Package | Description |
---|---|
apps | |
data | |
data.compartments | |
fitters | |
imaging | |
inverters | |
misc | |
models | |
models.compartments | |
numerics | |
sphfunc | |
tractography |
Modifier and Type | Method and Description |
---|---|
static RealMatrix |
InversionStats.dyadic(double[] dir)
Computes the dyadic of a direction.
|
static RealMatrix |
Reorient.getFS_Reorientation(RealMatrix F)
Computes the finite strain strategy reorientation matrix.
|
static RealMatrix |
Reorient.getJacobian(ScalarImage transX,
ScalarImage transY,
ScalarImage transZ,
double posX,
double posY,
double posZ)
Computes the Jacobian of the image transformation at point
(posX, posY, posZ).
|
static RealMatrix |
Reorient.readFSL_Affine(java.lang.String filename)
Reads an affine transformation from a file in the format output
by FSL's flirt program into a matrix object.
|
Modifier and Type | Method and Description |
---|---|
static RealMatrix |
Reorient.getFS_Reorientation(RealMatrix F)
Computes the finite strain strategy reorientation matrix.
|
Modifier and Type | Method and Description |
---|---|
static RealMatrix |
StandardTestFunctions.getRotationMatrix()
returns the rotation matrix transform
|
Modifier and Type | Method and Description |
---|---|
static void |
StandardTestFunctions.setTransformation(RealMatrix transformation)
Sets the transformation.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
Zeppelin.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
Tensor.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
CylinderGPD.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
CompartmentModel.getJacobian(double[] modParams,
DW_Scheme scheme)
Get Jacobian for each compartment separately.
|
RealMatrix |
Zeppelin.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Tensor.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Stick.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
SphereGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
ListDistributionCompartment.getSignals(double[] params,
DW_Scheme scheme) |
RealMatrix |
GammaDistribRadiiCylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Dot.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CylinderGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CompartmentModel.getSignals(double[] modParams,
DW_Scheme scheme)
sum up the signals from each compartment
|
RealMatrix |
Ball.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrosticks.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrocylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
Codec.getJacobian(double[] optParams)
Computes the jacobian of the encoding, specifically d(model
parameters)/d(optimization parameters).
|
Modifier and Type | Field and Description |
---|---|
RealMatrix |
MetaImageHeader.transformation
TransformMatrix, a 3x3 rotation matrix.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
DW_Scheme.getB_Matrix()
The B-matrix B is defined as follows.
|
RealMatrix |
ImageHeader.getPhysicalToVoxelTransform()
Gets the transformation matrix R that is the inverse of the voxel to physical space transformation.
|
RealMatrix |
Nifti1Dataset.getVoxelToPhysicalTransform()
Gets the transformation matrix R that provides a transformation from a = (i, j, k, 1) in
voxel space to b = (x, y, z, 1) in physical space.
|
RealMatrix |
MetaImageHeader.getVoxelToPhysicalTransform()
Will use TransformMatrix + Offset, because it's not clear what coordinates CenterOfRotation uses
|
abstract RealMatrix |
ImageHeader.getVoxelToPhysicalTransform()
Gets the transformation matrix R that provides a transformation from a = (i, j, k, 1) in
voxel space to b = (x, y, z, 1) in physical space
|
RealMatrix |
AnalyzeHeader.getVoxelToPhysicalTransform()
Gets the transformation matrix R that provides a transformation from a = (i, j, k, 1) in
voxel space to b = (x, y, z, 1) in physical space.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix[] |
WeightedLinearDT_Inversion.computeWeightedFit(double[] data)
Solves W*Y = W*X*B for B.
|
RealMatrix[] |
WeightedLinearDT_Inversion.computeWeightedFit(double[] data,
double[] olsSolution)
Solves W*Y = W*X*B for B.
|
RealMatrix |
LinearInversion.getMatrix()
Returns the linear inversion matrix.
|
RealMatrix |
LinearDT_Inversion.getMatrix()
Returns the linear inversion matrix.
|
Modifier and Type | Method and Description |
---|---|
double |
WeightedLinearDT_Inversion.computeNoiseVariance(RealMatrix[] weightedSolution)
Computes the noise variance \sigma^2 = (Y - XB)^T W^2 (Y - XB) / (DOF), where
DOF is the number of degrees of freedom in the model.
|
double[] |
WeightedLinearDT_Inversion.computeResidualVector(RealMatrix[] weightedSolution) |
Modifier and Type | Method and Description |
---|---|
RealMatrix |
DT.toMatrix() |
Modifier and Type | Method and Description |
---|---|
DT |
DT.iTransform(RealMatrix trans)
Applies a similarity transform to the diffusion tensor using the linear
transformation matrix supplied.
|
DT |
DT.ppd(RealMatrix jac)
Reorients the tensor using the PPD algorithm.
|
static double[][] |
SphericalPoints.rotatePointSet(double[][] pointSet,
RealMatrix rot)
Rotates a list of points.
|
DT |
DT.transform(RealMatrix trans)
Applies a similarity transform to the diffusion tensor using the linear
transformation matrix supplied.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
ParametricModel.getJacobian_old(double[] modParams,
DW_Scheme scheme)
Computes the Jacobian of the model numerically.
|
RealMatrix |
ParametricModel.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
ParametricModel.getJacobian(double[] modParams,
DW_Scheme scheme,
int index)
Computes the Jacobian of the model numerically.
|
abstract RealMatrix |
ParametricModel.getSignals(double[] modParams,
DW_Scheme scheme)
Returns a list of signals for the specified scheme from the
model using the specified model parameters.
|
RealMatrix |
BallAndStickModel.getSignals(double[] modParams,
DW_Scheme scheme) |
Modifier and Type | Method and Description |
---|---|
RealMatrix |
Zeppelin.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
Tensor.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
Stick.getJacobian(double[] modParams,
DW_Scheme scheme) |
RealMatrix |
CompartmentModel.getJacobian(double[] modParams,
DW_Scheme scheme)
Get Jacobian for each compartment separately.
|
RealMatrix |
Ball.getJacobian(double[] modParams,
DW_Scheme scheme)
Compute the jacobian of the signal.
|
RealMatrix |
Zeppelin.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Tensor.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Stick.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
SphereGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
ListDistributionCompartment.getSignals(double[] params,
DW_Scheme scheme) |
RealMatrix |
GDRCylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Dot.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CylinderGPD.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
CompartmentModel.getSignals(double[] modParams,
DW_Scheme scheme)
sum up the signals from each compartment
|
RealMatrix |
Ball.getSignals(double[] params,
DW_Scheme scheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrosticks.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line
in the scheme given.
|
RealMatrix |
Astrocylinders.getSignals(double[] params,
DW_Scheme rawScheme)
generates signals from this compartment for each line in the scheme
given.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
RealMatrix.add(RealMatrix m)
Adds matrices.
|
RealMatrix |
RealMatrix.adjoint()
Computes the adjoint matrix.
|
static RealMatrix |
ACG_Fitter.findA(Vector3D[] sampleVecs)
Finds the covariance matrix A of the ACG
distribution.
|
static RealMatrix |
Rotations.getRotMat(double[] r,
double theta)
Computes the rotation matrix that rotates by angle theta about axis r =
(rx, ry, rz).
|
static RealMatrix |
Rotations.getRotMat(double alpha,
double beta,
double theta)
Computes the rotation matrix that rotates by angle theta about axis
(alpha, beta).
|
static RealMatrix |
Rotations.getRotMat(Vector3D r,
double theta)
Computes the rotation matrix that rotates by angle theta about axis
r = (rx, ry, rz).
|
static RealMatrix |
Rotations.getRotMat(Vector3D vec,
Vector3D targetAxis)
Get rotation matrix of one vector onto another vector.
|
static RealMatrix |
RealMatrix.identity(int rows)
Returns a square identity matrix.
|
RealMatrix |
RealMatrix.inverse()
Inverts a matrix inefficiently by computing the determinant and adjoint.
|
RealMatrix[] |
RealMatrix.jacobi()
Does the jacobi transformation.
|
RealMatrix |
RealMatrix.luinvert()
Does LU inversion.
|
RealMatrix |
RealMatrix.negate()
Negates the matrix.
|
RealMatrix |
RealMatrix.product(RealMatrix m)
Multiplies matrices.
|
RealMatrix |
RealMatrix.pseudoInv() |
RealMatrix |
RealMatrix.pseudoInv(double svThresh) |
static RealMatrix |
Rotations.randomRotMat()
Generates a random rotation matrix with random seed taken from the clock
time.
|
static RealMatrix |
Rotations.randomRotMat(int seed)
Generates a seeded random rotation matrix.
|
static RealMatrix |
Rotations.randomRotMat(java.util.Random r)
Generates a random rotation matrix drawing using the random number
generator provided.
|
RealMatrix |
RealMatrix.scalarMult(double scalar)
Multiplies the matrix by a scalar and returns the result leaving
the original unchanged.
|
RealMatrix |
RealMatrix.sub(RealMatrix m)
Subtracts matrices.
|
RealMatrix[] |
RealMatrix.svd()
Computes the singular value decomposition U, S and V of the matrix A, so
that A = U S V^T.
|
static RealMatrix |
SphericalDistributionFitter.tBar(Vector3D[] sampleVecs) |
RealMatrix |
Vector3D.toRealMatrix() |
RealMatrix |
RealMatrix.transpose()
Computes the transpose.
|
Modifier and Type | Method and Description |
---|---|
RealMatrix |
RealMatrix.add(RealMatrix m)
Adds matrices.
|
RealMatrix |
RealMatrix.product(RealMatrix m)
Multiplies matrices.
|
static Vector3D |
Rotations.rotateVector(Vector3D original,
RealMatrix rot)
Apply a rotation matric to a vector.
|
static EigenSystem3D |
EigenSystem3D.sort(RealMatrix A)
Sorts eigen system by eigenvalue, greatest first.
|
RealMatrix |
RealMatrix.sub(RealMatrix m)
Subtracts matrices.
|
static EigenSystem3D |
SphericalDistributionFitter.tBarEigenSystem(RealMatrix tBar) |
Point3D |
Point3D.transform(RealMatrix aff)
Transform a point by a 4D Affine matrix.
|
static double[] |
Rotations.transformPoint(RealMatrix mat,
double[] point)
Applies a 3D transformation matrix to a point.
|
Constructor and Description |
---|
ACG_Distribution(RealMatrix A,
java.util.Random r) |
Modifier and Type | Method and Description |
---|---|
RealMatrix |
SphericalFunction.getHessian(double[] x)
Computes the Hessian of the function at the specified
point.
|
RealMatrix |
SphericalFunction.getHessian(PD pd)
Computes the Hessian of the function at the specified
point.
|
Modifier and Type | Method and Description |
---|---|
void |
StreamlineROI_Filter.setTransIntoSeedSpace(RealMatrix matrix)
Sets the transformation that warps the streamlines from diffusion space into seed space.
|
void |
Tract.transform(RealMatrix trans) |