int pioReadAttributeDouble (PIOObject pioObject,
const char* attr_name, double* attr_value)
{
if (pioHasAttribute(pioObject, attr_name))
{
H5LTget_attribute_double(pioObject.identifier, ".",
attr_name, attr_value);
return 1;
}
else {
return -1;
}
}
int_f
nh5ltget_attribute_double_c(hid_t_f *loc_id,
int_f *namelen,
_fcd dsetname,
int_f *attrnamelen,
_fcd attrname,
void *buf)
{
int ret_value = -1;
herr_t ret;
hid_t c_loc_id;
char *c_name = NULL;
char *c_attrname = NULL;
int c_namelen;
int c_attrnamelen;
/*
* convert FORTRAN name to C name
*/
c_namelen = (int)*namelen;
c_name = (char *)HD5f2cstring(dsetname, c_namelen);
if (c_name == NULL)
goto done;
c_attrnamelen = (int)*attrnamelen;
c_attrname = (char *)HD5f2cstring(attrname, c_attrnamelen);
if (c_attrname == NULL)
goto done;
/*
* call H5LTget_attribute_int function.
*/
c_loc_id = (hid_t)*loc_id;
ret = H5LTget_attribute_double(c_loc_id,c_name,c_attrname,buf);
if (ret < 0)
goto done;
ret_value = 0;
done:
if(c_name!=NULL)
free(c_name);
if(c_attrname!=NULL)
free(c_attrname);
return ret_value;
}
static herr_t make_attributes( hid_t loc_id, const char* obj_name )
{
int rank_out;
hsize_t *dims_out = 0;
H5T_class_t type_class;
size_t type_size;
int i;
char attr_str_in[] = {"My attribute"};
char attr_str_out[20];
char attr_char_in[5] = {1,2,3,4,5};
char attr_char_out[5];
short attr_short_in[5] = {1,2,3,4,5};
short attr_short_out[5];
int attr_int_in[5] = {1,2,3,4,5};
int attr_int_out[5];
long attr_long_in[5] = {1,2,3,4,5};
long attr_long_out[5];
float attr_float_in[5] = {1,2,3,4,5};
float attr_float_out[5];
double attr_double_in[5] = {1,2,3,4,5};
double attr_double_out[5];
unsigned char attr_uchar_in[5] = {1,2,3,4,5};
unsigned char attr_uchar_out[5];
unsigned short attr_ushort_in[5] = {1,2,3,4,5};
unsigned short attr_ushort_out[5];
unsigned int attr_uint_in[5] = {1,2,3,4,5};
unsigned int attr_uint_out[5];
unsigned long attr_ulong_in[5] = {1,2,3,4,5};
unsigned long attr_ulong_out[5];
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_string");
/* Set the attribute */
if ( H5LTset_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_in ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_string test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_string");
/* Get the attribute */
if ( H5LTget_attribute_string( loc_id, obj_name, ATTR1_NAME, attr_str_out ) < 0 )
return -1;
if ( strcmp( attr_str_in, attr_str_out ) != 0 )
{
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_char");
/* Set the attribute */
if ( H5LTset_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_char test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_char");
/* Get the attribute */
if ( H5LTget_attribute_char( loc_id, obj_name, ATTR2_NAME, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR2_NAME, H5T_NATIVE_CHAR, attr_char_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_char_in[i] != attr_char_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_short");
/* Set the attribute */
if ( H5LTset_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_short test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_short");
/* Get the attribute */
if ( H5LTget_attribute_short( loc_id, obj_name, ATTR3_NAME, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR3_NAME, H5T_NATIVE_SHORT, attr_short_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_short_in[i] != attr_short_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_int");
/* Set the attribute */
if ( H5LTset_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_int");
/* Get the attribute */
if ( H5LTget_attribute_int( loc_id, obj_name, ATTR4_NAME, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR4_NAME, H5T_NATIVE_INT, attr_int_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_int_in[i] != attr_int_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_long");
/* Set the attribute */
if ( H5LTset_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_long");
/* Get the attribute */
if ( H5LTget_attribute_long( loc_id, obj_name, ATTR5_NAME, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR5_NAME, H5T_NATIVE_LONG, attr_long_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_long_in[i] != attr_long_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uchar");
/* Set the attribute */
if ( H5LTset_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_uchar test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uchar");
/* Get the attribute */
if ( H5LTget_attribute_uchar( loc_id, obj_name, ATTR6_NAME, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR6_NAME, H5T_NATIVE_UCHAR, attr_uchar_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uchar_in[i] != attr_uchar_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ushort");
/* Set the attribute */
if ( H5LTset_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ushort test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ushort");
/* Get the attribute */
if ( H5LTget_attribute_ushort( loc_id, obj_name, ATTR7_NAME, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR7_NAME, H5T_NATIVE_USHORT, attr_ushort_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ushort_in[i] != attr_ushort_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_uint");
/* Set the attribute */
if ( H5LTset_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_int test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_uint");
/* Get the attribute */
if ( H5LTget_attribute_uint( loc_id, obj_name, ATTR8_NAME, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR8_NAME, H5T_NATIVE_UINT, attr_uint_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_uint_in[i] != attr_uint_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_ulong test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_ulong");
/* Set the attribute */
if ( H5LTset_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_long test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ulong");
/* Get the attribute */
if ( H5LTget_attribute_ulong( loc_id, obj_name, ATTR9_NAME, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR9_NAME, H5T_NATIVE_ULONG, attr_ulong_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_ulong_in[i] != attr_ulong_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_float");
/* Set the attribute */
if ( H5LTset_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_float test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_float");
/* Get the attribute */
if ( H5LTget_attribute_float( loc_id, obj_name, ATTR10_NAME, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR10_NAME, H5T_NATIVE_FLOAT, attr_float_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_float_in[i] != attr_float_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTset_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTset_attribute_double");
/* Set the attribute */
if ( H5LTset_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_in, (size_t)5 ) < 0 )
return -1;
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_double test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_double");
/* Get the attribute */
if ( H5LTget_attribute_double( loc_id, obj_name, ATTR11_NAME, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
/* Get the attribute */
if ( H5LTget_attribute( loc_id, obj_name, ATTR11_NAME, H5T_NATIVE_DOUBLE, attr_double_out ) < 0 )
return -1;
for (i = 0; i < 5; i++)
{
if ( attr_double_in[i] != attr_double_out[i] ) {
return -1;
}
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_ndims test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_ndims");
if ( H5LTget_attribute_ndims( loc_id, obj_name, ATTR2_NAME, &rank_out ) < 0 )
return -1;
if ( rank_out != 1 ) {
return -1;
}
PASSED();
/*-------------------------------------------------------------------------
* H5LTget_attribute_info test
*-------------------------------------------------------------------------
*/
TESTING("H5LTget_attribute_info");
dims_out = (hsize_t*) malloc( sizeof(hsize_t) * rank_out );
if ( H5LTget_attribute_info( loc_id, obj_name, ATTR2_NAME, dims_out, &type_class,
&type_size) < 0 )
return -1;
for (i = 0; i < rank_out; i++)
{
if ( dims_out[i] != 5 ) {
return -1;
}
}
if ( type_class != H5T_INTEGER ) {
return -1;
}
if ( dims_out )
free( dims_out );
PASSED();
return 0;
}
int main(int argc, char *argv[]) {
progname = argv[0];
int show_usage = 0;
int outrate = 1, timesteps = 17;
char *infile = NULL, *prefix = NULL;
int optc;
while ((optc = getopt_long(argc, argv, GETOPTS, long_opts, NULL)) != -1) {
switch (optc) {
case 'i':
if (infile != NULL) {
free(infile);
}
infile = strdup(optarg);
break;
case 'p':
if (prefix != NULL) {
free(prefix);
}
prefix = strdup(optarg);
break;
case 'r':
outrate = atoi(optarg);
break;
case 't':
timesteps = atoi(optarg);
if (timesteps < 1) {
fprintf(stderr, "Invalid value for timesteps: %s, must be a number greater than 1.\n", optarg);
show_usage = 1;
}
break;
default:
show_usage = 1;
}
}
if (show_usage == 1 || optind < argc || infile == NULL || prefix == NULL) {
print_usage();
return EXIT_FAILURE;
}
// READ FILE
hsize_t dims[2];
hid_t file_id;
if ((file_id = H5Fopen(infile, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) {
print_usage();
return EXIT_FAILURE;
}
if (H5LTget_dataset_info(file_id, CCILK_DATASET, dims, NULL, NULL) < 0) {
print_usage();
return EXIT_FAILURE;
}
size_t rows = dims[0];
size_t cols = dims[1];
double *data = malloc(rows * cols * sizeof(double));
double *next = malloc(rows * cols * sizeof(double));
double width, depth, nu, sigma;
if (H5LTread_dataset_double(file_id, CCILK_DATASET, data) < 0
|| H5LTget_attribute_double(file_id, "/domain/", "width", &width) < 0
|| H5LTget_attribute_double(file_id, "/domain/", "depth", &depth) < 0
|| H5LTget_attribute_double(file_id, "/properties/", "nu", &nu) < 0
|| H5LTget_attribute_double(file_id, "/properties/", "sigma", &sigma) < 0) {
fprintf(stderr, "Encountered an issue reading the dataset\n");
return EXIT_FAILURE;
};
printf("Width: %f dept %f\n", width, depth);
simulate(data, next, rows, cols, width, depth, nu, sigma, outrate, timesteps, prefix);
free(data);
H5Fclose(file_id);
return EXIT_SUCCESS;
}
/*----------------------------------------------------------------------
NAME: read_epoch_time
PURPOSE: Reads the requested epoch time attribute from the ancillary
data file
RETURNS: Integer status code of SUCCESS or ERROR
-------------------------------------------------------------------------*/
static int read_epoch_time
(
hid_t hdf_file_id, /* I: Open ancillary data file handle */
const char *epoch_name, /* I: Epoch time name */
double epoch_time[3] /* O: Array containing epoch time components */
)
{
herr_t hdf_error_status = -1; /* HDF5 error status code */
hsize_t epoch_dims = 0; /* Epoch array dimension */
H5T_class_t type_class; /* Type class identifier */
size_t type_size = 0; /* Size of datatype in bytes */
int rank = 0; /* Number of dimensions for the
epoch time attribute */
/* Verify the epoch time array attribute has an array dimension of 1 */
hdf_error_status = H5LTget_attribute_ndims(hdf_file_id, "/",
epoch_name, &rank);
if (hdf_error_status < 0)
{
IAS_LOG_ERROR("Retrieving epoch time attribute dimensions");
return ERROR;
}
if (rank != 1) /* Should only be 1D array */
{
IAS_LOG_ERROR("Invalid rank %d detected for epoch time array, "
"should be 1", rank);
return ERROR;
}
/* The epoch time attribute should be a 1D, 3-element array of datatype
double */
hdf_error_status = H5LTget_attribute_info(hdf_file_id, "/",
epoch_name, &epoch_dims, &type_class, &type_size);
if ((hdf_error_status < 0) || (epoch_dims != 3)
|| (type_class != H5T_FLOAT)
|| (type_size != sizeof(double)))
{
IAS_LOG_ERROR("Invalid epoch time array dimensions/datatype class/"
"datatype size information");
return ERROR;
}
/* Now get the epoch time components */
hdf_error_status = H5LTget_attribute_double(hdf_file_id, "/",
epoch_name, epoch_time);
if (hdf_error_status < 0)
{
IAS_LOG_ERROR("Retrieving epoch time attribute values");
return ERROR;
}
/* Done */
return SUCCESS;
}
int SpIO_FreadModel(const SpFile *sfp, const SpFile *popsfp, SpModel *model, int *read_pops)
{
int status = 0;
Deb_ASSERT(model->parms.mol == NULL);
Deb_ASSERT(model->grid == NULL);
#if 1
/* pre-check format version */
if(!status){
const char *default_format = "SPARX format v3";
char *format = NULL;
status = SpIO_H5GetAttribute_string(sfp->h5f_id, "/", "format", &format);
if(strncmp(format, default_format, strlen("SPARX format v3"))){
printf("The format is not '%s' (%s)\n", default_format, format);
status = 1;
}
free(format);
}
#endif
/* Read coordinate name */
if(!status){
char *coordinate = NULL;
status = SpIO_H5GetAttribute_string(sfp->h5f_id, "/", "geom", &coordinate);
/* Load molecule if present */
if(strlen(coordinate) > 0) {
DatINode *geom = Dat_IList_NameLookup(GEOM_TYPES, coordinate);
model->parms.geom = geom->idx;
}
free(coordinate);
}
herr_t hstatus;
/* Read T_cmb */
if(!status) {
hstatus = H5LTget_attribute_double(sfp->h5f_id, "/", "T_cmb", &model->parms.T_cmb);
if(hstatus < 0)
status = 1;
}
/* Read T_in */
if(!status) {
hstatus = H5LTget_attribute_double(sfp->h5f_id, "/", "T_in", &model->parms.T_in);
if(hstatus < 0)
status = 1;
}
/* Read molecule name */
if(!status){
char *mol_name = NULL;
status = SpIO_H5GetAttribute_string(sfp->h5f_id, "/", "molec", &mol_name);
/* Load molecule if present */
if(strlen(mol_name) > 0) {
if(!(model->parms.mol = SpIO_FreadMolec(mol_name)))
status = 1;
}
free(mol_name);
}
/* Read pops-switch */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "pops", &model->parms.pops);
if(hstatus < 0)
status = 1;
}
/* Read dust-switch */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "dust", &model->parms.dust);
if(hstatus < 0)
status = 1;
}
/* Read polariz-switch */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "polariz", &model->parms.polariz);
if(hstatus < 0)
status = 1;
}
/* Read z (zeeman splitting) factor */
if(!status) {
hstatus = H5LTget_attribute_int(sfp->h5f_id, "/", "z", &model->parms.z);
if(hstatus < 0)
status = 1;
}
#if 0
/* Set velocity field: the "velfield" attribute is expected
* to contain a Python function named "Vgas((x1,x2,x3),(min1,min2,min3),(max1,max2,max3)" where
* (x1,x2,x3) are the three coordinates of the ray position, (min1,min2,min3) are the lower
* bounds of the bounding box, and (max1,max2,max3) are the upper baounds of the bounding
* box. An example Vgas function would be:
* def Vgas((x1, x2, x3), (min1, min2, min3), (max1, max2, max3)):"
* return [0,0,0]"
*/
if(!status) {
char *velfield = NULL;
//if(!strncmp(velfield, "grid", strlen(velfield))) {
if(!strncmp(velfield, "grid", strlen("grid"))) {
model->parms.velfield = NULL;
}
else {
status = PyRun_SimpleString(velfield);
PyObject *__main__ = NULL, *ret = NULL;
__main__ = PyImport_AddModule("__main__");
model->parms.velfield = PyObject_GetAttrString(__main__, "Vgas");
Py_INCREF(model->parms.velfield);
/* Try calling the function and make sure it returns a sequence of length 3 */
char format[] = "(d,d,d),(d,d,d),(d,d,d)";
ret = PyObject_CallFunction(model->parms.velfield, format, 0, 0, 0, 0, 0, 0, 0, 0, 0);
if(!PySequence_Check(ret)) {
PyWrErr_SetString(PyExc_Exception, "Vgas() does not return a vector!");
status = 1;
}
}
free(velfield);
}
#endif
/* Load grid */
if(!status)
status =
SpIO_H5ReadGrid(
sfp->h5f_id,
(*read_pops) ? popsfp->h5f_id : NULL,
&model->grid,
&model->parms,
read_pops
);
/* Cleanup */
if(status)
PyWrErr_SetString(PyExc_Exception, "Error reading model from file `%s'", sfp->name);
return status;
}
