Updating lbpm_uCT_pp.cpp
This commit is contained in:
Mark Berrill
parent
ceb85c2cd0
commit
f1239ada97
@ -24,7 +24,7 @@ namespace IO {
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* silo - Silo
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* @param[in] append Append any existing data (default is false)
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*/
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void initialize( const std::string& path="", const std::string& format="new", bool append=false );
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void initialize( const std::string& path="", const std::string& format="silo", bool append=false );
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/*!
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File diff suppressed because it is too large
Load Diff
@ -1002,7 +1002,7 @@ Array<TYPE, FUN, Allocator> Array<TYPE, FUN, Allocator>::coarsen(
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throw std::invalid_argument( "Array must be multiple of filter size" );
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}
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Array<TYPE, FUN, Allocator> y( S2 );
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if ( d_size.ndim() <= 3 )
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if ( d_size.ndim() > 3 )
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throw std::logic_error( "Function programmed for more than 3 dimensions" );
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const auto &Nh = filter.d_size;
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for ( size_t k1 = 0; k1 < y.d_size[2]; k1++ ) {
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@ -30,463 +30,415 @@
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int main(int argc, char **argv)
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{
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// Initialize MPI
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Comm_rank(comm,&rank);
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MPI_Comm_size(comm,&nprocs);
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{
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Utilities::setErrorHandlers();
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PROFILE_START("Main");
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//std::vector<std::string> filenames;
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if ( argc<2 ) {
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if ( rank == 0 ){
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printf("At least one filename must be specified\n");
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}
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return 1;
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}
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std::string filename = std::string(argv[1]);
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if ( rank == 0 ){
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printf("Input data file: %s\n",filename.c_str());
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}
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auto db = std::make_shared<Database>( filename );
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auto domain_db = db->getDatabase( "Domain" );
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auto uct_db = db->getDatabase( "uCT" );
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auto analysis_db = db->getDatabase( "Analysis" );
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// Read domain values
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auto L = domain_db->getVector<double>( "L" );
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auto size = domain_db->getVector<int>( "n" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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int BoundaryCondition = domain_db->getScalar<int>( "BC" );
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int nx = size[0];
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int ny = size[1];
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int nz = size[2];
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double Lx = L[0];
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double Ly = L[1];
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double Lz = L[2];
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int nprocx = nproc[0];
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int nprocy = nproc[1];
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int nprocz = nproc[2];
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auto InputFile=uct_db->getScalar<std::string>( "InputFile" );
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auto target=uct_db->getScalar<int>("target");
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auto background=uct_db->getScalar<int>("background");
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auto rough_cutoff=uct_db->getScalar<float>( "rough_cutoff" );
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auto lamda=uct_db->getScalar<float>( "lamda" );
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auto nlm_sigsq=uct_db->getScalar<float>( "nlm_sigsq" );
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auto nlm_depth=uct_db->getScalar<int>( "nlm_depth" );
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auto cx=uct_db->getScalar<int>( "center_x" );
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auto cy=uct_db->getScalar<int>( "center_y" );
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auto cz=uct_db->getScalar<int>( "center_z" );
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auto CylRad=uct_db->getScalar<float>( "cylinder_radius" );
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//.......................................................................
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// Reading the domain information file
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//.......................................................................
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// std::shared_ptr<Domain> Dm ();
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//for (int i=0; i<Dm->Nx*Dm->Ny*Dm->Nz; i++) Dm->id[i] = 1;
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//Dm->CommInit();
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// Check that the number of processors >= the number of ranks
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if ( rank==0 ) {
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printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
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printf("Number of MPI ranks used: %i \n", nprocs);
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printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
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}
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if ( nprocs < nprocx*nprocy*nprocz ){
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ERROR("Insufficient number of processors");
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}
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// Determine the maximum number of levels for the desired coarsen ratio
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int ratio[3] = {2,2,2};
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//std::vector<size_t> ratio = {4,4,4};
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// need to set up databases for each level of the mesh
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std:vector<Database> multidomain_db;
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std::vector<int> Nx(1,nx), Ny(1,ny), Nz(1,nz);
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while ( Nx.back()%ratio[0]==0 && Nx.back()>8 &&
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Ny.back()%ratio[1]==0 && Ny.back()>8 &&
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Nz.back()%ratio[2]==0 && Nz.back()>8 )
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{
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Nx.push_back( Nx.back()/ratio[0] );
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Ny.push_back( Ny.back()/ratio[1] );
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Nz.push_back( Nz.back()/ratio[2] );
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// clone the domain and create coarse version based on Nx,Ny,Nz
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//multidomain_db.push_back();
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}
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int N_levels = Nx.size();
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// Initialize the domain
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std::vector<std::shared_ptr<Domain>> Dm(N_levels);
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for (int i=0; i<N_levels; i++) {
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// This line is no good -- will create identical Domain structures instead of
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// Need a way to define a coarse structure for the coarse domain (see above)
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Dm[i].reset( new Domain(domain_db, comm) );
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int N = (Nx[i]+2)*(Ny[i]+2)*(Nz[i]+2);
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for (int n=0; n<N; n++){
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Dm[i]->id[n] = 1;
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}
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Dm[i]->CommInit();
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}
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// array containing a distance mask
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Array<float> MASK(Nx[0]+2,Ny[0]+2,Nz[0]+2);
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// Create the level data
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std::vector<Array<char>> ID(N_levels);
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std::vector<Array<float>> LOCVOL(N_levels);
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std::vector<Array<float>> Dist(N_levels);
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std::vector<Array<float>> MultiScaleSmooth(N_levels);
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std::vector<Array<float>> Mean(N_levels);
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std::vector<Array<float>> NonLocalMean(N_levels);
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std::vector<std::shared_ptr<fillHalo<double>>> fillDouble(N_levels);
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std::vector<std::shared_ptr<fillHalo<float>>> fillFloat(N_levels);
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std::vector<std::shared_ptr<fillHalo<char>>> fillChar(N_levels);
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for (int i=0; i<N_levels; i++) {
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ID[i] = Array<char>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
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LOCVOL[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
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Dist[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
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MultiScaleSmooth[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
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Mean[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
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NonLocalMean[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
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ID[i].fill(0);
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LOCVOL[i].fill(0);
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Dist[i].fill(0);
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MultiScaleSmooth[i].fill(0);
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Mean[i].fill(0);
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NonLocalMean[i].fill(0);
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fillDouble[i].reset(new fillHalo<double>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
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fillFloat[i].reset(new fillHalo<float>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
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fillChar[i].reset(new fillHalo<char>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
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}
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// Read the subvolume of interest on each processor
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PROFILE_START("ReadVolume");
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int fid = netcdf::open(InputFile,netcdf::READ);
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std::string varname("VOLUME");
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netcdf::VariableType type = netcdf::getVarType( fid, varname );
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std::vector<size_t> dim = netcdf::getVarDim( fid, varname );
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if ( rank == 0 ) {
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printf("Reading %s (%s)\n",varname.c_str(),netcdf::VariableTypeName(type).c_str());
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printf(" dims = %i x %i x %i \n",int(dim[0]),int(dim[1]),int(dim[2]));
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}
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{
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RankInfoStruct info( rank, nprocx, nprocy, nprocz );
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int x = info.ix*nx;
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int y = info.jy*ny;
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int z = info.kz*nz;
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// Read the local data
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Array<short> VOLUME = netcdf::getVar<short>( fid, varname, {x,y,z}, {nx,ny,nz}, {1,1,1} );
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// Copy the data and fill the halos
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LOCVOL[0].fill(0);
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fillFloat[0]->copy( VOLUME, LOCVOL[0] );
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fillFloat[0]->fill( LOCVOL[0] );
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}
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netcdf::close( fid );
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MPI_Barrier(comm);
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PROFILE_STOP("ReadVolume");
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if (rank==0) printf("Read complete\n");
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// Filter the original data
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filter_src( *Dm[0], LOCVOL[0] );
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// Set up the mask to be distance to cylinder (crop outside cylinder)
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// float CylRad=900;
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for (int k=0;k<Nz[0]+2;k++) {
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for (int j=0;j<Ny[0]+2;j++) {
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for (int i=0;i<Nx[0]+2;i++) {
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int iproc = Dm[0]->iproc();
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int jproc = Dm[0]->jproc();
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int kproc = Dm[0]->kproc();
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int x=iproc*Nx[0]+i-1;
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int y=jproc*Ny[0]+j-1;
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int z=kproc*Nz[0]+k-1;
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//int cx = 0.5*nprocx*Nx[0];
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//int cy = 0.5*nprocy*Ny[0];
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//int cz = 0.5*nprocz*Nz[0];
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// distance from the center line
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MASK(i,j,k) = CylRad - sqrt(float((z-cz)*(z-cz) + (y-cy)*(y-cy)) );
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}
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}
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}
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// Compute the means for the high/low regions
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// (should use automated mixture model to approximate histograms)
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//float THRESHOLD = 0.05*maxReduce( Dm[0]->Comm, std::max( LOCVOL[0].max(), fabs(LOCVOL[0].min()) ) );
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float THRESHOLD=0.5*float(target+background);
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float mean_plus=0;
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float mean_minus=0;
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int count_plus=0;
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int count_minus=0;
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for (int k=1;k<Nz[0]+1;k++) {
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for (int j=1;j<Ny[0]+1;j++) {
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for (int i=1;i<Nx[0]+1;i++) {
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if (MASK(i,j,k) > 0.f ){
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auto tmp = LOCVOL[0](i,j,k);
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/* if ((tmp-background)*(tmp-target) > 0){
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// direction to background / target is the same
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if (fabs(tmp-target) > fabs(tmp-background)) tmp=background; // tmp closer to background
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else tmp=target; // tmp closer to target
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}
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*/
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if ( tmp > THRESHOLD ) {
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mean_plus += tmp;
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count_plus++;
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} else if ( tmp < -THRESHOLD ) {
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mean_minus += tmp;
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count_minus++;
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}
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}
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}
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}
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}
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mean_plus = sumReduce( Dm[0]->Comm, mean_plus ) / sumReduce( Dm[0]->Comm, count_plus );
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mean_minus = sumReduce( Dm[0]->Comm, mean_minus ) / sumReduce( Dm[0]->Comm, count_minus );
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if (rank==0) printf(" Region 1 mean (+): %f, Region 2 mean (-): %f \n",mean_plus, mean_minus);
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MPI_Barrier(comm);
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// Scale the source data to +-1.0
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for (size_t i=0; i<LOCVOL[0].length(); i++) {
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if (MASK(i) < 0.f){
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LOCVOL[0](i) = 1.0;
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}
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else if ( LOCVOL[0](i) >= 0 ) {
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LOCVOL[0](i) /= mean_plus;
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LOCVOL[0](i) = std::min( LOCVOL[0](i), 1.0f );
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} else {
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LOCVOL[0](i) /= -mean_minus;
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LOCVOL[0](i) = std::max( LOCVOL[0](i), -1.0f );
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}
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}
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// Fill the source data for the coarse meshes
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PROFILE_START("CoarsenMesh");
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for (int i=1; i<N_levels; i++) {
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Array<float> filter(ratio[0],ratio[1],ratio[2]);
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filter.fill(1.0f/filter.length());
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Array<float> tmp(Nx[i-1],Ny[i-1],Nz[i-1]);
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fillFloat[i-1]->copy( LOCVOL[i-1], tmp );
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Array<float> coarse = tmp.coarsen( filter );
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fillFloat[i]->copy( coarse, LOCVOL[i] );
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fillFloat[i]->fill( LOCVOL[i] );
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if (rank==0){
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printf("Coarsen level %i \n",i);
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printf(" Nx=%i, Ny=%i, Nz=%i \n",int(tmp.size(0)),int(tmp.size(1)),int(tmp.size(2)) );
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printf(" filter_x=%i, filter_y=%i, filter_z=%i \n",int(filter.size(0)),int(filter.size(1)),int(filter.size(2)) );
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printf(" ratio= %i,%i,%i \n",int(ratio[0]),int(ratio[1]),int(ratio[2]) );
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}
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MPI_Barrier(comm);
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}
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PROFILE_STOP("CoarsenMesh");
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// Initialize the coarse level
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PROFILE_START("Solve full mesh");
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if (rank==0)
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printf("Initialize full mesh\n");
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solve( LOCVOL[0], Mean[0], ID[0], Dist[0], MultiScaleSmooth[0],
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NonLocalMean[0], *fillFloat[0], *Dm[0], nprocx,
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rough_cutoff, lamda, nlm_sigsq, nlm_depth);
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PROFILE_STOP("Solve full mesh");
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MPI_Barrier(comm);
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/* // Initialize the coarse level
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PROFILE_START("Solve coarse mesh");
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if (rank==0)
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printf("Initialize coarse mesh\n");
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solve( LOCVOL.back(), Mean.back(), ID.back(), Dist.back(), MultiScaleSmooth.back(),
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NonLocalMean.back(), *fillFloat.back(), *Dm.back(), nprocx );
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PROFILE_STOP("Solve coarse mesh");
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MPI_Barrier(comm);
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// Refine the solution
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PROFILE_START("Refine distance");
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if (rank==0)
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printf("Refine mesh\n");
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for (int i=int(Nx.size())-2; i>=0; i--) {
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if (rank==0)
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printf(" Refining to level %i\n",int(i));
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refine( Dist[i+1], LOCVOL[i], Mean[i], ID[i], Dist[i], MultiScaleSmooth[i],
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NonLocalMean[i], *fillFloat[i], *Dm[i], nprocx, i );
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}
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PROFILE_STOP("Refine distance");
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MPI_Barrier(comm);
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// Perform a final filter
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PROFILE_START("Filtering final domains");
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if (rank==0)
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printf("Filtering final domains\n");
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Array<float> filter_Mean, filter_Dist1, filter_Dist2;
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filter_final( ID[0], Dist[0], *fillFloat[0], *Dm[0], filter_Mean, filter_Dist1, filter_Dist2 );
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PROFILE_STOP("Filtering final domains");
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*/
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//removeDisconnected( ID[0], *Dm[0] );
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/*
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// Write the distance function to a netcdf file
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const char* netcdf_filename = "Distance.nc";
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// Initialize MPI
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int rank, nprocs;
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MPI_Init(&argc,&argv);
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MPI_Comm comm = MPI_COMM_WORLD;
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MPI_Comm_rank(comm,&rank);
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MPI_Comm_size(comm,&nprocs);
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{
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RankInfoStruct info( rank, nprocx, nprocy, nprocz );
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std::vector<int> dim = { Nx[0]*nprocx, Ny[0]*nprocy, Nz[0]*nprocz };
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int fid = netcdf::open( netcdf_filename, netcdf::CREATE, MPI_COMM_WORLD );
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auto dims = netcdf::defDim( fid, {"X", "Y", "Z"}, dim );
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Array<float> data(Nx[0],Ny[0],Nz[0]);
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fillFloat[0]->copy( Dist[0], data );
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netcdf::write( fid, "Distance", dims, data, info );
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Utilities::setErrorHandlers();
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PROFILE_START("Main");
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//std::vector<std::string> filenames;
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if ( argc<2 ) {
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if ( rank == 0 ){
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printf("At least one filename must be specified\n");
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}
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return 1;
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}
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std::string filename = std::string(argv[1]);
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if ( rank == 0 ){
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printf("Input data file: %s\n",filename.c_str());
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}
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auto db = std::make_shared<Database>( filename );
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auto domain_db = db->getDatabase( "Domain" );
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auto uct_db = db->getDatabase( "uCT" );
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auto analysis_db = db->getDatabase( "Analysis" );
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// Read domain values
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auto L = domain_db->getVector<double>( "L" );
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auto size = domain_db->getVector<int>( "n" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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int BoundaryCondition = domain_db->getScalar<int>( "BC" );
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int nx = size[0];
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int ny = size[1];
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int nz = size[2];
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double Lx = L[0];
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double Ly = L[1];
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double Lz = L[2];
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int nprocx = nproc[0];
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int nprocy = nproc[1];
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int nprocz = nproc[2];
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auto InputFile = uct_db->getScalar<std::string>( "InputFile" );
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auto target = uct_db->getScalar<int>("target");
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auto background = uct_db->getScalar<int>("background");
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auto rough_cutoff = uct_db->getScalar<float>( "rough_cutoff" );
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auto lamda = uct_db->getScalar<float>( "lamda" );
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auto nlm_sigsq = uct_db->getScalar<float>( "nlm_sigsq" );
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auto nlm_depth = uct_db->getScalar<int>( "nlm_depth" );
|
||||
auto center = uct_db->getVector<int>( "center" );
|
||||
auto CylRad = uct_db->getScalar<float>( "cylinder_radius" );
|
||||
auto maxLevels = uct_db->getScalar<int>( "max_levels" );
|
||||
std::vector<int> offset( 3, 0 );
|
||||
if ( uct_db->keyExists( "offset" ) )
|
||||
offset = uct_db->getVector<int>( "offset" );
|
||||
|
||||
// Check that the number of processors >= the number of ranks
|
||||
if ( rank==0 ) {
|
||||
printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
|
||||
printf("Number of MPI ranks used: %i \n", nprocs);
|
||||
printf("Full domain size: %i x %i x %i \n",nx*nprocx,ny*nprocy,nz*nprocz);
|
||||
}
|
||||
if ( nprocs < nprocx*nprocy*nprocz ){
|
||||
ERROR("Insufficient number of processors");
|
||||
}
|
||||
|
||||
// Determine the maximum number of levels for the desired coarsen ratio
|
||||
int ratio[3] = {2,2,2};
|
||||
//std::vector<size_t> ratio = {4,4,4};
|
||||
// need to set up databases for each level of the mesh
|
||||
std::vector<std::shared_ptr<Database>> multidomain_db(1,domain_db);
|
||||
std::vector<int> Nx(1,nx), Ny(1,ny), Nz(1,nz);
|
||||
while ( Nx.back()%ratio[0]==0 && Nx.back()>8 &&
|
||||
Ny.back()%ratio[1]==0 && Ny.back()>8 &&
|
||||
Nz.back()%ratio[2]==0 && Nz.back()>8 &&
|
||||
(int) Nx.size() < maxLevels )
|
||||
{
|
||||
Nx.push_back( Nx.back()/ratio[0] );
|
||||
Ny.push_back( Ny.back()/ratio[1] );
|
||||
Nz.push_back( Nz.back()/ratio[2] );
|
||||
// clone the domain and create coarse version based on Nx,Ny,Nz
|
||||
auto db2 = domain_db->cloneDatabase();
|
||||
db2->putVector<int>( "n", { Nx.back(), Ny.back(), Nz.back() } );
|
||||
multidomain_db.push_back(db2);
|
||||
}
|
||||
int N_levels = Nx.size();
|
||||
|
||||
// Initialize the domain
|
||||
std::vector<std::shared_ptr<Domain>> Dm(N_levels);
|
||||
for (int i=0; i<N_levels; i++) {
|
||||
// This line is no good -- will create identical Domain structures instead of
|
||||
// Need a way to define a coarse structure for the coarse domain (see above)
|
||||
Dm[i].reset( new Domain(multidomain_db[i], comm) );
|
||||
int N = (Nx[i]+2)*(Ny[i]+2)*(Nz[i]+2);
|
||||
for (int n=0; n<N; n++){
|
||||
Dm[i]->id[n] = 1;
|
||||
}
|
||||
Dm[i]->CommInit();
|
||||
}
|
||||
|
||||
// array containing a distance mask
|
||||
Array<float> MASK(Nx[0]+2,Ny[0]+2,Nz[0]+2);
|
||||
MASK.fill(0);
|
||||
|
||||
// Create the level data
|
||||
std::vector<Array<char>> ID(N_levels);
|
||||
std::vector<Array<float>> LOCVOL(N_levels);
|
||||
std::vector<Array<float>> Dist(N_levels);
|
||||
std::vector<Array<float>> MultiScaleSmooth(N_levels);
|
||||
std::vector<Array<float>> Mean(N_levels);
|
||||
std::vector<Array<float>> NonLocalMean(N_levels);
|
||||
std::vector<std::shared_ptr<fillHalo<double>>> fillDouble(N_levels);
|
||||
std::vector<std::shared_ptr<fillHalo<float>>> fillFloat(N_levels);
|
||||
std::vector<std::shared_ptr<fillHalo<char>>> fillChar(N_levels);
|
||||
for (int i=0; i<N_levels; i++) {
|
||||
ID[i] = Array<char>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
|
||||
LOCVOL[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
|
||||
Dist[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
|
||||
MultiScaleSmooth[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
|
||||
Mean[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
|
||||
NonLocalMean[i] = Array<float>(Nx[i]+2,Ny[i]+2,Nz[i]+2);
|
||||
ID[i].fill(0);
|
||||
LOCVOL[i].fill(0);
|
||||
Dist[i].fill(0);
|
||||
MultiScaleSmooth[i].fill(0);
|
||||
Mean[i].fill(0);
|
||||
NonLocalMean[i].fill(0);
|
||||
fillDouble[i].reset(new fillHalo<double>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
|
||||
fillFloat[i].reset(new fillHalo<float>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
|
||||
fillChar[i].reset(new fillHalo<char>(Dm[i]->Comm,Dm[i]->rank_info,{Nx[i],Ny[i],Nz[i]},{1,1,1},0,1) );
|
||||
}
|
||||
|
||||
// Read the subvolume of interest on each processor
|
||||
PROFILE_START("ReadVolume");
|
||||
int fid = netcdf::open(InputFile,netcdf::READ);
|
||||
std::string varname("VOLUME");
|
||||
auto type = netcdf::getVarType( fid, varname );
|
||||
auto dim = netcdf::getVarDim( fid, varname );
|
||||
if ( rank == 0 ) {
|
||||
printf("Reading %s (%s)\n",varname.c_str(),netcdf::VariableTypeName(type).c_str());
|
||||
printf(" dims = %i x %i x %i \n",int(dim[0]),int(dim[1]),int(dim[2]));
|
||||
}
|
||||
{
|
||||
// Read the local data
|
||||
int x = Dm[0]->iproc()*nx + offset[0];
|
||||
int y = Dm[0]->jproc()*ny + offset[1];
|
||||
int z = Dm[0]->kproc()*nz + offset[2];
|
||||
Array<short> VOLUME = netcdf::getVar<short>( fid, varname, {x,y,z}, {nx,ny,nz}, {1,1,1} );
|
||||
// Copy the data and fill the halos
|
||||
LOCVOL[0].fill(0);
|
||||
fillFloat[0]->copy( VOLUME, LOCVOL[0] );
|
||||
fillFloat[0]->fill( LOCVOL[0] );
|
||||
}
|
||||
netcdf::close( fid );
|
||||
MPI_Barrier(comm);
|
||||
PROFILE_STOP("ReadVolume");
|
||||
if (rank==0) printf("Read complete\n");
|
||||
|
||||
|
||||
// Filter the original data
|
||||
filter_src( *Dm[0], LOCVOL[0] );
|
||||
|
||||
// Set up the mask to be distance to cylinder (crop outside cylinder)
|
||||
for (int k=0;k<Nz[0]+2;k++) {
|
||||
for (int j=0;j<Ny[0]+2;j++) {
|
||||
for (int i=0;i<Nx[0]+2;i++) {
|
||||
int x=Dm[0]->iproc()*Nx[0]+i-1;
|
||||
int y=Dm[0]->jproc()*Ny[0]+j-1;
|
||||
int z=Dm[0]->kproc()*Nz[0]+k-1;
|
||||
int cx = center[0] - offset[0];
|
||||
int cy = center[1] - offset[1];
|
||||
int cz = center[2] - offset[2];
|
||||
// distance from the center line
|
||||
MASK(i,j,k) = CylRad - sqrt(float((z-cz)*(z-cz) + (y-cy)*(y-cy)) );
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Compute the means for the high/low regions
|
||||
// (should use automated mixture model to approximate histograms)
|
||||
//float THRESHOLD = 0.05*maxReduce( Dm[0]->Comm, std::max( LOCVOL[0].max(), fabs(LOCVOL[0].min()) ) );
|
||||
double THRESHOLD=0.5*(target+background);
|
||||
double mean_plus=0;
|
||||
double mean_minus=0;
|
||||
int count_plus=0;
|
||||
int count_minus=0;
|
||||
for (int k=1;k<Nz[0]+1;k++) {
|
||||
for (int j=1;j<Ny[0]+1;j++) {
|
||||
for (int i=1;i<Nx[0]+1;i++) {
|
||||
if (MASK(i,j,k) > 0.f ){
|
||||
auto tmp = LOCVOL[0](i,j,k);
|
||||
/* if ((tmp-background)*(tmp-target) > 0){
|
||||
// direction to background / target is the same
|
||||
if (fabs(tmp-target) > fabs(tmp-background)) tmp=background; // tmp closer to background
|
||||
else tmp=target; // tmp closer to target
|
||||
}
|
||||
*/
|
||||
if ( tmp > THRESHOLD ) {
|
||||
mean_plus += tmp;
|
||||
count_plus++;
|
||||
} else if ( tmp < -THRESHOLD ) {
|
||||
mean_minus += tmp;
|
||||
count_minus++;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
ASSERT( count_plus > 0 && count_minus > 0 );
|
||||
mean_plus = sumReduce( Dm[0]->Comm, mean_plus ) / sumReduce( Dm[0]->Comm, count_plus );
|
||||
mean_minus = sumReduce( Dm[0]->Comm, mean_minus ) / sumReduce( Dm[0]->Comm, count_minus );
|
||||
if (rank==0) printf(" Region 1 mean (+): %f, Region 2 mean (-): %f \n",mean_plus, mean_minus);
|
||||
|
||||
|
||||
MPI_Barrier(comm);
|
||||
// Scale the source data to +-1.0
|
||||
for (size_t i=0; i<LOCVOL[0].length(); i++) {
|
||||
if (MASK(i) < 0.f){
|
||||
LOCVOL[0](i) = 1.0;
|
||||
}
|
||||
else if ( LOCVOL[0](i) >= 0 ) {
|
||||
LOCVOL[0](i) /= mean_plus;
|
||||
LOCVOL[0](i) = std::min( LOCVOL[0](i), 1.0f );
|
||||
} else {
|
||||
LOCVOL[0](i) /= -mean_minus;
|
||||
LOCVOL[0](i) = std::max( LOCVOL[0](i), -1.0f );
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// Fill the source data for the coarse meshes
|
||||
PROFILE_START("CoarsenMesh");
|
||||
for (int i=1; i<N_levels; i++) {
|
||||
Array<float> filter(ratio[0],ratio[1],ratio[2]);
|
||||
filter.fill(1.0f/filter.length());
|
||||
Array<float> tmp(Nx[i-1],Ny[i-1],Nz[i-1]);
|
||||
fillFloat[i-1]->copy( LOCVOL[i-1], tmp );
|
||||
Array<float> coarse = tmp.coarsen( filter );
|
||||
fillFloat[i]->copy( coarse, LOCVOL[i] );
|
||||
fillFloat[i]->fill( LOCVOL[i] );
|
||||
if (rank==0){
|
||||
printf("Coarsen level %i \n",i);
|
||||
printf(" Nx=%i, Ny=%i, Nz=%i \n",int(tmp.size(0)),int(tmp.size(1)),int(tmp.size(2)) );
|
||||
printf(" filter_x=%i, filter_y=%i, filter_z=%i \n",int(filter.size(0)),int(filter.size(1)),int(filter.size(2)) );
|
||||
printf(" ratio= %i,%i,%i \n",int(ratio[0]),int(ratio[1]),int(ratio[2]) );
|
||||
}
|
||||
MPI_Barrier(comm);
|
||||
}
|
||||
PROFILE_STOP("CoarsenMesh");
|
||||
|
||||
// Initialize the coarse level
|
||||
PROFILE_START("Solve coarse mesh");
|
||||
if (rank==0)
|
||||
printf("Initialize full mesh\n");
|
||||
solve( LOCVOL.back(), Mean.back(), ID.back(), Dist.back(), MultiScaleSmooth.back(),
|
||||
NonLocalMean.back(), *fillFloat.back(), *Dm.back(), nprocx,
|
||||
rough_cutoff, lamda, nlm_sigsq, nlm_depth);
|
||||
PROFILE_STOP("Solve coarse mesh");
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// Refine the solution
|
||||
PROFILE_START("Refine distance");
|
||||
if (rank==0)
|
||||
printf("Refine mesh\n");
|
||||
for (int i=N_levels-2; i>=0; i--) {
|
||||
if (rank==0)
|
||||
printf(" Refining to level %i\n",i);
|
||||
refine( Dist[i+1], LOCVOL[i], Mean[i], ID[i], Dist[i], MultiScaleSmooth[i],
|
||||
NonLocalMean[i], *fillFloat[i], *Dm[i], nprocx, i,
|
||||
rough_cutoff, lamda, nlm_sigsq, nlm_depth);
|
||||
}
|
||||
PROFILE_STOP("Refine distance");
|
||||
MPI_Barrier(comm);
|
||||
|
||||
// Perform a final filter
|
||||
PROFILE_START("Filtering final domains");
|
||||
if (rank==0)
|
||||
printf("Filtering final domains\n");
|
||||
Array<float> filter_Mean, filter_Dist1, filter_Dist2;
|
||||
filter_final( ID[0], Dist[0], *fillFloat[0], *Dm[0], filter_Mean, filter_Dist1, filter_Dist2 );
|
||||
PROFILE_STOP("Filtering final domains");
|
||||
//removeDisconnected( ID[0], *Dm[0] );
|
||||
|
||||
// Write the distance function to a netcdf file
|
||||
/* const char* netcdf_filename = "Distance.nc";
|
||||
{
|
||||
RankInfoStruct info( rank, nprocx, nprocy, nprocz );
|
||||
std::vector<int> dim = { Nx[0]*nprocx, Ny[0]*nprocy, Nz[0]*nprocz };
|
||||
int fid = netcdf::open( netcdf_filename, netcdf::CREATE, MPI_COMM_WORLD );
|
||||
auto dims = netcdf::defDim( fid, {"X", "Y", "Z"}, dim );
|
||||
Array<float> data(Nx[0],Ny[0],Nz[0]);
|
||||
fillFloat[0]->copy( Dist[0], data );
|
||||
netcdf::write( fid, "Distance", dims, data, info );
|
||||
netcdf::close( fid );
|
||||
} */
|
||||
|
||||
// Write the results
|
||||
if (rank==0) printf("Setting up visualization structure \n");
|
||||
std::vector<IO::MeshDataStruct> meshData(N_levels);
|
||||
for (size_t i=0; i<Nx.size(); i++) {
|
||||
// Mesh
|
||||
meshData[i].meshName = "image_" + std::to_string( i );
|
||||
meshData[i].mesh = std::make_shared<IO::DomainMesh>(Dm[i]->rank_info,Nx[i],Ny[i],Nz[i],Lx,Ly,Lz);
|
||||
// Source data
|
||||
auto OrigData = std::make_shared<IO::Variable>();
|
||||
OrigData->name = "Source_Data_" + std::to_string( i );
|
||||
OrigData->type = IO::VariableType::VolumeVariable;
|
||||
OrigData->dim = 1;
|
||||
OrigData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(OrigData);
|
||||
fillDouble[i]->copy( LOCVOL[i], OrigData->data );
|
||||
// Non-Local Mean
|
||||
auto NonLocMean = std::make_shared<IO::Variable>();
|
||||
NonLocMean->name = "NonLocal_Mean_" + std::to_string( i );
|
||||
NonLocMean->type = IO::VariableType::VolumeVariable;
|
||||
NonLocMean->dim = 1;
|
||||
NonLocMean->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(NonLocMean);
|
||||
fillDouble[i]->copy( NonLocalMean[i], NonLocMean->data );
|
||||
// Segmented Data
|
||||
auto SegData = std::make_shared<IO::Variable>();
|
||||
SegData->name = "Segmented_Data_" + std::to_string( i );
|
||||
SegData->type = IO::VariableType::VolumeVariable;
|
||||
SegData->dim = 1;
|
||||
SegData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(SegData);
|
||||
fillDouble[i]->copy( ID[i], SegData->data );
|
||||
// Signed Distance
|
||||
auto DistData = std::make_shared<IO::Variable>();
|
||||
DistData->name = "Signed_Distance_" + std::to_string( i );
|
||||
DistData->type = IO::VariableType::VolumeVariable;
|
||||
DistData->dim = 1;
|
||||
DistData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(DistData);
|
||||
fillDouble[i]->copy( Dist[i], DistData->data );
|
||||
// Smoothed Data
|
||||
auto SmoothData = std::make_shared<IO::Variable>();
|
||||
SmoothData->name = "Smoothed_Data_" + std::to_string( i );
|
||||
SmoothData->type = IO::VariableType::VolumeVariable;
|
||||
SmoothData->dim = 1;
|
||||
SmoothData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(SmoothData);
|
||||
fillDouble[i]->copy( MultiScaleSmooth[i], SmoothData->data );
|
||||
|
||||
}
|
||||
#if 0
|
||||
std::shared_ptr<IO::Variable> filter_Mean_var( new IO::Variable() );
|
||||
filter_Mean_var->name = "Mean";
|
||||
filter_Mean_var->type = IO::VariableType::VolumeVariable;
|
||||
filter_Mean_var->dim = 1;
|
||||
filter_Mean_var->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(filter_Mean_var);
|
||||
fillDouble[0]->copy( filter_Mean, filter_Mean_var->data );
|
||||
std::shared_ptr<IO::Variable> filter_Dist1_var( new IO::Variable() );
|
||||
filter_Dist1_var->name = "Dist1";
|
||||
filter_Dist1_var->type = IO::VariableType::VolumeVariable;
|
||||
filter_Dist1_var->dim = 1;
|
||||
filter_Dist1_var->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(filter_Dist1_var);
|
||||
fillDouble[0]->copy( filter_Dist1, filter_Dist1_var->data );
|
||||
std::shared_ptr<IO::Variable> filter_Dist2_var( new IO::Variable() );
|
||||
filter_Dist2_var->name = "Dist2";
|
||||
filter_Dist2_var->type = IO::VariableType::VolumeVariable;
|
||||
filter_Dist2_var->dim = 1;
|
||||
filter_Dist2_var->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(filter_Dist2_var);
|
||||
fillDouble[0]->copy( filter_Dist2, filter_Dist2_var->data );
|
||||
#endif
|
||||
MPI_Barrier(comm);
|
||||
if (rank==0) printf("Writing output \n");
|
||||
// Write visulization data
|
||||
IO::writeData( 0, meshData, comm );
|
||||
if (rank==0) printf("Finished. \n");
|
||||
|
||||
// Compute the Minkowski functionals
|
||||
MPI_Barrier(comm);
|
||||
auto Averages = std::make_shared<Minkowski>(Dm[0]);
|
||||
|
||||
Array <char> phase_label(Nx[0]+2,Ny[0]+2,Nz[0]+2);
|
||||
Array <double> phase_distance(Nx[0]+2,Ny[0]+2,Nz[0]+2);
|
||||
// Analyze the wetting fluid
|
||||
for (int k=1;k<Nz[0]+1;k++) {
|
||||
for (int j=1;j<Ny[0]+1;j++) {
|
||||
for (int i=1;i<Nx[0]+1;i++) {
|
||||
int n = k*Nx[0]*Ny[0]+j*Nx[0]+i;
|
||||
if (!(Dm[0]->id[n] > 0)){
|
||||
// Solid phase
|
||||
phase_label(i,j,k) = 0;
|
||||
}
|
||||
else if (Dist[0](i,j,k) < 0.0){
|
||||
// wetting phase
|
||||
phase_label(i,j,k) = 1;
|
||||
}
|
||||
else {
|
||||
// non-wetting phase
|
||||
phase_label(i,j,k) = 0;
|
||||
}
|
||||
phase_distance(i,j,k) =2.0*double(phase_label(i,j,k))-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
CalcDist(phase_distance,phase_label,*Dm[0]);
|
||||
Averages->ComputeScalar(phase_distance,0.f);
|
||||
Averages->PrintAll();
|
||||
}
|
||||
*/
|
||||
|
||||
{
|
||||
// Write the results
|
||||
if (rank==0) printf("Setting up visualization structure \n");
|
||||
// std::vector<IO::MeshDataStruct> meshData(N_levels);
|
||||
std::vector<IO::MeshDataStruct> meshData(1);
|
||||
// for (size_t i=0; i<Nx.size(); i++) {
|
||||
// Mesh
|
||||
meshData[0].meshName = "image";
|
||||
meshData[0].mesh = std::shared_ptr<IO::DomainMesh>( new IO::DomainMesh(Dm[0]->rank_info,Nx[0],Ny[0],Nz[0],Lx,Ly,Lz) );
|
||||
// Source data
|
||||
std::shared_ptr<IO::Variable> OrigData( new IO::Variable() );
|
||||
OrigData->name = "Source Data";
|
||||
OrigData->type = IO::VariableType::VolumeVariable;
|
||||
OrigData->dim = 1;
|
||||
OrigData->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(OrigData);
|
||||
fillDouble[0]->copy( LOCVOL[0], OrigData->data );
|
||||
// Non-Local Mean
|
||||
std::shared_ptr<IO::Variable> NonLocMean( new IO::Variable() );
|
||||
NonLocMean->name = "Non-Local Mean";
|
||||
NonLocMean->type = IO::VariableType::VolumeVariable;
|
||||
NonLocMean->dim = 1;
|
||||
NonLocMean->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(NonLocMean);
|
||||
fillDouble[0]->copy( NonLocalMean[0], NonLocMean->data );
|
||||
std::shared_ptr<IO::Variable> SegData( new IO::Variable() );
|
||||
SegData->name = "Segmented Data";
|
||||
SegData->type = IO::VariableType::VolumeVariable;
|
||||
SegData->dim = 1;
|
||||
SegData->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(SegData);
|
||||
fillDouble[0]->copy( ID[0], SegData->data );
|
||||
// Signed Distance
|
||||
std::shared_ptr<IO::Variable> DistData( new IO::Variable() );
|
||||
DistData->name = "Signed Distance";
|
||||
DistData->type = IO::VariableType::VolumeVariable;
|
||||
DistData->dim = 1;
|
||||
DistData->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(DistData);
|
||||
fillDouble[0]->copy( Dist[0], DistData->data );
|
||||
// Smoothed Data
|
||||
std::shared_ptr<IO::Variable> SmoothData( new IO::Variable() );
|
||||
SmoothData->name = "Smoothed Data";
|
||||
SmoothData->type = IO::VariableType::VolumeVariable;
|
||||
SmoothData->dim = 1;
|
||||
SmoothData->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(SmoothData);
|
||||
fillDouble[0]->copy( MultiScaleSmooth[0], SmoothData->data );
|
||||
|
||||
/*// Segmented Data
|
||||
std::shared_ptr<IO::Variable> SegData( new IO::Variable() );
|
||||
SegData->name = "Segmented Data";
|
||||
SegData->type = IO::VariableType::VolumeVariable;
|
||||
SegData->dim = 1;
|
||||
SegData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(SegData);
|
||||
fillDouble[i]->copy( ID[i], SegData->data );
|
||||
// Signed Distance
|
||||
std::shared_ptr<IO::Variable> DistData( new IO::Variable() );
|
||||
DistData->name = "Signed Distance";
|
||||
DistData->type = IO::VariableType::VolumeVariable;
|
||||
DistData->dim = 1;
|
||||
DistData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(DistData);
|
||||
fillDouble[i]->copy( Dist[i], DistData->data );
|
||||
// Smoothed Data
|
||||
std::shared_ptr<IO::Variable> SmoothData( new IO::Variable() );
|
||||
SmoothData->name = "Smoothed Data";
|
||||
SmoothData->type = IO::VariableType::VolumeVariable;
|
||||
SmoothData->dim = 1;
|
||||
SmoothData->data.resize(Nx[i],Ny[i],Nz[i]);
|
||||
meshData[i].vars.push_back(SmoothData);
|
||||
fillDouble[i]->copy( MultiScaleSmooth[i], SmoothData->data );
|
||||
|
||||
}
|
||||
#if 0
|
||||
std::shared_ptr<IO::Variable> filter_Mean_var( new IO::Variable() );
|
||||
filter_Mean_var->name = "Mean";
|
||||
filter_Mean_var->type = IO::VariableType::VolumeVariable;
|
||||
filter_Mean_var->dim = 1;
|
||||
filter_Mean_var->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(filter_Mean_var);
|
||||
fillDouble[0]->copy( filter_Mean, filter_Mean_var->data );
|
||||
std::shared_ptr<IO::Variable> filter_Dist1_var( new IO::Variable() );
|
||||
filter_Dist1_var->name = "Dist1";
|
||||
filter_Dist1_var->type = IO::VariableType::VolumeVariable;
|
||||
filter_Dist1_var->dim = 1;
|
||||
filter_Dist1_var->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(filter_Dist1_var);
|
||||
fillDouble[0]->copy( filter_Dist1, filter_Dist1_var->data );
|
||||
std::shared_ptr<IO::Variable> filter_Dist2_var( new IO::Variable() );
|
||||
filter_Dist2_var->name = "Dist2";
|
||||
filter_Dist2_var->type = IO::VariableType::VolumeVariable;
|
||||
filter_Dist2_var->dim = 1;
|
||||
filter_Dist2_var->data.resize(Nx[0],Ny[0],Nz[0]);
|
||||
meshData[0].vars.push_back(filter_Dist2_var);
|
||||
fillDouble[0]->copy( filter_Dist2, filter_Dist2_var->data );
|
||||
#endif
|
||||
*/
|
||||
MPI_Barrier(comm);
|
||||
if (rank==0) printf("Writing output \n");
|
||||
// Write visulization data
|
||||
IO::writeData( 0, meshData, comm );
|
||||
if (rank==0) printf("Finished. \n");
|
||||
}
|
||||
|
||||
// Compute the Minkowski functionals
|
||||
MPI_Barrier(comm);
|
||||
std::shared_ptr<Minkowski> Averages(new Minkowski(Dm[0]));
|
||||
|
||||
Array <char> phase_label(Nx[0],Ny[0],Nz[0]);
|
||||
Array <double> phase_distance(Nx[0],Ny[0],Nz[0]);
|
||||
// Analyze the wetting fluid
|
||||
for (int k=1;k<Nz[0]+1;k++) {
|
||||
for (int j=1;j<Ny[0]+1;j++) {
|
||||
for (int i=1;i<Nx[0]+1;i++) {
|
||||
int n = k*Nx[0]*Ny[0]+j*Nx[0]+i;
|
||||
if (!(Dm[0]->id[n] > 0)){
|
||||
// Solid phase
|
||||
phase_label(i,j,k) = 0;
|
||||
}
|
||||
else if (Dist[0](i,j,k) < 0.0){
|
||||
// wetting phase
|
||||
phase_label(i,j,k) = 1;
|
||||
}
|
||||
else {
|
||||
// non-wetting phase
|
||||
phase_label(i,j,k) = 0;
|
||||
}
|
||||
phase_distance(i,j,k) =2.0*double(phase_label(i,j,k))-1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
CalcDist(phase_distance,phase_label,*Dm[0]);
|
||||
Averages->ComputeScalar(phase_distance,0.f);
|
||||
Averages->PrintAll();
|
||||
}
|
||||
PROFILE_STOP("Main");
|
||||
PROFILE_SAVE("lbpm_uCT_pp",true);
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
return 0;
|
||||
PROFILE_STOP("Main");
|
||||
PROFILE_SAVE("lbpm_uCT_pp",true);
|
||||
MPI_Barrier(comm);
|
||||
MPI_Finalize();
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user