CIBC:Documentation:SCIRun:Reference:BioPSE
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Contents |
BioPSE Reference
Package Description
Module Reference
DataIO
- ImportDenseMatrixFromRaw
- The RawtoDenseMatrix mdoule reads CVRTI potentials, with output as a DenseMatrix.
Forward
- ApplyFEMCurrentSource
- The ApplyFEMCurrentSource module builds the right-hand side (ColumnMatrix) to reflect monopolar and dipolar current sources for finite-element based bioelectric field problems.
- ApplyFEMElectrodeSource
- Due to course current dipoles, the ApplyFEMElectrodeSource module changes and recreates the right-hand side (RHS) for the Finite Elements discretization approach.
- ApplyFEMVoltageSource
- The module changes/creates the right-hand side (RHS) and forward matrices for voltgage (Dirichlet) boundary conditions.
- BuildBEMSrcToInfTransferMatrix
- FILL THIS IN
- BuildBEMatrix
- The module solves a discretized model of Laplace's equation in a 3D volume conductor model using "surface method", given a particular type of boundary condition.
- BuildEITMatrix
- The module solves a discretized model of Laplace's equation in a 3D volume conductor model using "surface method", given a particular type of boundary condition.
- BuildFEMatrix
- The module sets up a mesh with conductivity tensors for bioelectric field problems.
- CalculateCurrentDensity
- Compute the current density vector field
- ConvertFieldDataFromIndicesToTensors
- Change a Field of ints, into a Field of Tensors.
- ConvertFieldDataFromTensorsToIndices
- Change a Field of ints, into a Field of Tensors.
- CreateAnisoSphereParameters
- CreateAnisoSphereParameters implements a four-layer anisotropic spherical volume conductor.
- CreateDiscreteAnisoSpheres
- Scale the geometry of a sphere to a requested size and assign a conductivity tensor to each cell.
- GetActivationTimes
- Accepts a matrix of potentials on a surface and calculates the activation times by selecting the lowest (most negative) derivative.
- InsertElectrodes
- Insert electrodes into a finite element mesh.
- InsertVoltageSource
- Insert electrodes into a finite element mesh.
- IntegrateCurrent
- Compute the current across a surface.
- SetWireElectrodePotential
- Configure an electrode.
- SetWireElectrodeProperties
- Configure an electrode.
- SimulateDipoleInAnisoSpheresAnalytically
- Due to a specified dipole, the potential on the outer sphere of a four layer spherical volume conductor is computed.
- SimulateDipoleInSphereAnalytically
- Due to the specified dipoles, the SimulateDipoleInSphereAnalytically module fills the sphere field with potentials values.
- SimulateForwardMagneticField
- Calculation of magnetic field at given detector points due to specificed dipoles.
Inverse
- BuildSurfaceLaplacianMatrix
- Transform attributes
- OptimizeConductivities
- Summary not available yet.
- OptimizeDipole
- Summary not available yet.
- SolveInverseProblemWithTSVD
- Solve inverse problem using Truncated SVD.
- SolveInverseProblemWithTikhonov
- This module applies SolveInverseProblemWithTikhonov regularization to an existing forward model, with flexible control of regularization type and parameters. Currently, the module solves the inverse problem in a single time-instant. This module requires a forward model matrix, geometries for the associated surfaces, and some remote boundary conditions, i.e., torso or head surface potentials.
- SolveInverseProblemWithTikhonovSVD
- Solve inverse problem using Tikhonov regularization by using SVD.
LeadField
- BuildElemLeadField
- Summary not available yet.
- BuildLeadFieldSourcesFromElectricCurrentMatrix
- Assign data to a field.
- CalculateMisfitField
- Summary not available yet.
Modeling
- AbsorbSegFieldIslands
- Create and process a segmented volume: erosion/dilation/open/close/absorb.
- ConvertSegFieldToLatVol
- Create a LatVolField from a SegLatVolField -- choose a quantity to store as the data.
- ConvertSegFieldToSepSurfs
- Create Separating surfaces from a SegLatVolField.
- ConvertSepSurfToQuadSurf
- Change the Separating Surface into a QuadSurf.
- GetSingleSurfaceFromSepSurfs
- Extract a single QuadSurf (one connected component) from a Separating Surface.
- SetConductivities
- Change the conductivity tensors in a field.
NeuroFEM
- InterfaceWithNeuroFEMForward
- Invoke the NeuroFEM ipm program to solve the forward problem for the inputs.
- InterfaceWithNeuroFEMInverse
- Invoke the NeuroFEM ipm program to solve the input problem for the inputs.
Visualization
- ShowAndEditDipoles
- Summary not available yet.
- ViewLeadSignals
- The ViewLeadSignals module graphs a Matrix that has rows of potentials.
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