/** read solution sizes */
static int read_nvnunrnl (hid_t file_id, int *nv, int *nr, int *nl)
{
if (H5Lexists (file_id, "/fclib_global", H5P_DEFAULT))
{
IO (H5LTread_dataset_int (file_id, "/fclib_global/M/n", nv));
IO (H5LTread_dataset_int (file_id, "/fclib_global/H/n", nr));
if (H5Lexists (file_id, "/fclib_global/G", H5P_DEFAULT))
{
IO (H5LTread_dataset_int (file_id, "/fclib_global/G/n", nl));
}
else *nl = 0;
}
else if (H5Lexists (file_id, "/fclib_local", H5P_DEFAULT))
{
*nv = 0;
IO (H5LTread_dataset_int (file_id, "/fclib_local/W/n", nr));
if (H5Lexists (file_id, "/fclib_local/R", H5P_DEFAULT))
{
IO (H5LTread_dataset_int (file_id, "/fclib_local/R/n", nl));
}
else *nl = 0;
}
else
{
fprintf (stderr, "ERROR: neither global nor local problem has been stored. Global or local have to be stored before solutions or guesses\n");
return 0;
}
return 1;
}
int read_input_config(char *input_file, struct input_config *cfg) {
herr_t err = 0;
size_t type_size;
hid_t input_file_id;
void *p = NULL;
cfg->rng_family = NULL;
cfg->levy_seed_family = NULL;
cfg->levy_seed_parameters = NULL;
cfg->levy_basis_dimension = NULL;
cfg->levy_basis_resolution = NULL;
input_file_id = H5Fopen(input_file, H5F_ACC_RDONLY, H5P_DEFAULT);
err = H5LTget_dataset_info(input_file_id, "/rng_family", NULL, NULL, &type_size);
cfg->rng_family = malloc(type_size * sizeof(char));
err = H5LTread_dataset_string(input_file_id, "/rng_family", cfg->rng_family);
err = H5LTread_dataset_int(input_file_id, "/rng_seed", &cfg->rng_seed);
err = H5LTget_dataset_info(input_file_id, "/levy_seed_family", NULL, NULL, &type_size);
cfg->levy_seed_family = malloc(type_size * sizeof(char));
err = H5LTread_dataset_string(input_file_id, "/levy_seed_family", cfg->levy_seed_family);
err = H5LTread_dataset_int(input_file_id, "/levy_seed_dimension", &cfg->levy_seed_dimension);
if (strcmp(cfg->levy_seed_family, "normal") == 0) {
p = (struct normal_seed_parameters *)malloc(sizeof(struct normal_seed_parameters));
err = read_normal_seed_parameters(input_file_id, p);
cfg->levy_seed_parameters = (void *)p;
}
else if (strcmp(cfg->levy_seed_family, "generalised hyperbolic") == 0) {
printf("Error: GH not yet supported.\n");
err = -1;
goto cleanup;
}
else {
printf("Error: Unsupported Levy seed.\n");
err = -1;
goto cleanup;
}
err = H5LTread_dataset_int(input_file_id, "/levy_basis_rank", &cfg->levy_basis_rank);
cfg->levy_basis_dimension = malloc(cfg->levy_basis_rank * sizeof(int));
cfg->levy_basis_resolution = malloc(cfg->levy_basis_rank * sizeof(double));
err = H5LTread_dataset_int(input_file_id, "/levy_basis_dimension", cfg->levy_basis_dimension);
err = H5LTread_dataset_double(input_file_id, "/levy_basis_resolution", cfg->levy_basis_resolution);
cleanup:
if (input_file_id >= 0) H5Fclose(input_file_id);
return (int)err;
}
int hdf5_load_int(hid_t loc_id, const string& dataset_name) {
int val;
herr_t status = H5LTread_dataset_int(loc_id, dataset_name.c_str(), &val);
CHECK_GE(status, 0)
<< "Failed to load int dataset with name " << dataset_name;
return val;
}
/* ------- begin -------------------------- readConvergence.c --- */
void readConvergence(void) {
/* This is a self-contained function to read the convergence matrix,
written by RH. */
const char routineName[] = "readConvergence";
char *atmosID;
int ncid, ncid_mpi, nx, ny;
size_t attr_size;
hid_t plist;
H5T_class_t type_class;
mpi.rh_converged = matrix_int(mpi.nx, mpi.ny);
/* --- Open the inputdata file --- */
if (( plist = H5Pcreate(H5P_FILE_ACCESS )) < 0) HERR(routineName);
if (( H5Pset_fapl_mpio(plist, mpi.comm, mpi.info) ) < 0) HERR(routineName);
if (( ncid = H5Fopen(INPUTDATA_FILE, H5F_ACC_RDWR, plist) ) < 0)
HERR(routineName);
if (( H5Pclose(plist) ) < 0) HERR(routineName);
/* Get ncid of the MPI group */
if (( ncid_mpi = H5Gopen(ncid, "mpi", H5P_DEFAULT) ) < 0) HERR(routineName);
/* --- Consistency checks --- */
/* Check that atmosID is the same */
if (( H5LTget_attribute_info(ncid, "/", "atmosID", NULL, &type_class,
&attr_size) ) < 0) HERR(routineName);
atmosID = (char *) malloc(attr_size + 1);
if (( H5LTget_attribute_string(ncid, "/", "atmosID", atmosID) ) < 0)
HERR(routineName);
if (!strstr(atmosID, atmos.ID)) {
sprintf(messageStr,
"Indata file was calculated for different atmosphere (%s) than current",
atmosID);
Error(WARNING, routineName, messageStr);
}
free(atmosID);
/* Check that dimension sizes match */
if (( H5LTget_attribute_int(ncid, "/", "nx", &nx) ) < 0) HERR(routineName);
if (nx != mpi.nx) {
sprintf(messageStr,
"Number of x points mismatch: expected %d, found %d.",
mpi.nx, (int)nx);
Error(WARNING, routineName, messageStr);
}
if (( H5LTget_attribute_int(ncid, "/", "ny", &ny) ) < 0) HERR(routineName);
if (ny != mpi.ny) {
sprintf(messageStr,
"Number of y points mismatch: expected %d, found %d.",
mpi.ny, (int)ny);
Error(WARNING, routineName, messageStr);
}
/* --- Read variable --- */
if (( H5LTread_dataset_int(ncid_mpi, CONV_NAME,
mpi.rh_converged[0]) ) < 0) HERR(routineName);
/* --- Close inputdata file --- */
if (( H5Gclose(ncid_mpi) ) < 0) HERR(routineName);
if (( H5Fclose(ncid) ) < 0) HERR(routineName);
return;
}
herr_t read_normal_seed_parameters(hid_t loc_id, struct normal_seed_parameters *p) {
herr_t err = 0;
err = H5LTread_dataset_int(loc_id, "/levy_seed_dimension", &p->dimension);
p->mean = malloc(p->dimension * sizeof(double));
p->covariance = malloc(p->dimension * p->dimension * sizeof(double));
err = H5LTread_dataset_double(loc_id, "/levy_seed_parameters/mean", p->mean);
err = H5LTread_dataset_double(loc_id, "/levy_seed_parameters/covariance", p->covariance);
return err;
}
/** read local problem;
* return problem on success; NULL on failure */
struct fclib_local* fclib_read_local (const char *path)
{
struct fclib_local *problem;
hid_t file_id, main_id, id;
if ((file_id = H5Fopen (path, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
{
fprintf (stderr, "ERROR: opening file failed\n");
return NULL;
}
if (!H5Lexists (file_id, "/fclib_local", H5P_DEFAULT))
{
fprintf (stderr, "ERROR: spurious input file %s :: fclib_local group does not exists", path);
return NULL;
}
MM (problem = calloc (1, sizeof (struct fclib_local)));
IO (main_id = H5Gopen (file_id, "/fclib_local", H5P_DEFAULT));
IO (H5LTread_dataset_int (file_id, "/fclib_local/spacedim", &problem->spacedim));
IO (id = H5Gopen (file_id, "/fclib_local/W", H5P_DEFAULT));
problem->W = read_matrix (id);
IO (H5Gclose (id));
if (H5Lexists (file_id, "/fclib_local/V", H5P_DEFAULT))
{
IO (id = H5Gopen (file_id, "/fclib_local/V", H5P_DEFAULT));
problem->V = read_matrix (id);
IO (H5Gclose (id));
IO (id = H5Gopen (file_id, "/fclib_local/R", H5P_DEFAULT));
problem->R = read_matrix (id);
IO (H5Gclose (id));
}
IO (id = H5Gopen (file_id, "/fclib_local/vectors", H5P_DEFAULT));
read_local_vectors (id, problem);
IO (H5Gclose (id));
if (H5Lexists (file_id, "/fclib_local/info", H5P_DEFAULT))
{
IO (id = H5Gopen (file_id, "/fclib_local/info", H5P_DEFAULT));
problem->info = read_problem_info (id);
IO (H5Gclose (id));
}
IO (H5Gclose (main_id));
IO (H5Fclose (file_id));
return problem;
}
/** read global problem;
* return problem on success; NULL on failure */
struct fclib_global* fclib_read_global (const char *path)
{
struct fclib_global *problem;
hid_t file_id, main_id, id;
if ((file_id = H5Fopen (path, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0)
{
fprintf (stderr, "ERROR: opening file failed\n");
return NULL;
}
MM (problem = calloc (1, sizeof (struct fclib_global)));
IO (main_id = H5Gopen (file_id, "/fclib_global", H5P_DEFAULT));
IO (H5LTread_dataset_int (file_id, "/fclib_global/spacedim", &problem->spacedim));
IO (id = H5Gopen (file_id, "/fclib_global/M", H5P_DEFAULT));
problem->M = read_matrix (id);
IO (H5Gclose (id));
IO (id = H5Gopen (file_id, "/fclib_global/H", H5P_DEFAULT));
problem->H = read_matrix (id);
IO (H5Gclose (id));
if (H5Lexists (file_id, "/fclib_global/G", H5P_DEFAULT))
{
IO (id = H5Gopen (file_id, "/fclib_global/G", H5P_DEFAULT));
problem->G = read_matrix (id);
IO (H5Gclose (id));
}
IO (id = H5Gopen (file_id, "/fclib_global/vectors", H5P_DEFAULT));
read_global_vectors (id, problem);
IO (H5Gclose (id));
if (H5Lexists (file_id, "/fclib_global/info", H5P_DEFAULT))
{
IO (id = H5Gopen (file_id, "/fclib_global/info", H5P_DEFAULT));
problem->info = read_problem_info (id);
IO (H5Gclose (id));
}
IO (H5Gclose (main_id));
IO (H5Fclose (file_id));
return problem;
}
void PHDF5fileClass::ReadPHDF5param(){
herr_t status;
string dname;
int datadims[3];
double L[3];
dname = "/Parameters/ncell";
status = H5LTread_dataset_int(file_id, dname.c_str(), datadims);
dname = "/Parameters/LxLyLz";
status = H5LTread_dataset_double(file_id, dname.c_str(), L);
ndim = 3;
if (datadims[0]<=1 || datadims[1]<=1 || datadims[2]<=1) ndim = 2;
for (int i=0; i<ndim; i++){
dim[i] = datadims[i];
LxLyLz[i] = L[i];
}
}
/** read initial guesses;
* return vector of guesses on success; NULL on failure;
* output numebr of guesses in the variable pointed by 'number_of_guesses' */
struct fclib_solution* fclib_read_guesses (const char *path, int *number_of_guesses)
{
struct fclib_solution *guesses;
hid_t file_id, main_id, id;
int nv, nr, nl, i;
char num [128];
if ((file_id = H5Fopen (path, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) /* overwrite */
{
fprintf (stderr, "ERROR: opening file failed\n");
return 0;
}
if (! read_nvnunrnl (file_id, &nv, &nr, &nl)) return 0;
if (H5Lexists (file_id, "/guesses", H5P_DEFAULT))
{
IO (main_id = H5Gopen (file_id, "/guesses", H5P_DEFAULT));
IO (H5LTread_dataset_int (file_id, "/guesses/number_of_guesses", number_of_guesses));
MM (guesses = malloc ((*number_of_guesses) * sizeof (struct fclib_solution)));
for (i = 0; i < *number_of_guesses; i ++)
{
snprintf (num, 128, "%d", i+1);
IO (id = H5Gopen (main_id, num, H5P_DEFAULT));
read_solution (id, nv, nr, nl, &guesses [i]);
IO (H5Gclose (id));
}
IO (H5Gclose (main_id));
}
IO (H5Fclose (file_id));
return guesses;
}
void bright::Reactor1G::loadlib(std::string lib)
{
// Loads Apporiate Libraries for Reactor and makes them into Burnup Parameters [F, pi(F), di(F), BUi(F), Tij(F)].
// HDF5 types
hid_t rlib;
herr_t rstat;
rlib = H5Fopen (lib.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT); //Recator Library
// Initializes Burnup Parameters...
hsize_t dimFromIso[1];
hsize_t dimToIso[1];
rstat = H5LTget_dataset_info(rlib, "/FromIso_zz", dimFromIso, NULL, NULL);
rstat = H5LTget_dataset_info(rlib, "/ToIso_zz", dimToIso, NULL, NULL);
#ifdef _WIN32
int * FromIso;
int * ToIso;
FromIso = new int [dimFromIso[0]];
ToIso = new int [dimToIso[0]];
#else
int FromIso [dimFromIso[0]];
int ToIso [dimToIso[0]];
#endif
rstat = H5LTread_dataset_int(rlib, "/FromIso_zz", FromIso);
rstat = H5LTread_dataset_int(rlib, "/ToIso_zz", ToIso);
I.clear();
I.insert(&FromIso[0], &FromIso[dimFromIso[0]]);
J.clear();
J.insert(&ToIso[0], &ToIso[dimToIso[0]]);
// Get Fluence Vector
hsize_t dimsF[1]; // Read in number of data points
rstat = H5LTget_dataset_info(rlib, "/Fluence", dimsF, NULL, NULL);
int lenF = dimsF[0];
// Make temp array
#ifdef _WIN32
float * tempF;
tempF = new float [lenF];
#else
float tempF [lenF];
#endif
rstat = H5LTread_dataset_float(rlib, "/Fluence", tempF);
F.assign(&tempF[0], &tempF[lenF]); // Fluence in [n/kb]
for (nuc_iter i = I.begin(); i != I.end(); i++ )
{
std::string iso = pyne::nucname::name(*i);
// Build BUi_F_
#ifdef _WIN32
float * tempBUi;
tempBUi = new float [lenF];
#else
float tempBUi [lenF];
#endif
rstat = H5LTread_dataset_float(rlib, ("/Burnup/" + iso).c_str(), tempBUi);
BUi_F_[*i].assign(&tempBUi[0], &tempBUi[lenF]);
// Build pi_F_
#ifdef _WIN32
float * temppi;
temppi = new float [lenF];
#else
float temppi [lenF];
#endif
rstat = H5LTread_dataset_float(rlib, ("/Production/" + iso).c_str(), temppi);
pi_F_[*i].assign(&temppi[0], &temppi[lenF]);
pi_F_[*i][0] = pyne::solve_line(0.0, F[2], pi_F_[*i][2], F[1], pi_F_[*i][1]);
// Build di_F_
#ifdef _WIN32
float * tempdi;
tempdi = new float [lenF];
#else
float tempdi [lenF];
#endif
rstat = H5LTread_dataset_float(rlib, ("/Destruction/" + iso).c_str(), tempdi);
di_F_[*i].assign(&tempdi[0], &tempdi[lenF]);
di_F_[*i][0] = pyne::solve_line(0.0, F[2], di_F_[*i][2], F[1], di_F_[*i][1]);
// Build Tij_F_
for (int jn = 0; jn < dimToIso[0] ; jn++)
{
int j = ToIso[jn];
std::string jso = pyne::nucname::name(j);
#ifdef _WIN32
float * tempTij;
tempTij = new float [lenF];
#else
float tempTij [lenF];
#endif
rstat = H5LTread_dataset_float(rlib, ("/Transmutation/" + iso + "/" + jso).c_str(), tempTij);
Tij_F_[*i][j].assign(&tempTij[0], &tempTij[lenF]);
};
};
rstat = H5Fclose(rlib);
// Now get microscopic XS data from KAERI...
// ...But only if the disadvantage factor is used.
if (!use_zeta)
return;
// HDF5 types
hid_t kdblib; // KaeriData.h5 file reference
herr_t kdbstat; // File status
hsize_t xs_nfields, xs_nrows; // Number of rows and fields (named columns) in XS table
// open the file
kdblib = H5Fopen ( (bright::BRIGHT_DATA + "/KaeriData.h5").c_str(), H5F_ACC_RDONLY, H5P_DEFAULT); // KAERI Data Library
// Get Thermal Mawell Average Table & Field Data Dimensions
kdbstat = H5TBget_table_info(kdblib, "/XS/ThermalMaxwellAve", &xs_nfields, &xs_nrows);
// Creating an empy array of character strings is tricky,
// because character strings are arrays themselves!
char ** xs_field_names = new char * [xs_nfields];
for (int n = 0; n < xs_nfields; n++)
xs_field_names[n] = new char [50];
#ifdef _WIN32
size_t * xs_field_sizes;
size_t * xs_field_offsets;
xs_field_sizes = new size_t [xs_nfields];
xs_field_offsets = new size_t [xs_nfields];
#else
size_t xs_field_sizes [xs_nfields];
size_t xs_field_offsets [xs_nfields];
#endif
size_t xs_type_size;
kdbstat = H5TBget_field_info(kdblib, "/XS/ThermalMaxwellAve", xs_field_names, xs_field_sizes, xs_field_offsets, &xs_type_size);
// Read the "isozz" column so that we can inteligently pick out our data
int isozz_n = bright::find_index_char( (char *) "isozz", xs_field_names, xs_nfields);
int * isozz = new int [xs_nrows];
const size_t temp_xs_field_sizes_isozz_n [1] = {xs_field_sizes[isozz_n]};
kdbstat = H5TBread_fields_name(kdblib, "/XS/ThermalMaxwellAve", xs_field_names[isozz_n], 0, xs_nrows, sizeof(int), 0, temp_xs_field_sizes_isozz_n, isozz);
// Now, load the XS that we need.
// NOTE: This maps metastable isotopes to their stable versions if they can't be found!
int sigma_a_n = bright::find_index_char( (char *) "sigma_a", xs_field_names, xs_nfields);
int sigma_s_n = bright::find_index_char( (char *) "sigma_s", xs_field_names, xs_nfields);
for (std::set<int>::iterator i = bright::track_nucs.begin(); i != bright::track_nucs.end(); i++)
{
int iso_n = bright::find_index<int>(*i, isozz, xs_nrows);
if (iso_n < 0)
iso_n = bright::find_index<int>(10*((*i)/10), isozz);
if (iso_n < 0)
{
sigma_a_therm[*i] = 0.0;
sigma_s_therm[*i] = 0.0;
continue;
};
double * iso_sig_a = new double [1];
double * iso_sig_s = new double [1];
const size_t temp_xs_field_sizes_sigma_a_n [1] = {xs_field_sizes[sigma_a_n]};
const size_t temp_xs_field_sizes_sigma_s_n [1] = {xs_field_sizes[sigma_s_n]};
kdbstat = H5TBread_fields_name(kdblib, "/XS/ThermalMaxwellAve", xs_field_names[sigma_a_n], iso_n, 1, sizeof(double), 0, temp_xs_field_sizes_sigma_a_n, iso_sig_a);
kdbstat = H5TBread_fields_name(kdblib, "/XS/ThermalMaxwellAve", xs_field_names[sigma_s_n], iso_n, 1, sizeof(double), 0, temp_xs_field_sizes_sigma_s_n, iso_sig_s);
sigma_a_therm[*i] = iso_sig_a[0];
sigma_s_therm[*i] = iso_sig_s[0];
};
kdbstat = H5Fclose(kdblib);
return;
};
static int test_dsets( void )
{
int rank = 2;
hsize_t dims[2] = {2,3};
hid_t file_id;
hid_t dataset_id;
char data_char_in[DIM] = {1,2,3,4,5,6};
char data_char_out[DIM];
short data_short_in[DIM] = {1,2,3,4,5,6};
short data_short_out[DIM];
int data_int_in[DIM] = {1,2,3,4,5,6};
int data_int_out[DIM];
long data_long_in[DIM] = {1,2,3,4,5,6};
long data_long_out[DIM];
float data_float_in[DIM] = {1,2,3,4,5,6};
float data_float_out[DIM];
double data_double_in[DIM] = {1,2,3,4,5,6};
double data_double_out[DIM];
const char *data_string_in = "This is a string";
char data_string_out[20];
int i;
/* Create a new file using default properties. */
file_id = H5Fcreate( FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/*-------------------------------------------------------------------------
* H5LTmake_dataset test
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset");
/* Make dataset */
if ( H5LTmake_dataset( file_id, DSET0_NAME, rank, dims, H5T_NATIVE_INT, data_int_in ) < 0 )
goto out;
/* Read dataset using the basic HDF5 API */
if ( ( dataset_id = H5Dopen2(file_id, DSET0_NAME, H5P_DEFAULT) ) < 0 )
goto out;
if ( H5Dread ( dataset_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, data_int_out ) < 0 )
goto out;
if ( H5Dclose( dataset_id ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* read using the LT function H5LTread_dataset
*-------------------------------------------------------------------------
*/
TESTING("H5LTread_dataset");
if ( H5LTread_dataset( file_id, DSET0_NAME, H5T_NATIVE_INT, data_int_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* test the H5LTmake_dataset_ functions
*-------------------------------------------------------------------------
*/
/*-------------------------------------------------------------------------
* H5LTmake_dataset_char
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_char");
/* Make dataset char */
if ( H5LTmake_dataset_char( file_id, DSET1_NAME, rank, dims, data_char_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET1_NAME, H5T_NATIVE_CHAR, data_char_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_char_in[i] != data_char_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_char( file_id, DSET1_NAME, data_char_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_char_in[i] != data_char_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_short
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_short");
/* Make dataset short */
if ( H5LTmake_dataset_short( file_id, DSET2_NAME, rank, dims, data_short_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET2_NAME, H5T_NATIVE_SHORT, data_short_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_short_in[i] != data_short_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_short( file_id, DSET2_NAME, data_short_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_short_in[i] != data_short_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_int
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_int");
/* Make dataset int */
if ( H5LTmake_dataset_int( file_id, DSET3_NAME, rank, dims, data_int_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET3_NAME, H5T_NATIVE_INT, data_int_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_int( file_id, DSET3_NAME, data_int_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_int_in[i] != data_int_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_long
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_long");
/* Make dataset long */
if ( H5LTmake_dataset_long( file_id, DSET4_NAME, rank, dims, data_long_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET4_NAME, H5T_NATIVE_LONG, data_long_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_long_in[i] != data_long_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_long( file_id, DSET4_NAME, data_long_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_long_in[i] != data_long_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_float
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_float");
/* Make dataset float */
if ( H5LTmake_dataset_float( file_id, DSET5_NAME, rank, dims, data_float_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET5_NAME, H5T_NATIVE_FLOAT, data_float_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_float_in[i] != data_float_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_float( file_id, DSET5_NAME, data_float_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_float_in[i] != data_float_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_double
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_double");
/* Make dataset double */
if ( H5LTmake_dataset_double( file_id, DSET6_NAME, rank, dims, data_double_in ) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset( file_id, DSET6_NAME, H5T_NATIVE_DOUBLE, data_double_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_double_in[i] != data_double_out[i] ) {
goto out;
}
}
/* Read dataset */
if ( H5LTread_dataset_double( file_id, DSET6_NAME, data_double_out ) < 0 )
goto out;
for (i = 0; i < DIM; i++)
{
if ( data_double_in[i] != data_double_out[i] ) {
goto out;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTmake_dataset_string
*-------------------------------------------------------------------------
*/
TESTING("H5LTmake_dataset_string");
/* Make dataset string */
if ( H5LTmake_dataset_string(file_id,DSET7_NAME,data_string_in) < 0 )
goto out;
/* Read dataset */
if ( H5LTread_dataset_string(file_id,DSET7_NAME,data_string_out) < 0 )
goto out;
if ( strcmp(data_string_in,data_string_out) != 0 )
goto out;
/*-------------------------------------------------------------------------
* end tests
*-------------------------------------------------------------------------
*/
/* Close the file. */
H5Fclose( file_id );
PASSED();
return 0;
out:
/* Close the file. */
H5_FAILED();
return -1;
}
void HDF5GeneralDataLayer<Dtype>::LoadGeneralHDF5FileData(const char* filename) {
DLOG(INFO) << "Loading The general HDF5 file" << filename;
hid_t file_id = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if (file_id < 0) {
LOG(ERROR) << "Failed opening HDF5 file" << filename;
}
HDF5GeneralDataParameter data_param = this->layer_param_.hdf5_general_data_param();
int fieldNum = data_param.field_size();
hdf_blobs_.resize(fieldNum);
const int MIN_DATA_DIM = 1;
const int MAX_DATA_DIM = 4;
for(int i = 0; i < fieldNum; ++i){
//LOG(INFO) << "Data type: " << data_param.datatype(i).data();
if(i < data_param.datatype_size() &&
strcmp(data_param.datatype(i).data(), "int8") == 0){
// We take out the io functions here
const char* dataset_name_ = data_param.field(i).data();
hdf_blobs_[i] = shared_ptr<Blob<Dtype> >(new Blob<Dtype>());
CHECK(H5LTfind_dataset(file_id, dataset_name_))
<< "Failed to find HDF5 dataset " << dataset_name_;
// Verify that the number of dimensions is in the accepted range.
herr_t status;
int ndims;
status = H5LTget_dataset_ndims(file_id, dataset_name_, &ndims);
CHECK_GE(status, 0) << "Failed to get dataset ndims for " << dataset_name_;
CHECK_GE(ndims, MIN_DATA_DIM);
CHECK_LE(ndims, MAX_DATA_DIM);
// Verify that the data format is what we expect: int8
std::vector<hsize_t> dims(ndims);
H5T_class_t class_;
status = H5LTget_dataset_info(file_id, dataset_name_, dims.data(), &class_, NULL);
CHECK_GE(status, 0) << "Failed to get dataset info for " << dataset_name_;
CHECK_EQ(class_, H5T_INTEGER) << "Expected integer data";
vector<int> blob_dims(dims.size());
for (int j = 0; j < dims.size(); ++j) {
blob_dims[j] = dims[j];
}
hdf_blobs_[i]->Reshape(blob_dims);
std::cout<<"Trying to allocate memories!\n";
int* buffer_data = new int[hdf_blobs_[i]->count()];
std::cout<<"Memories loaded!!!\n";
status = H5LTread_dataset_int(file_id, dataset_name_, buffer_data);
CHECK_GE(status, 0) << "Failed to read int8 dataset " << dataset_name_;
Dtype* target_data = hdf_blobs_[i]->mutable_cpu_data();
for(int j = 0; j < hdf_blobs_[i]->count(); j++){
//LOG(INFO) << Dtype(buffer_data[j]);
target_data[j] = Dtype(buffer_data[j]);
}
delete buffer_data;
}else{
// The dataset is still the float32 datatype
hdf_blobs_[i] = shared_ptr<Blob<Dtype> >(new Blob<Dtype>());
hdf5_load_nd_dataset(file_id, data_param.field(i).data(),
MIN_DATA_DIM, MAX_DATA_DIM, hdf_blobs_[i].get());
}
}
herr_t status = H5Fclose(file_id);
CHECK_GE(status, 0) << "Failed to close HDF5 file " << filename;
for(int i = 1; i < fieldNum; ++i){
CHECK_EQ(hdf_blobs_[0]->num(), hdf_blobs_[i]->num());
}
data_permutation_.clear();
data_permutation_.resize(hdf_blobs_[0]->shape(0));
for (int i = 0; i < hdf_blobs_[0]->shape(0); i++)
data_permutation_[i] = i;
//TODO: DATA SHUFFLE
//LOG(INFO) << "Successully loaded " << data_blob_.num() << " rows";
}
/*+++++++++++++++++++++++++ SDMF version 2.4 ++++++++++++++++++++++++++++++*/
float SDMF_orbitPhaseDiff( int orbit )
{
register hsize_t ni;
char rsp_file[MAX_STRING_LENGTH];
hsize_t nfields, num_roe;
hid_t file_id;
int *orbitList = NULL;
float orbitPhaseDiff = 0.092f;
const char roe_flname[] = "ROE_EXC_all.h5";
const char roe_tblname[] = "roe_entry";
/*
* open output HDF5-file
*/
(void) snprintf( rsp_file, MAX_STRING_LENGTH, "./%s", roe_flname );
H5E_BEGIN_TRY {
file_id = H5Fopen( rsp_file, H5F_ACC_RDONLY, H5P_DEFAULT );
} H5E_END_TRY;
if ( file_id < 0 ) {
(void) snprintf( rsp_file, MAX_STRING_LENGTH,
"%s/%s", DATA_DIR, roe_flname );
file_id = H5Fopen( rsp_file, H5F_ACC_RDONLY, H5P_DEFAULT );
if ( file_id < 0 )
NADC_GOTO_ERROR( NADC_ERR_HDF_FILE, rsp_file );
}
/*
* read info_h5 records
*/
(void) H5TBget_table_info( file_id, roe_tblname, &nfields, &num_roe );
/*
* read Orbit column
*/
if ( num_roe == 0 ) return orbitPhaseDiff;
orbitList = (int *) malloc( num_roe * sizeof( int ));
if ( orbitList == NULL )
NADC_GOTO_ERROR( NADC_ERR_ALLOC, "orbitList" );
if ( H5LTread_dataset_int( file_id, "orbitList", orbitList ) < 0 )
NADC_GOTO_ERROR( NADC_ERR_HDF_RD, "orbitList" );
for ( ni = 0; ni < num_roe; ni++ ) {
if ( orbitList[ni] == orbit ) break;
}
if ( ni < num_roe ) {
double ECL_Exit, ECL_Entry, Period;
const size_t field_offset = 0;
const size_t dst_sizes = sizeof( double );
H5TBread_fields_name( file_id, roe_tblname, "ECL_EXIT", ni, 1,
sizeof(double), &field_offset, &dst_sizes,
&ECL_Exit );
H5TBread_fields_name( file_id, roe_tblname, "ECL_ENTRY", ni, 1,
sizeof(double), &field_offset, &dst_sizes,
&ECL_Entry );
H5TBread_fields_name( file_id, roe_tblname, "PERIOD", ni, 1,
sizeof(double), &field_offset, &dst_sizes,
&Period );
orbitPhaseDiff = (float) ((ECL_Entry - ECL_Exit) / Period - 0.5) / 2;
}
(void) H5Fclose( file_id );
done:
if ( orbitList != NULL ) free( orbitList );
return orbitPhaseDiff;
}
/** read matrix */
struct fclib_matrix* read_matrix (hid_t id)
{
struct fclib_matrix *mat;
MM (mat = malloc (sizeof (struct fclib_matrix)));
IO (H5LTread_dataset_int (id, "nzmax", &mat->nzmax));
IO (H5LTread_dataset_int (id, "m", &mat->m));
IO (H5LTread_dataset_int (id, "n", &mat->n));
IO (H5LTread_dataset_int (id, "nz", &mat->nz));
if (mat->nz >= 0) /* triplet */
{
MM (mat->p = malloc (sizeof (int [mat->nz])));
MM (mat->i = malloc (sizeof (int [mat->nz])));
IO (H5LTread_dataset_int (id, "p", mat->p));
IO (H5LTread_dataset_int (id, "i", mat->i));
}
else if (mat->nz == -1) /* csc */
{
MM (mat->p = malloc (sizeof (int [mat->n+1])));
MM (mat->i = malloc (sizeof (int [mat->nzmax])));
IO (H5LTread_dataset_int (id, "p", mat->p));
IO (H5LTread_dataset_int (id, "i", mat->i));
}
else if (mat->nz == -2) /* csr */
{
MM (mat->p = malloc (sizeof (int [mat->m+1])));
MM (mat->i = malloc (sizeof (int [mat->nzmax])));
IO (H5LTread_dataset_int (id, "p", mat->p));
IO (H5LTread_dataset_int (id, "i", mat->i));
}
else ASSERT (0, "ERROR: unkown sparse matrix type => fclib_matrix->nz = %d\n", mat->nz);
MM (mat->x = malloc (sizeof (double [mat->nzmax])));
IO (H5LTread_dataset_double (id, "x", mat->x));
if (H5LTfind_dataset (id, "conditioning"))
{
H5T_class_t class_id;
hsize_t dim;
size_t size;
MM (mat->info = malloc (sizeof (struct fclib_matrix_info)));
if (H5LTfind_dataset (id, "comment"))
{
IO (H5LTget_dataset_info (id, "comment", &dim, &class_id, &size));
MM (mat->info->comment = malloc (sizeof (char [size])));
IO (H5LTread_dataset_string (id, "comment", mat->info->comment));
}
else mat->info->comment = NULL;
IO (H5LTread_dataset_double (id, "conditioning", &mat->info->conditioning));
IO (H5LTread_dataset_double (id, "determinant", &mat->info->determinant));
IO (H5LTread_dataset_int (id, "rank", &mat->info->rank));
}
else
{
mat->info = NULL;
}
return mat;
}
