Commit 2389e7a0 authored by Giovanni La Mura's avatar Giovanni La Mura
Browse files

Implement HDF5 configuration binary output

parent 0bcc235f

src/cluster/Makefile

+7 −4
Original line number Diff line number Diff line
@@ -3,8 +3,8 @@ FC=gfortran 
FCFLAGS=-std=legacy -O3

LFLAGS=

CXX=g++

CXXFLAGS=-O2 -ggdb -pg -coverage

CXXLFLAGS=

CXXFLAGS=-O3 -ggdb -pg -coverage

CXXLFLAGS=-L/usr/lib64 -lhdf5_hl -lhdf5



all: clu edfb np_cluster
@@ -14,8 +14,8 @@ clu: clu.o 
edfb: edfb.o

	$(FC) $(FCFLAGS) -o $(BUILDDIR)/edfb $(BUILDDIR)/edfb.o $(LFLAGS)



np_cluster: $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o

	$(CXX) $(CXXFLAGS) $(CXXLFLAGS) -o $(BUILDDIR)/np_cluster $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o

np_cluster: $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o

	$(CXX) $(CXXFLAGS) $(CXXLFLAGS) -o $(BUILDDIR)/np_cluster $(BUILDDIR)/np_cluster.o $(BUILDDIR)/Commons.o $(BUILDDIR)/Configuration.o $(BUILDDIR)/file_io.o $(BUILDDIR)/Parsers.o $(BUILDDIR)/sph_subs.o $(BUILDDIR)/clu_subs.o $(BUILDDIR)/cluster.o



$(BUILDDIR)/np_cluster.o:

	$(CXX) $(CXXFLAGS) -c np_cluster.cpp -o $(BUILDDIR)/np_cluster.o
@@ -26,6 +26,9 @@ $(BUILDDIR)/Commons.o: 
$(BUILDDIR)/Configuration.o:

	$(CXX) $(CXXFLAGS) -c ../libnptm/Configuration.cpp -o $(BUILDDIR)/Configuration.o



$(BUILDDIR)/file_io.o:

	$(CXX) $(CXXFLAGS) -c ../libnptm/file_io.cpp -o $(BUILDDIR)/file_io.o



$(BUILDDIR)/Parsers.o:

	$(CXX) $(CXXFLAGS) -c ../libnptm/Parsers.cpp -o $(BUILDDIR)/Parsers.o

src/cluster/cluster.cpp

+3 −2
Original line number Diff line number Diff line 
/*! \file cluster.cpp

 */

#include <cstdio>

#include <complex>

#include <exception>

#include <fstream>

#include <string>

#include <complex>



#ifndef INCLUDE_CONFIGURATION_H_

#include <exception>

#include "../include/Configuration.h"

#endif
@@ -42,6 +42,7 @@ void cluster(string config_file, string data_file, string output_path) { 
  }

  sconf->write_formatted(output_path + "/c_OEDFB");

  sconf->write_binary(output_path + "/c_TEDF");

  sconf->write_binary(output_path + "/c_TEDF.hd5", "HDF5");

  GeometryConfiguration *gconf = NULL;

  try {

    gconf = GeometryConfiguration::from_legacy(data_file);

src/include/Configuration.h

+48 −4
Original line number Diff line number Diff line
@@ -218,6 +218,51 @@ protected: 
  //! \brief Flag to control whether to add an external layer.

  bool use_external_sphere;



  /*! \brief Build configuration from a HDF5 binary input file.

   *

   * This is the function called by the public method `from_binary()` in case of

   * HDF5 mode selection. This function creates a configuration structure from

   * a binary file written according to the HDF5 format standard.

   *

   * \param file_name: `string` Name of the binary configuration data file.

   * \return config: `ScattererConfiguration*` Pointer to object containing the

   * scatterer configuration data.

   */

  static ScattererConfiguration *from_hdf5(std::string file_name);

  

  /*! \brief Build configuration from legacy binary input file.

   *

   * This is the function called by the public method `from_binary()` in case of

   * legacy mode selection. This function creates a configuration structure from

   * a binary file written according to the proprietary mode used by the original

   * FORTRAN code.

   *

   * \param file_name: `string` Name of the binary configuration data file.

   * \return config: `ScattererConfiguration*` Pointer to object containing the

   * scatterer configuration data.

   */

  static ScattererConfiguration *from_legacy(std::string file_name);



  /*! \brief Write the scatterer configuration data to HDF5 binary output.

   *

   * This function is invoked by the public method `write_binary()` with the

   * "HDF5" format mode. It undertakes the task of writing the configuration

   * information to a binary file using the standard HDF5 format.

   *

   * \param file_name: `string` Name of the binary configuration data file.

   */

  void write_hdf5(std::string file_name);

  

  /*! \brief Write the scatterer configuration data to legacy binary output.

   *

   * This function is invoked by the public method `write_binary()` with the

   * "LEGACY" format mode. It undertakes the task of writing the configuration

   * information to a binary file using a proprietary format, as it was done

   * originally in the FORTRAN code.

   *

   * \param file_name: `string` Name of the binary configuration data file.

   */

  void write_legacy(std::string file_name);

public:

  /*! \brief Build a scatterer configuration structure.

   *
@@ -306,11 +351,10 @@ public: 
   * be useful to save the configuration data. `ScattererConfiguration.write_binary()`

   * performs the operation of saving the configuration in binary format. This function

   * can work in legacy mode, to write backward compatible configuration files, as well

   * as by wrapping the data into common scientific formats (NB: this last option still

   * needs to be implemented).

   * as by wrapping the data into common scientific formats.

   *

   * \param file_name: `string` Name of the file to be written.

   * \param mode: `string` Binary encoding. Can be one of "LEGACY", ... . Optional

   * \param mode: `string` Binary encoding. Can be one of ["LEGACY", "HDF5"] . Optional

   * (default is "LEGACY").

   */

  void write_binary(std::string file_name, std::string mode="LEGACY");

src/include/file_io.h

+0 −4
Original line number Diff line number Diff line
@@ -120,10 +120,6 @@ class HDFFile { 
   */

  bool is_open() { return file_open_flag; }

  

  /* ! \brief Read data from attached file.

   */

  // herr_t read();

  

  /*! \brief Write data to attached file.

   *

   * \param dataset_name: `string` Name of the dataset to write to.

src/libnptm/Configuration.cpp

+237 −124
Original line number Diff line number Diff line
@@ -4,9 +4,11 @@ 
#include <cmath>

#include <complex>

#include <cstdio>

#include <exception>

#include <fstream>

#include <regex>

#include <string>

#include "hdf5.h"



#ifndef INCLUDE_LIST_H_

#include "../include/List.h"
@@ -20,6 +22,10 @@ 
#include "../include/Configuration.h"

#endif



#ifndef INCLUDE_FILE_IO_H_

#include "../include/file_io.h"

#endif



using namespace std;



GeometryConfiguration::GeometryConfiguration(
@@ -203,7 +209,7 @@ ScattererConfiguration::ScattererConfiguration( 
  radii_of_spheres = ros_vector;

  nshl_vec = nshl_vector;

  rcf = rcf_vector;

  idfc = dielectric_func_type,

  idfc = dielectric_func_type;

  dc0_matrix = dc_matrix;

  use_external_sphere = is_external;

  exdc = ex;
@@ -248,6 +254,24 @@ ScattererConfiguration::~ScattererConfiguration() { 
}



ScattererConfiguration* ScattererConfiguration::from_binary(string file_name, string mode) {

  ScattererConfiguration *conf = NULL;

  if (mode.compare("LEGACY") == 0) {

    conf = ScattererConfiguration::from_legacy(file_name);

  } else if (mode.compare("HDF5") == 0) {

    conf = ScattererConfiguration::from_hdf5(file_name);

  } else {

    string message = "Unknown format mode: \"" + mode + "\"";

    throw UnrecognizedConfigurationException(message);

  }

  return conf;

}



ScattererConfiguration* ScattererConfiguration::from_hdf5(string file_name) {

  ScattererConfiguration *conf = NULL;

  return conf;

}



ScattererConfiguration* ScattererConfiguration::from_legacy(string file_name) {

  int nsph;

  int *iog;

  double _exdc, _wp, _xip;
@@ -257,7 +281,7 @@ ScattererConfiguration* ScattererConfiguration::from_binary(string file_name, st 
  double *ros_vector;

  double **rcf_vector;

  complex<double> ***dc0m;

  if (mode.compare("LEGACY") == 0) { // Legacy mode was chosen.

  

  int max_ici = 0;

  fstream input;

  input.open(file_name.c_str(), ios::in | ios::binary);
@@ -302,10 +326,11 @@ ScattererConfiguration* ScattererConfiguration::from_binary(string file_name, st 
      }

    }

    dc0m = new complex<double>**[max_ici];

    int dim3 = (_idfc == 0) ? nxi : 1;

    for (int dim1 = 0; dim1 < max_ici; dim1++) {

      dc0m[dim1] = new complex<double>*[nsph];

      for (int dim2 = 0; dim2 < nsph; dim2++) {

	  dc0m[dim1][dim2] = new complex<double>[nxi]();

	dc0m[dim1][dim2] = new complex<double>[dim3]();

      }

    }

    for (int jxi468 = 1; jxi468 <= nxi; jxi468++) {
@@ -327,10 +352,7 @@ ScattererConfiguration* ScattererConfiguration::from_binary(string file_name, st 
    OpenConfigurationFileException ex(file_name);

    throw ex;

  }

  } else { // A different binary format was chosen.

    //TODO: this part is not yet implemented.

    //      Functions to write optimized file formats may be invoked here.

  }

    

  ScattererConfiguration *conf = new ScattererConfiguration(

							    nsph,

							    xi_vec,
@@ -511,20 +533,10 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(string dedfb_file_nam 
      }

    }

  }

  //last_read_line++;

  int *iog_vector = new int[nsph]();

  double *ros_vector = new double[nsph]();

  double **rcf_vector = new double*[nsph];

  int *nshl_vector = new int[nsph]();

  /*for (int i = 0; i < nsph; i++) {

    string read_format = "";

    for (int j = 0; j < (i % 15); j++) read_format += " %*d";

    read_format += " %d";

    sscanf(file_lines[last_read_line].c_str(), read_format.c_str(), (iog_vector + i));

    if (i > 0 && i % 15 == 0) {

    last_read_line++;

    }

    }*/

  int filled_iogs = 0;

  re = regex("[0-9]+");

  while (filled_iogs < nsph) {
@@ -561,8 +573,6 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(string dedfb_file_nam 
    rcf_vector[i113 - 1] = new double[nsh]();

    for (int ns = 0; ns < nsh; ns++) {

      double ns_rcf;

      //int ns_rcf_exp;

      //sscanf(file_lines[++last_read_line].c_str(), " %lf D%d", &ns_rcf, &ns_rcf_exp);

      str_target = file_lines[++last_read_line];

      regex_search(str_target, m, re);

      str_number = m.str();
@@ -573,10 +583,11 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(string dedfb_file_nam 
    }

  }

  complex<double> ***dc0m = new complex<double>**[max_ici];

  int dim3 = (_idfc == 0) ? nxi : 1;

  for (int dim1 = 0; dim1 < max_ici; dim1++) {

    dc0m[dim1] = new complex<double>*[nsph];

    for (int dim2 = 0; dim2 < nsph; dim2++) {

      dc0m[dim1][dim2] = new complex<double>[nxi]();

      dc0m[dim1][dim2] = new complex<double>[dim3]();

    }

  }

  re = regex("-?[0-9]+\\.[0-9]+([eEdD][-+]?[0-9]+)?");
@@ -589,8 +600,6 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(string dedfb_file_nam 
      if (i162 == 1) ici = ici + ies;

      for (int i157 = 0; i157 < ici; i157++) {

	double dc0_real, dc0_img;

	//int dc0_real_exp, dc0_img_exp;

	//sscanf(file_lines[++last_read_line].c_str(), " (%lf D%d, %lf D%d)", &dc0_real, &dc0_real_exp, &dc0_img, &dc0_img_exp);

	str_target = file_lines[++last_read_line];

	regex_search(str_target, m, re);

	string str_number = m.str();
@@ -603,7 +612,7 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(string dedfb_file_nam 
	str_number = regex_replace(str_number, regex("D"), "e");

	str_number = regex_replace(str_number, regex("d"), "e");

	dc0_img = stod(str_number);

	dc0m[i157][i162 - 1][jxi468 - 1] = std::complex<double>(dc0_real, dc0_img);

	dc0m[i157][i162 - 1][jxi468 - 1] = complex<double>(dc0_real, dc0_img);

      }

    }

  }
@@ -676,11 +685,117 @@ void ScattererConfiguration::print() { 
}



void ScattererConfiguration::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 UnrecognizedConfigurationException(message);

  }

}



void ScattererConfiguration::write_hdf5(string file_name) {

  const double two_pi = acos(0.0) * 4.0;

  const double evc = 6.5821188e-16;

  int ies = (use_external_sphere)? 1 : 0;

  int max_ici = 0;

  bool is_new_vector = false;

  if (mode.compare("LEGACY") == 0) { // Legacy mode was chosen.

  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, "NSPH");

  rec_type_list.set(0, "INT32_(1)");

  rec_ptr_list.set(0, &number_of_spheres);

  rec_name_list.append("IOGVEC");

  str_type = "INT32_(" + to_string(number_of_spheres) + ")";

  rec_type_list.append(str_type);

  rec_ptr_list.append(iog_vec);

  rec_name_list.append("EXDC");

  rec_type_list.append("FLOAT64_(1)");

  rec_ptr_list.append(&exdc);

  rec_name_list.append("WP");

  rec_type_list.append("FLOAT64_(1)");

  rec_ptr_list.append(&wp);

  rec_name_list.append("XIP");

  rec_type_list.append("FLOAT64_(1)");

  rec_ptr_list.append(&xip);

  rec_name_list.append("IDFC");

  rec_type_list.append("INT32_(1)");

  rec_ptr_list.append(&idfc);

  rec_name_list.append("NXI");

  rec_type_list.append("INT32_(1)");

  rec_ptr_list.append(&number_of_scales);

  rec_name_list.append("XIVEC");

  str_type = "FLOAT64_(" + to_string(number_of_scales) + ")";

  rec_type_list.append(str_type);

  rec_ptr_list.append(scale_vec);

  for (int i115 = 1; i115 <= number_of_spheres; i115++) {

    if (iog_vec[i115 - 1] < i115) continue;

    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]));

    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];

    if (i115 == 1) nsh += ies;

    if (max_ici < (nsh + 1) / 2) max_ici = nsh + 1 / 2;

    str_name = "RCF_" + to_string(i115);

    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]));

  }



  int dim3 = (idfc == 0) ? number_of_scales : 1;

  int dc0m_size = 2 * dim3 * number_of_spheres * max_ici;

  double *dc0m = new double[dc0m_size];

  int dc0_index = 0;

  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 ici = (nsh + 1) / 2;

      if (i162 == 1) ici = ici + ies;

      for (int i157 = 0; i157 < ici; i157++) {

	double dc0_real, dc0_imag;

	dc0_real = dc0_matrix[i157][i162 - 1][jxi468 - 1].real();

	dc0_imag = dc0_matrix[i157][i162 - 1][jxi468 - 1].imag();

	dc0m[dc0_index++] = dc0_real;

	dc0m[dc0_index++] = dc0_imag;

      }

    }

  }

  str_type = "FLOAT64_(" + to_string(dc0m_size) + ")";

  rec_name_list.append("DC0M");

  rec_type_list.append(str_type);

  rec_ptr_list.append(dc0m);



  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, "c_TEDF.hd5", 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();

  

  // Clean memory

  delete[] dc0m;

  delete[] rec_names;

  delete[] rec_types;

  delete[] rec_pointers;

  delete hdf_file;

}



void ScattererConfiguration::write_legacy(string file_name) {

  const double two_pi = acos(0.0) * 4.0;

  const double evc = 6.5821188e-16;

  fstream output;

  int ies = (use_external_sphere)? 1 : 0;

  output.open(file_name.c_str(), ios::out | ios::binary);
@@ -700,7 +815,6 @@ void ScattererConfiguration::write_binary(string file_name, string mode) { 
    output.write(reinterpret_cast<char *>(&(radii_of_spheres[i115 - 1])), sizeof(double));

    int nsh = nshl_vec[i115 - 1];

    if (i115 == 1) nsh += ies;

      if (max_ici < (nsh + 1) / 2) max_ici = (nsh + 1) / 2;

    for (int nsi = 0; nsi < nsh; nsi++)

      output.write(reinterpret_cast<char *>(&(rcf[i115 - 1][nsi])), sizeof(double));

  }
@@ -725,7 +839,6 @@ void ScattererConfiguration::write_binary(string file_name, string mode) { 
  }

  output.close();

}

}



void ScattererConfiguration::write_formatted(string file_name) {

  const double evc = 6.5821188e-16;