Implement HDF5 I/O of transition matrix for SPHERE (1640c3c5) · Commits · Giacomo Mulas / NP_TMcode

src/include/TransitionMatrix.h

+42 −2

Original line number	Diff line number	Diff line
		@@ -47,6 +47,22 @@ class TransitionMatrix {
		//! Matrix shape
		int *shape;

		/*! \brief Build transition matrix from a HDF5 binary input file.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		* \return config: `TransitionMatrix *` Pointer to object containing the
		* transition matrix data.
		*/
		static TransitionMatrix *from_hdf5(std::string file_name);

		/*! \brief Build transition matrix from a legacy binary input file.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		* \return config: `TransitionMatrix *` Pointer to object containing the
		* transition matrix data.
		*/
		static TransitionMatrix *from_legacy(std::string file_name);

		/*! \brief Write the Transition Matrix to HDF5 binary output.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		@@ -59,6 +75,20 @@ class TransitionMatrix {
		*/
		void write_legacy(std::string file_name);
		public:
		/*! \brief Default Transition Matrix instance constructor.
		*
		* \param _is: `int` Matrix type identifier
		* \param _lm: `int` Maximum field expansion order.
		* \param _vk: `double`
		* \param _exri: `double`
		* \param _elements: `complex<double> *` Vectorized elements of the matrix.
		* \param _radius: `double` Radius for the single sphere case (defaults to 0.0).
		*/
		TransitionMatrix(
		int _is, int _lm, double _vk, double _exri, std::complex<double> *_elements,
		double _radius=0.0
		);

		/*! \brief Transition Matrix instance constructor for single sphere.
		*
		* \param _lm: `int` Maximum field expansion order.
		@@ -81,12 +111,22 @@ class TransitionMatrix {
		* \param _exri: `double`
		* \param _am0m: Matrix of complex.
		*/
		TransitionMatrix(int _nlemt, int _lm, double _vk, double _exri, std::complex<double> **am0m);
		TransitionMatrix(int _nlemt, int _lm, double _vk, double _exri, std::complex<double> **_am0m);

		/*! \brief Transition Matrix instance destroyer.
		*/
		~TransitionMatrix();

		/*! \brief Build transition matrix from binary input file.
		*
		* \param file_name: `string` Name of the binary configuration data file.
		* \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"]. Optional
		* (default is "LEGACY").
		* \return config: `TransitionMatrix *` Pointer to object containing the transition
		* matrix data.
		*/
		static TransitionMatrix* from_binary(std::string file_name, std::string mode="LEGACY");

		/*! \brief Write the Transition Matrix to a binary file.
		*
		* \param file_name: `string` Name of the file to be written.

src/include/file_io.h

+17 −0

Original line number	Diff line number	Diff line
		@@ -120,6 +120,23 @@ class HDFFile {
		*/
		bool is_open() { return file_open_flag; }

		/*! \brief Read data from attached file.
		*
		* \param dataset_name: `string` Name of the dataset to read from.
		* \param data_type: `string` Memory data type identifier.
		* \param buffer: `hid_t` Starting address of the memory sector to store the data.
		* \param mem_space_id: `hid_t` Memory data space identifier (defaults to `H5S_ALL`).
		* \param file_space_id: `hid_t` File space identifier (defaults to `H5S_ALL`).
		* \param dapl_id: `hid_t` Data access property list identifier (defaults to `H5P_DEFAULT`).
		* \param dxpl_id: `hid_t` Data transfer property list identifier (defaults to `H5P_DEFAULT`).
		* \return status: `herr_t` Exit status of the operation.
		*/
		herr_t read(
		std::string dataset_name, std::string data_type, void *buffer,
		hid_t mem_space_id=H5S_ALL, hid_t file_space_id=H5S_ALL,
		hid_t dapl_id=H5P_DEFAULT, hid_t dxpl_id=H5P_DEFAULT
		);

		/*! \brief Write data to attached file.
		*
		* \param dataset_name: `string` Name of the dataset to write to.

src/libnptm/TransitionMatrix.cpp

+201 −4

Original line number	Diff line number	Diff line
		@@ -5,11 +5,20 @@
		#include <complex>
		#include <exception>
		#include <fstream>
		#include <hdf5.h>

		#ifndef INCLUDE_LIST_H_
		#include "../include/List.h"
		#endif

		#ifndef INCLUDE_TRANSITIONMATRIX_H_
		#include "../include/TransitionMatrix.h"
		#endif

		#ifndef INCLUDE_FILE_IO_H_
		#include "../include/file_io.h"
		#endif

		using namespace std;

		TransitionMatrix::~TransitionMatrix() {
		@@ -17,6 +26,27 @@ TransitionMatrix::~TransitionMatrix() {
		if (shape != NULL) delete[] shape;
		}

		TransitionMatrix::TransitionMatrix(
		int _is, int _lm, double _vk, double _exri, std::complex<double> *_elements,
		double _radius
		) {
		is = _is;
		l_max = _lm;
		vk = _vk;
		exri = _exri;
		elements = _elements;
		sphere_radius = _radius;
		shape = new int[2]();
		if (is == 1111) {
		shape[0] = l_max;
		shape[1] = 2;
		} else if (is == 1) {
		const int nlemt = 2 * l_max * (l_max + 2);
		shape[0] = nlemt;
		shape[1] = nlemt;
		}
		}

		TransitionMatrix::TransitionMatrix(
		int _lm, double _vk, double _exri, complex<double> **_rmi,
		complex<double> **_rei, double _sphere_radius
		@@ -38,7 +68,7 @@ TransitionMatrix::TransitionMatrix(

		TransitionMatrix::TransitionMatrix(
		int _nlemt, int _lm, double _vk, double _exri,
		std::complex<double> **am0m
		std::complex<double> **_am0m
		) {
		is = 1;
		shape = new int[2];
		@@ -50,8 +80,122 @@ TransitionMatrix::TransitionMatrix(
		sphere_radius = 0.0;
		elements = new complex<double>[_nlemt * _nlemt]();
		for (int ei = 0; ei < _nlemt; ei++) {
		for (int ej = 0; ej < _nlemt; ej++) elements[_nlemt * ei + ej] = am0m[ei][ej];
		for (int ej = 0; ej < _nlemt; ej++) elements[_nlemt * ei + ej] = _am0m[ei][ej];
		}
		}

		TransitionMatrix* TransitionMatrix::from_binary(string file_name, string mode) {
		TransitionMatrix *tm = NULL;
		if (mode.compare("LEGACY") == 0) {
		tm = TransitionMatrix::from_legacy(file_name);
		} else if (mode.compare("HDF5") == 0) {
		tm = TransitionMatrix::from_hdf5(file_name);
		} else {
		string message = "Unknown format mode: \"" + mode + "\"";
		throw UnrecognizedFormatException(message);
		}
		return tm;
		}

		TransitionMatrix* TransitionMatrix::from_hdf5(string file_name) {
		TransitionMatrix *tm = NULL;
		unsigned int flags = H5F_ACC_RDONLY;
		HDFFile *hdf_file = new HDFFile(file_name, flags);
		herr_t status = hdf_file->get_status();
		if (status == 0) {
		int _is;
		int _lm;
		double _vk;
		double _exri;
		// This vector will be passed to the new object. DO NOT DELETE HERE!
		complex<double> *_elements;
		double _radius = 0.0;
		status = hdf_file->read("/IS", "INT32", &_is);
		status = hdf_file->read("/L_MAX", "INT32", &_lm);
		status = hdf_file->read("/VK", "FLOAT64", &_vk);
		status = hdf_file->read("/EXRI", "FLOAT64", &_exri);
		if (_is == 1111) {
		int num_elements = 2 * _lm;
		double file_vector = new double[2 num_elements]();
		hid_t file_id = hdf_file->get_file_id();
		hid_t dset_id = H5Dopen2(file_id, "/ELEMENTS", H5P_DEFAULT);
		status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, file_vector);
		_elements = new complex<double>[num_elements]();
		for (int ei = 0; ei < num_elements; ei++) {
		_elements[ei] = complex<double>(file_vector[2 * ei], file_vector[2 * ei + 1]);
		}
		status = H5Dclose(dset_id);
		status = hdf_file->read("/RADIUS", "FLOAT64", &_radius);
		tm = new TransitionMatrix(_is, _lm, _vk, _exri, _elements, _radius);
		delete[] file_vector;
		} else if (_is == 1) {
		int nlemt = 2 * _lm * (_lm + 2);
		int num_elements = nlemt * nlemt;
		double file_vector = new double[2 num_elements]();
		hid_t file_id = hdf_file->get_file_id();
		hid_t dset_id = H5Dopen2(file_id, "/ELEMENTS", H5P_DEFAULT);
		status = H5Dread(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, file_vector);
		_elements = new complex<double>[num_elements]();
		for (int ei = 0; ei < num_elements; ei++) {
		_elements[ei] = complex<double>(file_vector[2 * ei], file_vector[2 * ei + 1]);
		}
		status = H5Dclose(dset_id);
		status = hdf_file->read("/RADIUS", "FLOAT64", &_radius);
		tm = new TransitionMatrix(_is, _lm, _vk, _exri, _elements, _radius);
		delete[] file_vector;
		}
		status = hdf_file->close();
		} else {
		printf("ERROR: could not open file \"%s\"\n", file_name.c_str());
		}
		return tm;
		}

		TransitionMatrix* TransitionMatrix::from_legacy(string file_name) {
		fstream ttms;
		TransitionMatrix *tm = NULL;
		ttms.open(file_name, ios::binary \| ios::in);
		if (ttms.is_open()) {
		int num_elements = 0;
		int _is;
		int _lm;
		double _vk;
		double _exri;
		// This vector will be passed to the new object. DO NOT DELETE HERE!
		complex<double> *_elements;
		double _radius = 0.0;
		ttms.read(reinterpret_cast<char *>(&_is), sizeof(int));
		ttms.read(reinterpret_cast<char *>(&_lm), sizeof(int));
		ttms.read(reinterpret_cast<char *>(&_vk), sizeof(double));
		ttms.read(reinterpret_cast<char *>(&_exri), sizeof(double));
		if (_is == 1111) {
		num_elements = _lm * 2;
		_elements = new complex<double>[num_elements]();
		for (int ei = 0; ei < num_elements; ei++) {
		double vreal, vimag;
		ttms.read(reinterpret_cast<char *>(&vreal), sizeof(double));
		ttms.read(reinterpret_cast<char *>(&vimag), sizeof(double));
		_elements[ei] = complex<double>(vreal, vimag);
		}
		double _radius;
		ttms.read(reinterpret_cast<char *>(&_radius), sizeof(double));
		tm = new TransitionMatrix(_is, _lm, _vk, _exri, _elements, _radius);
		} else if (_is == 1) {
		int nlemt = 2 * _lm * (_lm + 2);
		num_elements = nlemt * nlemt;
		_elements = new complex<double>[num_elements]();
		for (int ei = 0; ei < num_elements; ei++) {
		double vreal, vimag;
		ttms.read(reinterpret_cast<char *>(&vreal), sizeof(double));
		ttms.read(reinterpret_cast<char *>(&vimag), sizeof(double));
		_elements[ei] = complex<double>(vreal, vimag);
		}
		tm = new TransitionMatrix(_is, _lm, _vk, _exri, _elements);
		}
		} else {
		printf("ERROR: could not open file \"%s\"\n", file_name.c_str());
		}
		return tm;
		}

		void TransitionMatrix::write_binary(string file_name, string mode) {
		@@ -66,8 +210,61 @@ void TransitionMatrix::write_binary(string file_name, string mode) {
		}

		void TransitionMatrix::write_hdf5(string file_name) {
		// TODO: needs implementation.
		return;
		if (is == 1 \|\| is == 1111) {
		List<string> rec_name_list(1);
		List<string> rec_type_list(1);
		List<void *> rec_ptr_list(1);
		string str_type, str_name;
		rec_name_list.set(0, "/IS");
		rec_type_list.set(0, "INT32_(1)");
		rec_ptr_list.set(0, &is);
		rec_name_list.append("/L_MAX");
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&l_max);
		rec_name_list.append("/VK");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&vk);
		rec_name_list.append("/EXRI");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&exri);
		rec_name_list.append("/ELEMENTS");
		str_type = "FLOAT64_(" + to_string(shape[0]) + "," + to_string(2 * shape[1]) + ")";
		rec_type_list.append(str_type);
		// The (N x M) matrix of complex is converted to a (N x 2M) matrix of double,
		// where REAL(E_i,j) -> E_i,(2 j) and IMAG(E_i,j) -> E_i,(2 j + 1)
		double ptr_elements = new double[shape[0] 2 * shape[1]]();
		for (int ei = 0; ei < shape[0]; ei++) {
		for (int ej = 0; ej < shape[1]; ej++) {
		ptr_elements[ei * (2 * ej)] = elements[shape[1] * ei + ej].real();
		ptr_elements[ei * (2 * ej) + 1] = elements[shape[1] * ei + ej].imag();
		}
		}
		rec_ptr_list.append(ptr_elements);
		if (is == 1111) {
		rec_name_list.append("/RADIUS");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&sphere_radius);
		}

		string *rec_names = rec_name_list.to_array();
		string *rec_types = rec_type_list.to_array();
		void **rec_pointers = rec_ptr_list.to_array();
		const int rec_num = rec_name_list.length();
		FileSchema schema(rec_num, rec_types, rec_names);
		HDFFile *hdf_file = HDFFile::from_schema(schema, file_name, H5F_ACC_TRUNC);
		for (int ri = 0; ri < rec_num; ri++)
		hdf_file->write(rec_names[ri], rec_types[ri], rec_pointers[ri]);
		hdf_file->close();

		delete[] ptr_elements;
		delete[] rec_names;
		delete[] rec_types;
		delete[] rec_pointers;
		delete hdf_file;
		} else {
		string message = "Unrecognized matrix data.";
		throw UnrecognizedFormatException(message);
		}
		}

		void TransitionMatrix::write_legacy(string file_name) {

src/libnptm/file_io.cpp

+43 −1

Original line number	Diff line number	Diff line
		@@ -47,7 +47,10 @@ string* FileSchema::get_record_types() {

		HDFFile::HDFFile(string name, unsigned int flags, hid_t fcpl_id, hid_t fapl_id) {
		file_name = name;
		if (flags == H5F_ACC_EXCL \|\| flags == H5F_ACC_TRUNC)
		file_id = H5Fcreate(name.c_str(), flags, fcpl_id, fapl_id);
		else if (flags == H5F_ACC_RDONLY \|\| flags == H5F_ACC_RDWR)
		file_id = H5Fopen(name.c_str(), flags, fapl_id);
		id_list = new List<hid_t>(1);
		id_list->set(0, file_id);
		if (file_id != H5I_INVALID_HID) file_open_flag = true;
		@@ -132,6 +135,45 @@ HDFFile* HDFFile::from_schema(
		return hdf_file;
		}

		herr_t HDFFile::read(
		string dataset_name, string data_type, void *buffer,
		hid_t mem_space_id, hid_t file_space_id, hid_t dapl_id,
		hid_t dxpl_id
		) {
		string known_types[] = {"INT32", "FLOAT64"};
		regex re;
		smatch m;
		bool found_type = false;
		int type_index = 0;
		while (!found_type) {
		re = regex(known_types[type_index++]);
		found_type = regex_search(data_type, m, re);
		if (type_index == 2) break;
		}
		if (found_type) {
		hid_t dataset_id = H5Dopen2(file_id, dataset_name.c_str(), dapl_id);
		hid_t mem_type_id;
		switch (type_index) {
		case 1:
		mem_type_id = H5T_NATIVE_INT; break;
		case 2:
		mem_type_id = H5T_NATIVE_DOUBLE; break;
		default:
		throw runtime_error("Unrecognized data type \"" + data_type + "\"");
		}
		if (dataset_id != H5I_INVALID_HID) {
		status = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, dxpl_id, buffer);
		if (status == 0) status = H5Dclose(dataset_id);
		else status = (herr_t)-2;
		} else {
		status = (herr_t)-1;
		}
		} else {
		throw runtime_error("Unrecognized data type \"" + data_type + "\"");
		}
		return status;
		}

		herr_t HDFFile::write(
		string dataset_name, string data_type, const void *buffer,
		hid_t mem_space_id, hid_t file_space_id, hid_t dapl_id,

src/sphere/sphere.cpp

+4 −2

Original line number	Diff line number	Diff line
		@@ -292,8 +292,10 @@ void sphere(string config_file, string data_file, string output_path) {
		if (sconf->idfc >= 0 and nsph == 1 and jxi == gconf->jwtm) {
		// This is the condition that writes the transition matrix to output.
		TransitionMatrix ttms(gconf->l_max, vk, exri, c1->rmi, c1->rei, sconf->radii_of_spheres[0]);
		string ttms_name = output_path + "/c_TTMS";
		ttms.write_binary(ttms_name, "LEGACY");
		string ttms_name = output_path + "/c_TTMS.hd5";
		ttms.write_binary(ttms_name, "HDF5");
		ttms_name = output_path + "/c_TTMS";
		ttms.write_binary(ttms_name);
		}
		double cs0 = 0.25 * vk * vk * vk / half_pi;
		//printf("DEBUG: cs0 = %lE\n", cs0);