AccessTraceReader::AccessTraceReader(std::string _fname) : fname(_fname.c_str()) {
hid_t fid = H5Fopen(fname.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (fid == H5I_INVALID_HID) panic("Could not open HDF5 file %s", fname.c_str());
// Check that the trace finished
hid_t fAttr = H5Aopen(fid, "finished", H5P_DEFAULT);
uint32_t finished;
H5Aread(fAttr, H5T_NATIVE_UINT, &finished);
H5Aclose(fAttr);
if (!finished) panic("Trace file %s unfinished (halted simulation?)", fname.c_str());
// Populate numRecords & numChildren
hsize_t nPackets;
hid_t table = H5PTopen(fid, "accs");
if (table == H5I_INVALID_HID) panic("Could not open HDF5 packet table");
H5PTget_num_packets(table, &nPackets);
numRecords = nPackets;
hid_t ncAttr = H5Aopen(fid, "numChildren", H5P_DEFAULT);
H5Aread(ncAttr, H5T_NATIVE_UINT, &numChildren);
H5Aclose(ncAttr);
curFrameRecord = 0;
cur = 0;
max = MIN(PT_CHUNKSIZE, numRecords);
buf = max? gm_calloc<PackedAccessRecord>(max) : nullptr;
if (max) {
H5PTread_packets(table, 0, max, buf);
}
H5PTclose(table);
H5Fclose(fid);
}
char AH5_write_str_root_attr(hid_t loc_id, const char *attr_name, const char *wdata)
{
char success = AH5_FALSE;
hid_t aid = H5Screate(H5S_SCALAR);
hid_t atype = H5Tcopy(H5T_C_S1);
htri_t attr_exists = H5Aexists(loc_id, attr_name);
hid_t attr = -1;
H5Tset_size(atype, strlen(wdata));
if (atype >= 0) {
if (attr_exists == 0) {
attr = H5Acreate(loc_id, attr_name, atype, aid, H5P_DEFAULT, H5P_DEFAULT);
} else if (attr_exists > 0) {
attr = H5Aopen(loc_id, attr_name, H5P_DEFAULT);
}
if (attr && H5Awrite(attr, atype, wdata) >= 0 && H5Aclose(attr) >= 0)
success = AH5_TRUE;
}
success &= (H5Tclose(atype) >= 0);
success &= (H5Sclose(aid) >= 0);
return success;
}
int
e5_write_attr_list_double(
hid_t e5_group_id, e5_attr_double* e5_attr_list)
{
int i;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr_double *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(H5Aexists(e5_group_id, attr->name) <= 0)
e5_attribute_id = H5Acreate(e5_group_id, attr->name, H5T_IEEE_F64LE, e5_dataspace_id, H5P_DEFAULT);
else
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
e5_info(e5_group_id, "Adding attribute [type='double', name='%s', value='%f']\n", attr->name, attr->value);
H5Awrite(e5_attribute_id, H5T_NATIVE_DOUBLE, &(attr->value));
H5Aclose(e5_attribute_id);
}
H5Sclose(e5_dataspace_id);
return E5_SUCCESS;
}
static int readIntAttribute(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
herr_t status;
int iVal = -1;
hsize_t n = 0;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen(_iDatasetId, _pstName, H5P_DEFAULT);
if (iAttributeId < 0)
{
return -1;
}
status = H5Aread(iAttributeId, H5T_NATIVE_INT, &iVal);
if (status < 0)
{
return -1;
}
status = H5Aclose(iAttributeId);
if (status < 0)
{
return -1;
}
}
return iVal;
}
estatus_t
e5_write_attr_list_str(
hid_t e5_group_id, e5_attr_str* e5_attr_list)
{
int i;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
hid_t e5_string_type = H5Tcopy(H5T_C_S1);
H5Tset_size(e5_string_type, E5_MAX_ATTR_STRING_LENGTH);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr_str *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(attr->value == 0 || strlen(attr->value) < 1)
continue;
if(H5Aexists(e5_group_id, attr->name) <= 0)
e5_attribute_id = H5Acreate(e5_group_id, attr->name, e5_string_type, e5_dataspace_id, H5P_DEFAULT);
else
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
e5_info(e5_group_id, "Adding attribute [type='string', name='%s', value='%s']\n", attr->name, attr->value);
H5Awrite(e5_attribute_id, e5_string_type, &(attr->value));
H5Aclose(e5_attribute_id);
}
H5Sclose(e5_dataspace_id);
return E5_SUCCESS;
}
void DCAttribute::writeAttribute(const char* name, const hid_t type, hid_t parent,
uint32_t ndims, const Dimensions dims, const void* src)
throw (DCException)
{
hid_t attr = -1;
if (H5Aexists(parent, name))
attr = H5Aopen(parent, name, H5P_DEFAULT);
else
{
hid_t dsp;
if( ndims == 1 && dims.getScalarSize() == 1 )
dsp = H5Screate(H5S_SCALAR);
else
dsp = H5Screate_simple( ndims, dims.getPointer(), dims.getPointer() );
attr = H5Acreate(parent, name, type, dsp, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(dsp);
}
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened or created"));
if (H5Awrite(attr, type, src) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be written"));
}
H5Aclose(attr);
}
estatus_t
e5_read_attr_list_float(
hid_t e5_group_id, e5_attr_float* e5_attr_list)
{
int i;
hid_t e5_attribute_id;
estatus_t status = E5_SUCCESS;
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr_float *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(H5Aexists(e5_group_id, attr->name) <= 0)
{
status = E5_INVALID_ATTRIBUTE;
e5_error(e5_group_id, status, "Specified attribute '%s' does not exist\n", attr->name);
continue;
}
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
H5Aread(e5_attribute_id, H5T_NATIVE_FLOAT, &(attr->value));
H5Aclose(e5_attribute_id);
e5_info(e5_group_id, "Read attribute [type='float', name='%s', value='%f']\n", attr->name, attr->value);
}
return status;
}
void write_internal(hdf5dataset& hdataset, const std::string& name, hid_t type_id, const void* buffer, bool overwrite)
{
bool exists = H5Aexists(hdataset.handle(), name.c_str());
hid_t attribute_id = -1;
if(exists && overwrite)
{
attribute_id = H5Aopen(hdataset.handle(), name.c_str(), H5P_DEFAULT);
//H5Ldelete(_hfile.handle(), name.c_str(), H5P_DEFAULT);
}
else if(exists && !overwrite)
throw std::runtime_error("Attribute already exists: (" + name + ")");
else
{
hsize_t dims = 1;
hid_t space_id = H5Screate_simple(1, &dims, NULL);
attribute_id = H5Acreate(hdataset.handle(), name.c_str(), type_id, space_id, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(space_id);
}
if(attribute_id < 0)
throw std::runtime_error("Error creating or opening attribute () in file (" + name + ")");
H5Awrite(attribute_id, type_id, buffer);
H5Tclose(type_id);
H5Aclose(attribute_id);
}
escdf_errno_t utils_hdf5_check_attr(hid_t loc_id, const char *name,
hsize_t *dims, unsigned int ndims,
hid_t *attr_pt)
{
hid_t attr_id, dtspace_id;
if ((attr_id = H5Aopen(loc_id, name, H5P_DEFAULT)) < 0)
RETURN_WITH_ERROR(attr_id);
/* Check space dimensions. */
if ((dtspace_id = H5Aget_space(attr_id)) < 0) {
DEFER_FUNC_ERROR(dtspace_id);
goto cleanup_attr;
}
if (utils_hdf5_check_shape(dtspace_id, dims, ndims) != ESCDF_SUCCESS) {
goto cleanup_dtspace;
}
H5Sclose(dtspace_id);
if (attr_pt)
*attr_pt = attr_id;
else
H5Aclose(attr_id);
return ESCDF_SUCCESS;
cleanup_dtspace:
H5Sclose(dtspace_id);
cleanup_attr:
H5Aclose(attr_id);
return ESCDF_ERROR;
}
estatus_t
e5_read_attr_list_str(
hid_t e5_group_id, e5_attr_str* e5_attr_list)
{
int i;
estatus_t status = E5_SUCCESS;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
hid_t e5_string_type = H5Tcopy(H5T_C_S1);
H5Tset_size(e5_string_type, E5_MAX_ATTR_STRING_LENGTH);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr_str *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(H5Aexists(e5_group_id, attr->name) <= 0)
{
status = E5_INVALID_ATTRIBUTE;
e5_error(e5_group_id, status, "Specified attribute '%s' does not exist\n", attr->name);
continue;
}
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
H5Aread(e5_attribute_id, e5_string_type, &(attr->value));
H5Aclose(e5_attribute_id);
e5_info(e5_group_id, "Read attribute [type='str', name='%s', value='%s']\n", attr->name, attr->value);
}
H5Sclose(e5_dataspace_id);
return status;
}
estatus_t
e5_write_attr_list(
hid_t e5_group_id, e5_attr* e5_attr_list)
{
int i;
eid_t status = E5_SUCCESS;
hid_t e5_attribute_id;
hid_t e5_dataspace_id = H5Screate(H5S_SCALAR);
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
if(e5_is_valid_type(e5_attr_list[i].type) != E5_TRUE)
{
status = E5_INVALID_TYPE;
e5_error(e5_group_id, status, "Invalid type requested for attribute [type='%d', name='%s', value='%p']\n", attr->type, attr->name, attr->value);
continue;
}
hid_t hdf_type = e5_convert_type_to_hdf(e5_attr_list[i].type);
hid_t hdf_format = e5_convert_format_to_hdf(e5_attr_list[i].type);
if(H5Aexists(e5_group_id, attr->name) <= 0)
e5_attribute_id = H5Acreate(e5_group_id, attr->name, hdf_type, e5_dataspace_id, H5P_DEFAULT);
e5_info(e5_group_id, "Adding attribute [type='integer', name='%s', value='%d']\n", attr->name, attr->value);
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
H5Awrite(e5_attribute_id, hdf_format, &(attr->value));
H5Aclose(e5_attribute_id);
}
H5Sclose(e5_dataspace_id);
return E5_SUCCESS;
}
hid_t seissol::checkpoint::h5::Fault::initFile(int odd, const char* filename)
{
hid_t h5file;
if (loaded()) {
// Open the file
h5file = open(filename, false);
checkH5Err(h5file);
// Fault writer
m_h5timestepFault[odd] = H5Aopen(h5file, "timestep_fault", H5P_DEFAULT);
checkH5Err(m_h5timestepFault[odd]);
// Data
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
m_h5data[odd][i] = H5Dopen(h5file, VAR_NAMES[i], H5P_DEFAULT);
checkH5Err(m_h5data[odd][i]);
}
} else {
// Create the file
hid_t h5plist = H5Pcreate(H5P_FILE_ACCESS);
checkH5Err(h5plist);
checkH5Err(H5Pset_libver_bounds(h5plist, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST));
#ifdef USE_MPI
checkH5Err(H5Pset_fapl_mpio(h5plist, comm(), MPI_INFO_NULL));
#endif // USE_MPI
h5file = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, h5plist);
checkH5Err(h5file);
checkH5Err(H5Pclose(h5plist));
// Create scalar dataspace for attributes
hid_t h5spaceScalar = H5Screate(H5S_SCALAR);
checkH5Err(h5spaceScalar);
// Fault writer
m_h5timestepFault[odd] = H5Acreate(h5file, "timestep_fault",
H5T_STD_I32LE, h5spaceScalar, H5P_DEFAULT, H5P_DEFAULT);
checkH5Err(m_h5timestepFault[odd]);
int t = 0;
checkH5Err(H5Awrite(m_h5timestepFault[odd], H5T_NATIVE_INT, &t));
checkH5Err(H5Sclose(h5spaceScalar));
// Variables
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
h5plist = H5Pcreate(H5P_DATASET_CREATE);
checkH5Err(h5plist);
checkH5Err(H5Pset_layout(h5plist, H5D_CONTIGUOUS));
checkH5Err(H5Pset_alloc_time(h5plist, H5D_ALLOC_TIME_EARLY));
m_h5data[odd][i] = H5Dcreate(h5file, VAR_NAMES[i], H5T_IEEE_F64LE, m_h5fSpaceData,
H5P_DEFAULT, h5plist, H5P_DEFAULT);
checkH5Err(m_h5data[odd][i]);
checkH5Err(H5Pclose(h5plist));
}
}
return h5file;
}
hdf5attribute::hdf5attribute(hdf5dataset& hdataset, const std::string& name)
{
_attribute_id = H5Aopen(hdataset.handle(), name.c_str(), H5P_DEFAULT);
if(_attribute_id < 0)
throw std::runtime_error("Failed to open attribute (" + name + ") in dataset (" + "not available" + ") file (" + "not available" + ")");
_type_id = H5Aget_type(_attribute_id);
}
/*-------------------------------------------------------------*/
static void validateFloat3Attribute(pNXVcontext self,
hid_t dpField, char *name)
{
hid_t attID, attType, attSpace;
H5T_class_t h5class;
hsize_t dims[2], maxDims[2];
char fname[512];
memset(fname,0,sizeof(fname));
H5Iget_name(dpField,fname,sizeof(fname));
if(!H5LTfind_attribute(dpField,name)){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Missing attribute %s on %s",
name, fname);
NXVlog(self);
self->errCount++;
} else {
attID = H5Aopen(dpField,name,H5P_DEFAULT);
assert(attID >= 0);
attType = H5Aget_type(attID);
assert(attType >= 0);
h5class = H5Tget_class(attType);
if(h5class != H5T_FLOAT){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"%s attribute on %s is of wrong type, expected float",
name, fname);
NXVlog(self);
self->errCount++;
} else {
attSpace = H5Aget_space(attID);
if(H5Sget_simple_extent_ndims(attSpace) != 1){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"%s attribute on %s is of wrong rank, expected 1",
name, fname);
NXVlog(self);
self->errCount++;
} else {
H5Sget_simple_extent_dims(attSpace,dims,maxDims);
if(dims[0] != 3){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"%s attribute on %s is of wrong size, expected 3",
name, fname);
NXVlog(self);
self->errCount++;
}
}
H5Sclose(attSpace);
}
H5Tclose(attType);
H5Aclose(attID);
}
}
/*--------------------------------------------------------------
This validates the lesser depends_on chain fields like
vector, offset and transformation_type
----------------------------------------------------------------*/
static void validateDependsOnAttributes(pNXVcontext self,hid_t dpField)
{
char fname[512], transData[512];
hid_t attID, attType, attSpace;
H5T_class_t h5class;
memset(fname,0,sizeof(fname));
memset(transData,0,sizeof(transData));
H5Iget_name(dpField,fname,sizeof(fname));
/*
deal with transformation_type
*/
if(!H5LTfind_attribute(dpField,"transformation_type")){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"Missing attribute transformation_type on %s",
fname);
NXVlog(self);
self->errCount++;
} else {
attID = H5Aopen(dpField,"transformation_type",H5P_DEFAULT);
assert(attID >= 0);
attType = H5Aget_type(attID);
assert(attType >= 0);
h5class = H5Tget_class(attType);
if(h5class != H5T_STRING){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"transformation_type on %s is of wrong type, expected string",
fname);
NXVlog(self);
self->errCount++;
} else {
H5NXget_attribute_string(self->fileID, fname,
"transformation_type",transData);
if(strcmp(transData,"translation") != 0
&& strcmp(transData,"rotation") != 0){
NXVsetLog(self,"sev","error");
NXVprintLog(self,"message",
"transformation_type on %s contains bad data: %s",
fname,
"expected rotation or translation");
NXVlog(self);
self->errCount++;
}
}
H5Tclose(attType);
H5Aclose(attID);
}
validateFloat3Attribute(self,dpField,"offset");
validateFloat3Attribute(self,dpField,"vector");
}
bool seissol::checkpoint::h5::Wavefield::validate(hid_t h5file) const
{
// Turn of error printing
H5ErrHandler errHandler;
// Check #partitions
hid_t h5attr = H5Aopen(h5file, "partitions", H5P_DEFAULT);
if (h5attr < 0) {
logWarning(rank()) << "Checkpoint does not have a partition attribute.";
return false;
}
int p;
herr_t err = H5Aread(h5attr, H5T_NATIVE_INT, &p);
checkH5Err(H5Aclose(h5attr));
if (err < 0 || p != partitions()) {
logWarning(rank()) << "Partitions in checkpoint do not match.";
return false;
}
// Check dimensions
hid_t h5data = H5Dopen(h5file, "values", H5P_DEFAULT);
if (h5data < 0) {
logWarning(rank()) << "Checkpoint does not contains a data array.";
return false;
}
hid_t h5space = H5Dget_space(h5data);
checkH5Err(H5Dclose(h5data));
if (h5space < 0) {
logWarning(rank()) << "Could not get space identifier in checkpoint.";
return false;
}
bool isValid = true;
int dims = H5Sget_simple_extent_ndims(h5space);
if (dims != 1) {
isValid = false;
logWarning(rank()) << "Number of dimensions in checkpoint does not match.";
} else {
hsize_t dimSize;
if (H5Sget_simple_extent_dims(h5space, &dimSize, 0L) != 1) {
isValid = false;
logWarning(rank()) << "Could not get dimension sizes of checkpoint.";
} else {
if (dimSize != numTotalElems()) {
isValid = false;
logWarning(rank()) << "Number of elements in checkpoint does not match.";
}
}
}
checkH5Err(H5Sclose(h5space));
return isValid;
}
void
HDF5Attribute::open(const HDF5Id location_id, const String &name)
{
if (isValid()) {
THROW(Iex::IoExc, "Tried to open attribute that has already "
"been opened or created");
}
m_id = H5Aopen(location_id, name.c_str(), H5P_DEFAULT);
}
H5Attribute::H5Attribute(H5Object & _parent, const std::string & _name) : H5Object(_parent, _name)
{
if (H5Aexists(getParent().getH5Id(), name.c_str()) <= 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot open attribute: %s"), name.c_str());
}
attr = H5Aopen(getParent().getH5Id(), name.c_str(), H5P_DEFAULT);
if (attr < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot open attribute: %s"), name.c_str());
}
}
//--------------------------------------------------------------------------
// Function: H5Object::openAttribute
///\brief Opens an attribute given its name.
///\param name - IN: Name of the attribute
///\return Attribute instance
///\exception H5::AttributeIException
// Programmer Binh-Minh Ribler - 2000
//--------------------------------------------------------------------------
Attribute H5Object::openAttribute( const char* name ) const
{
hid_t attr_id = H5Aopen(getId(), name, H5P_DEFAULT);
if( attr_id > 0 )
{
Attribute attr( attr_id );
return( attr );
}
else
{
throw AttributeIException(inMemFunc("openAttribute"), "H5Aopen failed");
}
}
void
ReadStringsT( hid_t iParent,
const std::string &iAttrName,
size_t iNumStrings,
StringT *oStrings )
{
ABCA_ASSERT( iParent >= 0, "Invalid parent in ReadStringsT" );
// Open the attribute.
hid_t attrId = H5Aopen( iParent, iAttrName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( attrId >= 0,
"Couldn't open attribute named: " << iAttrName );
AttrCloser attrCloser( attrId );
// Checking code.
{
hid_t attrFtype = H5Aget_type( attrId );
DtypeCloser dtypeCloser( attrFtype );
hid_t nativeDtype = GetNativeDtype<CharT>();
ABCA_ASSERT( H5Tget_class( attrFtype ) ==
H5Tget_class( nativeDtype ) &&
H5Tget_sign( attrFtype ) ==
H5Tget_sign( nativeDtype ),
"Invalid datatype for stringT" );
}
hid_t attrSpace = H5Aget_space( attrId );
ABCA_ASSERT( attrSpace >= 0,
"Couldn't get dataspace for attribute: " << iAttrName );
DspaceCloser dspaceCloser( attrSpace );
hssize_t numPoints = H5Sget_simple_extent_npoints( attrSpace );
ABCA_ASSERT( numPoints > 0,
"Degenerate string dimensions in ReadStringsT" );
// Create temporary char storage buffer.
std::vector<CharT> charStorage( ( size_t )( 1 + numPoints ),
( CharT )0 );
// Read into it.
herr_t status = H5Aread( attrId, GetNativeDtype<CharT>(),
( void * )&charStorage.front() );
ABCA_ASSERT( status >= 0, "Couldn't read from attribute: " << iAttrName );
// Extract 'em.
ExtractStrings( oStrings, ( const CharT * )&charStorage.front(),
1 + numPoints, iNumStrings );
}
int hdf5_read(void *output, hid_t file, char *n_group, char *n_dset, char *n_attr, int c){
hid_t memtype, type, group=-1, dset=-1, attr=-1, tmp_id, space;
herr_t status;
size_t sdim;
int ndims;
tmp_id = file;
if(strlen(n_group)>0){
group = H5Gopen(tmp_id, n_group, H5P_DEFAULT);
tmp_id = group;
}
if(strlen(n_dset)>0){
dset = H5Dopen(tmp_id, n_dset, H5P_DEFAULT);
tmp_id = dset;
}
if(strlen(n_attr)>0){
attr = H5Aopen(tmp_id, n_attr, H5P_DEFAULT);
tmp_id = attr;
}
if(c == 'c'){
memtype = H5Tcopy (H5T_C_S1);
type = H5Aget_type (tmp_id);
sdim = H5Tget_size (type);
sdim++;
status = H5Tset_size (memtype, sdim);
}
else if(c == 'd'){
memtype = H5T_NATIVE_DOUBLE;
}
else if(c == 'i' || c == 'n'){
memtype = H5T_NATIVE_INT;
}
else if(c == 'f'){
memtype = H5T_NATIVE_FLOAT;
}
if (tmp_id == attr){
status = H5Aread(tmp_id, memtype, output);
}
else if(tmp_id == dset && c == 'n'){
space = H5Dget_space (dset);
ndims = H5Sget_simple_extent_dims (space, output, NULL);
}
else{
return(-1);
}
return(1);
}
estatus_t
e5_read_attr_list(
hid_t e5_group_id, e5_attr* e5_attr_list)
{
int i;
estatus_t status = E5_SUCCESS;
hid_t h5_type;
hid_t h5_native_type;
hid_t h5_space;
hid_t e5_attribute_id;
for(i = 0; e5_attr_list && e5_attr_list[i].name != 0; i++)
{
e5_attr *attr = &e5_attr_list[i];
if(attr->name == 0 || strlen(attr->name) < 1)
continue;
e5_info(e5_group_id, "Reading attribute [name='%s']\n", attr->name);
if(H5Aexists(e5_group_id, attr->name) <= 0)
{
status = E5_INVALID_ATTRIBUTE;
e5_error(e5_group_id, status, "Invalid name requested for attribute [type='%d', name='%s', value='%p']\n", attr->type, attr->name, attr->value);
continue;
}
e5_attribute_id = H5Aopen(e5_group_id, attr->name, H5P_DEFAULT);
h5_type = H5Aget_type(e5_attribute_id);
h5_space = H5Aget_space(e5_attribute_id);
h5_native_type = e5_get_native_h5_type(h5_type);
attr->type = e5_convert_hdf_type(h5_type);
if(e5_is_valid_type(attr->type) != E5_TRUE)
{
status = E5_INVALID_TYPE;
e5_error(e5_group_id, status, "Invalid type requested for attribute [type='%d', name='%s', value='%p']\n", attr->type, attr->name, attr->value);
continue;
}
H5Aread(e5_attribute_id, h5_native_type, attr->value);
H5Aclose(e5_attribute_id);
e5_info(e5_group_id, "Read attribute [type='%s', name='%s', value='%p']\n",
e5_typename(attr->type), attr->name, attr->value);
}
return status;
}
//-*****************************************************************************
void
ReadTimeSamples( hid_t iParent,
std::vector < AbcA::TimeSamplingPtr > & oTimeSamples )
{
oTimeSamples.clear();
// add the intrinsic default sampling
AbcA::TimeSamplingPtr ts( new AbcA::TimeSampling() );
oTimeSamples.push_back( ts );
uint32_t i = 1;
AbcA::TimeSamplingType tst;
std::string tstname = "1";
// keep trying to read till we can't find anymore
while ( ReadTimeSamplingType( iParent, tstname, tst ) )
{
// try to open the time samples attribute
std::string timeName = tstname + ".time";
hid_t aid = H5Aopen( iParent, timeName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( aid >= 0,
"Couldn't open time samples named: " << timeName );
AttrCloser attrCloser( aid );
// figure out how big it is
hid_t sid = H5Aget_space( aid );
ABCA_ASSERT( sid >= 0,
"Couldn't get dataspace for time samples: " << timeName );
DspaceCloser dspaceCloser( sid );
hssize_t numPoints = H5Sget_simple_extent_npoints( sid );
ABCA_ASSERT( numPoints > 0, "No time samples data: " << timeName );
std::vector < chrono_t > times(numPoints);
// do the read
herr_t status = H5Aread( aid, H5T_NATIVE_DOUBLE, &(times.front()) );
ABCA_ASSERT( status >= 0, "Can't read time samples: " << timeName );
// create the TimeSampling and add it to our vector
ts.reset( new AbcA::TimeSampling(tst, times) );
oTimeSamples.push_back( ts );
// increment to try and read the next one
i++;
std::stringstream strm;
strm << i;
tstname = strm.str();
}
}
void seissol::checkpoint::h5::Fault::load(int ×tepFault)
{
if (numSides() == 0)
return;
logInfo(rank()) << "Loading fault checkpoint";
seissol::checkpoint::CheckPoint::load();
hid_t h5file = open(linkFile());
checkH5Err(h5file);
// Attributes
hid_t h5attr = H5Aopen(h5file, "timestep_fault", H5P_DEFAULT);
checkH5Err(h5attr);
checkH5Err(H5Aread(h5attr, H5T_NATIVE_INT, ×tepFault));
checkH5Err(H5Aclose(h5attr));
// Set the memory space (this is the same for all variables)
hsize_t count[2] = {numSides(), numBndGP()};
hid_t h5memSpace = H5Screate_simple(2, count, 0L);
checkH5Err(h5memSpace);
checkH5Err(H5Sselect_all(h5memSpace));
// Offset for the file space
hsize_t fStart[2] = {fileOffset(), 0};
// Read the data
for (unsigned int i = 0; i < NUM_VARIABLES; i++) {
hid_t h5data = H5Dopen(h5file, VAR_NAMES[i], H5P_DEFAULT);
checkH5Err(h5data);
hid_t h5fSpace = H5Dget_space(h5data);
checkH5Err(h5fSpace);
// Read the data
checkH5Err(H5Sselect_hyperslab(h5fSpace, H5S_SELECT_SET, fStart, 0L, count, 0L));
checkH5Err(H5Dread(h5data, H5T_NATIVE_DOUBLE, h5memSpace, h5fSpace,
h5XferList(), data(i)));
checkH5Err(H5Sclose(h5fSpace));
checkH5Err(H5Dclose(h5data));
}
checkH5Err(H5Sclose(h5memSpace));
checkH5Err(H5Fclose(h5file));
}
void
ReadStringT<std::string,char>( hid_t iParent,
const std::string &iAttrName,
std::string &oString )
{
ABCA_ASSERT( iParent >= 0, "Invalid parent in ReadStringT" );
// Open the attribute.
hid_t attrId = H5Aopen( iParent, iAttrName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( attrId >= 0,
"Couldn't open attribute named: " << iAttrName );
AttrCloser attrCloser( attrId );
// Checking code.
hid_t attrFtype = H5Aget_type( attrId );
DtypeCloser dtypeCloser( attrFtype );
ssize_t numChars = H5Tget_size( attrFtype );
ABCA_ASSERT( numChars >= 0,
"ReadStringT() H5Aget_size() failed" );
// Read and check space
{
hid_t attrSpace = H5Aget_space( attrId );
ABCA_ASSERT( attrSpace >= 0,
"Couldn't get dataspace for attribute: " << iAttrName );
DspaceCloser dspaceCloser( attrSpace );
H5S_class_t attrSpaceClass = H5Sget_simple_extent_type( attrSpace );
ABCA_ASSERT( attrSpaceClass == H5S_SCALAR,
"Tried to read non-scalar attribute: " << iAttrName
<< " as scalar" );
}
// Create temporary char storage buffer.
std::vector<char> charStorage( ( size_t )( 1 + numChars ),
( char )0 );
// Read into it.
herr_t status = H5Aread( attrId, attrFtype,
( void * )&charStorage.front() );
ABCA_ASSERT( status >= 0, "Couldn't read from attribute: " << iAttrName );
// Return it.
oString = ( const char * )&charStorage.front();
}
bool Hdf5Dataset::open()
{
const char *filepath = this->path_.c_str();
const char *name = this->filename_.c_str();
char fullpath[100];
strcpy(fullpath, filepath);
strcat(fullpath, name);
ROS_INFO("Opening map %s", this->filename_.c_str());
this->file_ = H5Fopen(fullpath, H5F_ACC_RDONLY, H5P_DEFAULT);
this->group_poses_ = H5Gopen(this->file_, "/Poses", H5P_DEFAULT);
this->poses_dataset_ = H5Dopen(this->group_poses_, "poses_dataset", H5P_DEFAULT);
this->group_spheres_ = H5Gopen(this->file_, "/Spheres", H5P_DEFAULT);
this->sphere_dataset_ = H5Dopen(this->group_spheres_, "sphere_dataset", H5P_DEFAULT);
this->attr_ = H5Aopen(this->sphere_dataset_, "Resolution", H5P_DEFAULT);
herr_t ret = H5Aread(this->attr_, H5T_NATIVE_FLOAT, &this->res_);
}
/*
* Class: hdf_hdf5lib_H5
* Method: _H5Aopen
* Signature: (JLjava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Aopen
(JNIEnv *env, jclass clss, jlong obj_id, jstring name, jlong access_plist)
{
hid_t retVal = -1;
const char *aName;
PIN_JAVA_STRING(name, aName);
if (aName != NULL) {
retVal = H5Aopen((hid_t)obj_id, aName, (hid_t)access_plist);
UNPIN_JAVA_STRING(name, aName);
if (retVal < 0)
h5libraryError(env);
}
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Aopen */
void DCAttribute::readAttribute(const char* name, hid_t parent, void* dst)
throw (DCException)
{
hid_t attr = H5Aopen(parent, name, H5P_DEFAULT);
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened for reading"));
hid_t attr_type = H5Aget_type(attr);
if (attr_type < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Could not get type of attribute"));
}
if (H5Aread(attr, attr_type, dst) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be read"));
}
H5Aclose(attr);
}
// from scrappie
float fast5_read_float_attribute(hid_t group, const char *attribute) {
float val = NAN;
if (group < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "Invalid group passed to %s:%d.", __FILE__, __LINE__);
#endif
return val;
}
hid_t attr = H5Aopen(group, attribute, H5P_DEFAULT);
if (attr < 0) {
#ifdef DEBUG_FAST5_IO
fprintf(stderr, "Failed to open attribute '%s' for reading.", attribute);
#endif
return val;
}
H5Aread(attr, H5T_NATIVE_FLOAT, &val);
H5Aclose(attr);
return val;
}
/// Return the attribute name of obj, and "" if the attribute does not exist.
void h5_read_attribute(hid_t id, std::string const &name, std::string & s) {
s = "";
// if the attribute is not present, return 0
if (H5LTfind_attribute(id, name.c_str()) == 0) return; // not present
attribute attr = H5Aopen(id, name.c_str(), H5P_DEFAULT);
if (!attr.is_valid()) TRIQS_RUNTIME_ERROR << "Cannot open the attribute " << name;
dataspace space = H5Aget_space(attr);
int rank = H5Sget_simple_extent_ndims(space);
if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string attribute and got rank !=0";
datatype strdatatype = H5Aget_type(attr);
std::vector<char> buf(H5Aget_storage_size(attr) + 1, 0x00);
auto err = H5Aread(attr, strdatatype, (void *)(&buf[0]));
if (err < 0) TRIQS_RUNTIME_ERROR << "Cannot read the attribute " << name;
s.append(&(buf.front()));
}
