 |
SMILX
1.01
|
|
SMILX
1.01
|
Represents a deformable model (i.e. a model with cells and scalar values that has special members for interacting with images). More...
#include <milxDeformableModel.h>
Public Member Functions | |
| DeformableModel () | |
| Standard constructor. | |
| DeformableModel (vtkSmartPointer< vtkPolyData > model) | |
| Constructor that copies the input model. | |
| virtual | ~DeformableModel () |
| Standard Destructor. | |
| template<typename TImage > | |
| void | ApplyOrientation (itk::SmartPointer< TImage > image, const bool applyOrigin=true, const bool flipY=false) |
| Apply the orientation of an image to a model. More... | |
| template<typename TImage > | |
| itk::SmartPointer< TImage > | VoxeliseAsITKImage (const unsigned char insideValue, double *spacing, double *bounds=NULL, const size_t padVoxels=1) |
| Convert a model to voxelised (imaging) data. More... | |
| template<typename MeshType > | |
| itk::SmartPointer< MeshType > | ConvertVTKPolyDataToITKMesh () |
| Convert the current vtkPolyData to an itk::Mesh. | |
| template<typename MeshType > | |
| void | ConvertITKMeshToVTKPolyData (itk::SmartPointer< MeshType > mesh) |
| Convert an itk::Mesh to the current vtkPolyData. | |
| template<typename TImage > | |
| void | ApplyOrientationCollection (vtkSmartPointer< vtkPolyDataCollection > collection, itk::SmartPointer< TImage > refImage, const bool applyOrigin=true, const bool flipY=false) |
| Apply orientation/direction of a reference image to a collection of models. | |
| template<typename TImage > | |
| void | VoxeliseCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const coordinateType spacing, std::vector< typename itk::SmartPointer< TImage > > &images) |
| Voxelise a collection of models with isotropic spacing given. A vector of image pointers in set to 'images'. More... | |
 Public Member Functions inherited from milx::Model | |
| Model () | |
| Standard constructor. | |
| Model (vtkSmartPointer< vtkPolyData > model) | |
| Constructor that copies the input model. | |
| virtual | ~Model () |
| Standard Destructor. | |
| void | AddInput (vtkSmartPointer< vtkPolyData > model) |
| Assigns and coninually appends meshes provided to the class. | |
| void | AddArray (vtkSmartPointer< vtkDataArray > array) |
| Appends an array to the model. | |
| void | SetInput (vtkSmartPointer< vtkPolyData > model) |
| Assigns the input model to class. More... | |
| void | SetInputData (vtkSmartPointer< vtkPolyData > model) |
| Assigns the input model to class. Same as SetInput and meant for VTK version > 5. | |
| void | SetTransform (vtkSmartPointer< vtkAbstractTransform > newTransform) |
| Transforms the model by given transform. | |
| void | SetGraph (vtkSmartPointer< vtkMutableUndirectedGraph > graph) |
| Converts a graph to polydata/mesh ready for display. | |
| void | SetPoints (vtkSmartPointer< vtkPoints > modelPoints) |
| Assign points to the model. | |
| void | SetPolys (vtkSmartPointer< vtkCellArray > modelPolys) |
| Assign polygons to the model via the array given. | |
| void | SetVectors (vtkSmartPointer< vtkDataArray > modelVectors) |
| Sets the vector field of the mesh (vectors per vertex of the surface) | |
| void | SetScalars (vtkSmartPointer< vtkDataArray > modelScalars) |
| Sets the scalar field of the mesh (values per vertex of the surface) | |
| void | SetActiveScalars (std::string nameOfArray) |
| Sets the array of name as the scalar field of the mesh (values per vertex of the surface) | |
| vtkSmartPointer< vtkPolyData > & | Result () |
| Returns the current model, i.e. the result of the latest operation. More... | |
| vtkSmartPointer< vtkPolyData > & | PreviousResult () |
| Returns the previous model, i.e. the result of the penultimate operation. More... | |
| vtkSmartPointer< vtkPolyData > & | GetInput () |
| Returns the input model, i.e. the very most initial model. More... | |
| vtkSmartPointer< vtkPolyData > & | GetOutput () |
| Returns the current model, i.e. the result of the latest operation ITK/VTK style. | |
| vtkAlgorithmOutput * | GetProducerPort () |
| Returns the current model, i.e. the result of the latest operation ITK/VTK style. | |
| vtkIdType | GetNumberOfPoints () |
| Returns the total number of points of the model currently held. | |
| vtkIdType | GetNumberOfArrays () |
| Returns the total number of point-based arrays in the model. | |
| vtkSmartPointer< vtkTransform > & | GetTransform () |
| Returns the current net transform applied to the model, i.e. concatenations of all (rigid/linear) transforms. | |
| vtkSmartPointer< vtkPoints > | GetPoints () |
| Returns the points of the model. | |
| vtkSmartPointer< vtkDataArray > | GetScalars () |
| Returns the active scalars of the model. | |
| void | GetScalarRange (double *range) |
| Returns the scalar range of the model. | |
| vtkSmartPointer< vtkDataArray > | GetVectors () |
| Returns the active vectors of the model. | |
| vtkSmartPointer< vtkDataArray > | GetNormals () |
| Returns the normal vectors of the model. | |
| vtkSmartPointer< vtkDataArray > | GetTensors () |
| Returns the active tensors (3x3 matrix per vertex) of the model. | |
| void | Update () |
| Updates the model to be the most current. | |
| void | Clean () |
| Removes duplicate points etc. from model. More... | |
| void | Triangulate () |
| Ensures the polygons in the model are triangulated. Useful when some filters required triangulation before use. More... | |
| void | MatchInformation (vtkSmartPointer< vtkPolyData > matchMesh, const bool rescale) |
| Matches the centroid and centroid scale of the model to the one given. | |
| void | IterativeClosestPointsRegistration (vtkSmartPointer< vtkPolyData > fixedMesh, const bool similarity=false, const int maxPoints=1024) |
| Computes the ICP registration of the current mesh to the one provided. | |
| void | LandmarkBasedRegistration (vtkSmartPointer< vtkPolyData > fixedMesh, const bool similarity=false) |
| Computes the landmark transform registration of the current mesh to the one provided. Requires point correspondence and same number of points. | |
| void | Decimate (const float reduceFactor) |
| Decimate the mesh (in terms of points) using the Decimate PRO. Generally use QuadricDecimate() instead. More... | |
| void | QuadricDecimate (const float reduceFactor) |
| Decimate the mesh (in terms of points) using the Quadric algorithm. More... | |
| void | ClusterDecimate () |
| Decimate the mesh (in terms of points) using the Quadric Clustering algorithm. More... | |
| void | LaplacianSmoothing (const int iterations) |
| Smooth the mesh (in terms of points) using the Laplacian algorithm. It is unstable, use WindowedSincSmoothing() instead unless massive non-edge preserving smoothing is required. | |
| void | WindowedSincSmoothing (const int iterations, const float passBand=0.1) |
| Smooth the mesh (in terms of points) using the Taubin (1995) optimal filter. | |
| void | Curvature (const bool meanCurvature=true) |
| Compute the curvature (using Laplace-Beltrami operator) of the mesh. | |
| void | Gradient () |
| Compute the gradient (using Laplace-Beltrami operator) of the scalars on the mesh. | |
| void | DistanceMap (vtkSmartPointer< vtkPoints > loopPoints) |
| Compute the distance map of the mesh points given a loop (as points) assumed to be on the mesh surface. | |
| void | GaussianWeightScalars (float stddev, float clampValue) |
| Evaluate the Gaussian function with the given standard deviation for all values of the scalars on the mesh. More... | |
| void | Rotate (const bool xAxis, const bool yAxis, const bool zAxis, const float angle, const coordinate centre) |
| Rotate the mesh along the selected axes from the centre by angle. More... | |
| void | Flip (const bool xAxis, const bool yAxis, const bool zAxis) |
| Flip the mesh along the selected axes. More... | |
| void | Clip (const coordinateType belowValue, const coordinateType aboveValue) |
| Clip the mesh based on a scalar threshold of the mesh scalars. More... | |
| void | Threshold (const coordinateType belowVal, const coordinateType aboveVal, const coordinateType outsideVal) |
| Threshold the scalars on the mesh based on a levels provided. | |
| void | Threshold (const coordinateType belowVal, const coordinateType aboveVal, const coordinateType insideVal, const coordinateType outsideVal) |
| Threshold the scalars on the mesh based on a levels provided. Inside value means a binary threshold is effectively done. | |
| void | Mask (vtkSmartPointer< vtkPolyData > maskMesh) |
| Mask the scalars on the mesh based on values of maskMesh being >= 1. | |
| void | IsoSurface (vtkSmartPointer< vtkImageData > img, double minValue) |
| vtkSmartPointer< vtkImageData > | Voxelise (const unsigned char insideValue, double *spacing, double *bounds=NULL, const size_t padVoxels=1) |
| void | DelaunayGraph3D () |
| Compute the Delaunay 3D graph of the points in the mesh. More... | |
| void | Delaunay2DTriangulation () |
| Compute the Delaunay 2D triangluation of the points in the mesh. More... | |
| void | DelaunayTriangulation () |
| Compute the Delaunay 3D triangluation of the points in the mesh. | |
| void | Append (vtkSmartPointer< vtkPolyData > model) |
| Appends the model provided to the member into the current model. | |
| void | Scale (const coordinateType scale, const bool useCentroid=true) |
| void | GenerateVertices () |
| Generate (only) vertices for display from point data. Good for when only points in mesh. | |
| void | GenerateVertexScalars () |
| Generate vertex scalars for display from point data. This colours the mesh by point ids. | |
| void | GenerateVerticesAs2DGlyphs (const GlyphType glyphType) |
| Generate (only) vertices (as 2D glyphs like crosses etc.) for display from point data. Good for when only points in mesh. | |
| void | GenerateTubes () |
| Generate tubes along edges of the mesh. | |
| void | GeneratePointModel (const double newScale) |
| Generate spheres of scaling for each point of the mesh. | |
| void | GenerateSpheres (const double newScale) |
| Generate spheres of scaling for each point of the mesh. Same as GeneratePointModel(). | |
| void | GenerateSampledPoints (const double distance) |
| Generate sampled points (only points) for the mesh at given spacing on triangles. | |
| void | GenerateVectorField (const double newScale=0.0, const bool useNormals=false) |
| Generate vector field for vectors present (as an array) in the mesh at given scaling. More... | |
| void | GenerateTensorField (const double newScale=0.0) |
| Generate tensor field for tensors present (as an array) in the mesh at given scaling. More... | |
| void | GenerateHedgehog (const double newScale=0.0) |
| Generate a line field for vectors present (as an array) in the mesh at given scaling. More... | |
| void | GenerateNormals (const int pointNormals=0) |
| Generate normal vectors for each point on the mesh. If pointNormals is (0,1,2), then normals are for (points,cells,both). | |
| void | GenerateKMeansClustering (int numberOfClusters) |
| Generate k-means clustering for the point positions in the mesh. | |
| void | GenerateQuantisedPoints (float quantiseFactor) |
| Generate points of the mesh to have integral cordinates. | |
| void | GenerateCappedBoundaries () |
| Generate capped boundaries for open meshes. This closes off open ends of a mesh. | |
| void | GenerateRegions () |
| Generate connected regions for the mesh labelled by scalar values. | |
| void | GenerateElevation (double x, double y, double z) |
| Generate scalar field for the mesh proportional to the elevation (dot product) with a given vector/direction. | |
| void | GenerateElevation () |
| Generate scalar field for the mesh proportional to the elevation in the z-direction. | |
| void | ResetScalars () |
| Resets the scalars to zero of the current model. More... | |
| void | FillScalars (const coordinateType value) |
| Sets all the scalars of the current model to value. More... | |
| void | RemoveScalars () |
| Removes all the scalars from the current model. Same as ClearScalars() | |
| void | RemoveArrays () |
| Removes all the arrays from the current model. Same as ClearArrayss() | |
| void | ConcatenateCollection (vtkSmartPointer< vtkPolyDataCollection > collection) |
| Concatenates all the models in the collection together into one model. More... | |
| void | ScaleCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const coordinateType scale) |
| Scales the coordinates of each point in all the models in the collection. More... | |
| void | SmoothCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const size_t iterations) |
| Smoothes all points in all the models in the collection using the Windowed Sinc algorithm. More... | |
| void | LaplacianCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const size_t iterations) |
| Smoothes all points in all the models in the collection using the Laplacian algorithm. More... | |
| void | FlipCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const bool xAxis, const bool yAxis, const bool zAxis) |
| Flips all points in all the models in the collection using the axis provided. More... | |
| void | DecimateCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const coordinateType factor) |
| Decimates all points in all the models in the collection using the Quadric algorithm algorithm. More... | |
| void | SplitCollection (vtkSmartPointer< vtkPolyDataCollection > collection, vtkSmartPointer< vtkPolyDataCollection > components, std::vector< vtkSmartPointer< vtkPolyDataCollection > > &splitCollections) |
| Splits each of the models in the collection into a collection of models. More... | |
| void | ScalarDifferenceCollection (vtkSmartPointer< vtkPolyDataCollection > collection) |
| Computes the difference in scalars cummulatively over the collection wrt the first mesh assuming the meshes have the same number of points. More... | |
| void | ScalarDifferenceCollection (vtkSmartPointer< vtkPolyDataCollection > collection1, vtkSmartPointer< vtkPolyDataCollection > collection2, vtkSmartPointer< vtkPolyDataCollection > &results) |
| void | ScalarThresholdCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const coordinateType aboveVal, const coordinateType belowVal) |
| Computes the Threshold of scalar values of meshes in place over the collection wrt the first mesh assuming the meshes have the same number of points. More... | |
| void | ClipCollection (vtkSmartPointer< vtkPolyDataCollection > collection, const coordinateType aboveVal, const coordinateType belowVal) |
| Computes the Clipping of models via the Threshold of scalar values in place over the collection. More... | |
| void | ScalarStatisticsCollection (vtkSmartPointer< vtkPolyDataCollection > collection) |
| Computes the statistics (min, max, variance etc.) of the scalars over the collection assuming the meshes have the same number of points. More... | |
| void | ScalarRemoveCollection (vtkSmartPointer< vtkPolyDataCollection > collection) |
| Removes the scalars over the collection assuming the meshes have the same number of points. More... | |
| void | ScalarCopyCollection (vtkSmartPointer< vtkPolyDataCollection > collection) |
| Copies the scalars over the collection (from the first mesh) assuming the meshes have the same number of points. More... | |
| double | MeanSquaredErrorCollection (vtkSmartPointer< vtkPolyDataCollection > collection) |
| Computes the MSE of all models in collection accummulatively. | |
| vtkSmartPointer< vtkPolyDataCollection > | ProcrustesAlignCollection (vtkSmartPointer< vtkPolyDataCollection > collection, bool rigid=false) |
| Aligns the collection to the mean mesh (computed internally) of the collection assuming the meshes have the same number of points and correspondence. More... | |
| vtkSmartPointer< vtkPolyDataCollection > | IterativeClosestPointsAlignCollection (vtkSmartPointer< vtkPolyDataCollection > collection, bool rigid=false, vtkSmartPointer< vtkTransformCollection > tCollection=0) |
| Aligns the collection to the mean mesh (computed internally) of the collection without needing correspondence. More... | |
Static Public Member Functions | |
| template<typename TImage > | |
| static vtkSmartPointer< vtkFloatArray > | SurfaceScalarsFromImage (vtkSmartPointer< vtkPolyData > surface, itk::SmartPointer< TImage > img, const bool absoluteValues) |
| Returns the scalars of the mesh (float values per vertex) according to the values found within the image at corresponding pixel locations for each vertex. More... | |
| template<typename TImage > | |
| static void | MarkSurfaceInsideImage (vtkSmartPointer< vtkPolyData > &surface, itk::SmartPointer< TImage > img, vtkFloatArray *weights, const float outsideValue=0.0) |
| Mark existing surface with all parts outside the image as 'outsideValue' value. Inside will remain the same scalars if present, else will be marked as 1.0. Uses include weights for the missing data etc. | |
| Static Public Member Functions inherited from milx::Model | |
| static void | Scale (vtkSmartPointer< vtkPolyData > model, const coordinateType scale, const bool useCentroid=true) |
| Scales the coordinates of each point in the model provided by scale. More... | |
| static void | ClearScalars (vtkSmartPointer< vtkPolyData > &mesh) |
| Removes all the scalars from the current model. More... | |
| static void | ClearArrays (vtkSmartPointer< vtkPolyData > &mesh) |
| Removes all the arrays from the current model. More... | |
| static void | ScalarDifference (vtkSmartPointer< vtkPolyData > model1, vtkSmartPointer< vtkPolyData > model2, vtkSmartPointer< vtkPolyData > result) |
| Calculates differences within scalars of two meshes assuming the meshes have the same number of points. More... | |
| static void | ThresholdScalars (vtkSmartPointer< vtkPolyData > model, const coordinateType aboveVal, const coordinateType belowVal, const coordinateType outsideVal) |
| Thresholds scalar values of mesh in place. More... | |
| static void | BinaryThresholdScalars (vtkSmartPointer< vtkPolyData > model, const coordinateType aboveVal, const coordinateType belowVal, const coordinateType insideVal=1.0, const coordinateType outsideVal=0.0) |
| Thresholds scalar values of mesh in place. Scalars outside the given range is set to outsideVal and scalars inside the range set to insideVal. More... | |
| static void | MaskScalars (vtkSmartPointer< vtkPolyData > model1, vtkSmartPointer< vtkPolyData > model2) |
| Masks the scalars in model1 with scalars in model2. Only values corresponding to >= 1 in model2 are kept in model1. | |
| static vtkSmartPointer< vtkMatrix4x4 > | ProcrustesAlign (vtkSmartPointer< vtkPolyData > source, vtkSmartPointer< vtkPolyData > target, bool rigid=false) |
| Aligns the source mesh to target mesh assuming the meshes have the same number of points and correspondence. The transform is applied in-place to the source mesh. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from milx::Model | |
| bool | IsCurrentModel () |
| void | UpdateModelState (vtkSmartPointer< vtkPolyDataAlgorithm > filter) |
| void | UpdateModelStateFromModel (vtkSmartPointer< vtkPolyData > mesh) |
| Protected Attributes inherited from milx::Model | |
| vtkSmartPointer< vtkPolyData > | InputModel |
| Holds the initial model in the pipeline. | |
| vtkSmartPointer< vtkPolyData > | CurrentModel |
| Holds the current model in the pipeline. | |
| vtkSmartPointer< vtkPolyData > | PreviousModel |
| Holds the previous model in the pipeline. | |
| vtkSmartPointer< vtkTransform > | CurrentTransform |
| transform applied to model | |
| bool | InternalInPlaceOperation |
| Used by the collection members to assign via pointers rather than deep copys. | |
Represents a deformable model (i.e. a model with cells and scalar values that has special members for interacting with images).
It also handles interaction with ITK images and meshes.
Definition at line 52 of file milxDeformableModel.h.
1.8.13