Sisyphe.core.sisypheFiducialBox

External packages/modules

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

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

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

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

class Sisyphe.core.sisypheFiducialBox.SisypheFiducialBox

Description

This class detects the Elekta Leksell frame’s fiducial markers. It computes a rigid transformation to calculate coordinates between the geometric Leksell reference and the image coordinates, and vice versa.

Inheritance

QObject -> SisypheFiducialBox

Creation: 26/07/2022 Last revision: 11/12/2023

ProgressTextChanged

Private attributes

_nbfid int, fiducials count (6 or 9) _fidtol float, distance tolerance of fiducial markers _fidlist dict, fiducial markers coordinates _errorlist dict, fiducial markers errors _errorstats dict, fiducial markers errors statistics _volume SisypheVolume _trf SisypheTransform

addTransformToVolume() → None

Add the calculated geometric transformation to the Sisyphe.core.sisypheTransform.SisypheTransforms attribute of the processed volume.

calcErrors() → None

Calculate errors i.e. euclidean distances between coordinates of the detected fiducial markers and their theoretical coordinates in mm.

calcTransform() → None

Calculate rigid transformation between image and Leksell geometric reference.

execute(vol: SisypheVolume) → None

Execute Leksell fiducial markers detection to calculate rigid transformation between image and Leksell geometric reference.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

PySisyphe volume

getAllMarkers() → dict[int, dict[int, list[float]]]

Get all fiducial markers coordinates.

Marker indexes (axial slice):

• Left markers: 0 posterior, 1 middle, 2 anterior

• right markers: 3 anterior, 4 middle, 5 posterior

• anterior markers: 6 right, 7 middle, 8 left

Returns

dict[int, dict[int, list[float]]

• key int, slice index

• value dict[int, float]

  • key int, marker index (6 or 9 markers)

  • value list[float, float, float], list of x, y, z fiducial marker coordinates

getErrorStatistics() → dict[str, float]

Get errors statistics.

Returns

dict[str, float]

str keys, float values

• ‘Mean’ mean error

• ‘RMS’ root-mean-square error

• ‘Median’ median error

• ‘Std’ standard deviation error

• ‘25th’ first quantile error

• ‘75th’ third quantile error

• ‘Min’ minimum error

• ‘Max’ maximum error

getErrors() → dict[int, dict[int, float]] | None

Get errors i.e. euclidean distances between coordinates of the detected fiducial markers and their theoretical coordinates in mm.

Marker indexes (axial slice):

• Left markers: 0 posterior, 1 middle, 2 anterior

• right markers: 3 anterior, 4 middle, 5 posterior

• anterior markers: 6 right, 7 middle, 8 left

Returns

dict[int, dict[int, float]],

• key int, slice index

• value dict[int, float]

  • key int, marker index (6 or 9 markers)

  • value float, euclidean distance error in mm

classmethod getFileExt() → str

Get SisypheFiducialBox file extension.

Returns

str

‘.xfid’

classmethod getFilterExt() → str

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

Returns

str

‘PySisyphe Fiducial markers (.xfid)’

getMarker(n: int, m: int) → list[float]

Get coordinates of a fiducial marker.

Marker indexes (axial slice):

• Left markers: 0 posterior, 1 middle, 2 anterior

• right markers: 3 anterior, 4 middle, 5 posterior

• anterior markers: 6 right, 7 middle, 8 left

Parameters

nint

slice index

mint

marker index

Returns

list[float]

x, y, z fiducial marker coordinates

getMarkersCount() → int

Get fiducial markers count.

Two possible configurations:

• 6: 3 to the left and 3 to the right

• 9: 3 to the left, 3 to the right, 3 to the front (front markers are optional)

Marker indexes (axial slice):

• Left markers: 0 posterior, 1 middle, 2 anterior

• right markers: 3 anterior, 4 middle, 5 posterior

• anterior markers: 6 right, 7 middle, 8 left

Returns

bool

True if slice index is valid (i.e. less than slice count)

getSliceMarkers(n: int) → dict[int, list[float]]

Get coordinates of fiducial markers in a slice.

Marker indexes (axial slice):

• Left markers: 0 posterior, 1 middle, 2 anterior

• right markers: 3 anterior, 4 middle, 5 posterior

• anterior markers: 6 right, 7 middle, 8 left

Parameters

nint

slice index

Returns

dict[int, list[float]]

• key int, marker index

• value list[float], x, y, z fiducial marker coordinates

getSliceNumbers() → list[int]

Get list of valid slice indexes (i.e. slices with at least 6 or 9 fiducial markers depending on configuration).

Returns

list[int]

list of valid indexes

getTransform() → SisypheTransform

Get rigid transformation between image and Leksell geometric reference.

Returns

Sisyphe.core.SisypheTransform.SisypheTransform

rigid transformation

getVolume() → SisypheVolume

Get PySisyphe volume

Returns

Sisyphe.core.sisypheVolume.SisypheVolume

volume to process

hasErrors() → bool

Checks whether errors are calculated.

Returns

bool

True if errors are calculated

hasSlice(n: int) → bool

Check whether slice index is valid (i.e. it contains at least 6 or 9 fiducial markers depending on configuration).

Returns

bool

True if slice index is valid

hasTransform() → bool

Checks whether rigid transformation between image and Leksell geometric reference is calculated.

Returns

bool

True if rigid transformation is calculated

hasVolume() → bool

Check whether PySisyphe volume to process is available.

Returns

bool

True if PySisyphe volume is defined

hasXML(filename: str) → bool

Check that fiducial markers coordinates file (.xfid) exists.

Parameters

filenamestr

file name, file extension is replaced by .xfid if necessary

Returns

bool

True if file name exists

isEmpty() → bool

Check that fiduciary marker coordinates are calculated.

Returns

bool

True if fiduciary marker coordinates are calculated

loadFromXML(filename: str) → None

Load fiducial markers coordinates file (.xfid).

Parameters

filenamestr

file name (.xfid)

markersSearch(vol: SisypheVolume, slc: int | None = None) → bool

Leksell fiducial markers detection in a slice.

Parameters

volSisyphe.core.sisypheVolume.SisypheVolume

PySisyphe volume

slcint

slice index

Returns

bool

False if no frame or frame detection failed

removeFrontPlateMarkers() → None

Remove front fiducial markers. Six markers configuration, 3 on the left and 3 on the right.

Marker indexes (axial slice):

• Left markers: 0 posterior, 1 middle, 2 anterior

• right markers: 3 anterior, 4 middle, 5 posterior

• anterior markers: 6 right, 7 middle, 8 left

removeSliceMarkers(n: int) → None

Removes all fiduciary markers from a slice.

Parameters

nint

slice index

saveToXML(filename: str) → None

Save fiducial markers coordinates file (.xfid).

Parameters

filenamestr

file name (.xfid)

setVolume(v: SisypheVolume) → None

Set PySisyphe volume to process.

Parameters

vSisyphe.core.sisypheVolume.SisypheVolume

volume to process