Sisyphe.core.sisypheXml

External packages/modules

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

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

class Sisyphe.core.sisypheXml.AbstractXml(filename: str)

Description

Abstract ancestor class of XmlVolume, XmlRoi and XmlStreamlines classes. These classes provide direct access to the xml fields in PySisyphe Volume (.xvol), Roi (.xroi) and Streamlines (.xtracts) files.

Inheritance

object -> AbstractXml

Creation: 08/09/2022 Last revision: 16/12/2023

getFieldList() → list[str]

Get field list in the current AbstractXml instance.

Returns

list[str]: list of field names

getFieldNodes(field: str) → NodeList

Get field nodes in the current AbstractXml instance.

Parameters

fieldstr: field name

Returns

xml.dom.minicompat.NodeList: list of nodes

getFieldValues(field: str) → str | list[str] | None

Get field value(s) in the current AbstractXml instance.

Parameters

fieldstr: field name

Returns

str | list[str]: field value(s)

hasField(field: str) → bool

Check whether a field is in the current AbstractXml instance.

Parameters

fieldstr: field name

Returns

bool: True if field is defined

class Sisyphe.core.sisypheXml.XmlROI(filename: str)

Description

Class for accessing the xml fields of the PySisyphe ROI (.xroi).

Inheritance

object -> AbstractXml -> XmlROI

Creation: 08/09/2022 Last revision: 16/12/2023

getAlpha() → int

Get int format opacity attribute of the current XmlROI instance.

Returns

int: Roi opacity, between 0 and 255

getColor() → list[int]

Get int format color attribute of the current XmlROI instance.

Returns

list[int]: Roi color, red, green, blue components between 0 and 255

getFOV() → list[float]

Get field of view attribute of the current XmlROI instance.

Returns

list[float]: Roi FOV in x, y and z axes

getFloatAlpha() → float

Get float format opacity attribute of the current XmlROI instance.

Returns

float: Roi opacity between 0.0 and 1.0

getFloatColor() → list[float]

Get float format color attribute of the current XmlROI instance.

Returns

list[float]: Roi color, red, green, blue components between 0.0 and 1.0

getID() → str

Get reference ID attribute of the current XmlROI instance.

Returns

str: Roi ID

getName() → str

Get name attribute of the current XmlROI instance.

Returns

str: Roi name

getQColor() → QColor

Get QColor attribute of the current XmlROI instance.

Returns

PyQt5.QtGui.QColor: Roi color

getSize() → list[int]

Get image size attribute of the current XmlROI instance.

Returns

list[int]: Roi size in x, y and z axes

getSpacing() → list[float]

Get image spacing (i.e. voxel size in each dimension) attribute of the current XmlROI instance.

Returns

list[float]: Roi spacing in x, y and z axes

class Sisyphe.core.sisypheXml.XmlStreamlines(filename: str)

Description

Class for accessing the xml fields of the PySisyphe Streamlines (.xtracts).

Inheritance

object -> AbstractXml -> XmlStreamlines

Creation: 29/08/2024

getAffineTransform() → ndarray

Get affine transform attribute of the current XmlStreamlines instance.

Returns

numpy.ndarray: Affine transform

getAlpha() → int

Get int format opacity attribute of the current XmlStreamlines instance.

Returns

int: Streamlines opacity, between 0 and 255

getColor() → list[int]

Get int format color attribute of the current XmlStreamlines instance.

Returns

list[int]: Streamlines color, red, green, blue components between 0 and 255

getFOV() → list[float]

Get field of view attribute of the current XmlStreamlines instance.

Returns

list[float]: Streamlines FOV in x, y and z axes

getFloatAlpha() → float

Get float format opacity attribute of the current XmlStreamlines instance.

Returns

float: Streamlines opacity between 0.0 and 1.0

getFloatColor() → list[float]

Get float format color attribute of the current XmlStreamlines instance.

Returns

list[float]: Streamlines color, red, green, blue components between 0.0 and 1.0

getID() → str

Get reference ID attribute of the current XmlStreamlines instance.

Returns

str: Streamlines ID

getLineWidth() → float

Get line width attribute of the current XmlStreamlines instance.

Returns

float: Streamlines line width in mm

getLut() → str

Get lut name attribute of the current XmlStreamlines instance.

Returns

str: Streamlines lut name

getName() → str

Get name attribute of the current XmlStreamlines instance.

Returns

str: Streamlines name

getQColor() → QColor

Get QColor attribute of the current XmlStreamlines instance.

Returns

PyQt5.QtGui.QColor: Streamlines color

getSize() → list[int]

Get image size attribute of the current XmlStreamlines instance.

Returns

list[int]: Streamlines size in x, y and z axes

getSpacing() → list[float]

Get image spacing (i.e. voxel size in each dimension) attribute of the current XmlStreamlines instance.

Returns

list[float]: Streamlines spacing in x, y and z axes

isAtlas() → bool

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

Returns

bool: True if atlas streamlines

isCentroid() → bool

Check whether the current SisypheStreamlines instance is a centroid streamline.

Returns

bool: True if centroid streamline

isRegularStep() → bool

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.

isWhole() → bool

Check whether streamlines of the current SisypheStreamlines instance have been generated from whole brain seeds.

Returns

bool: True if whole brain streamlines

class Sisyphe.core.sisypheXml.XmlVolume(filename: str)

Description

Class for accessing the xml fields of the PySisyphe volume (.xvol).

Inheritance

object -> AbstractXml -> XmlVolume

Creation: 08/09/2022 Last revision: 16/12/2023

getComponents() → int

Get number of components attribute of the current XmlVolume instance.

Returns

int: number of components (1 for 3D volume, > 1 for 4D multi-components volume)

getDatatype() → str

Get datatype attribute of the current XmlVolume instance.

Returns

str: numpy datatype format

getDateOfBirthdayAsDate() → date

Get patient’s date of birth attribute of the current XmlVolume instance.

Returns

datetime.date: patient’s birthdate

getDateOfBirthdayAsString() → str

Get patient’s date of birth attribute of the current XmlVolume instance.

Returns

str: patient’s birthdate

getDateOfScanAsDate() → date

Get date of scan attribute of the current XmlVolume instance.

Returns

datetime.date: date of scan

getDateOfScanAsString() → str

Get date of scan attribute of the current XmlVolume instance.

Returns

str: date of scan

getDirections() → list[float]

Get directions attribute of the current XmlVolume instance. Direction vectors of image axes in RAS+ coordinates system.

PySisyphe uses RAS+ world coordinates system convention (as MNI, Nibabel, Dipy…) with origin to corner of the voxel

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

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

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

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

First vector, x-axis image direction, [1.0, 0.0, 0.0]

Second vector, y-axis image direction, [0.0, 1.0, 0.0]

Third vector, z-axis image direction, [0.0, 0.0, 1.0]

Returns

list[float]: volume directions

getFOV() → list[float]

Get field of view attribute of the current XmlVolume instance.

Returns

list[float]: volume FOV in x, y and z axes

getFirstname() → str

Get patient firstname of the current XmlVolume instance.

Returns

str: patient firstname

getFrame() → int

Get frame attribute of the current XmlVolume instance.

Returns

str: frame (‘UNKNOWN’, ‘NO FRAME’, ‘LEKSELL’)

getGender() → str

Get patient gender attribute of the current XmlVolume instance.

Returns

str: patient gender (‘Male’, ‘Female’, ‘Unknown’)

getID() → str

Get ID attribute of the current XmlVolume instance.

Returns

str: Volume ID (space ID)

getIntercept() → float

Get intercept attribute of the current XmlVolume instance. Used for linear transformation of scalar values displayed in the PySisyphe interface. displayed value = slope x scalar value + intercept

Returns

float: intercept attribute

getLastname() → str

Get patient lastname attribute of the current XmlVolume instance.

Returns

str: patient lastname

getModality() → str

Get modality attribute of the current XmlVolume instance.

Returns

str: modality

getNumberOfComponentsPerPixel() → int

Get number of components attribute of the current XmlVolume instance.

Returns

int: number of components (1 for 3D volume, > 1 for 4D multi-components volume)

getOrientation() → str

Get orientation attribute of the current XmlVolume instance.

Returns

str: ‘axial’, ‘coronal’, ‘sagittal’

getOrigin() → list[float]

Get origin coordinates (world reference) attribute of the current XmlVolume instance.

Returns

list[float]: origin coordinates of the volume

getRange() → tuple[float, float]

Get minimum and maximum scalar values in the image array of the current XmlVolume instance.

Returns

tuple[float, float]: minimum and maximum scalar values in the image array

getRangeMax() → float

Get maximum scalar value in the image array of the current XmlVolume instance.

Returns

float: maximum scalar value in the image array

getRangeMin() → float

Get minimum scalar value in the image array of the current XmlVolume instance.

Returns

float: minimum scalar value in the image array

getRawName() → str

Get array field value of the current XmlVolume instance.

Returns

str: ‘self’ if array image is saved in a binary part of the xvol file (single format) or file name with raw extension if image array is saved in a separate file

getSequence() → str

Get sequence attribute of the current XmlVolume instance.

Returns

str: sequence

getSize() → list[int]

Get image size attribute of the current XmlVolume instance.

Returns

list[int]: volume size in x, y and z axes

getSlope() → float

Get slope attribute of the current XmlVolume instance. Used for linear transformation of scalar values displayed in the PySisyphe interface. displayed value = slope x scalar value + intercept

Returns

float: slope attribute

getSpacing() → list[float]

Get image spacing (i.e. voxel size in each dimension) attribute of the current XmlVolume instance.

Returns

list[float]: volume spacing in x, y and z axes

getUnit() → str

Get unit attribute of the current XmlVolume instance.

Returns

str: unit

getWindow() → tuple[float, float]

Get minimum and maximum windowing values of the current XmlVolume instance.

Returns

tuple[float, float]: minimum and maximum windowing values

getWindowMax() → float

Get maximum windowing value of the current XmlVolume instance.

Returns

float: maximum windowing value

getWindowMin() → float

Get minimum windowing value of the current XmlVolume instance.

Returns

float: minimum windowing value