CIBC:Documentation:SCIRun:Reference:SCIRun
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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.
- MapFieldDataToNodeCoordinate
- Replace a mesh coordinate with the scalar field data values.
- Deprecated in SCIRun 4.6.
- ResampleRegularMesh
- Resample a regular mesh, such as a LatVol.
- 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.
- 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).
- 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).
- 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).
- 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
- 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.
- 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
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
- 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.
- 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.
- 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.
- 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.
- 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.
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
- 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.
- 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.
- 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.
- ExtractPlanarSliceFromField
- Deprecated. This module reduces the dimension of a topologically regular field by 1 dimension.
- 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.
- 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.
- GetFieldBoundary
- This module extracts a boundary surface from a volume field.
- 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.
- 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.
- 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.
Render
- CreateAndEditCameraPath
- Deprecated. Interactive tool to edit and playback camera path in <modref text="SCIRun"text="Viewer"></modref>.
- 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
String
- CreateString
- This module can be used to create a string.
- GetFileName
- This Module gets a filename and stores it in a string.
- 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.
- 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.
- ShowTextureVolume
- This module implements a volume renderer using 3D texture hardware.
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