Sisyphe.core.sisypheROI

External packages/modules

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

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

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

• pandas, data analysis and manipulation tool, https://pandas.pydata.org/

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

• radiomics, radiomics features and texture analysis, https://pyradiomics.readthedocs.io/en/latest/

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

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

• scikit-image, image processing, https://scikit-image.org/

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

class Sisyphe.core.sisypheROI.SisypheROI(image: str | Image | ndarray | vtkImageData | ANTsImage | SisypheImage | None = None, copy: bool = True, **kargs)

Description

PySisyphe region-of-interest (ROI) binary image class.

Scope of methods:

• display management (color, opacity, visibility),

• flip/shift,

• morphology operators (dilate, erode, closing, opening),

• fill holes,

• blob (connected component),

• 2D shape drawing (line, disk, ellipse, square, rectangle, polygon),

• 3D shape drawing (cube, Parallelepiped, sphere),

• mesh conversion,

• IO methods (native format and BrainVoyager VOI format),

• methods inherited from the SisypheImage class.

Inheritance

object -> SisypheImage -> SisypheBinaryImage -> SisypheROI

Creation: 08/09/2022 Last revision: 21/09/2024

classmethod addInstance() → None

Increment the SisypheROI instance count. This class method is called by the constructor.

clear() → None

Clear the ROI image of the current SisypheROI instance (Filling roi with 0).

clearBorderBlobs()

Clear blob(s) connected to the border of the current SisypheROI instance. The current SisypheROI instance is overwritten.

copy() → SisypheROI

SisypheROI copy of the current SisypheROI instance.

Returns

SisypheROI

roi copy

copyAttributesFrom(roi: SisypheROI) → None

Copy the attributes (reference ID, name, file name, color, opacity) of the parameter SisypheROI instance to the current SisypheROI instance.

Parameters

roiSisypheROI

roi from which attributes are copied

copyAttributesTo(roi: SisypheROI) → None

Copy the attributes (reference ID, name, file name, color, opacity) of the current SisypheROI instance to the parameter SisypheROI instance.

Parameters

roiSisypheROI

roi where attributes are copied

copyToSisypheVolume() → SisypheVolume

Copy fo the SisypheROI instance to a SisypheVolume instance. Deep copy of the SimpleITK image attribute. Image buffer is not shared between SisypheROI and SisypheVolume instances.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

deep copy of roi

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

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

Parameters

docminidom.Document

xml document

singlebool

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

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

createXMLOld(doc: Document) → None

Deprecated, use createXML() method

drawCube(p: list[int] | tuple[int, int, int], extent: int) → None

Draw a cube in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extentint

length of cube sides (in voxels)

drawDisk(p: list[int] | tuple[int, int, int], radius: int, orient: int = 0) → None

Draw a disk in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z center point coordinates

radiusint

disk radius (in voxels)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawEllipse(p: list[int] | tuple[int, int, int], radius: list[int] | tuple[int, int], rot: float = 0.0, orient: int = 0) → None

Draw an ellipse in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z center point coordinates

radiustuple[int, int] | list[int, int]

radius in x and y axes (in voxels)

rotfloat

set the ellipse rotation in radians (between -pi and pi, default 0.0)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawLine(p0: list[int] | tuple[int, int, int], p1: list[int] | tuple[int, int, int], orient: int = 0) → None

Draw a line in the ROI image of the current SisypheROI instance. Line is drawn in a single slice (points p0 and p1 must be within the same slice)

Parameters

p0tuple[int, int, int] | list[int, int, int]

x, y, z first point coordinates

p1tuple[int, int, int] | list[int, int, int]

x, y, z second point coordinates

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawParallelepiped(p: list[int] | tuple[int, int, int], extent: list[int] | tuple[int, int, int]) → None

Draw a parallelepiped in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extenttuple[int, int, int] | list[int, int, int]

width, height and depth (in voxels)

drawPolygon(p: list[list[int]], orient: int = 0) → None

Draw a polygon in the ROI image of the current SisypheROI instance. Polygon is drawn in a single slice (all points must be within the same slice).

Parameters

plist[list[int]]

• list of 3 list[int]:

  • first list[int], x coordinates of points

  • second list[int], y coordinates of points

  • third list[int], z coordinates of points

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawRectangle(p: list[int] | tuple[int, int, int], extent: list[int] | tuple[int, int], orient: int = 0) → None

Draw a rectangle in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extenttuple[int, int] | list[int, int]

width and height (in voxels)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawSphere(p: list[int] | tuple[int, int, int], radius: int) → None

Draw a sphere in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z center coordinates

radiusint

sphere radius (in voxels)

drawSquare(p: list[int] | tuple[int, int, int], extent: int, orient: int = 0) → None

Draw a square in the ROI image of the current SisypheROI instance.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extentint

length of square sides (in voxels)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

fillHoles() → None

Fill holes in the ROI image of the current SisypheROI instance. The current SisypheROI instance is overwritten.

flip(fx: bool = False, fy: bool = False, fz: bool = False) → None

Flip ROI image axes of the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

fxbool

flip x-axis if True (default False)

fybool

flip y-axis if True (default False)

fzbool

flip z-axis if True (default False)

fromIndexes(idx: list | ndarray) → None

Set voxels from a list of indexes (x, y, z).

Parameters

idxlist | ndarray

list of voxels indexes

getAlpha() → float

Set the ROI opacity of the current SisypheROI instance.

Returns

float

opacity, between 0.0 and 1.0

getBlobCount() → int

Get the number of blobs (connected components) in the ROI image of the current SisypheROI instance.

Returns

int

number of blobs

getBlobLargerThan(n: int) → SisypheROI

Remove blobs (connected components) with less than n voxels from the ROI image of a copy of the current SisypheROI instance.

Returns

SisypheROI

processed roi

getClearBorderBlobs() → SisypheROI

Clear blob(s) connected to the border of the current SisypheROI instance.

Returns

SisypheROI

processed roi

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

Get the roi color of the current SisypheROI instance.

Returns

tuple[float, float, float]

roi color, red, green, blue (0.0 <= value <= 1.0)

getCompression() → bool

Get the gzip file compression attribute of the current SisypheROI instance. PySisyphe ROI format (.xroi) can be optionally gzipped.

Returns

bool

True if compression is on

getDirname() → str

Get path part (dirname) of the file name attribute of the current SisypheROI instance.

Returns

str

path part of the file name attribute

getDistanceMap(blob: int = 0, output: str = 'xvol') → Image | ndarray | SisypheVolume

Calculates the Euclidean distance transform of the current SisypheROI instance.

Parameters

blobint

blob index or 0 (all image, default)

outputstr

output image type: ‘sitk’, ‘numpy’, ‘xvol’

Returns

SimpleITK.Image | numpy.ndarray | Sisyphe.core.sisypheVolume.SisypheVolume

distance map

getEulerNumber(connectivity: int = 26) → int

Calculate the Euler characteristic of the current SisypheROI instance. The Euler number is obtained as the number of blobs plus the number of holes, minus the number of tunnels, or loops.

Parameters

connectivityint

6 or 26

Returns

int

Euler number

classmethod getFileExt() → str

Get SisypheROI file extension.

Returns

str

‘.xroi’

getFilename() → str

Get the file name attribute of the current SisypheROI instance. This file name is used by save() method.

Returns

str

file name

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

Get prefix (if any) from the file name attribute of the current SisypheROI instance.

Parameters

sepstr

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

Returns

str

prefix

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

Get suffix (if any) from the file name attribute of the current SisypheROI instance.

Parameters

sepstr

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

Returns

str

suffix

getFillHoles() → SisypheROI

Fill holes in the ROI image of a copy of the current SisypheROI instance.

Returns

SisypheROI

roi without hole

classmethod getFilterExt() → str

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

Returns

str

‘PySisyphe ROI (.xroi)’

getFlip(fx: bool = False, fy: bool = False, fz: bool = False) → SisypheROI

Flip ROI image axes of a copy of the current SisypheROI instance.

Parameters

fxbool

flip x-axis if True (default False)

fybool

flip y-axis if True (default False)

fzbool

flip z-axis if True (default False)

Returns

SisypheROI

flipped roi

classmethod getInstancesCount() → int

Get the SisypheROI instance count.

Returns

int

instance count

getLut() → SisypheLut

Get the look-up table colormap attribute of the current SisypheROI instance. The Lut attribute exists only for compatibility with SisypheImage ancestor class and display widgets. All lut elements have the same color, i.e. the color attribute of the current SisypheROI instance.

Returns

Sisyphe.core.sisypheLUT.SisypheLut

roi lut

getMajorBlob() → SisypheROI

Clear all blobs (connected components) except the major one (most voxels) in the ROI image of a copy of the current SisypheROI instance.

Returns

SisypheROI

processed roi

getMorphoClosing(radius: int = 1, struct: int = 1) → SisypheROI

ROI image morphological closing of a copy of the current SisypheROI instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROI

morphology closing roi

getMorphoDilate(radius: int = 1, struct: int = 1) → SisypheROI

ROI image morphological dilatation of a copy of the current SisypheROI instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROI

dilated roi

getMorphoErode(radius: int = 1, struct: int = 1) → SisypheROI

ROI image morphological erosion of a copy of the current SisypheROI instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROI

eroded roi

getMorphoOpening(radius: int = 1, struct: int = 1) → SisypheROI

ROI image morphological opening of a copy of the current SisypheROI instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROI

morphology opening roi

getName() → str

Get the name attribute of the current SisypheMesh instance.

Returns

str

roi name

getPruning(blob: int = 0) → SisypheROI

Remove “spurs” of less than a certain length in the current SisypheROI instance.

Parameters

blobint

blob index or 0 (whole image, default)

Returns

SisypheROI

processed roi

getQColor() → QColor

Get the mesh color (as QColor) of the current SisypheROI instance.

Returns

PyQt5.QtGui.QColor

roi color

getReferenceID() → str

Get reference ID attribute of the current SisypheROI instance. A ROI is defined in the space of a reference SisypheVolume whose ID is the reference ID.

Returns

str

reference ID

classmethod getRegExp() → str

Get the regular expression filter applied to roi name attribute.

Returns

str

regular expression filter

getRemoveBlobByDistance(d: float) → SisypheROI

Remove blobs until the remaining ones are spaced more than a given distance from one another. By default, smaller objects are removed first.

Parameters

dfloat

minimal distance between blobs in mm

Returns

SisypheROI

processed roi

getShift(sx: int = 0, sy: int = 0, sz: int = 0) → SisypheROI

ROI image shift of a copy of the current SisypheROI instance.

Parameters

sxint

shift of sx voxels in x-axis (default 0)

syint

shift of sy voxels in y-axis (default 0)

szint

shift of sz voxels in z-axis (default 0)

Returns

SisypheROI

shifted roi

getSisypheVolume() → SisypheVolume

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

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

shallow copy of roi

getSkeletonize(blob: int = 0) → SisypheROI

Calculate the skeleton of the current SisypheROI instance.

Parameters

blobint

blob index or 0 (whole image, default)

Returns

SisypheROI

skeleton roi

getVisibility() → bool

Get the ROI visibility of the current SisypheROI instance.

Returns

bool

True if visible

getVtkContourActor() → vtkActor

Create a 3D contour of the ROI mask of the current SisypheROI instance (uses vtk.vtkContourFilter).

Returns

vtk.vtkActor

vtkActor surface of roi

getVtkContourPolyData() → vtkPolyData

Create a 3D contour of the ROI mask of the current SisypheROI instance (uses vtk.vtkContourFilter).

Returns

vtk.vtkPolyData

vtkPolydata surface of roi

getVtkMarchingCubeContourActor() → vtkActor

Create a 3D contour of the ROI mask of the current SisypheROI instance (uses vtk.vtkMarchingCubes).

Returns

vtk.vtkActor

vtkActor surface of roi

getVtkMarchingCubeContourPolyData() → vtkPolyData

Create a 3D contour of the ROI mask of the current SisypheROI instance (uses vtk.vtkMarchingCubes).

Returns

vtk.vtkPolyData

vtkPolydata surface of roi

getvtkLookupTable() → vtkLookupTable

Get the look-up table colormap attribute of the current SisypheROI instance. The Lut attribute exists only for compatibility with SisypheImage ancestor class and display widgets. All lut elements have the same color, i.e. the color attribute of the current SisypheROI instance.

Returns

vtk.vtkLookupTable

roi lut

hasFilename() → bool

Check whether the current SisypheROI instance file name attribute is defined (!= ‘’)

Returns

bool

True if file name attribute is defined

hasReferenceID() → bool

Check if the reference ID of the current SisypheROI instance is defined (not ‘’).

Returns

bool

True if reference ID is defined

load(filename: str) → None

Load the current SisypheROI instance from a PySisyphe ROI (.xroi) file.

Parameters

filenamestr

PySisyphe ROI file name

loadFromBrainVoyagerVOI(vmr: str, voi: str, index: int = 0) → None

Load the current SisypheROI instance from BrainVoyager files. BrainVoyager’s ROI format can include several ROIs, an index parameter is provided to select the ROI to be loaded.

Parameters

vmrstr

BrainVoyager image file name (.vmr)

voistr

BrainVoyager ROI file name (.voi)

indexint

ROI index in the BrainVoyager ROI file

loadFromSisyphe(filename: str, index: int = 0) → None

Load the current SisypheROI instance from old Sisyphe ROI (.roi) file.

Parameters

filenamestr

old Sisyphe ROI file name

indexint

ROI index in the old Sisyphe ROI file (default 0, first ROI)

loadOld(filename: str) → None

Deprecated, use load() method

morphoClosing(radius: int = 1, struct: int = 1) → None

ROI image morphological closing of the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

morphoDilate(radius: int = 1, struct: int = 1) → None

ROI image morphological dilatation of the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

morphoErode(radius: int = 1, struct: int = 1) → None

ROI image morphological erosion of the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

morphoOpening(radius: int = 1, struct: int = 1) → None

ROI image morphological opening of the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

classmethod openROI(filename: str) → SisypheROI

Create a SisypheROI instance from a PySisyphe ROI (.xroi) file format.

Parameters

filenamestr

PySisyphe ROI file name

Returns

SisypheROI

loaded ROI

parseXML(doc: Document) → dict

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

Parameters

docminidom.Document

xml document

Returns

dict[str] Keys: - ‘size’, list[int], image size in each axis - ‘spacing’, list[float], voxel size in each axis - ‘array’, bytes, array image

parseXMLOld(doc: Document) → None

Deprecated, use parseXML() method

pruning(blob: int = 0)

Remove “spurs” of less than a certain length in the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

blobint

blob index or 0 (whole image, default)

removeBlobByDistance(d: float)

Remove blobs until the remaining ones are spaced more than a given distance from one another. By default, smaller objects are removed first. The current SisypheROI instance is overwritten.

Parameters

dfloat

minimal distance between blobs in mm

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

Save the current SisypheROI instance to a PySisyphe ROI (.xroi) file. This method uses the file name attribute of the current SisypheROI instance.

Parameters

filenamestr

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

singlebool

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

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

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

Save the current SisypheROI instance to PySisyphe ROI (.xroi) file.

Parameters

filenamestr

PySisypheROI file name

singlebool

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

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

saveAsOld(filename: str) → None

Deprecated, use saveAs() method

setAlpha(a: int | float) → None

Set the ROI opacity of the current SisypheROI instance.

Parameters

afloat | int

• float, opacity, between 0.0 and 1.0

• int, opacity, between 0 and 255

setColor(r: float | int | None = None, g: float | int | None = None, b: float | int | None = None, rgb: list[float] | tuple[float, float, float] | list[int] | tuple[int, int, int] | None = None)

Set the ROI color of the current SisypheROI instance.

Parameters

rfloat | None

roi color, 0.0 <= red <= 1.0

gfloat | None

roi color, 0.0 <= green <= 1.0

bfloat | None

roi color, 0.0 <= blue <= 1.0

rgbtuple[float, float, float] | None

roi color, red, green, blue (0.0 <= value <= 1.0)

setCompression(v: bool) → None

Set the compression attribute of the current SisypheROI instance. PySisyphe ROI format (.xroi) can be optionally gzipped.

Parameters

vbool

compression is enabled if True

setCompressionOff() → None

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

setCompressionOn() → None

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

setDefaultFilename() → None

Set default file name attribute of the current SisypheROI instance. This file name is used by save() method. Default file name = name attribute + roi file extension (.xroi)

setDefaultName() → None

Set default name attribute of the current SisypheROI instance. default name = ‘ROI’ + instance count.

setDirname(path: str) → None

Set path part (dirname) of the file name attribute of the current SisypheROI instance.

Parameters

pathstr

replacement dirname

setFilename(filename: str) → None

Set the file name attribute of the current SisypheROI instance. This file name is used by save() method.

Parameters

filenamestr

file name

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

Set a prefix to the file name attribute of the current SisypheROI instance.

Parameters

prefixstr

prefix to add

sepstr

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

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

Set a suffix to the file name attribute of the current SisypheROI instance.

Parameters

suffixstr

suffix to add

sepstr

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

setName(name: str) → None

Set the name attribute of the current SisypheROI instance.

Parameters

namestr

roi name

setPathFromVolume(volume: SisypheVolume) → None

Set path part (dirname) of the file name attribute of the current SisypheROI instance from the path part of the file name attribute of a SisypheVolume parameter.

Parameters

volumeSisyphe.core.sisypheVolume.SisypheVolume

volume used to replace dirname

setQColor(c: QColor) → None

Set the ROI color of the current SisypheROI instance from a QColor.

Parameters

cPyQt5.QtGui.QColor

roi color

setReferenceID(ID: SisypheROI | SisypheVolume | str) → None

Set the reference ID attribute of the current SisypheROI instance. A ROI is defined in the space of a reference SisypheVolume whose ID is the reference ID.

Parameters

IDstr | Sisyphe.core.sisypheROI.SisypheROI | Sisyphe.core.sisypheVolume.SisypheVolume

• str, ID

• SisypheROI’s reference ID attribute

• SisypheVolume’s ID attribute

setVisibility(v: bool) → None

Set the ROI visibility of the current SisypheROI instance.

Parameters

vbool

visible if True

setVisibilityOff() → None

Hide the current SisypheROI instance.

setVisibilityOn() → None

Show the current SisypheROI instance.

shift(sx: int = 0, sy: int = 0, sz: int = 0) → None

ROI image shift of the current SisypheROI instance. The current SisypheROI instance is overwritten.

Parameters

sxint

shift of sx voxels in x-axis (default 0)

syint

shift of sy voxels in y-axis (default 0)

szint

shift of sz voxels in z-axis (default 0)

toIndexes(numpy: bool = False) → list | ndarray

Get a list of voxels indexes (x, y, z).

Parameters

numpybool

return numpy ndarray if True, list otherwise

Returns

list | ndarray

list of voxels indexes

class Sisyphe.core.sisypheROI.SisypheROICollection

Description

Named list container of SisypheROI instances. Container key to address elements can be an int index, a roi name str or a SisypheROI instance (uses name attribute as str key).

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

Scope of methods:

• resampling (apply geometric transformation),

• converting to and from SisypheVolume label,

• setter and getter methods of sisypheROI instances in the collection,

• set operators (union, intersection, difference, symmetric difference),

• flip/shift,

• morphology operators (dilate, erode, closing, opening),

• fill holes,

• IO methods.

Inheritance

object -> SisypheROICollection

Creation: 08/09/2022 Last revision: 23/05/2024

append(value: SisypheROI | SisypheROICollection) → None

Append a SisypheROI element in the current SisypheROICollection instance container.

Parameters

valueSisypheROI | SisypheROICollection

ROI(s) to append

clear() → None

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

clearBorderBlobs()

Clear blob(s) connected to the border of the current SisypheROI instance.

copy() → SisypheROICollection

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

Returns

SisypheROICollection

shallow copy of the collection

copyToList() → list[SisypheROI]

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

Returns

list[SisypheROI]

shallow copy of the collection

count() → int

Get the number of SisypheROI elements in the current SisypheROICollection instance container.

Returns

int

number of SisypheROI elements

difference() → SisypheROI

Apply difference operator between sisypheROI instances in the current SisypheROICollection instance container.

Returns

SisypheROI

processed roi

fillHoles() → None

Fill holes of the SisypheROI instances in the current SisypheROICollection instance container.

flip(fx: bool = False, fy: bool = False, fz: bool = False) → None

Flip SisypheROI instances axes in the current SisypheROICollection instance container.

Parameters

fxbool

flip x-axis if True (default False)

fybool

flip y-axis if True (default False)

fzbool

flip z-axis if True (default False)

fromLabelVolume(v: SisypheVolume) → None

Convert a SisypheVolume instance of labels to SisypheROI images added to the current SisypheROICollection instance. Each scalar value in the SisypheVolume instance is converted to a SisypheROI image, these scalar values are used as int index in the current SisypheROICollection instance.

Parameters

vSisyphe.core.sisypheVolume.SisypheVolume

label volume

getBlobCount() → list[int]

Get the number of blobs (connected components) in the SisypheROI instances in a copy of the current SisypheROICollection instance.

Returns

list[int]

number of blobs in each SisypheROI instance

getBlobLargerThan(n: int) → SisypheROICollection

Remove blobs (connected components) with less than n voxels from the SisypheROI instances in a copy of the current SisypheROICollection instance.

Returns

SisypheROICollection

collection of processed roi(s)

getClearBorderBlobs() → SisypheROICollection

Clear blob(s) connected to the border of the current SisypheROI instance.

Returns

SisypheROICollection

collection of processed roi(s)

getEulerNumber(connectivity: int = 26) → list[int]

Calculate the Euler characteristic of the current SisypheROI instance. The Euler number is obtained as the number of blobs plus the number of holes, minus the number of tunnels, or loops.

Parameters

connectivityint

6 or 26

Returns

list[int]

Euler number(s)

getFillHoles() → SisypheROICollection

Fill holes of the SisypheROI instances in a copy of the current SisypheROICollection instance.

Returns

SisypheROICollection

collection of processed roi(s)

getFlip(fx: bool = False, fy: bool = False, fz: bool = False) → SisypheROICollection

Flip SisypheROI instances axes in a copy of the current SisypheROICollection instance.

Parameters

fxbool

flip x-axis if True (default False)

fybool

flip y-axis if True (default False)

fzbool

flip z-axis if True (default False)

Returns

SisypheROICollection

collection of flipped roi(s)

getList() → list[SisypheROI]

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

Returns

list[SisypheROI]

shallow copy of the collection

getMajorBlob() → SisypheROICollection

Clear all blobs (connected components) except the major one (most voxels) of the SisypheROI instances in a copy of the current SisypheROICollection instance.

Returns

SisypheROICollection

collection of processed roi(s)

getMorphoClosing(radius: int = 1, struct: int = 1) → SisypheROICollection

SisypheROI instances morphological closing in a copy of the current SisypheROICollection instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROICollection

collection of morphology closing roi(s)

getMorphoDilate(radius: int = 1, struct: int = 1) → SisypheROICollection

SisypheROI instances morphological dilatation in a copy of the current SisypheROICollection instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROICollection

collection of dilated roi(s)

getMorphoErode(radius: int = 1, struct: int = 1) → SisypheROICollection

SisypheROI instances morphological erosion in a copy of the current SisypheROICollection instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROICollection

collection of eroded roi(s)

getMorphoOpening(radius: int = 1, struct: int = 1) → SisypheROICollection

SisypheROI instances morphological opening in a copy of the current SisypheROICollection instance.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

Returns

SisypheROICollection

collection of morphology opening roi(s)

getReferenceID() → str

Get reference ID attribute of the current SisypheROICollection instance. All ROIs in the container are defined in the space of a reference SisypheVolume whose ID is the reference ID.

Returns

str

reference ID

getShift(sx: int = 0, sy: int = 0, sz: int = 0) → SisypheROICollection

SisypheROI instances shift in a copy of the current SisypheROICollection instance.

Parameters

sxint

shift of sx voxels in x-axis (default 0)

syint

shift of sy voxels in y-axis (default 0)

szint

shift of sz voxels in z-axis (default 0)

Returns

SisypheROICollection

collection of shifted roi(s)

getSkeletonize(blob: int = 0) → SisypheROICollection

Calculate the skeleton of the current SisypheROI instance.

Parameters

blobint

blob index or 0 (whole image, default)

Returns

SisypheROI

collection of skeleton roi(s)

hasReferenceID() → bool

Check if the reference ID of the current SisypheROICollection instance is defined (not ‘’).

Returns

bool

True if reference ID is defined

index(value: str | SisypheROI) → int

Index of a SisypheROI element in the current SisypheROICollection instance container.

Parameters

valuestr | SisypheROI

ROI name or ROI element

Returns

int

index

insert(key: int | str | SisypheROI, value: SisypheROI)

Insert a SisypheROI element at the position given by the key in the current SisypheROICollection instance container.

Parameters

keyint | str | SisypheROI

• int, index

• str, ROI name index

• SisypheROI, ROI index

valueSisypheROI

ROI to insert

intersection() → SisypheROI

Apply intersection operator between sisypheROI instances in the current SisypheROICollection instance container.

Returns

SisypheROI

processed roi

isEmpty() → bool

Checks if SisypheROICollection instance container is empty.

Returns

bool

True if container is empty

keys() → list[str]

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

Returns

list[str]

list of keys in the container

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

Load SisypheROI elements in the current SisypheROICollection instance container from a list of PySisyphe ROI (.xroi) file names.

Parameters

filenamesstr | list[str]

list of PySisyphe ROI (.xroi) file names

loadFromBrainVoyagerVOI(vmr: str, filenames: str | list[str]) → None

Load SisypheROI elements in the current SisypheROICollection instance container from a list of old Sisyphe ROI (.roi) file names.

Parameters

vmrstr

BrainVoyager reference volume (.vmr) file name

filenamesstr | list[str]

list of BrainVoyager ROI (.voi) file names

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

Load SisypheROI elements in the current SisypheROICollection instance container from a list of old Sisyphe ROI (.roi) file names.

Parameters

filenamesstr | list[str]

list of old Sisyphe ROI (.roi) file names

morphoClosing(radius: int = 1, struct: int = 1) → None

Morphological closing of the SisypheROI instances in the current SisypheROICollection instance container.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

morphoDilate(radius: int = 1, struct: int = 1) → None

Morphological dilatation of the SisypheROI instances in the current SisypheROICollection instance container.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

morphoErode(radius: int = 1, struct: int = 1) → None

Morphological erosion of the SisypheROI instances in the current SisypheROICollection instance container.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

morphoOpening(radius: int = 1, struct: int = 1) → None

Morphological opening of the SisypheROI instances in the current SisypheROICollection instance container.

Parameters

radiusint

structuring element radius (in voxels)

structint

structuring element shape, SimpleITK code (0 sitkAnnulus, 1 sitkBall, 2 sitkBox, 3 sitkCross)

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

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

Parameters

keyint | str | SisypheROI | None

• int, index of the SisypheROI to remove

• str, ROI name of the SisypheROI to remove

• SisypheROI to remove

• None, remove the last element

Returns

SisypheROI

element removed from the container

pruning(blob: int = 0)

Remove “spurs” of less than a certain length in the current SisypheROI instance.

Parameters

blobint

blob index or 0 (whole image, default)

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

Remove a SisypheROI element from the current SisypheROICollection instance container.

Parameters

valueint | str | SisypheROI

• int, index of the SisypheROI to remove

• str, ROI name of the SisypheROI to remove

• SisypheROI to remove

removeBlobByDistance(d: float)

Remove blobs until the remaining ones are spaced more than a given distance from one another. By default, smaller objects are removed first.

Parameters

dfloat

minimal distance between blobs in mm

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

Apply an affine geometric transformation to all the SisypheROI elements of the current SisypheROICollection instance container.

Parameters

trfSisypheTransform

affine geometric transformation

savebool

save resampled SisypheROI elements (default True)

dialogbool

dialog box to choice file name of each resampled SisypheROI element (default False)

prefixstr | None

prefix added to file name of the resampled SisypheROI elements (optional)

suffixstr | None

suffix added to file name of the resampled SisypheROI elements (optional)

waitDialogWait | None

progress bar dialog (optional)

reverse() → None

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

roiSTAPLECombination() → SisypheROI

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

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

Returns

SisypheROI

processed roi

roiVotingCombination() → SisypheROI

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

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

Returns

SisypheROI

processed roi

save() → None

Iteratively save SisypheROI elements in the current SisypheMeshCollection instance container.

setReferenceID(ID: SisypheROI | SisypheVolume | str) → None

Set reference ID attribute of the current SisypheROICollection instance. All ROIs in the container are defined in the space of a reference SisypheVolume whose ID is the reference ID.

Parameters

IDstr | Sisyphe.core.sisypheROI.SisypheROI | Sisyphe.core.sisypheVolume.SisypheVolume

• str, ID

• SisypheROI’s ID attribute

• SisypheVolume’s ID attribute

shift(sx: int = 0, sy: int = 0, sz: int = 0) → None

SisypheROI instances shift in the current SisypheROICollection instance container.

Parameters

sxint

shift of sx voxels in x-axis (default 0)

syint

shift of sy voxels in y-axis (default 0)

szint

shift of sz voxels in z-axis (default 0)

sort(reverse: bool = False)

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

Parameters

reversebool

sorting in reverse order

symmetricDifference() → SisypheROI

Apply symmetric difference operator between sisypheROI instances in the current SisypheROICollection instance container.

Returns

SisypheROI

processed roi

toLabelVolume() → SisypheVolume

Convert the current SisypheROICollection instance into a SisypheVolume instance of labels. The label value of each ROI in the SisypheVolume instance is its int index in the SisypheROICollection container.

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

label volume

union() → SisypheROI

Apply union operator between sisypheROI instances in the current SisypheROICollection instance container.

Returns

SisypheROI

processed roi

class Sisyphe.core.sisypheROI.SisypheROIDraw

Description

Processing class for SisypheROI instances with undo/redo management. Set input ROI with setROI method. Set input reference valume with SetVolume method.

Scope of methods:

• drawing,

• flip/shift,

• copy/cut/paste (global or blob),

• blob selection,

• morphology operators (global or blob),

• fill holes,

• thresholding (global or blob),

• region growing (global or blob),

• active contour,

• slice interpolation,

• shape statistics,

• descriptive statistics.

Most of these methods are available in 2D (slice) and 3D.

Inheritance

object -> SisypheROIDraw

Creation: 08/09/2022 Last revision: 24/03/2025

activeContour(x: int, y: int, z: int, seedradius: float = 2.0, sigma: float = 1.0, rms: float = 0.01, advec: float = 1.0, curv: float = 1.0, propag: float = 1.0, niter: int = 1000, algo: str = 'default', replace: bool = False) → None

Active contour, level set method of segmentation, in the SisypheROI image attribute. Iterative algorithm starting from a seed sphere.

See SimpleITK GeodesicActiveContourLevelSetImageFilter doc: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1GeodesicActiveContourLevelSetImageFilter.html

Parameters

xint

x-axis seed sphere coordinate

yint

y-axis seed sphere coordinate

zint

z-axis seed sphere coordinate

seedradiusfloat

radius in mm of the seed sphere centered on x, y, z (default 2.0). If roi[x, y, z] is not background (i.e. > 0), use blob as seed rather than sphere, seedradius parameter is then ignored.

sigmafloat

gaussian kernel parameter used to compute the magnitude of the gradient. The edge potential map of the level set algorithm is computed from the image gradient. Edge potential map is that it has values close to zero in regions near the edges and values close to one inside the shape itself. This map is the image from which the speed function will be calculated.

rmsfloat

convergence threshold (0.0 < rms < 1.0, default 0.01). rms is used to determine when the solution has converged. A lower value will result in a tighter-fitting solution, but will require more computations. Too low a value could put the solver into an infinite loop unless a reasonable number of iterations parameter is set.

curvfloat

curvature, larger -> smoother resulting contour (default 1.0). Controls the magnitude of the curvature values which are calculated on the evolving isophote. This is important in controlling the relative effect of curvature in the calculation. Default value is 1.0. Higher values relative to the other level set equation terms (propagation and advection) will give a smoother result.

advecfloat

advection, default 1.0. Controls the scaling of the vector advection field term relative to other terms in the level set equation

propagfloat

propagation speed (default 1.0). > 0 propagation outwards, < 0 propagating inwards controls the scaling of the scalar propagation (speed) term relative to other terms in the level set equation

niterint

maximum number of iterations (default 1000). Can be used to halt the solution after a specified number of iterations, overriding the rms halting criteria

algostr

algorithm ‘default’ SimpleITK GeodesicActiveContourLevelSetImageFilter or ‘shape’ SimpleITK ShapeDetectionLevelSetImageFilter

replacebool

• if True, segmented mask replaces previous voxels

• if False (default), | (or) logic between mask and previous voxels

activeContourSegmentation(x: int, y: int, z: int) → None

Active contour, level set method of segmentation, in the SisypheROI image attribute. Iterative algorithm starting from a seed sphere. This method used active contour attributes of the current SisypheDraw instance as parameters (seed radius, sigma, rms, advection weight, curvature weight, propagation weight, number of iterations, algorithm).

Parameters

xint

x-axis seed sphere coordinate

yint

y-axis seed sphere coordinate

zint

z-axis seed sphere coordinate

activeThresholdContour(x: int, y: int, z: int, seedradius: float = 2.0, factor: float = 3.0, rms: float = 0.01, curv: float = 1.0, propag: float = 1.0, thresholds: tuple[float, float] | None = None, niter: int = 1000, replace: bool = False) → None

Active contour, level set method of segmentation, in the SisypheROI image attribute. Iterative algorithm starting from a seed sphere.

See SimpleITK ThresholdSegmentationLevelSetImageFilter doc: https://simpleitk.org/doxygen/v1_0/html/classitk_1_1simple_1_1ThresholdSegmentationLevelSetImageFilter.html

Parameters

xint

x-axis seed sphere coordinate

yint

y-axis seed sphere coordinate

zint

z-axis seed sphere coordinate

seedradiusfloat

radius in mm of the seed sphere centered on x, y, z (default 2.0). If roi[x, y, z] is not background (i.e. > 0), use blob as seed rather than sphere, seedradius parameter is then ignored.

factorfloat

factor x standard deviation of signal in seed sphere to estimate lower and upper thresholds used by level set algorithm (default 3.0)

rmsfloat

convergence threshold (0.0 < rms < 1.0, default 0.01). rms is used to determine when the solution has converged. A lower value will result in a tighter-fitting solution, but will require more computations. Too low a value could put the solver into an infinite loop unless a reasonabl number of iterations parameter is set.

curvfloat

curvature, larger -> smoother resulting contour (default 1.0). Controls the magnitude of the curvature values which are calculated on the evolving isophote. This is important in controlling the relative effect of curvature in the calculation. Default value is 1.0. Higher values relative to the other level set equation terms (propagation and advection) will give a smoother result.

propagfloat

propagation speed (default 1.0). > 0 propagation outwards, < 0 propagating inwards controls the scaling of the scalar propagation (speed) term relative to other terms in the level set equation.

thresholdstuple[float, float] | None

Lower and upper thresholds used by level set algorithm. If None, threshold are computed from seed region (mean +/- factor * sigma)

niterint

maximum number of iterations (default 1000). Can be used to halt the solution after a specified number of iterations, overriding the rms halting criteria

replacebool

• if True, segmented mask replaces previous voxels

• if False (default), | (or) logic between mask and previous voxels

appendSliceToLIFO(i: int, dim: int, pile: int = 0) → None

Add a slice of the SisypheROI attribute in the LIFO undo/redo stack. This method is called by 2D processing methods if undo/redo abilities are enabled.

Parameters

iint

index of the slice

dimint

slice axis code, 0 z-axis, 1 y-axis, 2 x-axis

pileint

0 addBundle to LIFO undo stack, 1 addBundle to LIFO redo stack

appendVolumeToLIFO(pile: int = 0) → None

Add the whole volume of the SisypheROI attribute in the LIFO undo/redo stack. This method is called by 3D processing methods if undo/redo abilities are enabled.

Parameters

pileint

0 addBundle to LIFO undo stack, 1 addBundle to LIFO redo stack

appendXSliceToLIFO(i: int, pile: int = 0) → None

Add a sagittal slice of the SisypheROI attribute in the LIFO undo/redo stack. This method is called by 2D processing methods if undo/redo abilities are enabled.

Parameters

iint

x-axis index of the slice

pileint

0 addBundle to LIFO undo stack, 1 addBundle to LIFO redo stack

appendYSliceToLIFO(i: int, pile: int = 0) → None

Add a coronal slice of the SisypheROI attribute in the LIFO undo/redo stack. This method is called by 2D processing methods if undo/redo abilities are enabled.

Parameters

iint

y-axis index of the slice

pileint

0 addBundle to LIFO undo stack, 1 addBundle to LIFO redo stack

appendZSliceToLIFO(i: int, pile: int = 0) → None

Add an axial slice of the SisypheROI attribute in the LIFO undo/redo stack. This method is called by 2D processing methods if undo/redo abilities are enabled.

Parameters

iint

z-axis index of the slice

pileint

0 addBundle to LIFO undo stack, 1 addBundle to LIFO redo stack

backgroundSegment(algo: str = 'huang') → None

Automatic background segmentation of the SisypheROI image attribute.

Parameters

algostr

algorithm used to find the best threshold for separating a mask from the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’

backgroundSegmentSlice(sindex: int, dim: int, algo: str = 'huang') → None

Automatic background segmentation in a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

algostr

algorithm used to find the best separation threshold between a mask and the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’ (default ‘huang’)

binaryAND(rois: list[SisypheROI] | SisypheROICollection) → None

Binary “logic and” between the SisypheROI image attribute and a list of SisypheROI images (or SisypheROICollection).

Parameters

roislist[SisypheROI] | SisypheROICollection

rois to be processed

binaryINTERSECTION(rois: list[SisypheROI] | SisypheROICollection) → None

Binary “logic and” between the SisypheROI image attribute and a list of SisypheROI images (or SisypheROICollection).

Parameters

roislist[SisypheROI] | SisypheROICollection

rois to be processed

binaryNAND(rois: list[SisypheROI] | SisypheROICollection) → None

Binary “logic nand (not and)” between the SisypheROI image attribute and a list of SisypheROI images (or SisypheROICollection).

Parameters

roislist[SisypheROI] | SisypheROICollection

rois to be processed

binaryNOT() → None

Binary “not” of the SisypheROI image attribute.

binaryNotSlice(sindex: int, dim: int) → None

Apply the binary not operator in a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

binaryOR(rois: list[SisypheROI] | SisypheROICollection) → None

Binary “logic or” between the SisypheROI image attribute and a list of SisypheROI images (or SisypheROICollection).

Parameters

roislist[SisypheROI] | SisypheROICollection

rois to be processed

binaryUNION(rois: list[SisypheROI] | SisypheROICollection) → None

Binary “logic or” between the SisypheROI image attribute and a list of SisypheROI images (or SisypheROICollection).

Parameters

roislist[SisypheROI] | SisypheROICollection

rois to be processed

binaryXOR(rois: list[SisypheROI] | SisypheROICollection) → None

Binary “logic xor” between the SisypheROI image attribute and a list of SisypheROI images (or SisypheROICollection).

Parameters

roislist[SisypheROI] | SisypheROICollection

rois to be processed

blobFilterExtent(n: int) → None

Remove blobs (connected components) from the SisypheROI image attribute, according to their extent (number of voxels).

Parameters

nint

number of voxels threshold

blobFilterExtentSlice(sindex: int, dim: int, n: int) → None

Remove blobs (connected components) from a SisypheROI attribute slice, according to their extent (number of voxels).

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

nint

number of voxels threshold

blobRemove(x: int, y: int, z: int) → None

Remove the blob containing the voxel whose coordinates are transmitted, from the SisypheROI image attribute.

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

blobRemoveSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Remove the blob containing the voxel whose coordinates are transmitted, from a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

blobSelect(x: int, y: int, z: int) → None

Remove all blobs except the one containing the voxel whose coordinates are transmitted, from the SisypheROI image attribute.

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

blobSelectSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Remove all blobs except the one containing the voxel whose coordinates are transmitted, from a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

brush(x: int, y: int, z: int, dim: int) → None

Draw a brush-shape at the x, y, z coordinates of the SisypheROI image attribute. Brush-shape is defined with setBrushType() method, and size with setBrushRadius() method.

Parameters

xint

x-axis coordinate

yint

y-axis coordinate

zint

z-axis coordinate

dimint

slice orientation code

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

clear() → None

Clear the SisypheROI image attribute (i.e. all voxels to 0).

clearBorderBlob() → None

Remove all blobs (connected components) connected to image border.

clearBorderBlobSlice(sindex: int, dim: int) → None

Remove all blobs (connected components) connected to image border, from a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

clearClipboard() → None

Clear the clipboard attribute of the current SisypheROIDraw instance. The clipboard attribute is used as temporary buffer by copy/cut/paste methods.

clearLIFO() → None

Clear the LIFO undo/redo stacks.

clearSlice(sindex: int, dim: int) → None

Clear a SisypheROI attribute slice (i.e. all voxels to 0).

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

copyBlob(x: int, y: int, z: int) → None

Copy to clipboard the blob containing the voxel whose coordinates are transmitted, from the SisypheROI image attribute.

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

copyBlobSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Copy the blob containing the voxel whose coordinates are transmitted to clipboard, from a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

copySlice(sindex: int, dim: int) → None

Copy of a SisypheROI attribute slice to the clipboard.

Parameters

sindex :int

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

cutBlob(x: int, y: int, z: int) → None

Cut to clipboard the blob containing the voxel whose coordinates are transmitted, from the SisypheROI image attribute.

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

cutBlobSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Cut the blob containing the voxel whose coordinates are transmitted to clipboard, from a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

cutSlice(sindex: int, dim: int) → None

Cut of a SisypheROI attribute slice to the clipboard.

Parameters

sindex :int

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

drawCube(p: list[int] | tuple[int, int, int], extent: int) → None

Draw a cube in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extentint

length of cube sides (in voxels)

drawDisk(p: list[int] | tuple[int, int, int], radius: int, orient: int = 0) → None

Draw a disk in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z center point coordinates

radiusint

disk radius (in voxels)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawEllipse(p: list[int] | tuple[int, int, int], radius: list[int] | tuple[int, int], rot: float = 0.0, orient: int = 0) → None

Draw an ellipse in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z center point coordinates

radiustuple[int, int] | list[int, int]

radius in x and y axes (in voxels)

rotfloat

set the ellipse rotation in radians (between -pi and pi, default 0.0)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawLine(p0: list[int] | tuple[int, int, int], p1: list[int] | tuple[int, int, int], orient: int = 0) → None

Draw a line in the current SisypheROI image attribute. Line is drawn in a single slice (p0 and p1 must be within the same slice)

Parameters

p0tuple[int, int, int] | list[int, int, int]

x, y, z first point coordinates

p1tuple[int, int, int] | list[int, int, int]

x, y, z second point coordinates

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawParallelepiped(p: list[int] | tuple[int, int, int], extent: list[int] | tuple[int, int, int]) → None

Draw a parallelepiped in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extenttuple[int, int, int] | list[int, int, int]

width, height and depth (in voxels)

drawPolygon(p: list[list[int]], orient: int = 0) → None

Draw a polygon in the current SisypheROI image attribute. Polygon is drawn in a single slice (all points must be within the same slice).

Parameters

plist[list[int]]

list of 3 list[int]: - first list[int], x coordinates of points - second list[int], y coordinates of points - third list[int], z coordinates of points

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawRectangle(p: list[int] | tuple[int, int, int], extent: list[int] | tuple[int, int], orient: int = 0) → None

Draw a rectangle in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extenttuple[int, int] | list[int, int]

width and height (in voxels)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

drawSphere(p: list[int] | tuple[int, int, int], radius: int) → None

Draw a sphere in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z center coordinates

radiusint

sphere radius (in voxels)

drawSquare(p: list[int] | tuple[int, int, int], extent: int, orient: int = 0) → None

Draw a square in the current SisypheROI image attribute.

Parameters

ptuple[int, int, int] | list[int, int, int]

x, y, z origin coordinates

extentint

length of square sides (in voxels)

orientint

slice orientation (0 axial, 1 coronal, 2 sagittal)

erase(x: int, y: int, z: int, dim: int) → None

Erase a brush-shape at the x, y, z coordinates of the SisypheROI image attribute. Brush-shape is defined with setBrushType() method, and size with setBrushRadius() method.

Parameters

xint

x-axis coordinate

yint

y-axis coordinate

zint

z-axis coordinate

dimint

slice orientation code

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

euclideanBlobDilate(x: int, y: int, z: int, mm: float = 0.0) → None

Expand a selected blob in the SisypheROI image attribute with a constant margin (in mm).

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

mmfloat

margin thickness in mm

euclideanBlobErode(x: int, y: int, z: int, mm: float = 0.0) → None

Shrink a selected blob in the SisypheROI image attribute with a constant margin (in mm).

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

mmfloat

margin thickness in mm

euclideanDilate(mm: float = 0.0) → None

Expand the SisypheROI image attribute with a constant margin (in mm)

Parameters

mmfloat

margin thickness in mm

euclideanErode(mm: float = 0.0) → None

Shrink the SisypheROI image attribute with a constant margin (in mm)

Parameters

mmfloat

margin thickness in mm

extractingValue(value: float, mask: bool = False, replace: bool = False) → None

Calculate a mask of the SisypheROI image attribute of voxels with a given scalar value in the reference SisypheVolume image attribute.

Parameters

valuefloat

scalar value in reference SisypheVolume attribute

maskbool

if True, & (and) logic between mask and previous voxels (default False)

replacebool

• if True, mask replaces previous voxels

• if False (default), | (or) logic between mask and previous voxels

extractingValueBlob(value: float, x: int, y: int, z: int) → None

Calculate a mask limited to a blob of the SisypheROI image attribute from voxels with a given scalar value in the reference SisypheVolume image attribute.

Parameters

valuefloat

scalar value in reference SisypheVolume attribute

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

extractingValueBlobSlice(sindex: int, dim: int, value: float, x: int, y: int, z: int) → None

Calculate a mask limited to the surface of a blob in a slice of the SisypheROI attribute from voxels with a given scalar value in the SisypheVolume reference attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

valuefloat

scalar value in reference SisypheVolume attribute

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

extractingValueSlice(sindex: int, dim: int, value: float, mask: bool = False, replace: bool = False) → None

Calculate a mask in a slice of the SisypheROI attribute of voxels with a given scalar value in the reference SisypheVolume attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

valuefloat

scalar value in reference SisypheVolume attribute

maskbool

if True, & (and) logic between mask and previous voxels of the slice (default False)

replacebool

• if True, mask replaces previous voxels of the slice

• if False (default), | (or) logic between mask and previous voxels of the slice

fillHoles() → None

Fill holes in the SisypheROI image attribute.

fillHolesAllSlices(dim: int) → None

Fill holes of the SisypheROI attribute. This method executes iteratively in 2D on all slices of the SisypheROI attribute.

Parameters

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

fillHolesSlice(sindex: int, dim: int, undo: bool | None = None)

Fill holes in a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

undobool | None

• if True, adds slice in the LIFO undo/redo stack

• if None, takes state of the undo attribute of the current SisypheROIDraw instance (see setUndo() method)

flip(flipx: bool, flipy: bool, flipz: bool) → None

Flip axes of the SisypheROI image attribute.

Parameters

flipxbool

flip x-slice-axis if True

flipybool

flip y-slice-axis if True

flipzbool

flip z-slice-axis if True

flipSlice(sindex: int, dim: int, flipx: bool, flipy: bool) → None

Flip axes of a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

flipxbool

flip x-slice-axis if True

flipybool

flip y-slice-axis if True

getActiveContourAdvectionWeight() → float

Get the active contour advection weight attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The advection attribute (default 1.0) controls the scaling of the vector advection field term relative to other terms in the level set equation.

Returns

float

active contour advection weight attribute

getActiveContourAlgorithm() → str

Get the active contour algorithm attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Returns

str

active contour algorithm attribute (‘geodesic’, ‘shape’ or ‘threshold’)

getActiveContourConvergence() → float

Get the active contour convergence attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The rms convergence attribute (0.0 < rms < 1.0, default 0.01) is used to determine when the solution has converged. A lower value will result in a tighter-fitting solution, but will require more computations. Too low a value could put the solver into an infinite loop unless a reasonable number of iterations parameter is set.

Returns

float

active contour convergence attribute

getActiveContourCurvatureWeight() → float

Get the active contour curvature weight attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The curvature attribute (default 1.0) controls the magnitude of the curvature values which are calculated on the evolving isophote. This is important in controlling the relative effect of curvature in the calculation. Default value is 1.0. Higher values relative to the other level set equation terms (propagation and advection) will give a smoother result.

Returns

float

active contour curvature weight attribute

getActiveContourFactor() → float

Get the active contour factorfactor attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The factor attribute is only used by the threshold version of the active contour algorithms, if threshold attributes are not defined. The formula factor x standard deviation of the signal within the seed sphere is used to estimate the lower and upper threshold parameters (default 3.0).

Returns

float

active contour factor attribute

getActiveContourNumberOfIterations() → int

Get the active contour number of iterations attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Returns

int

active contour number of iterations attribute

getActiveContourPropagationWeight() → float

Get the active contour propagation weight attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The propagation speed attribute (default 1.0) controls the scaling of the scalar propagation (speed) term relative to other terms in the level set equation. > 0 propagation outwards, < 0 propagating inwards.

Returns

float

active contour propagation weight attribute

getActiveContourSeedRadius() → float

Get the active contour seed radius attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Returns

float

active contour seed radius attribute, seed sphere radius in mm

getActiveContourSigma() → float

Get the active contour sigma attribute of the current SisypheDraw instance. This attribute is useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The sigma attribute is a gaussian kernel parameter used to compute the magnitude of the gradient. The edge potential map of the level set algorithm is computed from the image gradient. Edge potential map is that it has values close to zero in regions near the edges and values close to one inside the shape itself. This map is the image from which the speed function will be calculated.

Returns

float

active contour sigma attribute

getActiveContourThresholds() → tuple[float, float] | None

Get the active contour curvature weight attribute of the current SisypheDraw instance. These attributes are useb by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Lower and upper threshold attributes are only used by the threshold version of the active contour algorithms.

Returns

tuple[float, float]

active contour threshold attributes

getBrushRadius() → int

Get the radius (in voxels) of the brush used to hand-draw in the SisypheROI image.

Returns

int

brush radius in voxels

getBrushType() → str

Get the brush type, as str name, used to hand-draw in the SisypheROI image.

Brush types:

• ‘solid’ disc-shaped 2D brush

• ‘threshold’ voxels of the disc-shaped 2D brush surface with a scalar value over a threshold in the SisypheVolume reference

• ‘solid3’ sphere-shaped 3D brush

• ‘threshold3’ voxels in sphere-shaped 3D brush volume with a scalar value over a threshold in the SisypheVolume reference

Returns

str

brush type

getConfidenceConnectedIter() → int

Get the confidence connected number of iterations attribute of the current SisypheDraw instance.

Returns

int

confidence connected number of iterations attribute

getConfidenceConnectedSigma() → float

Get the confidence connected sigma attribute of the current SisypheDraw instance.

Returns

float

confidence connected sigma attribute

getIntensityStatistics() → dict[str, float]

Get the descriptive statistics of scalar values in the reference SisypheVolume image attribute masked by the SisypheROI image attribute.

Returns

dict[str, float]

key (str) / value (float)

• ‘count’ number of voxels

• ‘mean’ mean

• ‘median’ median

• ‘min’ minimum

• ‘max’ maximum

• ‘range’ maximum - minimum

• ‘perc25’ first quartile

• ‘perc75’ third quartile

• ‘var’ variance

• ‘std’ standard deviation

• ‘skewness’ skewness

• ‘kurtosis’ kurtosis

getMorphologyRadius() → float

Get the radius (in voxels) of the structuring element used in morphological methods (erosion, dilatation, opening, closing).

Returns

int

structuring element radius in voxels

getROI() → SisypheROI

Get the SisypheROI image attribute from the current SisypheROIDraw instance. This is the ROI image processed in the current SisypheROIDraw instance. Same space as reference SisypheVolume attribute (same size and spacing).

Returns

Sisyphe.core.sisypheROI.SisypheROI

roi to be processed

getShapeStatistics() → list[dict[str, float]]

Get the shape statistics of the SisypheROI image attribute.

Returns

dict[str, float]

key (str)

• ‘count’

• ‘boundingbox’

• ‘centroid’

• ‘elongation’

• ‘flatness’

• ‘principalaxes’

• ‘principalmoments’

• ‘perimeter’

• ‘physicalsize’

• ‘feretdiameter’

• ‘ellipsoiddiameter’

• ‘sphericalperimeter’

• ‘sphericalradius’

getSliceIntensityStatistics(sindex: int, dim: int) → dict[str, float]

Get the descriptive statistics of scalar values in a slice of the reference SisypheVolume image attribute masked by the SisypheROI image attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

Returns

dict[str, float]

key (str) / value (float)

• ‘count’ number of voxels

• ‘mean’ mean

• ‘median’ median

• ‘min’ minimum

• ‘max’ maximum

• ‘range’ maximum - minimum

• ‘perc25’ first quartile

• ‘perc75’ third quartile

• ‘var’ variance

• ‘std’ standard deviation

• ‘skewness’ skewness

• ‘kurtosis’ kurtosis

getStructElement() → str

Get the structuring element shape, as str name, used in morphological methods (erosion, dilatation, opening, closing).

Returns

str

structuring element: ‘ball’, ‘box’, ‘cross’ or ‘annulus’

getThickness() → float

Get the margin (in mm) used in euclidean expanding/shrinking methods (euclideanDilate, euclideanErode, 2D and 3D, whole and blob versions).

Returns

float

margin in mm

getThresholdMax() → float

Get the maximum value threshold used in some methods.

Returns

float

maximum value threshold

getThresholdMin() → float

Get the minimum value threshold used in some methods.

Returns

float

minimum value threshold

getThresholds() → tuple[float, float]

Get the minimum and maximum value thresholds used in some methods.

Returns

tuple[float, float]

minimum and maximum value thresholds

getUndo() → bool

Check whether undo/redo abilities of the current SisypheROIDraw instance are enabled. All ROI processing is stored in a LIFO stack if this option is enabled.

Returns

boolean

undo enabled if True

getVolume() → SisypheVolume

Get the reference SisypheVolume image attribute from the current SisypheROIDraw instance. Same space as SisypheROI attribute (same size and spacing). Many methods require a reference SisypheVolume (including segmentation methods).

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

reference volume

hasROI() → bool

Check whether the SisypheROI attribute of the current SisypheROIDraw instance is defined (not None). This is the ROI image processed in the current SisypheROIDraw instance.

Returns

bool

True if SisypheROI attribute is defined

hasThresholds() → bool

Check whether threshold attributes of the current SisypheROIDraw instance are defined.

Returns

bool

True if thresholds are defined

hasVolume() → bool

Check whether the reference SisypheVolume attribute of the current SisypheROIDraw instance is defined (not None).

Returns

bool

True if reference SisypheVolume attribute is defined

interpolateBetweenSlices(sindex1: int, sindex2: int, dim: int, replace=False) → None

Cavalieri’s interpolation method is used to fill in the slices of the SisypheROI attribute between two slices sent as parameters (sindex1 and sindex2).

Parameters

sindex1int

first slice index

sindex2int

last slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

replacebool

• if True, the interpolated slices replace the previous ones

• if False (default), interpolated slices are combined (or logical) with previous ones

interpolateEmptySlices(sindex: int, dim: int) → None

Empty slices are interpolated between two non-empty slices above and below. Non-empty slices are searched for above and below a starting slice given as parameter. Cavalieri’s interpolation method is used to fill in the empty slices of the SisypheROI attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

majorBlobSelect() → None

Remove all blobs (connected components) except the largest one, from the SisypheROI image attribute.

majorBlobSelectSlice(sindex: int, dim: int)

Remove all blobs (connected components) except for the largest one, from a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

maskSegment(algo: str = 'huang', morpho: str = '', niter: int = 1, kernel: int = 0, fill: str = '')

Automatic head/brain mask segmentation of the SisypheROI image attribute.

Parameters

algostr

algorithm used to find the best threshold for separating a mask from the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’

morphostr

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

niterint

number of binary morphology iterations

kernelint

structuring element size

fillstr

• ‘2d’, fill holes slice by slice

• ‘3d’, fill holes in 3D

• ‘’, no filling

maskSegment2(algo: str = 'huang', morphoiter: int = 2, kernel: int = 0)

Automatic head/brain mask segmentation of the SisypheROI image attribute.

Parameters

algostr

algorithm used to find the best threshold for separating a mask from the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’

morphoiterint

number of binary morphology iterations

kernelint

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

morphoBlobClosing(x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological closing of the SisypheROI image attribute. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoBlobDilate(x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological dilatation of the SisypheROI image attribute. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoBlobErode(x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological erosion of the SisypheROI image attribute. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoBlobOpening(x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological opening of the SisypheROI image attribute. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoClosing(radius: int | None = None, struct: int | None = None) → None

Morphological closing of the SisypheROI image attribute.

Parameters

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoDilate(radius: int | None = None, struct: int | None = None) → None

Morphological dilatation of the SisypheROI image attribute.

Parameters

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoErode(radius: int | None = None, struct: int | None = None) → None

Morphological erosion of the SisypheROI image attribute.

Parameters

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoOpening(radius: int | None = None, struct: int | None = None) → None

Morphological opening of the SisypheROI image attribute.

Parameters

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceBlobClosing(sindex: int, dim: int, x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological closing of a SisypheROI attribute slice. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

sindexint

slice index

dimint

slice orientation code, - 0 z-axis slice (axial), - 1 y-axis slice (coronal), - 2 x-axis slice (sagittal)

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceBlobDilate(sindex: int, dim: int, x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological dilatation of a SisypheROI attribute slice. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceBlobErode(sindex: int, dim: int, x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological erosion of a SisypheROI attribute slice. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceBlobOpening(sindex: int, dim: int, x: int, y: int, z: int, radius: int | None = None, struct: int | None = None) → None

Morphological opening of a SisypheROI attribute slice. Processing only applies to a blob selected by the coordinates of one of its voxels.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis coordinate of the voxel used for blob selection

yint

y-axis coordinate of the voxel used for blob selection

zint

z-axis coordinate of the voxel used for blob selection

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceClosing(sindex: int, dim: int, radius: int | None = None, struct: int | None = None) → None

Morphological closing of a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceDilate(sindex: int, dim: int, radius: int | None = None, struct: int | None = None) → None

Morphological dilatation of a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceErode(sindex: int, dim: int, radius: int | None = None, struct: int | None = None) → None

Morphological erosion of a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

morphoSliceOpening(sindex: int, dim: int, radius: int | None = None, struct: int | None = None) → None

Morphological opening of a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

radiusint | None

structuring element radius in voxels (Default is None). If None, get radius from the morphological radius attribute of the current SisypheROIDraw instance (see setMorphologyRadius() method)

structint | None

structuring element shape as SimpleITK int code (Default is None)

• 0 Annulus

• 1 disk

• 2 box

• 3 cross

• if None, get structuring element shape from the structuring element attribute of the current SisypheROIDraw instance (see setStructElement() method)

notMaskSegment2(algo: str = 'huang', morphoiter: int = 2, kernel: int = 0)

Automatic background mask segmentation of the SisypheROI image attribute.

Parameters

algostr

algorithm used to find the best threshold for separating a mask from the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’

morphoiterint

number of binary morphology iterations

kernelint

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

objectSegment(algo: str = 'huang') → None

Automatic mask segmentation of the SisypheROI image attribute.

Parameters

algostr

algorithm used to find the best threshold for separating a mask from the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’

objectSegmentSlice(sindex: int, dim: int, algo: str = 'huang') → None

Automatic mask segmentation in a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

algostr

algorithm used to find the best separation threshold between a mask and the background. Available algorithm names : ‘mean’, ‘otsu’, ‘huang’, ‘renyi’, ‘yen’, ‘li’, ‘shanbhag’, ‘triangle’, ‘intermodes’, ‘maximumentropy’, ‘kittler’, ‘isodata’, ‘moments’ (default ‘huang’)

pasteBlob(x: int, y: int, z: int) → None

Paste the blob from clipboard at the position of the voxel whose coordinates are transmitted, into the SisypheROI image attribute.

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

pasteBlobSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Paste the blob from clipboard at the position of the voxel whose coordinates are transmitted, into a SisypheROI attribute slice.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

pasteSlice(sindex: int, dim: int) → None

Paste a SisypheROI attribute slice from the clipboard.

Parameters

sindex :int

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

popRedoLIFO() → None

Copy the last element (slice or whole ROI) of the LIFO redo stack to the SisypheROI attribute. Redo the last processing of the SisypheROI attribute.

popUndoLIFO() → None

Copy the last element (slice or whole ROI) of the LIFO undo stack to the SisypheROI attribute. Undo the last processing of the SisypheROI attribute.

regionGrowing(x: int, y: int, z: int, mask: bool = False, replace: bool = False) → None

Region growing from a seed voxel in the SisypheROI image attribute.

Parameters

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

maskbool

if True, & (and) logic between mask and previous voxels (default False)

replacebool

• if True, mask replaces previous voxels

• if False (default), | (or) logic between mask and previous voxels

regionGrowingBlob(x: int, y: int, z: int) → None

Region growing from a seed voxel limited to a blob in the SisypheROI image attribute.

Parameters

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

regionGrowingBlobSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Region growing from a seed voxel limited to the surface of a blob in a slice of the SisypheROI attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

regionGrowingConfidence(x: int, y: int, z: int, niter: int | None = None, multi: float | None = None, radius: int | None = None, mask: bool = False, replace: bool = False) → None

Region growing confidence from a seed voxel in the SisypheROI image attribute.

SimpleITK ConfidenceConnectedImageFilter doc: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ConfidenceConnectedImageFilter.html

This filter extracts a connected set of voxels whose voxel intensities are consistent with the voxel statistics of a seed point. The mean and variance across a neighborhood (8-connected, 26-connected, …) are calculated for a seed point. Then voxels connected to this seed point whose values are within the confidence interval for the seed point are grouped. The width of the confidence interval is controlled by the “multi” parameter (the confidence interval is the mean plus or minus the “multi” times the standard deviation). If the intensity variations across a segment were gaussian, a “multi” setting of 2.5 would define a confidence interval wide enough to capture 99% of samples in the segment.

After this initial segmentation is calculated, the mean and variance are re-calculated. All the voxels in the previous segmentation are used to calculate the mean the standard deviation (as opposed to using the voxels in the neighborhood of the seed point). The segmentation is then recalculated using these refined estimates for the mean and variance of the voxel values. This process is repeated for the specified number of iterations. Setting the number of iterations to zero stops the algorithm after the initial segmentation from the seed point.

Parameters

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

niterint | None

number of iteration (default None) if niter is None, niter = confidence connected iterations attribute of the current instance

multifloat | None

confidence interval = multi * standard deviation (default None) if multi is None, multi = confidence connected sigma attribute of the current instance

radiusint | None

neighborhood radius (default None) if radius is None, raidus = morphology radius attribute of the current instance

maskbool

if True, & (and) logic between mask and previous voxels (default False)

replacebool

• if True, mask replaces previous voxels

• if False, | (or) logic between mask and previous voxels

regionGrowingConfidenceBlob(x: int, y: int, z: int, niter: int | None = None, multi: float | None = None, radius: int | None = None) → None

Region growing confidence from a seed voxel limited to a blob in the SisypheROI image attribute.

See SimpleITK ConfidenceConnectedImageFilter doc: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ConfidenceConnectedImageFilter.html

This filter extracts a connected set of voxels whose voxel intensities are consistent with the voxel statistics of a seed point. The mean and variance across a neighborhood (8-connected, 26-connected, …) are calculated for a seed point. Then voxels connected to this seed point whose values are within the confidence interval for the seed point are grouped. The width of the confidence interval is controlled by the “multi” parameter (the confidence interval is the mean plus or minus the “multi” times the standard deviation). If the intensity variations across a segment were gaussian, a “multi” setting of 2.5 would define a confidence interval wide enough to capture 99% of samples in the segment.

After this initial segmentation is calculated, the mean and variance are re-calculated. All the voxels in the previous segmentation are used to calculate the mean the standard deviation (as opposed to using the voxels in the neighborhood of the seed point). The segmentation is then recalculated using these refined estimates for the mean and variance of the voxel values. This process is repeated for the specified number of iterations. Setting the number of iterations to zero stops the algorithm after the initial segmentation from the seed point.

Parameters

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

niterint | None

number of iteration (default None) if niter is None, niter = confidence connected iterations attribute of the current instance

multifloat

confidence interval = multi * standard deviation (default None) if multi is None, multi = confidence connected sigma attribute of the current instance

radiusint | None

neighborhood radius (default None) if radius is None, raidus = morphology radius attribute of the current instance

regionGrowingConfidenceBlobSlice(sindex: int, dim: int, x: int, y: int, z: int, niter: int | None = None, multi: float | None = None, radius: int | None = None) → None

Region growing confidence from a seed voxel limited to the surface of a blob in a slice of the SisypheROI attribute.

SimpleITK ConfidenceConnectedImageFilter doc: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ConfidenceConnectedImageFilter.html

This filter extracts a connected set of voxels whose voxel intensities are consistent with the voxel statistics of a seed point. The mean and variance across a neighborhood (8-connected, 26-connected, …) are calculated for a seed point. Then voxels connected to this seed point whose values are within the confidence interval for the seed point are grouped. The width of the confidence interval is controlled by the “multi” parameter (the confidence interval is the mean plus or minus the “multi” times the standard deviation). If the intensity variations across a segment were gaussian, a “multi” setting of 2.5 would define a confidence interval wide enough to capture 99% of samples in the segment.

After this initial segmentation is calculated, the mean and variance are re-calculated. All the voxels in the previous segmentation are used to calculate the mean the standard deviation (as opposed to using the voxels in the neighborhood of the seed point). The segmentation is then recalculated using these refined estimates for the mean and variance of the voxel values. This process is repeated for the specified number of iterations. Setting the number of iterations to zero stops the algorithm after the initial segmentation from the seed point.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

niterint | None

number of iteration (default None) if niter is None, niter = confidence connected iterations attribute of the current instance

multifloat | None

confidence interval = multi * standard deviation (default None) if multi is None, multi = confidence connected sigma attribute of the current instance

radiusint | None

neighborhood radius (default None) if radius is None, multi = morphology radius attribute of the current instance

regionGrowingConfidenceSlice(sindex: int, dim: int, x: int, y: int, z: int, niter: int | None = None, multi: float | None = None, radius: int | None = None, mask: bool = False, replace: bool = False) → None

Region growing confidence from a seed voxel in a slice of the SisypheROI attribute.

SimpleITK ConfidenceConnectedImageFilter doc: https://simpleitk.org/doxygen/latest/html/classitk_1_1simple_1_1ConfidenceConnectedImageFilter.html

This filter extracts a connected set of voxels whose voxel intensities are consistent with the voxel statistics of a seed point. The mean and variance across a neighborhood (8-connected, 26-connected, …) are calculated for a seed point. Then voxels connected to this seed point whose values are within the confidence interval for the seed point are grouped. The width of the confidence interval is controlled by the “multi” parameter (the confidence interval is the mean plus or minus the “multi” times the standard deviation). If the intensity variations across a segment were gaussian, a “multi” setting of 2.5 would define a confidence interval wide enough to capture 99% of samples in the segment.

After this initial segmentation is calculated, the mean and variance are re-calculated. All the voxels in the previous segmentation are used to calculate the mean the standard deviation (as opposed to using the voxels in the neighborhood of the seed point). The segmentation is then recalculated using these refined estimates for the mean and variance of the voxel values. This process is repeated for the specified number of iterations. Setting the number of iterations to zero stops the algorithm after the initial segmentation from the seed point.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

niterint | None

number of iteration (default None) if niter is None, niter = confidence connected iterations attribute of the current instance

multifloat | None

confidence interval = multi * standard deviation (default None) if multi is None, multi = confidence connected sigma attribute of the current instance

radiusint | None

neighborhood radius (default None) if radius is None, raidus = morphology radius attribute of the current instance

maskbool

if True, & (and) logic between mask and previous voxels of the slice (default False)

replacebool

• if True, mask replaces previous voxels of the slice

• if False (default), or logic between mask and previous voxels of the slice

regionGrowingSlice(sindex: int, dim: int, x: int, y: int, z: int, mask: bool = False, replace: bool = False) → None

Region growing from a seed voxel in a slice of the SisypheROI attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis seed voxel coordinate

yint

y-axis seed voxel coordinate

zint

z-axis seed voxel coordinate

maskbool

if True, & (and) logic between mask and previous voxels of the slice (default False)

replacebool

• if True, mask replaces previous voxels of the slice

• if False (default), or logic between mask and previous voxels of the slice

removeROI() → None

Remove the SisypheROI attribute to the current SisypheROIDraw instance.

seedFill(x: int, y: int, z: int) → None

Fill background voxels (i.e. 0 value) from a seed voxel in the SisypheROI. Filling algorithm starts from a seed voxel whose x, y and z coordinates are provided.

Parameters

xint

x-axis seed coordinate

yint

y-axis seed coordinate

zint

z-axis seed coordinate

seedFillSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Fill background voxels (i.e. 0 value) from a seed voxel in a SisypheROI attribute slice. Filling algorithm starts from a seed voxel whose x, y and z coordinates are provided.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis seed coordinate

yint

y-axis seed coordinate

zint

z-axis seed coordinate

setActiveContourAdvectionWeight(weight: float = 1.0) → None

Set the active contour advection weight attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Advection attribute (default 1.0) controls the scaling of the vector advection field term relative to other terms in the level set equation.

Parameters

weightfloat

active contour advection weight attribute

setActiveContourAlgorithm(algo: str = 'geodesic') → None

Set the active contour algorithm attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Parameters

algostr

active contour algorithm attribute (‘geodesic’, ‘shape’ or ‘threshold’)

setActiveContourConvergence(rms: float = 0.01) → None

Set the active contour convergence attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The rms convergence attribute (0.0 < rms < 1.0, default 0.01) is used to determine when the solution has converged. A lower value will result in a tighter-fitting solution, but will require more computations. Too low a value could put the solver into an infinite loop unless a reasonable number of iterations parameter is set.

Parameters

rmsfloat

active contour convergence attribute

setActiveContourCurvatureWeight(weight: float = 1.0) → None

Set the active contour curvature weight attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The curvature attribute (default 1.0) controls the magnitude of the curvature values which are calculated on the evolving isophote. This is important in controlling the relative effect of curvature in the calculation. Default value is 1.0. Higher values relative to the other level set equation terms (propagation and advection) will give a smoother result.

Parameters

weightfloat

active contour curvature weight attribute

setActiveContourFactor(factor: float = 2.0) → None

Set the active contour factor attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The factor attribute is only used by the threshold version of the active contour algorithms, if threshold attributes are not defined. The formula mean +/- factor x standard deviation of the signal within the seed sphere is used to estimate the lower and upper threshold parameters (default 3.0).

Parameters

factorfloat

active contour factor attribute

setActiveContourNumberOfIterations(niter: int = 1000) → None

Set the active contour number of iterations attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Parameters

niterint

active contour number of iterations attribute

setActiveContourPropagationWeight(weight: float = 1.0) → None

Set the active contour propagation weight attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The propagation speed attribute (default 1.0) controls the scaling of the scalar propagation (speed) term relative to other terms in the level set equation. > 0 propagation outwards, < 0 propagating inwards.

Parameters

weightfloat

active contour propagation weight attribute

setActiveContourSeedRadius(radius: float = 2.0) → None

Set the active contour seed radius attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Parameters

radiusfloat

active contour seed radius attribute, seed sphere radius in mm

setActiveContourSigma(sigma: float = 1.0) → None

Set the active contour sigma attribute of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

The sigma attribute is a gaussian kernel parameter used to compute the magnitude of the gradient. The edge potential map of the level set algorithm is computed from the image gradient. Edge potential map is that it has values close to zero in regions near the edges and values close to one inside the shape itself. This map is the image from which the speed function will be calculated.

Parameters

sigmafloat

active contour sigma attribute

setActiveContourThresholds(thresholds: tuple[float, float] | None) → None

Set the active contour threshold attributes of the current SisypheDraw instance. This attribute is used by the activeContourSegmentation() method. Active contour is an iterative level set method of segmentation, starting from a seed sphere.

Lower and upper threshold attributes are only used by the threshold version of the active contour algorithms.

Parameters

thresholdstuple[float, float]

Lower and upper thresholds

setBrushRadius(radius: int) → None

Set the radius (in voxels) of the brush used to hand-draw in the SisypheROI image.

Parameters

radiusint

brush radius in voxels

setBrushType(brushtype: int | str) → None

Set the brush type, as str name or int code, used to hand-draw in the SisypheROI image.

Parameters

brushtype int | str

name or int code

• 0 or ‘solid’ disc-shaped 2D brush

• 1 or ‘threshold’ thresholded voxels of the disc-shaped 2D brush surface

• 2 or ‘solid3’ sphere-shaped 3D brush

• 3 or ‘threshold3’ thresholded voxels in sphere-shaped 3D brush volume

setConfidenceConnectedIter(iters: int = 4) → None

Set the confidence connected number of iterations attribute of the current SisypheDraw instance.

Parameters

itersint

confidence connected number of iterations attribute

setConfidenceConnectedSigma(sigma: float = 2.0) → None

Set the confidence connected sigma attribute of the current SisypheDraw instance.

Parameters

sigmafloat

confidence connected sigma attribute

setFullRangeThreshold() → None

Set the minimum and maximum value thresholds to the minimum and maximum scalar values in the reference SisypheVolume instance. These thresholds are used in some processing methods.

setHuangThreshold(background: bool = False) → None

Set minimum and maximum value thresholds using Huang algorithm. These thresholds are used in some processing methods.

Parameters

backgroundbool

• True:

  • minimum threshold = minimum scalar value in the reference SisypheVolume instance

  • maximum threshold processed by Huang algorithm

• False:

  • minimum threshold processed by Huang algorithm

  • maximum threshold = maximum scalar value in the reference SisypheVolume instance

setMeanThreshold(background: bool = False) → None

Set minimum and maximum value thresholds using Mean algorithm. These thresholds are used in some processing methods.

Parameters

backgroundbool

• True:

  • minimum threshold = minimum scalar value in the reference SisypheVolume instance

  • maximum threshold processed by Mean algorithm

• False:

  • minimum threshold processed by Mean algorithm

  • maximum threshold = maximum scalar value in the reference SisypheVolume instance

setMorphologyRadius(radius: float) → None

Set the radius (in voxels) of the structuring element used in morphological methods (erosion, dilatation, opening, closing).

Parameters

radiusint

structuring element radius in voxels

setOtsuThreshold(background: bool = False) → None

Set minimum and maximum value thresholds using Otsu algorithm. These thresholds are used in some processing methods.

Parameters

backgroundbool

• True:

  • minimum threshold = minimum scalar value in the reference SisypheVolume instance

  • maximum threshold processed by Otsu algorithm

• False:

  • minimum threshold processed by Otsu algorithm

  • maximum threshold = maximum scalar value in the reference SisypheVolume instance

setROI(roi: SisypheROI) → None

Set the SisypheROI image attribute to the current SisypheROIDraw instance. This is the ROI image processed in the current SisypheROIDraw instance. Same space as reference SisypheVolume attribute (same size and spacing).

Parameters

roiSisyphe.core.sisypheROI.SisypheROI

roi to be processed

setStructElement(struct: str) → None

Set the structuring element shape, as str name, used in morphological methods (erosion, dilatation, opening, closing).

Parameters

structstr

structuring element: ‘ball’, ‘box’, ‘cross’ or ‘annulus’

setThickness(mm: float) → None

Set the margin (in mm) used in euclidean expanding/shrinking methods (euclideanDilate, euclideanErode, 2D and 3D, whole and blob versions).

Parameters

mmfloat

margin in mm

setThresholdMax(vmax: float) → None

Set the maximum value threshold used in some methods.

Parameters

vmaxfloat

maximum value threshold

setThresholdMin(vmin: float) → None

Set the minimum value threshold used in some methods.

Parameters

vminfloat

minimum value threshold

setThresholds(vmin: float, vmax: float) → None

Set the minimum and maximum value thresholds used in some methods.

Parameters

vminfloat

minimum value threshold

vmaxfloat

maximum value threshold

setUndo(v: bool) → None

Enables/disables undo/redo abilities of the current SisypheROIDraw instance. All ROI processing is stored in a LIFO stack if this option is enabled.

Parameters

vboolean

undo enabled if True

setUndoOff() → None

Disables undo/redo abilities of the current SisypheROIDraw instance. All ROI processing is stored in a LIFO stack if this option is enabled.

setUndoOn() → None

Enables undo/redo abilities of the current SisypheROIDraw instance. All ROI processing is stored in a LIFO stack if this option is enabled.

setVolume(volume: SisypheVolume) → None

Set the reference SisypheVolume image attribute to the current SisypheROIDraw instance. Same space as SisypheROI attribute (same size and spacing). Many methods require a reference SisypheVolume (including segmentation methods).

Parameters

volumeSisyphe.core.sisypheVolume.SisypheVolume

reference volume

shift(movex: int, movey: int, movez: int) → None

Image shift of the SisypheROI image attribute.

Parameters

movexint

shift in x-slice-axis (in voxels)

moveyint

shift in y-slice-axis (in voxels)

movezint

shift in z-slice-axis (in voxels)

shiftSlice(sindex: int, dim: int, movex: int, movey: int) → None

Image shift of a SisypheROI attribute slice.

Parameters

sindex :int

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

movexint

shift in x-slice-axis (in voxels)

moveyint

shift in y-slice-axis (in voxels)

solid3DBrush(x: int, y: int, z: int, c: int = 1) → None

Draw a sphere at the x, y, z coordinates of the SisypheROI image attribute. Disk radius is defined with setBrushRadius() method.

Parameters

xint

x-axis coordinate

yint

y-axis coordinate

zint

z-axis coordinate

cint

0 (erase) or 1 (draw)

solidBrush(x: int, y: int, z: int, c: int, dim: int) → None

Draw a disk at the x, y, z coordinates of the SisypheROI image attribute. Disk radius is defined with setBrushRadius() method.

Parameters

xint

x-axis coordinate

yint

y-axis coordinate

zint

z-axis coordinate

cint

0 (erase) or 1 (draw)

dimint

slice orientation code

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

threshold3DBrush(x: int, y: int, z: int) → None

Draw a sphere at the x, y, z coordinates of the SisypheROI image attribute. In this thresholded version, only voxels with scalar values above a threshold in the SisypheVolume reference are added. Disk radius is defined with setBrushRadius() method.

Parameters

xint

x-axis coordinate

yint

y-axis coordinate

zint

z-axis coordinate

thresholdBrush(x: int, y: int, z: int, dim: int) → None

Draw a disk at the x, y, z coordinates of the SisypheROI image attribute. In this thresholded version, only voxels with scalar values above a threshold in the SisypheVolume reference are added. Disk radius is defined with setBrushRadius() method.

Parameters

xint

x-axis coordinate

yint

y-axis coordinate

zint

z-axis coordinate

dimint

slice orientation code

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

thresholding(mask: bool = False, replace: bool = False) → None

Calculate a mask of the SisypheROI image attribute of voxels whose scalar value is greater than a threshold in the reference SisypheVolume image attribute.

Parameters

maskbool

if True, & (and) logic between mask and previous voxels (default False)

replacebool

• if True, mask replaces previous voxels

• if False (default), | (or) logic between mask and previous voxels

thresholdingBlob(x: int, y: int, z: int) → None

Calculate a mask limited to a blob of the SisypheROI image attribute of voxels whose scalar value is greater than a threshold in the reference image SisypheVolume attribute.

Parameters

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

thresholdingBlobSlice(sindex: int, dim: int, x: int, y: int, z: int) → None

Calculate a mask limited to the surface of a blob in a slice of the SisypheROI attribute of voxels whose scalar value is greater than a threshold in the reference SisypheVolume attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

xint

x-axis blob selection coordinate

yint

y-axis blob selection coordinate

zint

z-axis blob selection coordinate

thresholdingSlice(sindex: int, dim: int, mask: bool = False, replace: bool = False) → None

Calculate a mask in a slice of the SisypheROI attribute of voxels whose scalar value is greater than a threshold in the reference SisypheVolume attribute.

Parameters

sindexint

slice index

dimint

slice orientation code,

• 0 z-axis slice (axial),

• 1 y-axis slice (coronal),

• 2 x-axis slice (sagittal)

maskbool

if True, & (and) logic between mask and previous voxels of the slice (default False)

replacebool

• if True, mask replaces previous voxels of the slice

• if False, | (or) logic between mask and previous voxels of the slice

class Sisyphe.core.sisypheROI.SisypheROIFeatures(vol: SisypheVolume | None = None, rois: SisypheROICollection | None = None)

Description

Extract features (descriptive statistics, shape, texture) from SisypheROI and SisypheVolume instance(s).

Inheritance

object -> SisypheROIFeatures

Creation: 08/09/2022 Last revision: 15/12/2023

execute(progress: DialogWait | None = None) → None

Execute features calculation.

List of calculated features enabled by tag methods :

• setFirstOrderTag()

• setGrayLevelCooccurrenceMatrixTag()

• setGrayLevelSizeZoneMatrixTag()

• setGrayLevelRunLengthMatrixTag()

• setNeighbouringGrayToneDifferenceMatrixTag()

• setGrayLevelDependenceMatrixTag()

• setShapeTag()

Feature results are set in the pandas.DataFrame instance attribute of the current SisypheROIFeatures instance.

Parameters

progressSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

getDataFrame() → DataFrame

Get the pandas.DataFrame instance attribute of the current SisypheROIFeatures instance.

Returns

pandas.DataFrame

DataFrame, table of features

getFirstOrderTag() → bool

Get tag state of the FirstOrder features.

Returns

bool

True if enabled

getGrayLevelCooccurrenceMatrixTag() → bool

Get tag state of the GrayLevelCooccurrenceMatrix features.

Returns

bool

True if enabled

getGrayLevelDependenceMatrixTag() → bool

Get tag state of the GrayLevelDependenceMatrix features.

Returns

bool

True if enabled

getGrayLevelRunLengthMatrixTag() → bool

Get tag state of the GrayLevelRunLengthMatrix features.

Returns

bool

True if enabled

getGrayLevelSizeZoneMatrixTag() → bool

Get tag state of the GrayLevelSizeZoneMatrix features.

Returns

bool

True if enabled

getNeighbouringGrayToneDifferenceMatrixTag() → bool

Get tag state of the NeighbouringGrayToneDifferenceMatrix features.

Returns

bool

True if enabled

getROICollection() → SisypheROICollection

Get the SisypheROICollection attribute from the current SisypheROIFeatures instance. Same space as SisypheROICollection attribute (same image size and spacing).

Returns

SisypheROICollection

roi collection to be processed

getShapeTag() → bool

Get tag state of the Shape features.

Returns

bool

True if enabled

getVolume() → SisypheVolume

Get the reference SisypheVolume image attribute from the current SisypheROIFeatures instance. Same space as SisypheROICollection attribute (same image size and spacing).

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

reference volume

hasROICollection() → bool

Check whether the SisypheROICollection attribute of the current SisypheROIFeatures instance is defined (not None).

Returns

bool

True if SisypheROICollection attribute is defined

hasVolume() → bool

Check whether the reference SisypheVolume attribute of the current SisypheROIFeatures instance is defined (not None).

Returns

bool

True if reference SisypheVolume attribute is defined

saveToCSV(filename: str) → None

Save calculated features to a CSV file (.csv).

Parameters

filenamestr

csv file name

saveToXLSX(filename: str) → None

Save calculated features to an Excel file (.xlsx).

Parameters

filenamestr

Excel file name

setAllTagsOn() → None

Enables all features.

setFirstOrderTag(v: bool) → None

Enable/Disable the FirstOrder features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#radiomics.firstorder.RadiomicsFirstOrder

FirstOrder features : energy, total energy, entropy, 10th percentile, 90th percentile, minimum, maximum, mean, median, interquartile range, range, mean absolute deviation, robust mean absolute deviation, root mean squared, standard deviation

Parameters

vbool

enabled if True

setGrayLevelCooccurrenceMatrixTag(v: bool) → None

Enable/Disable the GrayLevelCooccurrenceMatrix (GLCM) features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#module-radiomics.glcm

GLCM features : autocorrelation, joint average, cluster prominence, cluster shade, cluster tendency, contrast, correlation, difference average, difference entropy, difference variance, dissimilarity, joint energy, joint entropy, homogeneity 1 and 2, informational measure of correlation 1 and 2, inverse difference moment, maximal correlation coefficient, inverse difference moment normalized, inverse difference, inverse difference normalized, inverse variance, maximum probability, sum average, sum variance, sum entropy, sum of squares

Parameters

vbool

enabled if True

setGrayLevelDependenceMatrixTag(v: bool) → None

Enable/Disable the GrayLevelDependenceMatrix (GLDM) features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#module-radiomics.gldm

GLDM features : small dependence emphasis, large dependence emphasis, gray level non-uniformity, gray level non-uniformity normalized, dependence non-uniformity, dependence non-uniformity normalized, gray level variance, dependence variance, dependence entropy, low gray level emphasis, high gray level emphasis, small dependence low gray level emphasis, small dependence high gray level emphasis, large dependence low gray level emphasis, large dependence high gray level emphasis

Parameters

vbool

enabled if True

setGrayLevelRunLengthMatrixTag(v: bool) → None

Enable/Disable the GrayLevelRunLengthMatrix (GLRLM) features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#module-radiomics.glrlm

GLRLM features : short run emphasis, long run emphasis, gray level non-uniformity, gray level non-uniformity normalized, run length non-uniformity, run length non-uniformity normalized, run percentage, gray level variance, run variance, run entropy, low gray level run emphasis, high gray level run emphasis, short run low gray level emphasis, short run high gray level emphasis, long run low gray level emphasis, long run high gray level emphasis

Parameters

vbool

enabled if True

setGrayLevelSizeZoneMatrixTag(v: bool) → None

Enable/Disable the GrayLevelSizeZoneMatrix (GLSZM) features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#module-radiomics.glszm

GLSZM features : small area emphasis, large area emphasis, gray level non-uniformity, gray level non-uniformity normalized, size-Zone non-uniformity, size-zone non-uniformity normalized, zone percentage, gray level variance, zone variance, zone entropy, low gray level zone emphasis, high gray level zone emphasis, small area low gray level emphasis, small area high gray level emphasis, large area low gray level emphasis, large area high gray level emphasis

Parameters

vbool

enabled if True

setNeighbouringGrayToneDifferenceMatrixTag(v: bool) → None

Enable/Disable the NeighbouringGrayToneDifferenceMatrix (NGTDM) features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#module-radiomics.ngtdm

NGTDM features : coarseness, contrast, busyness, complexity, strength

Parameters

vbool

enabled if True

setROICollection(rois: SisypheROICollection) → None

Set the SisypheROICollection attribute to the current SisypheROIFeatures instance. Same space as SisypheVolume attribute (same image size and spacing).

Parameters

roisSisypheROICollection

roi collection to be processed

setROICollectionFromLabelVolume(v: SisypheVolume) → None

Convert the SisypheVolume instance of labels to SisypheROI images added to a SisypheROICollection instance (see fromLabelVolume() docstrings of the SisypheROICollection class) and set it to the current SisypheROIFeatures instance.

Parameters

vSisyphe.core.sisypheVolume.SisypheVolume

label volume

setShapeTag(v: bool) → None

Enable/Disable the Shape features.

See https://pyradiomics.readthedocs.io/en/latest/features.html#module-radiomics.shape

Shape features : mesh volume, voxel volume, surface area, surface area to volume ratio, sphericity, compactness 1 and 2, spherical disproportion, maximum 3D diameter, maximum 2D diameter (slice), maximum 2D diameter (column), maximum 2D diameter (row), major axis length, minor Axis Length, least axis Length, elongation, flatness, mesh Surface, pixel surface, perimeter, perimeter to surface ratio, sphericity, spherical disproportion, maximum 2D diameter, major axis length, minor axis length, elongation

Parameters

vbool

enabled if True

setVolume(volume: SisypheVolume) → None

Set the reference SisypheVolume image attribute to the current SisypheROIFeatures instance. Same space as SisypheROICollection attribute (same image size and spacing).

Parameters

volumeSisyphe.core.sisypheVolume.SisypheVolume

reference volume

class Sisyphe.core.sisypheROI.SisypheROIHistogram(vol: SisypheVolume | None = None, rois: SisypheROICollection | None = None)

Description

Extract histograms from SisypheROICollection instance.

Inheritance

object -> SisypheROIHistogram

Creation: 08/09/2022 Last revision: 15/12/2023

execute(progress: DialogWait | None = None) → None

Execute histogram(s) calculation. Histogram results are set in the pandas.DataFrame instance attribute of the current SisypheROIFeatures instance.

Parameters

progressSisyphe.gui.dialogWait.DialogWait | None

progress bar dialog (optional)

getBins() → int

Get the histogram bins attribute of the current SisypheROIHistogram instance.

Returns

int

number of bins in the histogram

getDataFrame() → DataFrame

Get the pandas.DataFrame instance attribute of the current SisypheROIFeatures instance.

Returns

pandas.DataFrame

DataFrame histogram values

getHistograms(roi: SisypheROI, norm: bool = False) → tuple[DataFrame, DataFrame]

Calculate the histograms of a SisypheROI instance.

Parameters

roiSisypheROI

roi to be processed

normbool

histogram normalization if True (default False)

Returns

tuple[pandas.DataFrame, pandas.DataFrame]

• histogram in the first pandas.DataFrame

• cumulative histogram in the second pandas.DataFrame

getROICollection() → SisypheROICollection

Get the SisypheROICollection attribute from the current SisypheROIHistogram instance. Same space as SisypheROICollection attribute (same image size and spacing).

Returns

SisypheROICollection

roi collection to be processed

getVolume() → SisypheVolume

Get the reference SisypheVolume image attribute from the current SisypheROIHistogram instance. Same space as SisypheROICollection attribute (same image size and spacing).

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

reference volume

hasROICollection() → bool

Check whether the SisypheROICollection attribute of the current SisypheROIHistogram instance is defined (not None).

Returns

bool

True if SisypheROICollection attribute is defined

hasVolume() → bool

Check whether the reference SisypheVolume attribute of the current SisypheROIHistogram instance is defined (not None).

Returns

bool

True if reference SisypheVolume attribute is defined

saveToCSV(filename: str) → None

Save calculated histogram(s) to a CSV file (.csv).

Parameters

filenamestr

csv file name

saveToXLSX(filename: str) → None

Save calculated histogram(s) to an Excel file (.xlsx).

Parameters

filenamestr

Excel file name

setBins(v: int) → None

Set the histogram bins attribute of the current SisypheROIHistogram instance.

Parameters

vint

number of bins in the histogram

setROICollection(rois: SisypheROICollection) → None

Set the SisypheROICollection attribute to the current SisypheROIHistogram instance. Same space as SisypheVolume attribute (same image size and spacing).

Parameters

roisSisypheROICollection

roi collection to be processed

setROICollectionFromLabelVolume(v: SisypheVolume) → None

Convert the SisypheVolume instance of labels to SisypheROI images added to a SisypheROICollection instance (see fromLabelVolume() docstrings of the SisypheROICollection class) and set it to the current SisypheROIHistogram instance.

Parameters

vSisyphe.core.sisypheVolume.SisypheVolume

label volume

setVolume(volume: SisypheVolume) → None

Set the reference SisypheVolume image attribute to the current SisypheROIHistogram instance. Same space as SisypheROICollection attribute (same image size and spacing).

Parameters

volumeSisyphe.core.sisypheVolume.SisypheVolume

reference volume