int mcmc_set_table(mcmc_configuration config, const char* field_names[])
{
int n_param = config.n_param;
hid_t field_types[n_param];
size_t dst_offsets[n_param];
size_t dst_sizes[n_param];
size_t dst_size = n_param*sizeof(double);
int i;
for (i=0; i<n_param; i++)
{
field_types[i] = H5T_NATIVE_DOUBLE;
dst_sizes[i] = sizeof(double);
dst_offsets[i] = i*sizeof(double);
}
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
herr_t status;
status = H5TBmake_table("Traces", config.file_id, "Traces", n_param, 1,
dst_size, field_names, dst_offsets, field_types,
chunk_size, fill_data, compress, config.parameters);
status = H5TBmake_table("Proposed", config.file_id, "Proposed", n_param, 0,
dst_size, field_names, dst_offsets, field_types,
chunk_size, fill_data, compress, config.parameters);
}
void SCIA_WR_H5_LADS( struct param_record param, unsigned int nr_lads,
const struct lads_scia *lads )
/*@globals lads_size, lads_offs@*/
{
hid_t ads_id;
hsize_t adim;
hid_t lads_type[NFIELDS];
hid_t type_id, temp_type00, temp_type01;
const hbool_t compress = (param.flag_deflate == PARAM_SET) ? TRUE : FALSE;
const char *lads_names[NFIELDS] = {
"dsr_time", "attach_flag", "corner_grd"
};
/*
* check number of LADS records
*/
if ( nr_lads == 0 ) return;
/*
* create/open group /ADS
*/
ads_id = NADC_OPEN_HDF5_Group( param.hdf_file_id, "/ADS" );
if ( ads_id < 0 ) NADC_RETURN_ERROR( NADC_ERR_HDF_GRP, "/ADS" );
/*
* define user-defined data types of the Table-fields
*/
temp_type00 = H5Topen( param.hdf_file_id, "mjd", H5P_DEFAULT );
adim = NUM_CORNERS;
type_id = H5Topen( param.hdf_file_id, "coord", H5P_DEFAULT );
temp_type01 = H5Tarray_create( type_id, 1, &adim );
lads_type[0] = temp_type00;
lads_type[1] = H5T_NATIVE_UCHAR;
lads_type[2] = temp_type01;
/*
* create table
*/
(void) H5TBmake_table( "lads", ads_id, TBL_NAME, NFIELDS,
nr_lads, lads_size, lads_names, lads_offs,
lads_type, nr_lads, NULL, compress, lads );
/*
* close interface
*/
(void) H5Tclose( type_id );
(void) H5Tclose( temp_type00 );
(void) H5Tclose( temp_type01 );
(void) H5Gclose( ads_id );
}
/* Create a normal HL table just like the HL examples do */
static int create_hl_table(hid_t fid)
{
/* Calculate the offsets of the particle struct members in memory */
size_t part_offset[NFIELDS] = { HOFFSET( particle_t, name ),
HOFFSET( particle_t, lati ),
HOFFSET( particle_t, longi ),
HOFFSET( particle_t, pressure ),
HOFFSET( particle_t, temperature )
};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
herr_t status;
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, (size_t)16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/*------------------------------------------------------------------------
* H5TBmake_table
*-------------------------------------------------------------------------
*/
status=H5TBmake_table( "Table Title", fid, H5TB_TABLE_NAME, (hsize_t)NFIELDS,
(hsize_t)NRECORDS, sizeof(particle_t),
field_names, part_offset, field_type,
chunk_size, fill_data, compress, testPart );
if(status<0)
return -1;
else
return 0;
}
bool IbHdf5::writeRecords(Record2* recArray, int nRecords)
{
qDebug() << "In IbHdf5::writeRecords()";
qDebug() << " m_filePath:" << m_filePath;
// if (QFileInfo::exists(m_filePath)) {
// QFile::remove(m_filePath);
// }
// if (H5Lexists(m_fid, m_tableName.toLatin1().data(), H5P_DEFAULT) == TRUE) {
// qDebug() << "NUM HDF5 RECORDS IS:" << numRecords();
// H5TBdelete_record(m_fid, m_tableName.toLatin1().data(), 0, numRecords());
// }
if (H5Lexists(m_fid, m_tableName.toLatin1().data(), H5P_DEFAULT) == FALSE) {
qDebug() << " creating new HDF5 table for:" << m_tableName;
H5TBmake_table(m_tableName.toLatin1().data(), m_fid, m_tableName.toLatin1().data(),
m_nFields, nRecords, sizeof(Record2), m_fieldNames, m_dst_offset,
m_fieldType, m_chunkSize, m_fillData, m_compress, recArray);
}
else {
H5TBappend_records(m_fid, m_tableName.toLatin1().data(), (hsize_t)nRecords, sizeof(Record2), m_dst_offset, m_dst_sizes, recArray);
}
}
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_LV1_WR_H5_SRSN( struct param_record param, unsigned int nr_srsn,
const struct srsn_scia *srsn )
{
hid_t ads_id;
hsize_t adim;
herr_t stat;
hid_t srsn_type[NFIELDS];
const hbool_t compress = (param.flag_deflate == PARAM_SET) ? TRUE : FALSE;
const size_t srsn_size = sizeof( struct srsn_scia );
const char *srsn_names[NFIELDS] = {
"mjd", "flag_mds", "flag_neu", "sun_spec_id", "avg_asm", "avg_esm",
"avg_elev_sun", "dopp_shift", "wvlen_sun", "mean_sun",
"precision_sun", "accuracy_sun", "etalon", "pmd_mean", "pmd_out"
};
const size_t srsn_offs[NFIELDS] = {
HOFFSET( struct srsn_scia, mjd ),
HOFFSET( struct srsn_scia, flag_mds ),
HOFFSET( struct srsn_scia, flag_neu ),
HOFFSET( struct srsn_scia, sun_spec_id ),
HOFFSET( struct srsn_scia, avg_asm ),
HOFFSET( struct srsn_scia, avg_esm ),
HOFFSET( struct srsn_scia, avg_elev_sun ),
HOFFSET( struct srsn_scia, dopp_shift ),
HOFFSET( struct srsn_scia, wvlen_sun ),
HOFFSET( struct srsn_scia, mean_sun ),
HOFFSET( struct srsn_scia, precision_sun ),
HOFFSET( struct srsn_scia, accuracy_sun ),
HOFFSET( struct srsn_scia, etalon ),
HOFFSET( struct srsn_scia, pmd_mean ),
HOFFSET( struct srsn_scia, pmd_out )
};
/*
* check number of PMD records
*/
if ( nr_srsn == 0 ) return;
/*
* open/create group /ADS
*/
ads_id = NADC_OPEN_HDF5_Group( param.hdf_file_id, "/ADS" );
if ( ads_id < 0 ) NADC_RETURN_ERROR( NADC_ERR_HDF_GRP, "/ADS" );
/*
* write SRSN data sets
*/
adim = SCIENCE_PIXELS;
srsn_type[0] = H5Topen( param.hdf_file_id, "mjd", H5P_DEFAULT );
srsn_type[1] = H5Tcopy( H5T_NATIVE_UCHAR );
srsn_type[2] = H5Tcopy( H5T_NATIVE_UCHAR );
srsn_type[3] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( srsn_type[3], (size_t) 3 );
srsn_type[4] = H5Tcopy( H5T_NATIVE_FLOAT );
srsn_type[5] = H5Tcopy( H5T_NATIVE_FLOAT );
srsn_type[6] = H5Tcopy( H5T_NATIVE_FLOAT );
srsn_type[7] = H5Tcopy( H5T_NATIVE_FLOAT );
adim = SCIENCE_PIXELS;
srsn_type[8] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
srsn_type[9] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
srsn_type[10] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
srsn_type[11] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
srsn_type[12] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
adim = PMD_NUMBER;
srsn_type[13] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
srsn_type[14] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
stat = H5TBmake_table( "srsn", ads_id, "NEW_SUN_REFERENCE",
NFIELDS, 1, srsn_size, srsn_names,
srsn_offs, srsn_type, 1,
NULL, compress, srsn );
if ( stat < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, "srsn" );
/*
* close interface
*/
done:
(void) H5Tclose( srsn_type[0] );
(void) H5Tclose( srsn_type[1] );
(void) H5Tclose( srsn_type[2] );
(void) H5Tclose( srsn_type[3] );
(void) H5Tclose( srsn_type[4] );
(void) H5Tclose( srsn_type[5] );
(void) H5Tclose( srsn_type[6] );
(void) H5Tclose( srsn_type[7] );
(void) H5Tclose( srsn_type[8] );
(void) H5Tclose( srsn_type[9] );
(void) H5Tclose( srsn_type[10] );
(void) H5Tclose( srsn_type[11] );
(void) H5Tclose( srsn_type[12] );
(void) H5Tclose( srsn_type[13] );
(void) H5Tclose( srsn_type[14] );
(void) H5Gclose( ads_id );
}
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_OL2_WR_H5_CLD( struct param_record param, unsigned int nr_cld,
const struct cld_sci_ol *cld )
{
register unsigned int nr;
hid_t grp_id;
hbool_t compress;
hsize_t adim;
hvl_t *vdata;
hid_t cld_type[NFIELDS];
const char *cld_names[NFIELDS] = {
"dsr_time", "quality_flag", "integr_time", "pmd_read",
"cl_type_flags", "cloud_flags", "flag_output_flags",
"num_aero_param", "pmd_read_cl", "dsr_length",
"surface_pres", "cl_frac", "cl_frac_err", "cl_top_pres",
"cl_top_pres_err", "cl_opt_depth", "cl_opt_depth_err",
"cl_reflectance", "cl_reflectance_err",
"surface_reflectance", "surface_reflectance_err",
"aero_abso_ind", "aero_ind_diag"
};
/*
* check number of CLD records
*/
if ( nr_cld == 0 ) return;
/*
* set HDF5 boolean variable for compression
*/
if ( param.flag_deflate == PARAM_SET )
compress = TRUE;
else
compress = FALSE;
/*
* create group /MDS
*/
grp_id = NADC_OPEN_HDF5_Group( param.hdf_file_id, "/MDS" );
if ( grp_id < 0 ) NADC_RETURN_ERROR( NADC_ERR_HDF_GRP, "/MDS" );
/*
* define user-defined data types of the Table-fields
*/
cld_type[0] = H5Topen( param.hdf_file_id, "mjd", H5P_DEFAULT );
cld_type[1] = H5Tcopy( H5T_NATIVE_CHAR );
cld_type[2] = H5Tcopy( H5T_NATIVE_USHORT );
cld_type[3] = H5Tcopy( H5T_NATIVE_USHORT );
cld_type[4] = H5Tcopy( H5T_NATIVE_USHORT );
cld_type[5] = H5Tcopy( H5T_NATIVE_USHORT );
cld_type[6] = H5Tcopy( H5T_NATIVE_USHORT );
cld_type[7] = H5Tcopy( H5T_NATIVE_USHORT );
adim = 2;
cld_type[8] = H5Tarray_create( H5T_NATIVE_USHORT, 1, &adim );
cld_type[9] = H5Tcopy( H5T_NATIVE_UINT );
cld_type[10] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[11] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[12] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[13] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[14] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[15] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[16] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[17] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[18] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[19] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[20] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[21] = H5Tcopy( H5T_NATIVE_FLOAT );
cld_type[22] = H5Tcopy( H5T_NATIVE_FLOAT );
/*
* create table
*/
(void) H5TBmake_table( "Cloud end Aerosol MDS", grp_id, "cld", NFIELDS,
nr_cld, cld_size, cld_names, cld_offs,
cld_type, nr_cld, NULL, compress, cld );
/*
* close interface
*/
for ( nr = 0; nr < NFIELDS; nr++ ) (void) H5Tclose( cld_type[nr] );
/*
* +++++ create/write variable part of the CLOUDS_AEROSOL record
*/
adim = (hsize_t) nr_cld;
/*
* Additional aerosol parameters
*/
vdata = (hvl_t *) malloc( nr_cld * sizeof(hvl_t) );
if ( vdata == NULL ) NADC_RETURN_ERROR( NADC_ERR_ALLOC, "vdata" );
nr = 0;
do {
vdata[nr].len = (size_t) cld[nr].numaeropars;
if ( cld[nr].numaeropars > 0 ) {
vdata[nr].p = malloc( vdata[nr].len * sizeof(float) );
if ( vdata[nr].p == NULL ) {
free( vdata );
NADC_RETURN_ERROR( NADC_ERR_ALLOC, "vdata.p" );
}
(void) memcpy( vdata[nr].p , cld[nr].aeropars,
vdata[nr].len * sizeof(float) );
}
} while ( ++nr < nr_cld );
NADC_WR_HDF5_Vlen_Dataset( compress, grp_id, "aeropars",
H5T_NATIVE_FLOAT, 1, &adim, vdata );
/*
* close interface
*/
(void) H5Gclose( grp_id );
}
int main( void )
{
typedef struct Particle1
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle1;
/* Define an array of Particles */
Particle1 p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size1 = sizeof( Particle1 );
size_t dst_offset1[NFIELDS] = { HOFFSET( Particle1, name ),
HOFFSET( Particle1, lati ),
HOFFSET( Particle1, longi ),
HOFFSET( Particle1, pressure ),
HOFFSET( Particle1, temperature )};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int compress = 0;
Particle1 fill_data[1] = { "no data",-1,-1, -99.0f, -99.0 };
int fill_data_new[1] = { -100 };
hsize_t position;
herr_t status;
hsize_t nfields_out;
hsize_t nrecords_out;
/* Define the inserted field information */
hid_t field_type_new = H5T_NATIVE_INT;
int data[NRECORDS] = { 0,1,2,3,4,5,6,7 };
/* Initialize the field type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_11.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make the table */
status=H5TBmake_table( "Table Title",file_id,TABLE_NAME,NFIELDS,NRECORDS,
dst_size1,field_names, dst_offset1, field_type,
chunk_size, fill_data, compress, p_data );
/* Insert the new field at the end of the field list */
position = NFIELDS;
status=H5TBinsert_field( file_id, TABLE_NAME, "New Field", field_type_new, position,
fill_data_new, data );
/* Get table info */
status=H5TBget_table_info (file_id,TABLE_NAME, &nfields_out, &nrecords_out );
/* print */
printf ("Table has %d fields and %d records\n",(int)nfields_out,(int)nrecords_out);
/* Close the file. */
H5Fclose( file_id );
return 0;
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
Particle dst_buf[ NRECORDS + NRECORDS_INS ];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int compress = 0;
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} }; /* Fill value particle */
hsize_t start1; /* Record to start reading from 1st table */
hsize_t nrecords; /* Number of records to insert */
hsize_t start2; /* Record to start writing in 2nd table */
herr_t status;
int i;
hsize_t nfields_out;
hsize_t nrecords_out;
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_09.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make 2 tables: TABLE2_NAME is empty */
status=H5TBmake_table( "Table Title",file_id,TABLE1_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
status=H5TBmake_table( "Table Title",file_id,TABLE2_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, NULL );
/* Add 2 records from TABLE1_NAME to TABLE2_NAME */
start1 = 3;
nrecords = NRECORDS_INS;
start2 = 6;
status=H5TBadd_records_from( file_id, TABLE1_NAME, start1, nrecords, TABLE2_NAME, start2 );
/* read TABLE2_NAME: it should have 2 more records now */
status=H5TBread_table( file_id, TABLE2_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* Get table info */
status=H5TBget_table_info (file_id,TABLE2_NAME, &nfields_out, &nrecords_out );
/* print */
printf ("Table has %d fields and %d records\n",(int)nfields_out,(int)nrecords_out);
/* print it by rows */
for (i=0; i<nrecords_out; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* Close the file. */
H5Fclose( file_id );
return 0;
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
Particle dst_buf[NRECORDS+NRECORDS_ADD];
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( p_data[0].name),
sizeof( p_data[0].lati),
sizeof( p_data[0].longi),
sizeof( p_data[0].pressure),
sizeof( p_data[0].temperature)};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
herr_t status;
int i;
/* Append particles */
Particle particle_in[ NRECORDS_ADD ] =
{{ "eight",80,80, 8.0f, 80.0},
{"nine",90,90, 9.0f, 90.0} };
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_02.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* make a table */
status=H5TBmake_table( "Table Title",file_id,TABLE_NAME,NFIELDS,NRECORDS,
dst_size, field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
/* append two records */
status=H5TBappend_records(file_id, TABLE_NAME,NRECORDS_ADD, dst_size, dst_offset, dst_sizes,
&particle_in );
/* read the table */
status=H5TBread_table( file_id, TABLE_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* print it by rows */
for (i=0; i<NRECORDS+NRECORDS_ADD; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* Close the file. */
H5Fclose( file_id );
return 0;
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} }; /* Fill value particle */
int compress = 0;
hsize_t nfields_out;
hsize_t nrecords_out;
/* Initialize field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_06.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make a table */
H5TBmake_table( "Table Title",file_id,TABLE_NAME,NFIELDS,NRECORDS,dst_size,
field_names, dst_offset, field_type,
chunk_size, fill_data, compress, NULL);
/* Get table info */
H5TBget_table_info (file_id,TABLE_NAME, &nfields_out, &nrecords_out );
/* print */
printf ("Table has %d fields and %d records\n",(int)nfields_out,(int)nrecords_out);
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
/**
* Allocates memory for and initializes data structure
* that describes the HDF5 table used to store SNP data.
* A single SNPTab data structure should be created for
* each chromosome, and be freed after use.
*
*/
SNPTab *snp_tab_new(hid_t h5file, const char *chrom_name,
size_t max_record) {
herr_t status;
SNPTab *tab;
SNP snp_desc;
const char *field_names[] =
{"name", "pos", "allele1", "allele2"};
tab = my_malloc(sizeof(SNPTab));
tab->h5file = h5file;
/* set datatypes for each field */
tab->name_type = H5Tcopy(H5T_C_S1);
H5Tset_size(tab->name_type, SNP_MAX_NAME);
/* no longer store chromosome as each chromosome
* gets its own table
*/
/* tab->chrom_type = H5Tcopy(H5T_C_S1);
* H5Tset_size(tab->chrom_type, SNP_MAX_CHROM);
*/
tab->allele_type = H5Tcopy(H5T_C_S1);
H5Tset_size(tab->allele_type, SNP_MAX_ALLELE);
tab->field_type[0] = tab->name_type; /* name */
/* tab->field_type[1] = tab->chrom_type; */ /* chromosome */
tab->field_type[1] = H5T_NATIVE_LONG; /* pos */
tab->field_type[2] = tab->allele_type; /* allele1 */
tab->field_type[3] = tab->allele_type; /* allele2 */
/* sizes of record and each field */
tab->record_size = sizeof(SNP);
tab->field_size[0] = sizeof(snp_desc.name);
/* tab->field_size[1] = sizeof(snp_desc.chrom); */
tab->field_size[1] = sizeof(snp_desc.pos);
tab->field_size[2] = sizeof(snp_desc.allele1);
tab->field_size[3] = sizeof(snp_desc.allele2);
/* offsets of each field */
tab->field_offset[0] = HOFFSET(SNP, name);
/* tab->field_offset[1] = HOFFSET(SNP, chrom); */
tab->field_offset[1] = HOFFSET(SNP, pos);
tab->field_offset[2] = HOFFSET(SNP, allele1);
tab->field_offset[3] = HOFFSET(SNP, allele2);
/* title and name of table */
tab->title = util_str_concat(chrom_name, " SNPs", NULL);
tab->name = util_str_dup(chrom_name);
/* set chunk size and compression */
tab->chunk_size = SNPTAB_CHUNK_SIZE;
tab->compress = 1;
tab->n_record = 0;
tab->max_record = max_record;
status = H5TBmake_table(tab->title, tab->h5file, tab->name,
SNPTAB_N_FIELDS, tab->max_record,
tab->record_size, field_names,
tab->field_offset, tab->field_type,
tab->chunk_size, NULL, tab->compress, NULL);
if(status < 0) {
my_err("%s:%d: could not create SNP table\n", __FILE__, __LINE__);
}
return tab;
}
int FileIO::create(Setup *setup) {
hid_t file_plist = H5Pcreate(H5P_FILE_ACCESS);
#ifdef GKC_PARALLEL_MPI
// pass some information onto the underlying MPI_File_open call
MPI_Info file_info;
check(MPI_Info_create(&file_info), DMESG("File info"));
/*
H5Pset_sieve_buf_size(file_plist, 262144);
H5Pset_alignment(file_plist, 524288, 262144);
MPI_Info_set(file_info, (char *) "access_style" , (char *) "write_once");
MPI_Info_set(file_info, (char *) "collective_buffering", (char *) "true");
MPI_Info_set(file_info, (char *) "cb_block_size" , (char *) "1048576");
MPI_Info_set(file_info, (char *) "cb_buffer_size" , (char *) "4194304");
* */
check( H5Pset_fapl_mpio(file_plist, parallel->Comm[DIR_ALL], file_info), DMESG("Set MPI Property"));
#endif
file = check(H5Fcreate(outputFileName.c_str(), (overwriteFile ? H5F_ACC_TRUNC : H5F_ACC_EXCL),
H5P_DEFAULT, file_plist ), DMESG("H5FCreate : HDF5 File (File already exists ? use -f to overwrite) : " + outputFileName));
check( H5Pclose(file_plist), DMESG("H5Pclose"));
#ifdef GKC_PARALLEL_MPI
MPI_Info_free(&file_info);
#endif
//////////////////////////////////////////////////////////////// Info Group ////////////////////////////////////////////////////////
hid_t infoGroup = check(H5Gcreate(file, "/Info",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
check(H5LTset_attribute_string(infoGroup, ".", "Output", outputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Input", inputFileName.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Version", PACKAGE_VERSION), DMESG("H5LTset_attribute"));
// Some Simulation specific stuff
//check(H5LTset_attribute_string(infoGroup, ".", "Solver", ((setup->Solver & VL_LIN) ? "Linear" : "Non-Linear")), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "Type", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//heck(H5LTset_attribute_string(infoGroup, ".", "FFTSolverS", ((setup->VlasovType & VLASOV_LOCAL ) ? "Local" : "Global" )), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_string(infoGroup, ".", "Initial Condition", setup->PerturbationMethod.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Info", info.c_str()), DMESG("H5LTset_attribute"));
check(H5LTset_attribute_string(infoGroup, ".", "Config", setup->configFileString.c_str()), DMESG("H5LTset_attribute"));
H5Gclose(infoGroup);
/// Wrote setup constants, ugly here ////
hid_t constantsGroup = check(H5Gcreate(file, "/Constants",H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT), DMESG("Error creating group file for Phasespace : H5Gcreate"));
//
if (!setup->parser_constants.empty()) {
std::vector<std::string> const_vec = Setup::split(setup->parser_constants, ",");
for(int s = 0; s < const_vec.size(); s++) {
std::vector<std::string> key_value = Setup::split(const_vec[s],"=");
double value = Setup::string_to_double(key_value[1]);
int dim[] = { 1 };
// check(H5LTmake_dataset_double(constantsGroup, Setup::trimLower(key_value[0], false).c_str(), 1, dim, &value ), DMESG("Write Constants Attributes"));
check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &value, 1), DMESG("H5LTset_attribute"));
//check(H5LTset_attribute_double(constantsGroup, ".", Setup::trimLower(key_value[0], false).c_str(), &(Setup::string_to_double(key_value[1])), 1), DMESG("H5LTset_attribute"));
};
}
H5Gclose(constantsGroup);
// ********************* setup Table for CFL *****************88
cfl_table = new CFLTable();
cfl_offset[0] = HOFFSET( CFLTable, timeStep );
cfl_offset[1] = HOFFSET( CFLTable, time );
cfl_offset[2] = HOFFSET( CFLTable, Fx );
cfl_offset[3] = HOFFSET( CFLTable, Fy );
cfl_offset[4] = HOFFSET( CFLTable, Fz );
cfl_offset[5] = HOFFSET( CFLTable, Fv );
cfl_offset[6] = HOFFSET( CFLTable, total );
for(int i = 1; i < 7; i++) cfl_sizes[i] = sizeof(double); cfl_sizes[0] = sizeof(int);
hid_t cfl_type[7]; for(int i = 1; i < 7; i++) cfl_type [i] = H5T_NATIVE_DOUBLE; cfl_type[0] = H5T_NATIVE_INT;
const char *cfl_names[7];
cfl_names[0] = "timeStep";
cfl_names[1] = "time";
cfl_names[2] = "Fx"; cfl_names[3] = "Fy"; cfl_names[4] = "Fz"; cfl_names[5] = "Fv"; cfl_names[6] = "Total";
check(H5TBmake_table("cflTable", file, "cfl", (hsize_t) 7, (hsize_t) 0, sizeof(CFLTable), (const char**) cfl_names,
cfl_offset, cfl_type, 32, NULL, 0, cfl_table ), DMESG("H5Tmake_table : cfl"));
return HELIOS_SUCCESS;
}
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_WR_H5_MPH( struct param_record param,
const struct mph_envi *mph )
{
register unsigned short ni = 0;
hid_t mph_type[NFIELDS];
const int compress = 0;
const char *mph_names[NFIELDS] = {
"product_name", "proc_stage", "ref_doc",
"acquisition_station", "proc_center", "proc_time",
"software_version",
"sensing_start", "sensing_stop",
"phase", "cycle", "rel_orbit", "abs_orbit", "state_vector_time",
"delta_ut1",
"x_position", "y_position", "z_position",
"x_velocity", "y_velocity", "z_velocity",
"vector_source", "utc_sbt_time", "sat_binary_time", "clock_step",
"leap_utc", "leap_sign", "leap_err",
"product_err", "tot_size", "sph_size", "num_dsd", "dsd_size",
"num_data_sets"
};
/*
* define user-defined data types of the Table-fields
*/
mph_type[0] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[0], (size_t) ENVI_FILENAME_SIZE );
mph_type[1] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[1], (size_t) 2 );
mph_type[2] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[2], (size_t) 24 );
mph_type[3] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[3], (size_t) 21 );
mph_type[4] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[4], (size_t) 7 );
mph_type[5] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[5], (size_t) UTC_STRING_LENGTH );
mph_type[6] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[6], (size_t) 15 );
mph_type[7] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[7], (size_t) UTC_STRING_LENGTH );
mph_type[8] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[8], (size_t) UTC_STRING_LENGTH );
mph_type[9] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[9], (size_t) 2 );
mph_type[10] = H5Tcopy( H5T_NATIVE_SHORT );
mph_type[11] = H5Tcopy( H5T_NATIVE_INT );
mph_type[12] = H5Tcopy( H5T_NATIVE_INT );
mph_type[13] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[13], (size_t) UTC_STRING_LENGTH );
mph_type[14] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[15] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[16] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[17] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[18] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[19] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[20] = H5Tcopy( H5T_NATIVE_DOUBLE );
mph_type[21] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[21], (size_t) 3 );
mph_type[22] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[22], (size_t) UTC_STRING_LENGTH );
mph_type[23] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[24] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[25] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[25], (size_t) UTC_STRING_LENGTH );
mph_type[26] = H5Tcopy( H5T_NATIVE_SHORT );
mph_type[27] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[27], (size_t) 2 );
mph_type[28] = H5Tcopy( H5T_C_S1 );
(void) H5Tset_size( mph_type[28], (size_t) 2 );
mph_type[29] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[30] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[31] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[32] = H5Tcopy( H5T_NATIVE_UINT );
mph_type[33] = H5Tcopy( H5T_NATIVE_UINT );
/*
* create table
*/
(void) H5TBmake_table( "Main Product Header", param.hdf_file_id, "MPH",
NFIELDS, 1, mph_size, mph_names, mph_offs,
mph_type, 1, NULL, compress, mph );
/*
* create some attributes for quick access
*/
(void) H5LTset_attribute_int( param.hdf_file_id, "/", "abs_orbit",
&mph->abs_orbit, 1 );
/*
* close interface
*/
do {
(void) H5Tclose( mph_type[ni] );
} while ( ++ni < NFIELDS );
}
int SpIO_H5WriteTau(hid_t h5f_id, const Zone *zone)
{
SpPhys *pp = zone->data;
/* Just in case the programmer did something stupid */
Deb_ASSERT(pp->mol != NULL);
Deb_ASSERT(pp->tau != NULL);
herr_t hstatus = 0;
int status = 0;
size_t
i, j,
nrad = pp->mol->nrad,
record_size = sizeof(double) * nrad,
field_offset[nrad];
const char **field_names = Mem_CALLOC(nrad, field_names);
char **level_names = Mem_CALLOC(nrad, level_names);
hid_t field_type[nrad];
hsize_t chunk_size = 10;
int *fill_data = NULL, compress = 0;
double *tau = Mem_CALLOC(zone->nchildren * nrad, tau);
/* Init fields */
for(i = 0; i < nrad; i++) {
field_offset[i] = i * sizeof(double);
field_type[i] = H5T_NATIVE_DOUBLE;
level_names[i] = Mem_Sprintf("line%lu", (unsigned long)i);
field_names[i] = level_names[i];
}
/* Load data */
#define TAU(i, j)\
tau[(j) + nrad * (i)]
for(i = 0; i < zone->nchildren; i++) {
pp = zone->children[i]->data;
for(j = 0; j < nrad; j++) {
TAU(i, j) = pp->tau[j];
}
}
#undef TAU
/* Write table */
hstatus = H5TBmake_table(
"Level populations",
h5f_id,
"TAU",
(hsize_t)nrad,
(hsize_t)zone->nchildren,
record_size,
field_names,
field_offset,
field_type,
chunk_size,
fill_data,
compress,
tau
);
/* Cleanup */
for(i = 0; i < nrad; i++)
free(level_names[i]);
free(level_names);
free(field_names);
free(tau);
if(hstatus < 0)
status = Err_SETSTRING("Error writing `TAU' table");
return status;
}
int SpIO_H5WritePops(hid_t h5f_id, const Zone *zone)
{
SpPhys *pp = zone->data;
/* Just in case the programmer did something stupid */
Deb_ASSERT(pp->mol != NULL);
Deb_ASSERT(pp->pops[0] != NULL);
herr_t hstatus = 0;
int status = 0;
size_t
i, j,
nlev = pp->mol->nlev,
record_size = sizeof(double) * nlev,
field_offset[nlev];
const char **field_names = Mem_CALLOC(nlev, field_names);
char **level_names = Mem_CALLOC(nlev, level_names);
hid_t field_type[nlev];
hsize_t chunk_size = 10;
int *fill_data = NULL, compress = 0;
double *pops = Mem_CALLOC(zone->nchildren * nlev, pops);
/* Init fields */
for(i = 0; i < nlev; i++) {
field_offset[i] = i * sizeof(double);
field_type[i] = H5T_NATIVE_DOUBLE;
level_names[i] = Mem_Sprintf("lev%lu", (unsigned long)i);
field_names[i] = level_names[i];
}
/* Load data */
#define POPS(i, j)\
pops[(j) + nlev * (i)]
for(i = 0; i < zone->nchildren; i++) {
pp = zone->children[i]->data;
for(j = 0; j < nlev; j++) {
POPS(i, j) = pp->pops[0][j];
}
}
#undef POPS
/* Write table */
hstatus = H5TBmake_table(
"Level populations",
h5f_id,
"POPS",
(hsize_t)nlev,
(hsize_t)zone->nchildren,
record_size,
field_names,
field_offset,
field_type,
chunk_size,
fill_data,
compress,
pops
);
/* Cleanup */
for(i = 0; i < nlev; i++)
free(level_names[i]);
free(level_names);
free(field_names);
free(pops);
if(hstatus < 0)
status = Err_SETSTRING("Error writing `POPS' table");
return status;
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
Particle dst_buf[ 2 * NRECORDS ];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int compress = 0;
int *fill_data = NULL;
herr_t status;
hsize_t nfields_out;
hsize_t nrecords_out;
int i;
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_10.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make two tables */
status=H5TBmake_table( "Table Title",file_id,TABLE1_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
status=H5TBmake_table( "Table Title",file_id,TABLE2_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
/* Combine the two tables into a third in the same file */
status=H5TBcombine_tables( file_id, TABLE1_NAME, file_id, TABLE2_NAME, TABLE3_NAME );
/* read the combined table */
status=H5TBread_table( file_id, TABLE3_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* Get table info */
status=H5TBget_table_info (file_id,TABLE3_NAME, &nfields_out, &nrecords_out );
/* print */
printf ("Table has %d fields and %d records\n",(int)nfields_out,(int)nrecords_out);
/* print it by rows */
for (i=0; i<nrecords_out; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
/*------------------------------------------------------------------------- * Function: h5tbmake_table_c * * Purpose: Call H5TBmake_table * * Return: Success: 0, Failure: -1 * * Programmer: [email protected] * * Date: October 06, 2004 * * Comments: * * Modifications: * * *------------------------------------------------------------------------- */ int_f nh5tbmake_table_c(int_f *namelen1, _fcd name1, hid_t_f *loc_id, int_f *namelen, _fcd name, hsize_t_f *nfields, hsize_t_f *nrecords, size_t_f *type_size, size_t_f *field_offset, hid_t_f *field_types, hsize_t_f *chunk_size, int_f *compress, int_f *namelen2, /* field_names lenghts */ _fcd field_names) /* field_names */ { int ret_value = -1; herr_t ret; char *c_name; int c_namelen; char *c_name1; int c_namelen1; hsize_t num_elem; hsize_t i; int max_len=1; hid_t c_loc_id = *loc_id; hsize_t c_nfields = *nfields; hsize_t c_nrecords = *nrecords; hsize_t c_chunk_size = *chunk_size; size_t c_type_size = *type_size; size_t *c_field_offset; hid_t *c_field_types; char **c_field_names; char *tmp, *tmp_p; num_elem = *nfields; for (i=0; i < num_elem; i++) { if (namelen2[i] > max_len) max_len = namelen2[i]; } /* * Convert FORTRAN name to C name */ c_namelen = *namelen; c_name = (char *)HD5f2cstring(name, c_namelen); if (c_name == NULL) return ret_value; c_namelen1 = *namelen1; c_name1 = (char *)HD5f2cstring(name1, c_namelen1); if (c_name1 == NULL) return ret_value; c_field_offset = (size_t*)malloc(sizeof(size_t) * (size_t)c_nfields); if (!c_field_offset) return ret_value; c_field_types = (hid_t*)malloc(sizeof(hid_t) * (size_t)c_nfields); if (!c_field_types) return ret_value; for (i=0; i < num_elem; i++) { c_field_offset[i] = field_offset[i]; c_field_types[i] = field_types[i]; } /* * Allocate array of character pointers */ c_field_names = (char **)malloc((size_t)num_elem * sizeof(char *)); if (c_field_names == NULL) return ret_value; /* Copy data to long C string */ tmp = (char *)HD5f2cstring(field_names, (int)(max_len*num_elem)); if (tmp == NULL) { free(c_field_names); return ret_value; } /* * Move data from temorary buffer */ tmp_p = tmp; for (i=0; i < num_elem; i++) { c_field_names[i] = (char *) malloc((size_t)namelen2[i]+1); memcpy(c_field_names[i], tmp_p, (size_t)namelen2[i]); c_field_names[i][namelen2[i]] = '\0'; tmp_p = tmp_p + max_len; } /* * Call H5TBmake_table function. */ ret = H5TBmake_table(c_name1,c_loc_id,c_name,c_nfields,c_nrecords,c_type_size, c_field_names,c_field_offset,c_field_types,c_chunk_size,NULL,*compress,NULL); for (i=0; i < num_elem; i++) { free (c_field_names[i]); } free(c_field_names); free(tmp); free(c_field_offset); free(c_field_types); if (ret < 0) return ret_value; ret_value = 0; return ret_value; }
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
/* Define a subset of Particle, with latitude and longitude fields */
typedef struct Position
{
int lati;
int longi;
} Position;
/* Define a subset of Particle, with name and pressure fields */
typedef struct NamePressure
{
char name[16];
float pressure;
} NamePressure;
/* Calculate the type_size and the offsets of our struct members */
Particle dst_buf[NRECORDS];
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
size_t field_offset_pos[2] = { HOFFSET( Position, lati ),
HOFFSET( Position, longi )};
/* Initially no data */
Particle *p_data = NULL;
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} }; /* Fill value particle */
int compress = 0;
hsize_t nfields;
hsize_t start; /* Record to start reading/writing */
hsize_t nrecords; /* Number of records to read/write */
herr_t status;
int i;
/* Define new values for the field "Pressure" */
float pressure_in [NRECORDS_ADD] =
{ 0.0f,1.0f,2.0f};
int field_index_pre[1] = { 3 };
int field_index_pos[2] = { 1,2 };
/* Define new values for the fields "Latitude,Longitude" */
Position position_in[NRECORDS_ADD] = { {0,0},
{10,10},
{20,20} };
size_t field_sizes_pos[2]=
{
sizeof(position_in[0].longi),
sizeof(position_in[0].lati)
};
size_t field_sizes_pre[1]=
{
sizeof(float)
};
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "ex_table_05.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make the table */
status=H5TBmake_table( "Table Title", file_id, TABLE_NAME,NFIELDS,NRECORDS,
dst_size,field_names, dst_offset, field_type,
chunk_size, fill_data, compress, p_data );
/* Write the pressure field starting at record 2 */
nfields = 1;
start = 2;
nrecords = NRECORDS_ADD;
status=H5TBwrite_fields_index( file_id, TABLE_NAME, nfields, field_index_pre, start, nrecords,
sizeof( float ), 0, field_sizes_pre, pressure_in );
/* Write the new longitude and latitude information starting at record 2 */
nfields = 2;
start = 2;
nrecords = NRECORDS_ADD;
status=H5TBwrite_fields_index( file_id, TABLE_NAME, nfields, field_index_pos, start, nrecords,
sizeof( Position ), field_offset_pos, field_sizes_pos, position_in );
/* read the table */
status=H5TBread_table( file_id, TABLE_NAME, dst_size, dst_offset, dst_sizes, dst_buf );
/* print it by rows */
for (i=0; i<NRECORDS; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
int main( void )
{
Particle dst_buf[NRECORDS];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
Particle p = {"zero",0,0, 0.0f, 0.0};
size_t dst_sizes[NFIELDS] = { sizeof( p.name),
sizeof( p.lati),
sizeof( p.longi),
sizeof( p.pressure),
sizeof( p.temperature)};
/* Fill value particle */
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
hsize_t start; /* Record to start reading/writing */
hsize_t nrecords; /* Number of records to read/write */
herr_t status;
int i;
/* Define 2 new particles to write */
Particle particle_in[NRECORDS_WRITE] =
{ {"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0} };
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "h5_table_03.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/* Make the table */
status=H5TBmake_table( "Table Title",
file_id,
TABLE_NAME,
NFIELDS,
NRECORDS,
dst_size,
field_names,
dst_offset,
field_type,
chunk_size,
fill_data,
0, /* no compression */
NULL ); /* no data written */
/* Overwrite 2 records starting at record 0 */
start = 0;
nrecords = NRECORDS_WRITE;
status = H5TBwrite_records (file_id,
TABLE_NAME,
start,
nrecords,
dst_size,
dst_offset,
dst_sizes,
particle_in);
/* read the table */
status = H5TBread_table (file_id,
TABLE_NAME,
dst_size,
dst_offset,
dst_sizes,
dst_buf);
/* print it by rows */
for (i=0; i<NRECORDS; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose( file_id );
return 0;
}
int main( void )
{
Particle dst_buf[NRECORDS];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
size_t field_offset_pos[2] = { HOFFSET( Position, lati ),
HOFFSET( Position, longi )};
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t fileID;
hsize_t chunk_size = 10;
Particle fill_data[1] =
{ {"no data",-1,-1, -99.0f, -99.0} }; /* Fill value particle */
hsize_t start; /* Record to start reading/writing */
hsize_t nrecords; /* Number of records to read/write */
int compress = 0;
int n;
herr_t status;
Particle *p_data = NULL; /* Initially no data */
float pressure_in [NRECORDS_ADD] = /* Define new values for the field "Pressure" */
{ 0.0f,1.0f,2.0f};
Position position_in[NRECORDS_ADD] = {/* Define new values for "Latitude,Longitude" */
{0,0},
{10,10},
{20,20}};
NamePressure namepre_in[NRECORDS_ADD] =/* Define new values for "Name,Pressure" */
{ {"zero",0.0f},
{"one", 1.0f},
{"two", 2.0f},
};
size_t field_sizes_pos[2]=
{
sizeof(position_in[0].longi),
sizeof(position_in[0].lati)
};
size_t field_sizes_pre[1]=
{
sizeof(namepre_in[0].pressure)
};
/* Initialize the field field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/*__________________________________________________________________
Create a new file using default properties.
*/
fileID = H5Fcreate ("h5_table_04.h5",
H5F_ACC_TRUNC,
H5P_DEFAULT,
H5P_DEFAULT);
/*__________________________________________________________________
Make the table
*/
status = H5TBmake_table ("Table Title",
fileID,
TABLE_NAME,
NFIELDS,
NRECORDS,
dst_size,
field_names,
dst_offset,
field_type,
chunk_size,
fill_data,
compress,
p_data);
/*__________________________________________________________________
Write the pressure field starting at record 2.
*/
start = 2;
nrecords = NRECORDS_ADD;
status = H5TBwrite_fields_name (fileID,
TABLE_NAME,
"Pressure",
start,
nrecords,
sizeof( float ),
0,
field_sizes_pre,
pressure_in);
/*__________________________________________________________________
Write the new longitude and latitude information starting at
record 2.
*/
start = 2;
nrecords = NRECORDS_ADD;
status = H5TBwrite_fields_name (fileID,
TABLE_NAME,
"Latitude,Longitude",
start,
nrecords,
sizeof( Position ),
field_offset_pos,
field_sizes_pos,
position_in);
/*__________________________________________________________________
Read the table
*/
status = H5TBread_table (fileID,
TABLE_NAME,
dst_size,
dst_offset,
dst_sizes,
dst_buf);
/* print it by rows */
for (n=0; n<NRECORDS; n++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[n].name,
dst_buf[n].lati,
dst_buf[n].longi,
dst_buf[n].pressure,
dst_buf[n].temperature);
printf ("\n");
}
/*-------------------------------------------------------------------------
* end
*-------------------------------------------------------------------------
*/
/* close type */
H5Tclose( string_type );
/* close the file */
H5Fclose (fileID);
return 0;
}
bool stfio::exportHDF5File(const std::string& fName, const Recording& WData, ProgressInfo& progDlg) {
hid_t file_id = H5Fcreate(fName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
const int NRECORDS = 1;
const int NFIELDS = 3;
/* Calculate the size and the offsets of our struct members in memory */
size_t rt_offset[NFIELDS] = { HOFFSET( rt, channels ),
HOFFSET( rt, date ),
HOFFSET( rt, time )};
/* Define an array of root tables */
rt p_data;
p_data.channels = WData.size();
struct tm t = WData.GetDateTime();
std::size_t date_length = snprintf(p_data.date, DATELEN, "%04i-%02i-%02i", t.tm_year+1900, t.tm_mon+1, t.tm_mday);
std::size_t time_length = snprintf(p_data.time, TIMELEN, "%02i:%02i:%02i", t.tm_hour, t.tm_min, t.tm_sec);
// ensure that an undefine string is set to "\0", and that the terminating \0 is counted in string length
p_data.date[date_length++] = 0;
p_data.time[time_length++] = 0;
/* Define field information */
const char *field_names[NFIELDS] = { "channels", "date", "time" };
hid_t field_type[NFIELDS];
/* Initialize the field field_type */
hid_t string_type1 = H5Tcopy( H5T_C_S1 );
hid_t string_type2 = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type1, date_length);
H5Tset_size( string_type2, time_length);
field_type[0] = H5T_NATIVE_INT;
field_type[1] = string_type1;
field_type[2] = string_type2;
std::ostringstream desc;
desc << "Description of " << fName;
herr_t status = H5TBmake_table( desc.str().c_str(), file_id, "description", (hsize_t)NFIELDS, (hsize_t)NRECORDS, sizeof(rt),
field_names, rt_offset, field_type, 10, NULL, 0, &p_data );
if (status < 0) {
std::string errorMsg("Exception while writing description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
hid_t comment_group = H5Gcreate2( file_id,"/comment", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/* File comment. */
std::string description(WData.GetFileDescription());
if (description.length() <= 0) {
description = "No description";
}
status = H5LTmake_dataset_string(file_id, "/comment/description", description.c_str());
if (status < 0) {
std::string errorMsg("Exception while writing description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
std::string comment(WData.GetComment());
if (comment.length() <= 0) {
comment = "No comment";
}
status = H5LTmake_dataset_string(file_id, "/comment/comment", comment.c_str());
if (status < 0) {
std::string errorMsg("Exception while writing comment in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
H5Gclose(comment_group);
std::vector<std::string> channel_name(WData.size());
hid_t channels_group = H5Gcreate2( file_id,"/channels", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
for ( std::size_t n_c=0; n_c < WData.size(); ++n_c) {
/* Channel descriptions. */
std::ostringstream ossname;
ossname << WData[n_c].GetChannelName();
if ( ossname.str() == "" ) {
ossname << "ch" << (n_c);
}
channel_name[n_c] = ossname.str();
hsize_t dimsc[1] = { 1 };
hid_t string_typec = H5Tcopy( H5T_C_S1 );
std::size_t cn_length = channel_name[n_c].length();
if (cn_length <= 0) cn_length = 1;
H5Tset_size( string_typec, cn_length );
std::vector<char> datac(channel_name[n_c].length());
std::copy(channel_name[n_c].begin(),channel_name[n_c].end(), datac.begin());
std::ostringstream desc_path; desc_path << "/channels/ch" << (n_c);
status = H5LTmake_dataset(file_id, desc_path.str().c_str(), 1, dimsc, string_typec, &datac[0]);
if (status < 0) {
std::string errorMsg("Exception while writing channel name in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
std::ostringstream channel_path; channel_path << "/" << channel_name[n_c];
hid_t channel_group = H5Gcreate2( file_id, channel_path.str().c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (channel_group < 0) {
std::ostringstream errorMsg;
errorMsg << "Exception while creating channel group for "
<< channel_path.str().c_str();
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg.str());
}
/* Calculate the size and the offsets of our struct members in memory */
size_t ct_size = sizeof( ct );
size_t ct_offset[1] = { HOFFSET( rt, channels ) };
/* Define an array of channel tables */
ct c_data = { (int)WData[n_c].size() };
/* Define field information */
const char *cfield_names[1] = { "n_sections" };
hid_t cfield_type[1] = {H5T_NATIVE_INT};
std::ostringstream c_desc;
c_desc << "Description of channel " << n_c;
status = H5TBmake_table( c_desc.str().c_str(), channel_group, "description", (hsize_t)1, (hsize_t)1, ct_size,
cfield_names, ct_offset, cfield_type, 10, NULL, 0, &c_data );
if (status < 0) {
std::string errorMsg("Exception while writing channel description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
int max_log10 = 0;
if (WData[n_c].size() > 1) {
max_log10 = int(log10((double)WData[n_c].size()-1.0));
}
for (std::size_t n_s=0; n_s < WData[n_c].size(); ++n_s) {
int progbar =
// Channel contribution:
(int)(((double)n_c/(double)WData.size())*100.0+
// Section contribution:
(double)(n_s)/(double)WData[n_c].size()*(100.0/WData.size()));
std::ostringstream progStr;
progStr << "Writing channel #" << n_c + 1 << " of " << WData.size()
<< ", Section #" << n_s << " of " << WData[n_c].size();
progDlg.Update(progbar, progStr.str());
// construct a number with leading zeros:
int n10 = 0;
if (n_s > 0) {
n10 = int(log10((double)n_s));
}
std::ostringstream strZero; strZero << "";
for (int n_z=n10; n_z < max_log10; ++n_z) {
strZero << "0";
}
// construct a section name:
std::ostringstream section_name; section_name << WData[n_c][n_s].GetSectionDescription();
if ( section_name.str() == "" ) {
section_name << "sec" << n_s;
}
// create a child group in the channel:
std::ostringstream section_path;
section_path << channel_path.str() << "/" << "section_" << strZero.str() << n_s;
hid_t section_group = H5Gcreate2( file_id, section_path.str().c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// add data and description, store as 32 bit little endian independent of machine:
hsize_t dims[1] = { WData[n_c][n_s].size() };
std::ostringstream data_path;
data_path << section_path.str() << "/data";
Vector_float data_cp(WData[n_c][n_s].get().size()); /* 32 bit */
for (std::size_t n_cp = 0; n_cp < WData[n_c][n_s].get().size(); ++n_cp) {
data_cp[n_cp] = float(WData[n_c][n_s][n_cp]);
}
status = H5LTmake_dataset(file_id, data_path.str().c_str(), 1, dims, H5T_IEEE_F32LE, &data_cp[0]);
if (status < 0) {
std::string errorMsg("Exception while writing data in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
const int NSRECORDS = 1;
const int NSFIELDS = 3;
/* Calculate the size and the offsets of our struct members in memory */
size_t st_size = sizeof( st );
size_t st_offset[NSFIELDS] = { HOFFSET( st, dt ),
HOFFSET( st, xunits ),
HOFFSET( st, yunits )};
/* Define an array of root tables */
st s_data;
s_data.dt = WData.GetXScale();
if (WData.GetXUnits().length() < UNITLEN)
strcpy( s_data.xunits, WData.GetXUnits().c_str() );
if (WData[n_c].GetYUnits().length() < UNITLEN)
strcpy( s_data.yunits, WData[n_c].GetYUnits().c_str() );
/* Define field information */
const char *sfield_names[NSFIELDS] = { "dt", "xunits", "yunits" };
hid_t sfield_type[NSFIELDS];
/* Initialize the field field_type */
hid_t string_type4 = H5Tcopy( H5T_C_S1 );
hid_t string_type5 = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type4, 2);
std::size_t yu_length = WData[n_c].GetYUnits().length();
if (yu_length <= 0) yu_length = 1;
H5Tset_size( string_type5, yu_length );
sfield_type[0] = H5T_NATIVE_DOUBLE;
sfield_type[1] = string_type4;
sfield_type[2] = string_type5;
std::ostringstream sdesc;
sdesc << "Description of " << section_name.str();
status = H5TBmake_table( sdesc.str().c_str(), section_group, "description", (hsize_t)NSFIELDS, (hsize_t)NSRECORDS, st_size,
sfield_names, st_offset, sfield_type, 10, NULL, 0, &s_data );
if (status < 0) {
std::string errorMsg("Exception while writing section description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
throw std::runtime_error(errorMsg);
}
H5Gclose(section_group);
}
H5Gclose(channel_group);
}
H5Gclose(channels_group);
/* Terminate access to the file. */
status = H5Fclose(file_id);
if (status < 0) {
std::string errorMsg("Exception while closing file in stfio::exportHDF5File");
throw std::runtime_error(errorMsg);
}
/* Release all hdf5 resources */
status = H5close();
if (status < 0) {
std::string errorMsg("Exception while closing file in stfio::exportHDF5File");
throw std::runtime_error(errorMsg);
}
return (status >= 0);
}
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_LV1_WR_H5_SCPN( struct param_record param, unsigned int nr_scpn,
const struct scpn_scia *scpn )
{
hid_t ads_id;
hsize_t adim;
herr_t stat;
hid_t scpn_type[NFIELDS];
const hbool_t compress = (param.flag_deflate == PARAM_SET) ? TRUE : FALSE;
const size_t scpn_size = sizeof( struct scpn_scia );
const char *scpn_names[NFIELDS] = {
"mjd", "flag_mds", "orbit_phase", "srs_param", "num_lines",
"wv_error_calib", "sol_spec", "line_pos", "coeffs"
};
const size_t scpn_offs[NFIELDS] = {
HOFFSET( struct scpn_scia, mjd ),
HOFFSET( struct scpn_scia, flag_mds ),
HOFFSET( struct scpn_scia, orbit_phase ),
HOFFSET( struct scpn_scia, srs_param ),
HOFFSET( struct scpn_scia, num_lines ),
HOFFSET( struct scpn_scia, wv_error_calib ),
HOFFSET( struct scpn_scia, sol_spec ),
HOFFSET( struct scpn_scia, line_pos ),
HOFFSET( struct scpn_scia, coeffs )
};
/*
* check number of PMD records
*/
if ( nr_scpn == 0 ) return;
/*
* open/create group /ADS
*/
ads_id = NADC_OPEN_HDF5_Group( param.hdf_file_id, "/ADS" );
if ( ads_id < 0 ) NADC_RETURN_ERROR( NADC_ERR_HDF_GRP, "/ADS" );
/*
* write SCPN data sets
*/
adim = SCIENCE_PIXELS;
scpn_type[0] = H5Topen( param.hdf_file_id, "mjd", H5P_DEFAULT );
scpn_type[1] = H5Tcopy( H5T_NATIVE_UCHAR );
scpn_type[2] = H5Tcopy( H5T_NATIVE_FLOAT );
adim = SCIENCE_CHANNELS;
scpn_type[3] = H5Tarray_create( H5T_NATIVE_UCHAR, 1, &adim );
scpn_type[4] = H5Tarray_create( H5T_NATIVE_USHORT, 1, &adim );
scpn_type[5] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
adim = SCIENCE_PIXELS;
scpn_type[6] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
adim = 3 * SCIENCE_CHANNELS;
scpn_type[7] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
adim = NUM_SPEC_COEFFS * SCIENCE_CHANNELS;
scpn_type[8] = H5Tarray_create( H5T_NATIVE_DOUBLE, 1, &adim );
stat = H5TBmake_table( "scpn", ads_id, "NEW_SPECTRAL_CALIBRATION",
NFIELDS, 1, scpn_size, scpn_names,
scpn_offs, scpn_type, 1,
NULL, compress, scpn );
if ( stat < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, "scpn" );
/*
* close interface
*/
done:
(void) H5Tclose( scpn_type[0] );
(void) H5Tclose( scpn_type[1] );
(void) H5Tclose( scpn_type[2] );
(void) H5Tclose( scpn_type[3] );
(void) H5Tclose( scpn_type[4] );
(void) H5Tclose( scpn_type[5] );
(void) H5Tclose( scpn_type[6] );
(void) H5Tclose( scpn_type[7] );
(void) H5Tclose( scpn_type[8] );
(void) H5Gclose( ads_id );
}
int ias_rlut_write_linearization_params
(
const IAS_RLUT_IO *rlut_file, /* I: Open RLUT file */
const IAS_RLUT_LINEARIZATION_PARAMS *linearization_params,
/* I: Pointer to an array of data
structures containing the
linearization parameters for all
detectors in the current band/SCA */
int band_number, /* I: Current band number */
int sca_number, /* I: Current SCA number*/
int num_detectors /* I: Number of detectors in the
current band/SCA */
)
{
char bandsca_parameter_name[IAS_RLUT_BANDSCA_GROUP_NAME_LENGTH + 1];
/* Linearization parameter group
name for the current band/SCA */
const char *field_names[IAS_RLUT_PARAM_NFIELDS];
/* Name of each linearization
parameter */
size_t offsets[IAS_RLUT_PARAM_NFIELDS];/* Data offsets in
LINEARIZATION_PARAMS
data structure for each
field*/
size_t field_sizes[IAS_RLUT_PARAM_NFIELDS];
/* Size of each field */
hid_t field_types[IAS_RLUT_PARAM_NFIELDS];
/* Data type for each field */
hid_t fields_to_close[IAS_RLUT_PARAM_NFIELDS];
/* Flags indicating open
fields needing to be closed */
hid_t linearization_param_group_id; /* Root LINEARIZATION_PARAMETERS
group ID */
hid_t bandsca_group_id; /* SCA group ID */
hsize_t type_size; /* Size of base
LINEARIZATION_PARAMS
data structure */
herr_t hdf_status; /* HDF5 error status flag */
int status; /* IAS status flags */
int return_status = SUCCESS;
/* Make sure the RLUT file is actually open */
if ((rlut_file == NULL) || (rlut_file->file_id < 0))
{
IAS_LOG_ERROR("NULL pointer to IAS_RLUT_IO data block, or no RLUT "
"file has been opened");
return ERROR;
}
/* Construct the group name for the current band/SCA */
status = snprintf(bandsca_parameter_name, sizeof(bandsca_parameter_name),
"%s/Band%02d_SCA%02d", LINEARIZATION_PARAMS_GROUP_NAME, band_number,
sca_number);
if ((status < 0) || (status >= sizeof(bandsca_parameter_name)))
{
IAS_LOG_ERROR("Creating group name for band %d SCA %d "
"linearization parameters", band_number, sca_number);
return ERROR;
}
/* Open the root group */
linearization_param_group_id = H5Gopen(rlut_file->file_id,
LINEARIZATION_PARAMS_GROUP_NAME, H5P_DEFAULT);
if (linearization_param_group_id < 0)
{
IAS_LOG_ERROR("Opening root linearization parameters group");
return ERROR;
}
/* Create a new group for the current band/SCA within this group */
bandsca_group_id = H5Gcreate(linearization_param_group_id,
bandsca_parameter_name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (bandsca_group_id < 0)
{
IAS_LOG_ERROR("Creating group for band %d SCA %d linearization "
"parameters", band_number, sca_number);
H5Gclose(linearization_param_group_id);
return ERROR;
}
/* Build the table definition */
status = ias_rlut_build_linearization_params_table_description(offsets,
field_names, field_types, fields_to_close, field_sizes);
if (status != SUCCESS)
{
IAS_LOG_ERROR("Building linearization parameter table description");
H5Gclose(bandsca_group_id);
H5Gclose(linearization_param_group_id);
return ERROR;
}
/* Get the size of the data structure */
type_size = sizeof(*linearization_params);
/* Write the parameter set for the current band/SCA */
hdf_status = H5TBmake_table(LINEARIZATION_PARAMS_TABLE_NAME,
bandsca_group_id, LINEARIZATION_PARAMS_DATASET_NAME,
IAS_RLUT_PARAM_NFIELDS, num_detectors, type_size, field_names,
offsets, field_types, sizeof(IAS_RLUT_LINEARIZATION_PARAMS), NULL, 0,
linearization_params);
/* Cleanup the table description */
ias_rlut_cleanup_table_description(fields_to_close,
IAS_RLUT_PARAM_NFIELDS);
/* Check the return status from the write */
if (hdf_status < 0)
{
IAS_LOG_ERROR("Writing band %d SCA %d linearization parameter "
"table to RLUT file %s", band_number, sca_number,
rlut_file->filename);
return_status = ERROR;
}
/* Close the local SCA group */
hdf_status = H5Gclose(bandsca_group_id);
if (hdf_status < 0)
{
IAS_LOG_ERROR("Closing band %d SCA %d linearization parameter "
"group", band_number, sca_number);
return_status = ERROR;
}
/* Close the main linearization parameter group */
hdf_status = H5Gclose(linearization_param_group_id);
if (hdf_status < 0)
{
IAS_LOG_ERROR("Closing root LINEARIZATION_PARAMETERS group");
return_status = ERROR;
}
return return_status;
} /* END ias_rlut_write_linearization_params */
/*+++++++++++++++++++++++++ Main Program or Function +++++++++++++++*/
void SCIA_LV1_WR_H5_VLCP( struct param_record param, unsigned int nr_vlcp,
const struct vlcp_scia *vlcp )
{
hid_t gads_id;
hsize_t adim;
herr_t stat;
hid_t vlcp_type[NFIELDS];
const hbool_t compress = (param.flag_deflate == PARAM_SET) ? TRUE : FALSE;
const char *vlcp_names[NFIELDS] = {
"orbit_phase", "obm_pmd", "var_lc", "var_lc_error", "solar_stray",
"solar_stray_error", "pmd_stray", "pmd_stray_error", "pmd_dark",
"pmd_dark_error"
};
const size_t vlcp_size = sizeof( struct vlcp_scia );
const size_t vlcp_offs[NFIELDS] = {
HOFFSET( struct vlcp_scia, orbit_phase ),
HOFFSET( struct vlcp_scia, obm_pmd ),
HOFFSET( struct vlcp_scia, var_lc ),
HOFFSET( struct vlcp_scia, var_lc_error ),
HOFFSET( struct vlcp_scia, solar_stray ),
HOFFSET( struct vlcp_scia, solar_stray_error ),
HOFFSET( struct vlcp_scia, pmd_stray ),
HOFFSET( struct vlcp_scia, pmd_stray_error ),
HOFFSET( struct vlcp_scia, pmd_dark ),
HOFFSET( struct vlcp_scia, pmd_dark_error )
};
/*
* check number of RSPO records
*/
if ( nr_vlcp == 0 ) return;
/*
* open/create group /GADS
*/
gads_id = NADC_OPEN_HDF5_Group( param.hdf_file_id, "/GADS" );
if ( gads_id < 0 ) NADC_RETURN_ERROR( NADC_ERR_HDF_GRP, "/GADS" );
/*
* write VLCP data sets
*/
vlcp_type[0] = H5Tcopy( H5T_NATIVE_FLOAT );
adim = IR_CHANNELS + PMD_NUMBER;
vlcp_type[1] = H5Tcopy( H5T_NATIVE_FLOAT );
adim = IR_CHANNELS * CHANNEL_SIZE;
vlcp_type[2] = H5Tcopy( H5T_NATIVE_FLOAT );
vlcp_type[3] = H5Tcopy( H5T_NATIVE_FLOAT );
adim = SCIENCE_PIXELS;
vlcp_type[4] = H5Tcopy( H5T_NATIVE_FLOAT );
vlcp_type[5] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
adim = PMD_NUMBER;
vlcp_type[6] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
vlcp_type[7] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
adim = IR_PMD_NUMBER;
vlcp_type[8] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
vlcp_type[9] = H5Tarray_create( H5T_NATIVE_FLOAT, 1, &adim );
stat = H5TBmake_table( "vlcp", gads_id, "LEAKAGE_VARIABLE",
NFIELDS, nr_vlcp, vlcp_size, vlcp_names,
vlcp_offs, vlcp_type, 1,
NULL, compress, vlcp );
if ( stat < 0 ) NADC_GOTO_ERROR( NADC_ERR_HDF_DATA, "vlcp" );
/*
* close interface
*/
done:
(void) H5Tclose( vlcp_type[0] );
(void) H5Tclose( vlcp_type[1] );
(void) H5Tclose( vlcp_type[2] );
(void) H5Tclose( vlcp_type[3] );
(void) H5Tclose( vlcp_type[4] );
(void) H5Tclose( vlcp_type[5] );
(void) H5Tclose( vlcp_type[6] );
(void) H5Tclose( vlcp_type[7] );
(void) H5Tclose( vlcp_type[8] );
(void) H5Tclose( vlcp_type[9] );
(void) H5Gclose( gads_id );
}
int main(int argc, char *argv[])
{
(void)argc;
(void)argv;
typedef struct rt {
int channels;
char date[DATELEN];
char time[TIMELEN];
} rt;
// H5Fis_hdf5("/dev/null");
/*
* Create a new file using H5ACC_TRUNC access,
* default file creation properties, and default file
* access properties.
* Then close the file.
*/
const int NRECORDS = 1;
const int NFIELDS = 3;
char fName[] = "tmp.h5";
/* Calculate the size and the offsets of our struct members in memory */
size_t rt_offset[NFIELDS] = { HOFFSET( rt, channels ),
HOFFSET( rt, date ),
HOFFSET( rt, time )};
rt p_data;
p_data.channels = 1;
strcpy( p_data.date, "1234-Dec-31");
strcpy( p_data.time, "12:34:56");
hid_t file_id = H5Fcreate(fName, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Define field information */
const char *field_names[NFIELDS] = { "channels", "date", "time" };
hid_t field_type[NFIELDS];
/* Initialize the field field_type */
hid_t string_type1 = H5Tcopy( H5T_C_S1 );
hid_t string_type2 = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type1, strlen(p_data.date));
H5Tset_size( string_type2, strlen(p_data.time));
field_type[0] = H5T_NATIVE_INT;
field_type[1] = string_type1;
field_type[2] = string_type2;
std::ostringstream desc;
desc << "Description of " << fName;
herr_t status = H5TBmake_table( desc.str().c_str(), file_id, "description", (hsize_t)NFIELDS, (hsize_t)NRECORDS, sizeof(rt),
field_names, rt_offset, field_type, 10, NULL, 0, &p_data );
if (status < 0) {
perror("Exception while writing description in stfio::exportHDF5File");
H5Fclose(file_id);
H5close();
exit(-1);
}
H5Fclose(file_id);
return(0);
}
int main( void )
{
typedef struct Particle
{
char name[16];
int lati;
int longi;
float pressure;
double temperature;
} Particle;
Particle dst_buf[NRECORDS];
/* Calculate the size and the offsets of our struct members in memory */
size_t dst_size = sizeof( Particle );
size_t dst_offset[NFIELDS] = { HOFFSET( Particle, name ),
HOFFSET( Particle, lati ),
HOFFSET( Particle, longi ),
HOFFSET( Particle, pressure ),
HOFFSET( Particle, temperature )};
size_t dst_sizes[NFIELDS] = { sizeof( dst_buf[0].name),
sizeof( dst_buf[0].lati),
sizeof( dst_buf[0].longi),
sizeof( dst_buf[0].pressure),
sizeof( dst_buf[0].temperature)};
/* Define an array of Particles */
Particle p_data[NRECORDS] = {
{"zero",0,0, 0.0f, 0.0},
{"one",10,10, 1.0f, 10.0},
{"two", 20,20, 2.0f, 20.0},
{"three",30,30, 3.0f, 30.0},
{"four", 40,40, 4.0f, 40.0},
{"five", 50,50, 5.0f, 50.0},
{"six", 60,60, 6.0f, 60.0},
{"seven",70,70, 7.0f, 70.0}
};
/* Define field information */
const char *field_names[NFIELDS] =
{ "Name","Latitude", "Longitude", "Pressure", "Temperature" };
hid_t field_type[NFIELDS];
hid_t string_type;
hid_t file_id;
hsize_t chunk_size = 10;
int *fill_data = NULL;
int compress = 0;
herr_t status;
int i;
/* Initialize field_type */
string_type = H5Tcopy( H5T_C_S1 );
H5Tset_size( string_type, 16 );
field_type[0] = string_type;
field_type[1] = H5T_NATIVE_INT;
field_type[2] = H5T_NATIVE_INT;
field_type[3] = H5T_NATIVE_FLOAT;
field_type[4] = H5T_NATIVE_DOUBLE;
/* Create a new file using default properties. */
file_id = H5Fcreate( "h5_table_01.h5", H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
/*-------------------------------------------------------------------------
* H5TBmake_table
*-------------------------------------------------------------------------
*/
status=H5TBmake_table ("Table Title", /* Title of the table */
file_id, /* HDF5 object identifier to the file */
TABLE_NAME, /* Name of the table */
NFIELDS, /* Number of fields/columns */
NRECORDS, /* */
dst_size, /* Size of the struct/table row */
field_names, /* */
dst_offset, /* */
field_type, /* Type of the individual table fields */
chunk_size, /* Chunking size */
fill_data, /* */
compress, /* Enable/disable compression */
p_data /* Array with the table data */
);
/*-------------------------------------------------------------------------
* H5TBread_table
*-------------------------------------------------------------------------
*/
status = H5TBread_table (file_id, /* HDF5 object identifier */
TABLE_NAME, /* Name of the table */
dst_size, /* */
dst_offset, /* */
dst_sizes, /* */
dst_buf); /* Buffer to return the data */
/* print it by rows */
for (i=0; i<NRECORDS; i++) {
printf ("%-5s %-5d %-5d %-5f %-5f",
dst_buf[i].name,
dst_buf[i].lati,
dst_buf[i].longi,
dst_buf[i].pressure,
dst_buf[i].temperature);
printf ("\n");
}
/*-------------------------------------------------------------------------
* end
*-------------------------------------------------------------------------
*/
/* Release object identifiers */
H5Tclose (string_type);
H5Fclose (file_id);
return 0;
}
