CIBC:Documentation:SCIRun:Reference:SCIRun

From SCIRun Documentation Wiki
Jump to: navigation, search

SCIRun Reference

Package Description

The SCIRun Core contains general modules that are not specific to one application field. This documentation page contains documentation for each module in the SCIRun Core.


Module Reference

Bundle

CreateParameterBundle
Sets several parameters and collects them as a single bundle.
GetBundlesFromBundle
This module retrieves a bundle object from a bundle.
GetColorMapsFromBundle
This module retrieves a colormap object from a bundle.
GetFieldsFromBundle
This module retrieves a field object from a bundle.
GetMatricesFromBundle
This module retrieves a matrix object from a bundle.
GetNrrdsFromBundle
This module retrieves a nrrd object from a bundle.
GetStringsFromBundle
This module retrieves a string object from a bundle.
InsertBundlesIntoBundle
This module inserts a bundle object into a bundle.
InsertColorMapsIntoBundle
This module inserts a colormap object into a bundle.
InsertEnvironmentIntoBundle
Collects the current environment variables into a bundle.
InsertFieldsIntoBundle
This module inserts a field object into a bundle.
InsertMatricesIntoBundle
This module inserts a matrix object into a bundle.
InsertNrrdsIntoBundle
This module inserts a nrrd object into a bundle.
InsertStringsIntoBundle
This module inserts a string object into a bundle.
JoinBundles
This module merges the contents of multiple bundles into one bundle.
ReportBundleInfo
This module lists all the objects stored in a bundle.

ChangeFieldData

ApplyFilterToFieldData
Applies a dilate or erode filter to a regular mesh.
ApplyMappingMatrix
Apply a mapping matrix to project the data from one field onto the mesh of another field.
ApplyTriSurfPhaseFilter
Deprecated in SCIRun 4.7.
CalculateDistanceToField
Calculate the distance field to a mesh.
CalculateDistanceToFieldBoundary
Calculate the distance field to a boundary of a given mesh.
CalculateFieldData
Calculate new data for the field given a function that uses field data, node location and element properties as input.
CalculateFieldData2
Calculate new data for the field given a function that uses field data, node location and element properties as input, with a second input port for a second field.
CalculateFieldData3
Calculate new data for the field given a function that uses field data, node location and element properties as input, with a second and third input port for two additional fields.
CalculateFieldData4
Calculate new data for the field given a function that uses field data, node location and element properties as input, with input ports for three additional fields.
CalculateFieldData5
Calculate new data for the field given a function that uses field data, node location and element properties as input, with input ports for four additional fields.
CalculateFieldDataMetric
Reads in a field file(s), allows parser edits to the data, and exports 1 of 7 metrics selected by the user as a matrix file.
CalculateGradients
Compute the derivative of a scalar field and output it as a vector field.
CalculateInsideWhichField
Calculate inside which field of a number of given fields a certain element is located.
CalculateIsInsideField
Calculate whether an element of one field is inside the domain of another field.
CalculateLatVolGradientsAtNodes
Compute the derivative of a scalar lattice and output it as a vector lattice.
CalculateNodeNormals
Make a new vector field that points to the input point.
CalculateProfile
Samples image data surrounding mesh generated from segmentation.
CalculateSignedDistanceToField
Calculate the distance to a surface mesh and use the normal of the surface to determine on which side of the surface the element is located.
CalculateVectorMagnitudes
Computes the gradient of a field.
ConvertFieldBasis
ConvertFieldBasis can modify the location of data in the input field.
ConvertFieldDataType
ConvertFieldDataType is used to change the type of data associated with the field elements.
ConvertIndicesToFieldData
Convert a field with indices as data values into a field with values assigned to each index using a lookup table.
ConvertLatVolDataFromElemToNode
Make a new field with data at nodes instead of elements.
ConvertLatVolDataFromNodeToElem
Make a new field with data at elements instead of nodes.
CreateFieldData
This module assigns a value to each element or node of the mesh based on a given function, that is based on the location of nodes and elements and properties of the elements.
GetFieldData
This module will get the data associated with the nodes or the elements of a field and put them in a matrix.
MapFieldDataFromElemToNode
This module contains several filters for converting data that is stored in the elements to data that is stored in the nodes.
MapFieldDataFromNodeToElem
This module contains several filters for converting data that is stored in the nodes to data that is stored in the elements.
MapFieldDataFromSourceToDestination
The MapFieldDataFromSourceToDestination module takes two Fields as input, the first of which, Source, contains geometry and data values; the second, Destination, contains geometry only. MapFieldDataFromSourceToDestination takes a field and finds data values for the destination geometry and outputs the resulting Field.
MapFieldDataOntoElems
Maps data from one mesh to another mesh. The output mesh will have the data located on the elements.
MapFieldDataOntoNodes
Maps data from one mesh or point cloud to another mesh or point cloud. The output mesh will have the data located at the nodes.
MapFieldDataOntoNodesRadialbasis
Maps data centered on the nodes to another set of nodes using a radial basis.
MaskLatVolWithTriSurf
Convert a LatVolField into a MaskedLatVolField and apply the given function to mask it out.
ProjectLocalMaxOnSurface
Deprecated in SCIRun 4.6.
QueryFieldData
Query field data using a function.
RegisterWithCorrespondences
This module allows you to morph using a thin plate spline algorithm one point set or mesh to another point set or mesh.
SelectAndSetFieldData
This module selects a function based on the input values of the field and then applies this function to assign a new value to the field.
SelectAndSetFieldData3
This module selects a function based on the input values of the field and then applies this function to assign a new value to the field. This module contains two additional field ports to be used for selecting and setting data values.
SetFieldData
This module allows you to set the scalar, vector, or tensor entries of an array or single column matrix to the nodes or elements of a mesh.
SetFieldDataToConstantValue
Sets field data to a given scalar value on a new output field based on the input field geometry.
SmoothVecFieldMedian
This function smoothes vectors assigned to the elements of a mesh using a median filter.
SwapFieldDataWithMatrixEntries
Add and remove data from a field.

ChangeMesh

AlignMeshBoundingBoxes
Scales, translates, and deforms an input field to a defined alignment field.
CalculateMeshNodes
Calculate new positions for the node locations of the mesh.
CleanupTetMesh
This module tidies up node orientation and removes degenerate tetrahedral elements on a given tetrahedral mesh.
ConvertHexVolToTetVol
Convert a HexVolField into a TetVolField.
ConvertMeshCoordinateSystem
Convert mesh coordinate system.
ConvertMeshToIrregularMesh
This module loads a regular mesh and converts it to an irregular mesh.
ConvertMeshToPointCloud
Convert a structured field into an unstructured field for editing.
ConvertMeshToUnstructuredMesh
Convert a structured field into an unstructured field for editing.
ConvertQuadSurfToTriSurf
Convert a QuadSurfField into a TriSurfField.
EditMeshBoundingBox
EditMeshBoundingBox is used to transform the field geometry.
FlipSurfaceNormals
Changes the normal of the face of an element on a surface mesh by reordering how the nodes are ordered in the face definition.
GeneratePolarProjection
GeneratePolarProjectionOnImage
GetFieldNodes
MapFieldDataToNodeCoordinate
Replace a mesh coordinate with the scalar field data values.
Deprecated in SCIRun 4.6.
PadRegularMesh
ProjectPointsOntoMesh
RemoveUnusedNodes
ResampleRegularMesh
Resample a regular mesh, such as a LatVol.
ScaleFieldMeshAndData
SetFieldNodes
SmoothMesh
Deprecated in SCIRun 4.6.
SwapNodeLocationsWithMatrixEntries
Extract and change the positions of the nodes in a mesh.
TransformMeshWithFunction
Perform a specified functional transform on all of the points in a field.
''Deprecated in SCIRun 4.6.
TransformMeshWithTransform
Non-interactive geometric transform of a field.
TransformPlanarMesh
Non-interactive geometric transform of a field.

Converters

ConvertBundleToField
This module merges input bundle contents to an output field.
ConvertMatrixToField
This module converts a matrix into a field.
ConvertMatrixToString
This module converts a matrix into a string.

DataArrayMath

AppendDataArrays
This module appends various data arrays together.
CalculateDataArray
This module computes a new scalar, vector or tensor array based upon a combination of scalars, vectors, and tensors.
CreateDataArray
This module computes a new scalar, vector or tensor array based upon a combination of scalars, vectors, and tensors.
CreateDataArrayFromIndices
This module takes the elements of the input array and reorders them according to order specified in the index vector.
CreateTensorArray
This module creates a N by 9 matrix describing tensors. The tensors are constructed out of two orthogonal N by 3 arrays describing the eigenvectors for the system and 3 column vectors describing the eigenvalues.
CreateVectorArray
This module creates a vector out of arrays of scalars.
DecomposeTensorArrayIntoEigenVectors
This module decomposes the a N by 9 Matrix, representing an array of tensors into three N by 3 matrices which contain the eigenvectors of the system, numbered from the most significant to the least significant and three column vectors representing the three eigenvalues of the tensor.
ReplicateDataArray
This module takes a ScalarArray, VectorArray or TensorArray and replicates it n-fold.
ReportDataArrayInfo
ReportDataArrayMeasure
This module calculates a measure of the array.
SplitVectorArrayInXYZ
Decomposed the vector in the three cartesian coordinates.

DataIO

ReadBundle
This module reads a bundle from file (a SCIRun .bdl file).
ReadColorMap
This module reads a colormap from file (a SCIRun .cmap file).
ReadColorMap2
This module reads a colormap2D from file (a SCIRun .cmap2 file).
ReadField
This module reads a field from file (a SCIRun .fld file and various other formats using a plugin system).
ReadFieldArray
ReadMatrix
This module reads a matrix from file (a SCIRun .mat file and various other file formats using a plugin system).
ReadPath
This module reads a camera path from file (a SCIRun .path file).
ReadString
This module reads a string from file (an ASCII text file).
StreamACQFileFromDisk
StreamMatrixFromDisk
WriteBundle
This module writes a bundle to file (a SCIRun .bdl file).
WriteColorMap
This module writes a colormap to file (a SCIRun .cmap file).
WriteColorMap2D
This module writes a colormap2D to file (a SCIRun .cmap2 file).
WriteField
This module writes a field to file (a SCIRun .fld file and various other file formats using a plugin system).
WriteFieldArray
WriteMatrix
This module writes a matrix to file (a SCIRun .mat file and various other file formats using a plugin system).
WritePath
This module writes a camera path to file (a SCIRun .path file).
WriteString
This module writes a string to file (an ASCII text file).

FieldArray

ApplyTriSurfArrayPhaseFilter
ConvertCurveArrayToSurface
CreateFieldArrayFromData
Creates an array from a field and associated data. Additional fields can be added to this array so that the array contains multiple fields.
ExtractFieldArrayRange
Extracts a subset of an Fields grouped as an array based on the GUI inputs.
GeneratePolarProjectionForFieldArray
GeneratePolarProjectionOnImageForFieldArray
GetFieldFromFieldArray
Extracts a Field from and array of Fields stored as a FieldArray
InsertFieldIntoFieldArray
Insert a field into and array of fields. The GUI input allows you to choose the location in the array to insert the field.
MergeFieldArray
Insert a field into and array of fields. The GUI input allows you to choose the location in the array to insert the field.
ReportFieldArrayInfo
ReportFieldArrayInfo is used to view the attributes of the each field in the field array.

FiniteElements

BuildFEGridMapping
BuildFEGridMappingByDomain
BuildFEMatrix
BuildFESurfRHS
BuildFEVolRHS
BuildSurfaceResistorMatrix
DefinePeriodicBoundaries

Examples

TODO: these modules no longer exist, we need to point to the sample network directory instead.

GetInputField
Most basic example of Field Input in a SCIRun module.
GetInputFieldAndSendAsOutput
Most basic example of Field Output in a SCIRun module.
PrintHelloWorldToScreen
Most basic example SCIRun module.
SetFieldDataValues
Most basic example manipulating Field data in a SCIRun module.
SetTetVolFieldDataValues
Most basic example manipulating Field data in a SCIRun module.
SetTetVolFieldDataValuesToZero
Most basic example manipulating Field data in a SCIRun module.

Math

AddKnownsToLinearSystem
AddLinkedNodesToLinearSystem
AppendMatrix
Append the rows or columns of a matrix to a base matrix.
BuildNoiseColumnMatrix
This module creates a noise vector.
ChooseMatrix
This module takes in an arbitrary number of input matrices, and passes one of them downstream.
CollectMatrices
This module appends/replaces rows or columns of a matrix while looping through a network.
ComputeSVD
ConvertMappingMatrixToMaskVector
This module converts a Mapping Matrix to a Mask Vector.
ConvertMaskVectorToMappingMatrix
This module converts a Mask Vector to a Mapping Matrix.
ConvertMatrixType
This module casts a matrix into a different type.
CreateGeometricTransform
This module builds a 4x4 geometric transformation matrix.
CreateMatrix
This module lets the user create a small dense matrix manually.
CreateScalarMatrix
EvaluateLinAlgBinary
This module performs one of a number of selectable matrix operations using the two input matrices.
EvaluateLinAlgGeneral
This module performs a user defined linear algebra operation on up to five input matrices.
EvaluateLinAlgUnary
Performs one of a number of selectable unary matrix operations to the input matrix.
GetColumnOrRowFromMatrix
This module allows users to select a singe row or column from a matrix. The user can also select a range of rows or columns and send them to the output port one at a time.
GetSubmatrix
This module selects a subset of a matrix.
RemoveZeroRowsAndColumns
RemoveZerosFromMatrix
ReorderMatrixByCuthillMcKee
This module reorders a matrix to reduce the average bandwidth of the matrix.
ReorderMatrixByReverseCuthillMcKee
This module reorders a matrix to reduce the average bandwidth of the matrix.
ReportColumnMatrixMisfit
This module computes and visualizes the error between two vectors.
ReportMatrixColumnMeasure
This module computes a measure on each column of the input matrix and stores the result in the output matrix.
ReportMatrixInfo
This module is used to view the attributes of matrices.
ReportMatrixRowMeasure
This module computes a measure on each row of the input matrix and stores the result in the output matrix.
ReportRootMeanSquareError
This module computes the Root Mean Square Error from two input matrices and stores the result in the output matrix.
ResizeMatrix
This module resizes a matrix to a different size.
SelectSubMatrix
SetSubmatrix
SolveLinearSystem
This module is used to solve the linear system Ax=b, where A is a given Matrix, b is a given right-hand-side vector, and the user wants to find the solution vector x.
SolveMinNormLeastSqSystem
This module computes the minimal norm, least squared solution to a nx3 linear system.
SortMatrix

MiscField

BuildMappingMatrix
Build a mapping matrix -- a matrix that says how to project the data from one field onto the data of a second field.
BuildMatrixOfSurfaceNormals
The BuildMatrixOfSurfaceNormals calculates area weighted normal Vectors per node.
BuildPointCloudToLatVolMappingMatrix
Builds mapping matrix that projects data from a PointCloud to a LatVol
CalculateMeshCenter
CalculateMeshConnector
This module computes a connection between two meshes based on the minimal spatial distance between their nodes.
ChooseField
ChooseField takes in an arbitrary number of input fields, and pass one of them downstream, based on the port index typed in the UI.
CollectPointClouds
This module collects and joins PointClouds fields while iterating over a dataflow loop.
CoregisterPointClouds
CoregisterPointClouds the first three points of two PointCloudFields.
GenerateLinearSegments
GetMeshQualityField
ManageFieldSeries
Empty module; removed in SCIRun 4.6.
ReportFieldGeometryMeasures
Build a densematrix, where each row is a particular measure of the input Field (e.g. the x-values, or the element size).
ReportFieldInfo
ReportFieldInfo is used to view the attributes of fields.
ReportScalarFieldStats
Analyze data from a scalarfield.
ReportSearchGridInfo
Deprecated. Output a LatVolField that matches the search grid of the input field.
SelectFieldROIWithBoxWidget
Select data from a field.
SetFieldOrMeshStringProperty
Set a Property for a Field (or for its mesh).
SetFieldProperty
Set a Property for a Field.

NewField

ClipFieldByFunction
This module selects a subset of a field using a function.
ClipFieldByFunction2
This module selects a subset of one or two fields using a function.
ClipFieldByFunction3
This module selects a subset of one or more (up to three) fields using a function.
ClipFieldByMesh
Clip a mesh to another mesh.
ClipFieldToFieldOrWidget
This module selects a subset of a field using a field or a widget.
ClipFieldWithSeeds
ClipLatVolByIndicesOrWidget
This module selects data from a field.
ClipRasterFieldByIndices
Deprecated. This module subsamples a structured grid. It is posible to sub sample a particular region or sparsely sample the grid.
ClipVolumeByIsovalue
This module clips a scalar field to a specified isovalue.
CollectFields
This module collects and joins fields while iterating over a dataflow loop.
ConvertMatricesToMesh
This module constructs a mesh from raw matrix data.
CreateImage
This module constructs an ImageField that fits the source field.
CreateLatVol
This module constructs a LatVolField that fits the source field.
CreateStructHex
This module constructs a StructHexVolField that fits the source field.
ExtractIsosurfaceByFunction
ExtractPlanarSliceFromField
Deprecated. This module reduces the dimension of a topologically regular field by 1 dimension.
FairMesh
GenerateElectrode
GenerateMedialAxisPoints
GeneratePointSamplesFromField
This module places seed points in a field.
GeneratePointSamplesFromFieldOrWidget
This module generates samples from any type of input field and outputs the samples as a PointCloudField field.
GenerateSinglePointProbeFromField
This module generates a single probe.
GetAllSegmentationBoundaries
GetCentroidsFromMesh
This module computes a PointCloudField containing all of the element centers for a field.
GetDomainBoundary
This module extracts the boundaries of the different regions in a label map.
GetDomainStructure
GetFieldBoundary
This module extracts a boundary surface from a volume field.
GetSliceFromStructuredFieldByIndices
GetSliceFromStructuredFieldByIndices
This module reduces the dimension of a topologically regular field by 1 dimension.
InsertHexVolSheetAlongSurface
This module inserts a layer of hexes corresponding to the input TriSurfMesh.
InterfaceWithTetGen
This module interfaces with TetGen.
JoinFields
This module glues any number of input fields into one output field.
MatchDomainLabels
MergeFields
This module insers the elements from a field into a TetVol or TriSurf field.
MergeTriSurfs
This module self intersects all the triangles in a trisurf with each other so that none overlap.
RefineMesh
RefineMeshByIsoValue
Deprecated. This module refines a region of a mesh based on the value in the field.
RemoveHexVolSheet
This module removes a layer of hexes corresponding to the input edge ids.
SplitAndJoinFieldByDomain
Deprecated. This module split field by domain (a region with one single value) and then joins the fields together again, doubling all the nodes at the interfaces.
SplitFieldByConnectedRegion
SplitFieldByDomain
SplitNodesByDomain
SubsampleStructuredFieldByIndices

Render

CreateAndEditCameraPath
Deprecated. Interactive tool to edit and playback camera path in <modref text="SCIRun"text="Viewer"></modref>.
ShowAndEditCameraWidget
?
SynchronizeGeometry
Create a barrier to synchronize a set of geometry streams.
ViewAndEditSlices
Deprecated. The ViewAndEditSlices module displays orthogonal slices of a 3D Nrrd in a 2D OpenGL window.
ViewGraph
Deprecated. Renders input Nx2 matrices in a 2D graph
ViewScene
The ViewScene displays interactive graphical output to the computer screen. Use the ViewScene to see a geometry, or spatial data. The ViewScene provides access to many simulation parameters and controls, thus, indirectly initiates new iterations of the simulation steps important to computational steering.
ViewSlices
The ViewSlices module displays orthogonal slices of a 3D Nrrd in a 2D OpenGL window.

SignalProcessing

FilterPhaseData

String

CreateString
This module can be used to create a string.
GetFileName
This Module gets a filename and stores it in a string.
GetNetworkFileName
JoinStrings
This module merges multiple strings into one string.
PrintMatrixIntoString
This module does a sprintf with input matrices into a new string.
PrintStringIntoString
This module does a sprintf with input strings into a new string.
ReportStringInfo
This module can be used to display the contents of a string.
SplitFileName
This module splits a filename in: pathname, filename (base), and extension.

Time

Deprecated

TimeControls
Global time controls.

Visualization

ChooseColorMap
ChooseColorMap takes in an arbitrary number of input colormaps, and passes one of them downstream, based on the port index typed in the UI. Input port specification is 0 based (ie: first port is 0, 2nd port is 1, etc.)
ColorMap2DSemantics
Empty module; removed in SCIRun 4.6.
ConvertFieldsToTexture
This module builds a 3D Texture for use with an OpenGL volume renderer.
ConvertNrrdsToTexture
This module builds a 3D Texture for use with an OpenGL volume renderer.
CreateAndEditColorMap
Modify and create custom SCIRun ColorMaps.
CreateAndEditColorMap2D
CreateAndEditColorMap2D is used for interactively creating and editing ColorMap2 transfer functions for use in volume visualization.
CreateLightForViewer
Create light source object.
CreateScaleBar
CreateStandardColorMaps
A module that generates fixed Colormaps for visualization tools.
CreateViewerAxes
Generates Axes Geometry for rendering graphs.
CreateViewerCaption
Deprecated. Generates a title for rendering animations.
CreateViewerClockIcon
Generates a clock for rendering animations.
ExtractIsosurface
ExtractIsosurface extracts an isopotential surface from a scalar field.
GenerateStreamLines
The GenerateStreamLines module visualizes vector fields by generating curves that interpolate the vector of vectors in a Field.
GenerateStreamLinesWithPlacementHeuristic
Generate optimal stream lines
RescaleColorMap
RescaleColorMap allows the user to manually or automatically set the range of scalar values that map to the ColorMap. RescaleColorMap is an example of a module that has dynamic ports, because each time the user connects a Field module to the RescaleColorMap Field input port, another Field input port appears.
ShowColorMap
Display a ColorMap with index values.
ShowField
The ShowField module visualizes the geometry that makes up a Mesh inside a Field. When possible and if desireed, the field takes its color from the Data values that permeate the field.
ShowFieldGlyphs
The ShowField module visualizes the data that makes up a Field. If desired, the glyphs take their color from the Data values that permeate the field.
ShowLinePath
Shows a sequence of points, with coordinates in 3 dimensions, as a linearly interpolated curve.
ShowMatrix
Display a matrix as geometry.
ShowMeshBoundingBox
The ShowMeshBoundingBox Module renders a semented red-green-blue 3D grid around an arbitrary field
ShowPointPath
Shows a sequence of points, with coordinates in 3 dimensions, as a series of spheres located at the coordinates.
ShowString
This module puts the contents of a string in the viewer window.
ShowTextureSlices
This module is used to view slices of data using hardware 3D textures.
ShowTextureSurface
ShowTextureVolume
This module implements a volume renderer using 3D texture hardware.



Go back to Documentation:SCIRun:Reference