# CIBC:Documentation:SCIRun:Reference:SCIRun

From SCIRun Documentation Wiki

## Contents

**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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