/* * meshUtils.h * * * Created by Brian Patenaude on 04/04/2008. * Copyright 2008 University of Oxford All rights reserved. * */ /* Part of FSL - FMRIB's Software Library http://www.fmrib.ox.ac.uk/fsl fsl@fmrib.ox.ac.uk Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance Imaging of the Brain), Department of Clinical Neurology, Oxford University, Oxford, UK LICENCE FMRIB Software Library, Release 5.0 (c) 2012, The University of Oxford (the "Software") The Software remains the property of the University of Oxford ("the University"). 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You are not permitted under this Licence to use this Software commercially. Use for which any financial return is received shall be defined as commercial use, and includes (1) integration of all or part of the source code or the Software into a product for sale or license by or on behalf of Licensee to third parties or (2) use of the Software or any derivative of it for research with the final aim of developing software products for sale or license to a third party or (3) use of the Software or any derivative of it for research with the final aim of developing non-software products for sale or license to a third party, or (4) use of the Software to provide any service to an external organisation for which payment is received. If you are interested in using the Software commercially, please contact Isis Innovation Limited ("Isis"), the technology transfer company of the University, to negotiate a licence. Contact details are: innovation@isis.ox.ac.uk quoting reference DE/9564. */ #ifndef MESHUTILS_H #define MESHUTILS_H #include "newimage/newimageall.h" #include "fslvtkio/fslvtkio.h" //#include "shapeModel/shapeModel.h" //#include "meshclass/meshclass.h" //using namespace std; //using namespace fslvtkio; namespace meshutils { class meshUtils: public fslvtkio::fslvtkIO { public: meshUtils(); meshUtils(const string & fname, const fslvtkIO::DataType i); //convience method to read polydata void loadMesh(const std::string & meshname); float getMinX() { return Points.Column(1).Minimum(); } float getMaxX() { return Points.Column(1).Maximum(); } float getMinY() { return Points.Column(2).Minimum(); } float getMaxY() { return Points.Column(2).Maximum(); } float getMinZ() { return Points.Column(3).Minimum(); } float getMaxZ() { return Points.Column(3).Maximum(); } static void generateRandomMeshUsingScalar(const mesh::Mesh & m, const string & outname, const vector & scal, const int & N); // static void addModesToModelUsingMask(shapemodel::shapeModel * min, const vector & scal); // static void getConditionalMeanAndVariance(shapemodel::shapeModel * min, volume4D & iCondMean, volume4D & iCondVar , const volume & im, const int & mode, const float & bmin, const float & bmax, const float & res, const float & mean_offset); static void generateRandom6DOFMatrices( const string & outname, const int & N); int getNumberOfPolygons(){ return Polygons.Nrows(); } float interpolateScalar(const unsigned int & tri_index, const float & x, const float & y, const float& z ); static ReturnMatrix vectorOfVectorsToMatrix(const vector< vector > & vin); static void fileToVector(const string & fname, vector list); static vector fileToVector(const string & fname ); static ReturnMatrix readFlirtMat(const string & fname); static void writeFlirtMatrix(const Matrix & fmat, const string & fname); void getBounds(int *bounds, const float & xdim, const float & ydim,const float & zdim); static void getBounds(const mesh::Mesh & m, int *bounds,const float & xdim, const float & ydim,const float & zdim) ; template //instantiations are in .cc file void SurfDistToLabels(vector & dist, const volume & image); template //instantiations are in .cc file void SurfDistToLabels(vector & dist, const volume & image, const Tim & label); void SurfScalarsMeanAndStdev(vector meshList, Matrix & MeanPoints, Matrix & MeanScalars, Matrix & StDevScalars ); static void meshReg(mesh::Mesh & m, const Matrix & fmat); void meshReg(const Matrix & fmat); static void shift3DVertexMatrix(Matrix & mat, const float & tx, const float & ty, const float & tz ); static void shift3DVertexColumnVector(ColumnVector & mat, const float & tx, const float & ty, const float & tz ); static void shift3DMesh(mesh::Mesh & m, const float & tx, const float & ty, const float & tz ); static ReturnMatrix subSampleMatrix(const Matrix & m, const vector & vmask ); static ReturnMatrix subSample_Nby1_3D_Matrix(const Matrix & m, const vector & vmask ); void shiftPoints(const float & tx, const float & ty, const float & tz ); void scalePoints( const float & sx, const float & sy, const float & sz ); static ReturnMatrix shiftPolygonMatrix(const Matrix & mat, const int & shift ); void shiftPolygonMatrix( const int & shift ); static ReturnMatrix meshPointsToMatrix(const mesh::Mesh & m1); static bool checkLine(const float & p1, const float & p2, const float & test); static bool checkTriangleNeighbour(const short & tri0, const short & tri1, const short & tri2 , const short & ind0, const short & ind1, short & ind0new , short & ind1new); static void intersectionPoint(const float & ycut, const float & px0, const float & py0, const float & pz0, const float & dx, const float & dy, const float & dz, vector & px, vector & py, vector & pz); template void deformSurface(const volume & im, const float & maxit, const float & w_im, const float & wTang, const float & maxTri, const float & w_norm, const T & max_thresh,const unsigned int & interRate, const bool & enableInteraction, const string & name); //transformation matrix utilities static void preMultiplyGlobalRotation(Matrix & fmat, const Matrix & R); static void preMultiplyGlobalScale(Matrix & fmat, const float & s); static void preMultiplyGlobalScale(Matrix & fmat, const float & sx,const float & sy, const float & sz); static void preMultiplyTranslation(Matrix & fmat, const float & tx, const float & ty, const float & tz ); static ReturnMatrix getIdentityMatrix(const short N); //end of transofrmation matrix utilities //this should output the mask values as well as the truncated mesh template void sampleImageAtPoints(const volume & immask, vector & vsamples); void LQSurfaceReg(const Matrix & refPoints, Matrix & fmat, const int & dof); void combineMeshesWithVectorsAndScalars(const vector & meshlist); //template void findMidPointOfMidSlice(const volume & im, const Matrix & fmat, float & cx, float & cy, float & cz); vector sliceMesh(const float & ycut); void sampleMeshProfilesFromImage(const volume & image, const float & sample_interval, const unsigned int & ipp); static void warpMeshWithDefField(const string & fieldname, const string & meshname, const string & meshoutname, const float & dx, const float & dy, const float & dz); template< class T > void warpGridWithDefField(const volume4D & fieldname, const float & dx, const float & dy, const float & dz); template< class T > static void warpGridWithDefField(const volume4D & defField, vector & points_in, float warpSc,const float & dx, const float & dy, const float & dz); float drawTriangleScalars(volume& image, volume &count, const unsigned int & tri_index); //-----------------------VERTEX ANALYSIS STUFF-----------------------// //return linear transformation matrix Matrix reg_leastsq(const Matrix & TargetPoints, const short & dof); static void applyReg(Matrix & pts, const Matrix & fmat); static ReturnMatrix calculateRotation(const Matrix & Pts_src_dm, const Matrix & Pts_targ_dm); static ReturnMatrix calculateScale(const Matrix & Pts_src_dm, const Matrix & Pts_targ_dm, const bool & global); Matrix alignSurfaces(const string & src_list, const short & dof, const string & outname ); double maxScalar(); double meanScalar(); //-----------------------VERTEX ANALYSIS STUFF-----------------------// static float myatan2(const float & y, const float & x); template static void cartesianToSphericalCoord(vector & verts); template static void sphericalToCartesianCoord(vector & verts); static ReturnMatrix addSphericalCorrdinates( const Matrix & m1, const Matrix & m2 ); static ReturnMatrix subtractSphericalCoordinates( const Matrix & m1, const Matrix & m2 ); static ReturnMatrix averageSphericalCorrdinates( const Matrix & m1, const Matrix & m2 , int & N1, const int & N2); static void SVDarcSpherical( Matrix & m1, DiagonalMatrix & D, Matrix & U, Matrix & V); void getSphericalCoordFromCart(NEWMAT::Matrix & r, NEWMAT::Matrix & theta, NEWMAT::Matrix & phi); static void cartesianToSphericalCoord(NEWMAT::Matrix & verts); static void sphericalToCartesianCoord(NEWMAT::Matrix & verts); template static void cartesianToSphericalCoord(mesh::Mesh & m); template static void sphericalToCartesianCoord(mesh::Mesh & m); static void combinedSharedBoundaries(const string & mname1, const string & mname2 ); static void labelAndCombineSharedBoundaries(const string & mname1, const string & mname2, const string & mout1name ); //static void appendSharedBoundaryMask(const string & mname1, const string & mname2,const string & mbase, const string & mout1name, const bool & indexed, const bool & useSc2 ); ReturnMatrix appendSharedBoundaryMask(const Matrix & Points2 ); //this will sample the new set of points based on indices from mask then replace the original void sampleSharedBoundaryByMask(const Matrix & Points2); static void removeRow(Matrix & mat, int ind ); static ColumnVector sample_image_at_vertices(string meshname, string imagename); static void sample_image_at_verticesNN(const string & meshname, const string & imagename, const string & outname); static void sampleSumAndWrite(const string & meshname, const string & imagename, const string & outname); static void meshReg(const string & meshname, const string & fname, const string & outname, bool noinv ); static void draw_segment(volume& image, const mesh::Pt& p1, const mesh::Pt& p2, int label); static volume draw_mesh(const volume& image, const mesh::Mesh &m, int label); static volume make_mask_from_mesh(const volume & image, const mesh::Mesh& m, int label, int* bounds, const bool & sep_boundary); static void fillMesh(const string & imname, const string & meshname, const string & outname, const int & label, const bool & sep_boundary ); static bool findVertex(const Matrix & vert1,const Matrix & vert2, int ind1 ); static void applyFlirtThenSBmask(const string & mname1, const string & mname2,const string & mflirtname, const string & mout1name); static void do_work_uncentreMesh(const string & inim, const string & inmesh, const string & outmesh); static void do_work_MeshReg(const string & inim, const string & inmesh, const string & outmesh); static void subtractMeshes(const string & mesh1name, const string & mesh2name, const string & out); template static void warpMeshWithDefField(mesh::Mesh & m, const volume4D & defField, const Matrix & mat); static ReturnMatrix getDeformedVector(const ColumnVector & mean, const Matrix & modes, const ColumnVector & eigs, const vector & vars ); template void ugridToImage(NEWIMAGE::volume & im); private: volume image; }; } #endif