci values

bundleClusterConfidenceStatistics(mdf: int = 5, power: int = 1, subsample: int = 12, bundle: str = 'all') → dict[slice(<class 'str'>, <class 'float'>, None)]

Get the descriptive statistics of streamline cluster confidence index in a bundle of the current SisypheStreamlines instance.

Parameters

mdfint

maximum MDF distance (mm) that will be considered a ‘supporting’ streamline and included in cci calculation (default 5 mm)

powerint

power to which the MDF distance for each streamline will be raised to determine how much it contributes to the cci. High values of power make the contribution value degrade much faster. e.g., a streamline with 5 mm MDF similarity contributes 1/5 to the cci if power is 1, but only contributes 1/5^2 = 1/25 if power is 2 (default 1).

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time, each streamline is subsampled (default 12 points)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

dict[str: float]

descriptive statistics of streamline mean curvatures, keys(str), values (float) :

• ‘min’, minimum

• ‘perc5’, 5th percentile

• ‘perc25’, first quartile

• ‘median’, median

• ‘perc75’, third quartile

• ‘perc95’, 95th percentile

• ‘max’, maximum

• ‘std’, standard deviation

• ‘mean’, mean

• ‘skewness’, skewness

• ‘kurtosis’, kurtosis

bundleClustering(threshold: float | None = None, nbp: int = 12, metric: str = 'apd', minclustersize: int = 10, bundle: str = 'all') → tuple[SisypheBundleCollection, list[SisypheStreamlines]]

Create a new bundle with streamlines of a bundle selected by a clustering algorithm.

Parameters

thresholdfloat

maximum distance from a bundle for a streamline to be still considered as part of it. (Default 10 mm)

nbpint

streamlines are subsampled, number of points per streamline

metricstr

• ‘apd’ average pointwise euclidean distance (default)

• ‘cmd’ center of mass euclidean distance

• ‘mpd’ midpoint euclidean distance

• ‘lgh’ length

• ‘ang’ vector between endpoints

minclustersizeint

minimum cluster size (number of streamlines, default 10)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

tuple[SisypheBundleCollection, list[SisypheStreamlines]]

• SisypheBundleCollection, clusters

• list[SisypheStreamlines], centroid streamlines of clusters

bundleCosineDistanceBetweenEndVectors(bundle: str = 'all') → ndarray

Get the cosine distance between endpoint vectors of streamlines in a bundle of the current SisypheStreamlines instance. The cosine distance between two vector A and B is (A.B) / (||A||.||B||)

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

numpy.ndarray

cosine distance between endpoint vectors of streamlines

bundleEuclideanDistanceBetweenEndPoints(bundle: str = 'all') → ndarray

Get the euclidean distance between endpoint of streamlines in a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

numpy.ndarray

euclidean distance between endpoint vectors of streamlines

bundleFastClustering(threshold: float = 10.0, minclustersize: int = 10, bundle: str = 'all') → tuple[SisypheBundleCollection, list[SisypheStreamlines]]

Create a new bundle with streamlines of a bundle selected by a clustering algorithm (fast version).

Parameters

thresholdfloat

maximum distance from a bundle for a streamline to be still considered as part of it. (Default 10 mm)

minclustersizeint

minimum cluster size (number of streamlines, default 10)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

tuple[SisypheBundleCollection, dipy.tracking.Streamlines]

• SisypheBundleCollection, clusters

• list[SisypheStreamlines], centroid streamlines of clusters

bundleFromBundleModel(model: ArraySequence, threshold: float = 15.0, reduction: float = 10.0, pruning: float = 5.0, reductiondist: str = 'mam', pruningdist: str = 'mam', refine: bool = False, minlength: int = 50, bundle: str = 'all') → SisypheBundle

Create a new bundle with streamlines of a bundle selected by a model.

Parameters

modeldipy.tracking.Streamlines

streamlines used as model

thresholdfloat

distance threshold in mm for clustering streamlines (default 15.0)

reductionfloat

distance threshold in mm for bundle reduction (default 10.0)

pruningfloat

distance threshold in mm for bundle pruning (default 5.0)

reductiondiststr

• ‘mdf’ average pointwise euclidean distance

• ‘mam’ mean average minimum distance

pruningdiststr

• ‘mdf’ average pointwise euclidean distance

• ‘mam’ mean average minimum distance

refinebool

if True, two stage algorithm (recognize and refine), otherwise only recognize

minlengthint

minimum streamline size

bundlestr

bundle name or ‘all’ for all streamlines

Returns

SisypheBundle

bundle with indices of streamlines selected by model

bundleIntersectPlane(p: list[float] | tuple[float, float, float], planes: tuple[bool, bool, bool] | list[bool], include: bool = False, inplace: bool = False, bundle: str = 'all') → SisypheBundle

Create a new bundle with streamlines that cross (or not) a plane. A streamline is included/excluded if one of its points crosses the x-axis plane. A streamline is included/excluded if one of its points crosses the y-axis plane. A streamline is included/excluded if one of its points crosses the z-axis plane.

Parameters

ptuple[float, float, float] | list[float, float, float]

coordinates of plane center

planestuple[int, int, int] | list[int, int, int]

• first bool, x-axis inclusion/exclusion

• second bool, y-axis inclusion/exclusion

• third bool, z-axis, inclusion/exclusion

includebool

• True, streamlines that cross plane are included

• False, streamlines that cross plane are excluded

inplacebool

if True, the initial bundle of the current SisypheStreamlines instance is replaced (default False)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

SisypheBundle

bundle with indices of streamlines that cross the sphere

bundleIntersectSphere(p: list[float] | tuple[float, float, float], radius: float, include: bool = False, inplace: bool = False, bundle: str = 'all') → SisypheBundle

Create a new bundle from streamlines of a bundle in the current SisypheStreamlines instance that cross a sphere.

Parameters

ptuple[float, float, float] | list[float, float, float]

coordinates of sphere center

radiusfloat

sphere radius in mm

includebool

True for inclusion in sphere, otherwise exclusion from sphere (default False)

inplacebool

if True, the initial bundle of the current SisypheStreamlines instance is replaced (default False)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

SisypheBundle

bundle with indices of streamlines that cross the sphere

bundleLengthStatistics(bundle: str = 'all') → dict[slice(<class 'str'>, <class 'float'>, None)]

Get the descriptive statistics of streamline lengths in a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

dict[str: float]

descriptive statistics of streamline lengths, keys(str), values (float) :

• ‘min’, minimum

• ‘perc5’, 5th percentile

• ‘perc25’, first quartile

• ‘median’, median

• ‘perc75’, third quartile

• ‘perc95’, 95th percentile

• ‘max’, maximum

• ‘std’, standard deviation

• ‘mean’, mean

• ‘skewness’, skewness

• ‘kurtosis’, kurtosis

bundleLengths(bundle: str = 'all') → ndarray

Get the lengths of streamlines in a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

numpy.ndarray

streamline lengths

bundleMajorClusterCentroid(threshold: float = 10.0, bundle: str = 'all') → ArraySequence

Get the major cluster centroid streamline of a bundle.

Parameters

thresholdfloat

maximum distance from a bundle for a streamline to be still considered as part of it (Default 10 mm).

bundlestr

bundle name or ‘all’ for all streamlines

Returns

dipy.tracking.Streamlines

centroid streamlines

bundleMeanCurvatureStatistics(bundle: str = 'all') → dict[slice(<class 'str'>, <class 'float'>, None)]

Get the descriptive statistics of streamline mean curvatures in a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

dict[str: float]

descriptive statistics of streamline mean curvatures, keys(str), values (float) :

• ‘min’, minimum

• ‘perc5’, 5th percentile

• ‘perc25’, first quartile

• ‘median’, median

• ‘perc75’, third quartile

• ‘perc95’, 95th percentile

• ‘max’, maximum

• ‘std’, standard deviation

• ‘mean’, mean

• ‘skewness’, skewness

• ‘kurtosis’, kurtosis

bundleMeanCurvatures(bundle: str = 'all') → ndarray

Get the mean curvatures of streamlines in a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

numpy.ndarray

streamline mean curvatures

bundleRoiSelection(rois: SisypheROICollection, include: list[bool] | None = None, mode: str = 'any', tol: float | None = None, bundle: str = 'all') → SisypheBundle

Create a new bundle with streamlines of a bundle selected by ROI(s). These ROI(s) are used to perform virtual dissection. A streamline is included if any (or all) streamline point is within tol from inclusion ROI. A streamline is excluded if any (or all) streamline point is within tol from exclusion ROI.

Parameters

roisSisyphe.core.sisypheROI.SisypheROICollection

Container with ROIs (Sisyphe.core.sisypheROI.SisypheROI instances) used to select streamlines

includelist[bool] | None

• This list has the same number of elements as the ROI container. if list element is True, the ROI with the

same index is used as inclusion, otherwise the ROI is used as exclusion - if None, all ROIs are used as inclusion

modestr

• ‘any’ : any streamline point is within tol from ROI (Default)

• ‘all’ : all streamline points are within tol from ROI

• ‘end’ : either of the end-points is within tol from ROI

tolfloat | None

• If any coordinate in the streamline is within this distance, in mm, from the center of any voxel in the

ROI, the filtering criterion is set to True for this streamline, otherwise False. - if None (Default) tol is the distance between the center of each voxel and the corner of the voxel

bundlestr

bundle name or ‘all’ for all streamlines

Returns

SisypheBundle

bundle with indices of streamlines selected by ROI(s)

bundleScalarHistogramFromVolume(vol: SisypheVolume, bins: int = 10, bundle: str = 'all') → ndarray

Get scalar values histogram in a Sisyphe.core.sisypheVolume.SisypheVolume instance along the streamlines in a bundle of the current SisypheStreamline instance.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

volume used to get scalars

binsint

histogram bins (default 10)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

numpy.ndarray

histogram

bundleScalarStatisticsFromVolume(vol: SisypheVolume, bundle: str = 'all') → dict[slice(<class 'str'>, <class 'float'>, None)]

Get descriptive statistics of scalar values in a Sisyphe.core.sisypheVolume.SisypheVolume instance along the streamlines in a bundle of the current SisypheStreamline instance.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

volume used to get scalars

bundlestr

bundle name or ‘all’ for all streamlines

Returns

dict[str: float]

descriptive statistics dict, keys(str), values (float) :

• ‘min’, minimum

• ‘perc5’, 5th percentile

• ‘perc25’, first quartile

• ‘median’, median

• ‘perc75’, third quartile

• ‘perc95’, 95th percentile

• ‘max’, maximum

• ‘std’, standard deviation

• ‘mean’, mean

• ‘skewness’, skewness

• ‘kurtosis’, kurtosis

bundleScalarsFromVolume(vol: SisypheVolume, bundle: str = 'all') → list[ndarray]

Get scalar values in a Sisyphe.core.sisypheVolume.SisypheVolume instance along the streamlines in a bundle of the current SisypheStreamline instance.

Parameters

vol : Sisyphe.core.sisypheVolume.SisypheVolume bundle : str

bundle name or ‘all’ for all streamlines

Returns

list[numpy.ndarray]

scalar values

bundleStreamlinesLongerThan(bundle: str = 'all', l: float = 10.0) → SisypheBundle

Create a new bundle with streamlines whose lengths are longer than a threshold.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

lfloat

streamline length threshold in mm

Returns

SisypheBundle

bundle with indices of streamlines selected by a lengths threshold

bundleStreamlinesShorterThan(bundle: str = 'all', l: float = 10.0) → SisypheBundle

Create a new bundle with streamlines whose lengths are shorter than a threshold.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

lfloat

streamline length threshold in mm

Returns

SisypheBundle

bundle with indices of streamlines selected by a lengths threshold

bundleToConnectivityMatrix(vol: SisypheVolume, bundle: str = 'all') → DataFrame

Calculate the connectivity matrix of a bundle in the current SisypheStreamlines instance. The connectivity matrix is a square matrix with as many columns (rows) as there are labels in a label volume. Each element corresponds to the number of streamlines that start and end at each pair of labels in the label volume.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

label volume, Sisyphe.core.sisypheVolume.SisypheVolume must a label volume

bundlestr

bundle name or ‘all’ for all streamlines

Returns

pandas.DataFrame

connectivity matrix

bundleToDensityMap(bundle: str = 'all') → SisypheVolume

Calculate the density map of a bundle in the current SisypheStreamlines instance. The scalar values of this map are the number of unique streamlines that pass through each voxel.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

density map

bundleToMesh(threshold: int, perc: bool = False, fill: float = 1000.0, decimate: float = 1.0, clean: bool = False, smooth: str = 'sinc', niter: int = 10, factor: float = 0.1, algo: str = 'flying', largest: bool = False, bundle: str = 'all') → SisypheMesh

Convert a bundle of the current SisypheStreamlines instance to a mesh (Sisyphe.core.sisypheMesh.SisypheMesh instance).

Parameters

thresholdint

• absolute streamline count per voxel (if perc is False)

• percentile of streamline count per voxel distribution (if perc is True)

percbool

absolute (default False) or percentile (True) Threshold

fillfloat

identify and fill holes in mesh (default 1000.0)

decimatefloat

mesh points reduction percentage (between 0.0 and 1.0, default 1.0)

cleanbool

merge duplicate points, remove unused points and remove degenerate cells

smoothstr

smoothing algorithm, ‘sinc’ or ‘laplacian’

niterint

number of iterations of smoothing algorithm (default 20)

factorfloat

• lower values produce more smoothing (between 0.0 and 1.0)

• if smooth == ‘sinc’, passband factor

• if smooth == ‘laplacian’, relaxation factor

algostr

isosurface algorithm, ‘contour’, ‘marching’ or ‘flying’ (default)

largestbool

keep only the largest blob (default False)

bundlestr

bundle name or ‘all’ for all streamlines

Returns

Sisyphe.core.sisypheMesh.SisypheMesh

bundle mesh

bundleToPathLengthMap(roi: SisypheROI, bundle: str = 'all') → SisypheVolume

Calculate the path length map of a bundle in the current SisypheStreamlines instance. The scalar values of this map are the shortest path, along any streamline, between a reference roi and each voxel.

Parameters

roiSisyphe.core.sisypheROI.SisypheROI

reference roi

bundlestr

bundle name or ‘all’ for all streamlines

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

path length map

bundleToRoi(threshold: int = 10, perc: bool = False, bundle: str = 'all') → SisypheROI

Convert a bundle of the current SisypheStreamlines instance to a ROI (Sisyphe.core.sisypheROI.SisypheROI instance).

Parameters

thresholdint

• absolute streamline count per voxel (if perc is False)

• percentile of streamline count per voxel distribution (if perc is True)

percbool

absolute (default False) or percentile (True) Threshold

bundlestr

bundle name or ‘all’ for all streamlines

Returns

Sisyphe.core.sisypheROI.SisypheROI

bundle roi

changeStreamlinesSampling(factor: float, inplace: bool = False) → SisypheStreamlines | None

Subsample streamlines of the current SisypheStreamlines instance. This method apply a reduction in the number of points.

Parameters

factorfloat

reduction factor for the number of points (between 0.0 and 2.0)

inplacebool

if True, replace streamlines of the current SisypheStreamlines instance with compressed ones

Returns

SisypheStreamlines | None

resampled streamlines

changeStreamlinesStepSize(step: float, inplace: bool = False) → SisypheStreamlines | None

Change streamlines sampling of the current SisypheStreamlines instance. This method change the step size, in mm, between points.

Parameters

stepfloat

step size between points in mm

inplacebool

if True, replace streamlines of the current SisypheStreamlines instance with resampled ones

Returns

SisypheStreamlines | None

resampled streamlines

clearAffineAtlasTransformation() → None

Clear affine attribute of the current SisypheStreamlines instance. Affine attribute = affine transformation from ICBM152 HCP space to current space.

compressStreamlines(inplace: bool = False) → SisypheStreamlines | None

Compress streamlines of the current SisypheStreamlines instance.

Parameters

inplacebool

if True, replace streamlines of the current SisypheStreamlines instance with compressed ones

Returns

SisypheStreamlines | None

compressed streamlines

copyAttributesFrom(sl: SisypheStreamlines) → None

Copy attributes from SisypheStreamlines parameter to current SisypheStreamlines instance.

Parameters

sl: SisypheStreamlines

copy streamline attributes from sl

copyAttributesTo(sl: SisypheStreamlines) → None

Copy current SisypheStreamlines instance attributes to SisypheStreamlines parameter.

Parameters

sl: SisypheStreamlines

copy streamline attributes to sl

count() → int

Get the number of streamline elements in the current SisypheStreamlines instance.

Returns

int

number of streamline elements

createXML(doc: Document, bundle: str) → None

Write a bundle of the current SisypheStreamlines 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

bundlestr

bundle name or ‘all’ for all streamlines

getAffineAtlasTransformation() → ndarray | None

Get affine attribute of the current SisypheStreamlines instance. Affine attribute = affine transformation from ICBM152 HCP space to current space.

classmethod getAtlasBundleDirectory() → str

Get atlas bundles directory (~/templates/BUNDLES)

Returns

str

bundle model directory (~/templates/BUNDLES)

classmethod getAtlasBundleFilenameFromName(name: str) → str | None

Get atlas bundle filename from its name.

Parameters

namestr

atlas bundle long name

Returns

str | None

bundle filename

classmethod getAtlasBundleFilenameFromShortName(short: str) → str | None

Get atlas bundle filename from its short name.

Parameters

shortstr

atlas bundle short name

Returns

str | None

bundle filename

classmethod getAtlasBundleNames(whole: bool = True) → list[str]

Get names of atlas bundles.

Parameters

wholebool

if False, whole brain tractogram is removed from the list

Returns

str

names of atlas bundles

classmethod getAtlasBundleShortNames(whole: bool = True) → list[str]

Get short names of atlas bundles.

Parameters

wholebool

if False, whole brain tractogram is removed from the list

Returns

str

short names of atlas bundles

getAtlasTransformation() → ndarray | None

Get affine SisypheTransform of atlas coregistration.

Returns

numpy.ndarray | None

affine geometric transformation

getBundle(key: int | str) → SisypheBundle

Get a SisypheBundle of the current SisypheStreamlines instance.

Returns

SisypheBundle

bundle

getBundles() → SisypheBundleCollection

Get the SisypheBundleCollection attribute of the current SisypheStreamlines instance.

Returns

SisypheBundleCollection

bundles collection

getColorRepresentation(bundle: str = 'all') → int

Get the bundle color representation attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

int

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the streamline (x-axis

component in red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - 2, COLOR mode, solid color given by the color attribute of the current instance.

getColorRepresentationAsString(bundle: str = 'all') → str

Get the bundle color representation attribute of the current SisypheStreamlines instance from a str.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

str

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the streamline (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current instance.

getDWIFOV(decimals: int | None = None) → tuple[float, float, float]

Get the field of view (FOV) attribute of the current SisypheStreamlines instance. This is the spacing of the diffusion-weighted images used for the tracking process.

Parameters

decimalsint | None

number of decimals used to round values, if None no round

Returns

tuple[float, float, float]

field of view of diffusion-weighted images used to calculate streamlines

getDWIShape()

Get the shape attribute of the current SisypheStreamlines instance. This is the shape of the diffusion-weighted images used for the tracking process.

Returns

tuple[int, int, int] | list[int, int, int]

shape of the diffusion-weighted images used to calculate streamlines

getDWISpacing()

Get the spacing attribute of the current SisypheStreamlines instance. This is the spacing of the diffusion-weighted images used for the tracking process.

Returns

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

spacing of the diffusion-weighted images used to calculate streamlines

classmethod getDefaultName() → str

Get the default name of a SisypheStreamlines instance (name after initialization).

Returns

str

default name

getDirname() → str

Get the path part of the file name attribute of the current SisypheStreamlines instance. This file name is the default name used by IO methods.

Returns

str

default path

classmethod getFileExt() → str

Get SisypheStreamlines file extension.

Returns

str

‘.xtracts’

getFilename(bundle: str = 'all') → str

Get the bundle file name attribute of the current SisypheStreamlines instance. This file name is the default name used by IO methods.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

str

default bundle file name

classmethod getFilterExt() → str

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

Returns

str

‘PySisyphe Streamlines (.xtracts)’

getFloatColor(bundle: str = 'all') → list[float] | tuple[float, float, float]

Get the bundle color attribute of the current SisypheStreamlines instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

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

bundle color red, green, blue (each component between 0.0 and 1.0)

getIntColor(bundle: str = 'all') → list[int] | tuple[int, int, int]

Get the bundle color attribute of the current SisypheStreamlines instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

ctuple[int, int, int] | list[int, int, int]

bundle color red, green, blue (each component between 0 and 255)

getLineWidth(bundle: str = 'all') → float

Get the bundle line width attribute of the current SisypheStreamlines instance in mm.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

float

bundle line width in mm

getLongestStreamlineIndex(bundle: str = 'all') → int

Get index of the longest streamline in a bundle of the current SisypheStreamline instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

int

index of the longest streamline

getLut(bundle: str = 'all') → SisypheLut

Get the bundle look-up table colormap attribute of the current SisypheStreamlines instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

Sisyphe.core.sisypheLUT.SisypheLut

bundle lut

getName() → str

Get the name attribute of the current SisypheStreamlines instance.

Returns

str

streamlines name

getOpacity(bundle: str = 'all') → float

Get the bundle opacity attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

float

bundle opacity, between 0.0 (transparent) and 1.0 (opaque)

getQColor(bundle: str = 'all') → QColor

Get the bundle color attribute of the current SisypheStreamlines instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

cPyQt5.QtGui.QColor

bundle color

getReferenceID() → str

Get the reference ID attribute of the current SisypheStreamlines instance. This is the space ID of the diffusion weighted images used for the tracking process.

Returns

str

ID

classmethod getReferenceIDfromFile(filename: str) → str

Get the reference ID attribute from xtracts file. This is the space ID of the diffusion weighted images used for the tracking process.

Returns

str

ID

getShortestStreamlineIndex(bundle: str = 'all') → int

Get index of the shortest streamline in a bundle of the current SisypheStreamline instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

int

index of the shortest streamline

getSisypheStreamlinesFromBundle(bundle: str = 'all') → SisypheStreamlines

Get a new SisypheStreamlines from a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

SisypheStreamlines

streamlines of the bundle

getSisypheStreamlinesLongerThan(bundle: str = 'all', l: float = 10.0) → SisypheStreamlines | None

Get a new SisypheStreamlines from the streamlines of a bundle of the current SisypheStreamlines instance whose lengths are longer than a threshold.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

lfloat

streamline length threshold in mm

Returns

SisypheStreamlines | None

streamlines of a bundle longer than the threshold

getSisypheStreamlinesShorterThan(bundle: str = 'all', l: float = 10.0) → SisypheStreamlines | None

Get a new SisypheStreamlines from the streamlines of a bundle of the current SisypheStreamlines instance whose lengths are shorter than a threshold.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

lfloat

streamline length threshold in mm

Returns

SisypheStreamlines | None

streamlines of a bundle shorter than the threshold

classmethod getStepSize(sl: SisypheStreamlines | ArraySequence | ndarray) → tuple[bool, float]

Get whether step size of a streamline is regular.

Parameters

slSisypheStreamlines | dipy.tracking.Streamlines | numpy.ndarray

streamlines to test

Returns

tuple[bool, float]

True if regular step size, step size in mm (0.0 if non-regular step size)

getStreamlineIndexesSortedByLength(bundle: str = 'all') → list[int]

Get indices of streamlines sorted by length in a bundle of the current SisypheStreamline instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

list[int]

list of indices of streamlines sorted by length

getStreamlines() → ArraySequence

Get dipy.tracking.Streamlines of the current SisypheStreamlines instance.

Returns

dipy.tracking.Streamlines

streamlines

getStreamlinesFromBundle(bundle: str = 'all') → ArraySequence

Get dipy.tracking.Streamlines from a bundle of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

dipy.tracking.Streamlines

streamlines of the bundle

hasICBM152ReferenceID() → bool

Check whether the reference ID attribute of the current SisypheStreamlines instance is ICBM152.

Returns

bool

True if ID is ICBM152

hasReferenceID() → bool

Check whether the reference ID attribute of the current SisypheStreamlines instance is defined. This is the space ID of the diffusion weighted images used for the tracking process.

Returns

bool

True if ID is defined

hasRegularStep()

Check whether the streamlines of the current SisypheStreamlines instance are compressed.

By default, streamlines are uncompressed, with a regular step between points. Compression can be applied to streamlines i.e. a reduction in the number of points with non-uniform steps between points. The compression consists in merging consecutive segments that are nearly collinear. The merging is achieved by removing the point the two segments have in common. The linearization process ensures that every point being removed are within a certain margin of the resulting streamline.

Returns

bool

True, if not compressed with regular step between points.

hasSRI24ReferenceID() → bool

Check whether the reference ID attribute of the current SisypheStreamlines instance is SRI24.

Returns

bool

True if ID is SRI24

isAtlas() → bool

Check whether streamlines of the current SisypheStreamlines instance are atlas streamlines.

Returns

bool

True if atlas streamlines

classmethod isAtlasBundleName(name: str) → bool

Check whether name parameter is a valid atlas bundle name.

Parameters

namestr

atlas bundle name

Returns

bool

True if valid atlas bundle name

classmethod isAtlasBundleShortName(short: str) → bool

Check whether short name parameter is a valid atlas bundle short name.

Parameters

shortstr

atlas bundle short name

Returns

bool

True if valid atlas bundle short name

isAtlasRegistered() → bool

Check whether streamlines of the current SisypheStreamlines instance are coregistered with atlas.

Returns

bool

True if affine transformation to atlas is not empty

isCentroid() → bool

Check whether streamline(s) of the current SisypheStreamlines instance is (are) centroid streamline(s).

Returns

bool

True if centroid streamline(s)

isColorRepresentation(bundle: str = 'all') → bool

Check whether the bundle color representation of the current SisypheStreamlines instance is in COLOR mode. The bundle streamlines have a solid color given by the color attribute.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

bool

True if color representation

isDefaultName() → bool

Check whether the name attribute of the current SisypheStreamlines instance has a default value.

Returns

bool

True if ‘all’ or ‘tractogram’

isEmpty() → bool

Check whether the current SisypheStreamlines instance is empy (no streamline).

Returns

bool

True if empty

isRGBRepresentation(bundle: str = 'all') → bool

Check whether the bundle color representation of the current SisypheStreamlines instance is in RGB mode. Colors are derived from unit vector directed to next point of the streamline (x-axis component in red, y-axis component in green and z-axis component in blue).

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

bool

True if RGB representation

isScalarsRepresentation(bundle: str = 'all') → bool

Check whether the bundle color representation of the current SisypheStreamlines instance is in SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

Returns

bool

True if scalars representation

isStreamlineIntersectSphere(index: int, p: list[float] | tuple[float, float, float], radius: float) → bool

Check whether a streamline of the current SisypheStreamlines instance crosses a sphere.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

ptuple[float, float, float] | list[float, float, float]

coordinates of sphere center

radiusfloat

sphere radius in mm

Returns

bool

True if the streamline crosses the sphere

isWholeBrainTractogram() → bool

Check whether streamlines of the current SisypheStreamlines instance have been generated from whole brain seeds. Whole brain state is assumed if more than 50% brain mask voxels are used as seeds.

Returns

bool

True if whole brain seeds

load(filename: str) → None

Load the current SisypheStreamlines instance from a PySisyphe Streamlines (.xtracts) file.

Parameters

filenamestr

PySisyphe Streamlines file name

loadAtlasBundle(name: str = 'WHOLE')

Load an atlas bundle.

Parameters

namestr

atlas bundle name or short name

loadFromDpy(filename: str) → None

Load the current SisypheStreamlines instance from a dipy (.dpy) file.

Parameters

filenamestr

dipy file name

loadFromFib(filename: str) → None

Load the current SisypheStreamlines instance from a FIB (.fib) file.

Parameters

filenamestr

FIB file name

loadFromNumpy(filename: str) → None

Load the current SisypheStreamlines instance from a numpy (.npz) file.

Parameters

filenamestr

numpy file name

loadFromTck(filename: str) → None

Load the current SisypheStreamlines instance from a TCK (.tck) file.

Parameters

filenamestr

TCK file name

loadFromTrk(filename: str) → None

Load the current SisypheStreamlines instance from a TRK (.trk) file.

Parameters

filenamestr

TRK file name

loadFromVtk(filename: str) → None

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

Parameters

filenamestr

VTK file name

loadFromVtp(filename: str) → None

Load the current SisypheStreamlines instance from a VTP (.vtp) file.

Parameters

filenamestr

VTP file name

minimumClosestDistanceBetweenStreamlines(index1: int, index2: int) → float

Get the minimum distance between two streamlines of the current SisypheStreamline instance.

Parameters

index1int

first streamline index in the current SisypheStreamline instance

index2int

second streamline index in the current SisypheStreamline instance

Returns

float

minimum distance between the two streamlines in mm

classmethod openStreamlines(filename: str) → SisypheStreamlines

Create a SisypheStreamlines instance from a PySisyphe streamlines file (.xtracts).

Parameters

filenamestr

Diffusion model file name

Returns

SisypheStreamlines

loaded streamlines

parseXML(doc: Document) → dict

Read a bundle of the current SisypheStreamline 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

keys(str), values:

• ‘name’, str, bundle name

• ‘color’, list[float, float, float], red, green, blue color components

• ‘lut’, str, lut name

• ‘opacity’, float

• ‘width’, float, line width in mm

• ‘offsets’, tuple[float, float], streamlines data size

• ‘dtypes’, streamlines data type

renameBundle(old: str, new: str) → None

Rename a SisypheBundle of the current SisypheStreamlines instance.

Parameters

oldstr

Old bundle name

newstr

New bundle name

resampleAtlasBundle(bundle: str) → SisypheStreamlines | None

Resampling of atlas streamlines into the current SisypheStreamlines instance space.

Parameters

bundlestr

Atlas bundle name or short name

Returns

SisypheStreamlines | None

resampled streamlines

save(filename: str = '', bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a PySisyphe Streamlines (.xtracts) file. If the filename parameter is empty, uses the file name attribute of the current SisypheStreamlines instance.

Parameters

filenamestr

PySisyphe Streamlines file name

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToDpy(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a dipy (.dpy) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToFib(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a FIB (.fib) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToNumpy(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a numpy (.npz) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToTck(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a TCK (.tck) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToTrk(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a TRK (.trk) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToVtk(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a VTK (.vtk) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

saveToVtp(bundle: str = 'all') → None

Save a bundle of the current SisypheStreamlines instance to a VTP (.vtp) file. Uses the file name attribute of the current SisypheStreamlines instance.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines (default)

setAtlasStatus(v) → None

Set the atlas attribute of the current SisypheStreamlines instance. True if streamlines are atlas streamlines.

Parameters

v: bool

atlas status of streamlines

setAtlasTransformation(affine: ndarray) → None

Set affine SisypheTransform of atlas coregistration.

Parameters

affine: ndarray | None

affine geometric transformation

setCentroidStatus(v) → None

Set the centroid attribute of the current SisypheStreamlines instance. True if streamline(s) is (are) centroid streamline(s).

Parameters

v: bool

centroid status of streamline(s)

setColorRepresentation(v: int, bundle: str = 'all') → None

Set the bundle color representation attribute of the current SisypheStreamlines instance.

Parameters

vint

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the streamline (x-axis

component in red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - 2, COLOR mode, solid color given by the color attribute of the current instance.

bundlestr

bundle name or ‘all’ for all streamlines

setColorRepresentationAsString(v: str, bundle: str = 'all') → None

Set the bundle color representation attribute of the current SisypheStreamlines instance from a str.

Parameters

vstr

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the streamlineb(x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current instance.

bundlestr

bundle name or ‘all’ for all streamlines

setColorRepresentationToColor(bundle: str = 'all') → None

Set the bundle color representation attribute of the current SisypheStreamlines instance to COLOR mode. The bundle streamlines have a solid color given by the color attribute.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

setColorRepresentationToRGB(bundle: str = 'all') → None

Set the bundle color representation attribute of the current SisypheStreamlines instance to RGB mode. Colors are derived from unit vector directed to next point of the streamline (x-axis component in red, y-axis component in green and z-axis component in blue).

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

setColorRepresentationToScalars(bundle: str = 'all') → None

Set the bundle color representation attribute of the current SisypheStreamlines instance to SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute.

Parameters

bundlestr

bundle name or ‘all’ for all streamlines

setDWIShape(v: list[int] | tuple[int, int, int])

Set the shape attribute of the current SisypheStreamlines instance. This is the shape of the diffusion-weighted images used for the tracking process.

Parameters

vtuple[int, int, int] | list[int, int, int]

shape of the diffusion-weighted images used to calculate streamlines

setDWISpacing(v: list[float] | tuple[float, float, float])

Set the spacing attribute of the current SisypheStreamlines instance. This is the spacing of the diffusion-weighted images used for the tracking process.

Parameters

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

spacing of the diffusion-weighted images used to calculate streamlines

setFloatColor(c: list[float] | tuple[float, float, float], bundle: str = 'all') → None

Set the bundle color attribute of the current SisypheStreamlines instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

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

bundle color red, green, blue (each component between 0.0 and 1.0)

bundlestr

bundle name or ‘all’ for all streamlines

setIntColor(c: list[int] | tuple[int, int, int], bundle: str = 'all') → None

Set the bundle color attribute of the current SisypheStreamlines instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

ctuple[int, int, int] | list[int, int, int]

bundle color red, green, blue (each component between 0 and 255)

bundlestr

bundle name or ‘all’ for all streamlines

setLineWidth(v: float, bundle: str = 'all') → None

Set the bundle line width attribute of the current SisypheStreamlines instance in mm.

Parameters

vfloat

bundle line width in mm

bundlestr

bundle name or ‘all’ for all streamlines

setLut(lut: str | SisypheLut, bundle: str = 'all') → None

Set the bundle look-up table colormap attribute the current SisypheStreamlines instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Parameters

lutstr | Sisyphe.core.SisypheLUT.SisypheLut

look-up table colormap

bundlestr

bundle name or ‘all’ for all streamlines

setName(name: str = 'tractogram') → None

Set the name attribute of the current SisypheStreamlines instance.

Parameters

namestr

streamlines name

setOpacity(v: float, bundle: str = 'all') → None

Set the bundle opacity attribute of the current SisypheStreamlines instance.

Parameters

vfloat

bundle opacity, between 0.0 (transparent) and 1.0 (opaque)

bundlestr

bundle name or ‘all’ for all streamlines

setQColor(c: QColor, bundle: str = 'all') → None

Set the bundle color attribute of the current SisypheStreamlines instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

cPyQt5.QtGui.QColor

bundle color

bundlestr

bundle name or ‘all’ for all streamlines

setReferenceID(ID: str | SisypheVolume | SisypheDiffusionModel | SisypheStreamlines) → None

Set the reference ID attribute of the current SisypheStreamlines instance. This is the space ID of the diffusion-weighted images used for the tracking process. If the parameter is a SisypheVolume or SisypheDiffusionModel instance, this method also copies shape and spacing attributes to the current SisypheStreamlines instance.

Parameters

IDstr | Sisyphe.core.sisypheVolume.SisypheVolume | SisypheDiffusionModel | SisypheStreamlines

reference ID

setWholeBrainStatus(s: bool)

Set the whole brain attribute of the current SisypheStreamlines instance are atlas streamlines. Whole brain state is assumed if more than 50% brain mask voxels are used as seeds.

Parameters

s: bool

Whole brain state

setWholeBrainStatusFromMasks(brainmask: ndarray, seedmask: ndarray) → float

Set the whole brain status of the seeds used to generate streamlines of the current SisypheStreamlines instance. Whole brain state is assumed if more than 50% brain mask voxels are used as seeds.

Parameters

brainmasknumpy.ndarray

whole brain mask

seedmasknumpy.ndarray

seeding voxels mask

Returns

float

Ratio of brain mask voxels used as seeds

streamlineCenterOfMass(index: int) → list[float] | tuple[float, float, float]

Get the center of mass of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

tuple[float, float, float]

center of mass of the streamline

streamlineDistanceToMidPoint(index: int, p: list[float] | tuple[float, float, float]) → float

Get the distance between of a point and the mid-point of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

ptuple[float, float, float] | list[float, float, float]

point coordinates

Returns

tuple[float, float, float]

distance between of the given point and the mid-point of the streamline

streamlineFirstPoint(index: int) → list[float] | tuple[float, float, float]

Get the first point of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

tuple[float, float, float]

first point of the streamline

streamlineLastPoint(index: int) → list[float] | tuple[float, float, float]

Get the last point of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

tuple[float, float, float]

last point of the streamline

streamlineLength(index: int) → float

Get the length of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

float

streamline length

streamlineMeanCurvature(index: int) → float

Get the mean curvature of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

float

mean curvature of the streamline

streamlineMidPoint(index: int) → list[float] | tuple[float, float, float]

Get the mid-point of a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

tuple[float, float, float]

mid-point of the streamline

streamlinePointFromDistance(index: int, d: float, percent: bool = False) → list[float] | tuple[float, float, float]

Get a point at a given distance from the start along a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

dfloat

distance from the start, as ratio, or in mm

percentbool

if True, d is expressed as a ratio value, between 0.0 and 1.0. Otherwise, d is expressed as absolute value in mm

Returns

tuple[float, float, float]

point coordinates at distance d from the start along the streamline

streamlinePointIndex(index: int, p: list[float] | tuple[float, float, float], tol: float = 0.1) → int | None

Get the index a point in a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

ptuple[float, float, float] | list[float, float, float]

point coordinates

tolfloat

tolerance (default 0.1)

Returns

int | None

point index in the streamline of the current SisypheStreamlines instance. If point is not in the streamline, returns None

streamlinePointIndexFromDistance(index: int, d: float, percent: bool = False) → int

Get a point at a given distance from the start along a streamline of the current SisypheStreamlines instance.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

dfloat

distance from the start, as ratio, or in mm

percentbool

if True, d is expressed as a ratio value, between 0.0 and 1.0. Otherwise, d is expressed as absolute value in mm

Returns

int

point index at distance d from the start along the streamline

streamlinePrincipalDirection(index: int) → list[float] | tuple[float, float, float]

Get the principal direction of a streamline of the current SisypheStreamlines instance. PCA is used to calculate the 3 principal directions for a streamline.

Parameters

indexint

streamline index in the current SisypheStreamlines instance container

Returns

list[float, float, float]

unit vector of the principal direction

streamlineScalarHistogramFromVolume(index: int, vol: SisypheVolume, bins: int = 10) → ndarray

Get histogram of scalar values in a Sisyphe.core.sisypheVolume.SisypheVolume instance along a streamline of the current SisypheStreamline instance.

Parameters

indexint

streamline index in the current SisypheStreamline instance

volSisyphe.core.sisypheVolume.SisypheVolume

volume used to get scalars

binsint

histogram bins (default 10)

Returns

numpy.ndarray

histogram

streamlineScalarStatisticsFromVolume(index: int, vol: SisypheVolume) → dict[slice(<class 'str'>, <class 'float'>, None)]

Get descriptive statistics of scalar values in a Sisyphe.core.sisypheVolume.SisypheVolume instance along a streamline of the current SisypheStreamline instance.

Parameters

indexint

streamline index in the current SisypheStreamline instance

volSisyphe.core.sisypheVolume.SisypheVolume

volume used to get scalars

Returns

dict[str: float]

descriptive statistics dict, keys(str), values (float) :

• ‘min’, minimum

• ‘perc5’, 5th percentile

• ‘perc25’, first quartile

• ‘median’, median

• ‘perc75’, third quartile

• ‘perc95’, 95th percentile

• ‘max’, maximum

• ‘std’, standard deviation

• ‘mean’, mean

• ‘skewness’, skewness

• ‘kurtosis’, kurtosis

streamlineScalarsFromVolume(index: int, vol: SisypheVolume) → ndarray

Get scalar values in a Sisyphe.core.sisypheVolume.SisypheVolume instance along a streamline of the current SisypheStreamline instance.

Parameters

indexint

streamline index in the current SisypheStreamline instance

volSisyphe.core.sisypheVolume.SisypheVolume

volume used to get scalar values

Returns

numpy.ndarray

numpy ndarray of scalar values (same size as the number of points in the streamline)

streamlinesClusterConfidenceFiltering(mdf: int = 5, subsample: int = 12, power: int = 1, ccithreshold: float = 1.0) → SisypheStreamlines | None

Create a new bundle with streamlines of a bundle selected by a clustering confidence algorithm. Computes the cluster confidence index (cci), which is an estimation of the support a set of streamlines gives to a particular pathway. The cci provides a voting system where by each streamline (within a set tolerance) gets to vote on how much support it lends to. Outlier pathways score relatively low on cci, since they do not have many streamlines voting for them. These outliers can be removed by thresholding on the cci metric.

Parameters

mdfint

maximum MDF distance (mm) that will be considered a ‘supporting’ streamline and included in cci calculation (default 5 mm)

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time, each streamline is subsampled (default 12 points)

powerint

power to which the MDF distance for each streamline will be raised to determine how much it contributes to the cci. High values of power make the contribution value degrade much faster. e.g., a streamline with 5 mm MDF similarity contributes 1/5 to the cci if power is 1, but only contributes 1/5^2 = 1/25 if power is 2 (default 1).

ccithresholdfloat

cci threshold used to select streamlines

Returns

SisypheStreamlines | None

selected streamlines

streamlinesClustering(metric: str = 'apd', threshold: float | None = None, subsample: int = 12, minclustersize: int = 10) → list[SisypheStreamlines]

Streamlines clustering with various metric : average pointwise euclidean distance, center of mass distance, midpoint distance, length, angle between vector endpoints.

Parameters

metric: str

• ‘apd’: average pointwise euclidean distance (mm), default metric

• ‘cmd’: center of mass euclidean distance (mm)

• ‘mpd’: midpoint euclidean distance (mm)

• ‘lgh’: length (mm)

• ‘ang’: angle between vector endpoints (degrees)

thresholdfloat | None

metric value threshold :

• average pointwise euclidean distance, default 10 mm

• center of mass euclidean distance, default 5 mm

• midpoint euclidean distance, default 5 mm

• length, default 10 mm

• angle between vector endpoints, default 80°

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time (default 12 points)

minclustersizeint

minimum cluster size (number of streamlines, default 10)

Returns

list[SisypheStreamlines]

Streamlines clusters

streamlinesFromAtlas(atlas: SisypheStreamlines, threshold: float = 0.1, reduction: float = 25.0, pruning: float = 12.0, reductiondist: str = 'mdf', pruningdist: str = 'mdf', refine: bool = False, refinereduction: float = 12.0, refinepruning: float = 6.0, minlength: float = 50.0, wait: DialogWait | None = None) → SisypheStreamlines

Select streamlines from an atlas bundle. This function requires a model bundle (HCP bundle, ICBM152 space) and tries to extract similar looking bundle from the tractogram of the current SisypheStreamlines instance.

Parameters

atlasSisypheStreamlines

streamlines used as bundle model

thresholdfloat

mdf distance threshold for model bundle clustering (default 15.0). Get the centroids of the model bundle and work with centroids instead of all streamlines. This helps speed up processing.The larger the value of the threshold, the fewer centroids will be, and smaller the threshold value, the more centroids will be. If you prefer to use all the streamlines of the model bundle, you can set this threshold to 0.1 mm.

reductionfloat

distance threshold in mm for bundle reduction (default 25.0)

pruningfloat

distance threshold in mm for bundle pruning (default 12.0)

reductiondiststr

• ‘mdf’ average pointwise euclidean distance (default)

• ‘mam’ mean average minimum distance

pruningdiststr

• ‘mdf’ average pointwise euclidean distance (default)

• ‘mam’ mean average minimum distance

refinebool

if True, two stage algorithm (recognize and refine), otherwise only recognize

refinereductionfloat

distance threshold in mm for bundle reduction at refine stage (default 12.0)

refinepruningfloat

distance threshold in mm for bundle pruning at refine stage (default 6.0)

minlengthint

minimum streamline size

waitSisyphe.gui.dialogWait.DialogWait

progress dialog (optional)

Returns

SisypheStreamlines

streamlines selected by model

streamlinesMajorCentroid(threshold: float | None = None, subsample: int = 12) → SisypheStreamlines | None

Get the major cluster centroid streamline.

Parameters

thresholdfloat | None

maximum distance from a bundle for a streamline to be still considered as part of it (Default 10 mm).

subsampleint

number of points that are considered for each streamline in the calculation. To save on calculation time (default 12 points)

Returns

SisypheStreamlines | None

centroid streamline

streamlinesPlaneSelection(p: list[float] | tuple[float, float, float], planes: list[bool], include: bool = False) → SisypheStreamlines

Create a new bundle with streamlines that cross or do not cross a plane. A streamline is included/excluded if one of its points crosses the x-axis plane. A streamline is included/excluded if one of its points crosses the y-axis plane. A streamline is included/excluded if one of its points crosses the z-axis plane.

Parameters

ptuple[float, float, float] | list[float, float, float]

coordinates of sphere center

planestuple[int, int, int] | list[int, int, int]

• first bool, x-axis inclusion/exclusion

• second bool, y-axis inclusion/exclusion

• third bool, z-axis, inclusion/exclusion

includebool

• True, streamlines that cross plane are included

• False, streamlines that cross plane are excluded

Returns

SisypheStreamlines

selected streamlines

streamlinesRoiSelection(rois: SisypheROICollection, include: list[bool] | None = None, mode: str = 'any', tol: float | None = None, wait: DialogWait | None = None) → SisypheStreamlines

ROI(s) selection of streamlines in the current SisypheStreamline instance. These ROI(s) are used to perform virtual dissection. A streamline is included if any (or all) streamline point(s) is(are) within tol from inclusion ROI. A streamline is excluded if any (or all) streamline point(s) is(are) within tol from exclusion ROI.

Parameters

roisSisyphe.core.sisypheROI.SisypheROICollection

ROIs container used to select streamlines

includelist[bool] | None

• This list has the same number of elements as the ROI container. if list element is True, the ROI with the

same index is used as inclusion, otherwise the ROI is used as exclusion - if None, all ROIs are used as inclusion

modestr

• ‘any’ : any streamline point is within tol from ROI (Default)

• ‘all’ : all streamline points are within tol from ROI

• ‘end’ : either of the end-points is within tol from ROI

tolfloat | None

• If any coordinate in the streamline is within this distance, in mm, from the center of any voxel in the

ROI, the filtering criterion is set to True for this streamline, otherwise False. - if None (Default) tol is the distance between the center of each voxel and the corner of the voxel

waitSisyphe.gui.dialogWait.DialogWait | None

progress dialog (optional)

Returns

SisypheStreamlines

selected streamlines

streamlinesSphereSelection(p: list[float] | tuple[float, float, float], radius: float, include: bool = False) → SisypheStreamlines

Sphere selection of streamlines in the current SisypheStreamline instance. A streamline is included if any streamline point(s) is(are) within sphere. A streamline is excluded if any streamline point(s) is(are) within sphere.

Parameters

ptuple[float, float, float] | list[float, float, float]

coordinates of sphere center

radiusfloat

sphere radius in mm

includebool

True for inclusion in sphere, otherwise exclusion from sphere (default False)

Returns

SisypheStreamlines

selected streamlines

streamlinesToConnectivityMatrix(vol: SisypheVolume | None) → DataFrame

Calculate the connectivity matrix of the current SisypheStreamlines instance (all streamlines). The connectivity matrix is a square matrix with as many columns (rows) as there are labels in a label volume. Each element corresponds to the number of streamlines that start and end at each pair of labels in the label volume.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

label volume, Sisyphe.core.sisypheVolume.SisypheVolume must be a label volume

Returns

pandas.DataFrame

connectivity matrix

streamlinesToDensityMap() → SisypheVolume

Calculate the density map of the current SisypheStreamlines instance (all streamlines). The scalar values of this map are the number of unique streamlines that pass through each voxel.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

density map

streamlinesToPathLengthMap(roi: SisypheROI) → SisypheVolume

Calculate the path length map of the current SisypheStreamlines instance (all streamlines). The scalar values of this map are the shortest path, along any streamline, between a reference roi and each voxel.

Parameters

roiSisyphe.core.sisypheROI.SisypheROI

reference roi

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

path length map

class Sisyphe.core.sisypheTracts.SisypheTracking(model: SisypheDiffusionModel)

Description

Class to compute streamlines from diffusion model.

Attributes:

• name of the generated bundle (default ‘tractogram’)

• tracking algorithm

  • deterministic EuDX Euler integration

  • deterministic fiber orientation distribution

  • deterministic parallel transpor

  • deterministic closest peak direction

  • probabilistic bootstrap direction

  • probabilistic fiber orientation distribution

• seed voxels from

  • FA threshold

  • ROI

• seed count per voxel

• step size between streamline points

• stopping criterion

  • FA threshold

  • ROI

  • GM/WM/CSF Maps

Inheritance

object -> SisypheTracking

Creation: 29/10/2023 Last revision: 07/04/2025

computeTracking(wait: DialogWait | None = None) → SisypheStreamlines

Compute the fiber tracking according to the current SisypheTracking instance attributes (bundle name, diffusion model, tracking algorithm, seed method, seed count per voxel, step size and stopping criterion).

Parameters

wait: Sisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

Returns

SisypheStreamlines

streamlines

getBundleName() → str

Get the bundle name attribute of the current SisypheTracking instance.

Returns

str

name of the generated bundle

getMinLength() → float

Get the minimum length attribute of the current SisypheTracking instance. Streamlines with a length below this threshold are removed.

Returns

float

minimum length in mm

getMinSeparationAngleOfPeaks() → float

Get the minimum separation angle attribute of the current SisypheTracking instance. If two odf peaks are too close i.e. separation angle below this threshold, only the larger of the two is returned. This parameter is only ysed by the deterministic euler integration tracking algorithm.

Returns

float

minimum separation angle between peaks in degrees

getNumberOfPeaks() → int

Get the number of peaks attribute of the current SisypheTracking instance. Maximum number of odf peaks used by deterministic euler integration tracking algorithm.

Returns

int

maximum number of peaks

getRelativeThresholdOfPeaks() → float

Get the relative peak threshold attribute of the current SisypheTracking instance. Only return odf peaks greater than relative_peak_threshold * m where m is the largest peak. This parameter is only ysed by the deterministic euler integration tracking algorithm.

Returns

float

relative peak threshold (ratio, 0.0 to 1.0)

getSeedCountPerVoxel() → int

Get the seed count per voxel attribute of the current SisypheTracking instance. Number of streamlines generated per seed voxel.

Returns

int

number of streamlines generated per seed voxel

getSeeds() → ndarray

Get array of seeds from the current SisypheTracking instance.

Returns

numpy.ndarray

array of seeds

getStepSize() → float

Get the step size attribute of the current SisypheTracking instance. Step size (mm) between streamline points.

Returns

float

step size

getTrackingAlgorithm() → int

Get the tracking algorithm attribute of the current SisypheTracking instance as int code.

Returns

int

• 0 Deterministic EuDX Euler integration

• 1 Deterministic Fiber orientation distribution

• 2 Deterministic Parallel transport

• 3 Deterministic Closest peak direction

• 4 Probabilistic Bootstrap direction

• 5 Probabilistic Fiber orientation distribution

getTrackingAlgorithmAsString() → str

Get the tracking algorithm attribute of the current SisypheTracking instance.

Returns

str

• Deterministic EuDX Euler integration

• Deterministic Fiber orientation distribution

• Deterministic Parallel transport

• Deterministic Closest peak direction

• Probabilistic Bootstrap direction

• Probabilistic Fiber orientation distribution

setBundleName(name: str)

Set the bundle name attribute of the current SisypheTracking instance.

Parameters

namestr

name of the generated bundle

setMinLength(l: float = 0.0)

Set the minimum length attribute of the current SisypheTracking instance. Streamlines with a length below this threshold are removed.

Parameters

lfloat

minimum length in mm

setMinSeparationAngleOfPeaks(v: float)

Set the minimum separation angle attribute of the current SisypheTracking instance. If two odf peaks are too close i.e. separation angle below this threshold, only the larger of the two is returned. This parameter is only ysed by the deterministic euler integration tracking algorithm.

Parameters

vfloat

minimum separation angle between peaks in degrees

setNumberOfPeaks(v: int = 5)

Set the number of peaks attribute of the current SisypheTracking instance. Maximum number of odf peaks used by deterministic euler integration tracking algorithm.

Returns

int

maximum number of peaks (default 5)

setRelativeThresholdOfPeaks(v: float)

Set the relative peak threshold attribute of the current SisypheTracking instance. Only return odf peaks greater than relative_peak_threshold * m where m is the largest peak. This parameter is only ysed by the deterministic euler integration tracking algorithm.

Parameters

vfloat

relative peak threshold (ratio, 0.0 to 1.0)

setSeedCountPerVoxel(n: int = 1) → None

Set the seed count per voxel attribute of the current SisypheTracking instance. Number of streamlines generated per seed voxel.

Parameters

nint

number of streamlines generated per seed voxel

setSeedsFromFAThreshold(threshold: float) → None

Set seed voxels of the current SisypheTracking instance from FA threshold. Streamlines are generated from voxels whose FA value is above a given threshold.

Parameters

thresholdfloat

FA threshold

setSeedsFromRoi(roi: SisypheROI) → None

Set seed voxels of the current SisypheTracking instance from a ROI. Streamlines are generated from voxels belonging to the mask of a ROI.

Parameters

roiSisyphe.core.sisypheROI.SisypheROI

seed roi

setStepSize(stepsize: float = 0.5) → None

Set the step size attribute of the current SisypheTracking instance. Step size (mm) between streamline points (default 0.5).

Parameters

stepsizefloat

step size

setStoppingCriterionToFAThreshold(threshold: float = 0.1) → None

Set the stopping criterion attribute of the current SisypheTracking instance to FA threshold. Streamline reconstruction is stopped when the current point is in a voxel whose FA value is below a threshold.

Parameters

thresholdfloat

FA threshold (between 0.0 and 1.0, default 0.1)

setStoppingCriterionToMaps(gm: SisypheVolume(), wm: SisypheVolume(), csf: SisypheVolume()) → None

Set the stopping criterion attribute of the current SisypheTracking instance to maps. This stopping criterion uses gray matter, white matter and cerebro-spinal fluid maps. Streamline reconstruction is stopped when the current point is in a voxel belonging to gray matter (> 0.5), cerebro-spinal fluid (> 0.5) or background.

Parameters

gmSisyphe.core.sisypheVolume.SisypheVolume

gray matter probability map

wmSisyphe.core.sisypheVolume.SisypheVolume

white matter probability map

csfSisyphe.core.sisypheVolume.SisypheVolume

cerebro-spinal fluid probability map

setStoppingCriterionToROI(roi: SisypheROI) → None

Set the stopping criterion attribute of the current SisypheTracking instance to ROI. Streamline reconstruction is stopped when the current point is in a voxel belonging to the mask of a ROI.

Parameters

roiSisyphe.core.sisypheROI.SisypheROI

stopping criterion roi

setTrackingAlgorithm(alg: int = 0) → None

Set the tracking algorithm attribute of the current SisypheTracking instance as int code.

Parameters

algint

• 0 deterministic Euler integration

• 1 deterministic particle filtering

• 2 deterministic closest peak direction

• 3 deterministic fiber orientation distribution

• 4 probabilistic bootstrap direction

• 5 probabilistic fiber orientation distribution

setTrackingAlgorithmToDeterministicClosestPeakDirection() → None

Set the tracking algorithm attribute of the current SisypheTracking instance to deterministic closest peak direction.

setTrackingAlgorithmToDeterministicEulerIntegration() → None

Set the tracking algorithm attribute of the current SisypheTracking instance to deterministic Euler integration.

setTrackingAlgorithmToDeterministicFiberOrientationDistribution() → None

Set the tracking algorithm attribute of the current SisypheTracking instance to deterministic fiber orientation distribution.

setTrackingAlgorithmToDeterministicParallelTransport() → None

Set the tracking algorithm attribute of the current SisypheTracking instance to deterministic parallel transport.

setTrackingAlgorithmToProbabilisticBootstrapDirection() → None

Set the tracking algorithm attribute of the current SisypheTracking instance to probabilistic bootstrap direction.

setTrackingAlgorithmToProbabilisticFiberOrientationDistribution() → None

Set the tracking algorithm attribute of the current SisypheTracking instance to probabilistic fiber orientation distribution.

class Sisyphe.core.sisypheTracts.SisypheTract

Description

Class to manage streamline display (tract).

This class manages display attributes of tracts:

• Color representation

  • RGB mode, colors derived from unit vector directed to next point of the tract

  • CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute

  • COLOR mode, solid color given by the color attribute

• Color, used in COLOR mode

• Look-up table colormap, used in CMAP mode

• Line width

• Visibility

• Opacity

Inheritance

object -> SisypheTract

Creation: 26/10/2023 Last revision: 21/02/2025

clear() → None

Clear the current SisypheTract instance.

deepCopy() → SisypheTract

Deep copy of the current SisypheTract instance.

Returns

SisypheTract

deep copy of tract

getActiveScalars() → str | None

Get the name of the active scalar value associated with points in the current SisypheTract instance.

Returns

str | None

scalar value name

getActor() → vtkActor

Get the vtk.vtkActor attribute of the current SisypheTract instance.

Returns

vtk.vtkActor

vtkActor tract

getColorRepresentation() → int

Get the tract representation attribute of the current SisypheTract instance.

Returns

int

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis component in

red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current SisypheTract instance. - 2, COLOR mode, solid color given by the color attribute of the current SisypheTract instance.

getColorRepresentationAsString() → str

Get the tract representation attribute of the current SisypheTract instance from a str.

Returns

str

representation code

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current SisypheTract instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current SisypheTract instance.

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

Get the color attribute of the current SisypheTract instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Returns

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

color red, green, blue (each component between 0.0 and 1.0)

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

Get the color attribute of the current SisypheTract instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Returns

tuple[int, int, int] | list[int, int, int]

color red, green, blue (each component between 0 and 255)

getLineWidth() → float

Get the line width attribute of the current SisypheTract instance in mm.

Returns

float

line width in mm

getLut() → SisypheLut

Get the look-up table colormap attribute of the current SisypheTract instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Returns

Sisyphe.core.sisypheLUT.SisypheLut

tract lut

getOpacity() → float

Get the opacity attribute of the current SisypheTract instance.

Returns

float

opacity, between 0.0 (transparent) and 1.0 (opaque)

getPoints() → ndarray

Get the tract points of the current SisypheTract instance.

Returns

ndarray

shape(n, 3), n points.

getPolyData() → vtkPolyData

Get the vtk.vtkPolyData attribute of the current SisypheTract instance.

Returns

vtk.vtkPolyData

vtkPolydata tract

getQColor() → QColor

Get the color attribute of the current SisypheTract instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Returns

PyQt5.QtGui.QColor

tract color

getScalarNames() → list[str]

Get a list of scalar value names associated with points in the current SisypheTract instance.

Returns

list[str]

scalar value names

getVisibility() → bool

Get the visibility attribute of the current SisypheTract instance.

Returns

bool

True if visible

hasScalarNames() → bool

Check whether the current SisypheTract instance has associated scalar values.

Returns

bool

True if scalar values are defined

isColorRepresentation() → bool

Check whether the tract representation of the current SisypheTract instance is in COLOR mode. The tract has a solid color given by the color attribute of the current SisypheTract instance.

Returns

bool

True if color representation

isEmpty() → bool

Check whether the current SisypheTract instance is empty (no point)

Returns

bool

True if empty

isRGBRepresentation() → bool

Check whether the tract representation of the current SisypheTract instance is in RGB mode. Colors are derived from unit vector directed to next point of the tract (x-axis component in red, y-axis component in green and z-axis component in blue).

Returns

bool

True if RGB representation

isScalarsRepresentation() → bool

Check whether the tract representation of the current SisypheTract instance is in SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute of the current SisypheTract instance.

Returns

bool

True if scalrs representation

setActiveScalars(sc: str) → None

Set the name of the active scalar value associated with points in the current SisypheTract instance.

Parameters

scstr

scalar value name

setColorRepresentation(r: int) → None

Set the tract representation attribute of the current SisypheTract instance.

Parameters

rint

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis component in

red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current SisypheTract instance. - 2, COLOR mode, solid color given by the color attribute of the current SisypheTract instance.

setColorRepresentationAsString(r: str) → None

Set the tract representation attribute of the current SisypheTract instance from a str.

Parameters

rstr

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current SisypheTract instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current SisypheTract instance.

setColorRepresentationToColor() → None

Set the tract representation attribute of the current SisypheTract instance to COLOR mode. The tract has a solid color given by the color attribute of the current SisypheTract instance.

setColorRepresentationToRGB() → None

Set the tract representation attribute of the current SisypheTract instance to RGB mode. Colors are derived from unit vector directed to next point of the tract (x-axis component in red, y-axis component in green and z-axis component in blue).

setColorRepresentationToScalars() → None

Set the tract representation attribute of the current SisypheTract instance to SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute of the current SisypheTract instance.

setFloatColor(c: list[float] | tuple[float, float, float], update: bool = False) → None

Set the color attribute of the current SisypheTract instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

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

color red, green, blue (each component between 0.0 and 1.0)

updatebool

update color representation to solid color

setIntColor(c: list[int] | tuple[int, int, int], update: bool = False) → None

Set the color attribute of the current SisypheTract instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

ctuple[int, int, int] | list[int, int, int]

color red, green, blue (each component between 0 and 255)

updatebool

update color representation to solid color

setLineWidth(v: float)

Set the line width attribute of the current SisypheTract instance in mm.

Parameters

vfloat

line width in mm

setLut(lut: str | SisypheVolume | SisypheLut | vtkLookupTable | None = None, update: bool = False) → None

Set the look-up table colormap attribute of the current SisypheTract instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Parameters

lutstr | Sisyphe.core.sisypheVolume.SisypheVolume | Sisyphe.core.SisypheLUT.SisypheLut | vtk.vtkLookupTable | None

if None, set a default look-up table colormap (hot)

updatebool

update color representation to color map

setOpacity(v: float)

Set the opacity attribute of the current SisypheTract instance.

Parameters

vfloat

opacity, between 0.0 (transparent) and 1.0 (opaque)

setPoints(sl: ndarray, reg: bool = True) → None

Set the tract points of the current SisypheTract instance.

Parameters

slndarray

streamline of n points, shape(n, 3)

regbool

regular step between points of the streamline

setQColor(c: QColor, update: bool = False) → None

Set the color attribute of the current SisypheTract instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

cPyQt5.QtGui.QColor

color

updatebool

update color representation to solid color

setScalarsFromVolume(vol: SisypheVolume) → None

Set scalar values associated to each point of the current SisypheTract instance from a Sisyphe.core.sisypheVolume.SisypheVolume instance. The value associated with a point of the tract is the scalar value of the SisypheVolume voxel at the coordinates of that point.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

reference volume

setVisibility(v: bool)

Set the visibility attribute of the current SisypheTract instance.

Parameters

vbool

True if visible

visibilityOff() → None

Hide the current SisypheTract instance (set the visibility attribute to False).

visibilityOn() → None

Show the current SisypheTract instance (set the visibility attribute to True).

class Sisyphe.core.sisypheTracts.SisypheTractCollection

Description

Named (bundel name) list container of SisypheTract instances. Container Key = tuple[str, int], str bundle name, int index of a SisypheTract in the bundle

This class manages display attributes of bundles:

• Color representation

  • RGB mode, colors derived from unit vector directed to next point of the tract

  • CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute

  • COLOR mode, solid color given by the color attribute

• Color, used in COLOR mode

• Look-up table colormap, used in CMAP mode

• Line width

• Visibility

• Opacity

Inheritance

object -> SisypheTractCollection

Creation: 26/10/2023 Last revision: 20/02/2025

appendBundle(sl: SisypheStreamlines, bundle: str, wait: DialogWait | None = None) → None

Append streamlines to the current SisypheTractCollection instance container. These streamlines belong to a bundle identified by a bundle name given as parameter.

Parameters

sl : SisypheStreamlines bundle : str

Bundle name

waitSisyphe.gui.dialogWait.DialogWait | None

Progress bar dialog

bundleCount() → int

Get the number of bundles in the current SisypheTractCollection instance container.

Returns

int

Number of bundles

clear() → None

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

count() → int

Get the global number of SisypheTract elements in the current SisypheTractCollection instance container.

Returns

int

Number of SisypheTract elements

duplicateBundle(sl: SisypheStreamlines, select: SisypheBundle | None = None) → SisypheStreamlines

Duplicate a selection of streamlines belonging to a bundle of the current SisypheTractCollection instance container. The new bundle is called with the name attribute of the select instance (SisypheBundle parameter)

Parameters

sl : SisypheStreamlines select : SisypheBundle | None

streamlines duplicated in the new bundle. If None (default), no streamline selection (all streamlines are duplicated)

Returns

SisypheStreamlines

Streamlines of the new bundle

getActiveScalars(bundle: str = '') → str

Get the name of the active scalar value associated with tract points of a bundle in the current SisypheTractCollection instance.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected

Returns

str

scalar value name

getBundleNames() → list[str]

Get the bundle names in the current SisypheTractCollection instance container.

Returns

list[str]

list of bundle names

getColorRepresentation(bundle: str = '') → int

Get the color representation attribute of a bundle in the current SisypheTractCollection instance.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

int

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis component

in red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - 2, COLOR mode, solid color given by the color attribute of the current instance.

getColorRepresentationAsString(bundle: str = '') → str

Get the color representation attribute of a bundle in the current SisypheTractCollection instance from a str.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

str

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current instance.

getDict() → dict[slice(<class 'str'>, list[Sisyphe.core.sisypheTracts.SisypheTract], None)]

Get the current SisypheTractCollection instance container as dict (Shallow copy).

Returns

dict[str: list[SisypheTract]]

• str dict key, bundle name

• list[SisypheTract] dict value

getFloatColor(bundle: str = '') → list[float] | tuple[float, float, float]

Get the color attribute of a bundle in the current SisypheTractCollection instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

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

color red, green, blue (each component between 0.0 and 1.0)

getIntColor(bundle: str = '') → list[int] | tuple[int, int, int]

Get the color attribute of a bundle in the current SisypheTractCollection instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

tuple[int, int, int] | list[int, int, int]

color red, green, blue (each component between 0 and 255)

getLineWidth(bundle: str = '') → float

Get the line width attribute of a bundle in the current SisypheTractCollection instance in mm.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

float

line width in mm

getLut(bundle: str = '') → SisypheLut

Get the look-up table colormap attribute of a bundle in the current SisypheTractCollection instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

Sisyphe.core.sisypheLUT.SisypheLut

lut

getOpacity(bundle: str = '') → float

Get the opacity attribute of a bundle in the current SisypheTractCollection instance.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

float

opacity, between 0.0 (transparent) and 1.0 (opaque)

getQColor(bundle: str = '') → QColor

Get the color attribute of a bundle in the current SisypheTractCollection instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

PyQt5.QtGui.QColor

getRenderer() → vtkRenderer | None

Get the renderer in which the current SisypheTractCollection is displayed.

Returns

vtkRenderer | None

renderer

getScalarNames(bundle: str) → list[str]

Get a list of scalar value names associated with tract points in the current SisypheTractCollection instance.

Parameters

bundlestr

Bundle name, if bundle name is empty, the first bundle is selected

Returns

list[str]

scalar value names

getVisibility(bundle: str = '') → bool

Get the visibility attribute of a bundle in the current SisypheTractCollection instance.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

bool

True if visible

hasRenderer() → bool

Check whether a renderer has been defined to display the current SisypheTractCollection.

Returns

bool

True if renderer is defined i.e. not None

hasScalars(bundle: str = '') → bool

Check whether the bundle in the current SisypheTractCollection instance has associated scalar values.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected

Returns

bool

True if scalars are defined

isColorRepresentation(bundle: str = '') → bool

Check whether the color representation of a bundle is in COLOR mode. The tracts have a solid color given by the color attribute.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

bool

True if color representation

isEmpty() → bool

Check if SisypheTractCollection instance container is empty.

Returns

bool

True if empty

isRGBRepresentation(bundle: str = '') → bool

Check whether the color representation of a bundle is in RGB mode. Colors are derived from unit vector directed to next point of the tract (x-axis component in red, y-axis component in green and z-axis component in blue).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

bool

True if RGB representation

isScalarsRepresentation(bundle: str = '') → bool

Check whether the color representation of a bundle is in SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

Returns

bool

True if scalars representation

removeAllBundles() → None

Remove all bundles from the current SisypheTractCollection instance container.

removeBundle(bundle: str = '') → None

Remove a bundle from the current SisypheTractCollection instance container. This bundle is identified by a bundle name given as parameter.

Parameters

bundlestr

Bundle name. if bundle name is empty, removes the first bundle.

renameBundle(old: str, new: str) → None

Rename a bundle of the current SisypheTractCollection instance container.

Parameters

oldstr

Old bundle name

newstr

New bundle name

setActiveScalars(sc: str, bundle: str = '') → None

Set the name of the active scalar value associated with tract points of a bundle in the current SisypheTractCollection instance.

Parameters

scstr

scalar value name

bundlestr

bundle name, if bundle name is empty, the first bundle is selected

setColorRepresentation(v: int, bundle: str = '') → None

Set the color representation attribute of a bundle in the current SisypheTractCollection instance.

Parameters

vint

representation code:

• 0, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis component in

red, y-axis component in green and z-axis component in blue). - 1, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - 2, COLOR mode, solid color given by the color attribute of the current instance.

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setColorRepresentationAsString(v: str, bundle: str = '') → None

Set the color representation attribute of a bundle in the current SisypheTractCollection instance from a str.

Parameters

vstr

representation code:

• ‘rgb’, RGB mode, colors derived from unit vector directed to next point of the tract (x-axis

component in red, y-axis component in green and z-axis component in blue). - ‘scalars’, CMAP mode, colors derived from scalar values associated with points using the look-up table colormap attribute of the current instance. - ‘color’, COLOR mode, solid color given by the color attribute of the current instance.

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setColorRepresentationToColor(bundle: str = '') → None

Set the color representation attribute of the current SisypheTractCollection instance to COLOR mode. The tracts have a solid color given by the color attribute.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setColorRepresentationToRGB(bundle: str = '') → None

Set the color representation attribute of a bundle in the current SisypheTractCollection instance to RGB mode. Colors are derived from unit vector directed to next point of the tract (x-axis component in red, y-axis component in green and z-axis component in blue).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setColorRepresentationToScalars(bundle: str = '') → None

Set the color representation attribute of a bundle in the current SisypheTractCollection instance to SCALARS mode. Colors are derived from scalar values associated with points using the look-up table colormap attribute.

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setFloatColor(c: list[float] | tuple[float, float, float], bundle: str = '') → None

Set the color attribute of a bundle in the current SisypheTractCollection instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

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

color red, green, blue (each component between 0.0 and 1.0)

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setIntColor(c: list[int] | tuple[int, int, int], bundle: str = '') → None

Set the color attribute of a bundle in the current SisypheTractCollection instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

ctuple[int, int, int] | list[int, int, int]

color red, green, blue (each component between 0 and 255)

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setLineWidth(v: float, bundle: str = '') → None

Set the line width attribute of a bundle in the current SisypheTractCollection instance in mm.

Parameters

vfloat

line width in mm

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setLut(lut: SisypheLut, bundle: str = '') → None

Set the look-up table colormap attribute of a bundle in the current SisypheTractCollection instance. The look-up table colormap attribute is only used in CMAP mode representation (see setColorRepresentation() method).

Parameters

lutSisyphe.core.sisypheVolume.SisypheVolume | Sisyphe.core.SisypheLUT.SisypheLut | vtk.vtkLookupTable

lut

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setOpacity(v: float, bundle: str = '') → None

Set the opacity attribute of a bundle in the current SisypheTractCollection instance.

Parameters

vfloat

opacity, between 0.0 (transparent) and 1.0 (opaque)

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

setQColor(c: QColor, bundle: str = '') → None

Set the color attribute of a bundle in the current SisypheTractCollection instance. The color attribute is only used in COLOR mode representation (see setColorRepresentation() method).

Parameters

c : PyQt5.QtGui.QColor bundle : str

bundle name, if bundle name is empty, the first bundle is selected.

setRenderer(r: vtkRenderer | None)

Define the renderer in which the current SisypheTractCollection is displayed.

Parameters

rvtkRenderer | None

renderer

setScalarsFromVolume(vol: SisypheVolume, bundle: str, wait: DialogWait | None = None) → None

Set scalar values associated to each point of the tract elements from a Sisyphe.core.sisypheVolume.SisypheVolume instance. The value associated with a point of the tract is the scalar value of the SisypheVolume voxel at the coordinates of that point.

Parameters

vol : Sisyphe.core.sisypheVolume.SisypheVolume bundle : str

Bundle name, if bundle name is empty, the first bundle is selected

waitSisyphe.gui.dialogWait.DialogWait | None

Progress bar dialog (optional)

setVisibility(v: bool, bundle: str = '')

Set the visibility attribute of a bundle in the current SisypheTractCollection instance.

Parameters

vbool

visibility

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

tractCount(bundle: str = '') → int

Get the number of SisypheTract elements in a bundle of the current SisypheTractCollection instance container.

Parameters

bundlestr

Bundle name, if bundle = ‘’, returns the global number of tracts.

Returns

int

Number of SisypheTract elements in the bundle

unionBundle(bundle: str, lsl: list[SisypheStreamlines], wait: DialogWait | None = None) → SisypheStreamlines

Union of bundles of the current SisypheTractCollection instance container. The bundle updated is the bundle name attribute of the sl1 instance (SisypheStreamlines parameter)

Parameters

bundlestr

union bundle name

lsl : list[SisypheStreamlines] wait : Sisyphe.gui.dialogWait.DialogWait | None

Progress bar dialog (optional)

Returns

SisypheStreamlines

Streamlines union

updateBundle(sl: SisypheStreamlines, select: SisypheBundle) → SisypheStreamlines

Update streamlines belonging to a bundle of the current SisypheTractCollection instance container. The bundle updated is the bundle name attribute of the sl instance (SisypheStreamlines parameter)

Parameters

slSisypheStreamlines

Streamlines of the bundle to update

selectSisypheBundle

Streamlines selection of the bundle

Returns

SisypheStreamlines

Selected streamlines

visibilityOff(bundle: str = '') → None

Hide a bundle of the current SisypheTractCollection instance (set the visibility attribute to False).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.

visibilityOn(bundle: str = '') → None

Show a bundle of the current SisypheTractCollection instance (set the visibility attribute to True).

Parameters

bundlestr

bundle name, if bundle name is empty, the first bundle is selected.