geometry

Contains functions to convert between world coordinates, cube coordinates, and voxel indices, as well as functions to handle gantry and couch rotations.

matRad_getRotationMatrix(gantryAngle, couchAngle, system)

matRad function to return the rotation / transformation matrix for gantry and/or couch rotation. The Rotation matrix stands for a (1) counter-clockwise, (2) active rotation in the patient coordinate system that is performed on a (4) column vector (by premultiplying the matrix). Per change of one of these directions a matrix transpose of the returned matrix is required.

call

rotMat = matRad_getRotationMatrix(gantryAngle,couchAngle,type,system)

Input:

gantryAngle – beam/gantry angle
couchAngle – couch angle
system – optional coordinate system the transformation matrix is requested for. So far, only the default option ‘LPS’ is supported (right handed system).

Output:

rotMat – 3x3 matrix that performs an active rotation around the patient system origin via rotMat * x

References: https://en.wikipedia.org/wiki/Rotation_matrix (2017, Mar 1)

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_getIsoCenter(cst, ct, visBool)

computes the isocenter [mm] as the joint center of gravity of all volumes of interest that are labeled as target within the cst struct

call

isoCenter = matRad_getIsoCenter(cst,ct,visBool)

Input:

cst – matRad cst struct
ct – ct cube
visBool – toggle on/off visualization (optional)

Output:

isoCenter – isocenter in [mm]

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_world2cubeCoords(wCoord, gridStruct, allowOutside)

matRad function to convert world coordinates to cube coordinates

call

coord = world2cubeCoords(wCoord, ct)

Input:

wCoord – world coordinates array Nx3 (x,y,z) [mm]
gridStruct – can be matRad ct, dij.doseGrid, or the ctGrid required fields x,y,x,dimensions,resolution
allowOutside – indices not within the image bounds will be calculated optional, default is true

Output:

coord – cube coordinates (x,y,z) - Nx3 in mm

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_addMargin(mVOI, cst, vResolution, vMargin, bDiaElem)

matRad add margin function

call

mVOIEnlarged = matRad_addMargin(mVOI,cst,vResolution,vMargin,bDiaElem)

Input:

mVOI – image stack in dimensions of X x Y x Z holding ones for object and zeros otherwise
cst – matRad cst struct
vResolution ct resolution
vMargin – margin in mm
bDiaElem if true 26-connectivity is used otherwise 6-connectivity

Output:

mVOIEnlarged – enlarged VOI

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_cubeIndex2worldCoords(cubeIx, gridStruct)

matRad function to convert cube indices to world coordinates

call

coord = matRad_cubeIndex2worldCoords(vCoord, gridStruct)

Input:

cCoord – cube indices [i j k] (Nx3) or [linIx] (Nx1)
gridStruct – matRad ct struct or dij.doseGrid/ctGrid struct
allowOutside – indices not within the image bounds will be calculated optional, default is true

Output:

coord – worldCoordinates [x y z] (Nx3 in mm)

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_resizeCstToGrid(cst, vXgridOld, vYgridOld, vZgridOld, vXgridNew, vYgridNew, vZgridNew)

matRad function to resize the cst to a given resolution

call

cst = matRad_resizeCstToGrid(cst,vXgridOld,vYgridOld,vZgridOld,vXgridNew,vYgridNew,vZgridNew)

Input:

cst – matRad cst struct
vXgridOld – vector containing old spatial grid points in x [mm]
vYgridOld – vector containing old spatial grid points in y [mm]
vZgridOld – vector containing old spatial grid points in z [mm]
vXgridNew – vector containing new spatial grid points in x [mm]
vYgridNew – vector containing new spatial grid points in y [mm]
vZgridNew – vector containing new spatial grid points in z [mm]

Output:

cst – updated matRad cst struct containing new linear voxel indices

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_selectVoxelsFromCst(cstOnDoseGrid, doseGrid, selectionMode)

matRad function to get mask of the voxels (on dose grid) that are included in cst structures specified by selectionMode.

call

includeMask = matRad_getVoxelsOnCstStructs(cst,doseGrid,VdoseGrid,selectionMode)

Input:

cstOnDoseGrid – cstOnDoseGrid (voxel indexes included in cst{:,4} are referred to a cube of dimensions doseGrid.dimensions)
doseGrid – doseGrid struct containing field doseGrid.dimensions
selectionMode – define which method to apply to select cst structures. Choices: all, targetOnly, oarsOnly, objectivesOnly, robustnessOnly, [indexes]

Output:

includeMask – logical array #voxels in dose grid

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_cubeCoords2worldCoords(cCoord, gridStruct, allowOutside)

matRad function to convert cube coordinates to world coordinates

call

coord = matRad_worldToCubeCoordinates(vCoord, gridStruct)

Input:

cCoord – cube coordinates [vx vy vz] (Nx3 in mm)
gridStruct – matRad ct struct or dij.doseGrid/ctGrid struct
allowOutside – indices not within the image bounds will be calculated optional, default is true

Output:

coord – worldCoordinates [x y z] (Nx3 in mm)

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_world2cubeIndex(wCoord, gridStruct, allowOutside)

matRad function to convert world coordinates to cube indices

call

coord = world2cubeCoords(wCoord, ct)

Input:

wCoord – world coordinates array Nx3 (x,y,z) [mm]
gridStruct – can be matRad ct, dij.doseGrid, or the ctGrid required fields x,y,x,dimensions,resolution
allowOutside – If coordinates outside are allowed. False default.

Output:

index – cube index (i,j,k) honoring Matlab permuatation of i,j

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_getWorldAxes(gridStruct)

matRad function to compute and store world coordinates into ct.x

call

gridStruct = matRad_getWorldAxes(gridStruct)

gridStruct: can be ct, dij.doseGrid,dij.ctGrid

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_setOverlapPriorities(cst, ctDim)

function to handle overlap priorities during fluence optimization and dose calculation. If you have overlapping volumes of interest you need to inform matRad to which volume(s) the intersection voxels belong.

call

cst = matRad_considerOverlap(cst) [cst, overlapPriorityCube] = matRad_setOverlapPriorities(cst,ctDim)

Input:

cst – cst file
ctDim – (optional) dimension of the ct for overlap cube claculation

Output:

cst – updated cst file considering overlap priorities
overlapPriorityCube – (optional) cube visualizing the overlap priority

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.