Implement trapping configuration binary I/O and add it to library Makefile (ccf13828) · Commits · Giacomo Mulas / NP_TMcode

src/include/tfrfme.h

+123 −9

Original line number	Diff line number	Diff line
		@@ -6,6 +6,50 @@
		#ifndef INCLUDE_TFRFME_H_
		#define INCLUDE_TFRFME_H_

		/**
		* \brief Exception for unrecognized parameters.
		*/
		class MatrixOutOfBoundsException: public std::exception {
		protected:
		//! Description of the problem.
		std::string message;
		public:
		/**
		* \brief Exception instance constructor.
		*
		* \param problem: `string` Description of the problem that occurred.
		*/
		MatrixOutOfBoundsException(std::string problem) { message = problem; }
		/**
		* \brief Exception message.
		*/
		virtual const char* what() const throw() {
		return message.c_str();
		}
		};

		/**
		* \brief Exception for unrecognized parameters.
		*/
		class UnrecognizedParameterException: public std::exception {
		protected:
		//! Description of the problem.
		std::string message;
		public:
		/**
		* \brief Exception instance constructor.
		*
		* \param problem: `string` Description of the problem that occurred.
		*/
		UnrecognizedParameterException(std::string problem) { message = problem; }
		/**
		* \brief Exception message.
		*/
		virtual const char* what() const throw() {
		return message.c_str();
		}
		};

		/*! \brief Class to represent the trapping configuration.
		*/
		class TFRFME {
		@@ -51,28 +95,56 @@ class TFRFME {
		//! Vector of computed z positions
		double *zv;
		//! QUESTION: definition?
		complex<double> **wsum;
		std::complex<double> **wsum;

		/*! \brief Load a configuration instance from a HDF5 binary file.
		*
		* \param file_name: `string` Name of the file to be loaded.
		* \return instance: `TFRFME *` Pointer to a new trapping configuration
		* instance.
		*/
		static TFRFME *from_hdf5(std::string file_name);

		/*! \brief Load a configuration instance from a legacy binary file.
		*
		* \param file_name: `string` Name of the file to be loaded.
		* \return instance: `TFRFME *` Pointer to a new trapping configuration
		* instance.
		*/
		static TFRFME *from_legacy(std::string file_name);

		/*! \brief Save a configuration instance to a HDF5 binary file.
		*
		* \param file_name: `string` Name of the file to be loaded.
		*/
		void write_hdf5(std::string file_name);

		/*! \brief Save a configuration instance to a legacy binary file.
		*
		* \param file_name: `string` Name of the file to be loaded.
		*/
		void write_legacy(std::string file_name);

		public:
		/*! \briesf Trapping configuration instance constructor.
		/*! \brief Trapping configuration instance constructor.
		*/
		TFRFME(
		int _lmode, int _lm, int _nkv, int _nxv, int _nyv, int _nzv
		);

		/*! \briesf Trapping configuration instance destroyer.
		/*! \brief Trapping configuration instance destroyer.
		*/
		~TFRFME();

		/*! \briesf Load a trapping configuration instance from binary file.
		/*! \brief Load a trapping configuration instance from binary file.
		*
		* \param file_name: `string` Name of the file.
		* \param format: `string` Format of the file (can be either "HDF5"
		* \param mode: `string` Format of the file (can be either "HDF5"
		* or "LGEACY". Default is "LEGACY").
		* \return instance: `TFRFME *` Pointer to anewly created configuration
		* instance.
		*/
		TFRFME* from_binary(std::string file_name, std::string format="LEGACY");
		static TFRFME* from_binary(std::string file_name, std::string mode="LEGACY");

		/*! \brief Get an element from the WSUM matrix.
		*
		@@ -89,6 +161,27 @@ class TFRFME {
		*/
		double get_param(std::string param_name);

		/*! \brief Get the X coordinate of the computed point at given index.
		*
		* \param index: `int` Index of the requested point.
		* \return x: `double` X coordinate of the requested point.
		*/
		double get_x(int index) { return xv[index]; }

		/*! \brief Get the Y coordinate of the computed point at given index.
		*
		* \param index: `int` Index of the requested point.
		* \return y: `double` Y coordinate of the requested point.
		*/
		double get_y(int index) { return yv[index]; }

		/*! \brief Get the Z coordinate of the computed point at given index.
		*
		* \param index: `int` Index of the requested point.
		* \return z: `double` Z coordinate of the requested point.
		*/
		double get_z(int index) { return zv[index]; }

		/*! \brief Set an element in the WSUM matrix.
		*
		* \param row: `int` Row index of the element to be read.
		@@ -104,12 +197,33 @@ class TFRFME {
		*/
		void set_param(std::string param_name, double value);

		/*! \briesf Write a trapping configuration instance to binary file.
		/*! \brief Set the X coordinate of the computed point at given index.
		*
		* \param index: `int` Index of the requested point.
		* \param value: `double` X coordinate of the requested point.
		*/
		void set_x(int index, double value) { xv[index] = value; }

		/*! \brief Set the Y coordinate of the computed point at given index.
		*
		* \param index: `int` Index of the requested point.
		* \param value: `double` Y coordinate of the requested point.
		*/
		void set_y(int index, double value) { yv[index] = value; }

		/*! \brief Set the Z coordinate of the computed point at given index.
		*
		* \param index: `int` Index of the requested point.
		* \param value: `double` Z coordinate of the requested point.
		*/
		void set_z(int index, double value) { zv[index] = value; }

		/*! \brief Write a trapping configuration instance to binary file.
		*
		* \param file_name: `string` Name of the file.
		* \param format: `string` Format of the file (can be either "HDF5"
		* \param mode: `string` Format of the file (can be either "HDF5"
		* or "LGEACY". Default is "LEGACY").
		*/
		void write_binary(std::string file_name, std::string format="LEGACY");
		void write_binary(std::string file_name, std::string mode="LEGACY");
		};
		#endif

src/libnptm/Makefile

+2 −2

Original line number	Diff line number	Diff line
		@@ -19,9 +19,9 @@ endif
		include ../make.inc


		CXX_NPTM_OBJS=$(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/Parsers.o $(OBJDIR)/sph_subs.o $(OBJDIR)/clu_subs.o $(OBJDIR)/tra_subs.o $(OBJDIR)/TransitionMatrix.o
		CXX_NPTM_OBJS=$(OBJDIR)/Commons.o $(OBJDIR)/Configuration.o $(OBJDIR)/file_io.o $(OBJDIR)/Parsers.o $(OBJDIR)/sph_subs.o $(OBJDIR)/clu_subs.o $(OBJDIR)/tfrfme.o $(OBJDIR)/tra_subs.o $(OBJDIR)/TransitionMatrix.o

		CXX_NPTM_DYNOBJS=$(DYNOBJDIR)/Commons.o $(DYNOBJDIR)/Configuration.o $(DYNOBJDIR)/file_io.o $(DYNOBJDIR)/Parsers.o $(DYNOBJDIR)/sph_subs.o $(DYNOBJDIR)/clu_subs.o $(DYNOBJDIR)/tra_subs.o $(DYNOBJDIR)/TransitionMatrix.o
		CXX_NPTM_DYNOBJS=$(DYNOBJDIR)/Commons.o $(DYNOBJDIR)/Configuration.o $(DYNOBJDIR)/file_io.o $(DYNOBJDIR)/Parsers.o $(DYNOBJDIR)/sph_subs.o $(DYNOBJDIR)/clu_subs.o $(DYNOBJDIR)/tfrfme.o $(DYNOBJDIR)/tra_subs.o $(DYNOBJDIR)/TransitionMatrix.o


		all: $(BUILDDIR_NPTM)/libnptm.a $(BUILDDIR_NPTM)/libnptm.so

src/libnptm/TransitionMatrix.cpp

+1 −0

Original line number	Diff line number	Diff line
		@@ -6,6 +6,7 @@
		#include <exception>
		#include <fstream>
		#include <hdf5.h>
		#include <string>

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

src/libnptm/tfrfme.cpp

+288 −9

Original line number	Diff line number	Diff line
		@@ -4,10 +4,21 @@
		*/

		#include <complex>
		#include <exception>
		#include <fstream>
		#include <hdf5.h>
		#include <string>

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

		#ifndef INCLUDE_TFRFME_H_
		#include "../include/tfrfme.cpp"
		#include "../include/tfrfme.h"
		#endif

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

		using namespace std;
		@@ -46,24 +57,292 @@ TFRFME::~TFRFME() {
		delete[] wsum;
		}

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

		TFRFME* TFRFME::from_hdf5(string file_name) {
		TFRFME *instance = 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 lmode, lm, nkv, nxv, nyv, nzv;
		double vk, exri, an, ff, tra, spd, frsh, exril;
		status = hdf_file->read("LMODE", "INT32", &lmode);
		status = hdf_file->read("LM", "INT32", &lm);
		status = hdf_file->read("NKV", "INT32", &nkv);
		status = hdf_file->read("NXV", "INT32", &nxv);
		status = hdf_file->read("NYV", "INT32", &nyv);
		status = hdf_file->read("NZV", "INT32", &nzv);
		status = hdf_file->read("VK", "FLOAT64", &vk);
		status = hdf_file->read("EXRI", "FLOAT64", &exri);
		status = hdf_file->read("AN", "FLOAT64", &an);
		status = hdf_file->read("FF", "FLOAT64", &ff);
		status = hdf_file->read("TRA", "FLOAT64", &tra);
		status = hdf_file->read("SPD", "FLOAT64", &spd);
		status = hdf_file->read("FRSH", "FLOAT64", &frsh);
		status = hdf_file->read("EXRIL", "FLOAT64", &exril);
		instance = new TFRFME(lmode, lm, nkv, nxv, nyv, nzv);
		instance->set_param("vk", vk);
		instance->set_param("exri", exri);
		instance->set_param("an", an);
		instance->set_param("ff", ff);
		instance->set_param("tra", tra);
		instance->set_param("spd", spd);
		instance->set_param("frsh", frsh);
		instance->set_param("exril", exril);
		// DA QUI: aggiungere lettura di vettori e matrice.
		}
		return instance;
		}

		TFRFME* TFRFME::from_legacy(string file_name) {
		fstream input;
		TFRFME *instance = NULL;
		input.open(file_name.c_str(), ios::in \| ios::binary);
		if (input.is_open()) {
		int lmode, lm, nkv, nxv, nyv, nzv;
		double vk, exri, an, ff, tra, spd, frsh, exril;
		double dval, rval, ival;
		input.read(reinterpret_cast<char *>(&lmode), sizeof(int));
		input.read(reinterpret_cast<char *>(&lm), sizeof(int));
		input.read(reinterpret_cast<char *>(&nkv), sizeof(int));
		input.read(reinterpret_cast<char *>(&nxv), sizeof(int));
		input.read(reinterpret_cast<char *>(&nyv), sizeof(int));
		input.read(reinterpret_cast<char *>(&nzv), sizeof(int));
		input.read(reinterpret_cast<char *>(&vk), sizeof(double));
		input.read(reinterpret_cast<char *>(&exri), sizeof(double));
		input.read(reinterpret_cast<char *>(&an), sizeof(double));
		input.read(reinterpret_cast<char *>(&ff), sizeof(double));
		input.read(reinterpret_cast<char *>(&tra), sizeof(double));
		input.read(reinterpret_cast<char *>(&spd), sizeof(double));
		input.read(reinterpret_cast<char *>(&frsh), sizeof(double));
		input.read(reinterpret_cast<char *>(&exril), sizeof(double));
		instance = new TFRFME(lmode, lm, nkv, nxv, nyv, nzv);
		instance->set_param("vk", vk);
		instance->set_param("exri", exri);
		instance->set_param("an", an);
		instance->set_param("ff", ff);
		instance->set_param("tra", tra);
		instance->set_param("spd", spd);
		instance->set_param("frsh", frsh);
		instance->set_param("exril", exril);
		for (int xi = 0; xi < nxv; xi++) {
		input.read(reinterpret_cast<char *>(&dval), sizeof(double));
		instance->set_x(xi, dval);
		}
		for (int yi = 0; yi < nyv; yi++) {
		input.read(reinterpret_cast<char *>(&dval), sizeof(double));
		instance->set_y(yi, dval);
		}
		for (int zi = 0; zi < nzv; zi++) {
		input.read(reinterpret_cast<char *>(&dval), sizeof(double));
		instance->set_z(zi, dval);
		}
		int _nlmmt = 2 * lm * (lm + 2);
		int _nrvc = nxv * nyv * nzv;
		for (int wi = 0; wi < _nlmmt; wi++) {
		for (int wj = 0; wj < _nrvc; wj++) {
		input.read(reinterpret_cast<char *>(&rval), sizeof(double));
		input.read(reinterpret_cast<char *>(&ival), sizeof(double));
		complex<double> value(rval, ival);
		instance->set_matrix_element(wi, wj, value);
		} // wj loop
		} // wi loop
		} else {
		printf("ERROR: could not open input file \"%s\"\n", file_name.c_str());
		}
		return instance;
		}

		TFRFME::double get_param(string param_name) {
		std::complex<double> TFRFME::get_matrix_element(int row, int col) {
		return wsum[row][col];
		}

		double TFRFME::get_param(string param_name) {
		double value;
		if (param_name.compare("exri") == 0) value = exri;
		if (param_name.compare("vk") == 0) value = vk;
		else if (param_name.compare("exri") == 0) value = exri;
		else if (param_name.compare("an") == 0) value = an;
		else if (param_name.compare("ff") == 0) value = ff;
		else if (param_name.compare("tra") == 0) value = tra;
		else if (param_name.compare("spd") == 0) value = spd;
		else if (param_name.compare("frsh") == 0) value = frsh;
		else if (param_name.compare("exril") == 0) value = exril;
		//TODO: add else clause with exception.
		else {
		string message = "Unrecognized parameter name \"" + param_name + "\"";
		UnrecognizedParameterException ex(message);
		throw ex;
		}
		return value;
		}

		TFRFME::void write_binary(string file_name, string format) {
		return;
		void TFRFME::set_matrix_element(int row, int col, complex<double> value) {
		wsum[row][col] = value;
		}

		void TFRFME::set_param(string param_name, double value) {
		if (param_name.compare("vk") == 0) vk = value;
		else if (param_name.compare("exri") == 0) exri = value;
		else if (param_name.compare("an") == 0) an = value;
		else if (param_name.compare("ff") == 0) ff = value;
		else if (param_name.compare("tra") == 0) tra = value;
		else if (param_name.compare("spd") == 0) spd = value;
		else if (param_name.compare("frsh") == 0) frsh = value;
		else if (param_name.compare("exril") == 0) exril = value;
		else {
		string message = "Unrecognized parameter name \"" + param_name + "\"";
		UnrecognizedParameterException ex(message);
		throw ex;
		}
		}

		void TFRFME::write_binary(string file_name, string mode) {
		if (mode.compare("LEGACY") == 0) {
		write_legacy(file_name);
		} else if (mode.compare("HDF5") == 0) {
		write_hdf5(file_name);
		} /* else {
		string message = "Unknown format mode: \"" + mode + "\"";
		throw UnrecognizedFormatException(message);
		} */
		}

		void TFRFME::write_hdf5(string file_name) {
		List<string> rec_name_list(1);
		List<string> rec_type_list(1);
		List<void *> rec_ptr_list(1);
		string str_type;
		rec_name_list.set(0, "LMODE");
		rec_type_list.set(0, "INT32_(1)");
		rec_ptr_list.set(0, &lmode);
		rec_name_list.append("LM");
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&lm);
		rec_name_list.append("NKV");
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&nkv);
		rec_name_list.append("NXV");
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&nxv);
		rec_name_list.append("NYV");
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&nyv);
		rec_name_list.append("NZV");
		rec_type_list.append("INT32_(1)");
		rec_ptr_list.append(&nzv);
		rec_name_list.append("VK");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&lm);
		rec_name_list.append("EXRI");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&exri);
		rec_name_list.append("AN");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&an);
		rec_name_list.append("FF");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&ff);
		rec_name_list.append("TRA");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&tra);
		rec_name_list.append("SPD");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&spd);
		rec_name_list.append("FRSH");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&frsh);
		rec_name_list.append("EXRIL");
		rec_type_list.append("FLOAT64_(1)");
		rec_ptr_list.append(&exril);
		str_type = "FLOAT64_(" + to_string(nxv) + ")";
		rec_name_list.append("XVEC");
		rec_type_list.append(str_type);
		rec_ptr_list.append(xv);
		str_type = "FLOAT64_(" + to_string(nyv) + ")";
		rec_name_list.append("YVEC");
		rec_type_list.append(str_type);
		rec_ptr_list.append(yv);
		str_type = "FLOAT64_(" + to_string(nzv) + ")";
		rec_name_list.append("ZVEC");
		rec_type_list.append(str_type);
		rec_ptr_list.append(zv);
		rec_name_list.append("WSUM");
		str_type = "FLOAT64_(" + to_string(nlmmt) + "," + to_string(2 * nrvc) + ")";
		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)
		int num_elements = 2 * nlmmt * nrvc;
		double * ptr_elements = new double[num_elements]();
		for (int wi = 0; wi < nlmmt; wi++) {
		for (int wj = 0; wj < nrvc; wj++) {
		int index = (2 * nrvc) * wi + 2 * wj;
		ptr_elements[index] = wsum[wi][wj].real();
		ptr_elements[index + 1] = wsum[wi][wj].imag();
		} // wj loop
		} // wi loop
		rec_ptr_list.append(ptr_elements);

		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;
		}

		void TFRFME::write_legacy(string file_name) {
		fstream output;
		output.open(file_name.c_str(), ios::out \| ios::binary);
		if (output.is_open()) {
		output.write(reinterpret_cast<char *>(&lmode), sizeof(int));
		output.write(reinterpret_cast<char *>(&lm), sizeof(int));
		output.write(reinterpret_cast<char *>(&nkv), sizeof(int));
		output.write(reinterpret_cast<char *>(&nxv), sizeof(int));
		output.write(reinterpret_cast<char *>(&nyv), sizeof(int));
		output.write(reinterpret_cast<char *>(&nzv), sizeof(int));
		output.write(reinterpret_cast<char *>(&vk), sizeof(double));
		output.write(reinterpret_cast<char *>(&exri), sizeof(double));
		output.write(reinterpret_cast<char *>(&an), sizeof(double));
		output.write(reinterpret_cast<char *>(&ff), sizeof(double));
		output.write(reinterpret_cast<char *>(&tra), sizeof(double));
		output.write(reinterpret_cast<char *>(&spd), sizeof(double));
		output.write(reinterpret_cast<char *>(&frsh), sizeof(double));
		output.write(reinterpret_cast<char *>(&exril), sizeof(double));
		for (int xi = 0; xi < nxv; xi++)
		output.write(reinterpret_cast<char *>(&(xv[xi])), sizeof(double));
		for (int yi = 0; yi < nyv; yi++)
		output.write(reinterpret_cast<char *>(&(yv[yi])), sizeof(double));
		for (int zi = 0; zi < nzv; zi++)
		output.write(reinterpret_cast<char *>(&(zv[zi])), sizeof(double));
		for (int wi = 0; wi < nlmmt; wi++) {
		for (int wj = 0; wj < nrvc; wj++) {
		double rval = wsum[wi][wj].real();
		double ival = wsum[wi][wj].imag();
		output.write(reinterpret_cast<char *>(&rval), sizeof(double));
		output.write(reinterpret_cast<char *>(&ival), sizeof(double));
		} // wj loop
		} // wi loop
		} else { // Should never occur
		printf("ERROR: could not open output file \"%s\"\n", file_name.c_str());
		}
		}