int main(int argc, char *argv[]) { struct matrix_t *matrixA; struct sparse_matrix_t *sparseA; struct vector_t *x, *b; lsqr_input *input; lsqr_output *output; lsqr_work *work; /* zone temoraire de travail */ lsqr_func *func; /* func->mat_vec_prod -> APROD */ /* cmd line arg */ char *matrix_filename = NULL; char *vector_filename = NULL; char *sol_filename = NULL; int max_iter = -1; float damping = 0; if (argc != 4) { fprintf(stderr, "%s matrixfile vectorfile solutionfile\n", argv[0]); exit(1); } matrix_filename = strdup(argv[1]); vector_filename = strdup(argv[2]); sol_filename = strdup(argv[3]); /* read the matrix */ matrixA = read_matrix(matrix_filename); fprintf(stderr, "read*matrix: ok (size=%ldx%ld, %ld elements)\n", matrixA->nb_line, matrixA->nb_col, matrixA->nb_line * matrixA->nb_col); sparseA = sparsify(matrixA, SPARSE_COL_LINK); b = read_simple_vector(vector_filename); /*************************************************/ /* check compatibility between matrix and vector */ /*************************************************/ if (sparseA->nb_line != b->length) { fprintf(stderr, "Error, check your matrix/vector sizes (%ld/%ld)\n", sparseA->nb_line, b->length); exit(1); } /* init vector solution to zero */ x = new_vector(sparseA->nb_col); /* catch Ctrl-C signal */ signal(SIGINT, emergency_halt); /*************************************************************/ /* solve A.x = B */ /*************************************************************/ /* LSQR alloc */ alloc_lsqr_mem(&input, &output, &work, &func, sparseA->nb_line, sparseA->nb_col); fprintf(stderr, "alloc_lsqr_mem : ok\n"); /* defines the routine Mat.Vect to use */ func->mat_vec_prod = sparseMATRIXxVECTOR; /* Set the input parameters for LSQR */ input->num_rows = sparseA->nb_line; input->num_cols = sparseA->nb_col; input->rel_mat_err = .0; input->rel_rhs_err = .0; input->cond_lim = .0; input->lsqr_fp_out = stdout; input->rhs_vec = (dvec *) b; input->sol_vec = (dvec *) x; /* initial guess */ input->damp_val = damping; if (max_iter == -1) { input->max_iter = 4 * (sparseA->nb_col); } else { input->max_iter = max_iter; } /* resolution du systeme Ax=b */ lsqr(input, output, work, func, sparseA); write_vector((struct vector_t *) output->sol_vec, sol_filename); free_lsqr_mem(input, output, work, func); free_matrix(matrixA); /* check A^t.A */ /* * { struct sparse_matrix_t *AtA; AtA = AtransA (sparseA); * write_sparse_matrix(AtA, "AtA"); write_sparse_matrix(sparseA, * "A"); free_sparse_matrix (AtA); * * } */ free_sparse_matrix(sparseA); return (1); }
float optimize_smoothness(WPt& worlds_pts, const IntensityPerImage& left_intensities, const IntensityPerImage& right_intensities) { // copy to globals //assert(fromVector.size() == toVector.size()); //assert(fromVector.size() >= 3); //_fromVector = fromVector; // worlds_pts.resize(3); if (worlds_pts.size() < 3) { // too little points to opitimize return -1; } double max_z = -DBL_MAX; for (auto w = 0; w < worlds_pts.size();++w) { max_z = std::max(max_z, worlds_pts[w][2]); // max_z = std::max(max_z, (worlds_pts[w][1])); } double adjustment_rate = 1; std::vector<double> lambdas; lambdas.resize(worlds_pts.size() - 2); for (auto w = 0; w < worlds_pts.size();++w) { if (((w - 1) >= 0) && ((w) < (worlds_pts.size() - 1))) { double z_top = worlds_pts[w - 1][2]; double z_bottom = worlds_pts[w + 1][2]; double z_0 = worlds_pts[w][2]; // double z_top = worlds_pts[w - 1][1]; // double z_bottom = worlds_pts[w + 1][1]; // double z_0 = worlds_pts[w][1]; // double delta_z = ((z_top - z_bottom) + (z_0 - z_top) - (z_bottom - z_0)) / max_z; double delta_z = ((z_0 - z_top) - (z_bottom - z_0)) / max_z; // double delta_z = 0; double omega_i = std::min(left_intensities[w], right_intensities[w]); omega_i /= 255.0; // omega_i = 1.0; // double lambda_i = (1.0 - delta_z) * omega_i * adjustment_rate; double lambda_i = 0.99; lambdas[w - 1] = lambda_i; double y_top = worlds_pts[w - 1][1]; double y_bottom = worlds_pts[w + 1][1]; double y_0 = worlds_pts[w][1]; double y = worlds_pts[w][1]; double y_prime = w; } } #ifdef DEBUG for (auto i = 0u; i < lambdas.size(); ++i) { std::cout << std::setprecision(15) << lambdas[i] << std::endl; } #endif // allocate to globals lambdas_g = lambdas; // allocate structures for sparse linear least squares //printf("\tallocating for sparse linear least squares " //"(%i vectors)...\n", fromVector.size()); int num_rows = worlds_pts.size() - 2; int num_cols = worlds_pts.size(); lsqr_input *input = NULL; lsqr_output *output = NULL; lsqr_work *work = NULL; lsqr_func *func = NULL; alloc_lsqr_mem(&input, &output, &work, &func, num_rows, num_cols); input->num_rows = num_rows; input->num_cols = num_cols; input->damp_val = 0.0; input->rel_mat_err = 0.0; input->rel_rhs_err = 0.0; input->cond_lim = 0.0; input->max_iter = 10*input->num_cols; input->lsqr_fp_out = NULL; func->mat_vec_prod = lsqr_eval_for_opt; // set rhs vec for (auto j = 0; j < num_rows; ++j) { // input->rhs_vec->elements[j] = (1.0 - lambdas[j]) * worlds_pts[j+1][1]; input->rhs_vec->elements[j] = (1.0 - lambdas[j]) * worlds_pts[j+1][2]; } // set initial sol vec for (auto i = 0u; i<num_cols; i++) { // input->sol_vec->elements[i] = worlds_pts[i][1]; input->sol_vec->elements[i] = 0; } // call sparse linear least squares! printf("\t\tstarting (rows=%i, cols=%i)...\n", num_rows, num_cols); lsqr(input, output, work, func, NULL); double error = output->resid_norm; printf("\t\ttermination reason = %i\n", output->term_flag); printf("\t\tnum function calls = %i\n", output->num_iters); printf("\t\tremaining error = %lf\n", error); if (worlds_pts.size() > 0) { // double y_prev = worlds_pts[0][1]; double y_prev = worlds_pts[0][2]; for (auto i = 1u; i < worlds_pts.size() - 1; ++i) { // auto& y = worlds_pts[i][1]; auto& y = worlds_pts[i][2]; y = output->sol_vec->elements[i]; double y_diff = y - y_prev; std::cout << "y difference " << i << " : "<< y_diff << std::endl; y_prev = y; } auto i = worlds_pts.size() - 1; // auto& y = worlds_pts[i][1]; auto& y = worlds_pts[i][2]; double y_diff = y - y_prev; std::cout << "y difference " << i << " : "<< y_diff << std::endl; } // free memory free_lsqr_mem(input, output, work, func); return (error); }
int main(int argc, char *argv[]) { struct sparse_matrix_t *sparseA = NULL; struct vector_t *b = NULL; struct vector_t *x; struct mesh_t *mesh; char *xml_output; long int *compress2fat = NULL; struct vector_t *solution; struct vector_t *std_error_sol; long int fat_sol_nb_col; lsqr_input *input; lsqr_output *output; lsqr_work *work; /* zone temoraire de travail */ lsqr_func *func; /* func->mat_vec_prod -> APROD */ /* cmd line arg */ char *mesh_filename = NULL; char *importfilename = NULL; char *output_filename = NULL; char *sol_error_filename = NULL; char *log_filename = NULL; char *output_type = NULL; int max_iter; double damping, grad_damping; int use_ach = 0; /* ACH : tele-seismic inversion tomography */ int check_sparse = 0; /* check sparse matrix disable by default */ /* velocity model */ char *vmodel = NULL; struct velocity_model_t *vm = NULL; struct mesh_t **imported_mesh = NULL; char **xmlfilelist = NULL; int nb_xmlfile = 0; int i, j; int nb_irm = 0; struct irm_t **irm = NULL; int *nb_metacell = NULL; FILE *logfd; /*************************************************************/ parse_command_line(argc, argv, &mesh_filename, &vmodel, &importfilename, &log_filename, &output_filename, &output_type, &max_iter, &damping, &grad_damping, &use_ach, &check_sparse); if (use_ach) { fprintf(stderr, "Using ACH tomographic inversion\n"); } else { fprintf(stderr, "Using STANDARD tomographic inversion\n"); } /* load the velocity model */ if (vmodel) { char *myfile; vm = load_velocity_model(vmodel); if (!vm) { fprintf(stderr, "Can not initialize velocity model '%s'\n", vmodel); exit(1); } myfile = strdup(vmodel); fprintf(stderr, "Velocity model '%s' loaded\n", basename(myfile)); free(myfile); } else { vm = NULL; } /* Open log file */ if (!log_filename) { logfd = stdout; } else { if (!(logfd = fopen(log_filename, "w"))) { perror(log_filename); exit(1); } } /*check_write_access (output_filename); */ /**************************************/ /* test if we can open file to import */ /**************************************/ if (importfilename) { xmlfilelist = parse_separated_list(importfilename, ","); nb_xmlfile = 0; while (xmlfilelist[nb_xmlfile]) { if (access(xmlfilelist[nb_xmlfile], R_OK) == -1) { perror(xmlfilelist[nb_xmlfile]); exit(1); } nb_xmlfile++; } } else { fprintf(stderr, "No file to import ... exiting\n"); exit(0); } /****************************/ /* main mesh initialization */ /****************************/ mesh = mesh_init_from_file(mesh_filename); if (!mesh) { fprintf(stderr, "Error decoding %s.\n", mesh_filename); exit(1); } fprintf(stderr, "read %s ok\n", mesh_filename); /*****************************************/ /* check and initialize slice xml files */ /*****************************************/ if (nb_xmlfile) { int nb_sparse = 0; int nb_res = 0; int f; imported_mesh = (struct mesh_t **) malloc(sizeof(struct mesh_t *) * nb_xmlfile); assert(imported_mesh); for (i = 0; i < nb_xmlfile; i++) { imported_mesh[i] = mesh_init_from_file(xmlfilelist[i]); if (!imported_mesh[i]) { fprintf(stderr, "Error decoding %s.\n", mesh_filename); exit(1); } for (f = 0; f < NB_MESH_FILE_FORMAT; f++) { /* mandatory field : res, sparse, and irm if provided */ if (f == RES || f == SPARSE || f == IRM) { check_files_access(f, imported_mesh[i]->data[f], xmlfilelist[i]); } } if (imported_mesh[i]->data[SPARSE]) { nb_sparse += imported_mesh[i]->data[SPARSE]->ndatafile; } if (imported_mesh[i]->data[RES]) { nb_res += imported_mesh[i]->data[RES]->ndatafile; } if (imported_mesh[i]->data[IRM]) { nb_irm += imported_mesh[i]->data[IRM]->ndatafile; } } if (!nb_sparse || !nb_res) { fprintf(stderr, "Error no sparse or res file available !\n"); exit(0); } } /*********************************************/ /* read and import the sparse(s) matrix(ces) */ /*********************************************/ for (i = 0; i < nb_xmlfile; i++) { if (!imported_mesh[i]->data[SPARSE]) { continue; } for (j = 0; j < imported_mesh[i]->data[SPARSE]->ndatafile; j++) { sparseA = import_sparse_matrix(sparseA, imported_mesh[i]->data[SPARSE]-> filename[j]); } } if (check_sparse) { if (check_sparse_matrix(sparseA)) { exit(1); } } /*sparse_compute_length(sparseA, "length1.txt"); */ fat_sol_nb_col = sparseA->nb_col; show_sparse_stats(sparseA); /*********************************************/ /* read and import the residual time vector */ /*********************************************/ for (i = 0; i < nb_xmlfile; i++) { if (!imported_mesh[i]->data[RES]) { continue; } for (j = 0; j < imported_mesh[i]->data[RES]->ndatafile; j++) { b = import_vector(b, imported_mesh[i]->data[RES]->filename[j]); } } /*************************************************/ /* check compatibility between matrix and vector */ /*************************************************/ if (sparseA->nb_line != b->length) { fprintf(stderr, "Error, check your matrix/vector sizes (%ld/%ld)\n", sparseA->nb_line, b->length); exit(1); } /********************/ /* show memory used */ /********************/ #ifdef __APPLE__ { struct mstats memusage; memusage = mstats(); fprintf(stderr, "Memory used: %.2f MBytes\n", (float) (memusage.bytes_used) / (1024. * 1024)); } #else { struct mallinfo m_info; m_info = mallinfo(); fprintf(stderr, "Memory used: %.2f MBytes\n", (float) (m_info.uordblks + m_info.usmblks) / (1024. * 1024.)); } #endif /**************************************/ /* relative traveltime mode */ /**************************************/ if (use_ach) { int nb_evt_imported = 0; for (i = 0; i < nb_xmlfile; i++) { if (!imported_mesh[i]->data[EVT]) { continue; } for (j = 0; j < imported_mesh[i]->data[EVT]->ndatafile; j++) { relative_tt(sparseA, b, imported_mesh[i]->data[EVT]->filename[j]); nb_evt_imported++; } } if (!nb_evt_imported) { fprintf(stderr, "Error in ACH mode, can not import any .evt file !\n"); exit(1); } } /************************************************/ /* read the irregular mesh definition if needed */ /* one by layer */ /************************************************/ if (nb_irm) { int cpt = 0; struct mesh_offset_t **offset; int l; irm = (struct irm_t **) malloc(nb_irm * sizeof(struct irm_t *)); assert(irm); nb_metacell = (int *) calloc(nb_irm, sizeof(int)); assert(nb_metacell); make_mesh(mesh); for (i = 0; i < nb_xmlfile; i++) { if (!imported_mesh[i]->data[IRM]) { continue; } /* offset between meshes */ offset = compute_mesh_offset(mesh, imported_mesh[i]); for (l = 0; l < mesh->nlayers; l++) { if (!offset[l]) continue; fprintf(stderr, "\t%s, [%s] offset[layer=%d] : lat=%d lon=%d z=%d\n", xmlfilelist[i], MESH_FILE_FORMAT[IRM], l, offset[l]->lat, offset[l]->lon, offset[l]->z); } for (j = 0; j < imported_mesh[i]->data[IRM]->ndatafile; j++) { /* FIXME: read only once the irm file */ irm[cpt] = read_irm(imported_mesh[i]->data[IRM]->filename[j], &(nb_metacell[cpt])); import2mesh_irm_file(mesh, imported_mesh[i]->data[IRM]-> filename[j], offset); cpt++; } for (l = 0; l < mesh->nlayers; l++) { if (offset[l]) free(offset[l]); } free(offset); } metacell_find_neighbourhood(mesh); } /*sparse_compute_length(sparseA, "length1.txt"); */ fat_sol_nb_col = sparseA->nb_col; show_sparse_stats(sparseA); /***********************/ /* remove empty column */ /***********************/ fprintf(stderr, "starting compression ...\n"); sparse_compress_column(mesh, sparseA, &compress2fat); if (check_sparse) { if (check_sparse_matrix(sparseA)) { exit(1); } } show_sparse_stats(sparseA); /***************************************/ /* add gradient damping regularisation */ /***************************************/ if (fabs(grad_damping) > 1.e-6) { int nb_faces = 6; /* 1 cell may have 6 neighbours */ long int nb_lines = 0; char *regul_name; fprintf(stdout, "using gradient damping : %f\n", grad_damping); /* tmp file name */ regul_name = tempnam("/tmp", "regul"); if (!regul_name) { perror("lsqrsolve: "); exit(1); } if (nb_irm) { create_regul_DtD_irm(sparseA, compress2fat, mesh, regul_name, nb_faces, grad_damping, &nb_lines); } else { create_regul_DtD(sparseA, compress2fat, mesh, regul_name, nb_faces, grad_damping, &nb_lines); } sparse_matrix_resize(sparseA, sparseA->nb_line + sparseA->nb_col, sparseA->nb_col); sparseA = import_sparse_matrix(sparseA, regul_name); if (check_sparse) { if (check_sparse_matrix(sparseA)) { exit(1); } } vector_resize(b, sparseA->nb_line); unlink(regul_name); show_sparse_stats(sparseA); } /*********************************/ /* the real mesh is no more used */ /* keep only the light mesh */ /*********************************/ fprintf(stdout, "Time to free the real mesh and keep only the light structure\n"); free_mesh(mesh); mesh = mesh_init_from_file(mesh_filename); if (!mesh) { fprintf(stderr, "Error decoding %s.\n", mesh_filename); exit(1); } fprintf(stderr, "read %s ok\n", mesh_filename); /********************************/ /* init vector solution to zero */ /********************************/ x = new_vector(sparseA->nb_col); /*************************************************************/ /* solve A.x = B */ /* A = ray length in the cells */ /* B = residual travel time observed - computed */ /* x solution to satisfy the lsqr problem */ /*************************************************************/ /* LSQR alloc */ alloc_lsqr_mem(&input, &output, &work, &func, sparseA->nb_line, sparseA->nb_col); fprintf(stderr, "alloc_lsqr_mem : ok\n"); /* defines the routine Mat.Vect to use */ func->mat_vec_prod = sparseMATRIXxVECTOR; /* Set the input parameters for LSQR */ input->num_rows = sparseA->nb_line; input->num_cols = sparseA->nb_col; input->rel_mat_err = 1.0e-3; /* in km */ input->rel_rhs_err = 1.0e-2; /* in seconde */ /*input->rel_mat_err = 0.; input->rel_rhs_err = 0.; */ input->cond_lim = .0; input->lsqr_fp_out = logfd; /* input->rhs_vec = (dvec *) b; */ dvec_copy((dvec *) b, input->rhs_vec); input->sol_vec = (dvec *) x; /* initial guess */ input->damp_val = damping; if (max_iter == -1) { input->max_iter = 4 * (sparseA->nb_col); } else { input->max_iter = max_iter; } /* catch Ctrl-C signal */ signal(SIGINT, emergency_halt); /******************************/ /* resolution du systeme Ax=b */ /******************************/ lsqr(input, output, work, func, sparseA); fprintf(stderr, "*** lsqr ended (%ld iter) : %s\n", output->num_iters, lsqr_msg[output->term_flag]); if (output->term_flag == 0) { /* solution x=x0 */ exit(0); } /* uncompress the solution */ solution = uncompress_column((struct vector_t *) output->sol_vec, compress2fat, fat_sol_nb_col); /* uncompress the standard error on solution */ std_error_sol = uncompress_column((struct vector_t *) output->std_err_vec, compress2fat, fat_sol_nb_col); /* if irm file was provided, set the right value to each cell * from a given metacell */ if (irm) { irm_update(solution, irm, nb_metacell, nb_irm, mesh); free_irm(irm, nb_irm); free(nb_metacell); } /* write solution */ if (strchr(output_type, 'm')) { export2matlab(solution, output_filename, mesh, vm, output->num_iters, input->damp_val, grad_damping, use_ach); } if (strchr(output_type, 's')) { export2sco(solution, output_filename, mesh, vm, output->num_iters, input->damp_val, grad_damping, use_ach); } if (strchr(output_type, 'g')) { /* solution */ export2gmt(solution, output_filename, mesh, vm, output->num_iters, input->damp_val, grad_damping, use_ach); /* error on solution */ sol_error_filename = (char *) malloc(sizeof(char) * (strlen(output_filename) + strlen(".err") + 1)); sprintf(sol_error_filename, "%s.err", output_filename); export2gmt(std_error_sol, sol_error_filename, mesh, vm, output->num_iters, input->damp_val, grad_damping, use_ach); free(sol_error_filename); } /* save the xml enrichied with sections */ xml_output = (char *) malloc((strlen(output_filename) + strlen(".xml") + 1) * sizeof(char)); assert(xml_output); sprintf(xml_output, "%s.xml", output_filename); mesh2xml(mesh, xml_output); free(xml_output); /******************************************************/ /* variance reduction, ie how the model fits the data */ /* X = the final solution */ /* */ /* ||b-AX||² */ /* VR= 1 - -------- */ /* ||b||² */ /* */ /******************************************************/ { double norm_b; double norm_b_AX; double VR; /* variance reduction */ struct vector_t *rhs; /* right hand side */ rhs = new_vector(sparseA->nb_line); /* use copy */ dvec_copy((dvec *) b, (dvec *) rhs); norm_b = dvec_norm2((dvec *) rhs); /* does rhs = rhs + sparseA . output->sol_vec */ /* here rhs is overwritten */ dvec_scale((-1.0), (dvec *) rhs); sparseMATRIXxVECTOR(0, output->sol_vec, (dvec *) rhs, sparseA); dvec_scale((-1.0), (dvec *) rhs); norm_b_AX = dvec_norm2((dvec *) rhs); VR = 1 - (norm_b_AX * norm_b_AX) / (norm_b * norm_b); fprintf(stdout, "Variance reduction = %.2f%%\n", VR * 100); free_vector(rhs); } /********/ /* free */ /********/ if (vm) { free_velocity_model(vm); } free_mesh(mesh); free_sparse_matrix(sparseA); free_lsqr_mem(input, output, work, func); free_vector(solution); free_vector(std_error_sol); free(compress2fat); for (i = 0; i < nb_xmlfile; i++) { free(xmlfilelist[i]); free_mesh(imported_mesh[i]); } free(xmlfilelist); free(imported_mesh); return (0); }
double find_optimal_edge_zero_crossing(std::vector<cv::Point2f>& crossing_points) { // copy to globals //assert(fromVector.size() == toVector.size()); //assert(fromVector.size() >= 3); //_fromVector = fromVector; // worlds_pts.resize(3); if (crossing_points.size() < 3) { // too little points to opitimize return -1; } #ifdef DEBUG //for (auto i = 0u; i < lambdas.size(); ++i) { // std::cout << std::setprecision(15) << lambdas[i] << std::endl; //} #endif // allocate to globals crossing_points_g = crossing_points; // allocate structures for sparse linear least squares //printf("\tallocating for sparse linear least squares " //"(%i vectors)...\n", fromVector.size()); int num_rows = crossing_points.size(); int num_cols = 3; lsqr_input *input = NULL; lsqr_output *output = NULL; lsqr_work *work = NULL; lsqr_func *func = NULL; alloc_lsqr_mem(&input, &output, &work, &func, num_rows, num_cols); input->num_rows = num_rows; input->num_cols = num_cols; input->damp_val = 0.0; input->rel_mat_err = 0.0; input->rel_rhs_err = 0.0; input->cond_lim = 0.0; input->max_iter = 10*input->num_cols; input->lsqr_fp_out = NULL; func->mat_vec_prod = lsqr_eval_for_opt_; // set rhs vec for (auto j = 0; j < num_rows; ++j) { // input->rhs_vec->elements[j] = (1.0 - lambdas[j]) * worlds_pts[j+1][1]; input->rhs_vec->elements[j] = crossing_points[j].y; } // set initial sol vec for (auto i = 0u; i<num_cols; i++) { // input->sol_vec->elements[i] = worlds_pts[i][1]; input->sol_vec->elements[i] = 0; } // call sparse linear least squares! //printf("\t\tstarting (rows=%i, cols=%i)...\n", num_rows, num_cols); lsqr(input, output, work, func, NULL); double error = output->resid_norm; //printf("\t\ttermination reason = %i\n", output->term_flag); //printf("\t\tnum function calls = %i\n", output->num_iters); //printf("\t\tremaining error = %lf\n", error); double a = input->sol_vec->elements[0]; double b = input->sol_vec->elements[1]; double c = input->sol_vec->elements[2]; // solving for y = 0 double solution = 0.0; double discriminant = std::pow(b, 2) - (4 * a * c); if (discriminant < 0) { // something went wrong solution = -1; } else { double delta = std::sqrt(discriminant); double sol_1 = ((-1 * b) + delta) / (2 * a); double sol_2 = ((-1 * b) - delta) / (2 * a); if (sol_1 <= crossing_points[crossing_points.size() - 1].x && sol_1 >= crossing_points[0].x) { solution = sol_1; } else if (sol_2 <= crossing_points[crossing_points.size() - 1].x && sol_2 >= crossing_points[0].x) { solution = sol_2; } else { // something wrong happened solution = -1; } } // free memory free_lsqr_mem(input, output, work, func); return (solution); }