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Commit 49430428 authored by Giovanni La Mura's avatar Giovanni La Mura
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Optimize legacy configuration binary I/O format

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src/libnptm/Configuration.cpp
+ 127
− 155
View file @ 49430428
......@@ -234,21 +234,21 @@ ScattererConfiguration::ScattererConfiguration(
}
ScattererConfiguration::~ScattererConfiguration() {
int max_ici = 0;
int configurations = 0;
for (int i = 1; i <= number_of_spheres; i++) {
if (iog_vec[i - 1] < i) continue;
int nsh = nshl_vec[i - 1];
if (max_ici < (nsh + 1) / 2) max_ici = (nsh + 1) / 2;
configurations++;
}
for (int i = 0; i < max_ici; i++) {
for (int i = 0; i < configurations; i++) {
for (int j = 0; j < number_of_spheres; j++) {
delete[] dc0_matrix[i][j];
}
}
delete[] dc0_matrix;
for (int i = 0; i < number_of_spheres; i++) {
for (int i = 0; i < configurations; i++) {
delete[] rcf[i];
}
delete[] rcf;
delete[] nshl_vec;
delete[] radii_of_spheres;
delete[] iog_vec;
......@@ -430,88 +430,82 @@ ScattererConfiguration* ScattererConfiguration::from_dedfb(string dedfb_file_nam
}
}
int *iog_vector = new int[nsph]();
double *ros_vector = new double[nsph]();
double **rcf_vector = new double*[nsph];
int *nshl_vector = new int[nsph]();
int filled_iogs = 0;
str_target = file_lines[++last_read_line];
re = regex("[0-9]+");
while (filled_iogs < nsph) {
string str_target = file_lines[++last_read_line];
while(regex_search(str_target, m, re)) {
iog_vector[filled_iogs++] = stoi(m.str());
int configurations = 0;
for (int i = 1; i <= nsph; i++) {
bool success = regex_search(str_target, m, re);
if (success) {
iog_vector[i - 1] = stoi(m.str());
str_target = m.suffix().str();
if (filled_iogs == nsph) break;
if (iog_vector[i - 1] >= i) configurations++;
} else {
str_target = file_lines[++last_read_line];
i--;
}
}
int index = 0;
double *ros_vector = new double[configurations]();
int *nshl_vector = new int[configurations]();
double **rcf_vector = new double*[configurations];
for (int i113 = 1; i113 <= nsph; i113++) {
int i_val, nsh;
double ros_val;
if (iog_vector[i113 - 1] < i113) {
rcf_vector[i113 - 1] = new double[1]();
continue;
}
re = regex("[0-9]+");
if (iog_vector[i113 - 1] < i113) continue;
str_target = file_lines[++last_read_line];
regex_search(str_target, m, re);
i_val = stoi(m.str());
str_target = m.suffix();
nshl_vector[i113 - 1] = stoi(m.str());
str_target = m.suffix().str();
re = regex("-?[0-9]+\\.[0-9]+([eEdD][-+]?[0-9]+)?");
regex_search(str_target, m, re);
string str_number = m.str();
str_number = regex_replace(str_number, regex("D"), "e");
str_number = regex_replace(str_number, regex("d"), "e");
ros_val = stod(str_number);
nshl_vector[i113 - 1] = i_val;
if (max_ici < (i_val + 1) / 2) max_ici = (i_val + 1) / 2;
ros_vector[i113 - 1] = ros_val;
nsh = nshl_vector[i113 - 1];
ros_vector[i113 - 1] = stod(m.str());
int nsh = nshl_vector[i113 - 1];
if (i113 == 1) nsh += ies;
rcf_vector[i113 - 1] = new double[nsh]();
for (int ns = 0; ns < nsh; ns++) {
double ns_rcf;
for (int ns112 = 0; ns112 < nsh; ns112++) {
str_target = file_lines[++last_read_line];
regex_search(str_target, m, re);
str_number = m.str();
str_number = regex_replace(str_number, regex("D"), "e");
str_number = regex_replace(str_number, regex("d"), "e");
ns_rcf = stod(str_number);
rcf_vector[i113 - 1][ns] = ns_rcf;
}
}
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>[dim3]();
}
}
re = regex("-?[0-9]+\\.[0-9]+([eEdD][-+]?[0-9]+)?");
rcf_vector[i113 - 1][ns112] = stod(str_number);
} // ns112 loop
} // i113 loop
complex<double> ***dc0m = new complex<double>**[configurations];
complex<double> *dc0 = new complex<double>[configurations]();
for (int di = 0; di < configurations; di++) {
dc0m[di] = new complex<double>*[nsph];
for (int dj = 0; dj < nsph; dj++) dc0m[di][dj] = new complex<double>[nxi]();
} // di loop
for (int jxi468 = 1; jxi468 <= nxi; jxi468++) {
if (_idfc != 0 && jxi468 > 1) continue;
if (_idfc != 0 && jxi468 > 1) continue; // jxi468 loop
for (int i162 = 1; i162 <= nsph; i162++) {
if (iog_vector[i162 - 1] < i162) continue;
if (iog_vector[i162 - 1] >= i162) {
int nsh = nshl_vector[i162 - 1];
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++) {
double dc0_real, dc0_img;
int ici = (nsh + 1) / 2;
if (i162 == 1) ici += ies;
for (int ic157 = 0; ic157 < ici; ic157++) {
str_target = file_lines[++last_read_line];
regex_search(str_target, m, re);
string str_number = m.str();
str_number = regex_replace(str_number, regex("D"), "e");
str_number = regex_replace(str_number, regex("d"), "e");
dc0_real = stod(str_number);
double rval = stod(str_number);
str_target = m.suffix().str();
regex_search(str_target, m, re);
str_number = m.str();
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] = complex<double>(dc0_real, dc0_img);
}
}
}
double ival = stod(str_number);
dc0[ic157] = complex<double>(rval, ival);
dc0m[ic157][i162 - 1][jxi468 - 1] = dc0[ic157];
} // ic157 loop
}
} // i162 loop
} // jxi468 loop
delete[] dc0;
ScattererConfiguration *config = new ScattererConfiguration(
nsph,
......@@ -627,104 +621,83 @@ ScattererConfiguration* ScattererConfiguration::from_hdf5(string file_name) {
}
ScattererConfiguration* ScattererConfiguration::from_legacy(string file_name) {
int nsph;
int *iog;
int _nsph;
int *_iog_vec;
int _ies;
double _exdc, _wp, _xip;
int _idfc, nxi;
int *nshl_vector;
double *xi_vec;
double *ros_vector;
double **rcf_vector;
complex<double> ***dc0m;
int _idfc, _nxi;
int *_nshl_vec;
double *_xi_vec;
double *_ros_vec;
double **_rcf_vec;
complex<double> ***_dc0m;
int max_ici = 0;
fstream input;
input.open(file_name.c_str(), ios::in | ios::binary);
if (input.is_open()) {
input.read(reinterpret_cast<char *>(&nsph), sizeof(int));
iog = new int[nsph]();
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 *>(&_nsph), sizeof(int));
input.read(reinterpret_cast<char *>(&_ies), sizeof(int));
_iog_vec = new int[_nsph]();
for (int i = 0; i < _nsph; i++)
input.read(reinterpret_cast<char *>(&(_iog_vec[i])), sizeof(int));
input.read(reinterpret_cast<char *>(&_exdc), sizeof(double));
input.read(reinterpret_cast<char *>(&_wp), sizeof(double));
input.read(reinterpret_cast<char *>(&_xip), sizeof(double));
input.read(reinterpret_cast<char *>(&_idfc), sizeof(int));
input.read(reinterpret_cast<char *>(&nxi), sizeof(int));
try {
xi_vec = new double[nxi]();
} catch (const bad_alloc &ex) {
throw UnrecognizedConfigurationException("Wrong parameter set: invalid number of scales " + to_string(nxi));
}
for (int i = 0; i < nxi; i++) {
input.read(reinterpret_cast<char *>(&(xi_vec[i])), sizeof(double));
}
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)); // 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](); // 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)); // was not from IOG
}
}
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>[dim3]();
}
input.read(reinterpret_cast<char *>(&_nxi), sizeof(int));
_xi_vec = new double[_nxi]();
for (int i = 0; i < _nxi; i++)
input.read(reinterpret_cast<char *>(&(_xi_vec[i])), sizeof(double));
int configurations = 0;
for (int i = 1; i <= _nsph; i++) {
if (_iog_vec[i - 1] >= i) configurations++;
}
_nshl_vec = new int[configurations]();
_ros_vec = new double[configurations]();
_rcf_vec = new double*[configurations];
for (int i115 = 1; i115 <= _nsph; i115++) {
if (_iog_vec[i115 - 1] < i115) continue;
input.read(reinterpret_cast<char *>(&(_nshl_vec[i115 - 1])), sizeof(int));
input.read(reinterpret_cast<char *>(&(_ros_vec[i115 - 1])), sizeof(double));
int nsh = _nshl_vec[i115 - 1];
if (i115 == 1) nsh += _ies;
_rcf_vec[i115 - 1] = new double[nsh]();
for (int nsi = 0; nsi < nsh; nsi++)
input.read(reinterpret_cast<char *>(&(_rcf_vec[i115 - 1][nsi])), sizeof(double));
}
for (int jxi468 = 1; jxi468 <= nxi; jxi468++) {
_dc0m = new complex<double>**[configurations];
for (int di = 0; di < configurations; di++) {
_dc0m[di] = new complex<double>*[_nsph];
for (int dj = 0; dj < _nsph; dj++) _dc0m[di][dj] = new complex<double>[_nxi]();
} // di loop
for (int jxi468 = 1; jxi468 <= _nxi; jxi468++) {
if (_idfc != 0 && jxi468 > 1) continue;
for (int i162 = 1; i162 <= nsph; i162++) {
if (iog[i162 - 1] < i162) continue;
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 i162 = 1; i162 <= _nsph; 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_img;
input.read(reinterpret_cast<char *>(&dc0_real), sizeof(double));
input.read(reinterpret_cast<char *>(&dc0_img), sizeof(double));
dc0m[i157][i162 - 1][jxi468 - 1] = dc0_real + 1i * dc0_img;
double rval, ival;
input.read(reinterpret_cast<char *>(&rval), sizeof(double));
input.read(reinterpret_cast<char *>(&ival), sizeof(double));
_dc0m[i157][i162 - 1][jxi468 - 1] = complex<double>(rval, ival);
}
}
}
input.close();
} else { // Opening of the input file did not succeed.
OpenConfigurationFileException ex(file_name);
throw ex;
}
ScattererConfiguration *conf = new ScattererConfiguration(
nsph,
xi_vec,
nxi,
_nsph,
_xi_vec,
_nxi,
"XIV",
iog,
ros_vector,
nshl_vector,
rcf_vector,
_iog_vec,
_ros_vec,
_nshl_vec,
_rcf_vec,
_idfc,
dc0m,
false,
_dc0m,
(_ies == 1),
_exdc,
_wp,
_xip
......@@ -889,12 +862,11 @@ void ScattererConfiguration::write_hdf5(string file_name) {
}
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);
output.write(reinterpret_cast<char *>(&number_of_spheres), sizeof(int));
output.write(reinterpret_cast<char *>(&ies), sizeof(int));
for (int i = 0; i < number_of_spheres; i++)
output.write(reinterpret_cast<char *>(&(iog_vec[i])), sizeof(int));
output.write(reinterpret_cast<char *>(&exdc), sizeof(double));
......
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