Implement complete configuration I/O to HDF5 (a263301a) · Commits · Giacomo Mulas / NP_TMcode

src/libnptm/Configuration.cpp

+67 −24

Original line number	Diff line number	Diff line
		@@ -538,6 +538,7 @@ ScattererConfiguration* ScattererConfiguration::from_hdf5(string file_name) {
		unsigned int flags = H5F_ACC_RDONLY;
		HDFFile *hdf_file = new HDFFile(file_name, flags);
		herr_t status = hdf_file->get_status();
		string str_name, str_type;
		if (status == 0) {
		int nsph;
		int *iog;
		@@ -562,10 +563,47 @@ ScattererConfiguration* ScattererConfiguration::from_hdf5(string file_name) {
		if (iog[ci] < ci + 1) continue;
		configuration_count++;
		}
		nshl_vector = new int[configuration_count];
		ros_vector = new double[configuration_count];
		// DA QUI
		nshl_vector = new int[configuration_count]();
		ros_vector = new double[configuration_count]();
		rcf_vector = new double*[configuration_count];
		for (int i115 = 1; i115 <= nsph; i115++) {
		if (iog[i115 - 1] < i115) continue;
		str_name = "NSHL_" + to_string(iog[i115 - 1]);
		str_type = "INT32_(1)";
		status = hdf_file->read(str_name, str_type, (nshl_vector + i115 - 1));
		str_name = "ROS_" + to_string(iog[i115 - 1]);
		str_type = "FLOAT64_(1)";
		status = hdf_file->read(str_name, str_type, (ros_vector + i115 - 1));
		int nsh = nshl_vector[i115 - 1];
		rcf_vector[i115 - 1] = new double[nsh]();
		str_name = "RCF_" + to_string(iog[i115 - 1]);
		str_type = "FLOAT64_(" + to_string(nsh) + ")";
		status = hdf_file->read(str_name, str_type, (rcf_vector[i115 - 1]));
		}
		xi_vec = new double[nxi];
		str_name = "XIVEC";
		str_type = "FLOAT64_(" + to_string(nxi) + ")";
		status = hdf_file->read(str_name, str_type, xi_vec);

		int dim3 = (_idfc == 0) ? nxi : 1;
		int element_size = 2 * dim3 * nsph * configuration_count;
		double *elements = new double[element_size]();
		str_name = "DC0M";
		str_type = "FLOAT64_(" + to_string(element_size) + ")";
		status = hdf_file->read(str_name, str_type, elements);
		dc0m = new complex<double>**[configuration_count];
		for (int di = 0; di < configuration_count; di++) {
		dc0m[di] = new complex<double>*[nsph];
		for (int dj = 0; dj < nsph; dj++) {
		dc0m[di][dj] = new complex<double>[dim3]();
		for (int dk = 0; dk < dim3; dk++) {
		double rval = elements[(di * nsph) + (dj * dim3) + 2 * dk];
		double ival = elements[(di * nsph) + (dj * dim3) + 2 * dk + 1];
		dc0m[di][dj][dk] = complex<double>(rval, ival);
		}
		} // dj loop
		} // di loop
		delete[] elements;
		status = hdf_file->close();
		conf = new ScattererConfiguration(
		nsph,
		@@ -608,6 +646,11 @@ ScattererConfiguration* ScattererConfiguration::from_legacy(string file_name) {
		for (int i = 0; i < nsph; i++) {
		input.read(reinterpret_cast<char *>(&(iog[i])), sizeof(int));
		}
		int configuration_count = 0;
		for (int i115 = 1; i115 <= nsph; i115++) {
		if (iog[i115 - 1] < i115) continue;
		configuration_count++;
		}
		input.read(reinterpret_cast<char *>(&_exdc), sizeof(double));
		input.read(reinterpret_cast<char *>(&_wp), sizeof(double));
		input.read(reinterpret_cast<char *>(&_xip), sizeof(double));
		@@ -621,25 +664,25 @@ ScattererConfiguration* ScattererConfiguration::from_legacy(string file_name) {
		for (int i = 0; i < nxi; i++) {
		input.read(reinterpret_cast<char *>(&(xi_vec[i])), sizeof(double));
		}
		nshl_vector = new int[nsph]();
		ros_vector = new double[nsph]();
		rcf_vector = new double*[nsph];
		nshl_vector = new int[configuration_count]();
		ros_vector = new double[configuration_count]();
		rcf_vector = new double*[configuration_count];
		for (int i115 = 1; i115 <= nsph; i115++) {
		if (iog[i115 - 1] < i115) {
		rcf_vector[i115 - 1] = new double[1]();
		continue;
		}
		input.read(reinterpret_cast<char *>(&(nshl_vector[i115 - 1])), sizeof(int));
		input.read(reinterpret_cast<char *>(&(ros_vector[i115 - 1])), sizeof(double));
		int nsh = nshl_vector[i115 - 1];
		input.read(reinterpret_cast<char *>(&(nshl_vector[i115 - 1])), sizeof(int)); // was not from IOG
		input.read(reinterpret_cast<char *>(&(ros_vector[i115 - 1])), sizeof(double)); // was not from IOG
		int nsh = nshl_vector[i115 - 1]; // was not from IOG
		if (max_ici < (nsh + 1) / 2) max_ici = (nsh + 1) / 2;
		try {
		rcf_vector[i115 - 1] = new double[nsh]();
		rcf_vector[i115 - 1] = new double[nsh](); // was not from IOG
		} catch (const bad_alloc &ex) {
		throw UnrecognizedConfigurationException("Wrong parameter set: invalid number of layers " + to_string(nsh));
		}
		for (int nsi = 0; nsi < nsh; nsi++) {
		input.read(reinterpret_cast<char *>(&(rcf_vector[i115 - 1][nsi])), sizeof(double));
		input.read(reinterpret_cast<char *>(&(rcf_vector[i115 - 1][nsi])), sizeof(double)); // was not from IOG
		}
		}
		dc0m = new complex<double>**[max_ici];
		@@ -654,7 +697,7 @@ ScattererConfiguration* ScattererConfiguration::from_legacy(string file_name) {
		if (_idfc != 0 && jxi468 > 1) continue;
		for (int i162 = 1; i162 <= nsph; i162++) {
		if (iog[i162 - 1] < i162) continue;
		int nsh = nshl_vector[i162 - 1];
		int nsh = nshl_vector[iog[i162 - 1] - 1]; // was not from IOG
		int ici = (nsh + 1) / 2; // QUESTION: is integer division really intended here?
		for (int i157 = 0; i157 < ici; i157++) {
		double dc0_real, dc0_img;
		@@ -787,19 +830,19 @@ void ScattererConfiguration::write_hdf5(string file_name) {
		str_name = "NSHL_" + to_string(i115);
		rec_name_list.append(str_name);
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&(nshl_vec[i115 - 1]));
		rec_ptr_list.append(&(nshl_vec[i115 - 1])); // was not from IOG
		str_name = "ROS_" + to_string(i115);
		rec_name_list.append(str_name);
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&(radii_of_spheres[i115 - 1]));
		int nsh = nshl_vec[i115 - 1];
		rec_ptr_list.append(&(radii_of_spheres[i115 - 1])); // was not from IOG
		int nsh = nshl_vec[i115 - 1]; // was not from IOG
		if (i115 == 1) nsh += ies;
		if (max_ici < (nsh + 1) / 2) max_ici = nsh + 1 / 2;
		str_name = "RCF_" + to_string(i115);
		str_name = "RCF_" + to_string(i115); // was not from IOG
		str_type = "FLOAT64_(" + to_string(nsh) + ")";
		rec_name_list.append(str_name);
		rec_type_list.append(str_type);
		rec_ptr_list.append(&(rcf[i115 - 1][0]));
		rec_ptr_list.append(&(rcf[i115 - 1][0])); // was not from IOG
		}

		int dim3 = (idfc == 0) ? number_of_scales : 1;
		@@ -810,7 +853,7 @@ void ScattererConfiguration::write_hdf5(string file_name) {
		if (idfc != 0 && jxi468 > 1) continue;
		for (int i162 = 1; i162 <= number_of_spheres; i162++) {
		if (iog_vec[i162 - 1] < i162) continue;
		int nsh = nshl_vec[i162 - 1];
		int nsh = nshl_vec[i162 - 1]; // was not from IOG
		int ici = (nsh + 1) / 2;
		if (i162 == 1) ici = ici + ies;
		for (int i157 = 0; i157 < ici; i157++) {
		@@ -863,18 +906,18 @@ void ScattererConfiguration::write_legacy(string file_name) {
		output.write(reinterpret_cast<char *>(&(scale_vec[i])), sizeof(double));
		for (int i115 = 1; i115 <= number_of_spheres; i115++) {
		if (iog_vec[i115 - 1] < i115) continue;
		output.write(reinterpret_cast<char *>(&(nshl_vec[i115 - 1])), sizeof(int));
		output.write(reinterpret_cast<char *>(&(radii_of_spheres[i115 - 1])), sizeof(double));
		int nsh = nshl_vec[i115 - 1];
		output.write(reinterpret_cast<char *>(&(nshl_vec[i115 - 1])), sizeof(int)); // was not from IOG
		output.write(reinterpret_cast<char *>(&(radii_of_spheres[i115 - 1])), sizeof(double)); // was not from IOG
		int nsh = nshl_vec[i115 - 1]; // was not from IOG
		if (i115 == 1) nsh += ies;
		for (int nsi = 0; nsi < nsh; nsi++)
		output.write(reinterpret_cast<char *>(&(rcf[i115 - 1][nsi])), sizeof(double));
		output.write(reinterpret_cast<char *>(&(rcf[i115 - 1][nsi])), sizeof(double)); // was not from IOG
		}
		for (int jxi468 = 1; jxi468 <= number_of_scales; jxi468++) {
		if (idfc != 0 && jxi468 > 1) continue;
		for (int i162 = 1; i162 <= number_of_spheres; i162++) {
		if (iog_vec[i162 - 1] < i162) continue;
		int nsh = nshl_vec[i162 - 1];
		int nsh = nshl_vec[i162 - 1]; // was not from IOG
		int ici = (nsh + 1) / 2; // QUESTION: is integer division really intended here?
		if (i162 == 1) ici = ici + ies;
		for (int i157 = 0; i157 < ici; i157++) {