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
- GetBundlesFromBundle
- This module retrieves a bundle object from a bundle.
- GetColorMap2sFromBundle
- This module retrieves a colormap2 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.
- GetPathsFromBundle
- This module retrieves a path object from a bundle.
- GetStringsFromBundle
- This module retrieves a string object from a bundle.
- InsertBundlesIntoBundle
- This module inserts a bundle object into a bundle.
- InsertColorMap2sIntoBundle
- This module inserts a colormap2 object into a bundle.
- InsertColorMapsIntoBundle
- This module inserts a colormap object 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.
- InsertPathsIntoBundle
- This module inserts a path 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
- ApplyMappingMatrix
- Apply a mapping matrix to project the data from one field onto the mesh of another field.
- 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.
- CalculateFieldDataCompiled
- Perform a specified functional transform on all of the data in a field.
- CalculateFieldDataCompiled2
- Perform a specified functional transform to each pair of data elements in the two input fields.
- CalculateFieldDataCompiled3
- Perform a specified functional transform on all of the data in a field.
- 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.
- 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.
- 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.
- MaskLatVol
- Convert a LatVolField into a MaskedLatVolField and apply the given function to mask it out.
- MaskLatVolWithTriSurf
- Convert a LatVolField into a MaskedLatVolField and apply the given function to mask it out.
- 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.
- SelectAndSetFieldData2
- 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 one additional field port to be used for selecting and setting data values.
- 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.
- ReportMeshQualityMeasures
- Report the quality of the elements of the mesh.
- SwapFieldDataWithMatrixEntries
- Add and remove data from a field.
ChangeMesh
- ConvertHexVolToTetVol
- Convert a HexVolField into a TetVolField.
- ConvertMLVtoHV
- Convert a LatVolField to a HexVolField
- 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.
- ConvertRasterMeshToStructuredMesh
- Convert a regular lattice field into an structured field.
- ConvertTVtoMLV
- Convert a TetVolField to a MaskedLatVolField
- EditMeshBoundingBox
- EditMeshBoundingBox is used to transform the field geometry.
- MapFieldDataToNodeCoordinate
- Replace a mesh coordinate with the scalar fdata values.
- SmoothMesh
- Nodal movement to improve mesh quality.
- 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.
- TransformMeshWithTransform
- Non-interactive geometric transform of a field.
- TransformPlanarMesh
- Non-interactive geometric transform of a field.
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).
- WriteColorMap2
- 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).
Examples
- 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
- CollectMatrices
- This module appends/replaces rows or columns of a matrix while looping through a network.
- BuildNoiseColumnMatrix
- Performs the unary matrix operation transpose.
- ChooseMatrix
- ChooseMatrix takes in an arbitrary number of input matrices, and pass one of them downstream, based on the port index typed in the UI.
- ConvertMappingMatrixToMaskVector
- Converts a Mapping Matrix to a Mask Vector
- ConvertMaskVectorToMappingMatrix
- Converts a Mask Vector to a Mapping Matrix.
- ConvertMatrixType
- Casts a matrix
- CreateGeometricTransform
- Build a 4x4 geometric transformation matrix.
- CreateMatrix
- This module lets the user create a small dense matrix manually.
- EvaluateLinAlgBinary
- Performs one of a number of selectable matrix operations using the two input matrices.
- EvaluateLinAlgGeneral
- Do some linear algebra on input matrices.
- EvaluateLinAlgUnary
- Performs one of a number of selectable unary matrix operations to the input matrix.
- GetColumnMatrixFromMatrix
- The GetColumnMatrixFromMatrix module allows users to select a single 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. The GetColumnMatrixFromMatrix module has three input ports: Matrix, Weight Vector and Current Index, which may run concurrently or one at a time. This module allows the user to animate points on a mesh if computing a whole time series of results packaged within a row or column. As data propogates throughout the image, the Viewer window displays the animation of points on the mesh.
- GetSubmatrix
- Select a subset of a matrix.
- ReportColumnMatrixMisfit
- Compute and visualize error between two vectors.
- ReportMatrixInfo
- ReportMatrixInfo is used to view the attributes of matrices.
- SolveLinearSystem
- The SolveLinearSystem 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
- 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.
- CoregisterPointClouds
- CoregisterPointClouds the first three points of two PointCloudFields.
- 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
- 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
- Select a subset of a field.
- ClipFieldToFieldOrWidget
- Select a subset of a field.
- ClipLatVolByIndicesOrWidget
- Select data from a field.
- ClipRasterFieldByIndices
- The Field Sub Sample module sub samples a structured grid. It is posible to sub sample a particular region or sparsely sample the grid.
- ClipVolumeByIsovalue
- Clip a scalar field to a specified isovalue.
- ClipVolumeByIsovalueWithRefinement
- Clip a scalar field to a specified isovalue.
- ConvertMatricesToMesh
- Construct a mesh from raw matrix data.
- CreateImage
- Make an ImageField that fits the source field.
- CreateLatVol
- Make a LatVolField that fits the source field.
- CreateStructHex
- Make a StructHexVolField that fits the source field.
- ExtractPlanarSliceFromField
- The Field Slicer module reduces the dimension of a topologically regular field by 1 dimension.
- GeneratePointSamplesFromField
- Place seed points in a field.
- GeneratePointSamplesFromFieldOrWidget
- GeneratePointSamplesFromFieldOrWidget generates samples from any type of input field and outputs the samples as a PointCloudField field.
- GenerateSinglePointProbeFromField
- GenerateSinglePointProbeFromField values in a field.
- GetCentroidsFromMesh
- Computes a PointCloudField containing all of the element centers for a field.
- GetFieldBoundary
- The GetFieldBoundary module extracts a boundary surface from a volume field.
- GetHexVolSheetBasedOnEdgeIndices
- Removes a layer of hexes corresponding to the input edge ids.
- GetSliceFromLatVol
- The Field Slicer module reduces the dimension of a topologically regular field by 1 dimension.
- InsertHexVolSheetFromTriSurf
- Insert a layer of hexes corresponding to the input TriSurfMesh.
- InterfaceWithCamal
- InterfaceWithCamal will create a 3D volumetric mesh of tets in the supplied boundary mesh
- JoinFields
- JoinFields glues any number of input fields into one output field.
- MergeFields
- Insert the elements from a field into a TetVol or TriSurf field.
- MergeTriSurfs
- Self intersect all the triangles in a trisurf with each other so that none overlap.
Render
- CreateAndEditCameraPath
- 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
- The ViewAndEditSlices module displays orthogonal slices of a 3D Nrrd in a 2D OpenGL window.
- ViewGraph
- 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.
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
- 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.)
- 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.
- CreateStandardColorMaps
- A module that generates fixed Colormaps for visualization tools.
- CreateViewerAxes
- Generates Axes Geometry for rendering graphs.
- CreateViewerCaption
- 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. Where possible, the field takes its color from the Data values that permeate the field.
- ShowMatrix
- Display a matrix as geometry.
- ShowMeshBoundingBox
- The ShowMeshBoundingBox Module renders a semented red-green-blue 3D grid around an arbitrary field
- 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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