Package | Description |
---|---|
edu.stanford.rsl.conrad.geometry |
Contains classes to describe various projection geometries.
|
edu.stanford.rsl.conrad.geometry.motion |
Contains classes to model motion.
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edu.stanford.rsl.conrad.geometry.shapes.simple |
Contains classes to model simple shapes.
|
edu.stanford.rsl.conrad.geometry.splines |
Contains classes to model splines.
|
edu.stanford.rsl.conrad.geometry.trajectories |
Contains classes to model trajectories, i.e.
|
edu.stanford.rsl.conrad.geometry.transforms |
Contains classes to model transformations in 3D.
|
edu.stanford.rsl.conrad.numerics |
Contains Matrix and Vector objects and associated linear algebra operations.
|
edu.stanford.rsl.conrad.numerics.mathexpressions |
Contains classes to model the Forbild phantom language.
|
edu.stanford.rsl.conrad.opencl |
Contains classes to use OpenCL.
|
edu.stanford.rsl.conrad.phantom.xcat |
Contains classes to create a phantom that is similar to NCAT.
|
edu.stanford.rsl.conrad.physics |
Contains classes to physical effects related to x-rays.
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edu.stanford.rsl.conrad.reconstruction |
Contains classes to implement different reconstruction algorithms.
|
edu.stanford.rsl.conrad.reconstruction.iterative |
Contains classes to implement different iterative reconstruction algorithms.
|
edu.stanford.rsl.conrad.rendering |
Contains classes that model different ray tracers.
|
edu.stanford.rsl.conrad.utils |
Contains various utility classes.
|
edu.stanford.rsl.tutorial.motionEstimation |
This package contains a motion estimator.
|
Modifier and Type | Field and Description |
---|---|
static SimpleVector |
General.E_X |
static SimpleVector |
General.E_Y |
static SimpleVector |
General.E_Z |
Modifier and Type | Method and Description |
---|---|
static SimpleVector |
General.augmentToHomgeneous(SimpleVector v) |
SimpleVector |
Projection.computeCameraCenter()
Compute the camera center in world coordinates.
|
SimpleVector |
Projection.computeOffset(SimpleVector sizeUV)
This convenience method computes the offset from the image center to the principal point.
|
SimpleVector |
Projection.computePrincipalAxis()
Compute the principal axis direction in world coordinates.
|
SimpleVector |
Projection.computeRayDirection(SimpleVector p)
Computes the direction of the ray corresponding to a given pixel.
|
static SimpleVector |
General.crossProduct(SimpleVector v1,
SimpleVector v2) |
SimpleVector |
Axis.getAxisVector() |
SimpleVector |
Projection.getPrincipalPoint()
Returns the principal point in pixels.
|
SimpleVector |
Projection.getT()
Returns a const reference to the translation vector t.
|
static SimpleVector |
General.normalizeFromHomogeneous(SimpleVector v) |
Modifier and Type | Method and Description |
---|---|
static double |
General.angle(SimpleVector a,
SimpleVector b)
Computes the angle between two vectors;
|
static boolean |
General.areColinear(SimpleVector v1,
SimpleVector v2,
double delta) |
static SimpleVector |
General.augmentToHomgeneous(SimpleVector v) |
double |
Projection.computeDepth(SimpleVector v)
Computes a given point's Eucledian distance to the camera.
|
boolean |
Projection.computeGLMatrices(int imgMinU,
int imgMinV,
int imgSizeU,
int imgSizeV,
SimpleVector cubmin,
SimpleVector cubmax,
double[] glProjectionGlVec,
double[] glModelviewGlVec)
Compute the 4x4 OpenGL projection and modelview matrices from this Projection.
|
SimpleVector |
Projection.computeOffset(SimpleVector sizeUV)
This convenience method computes the offset from the image center to the principal point.
|
SimpleVector |
Projection.computeRayDirection(SimpleVector p)
Computes the direction of the ray corresponding to a given pixel.
|
double[] |
Projection.computeSourceToDetectorDistance(SimpleVector spacingUV)
This convenience method computes the source-to-detector distance in world corrdinate dimensions.
|
static SimpleMatrix |
General.createHomAffineMotionMatrix(SimpleMatrix A,
SimpleVector t) |
static SimpleMatrix |
General.createHomAffineMotionMatrix(SimpleVector t) |
static SimpleMatrix |
Rotations.createRotationMatrixAboutAxis(SimpleVector axis,
double angle) |
static SimpleVector |
General.crossProduct(SimpleVector v1,
SimpleVector v2) |
static double |
General.euclideanDistance(SimpleVector v1,
SimpleVector v2) |
static double |
Rotations.getRotationFromAtoB(SimpleVector a,
SimpleVector b)
Computes the angle (in radians) of the rotation from a to b (in the plane that is defined by (0,0,0), a, b).
|
static SimpleMatrix |
Rotations.getRotationMatrixFromAtoB(SimpleVector a,
SimpleVector b)
Computes the rotation matrix from a to b.
|
void |
Projection.initFromSKRT(double s,
SimpleMatrix K,
SimpleMatrix R,
SimpleVector t)
Set the projection's intrinsic and extrinsic parameters all at once.
|
boolean |
Projection.intersectRayWithCuboid(SimpleVector p,
SimpleVector cubmin,
SimpleVector cubmax,
double[] distanceNearFar,
SimpleVector C,
SimpleVector d)
Computes the two intersections of a ray with a cuboid, called entry and
exit point where the ray is defined by this projection and the given pixel.
|
static boolean |
General.intersectRayWithCuboid(SimpleVector origin,
SimpleVector dir,
SimpleVector cubmin,
SimpleVector cubmax,
double[] distanceNearAndFar)
Computes the two intersections of a ray with a cuboid, called entry and
exit point where the ray is specified by the given line origin and ray direction.
|
static SimpleVector |
General.normalizeFromHomogeneous(SimpleVector v) |
double |
Projection.project(SimpleVector volumePoint,
SimpleVector pixel)
Projects a given voxel to a pixel and determines its visibility.
|
void |
Axis.setAxis(SimpleVector newAxis) |
void |
Projection.setKFromDistancesSpacingsSizeOffset(double sourceToDetector,
SimpleVector spacingUV,
SimpleVector sizeUV,
SimpleVector offset,
double dir,
double skew)
Constructs the K matrix from distance and offset parameters.
|
void |
Projection.setPrincipalPointValue(SimpleVector p)
Sets the principal point in pixels.
|
double |
Projection.setRtFromCircularTrajectory(SimpleVector rotationCenter,
SimpleVector rotationAxis,
double sourceToAxisDistance,
SimpleVector centerToCameraAtZeroAngle,
Projection.CameraAxisDirection uDirection,
Projection.CameraAxisDirection vDirection,
double rotationAngle)
Constructs the extrinsic parameters (R and t) of this projection from the extrensic parameters
source-to-isocenter distance, rotation axis, rotation angle, and viewing axis.
|
void |
Projection.setTVector(SimpleVector t)
Set the translation part of the extrinsic parameters of the projection.
|
static void |
General.splitHomAffineMotionMatrix(SimpleMatrix At,
SimpleMatrix A,
SimpleVector t) |
Constructor and Description |
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Axis(SimpleVector axisvec) |
Constructor and Description |
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AffineMotionField(PointND transformationCenter,
SimpleMatrix rotMat,
SimpleVector translation)
Creates a new rotational and translation MotionField.
|
AffineMotionField(PointND transformationCenter,
SimpleVector axis,
double angle,
SimpleVector translation)
Creates a new rotational and translation MotionField.
|
CompressionMotionField(PointND min,
PointND max,
SimpleVector direction) |
MovingCenterRotationMotionField(PointND transformationCenter,
MotionField centerTransform,
SimpleVector rotationAxis,
double angle) |
PlanarMotionField(MotionField fullMotion,
SimpleVector planeNormal) |
RotationMotionField(PointND transformationCenter,
SimpleVector axis,
double angle)
Creates a new rotational MotionField.
|
Modifier and Type | Method and Description |
---|---|
SimpleVector |
PointND.getAbstractVector()
Returns the internal abstract vector to enable computations via the numerics library.
Changes to the vector will affect the point |
SimpleVector |
StraightLine.getDirection() |
SimpleVector |
Plane3D.getNormal() |
SimpleVector |
VectorPoint3D.getVector() |
Modifier and Type | Method and Description |
---|---|
void |
StraightLine.init(PointND point,
SimpleVector dir) |
void |
PointND.setCoordinates(SimpleVector coordinates) |
void |
StraightLine.setDirection(SimpleVector direction) |
void |
VectorPoint3D.setVector(SimpleVector vector) |
Constructor and Description |
---|
Plane3D(PointND point,
SimpleVector normal)
Creates a plane from a given point in the plane and a vector normal to the plane so that
![]() |
Plane3D(PointND p1,
SimpleVector dirU,
SimpleVector dirV)
Creates a plane from the given parametric representation
![]() |
Plane3D(SimpleVector normal,
double offset)
Creates a plane from the given normal form
![]() |
PointND(SimpleVector knotVector)
Creates a new point of the specified dimension
|
SortablePoint(SimpleVector add) |
StraightLine(PointND point,
SimpleVector dir)
Creates a StraightLine from point with direction dir
|
VectorPoint3D(double x,
double y,
double z,
SimpleVector vector)
Creates a new VectorPoint3D at coordinates (x, y, z).
|
VectorPoint3D(PointND point,
SimpleVector vector)
Creates a new VectorPoint3D at point.
|
Modifier and Type | Method and Description |
---|---|
SimpleVector |
SurfaceBSplineVolumePhantom.getBounds()
Returns an SimpleVector that specifies the bounding box of the BSpline Phantom with six entries:
Minimum X Coordinate Minimum Y Coordinate Minimum Z Coordinate Maximum X Coordinate Maximum Y Coordinate Maximum Z Coordinate |
SimpleVector |
SurfaceBSpline.getUKnots() |
SimpleVector |
SurfaceBSpline.getVKnots() |
Constructor and Description |
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BSpline(java.util.ArrayList<PointND> controlPoints,
SimpleVector knotVector)
Constructor for a BSpline using ArbitraryPoints and a weight vector as SimpleVector
|
SurfaceBSpline(java.util.ArrayList<PointND> controlPoints,
SimpleVector uKnots,
SimpleVector vKnots)
Constructor for a surface BSpline.
|
SurfaceBSpline(java.lang.String title,
java.util.ArrayList<PointND> list,
SimpleVector uKnots,
SimpleVector vKnots)
Constructor for a surface BSpline.
|
SurfaceUniformCubicBSpline(java.util.ArrayList<PointND> initialPoints,
SimpleVector uKnots,
SimpleVector vKnots) |
SurfaceUniformCubicBSpline(java.lang.String name,
java.util.ArrayList<PointND> controlPoints,
SimpleVector uKnots,
SimpleVector vKnots) |
UniformCubicBSpline(java.util.ArrayList<PointND> controlPoints,
SimpleVector knotVector) |
Modifier and Type | Method and Description |
---|---|
SimpleVector |
Trajectory.getRotationAxis() |
Modifier and Type | Method and Description |
---|---|
void |
Trajectory.setRotationAxis(SimpleVector rotationAxis) |
void |
CircularTrajectory.setTrajectory(int numProjectionMatrices,
double sourceToAxisDistance,
double averageAngularIncrement,
double detectorOffsetX,
double detectorOffsetY,
Projection.CameraAxisDirection uDirection,
Projection.CameraAxisDirection vDirection,
SimpleVector rotationAxis) |
Modifier and Type | Method and Description |
---|---|
SimpleVector |
Translation.getData() |
SimpleVector |
Translation.transform(SimpleVector dir)
Since directions are not altered by translation, this method returns a given input unaltered.
|
abstract SimpleVector |
Transform.transform(SimpleVector dir)
Transforms the given vector
|
SimpleVector |
ScaleRotate.transform(SimpleVector dir)
Applies scale-rotate transformation on a given direction
|
SimpleVector |
ComboTransform.transform(SimpleVector dir) |
Modifier and Type | Method and Description |
---|---|
SimpleVector |
Translation.transform(SimpleVector dir)
Since directions are not altered by translation, this method returns a given input unaltered.
|
abstract SimpleVector |
Transform.transform(SimpleVector dir)
Transforms the given vector
|
SimpleVector |
ScaleRotate.transform(SimpleVector dir)
Applies scale-rotate transformation on a given direction
|
SimpleVector |
ComboTransform.transform(SimpleVector dir) |
Constructor and Description |
---|
AffineTransform(SimpleMatrix scaleRotate,
SimpleVector translatorVec)
Initialize a new Affine transform;
|
Quaternion(double scaler,
SimpleVector vector) |
Translation(SimpleVector t)
Initialize a translation transform with a translation vector
|
Modifier and Type | Method and Description |
---|---|
SimpleVector |
SimpleVector.absoluted() |
static SimpleVector |
SimpleOperators.add(SimpleVector... addends)
Computes the sum of supplied vectors
|
SimpleVector |
SimpleVector.clone() |
static SimpleVector |
SimpleOperators.concatenateVertically(SimpleVector... parts)
Creates a new vector which is composed of all input vectors, stacked over each other.
|
SimpleVector |
SimpleVector.dividedBy(double divisor)
Returns a scaled instance of the vector.
|
static SimpleVector |
SimpleOperators.divideElementWise(SimpleVector v1,
SimpleVector v2)
Computes the element wise division of v1 by v2.
|
SimpleVector |
SimpleMatrix.getCol(int col)
Retrieve column from index col of matrix
|
SimpleVector |
SimpleMatrix.getDiag() |
SimpleVector |
SimpleMatrix.getRow(int row)
Retrieve row from index row of matrix
|
SimpleVector |
SimpleMatrix.getSubCol(int firstRow,
int col,
int sizeRows)
Returns a vector containing a sub column in current matrix.
|
SimpleVector |
SimpleMatrix.getSubRow(int row,
int firstCol,
int sizeCols)
Returns a vector containing a sub row in current matrix.
|
SimpleVector |
SimpleVector.getSubVec(int firstInd,
int size) |
static SimpleVector |
SimpleOperators.max(SimpleVector... vectors)
Computes and returns the element-wise maximum of all given vectors.
|
static SimpleVector |
SimpleOperators.min(SimpleVector... vectors)
Computes and returns the element-wise minimum of all given vectors.
|
SimpleVector |
SimpleVector.multipliedBy(double factor)
Returns a scaled instance of the vector.
|
static SimpleVector |
SimpleOperators.multiply(SimpleMatrix M,
SimpleVector v)
Performs a standard matrix-vector product.
|
static SimpleVector |
SimpleOperators.multiply(SimpleVector v,
SimpleMatrix M)
Performs a vector-matrix product, assuming a row vector.
|
static SimpleVector |
SimpleOperators.multiplyElementWise(SimpleVector... factors)
Multiplies the supplied vectors element wise
|
SimpleVector |
SimpleVector.negated() |
SimpleVector |
SimpleVector.normalizedL2() |
SimpleVector |
DecompositionRQ.solve(SimpleVector b)
Computes solution Vector
![]() ![]() |
SimpleVector |
DecompositionQR.solve(SimpleVector b)
Computes solution Vector
![]() ![]() |
static SimpleVector |
Solvers.solveLinearLeastSquares(SimpleMatrix A,
SimpleVector b)
Solves the linear least squares problem
![]() |
static SimpleVector |
Solvers.solveLinearSysytemOfEquations(SimpleMatrix A,
SimpleVector b)
Solves the linear system of equations
![]() |
static SimpleVector |
Solvers.solveLowerTriangular(SimpleMatrix L,
SimpleVector b)
Solves the linear system of equations L*x = b with a square,
lower-triangular matrix L using forward substitution.
|
static SimpleVector |
Solvers.solveUpperTriangular(SimpleMatrix U,
SimpleVector b)
Solves the linear system of equations U*x = b with a square,
upper-triangular matrix U using backward substitution.
|
static SimpleVector |
SimpleOperators.subtract(SimpleVector v1,
SimpleVector v2)
subtracts v2 from v1
|
Modifier and Type | Method and Description |
---|---|
void |
SimpleVector.add(SimpleVector... addends)
Method to add other vectors to this vector in place.
|
static SimpleVector |
SimpleOperators.add(SimpleVector... addends)
Computes the sum of supplied vectors
|
static SimpleMatrix |
SimpleOperators.concatenateHorizontally(SimpleVector... columns)
Creates a new matrix which is composed of all input column vectors, stacked next to each other.
|
static SimpleVector |
SimpleOperators.concatenateVertically(SimpleVector... parts)
Creates a new vector which is composed of all input vectors, stacked over each other.
|
static SimpleVector |
SimpleOperators.divideElementWise(SimpleVector v1,
SimpleVector v2)
Computes the element wise division of v1 by v2.
|
void |
SimpleVector.divideElementWiseBy(SimpleVector... divisors) |
static boolean |
SimpleOperators.equalElementWise(SimpleVector v1,
SimpleVector v2,
double delta) |
void |
SimpleVector.init(SimpleVector otherVec)
Initialize vector with otherVec
|
static SimpleVector |
SimpleOperators.max(SimpleVector... vectors)
Computes and returns the element-wise maximum of all given vectors.
|
static SimpleVector |
SimpleOperators.min(SimpleVector... vectors)
Computes and returns the element-wise minimum of all given vectors.
|
static SimpleVector |
SimpleOperators.multiply(SimpleMatrix M,
SimpleVector v)
Performs a standard matrix-vector product.
|
static SimpleVector |
SimpleOperators.multiply(SimpleVector v,
SimpleMatrix M)
Performs a vector-matrix product, assuming a row vector.
|
static SimpleVector |
SimpleOperators.multiplyElementWise(SimpleVector... factors)
Multiplies the supplied vectors element wise
|
void |
SimpleVector.multiplyElementWiseBy(SimpleVector... factors) |
static double |
SimpleOperators.multiplyInnerProd(SimpleVector v1,
SimpleVector v2)
Computes the inner product multiplication (dot product) of v1 and v2.
|
static SimpleMatrix |
SimpleOperators.multiplyOuterProd(SimpleVector v1,
SimpleVector v2)
Computes the outer product multiplication of v1 and v2; i.e v1 x v2
|
void |
SimpleMatrix.setColValue(int col,
SimpleVector newCol)
Replace col with newCol
|
void |
SimpleMatrix.setDiagValue(SimpleVector diag)
Replace diagonal entries of matrix with diag
|
void |
SimpleMatrix.setRowValue(int row,
SimpleVector newRow)
Replace row with newRow
|
void |
SimpleMatrix.setSubColValue(int firstRow,
int col,
SimpleVector subCol)
Replace the entries of sub column starting at [col,firstRow] with subCol
|
void |
SimpleMatrix.setSubRowValue(int row,
int firstCol,
SimpleVector subRow)
Replace the entries of sub row starting at [row,firstCol] with subRow
|
void |
SimpleVector.setSubVecValue(int firstInd,
SimpleVector subVector) |
SimpleVector |
DecompositionRQ.solve(SimpleVector b)
Computes solution Vector
![]() ![]() |
SimpleVector |
DecompositionQR.solve(SimpleVector b)
Computes solution Vector
![]() ![]() |
static SimpleVector |
Solvers.solveLinearLeastSquares(SimpleMatrix A,
SimpleVector b)
Solves the linear least squares problem
![]() |
static SimpleVector |
Solvers.solveLinearSysytemOfEquations(SimpleMatrix A,
SimpleVector b)
Solves the linear system of equations
![]() |
static SimpleVector |
Solvers.solveLowerTriangular(SimpleMatrix L,
SimpleVector b)
Solves the linear system of equations L*x = b with a square,
lower-triangular matrix L using forward substitution.
|
static SimpleVector |
Solvers.solveUpperTriangular(SimpleMatrix U,
SimpleVector b)
Solves the linear system of equations U*x = b with a square,
upper-triangular matrix U using backward substitution.
|
void |
SimpleVector.subtract(SimpleVector... subtrahends) |
static SimpleVector |
SimpleOperators.subtract(SimpleVector v1,
SimpleVector v2)
subtracts v2 from v1
|
Constructor and Description |
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SimpleVector(SimpleVector otherVec)
Creates a new vector from otherVec.
|
Modifier and Type | Method and Description |
---|---|
static SimpleVector |
Evaluator.getVectorValue(java.lang.String expression)
Evaluates the string literals in a string vector;
|
static SimpleVector |
Evaluator.getVectorValue(java.lang.String expression,
java.util.Map<java.lang.String,java.lang.Double> variablesMap)
Evaluates the string literals in a string vector and replaces variables with values in map;
|
Constructor and Description |
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OpenCLUniformSurfaceBSpline(java.lang.String title,
java.util.ArrayList<PointND> controlPoints,
SimpleVector uKnots,
SimpleVector vKnots,
com.jogamp.opencl.CLDevice device) |
OpenCLUniformTextureSurfaceBSpline(java.lang.String title,
java.util.ArrayList<PointND> controlPoints,
SimpleVector uKnots,
SimpleVector vKnots,
com.jogamp.opencl.CLDevice device) |
Modifier and Type | Method and Description |
---|---|
SimpleVector |
BreathingScene.getDiaphragmMotionVector_old(double initialTime,
double time) |
SimpleVector |
BreathingScene.getDiaphragmMotionVector(double initialTime,
double time)
Returns the Motion Vector of the top of the diaphragm from initialTime to time
|
Constructor and Description |
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PhysicalPoint(SimpleVector add) |
Modifier and Type | Method and Description |
---|---|
static void |
ModelBasedIterativeReconstruction.printSimpleVector(SimpleVector B) |
Modifier and Type | Method and Description |
---|---|
static void |
ModelBasedIterativeReconstruction.printSimpleVector(SimpleVector B) |
Modifier and Type | Method and Description |
---|---|
SimpleVector |
RayDetector.getPrincipalPointInMM() |
SimpleVector |
RayDetector.getPrincipalPointInPixels() |
Modifier and Type | Method and Description |
---|---|
static SimpleVector |
TestingTools.randVector(int len)
Randomly generates a vector of the given length.
|
Modifier and Type | Method and Description |
---|---|
static void |
TestingTools.assertEqualElementWise(SimpleVector v1,
SimpleVector v2,
double delta)
own assert for vectors
|
Modifier and Type | Method and Description |
---|---|
SimpleVector |
ThinPlateSplineInterpolation.interpolate(PointND pt)
Interpolation function
|