// JRC: This fat interface may not scale? What about
// scalar attributes?
herr_t VsH5Attribute::getDoubleVectorValue(std::vector<double>* dvals) {
herr_t err = 0;
size_t npoints;
hid_t atype = H5Aget_type(getId());
H5T_class_t type = H5Tget_class(atype);
hid_t aspace = H5Aget_space(getId());
size_t rank = H5Sget_simple_extent_ndims(aspace);
if (type != H5T_FLOAT) {
VsLog::warningLog() <<"VsH5Attribute::getDoubleVectorValue() - Requested attribute " <<getShortName()
<<" is not a floating point vector." <<std::endl;
dvals->resize(0);
return -1;
}
if (rank == 0) {
dvals->resize(1);
double v;
err = H5Aread(getId(), H5T_NATIVE_DOUBLE, &v);
(*dvals)[0] = v;
return err;
}
// rank>0
npoints = H5Sget_simple_extent_npoints(aspace);
double* v = new double[npoints];
err = H5Aread(getId(), H5T_NATIVE_DOUBLE, v);
dvals->resize(npoints);
for (size_t i = 0; i<npoints; ++i) {
(*dvals)[i] = v[i];
}
delete [] v;
return err;
}
int AMRreader::
getIntfInfo( hid_t gid )
{
hid_t aid = H5Aopen_name( gid, intf_np_name );
if( aid<0 ) {
nvert_=0;
debug1 << "Failed to find number of interface points.\n";
return -1;
}
else {
H5Aread( aid, H5T_NATIVE_INT, &nvert_ );
H5Aclose(aid);
}
debug2 << "nvert is " << nvert_ << "\n";
aid = H5Aopen_name( gid, intf_ne_name );
if( aid<0 ) {
nrect_=0;
debug1 << "Failed to find number of interface elements.\n";
return -2;
}
else {
H5Aread( aid, H5T_NATIVE_INT, &nrect_ );
H5Aclose(aid);
}
debug2 << "nrect is " << nrect_ << "\n";
return 0;
}
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);
}
/* Read and verify attribute for group or dataset. */
int read_attribute(hid_t obj_id, int this_type, int num)
{
hid_t aid;
hsize_t group_block[2]={1,1}, dset_block[2]={1, 8};
int i, mpi_rank, in_num, in_data[8], out_data[8], vrfy_errors = 0;
char attr_name[32];
MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
if(this_type == is_group) {
sprintf(attr_name, "Group Attribute %d", num);
aid = H5Aopen_name(obj_id, attr_name);
if(MAINPROCESS) {
H5Aread(aid, H5T_NATIVE_INT, &in_num);
vrfy_errors = dataset_vrfy(NULL, NULL, NULL, group_block,
&in_num, &num);
}
H5Aclose(aid);
}
else if(this_type == is_dset) {
sprintf(attr_name, "Dataset Attribute %d", num);
for(i=0; i<8; i++)
out_data[i] = i;
aid = H5Aopen_name(obj_id, attr_name);
if(MAINPROCESS) {
H5Aread(aid, H5T_NATIVE_INT, in_data);
vrfy_errors = dataset_vrfy(NULL, NULL, NULL, dset_block, in_data,
out_data);
}
H5Aclose(aid);
}
return vrfy_errors;
}
herr_t attribute_read(char *attribute_name, enum my_hdf5_types hdf5_type,
hid_t hdf5_file_handle, void *buf)
{
hid_t hdf5_attribute_id, hdf5_dataspace, hdf5_datatype;
herr_t hdf5_status = 0;
//here we get an identifier for a datatype
switch (hdf5_type)
{
case my_hdf5_int:
hdf5_datatype = H5Tcopy(H5T_NATIVE_INT);
break;
case my_hdf5_long:
hdf5_datatype = H5Tcopy(H5T_NATIVE_LONG);
break;
case my_hdf5_float:
hdf5_datatype = H5Tcopy(H5T_NATIVE_FLOAT);
break;
case my_hdf5_double:
hdf5_datatype = H5Tcopy(H5T_NATIVE_DOUBLE);
break;
default:
exit(-1);
break;
}
hdf5_dataspace = H5Screate(H5S_SCALAR);
hdf5_attribute_id =
H5Acreate(hdf5_file_handle, attribute_name, hdf5_datatype, hdf5_dataspace, H5P_DEFAULT); //here we 'create' an attribute
switch (hdf5_type)
{
case my_hdf5_int:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (int *) buf);
break;
case my_hdf5_long:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (long *) buf);
break;
case my_hdf5_float:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (float *) buf);
break;
case my_hdf5_double:
hdf5_status = H5Aread(hdf5_attribute_id, hdf5_datatype, (double *) buf);
break;
default:
exit(-1);
break;
}
H5Tclose(hdf5_datatype);
H5Aclose(hdf5_attribute_id);
H5Sclose(hdf5_dataspace);
return hdf5_status;
}
void AbstractHdf5Access::SetUnlimitedDatasetId()
{
// Now deal with the unlimited dimension
// In terms of an Unlimited dimension dataset:
// * Files pre - r16738 (inc. Release 3.1 and earlier) use simply "Time" for "Data"'s unlimited variable.
// * Files generated by r16738 - r18257 used "<DatasetName>_Time" for "<DatasetName>"'s unlimited variable,
// - These are not to be used and there is no backwards compatibility for them, since they weren't in a release.
// * Files post r18257 (inc. Release 3.2 onwards) use "<DatasetName>_Unlimited" for "<DatasetName>"'s
// unlimited variable,
// - a new attribute "Name" has been added to the Unlimited Dataset to allow it to assign
// any name to the unlimited variable. Which can then be easily read by Hdf5DataReader.
// - if this dataset is missing we look for simply "Time" to remain backwards compatible with Releases <= 3.1
if (DoesDatasetExist(mDatasetName + "_Unlimited"))
{
mUnlimitedDatasetId = H5Dopen(mFileId, (mDatasetName + "_Unlimited").c_str());
hid_t name_attribute_id = H5Aopen_name(mUnlimitedDatasetId, "Name");
hid_t unit_attribute_id = H5Aopen_name(mUnlimitedDatasetId, "Unit");
hid_t attribute_type = H5Aget_type(name_attribute_id);
// Read into it.
char* string_array = (char *)malloc(sizeof(char)*MAX_STRING_SIZE);
H5Aread( name_attribute_id, attribute_type, string_array);
std::string name_string(&string_array[0]);
mUnlimitedDimensionName = name_string;
H5Aread( unit_attribute_id, attribute_type, string_array);
std::string unit_string(&string_array[0]);
mUnlimitedDimensionUnit = unit_string;
free(string_array);
H5Tclose(attribute_type);
H5Aclose(name_attribute_id);
H5Aclose(unit_attribute_id);
}
else if (DoesDatasetExist("Time"))
{
mUnlimitedDimensionName = "Time";
mUnlimitedDimensionUnit = "msec";
mUnlimitedDatasetId = H5Dopen(mFileId, mUnlimitedDimensionName.c_str());
}
else
{
NEVER_REACHED;
}
mIsUnlimitedDimensionSet = true;
}
char HIntAttribute::read(int *data)
{
herr_t status = H5Aread(fObjectId, dataType(), data);
if(status < 0)
return 0;
return 1;
}
static herr_t get_attribute_mem(hid_t obj_id,
const char *attr_name,
hid_t mem_type_id,
void *data)
{
hid_t attr_id;
herr_t status;
attr_id = H5Aopen_name(obj_id, attr_name);
if (attr_id < 0)
return -1;
status = H5Aread(attr_id, mem_type_id, data);
if (status < 0)
{
H5Aclose(attr_id);
return -1;
}
status = H5Aclose(attr_id);
if (status < 0)
return -1;
return 0;
}
static herr_t get_attribute_disk(hid_t loc_id,
const char *attr_name,
void *attr_out)
{
hid_t attr_id;
hid_t attr_type;
herr_t status;
attr_id = H5Aopen_name(loc_id, attr_name);
if (attr_id < 0)
return -1;
attr_type = H5Aget_type(attr_id);
if (attr_type < 0)
goto out;
status = H5Aread(attr_id, attr_type, attr_out);
if (status < 0)
goto out;
status = H5Tclose(attr_type);
if (status < 0)
goto out;
status = H5Aclose(attr_id);
if (status < 0)
return -1;
return 0;
out:
H5Tclose(attr_type);
H5Aclose(attr_id);
return -1;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Aread
* Signature: (JJ[B)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Aread
(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jbyteArray buf)
{
herr_t status = -1;
jbyte *byteP;
jboolean isCopy;
if (buf == NULL) {
h5nullArgument( env,"H5Aread: buf is NULL");
} /* end if */
else {
byteP = ENVPTR->GetByteArrayElements(ENVPAR buf, &isCopy);
if (byteP == NULL) {
h5JNIFatalError( env,"H5Aread: buf is not pinned");
} /* end if */
else {
status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, byteP);
if (status < 0) {
ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, JNI_ABORT);
h5libraryError(env);
} /* end if */
else {
ENVPTR->ReleaseByteArrayElements(ENVPAR buf, byteP, 0);
} /* end else */
} /* end else */
} /* end else */
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Aread */
// read a complex float attribute
float_complex read_complex_attribute(hid_t loc_id, const char* path,
const char* name)
{
float_complex value;
float *buf;
hid_t attr_id, real_type_id;
;
hsize_t *dims;
herr_t status;
status = H5Aexists_by_name(loc_id, path, name, H5P_DEFAULT);
if (status < 0)
{
printf("attribut %s does not exist \n", name);
}
real_type_id = create_real_type_id();
attr_id = H5Aopen_by_name(loc_id, path, name, H5P_DEFAULT, H5P_DEFAULT);
status = H5Aread(attr_id, real_type_id, buf);
if (status < 0)
{
printf("Can't read attribute : %s\n", name);
}
value.re = buf[0]; value.im=buf[1];
return value;
}
/* read attribute value */
char* H5Dataset_read_attr_value(hid_t aid)
{
hid_t asid=-1, atid=-1;
int i, rank;
hsize_t *dims;
size_t size=1;
char *attr_buf=NULL;
asid = H5Aget_space(aid);
atid = H5Aget_type(aid);
rank = H5Sget_simple_extent_ndims(asid);
if (rank > 0) {
dims = (hsize_t *)malloc(rank * sizeof(hsize_t));
H5Sget_simple_extent_dims(asid, dims, NULL);
for (i=0; i<rank; i++) {
size *= (size_t)dims[i];
free(dims);
}
size *= H5Tget_size(atid);
attr_buf = (char *)malloc(size);
if (H5Aread( aid, atid, attr_buf) < 0) {
free(attr_buf);
attr_buf = NULL;
}
}
if( atid > 0) H5Tclose(atid);
if (asid > 0) H5Sclose(asid);
return attr_buf;
}
inline typename boost::enable_if<boost::is_same<T, std::string>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
}
catch (H5::AttributeIException const&) {
throw;
}
if (!has_scalar_space(attr)) {
throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
}
H5::DataType tid = attr.getDataType();
std::string value;
if (!tid.isVariableStr()) {
// read fixed-size string, allocate space in advance and let the HDF5
// library take care about NULLTERM and NULLPAD strings
value.resize(tid.getSize(), std::string::value_type());
attr.read(tid, &*value.begin());
}
else {
// read variable-length string, memory will be allocated by HDF5 C
// library and must be freed by us
char *c_str;
if (H5Aread(attr.getId(), tid.getId(), &c_str) < 0) {
throw H5::AttributeIException("Attribute::read", "H5Aread failed");
}
value = c_str; // copy '\0'-terminated string
free(c_str);
}
return value;
}
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;
}
static int readIntAttribute_v1(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
herr_t status;
hsize_t n = 0;
int iVal = -1;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name_v1, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen_by_name(_iDatasetId, ".", _pstName, H5P_DEFAULT, 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;
}
// Read string attribute <attr_name> given by address <path>
char AH5_read_str_attr(hid_t loc_id, const char *path, char *attr_name, char **rdata)
{
hid_t attr_id, filetype, memtype;
size_t sdim;
char success = AH5_FALSE;
if (AH5_path_valid(loc_id, path) || strcmp(path, ".") == 0)
if (H5Aexists_by_name(loc_id, path, attr_name, H5P_DEFAULT) > 0)
{
attr_id = H5Aopen_by_name(loc_id, path, attr_name, H5P_DEFAULT, H5P_DEFAULT);
filetype = H5Aget_type(attr_id);
sdim = H5Tget_size(filetype);
sdim++; // make a space for null terminator
*rdata = (char *) malloc(sdim * sizeof(char));
memtype = H5Tcopy(H5T_C_S1);
H5Tset_size(memtype, sdim);
if (H5Aread(attr_id, memtype, *rdata) >= 0)
success = AH5_TRUE;
else
free(*rdata);
H5Tclose(memtype);
H5Tclose(filetype);
H5Aclose(attr_id);
}
if (!success)
*rdata = NULL;
return success;
}
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;
}
bool read_attribute(const char * name, const H5ID & dataset, T & value)
{
H5ID attribute(H5Aopen_name(dataset, name), H5Aclose);
if (!attribute)
return false;
herr_t status = H5Aread(attribute, H5T_NATIVE_FLOAT, &value);
return status >= 0;
}
void
mhdf_getElemTypeName( mhdf_FileHandle file_handle,
const char* elem_handle,
char* buffer, size_t buf_len,
mhdf_Status* status )
{
FileHandle* file_ptr;
hid_t elem_id, type_id, attr_id;
char bytes[16];
herr_t rval;
API_BEGIN;
if (NULL == buffer || buf_len < 2)
{
mhdf_setFail( status, "invalid input" );
return;
}
buffer[0] = '\0';
file_ptr = (FileHandle*)(file_handle);
if (!mhdf_check_valid_file( file_ptr, status ))
return;
elem_id = mhdf_elem_group_from_handle( file_ptr, elem_handle, status );
if (elem_id < 0) return;
attr_id = H5Aopen_name( elem_id, ELEM_TYPE_ATTRIB );
H5Gclose( elem_id );
if (attr_id < 0)
{
mhdf_setFail( status, "Missing element type attribute. Invalid file." );
return;
}
type_id = H5Aget_type( attr_id );
assert( type_id > 0 );
rval = H5Aread( attr_id, type_id, bytes );
H5Aclose( attr_id );
if (rval < 0)
{
H5Tclose( type_id );
mhdf_setFail( status, "Failed to read element type attribute. Invalid file." );
return;
}
rval = H5Tenum_nameof( type_id, bytes, buffer, buf_len );
H5Tclose( type_id );
if (rval < 0)
{
mhdf_setFail( status, "Invalid datatype for element type attribute. Invalid file." );
return;
}
mhdf_setOkay( status );
API_END;
return ;
}
/* fetch num_cols and the col for a particular trackname */
void get_cols(chromosome_t *chromosome, char *trackname, hsize_t *num_cols,
hsize_t *col) {
hid_t attr, root, dataspace, datatype;
hsize_t data_size, cell_size, num_cells;
char *attr_data;
/* Tracknames are stored in the attributes of the root group of each file */
root = H5Gopen(chromosome->h5group, "/", H5P_DEFAULT);
assert(root >= 0);
attr = H5Aopen_name(root, "tracknames");
assert(attr >= 0);
dataspace = H5Aget_space(attr);
assert(dataspace >= 0);
assert(H5Sget_simple_extent_dims(dataspace, num_cols, NULL) == 1);
assert(H5Sclose(dataspace) >= 0);
if (trackname && col) {
datatype = H5Aget_type(attr);
assert(datatype >= 0);
assert(H5Tget_class(datatype) == H5T_STRING);
cell_size = H5Tget_size(datatype);
assert(cell_size > 0);
data_size = H5Aget_storage_size(attr);
assert(data_size > 0);
num_cells = data_size / cell_size;
/* allocate room for tracknames */
attr_data = xmalloc(data_size);
assert(attr_data);
assert(H5Aread(attr, datatype, attr_data) >= 0);
*col = 0;
for (*col = 0; *col <= num_cells; (*col)++) {
if (*col == num_cells) {
fprintf(stderr, "can't find trackname: %s\n", trackname);
free(attr_data);
exit(EXIT_FAILURE);
} else {
if (!strncmp(attr_data + (*col * cell_size), trackname, cell_size)) {
break;
}
}
}
/* clean up read tracknames */
free(attr_data);
}
assert(H5Aclose(attr) >= 0);
}
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 compare_and_read_scalar_attribute_internal(hid_t attribute_id, hid_t type_id, hid_t expected_type, void* buffer)
{
if(H5Tequal(type_id, expected_type))
{
herr_t status = H5Aread(attribute_id, type_id, buffer);
if(status >= 0)
return;
}
throw std::runtime_error("type mismatch");
}
void get_attr(hid_t loc, const char *name, hid_t mem_type_id, void *buf) {
hid_t attr;
attr = H5Aopen_name(loc, name);
assert(attr >= 0);
assert(H5Aread(attr, mem_type_id, buf) >= 0);
assert(H5Aclose(attr) >= 0);
}
static herr_t get_attribute_str(hid_t obj_id,
const char *attr_name,
char **data)
{
hid_t attr_id;
hid_t attr_type;
size_t type_size;
herr_t status;
*data = NULL;
attr_id = H5Aopen_name(obj_id, attr_name);
if (attr_id < 0)
return -1;
attr_type = H5Aget_type(attr_id);
if (attr_type < 0)
goto out;
/* Get the size */
type_size = H5Tget_size(attr_type);
if (type_size < 0)
goto out;
/* malloc enough space for the string, plus 1 for trailing '\0' */
*data = (char *)malloc(type_size + 1);
status = H5Aread(attr_id, attr_type, *data);
if (status < 0)
goto out;
/* Set the last character to '\0' in case we are dealing with
* null padded or space padded strings
*/
(*data)[type_size] = '\0';
status = H5Tclose(attr_type);
if (status < 0)
goto out;
status = H5Aclose(attr_id);
if (status < 0)
return -1;
return 0;
out:
H5Tclose(attr_type);
H5Aclose(attr_id);
if (*data)
free(*data);
return -1;
}
char HStringAttribute::read(std::string & str)
{
const int d = dataSpaceDimension();
char * t = new char[d + 1];
herr_t status = H5Aread(fObjectId, dataType(), t);
if(status < 0)
return 0;
t[d] = '\0';
str = std::string(t);
delete[] t;
return 1;
}
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);
}
herr_t
H5AreadVL_str
(JNIEnv *env, hid_t aid, hid_t tid, jobjectArray buf)
{
char **strs;
jstring jstr;
jint i;
jint n;
hid_t sid;
hsize_t dims[H5S_MAX_RANK];
herr_t status = -1;
n = ENVPTR->GetArrayLength(ENVPAR buf);
strs =(char**)HDcalloc((size_t)n, sizeof(char*));
if (strs == NULL) {
h5JNIFatalError(env, "H5AreadVL_str: failed to allocate buff for read variable length strings");
} /* end if */
else {
status = H5Aread(aid, tid, strs);
if (status < 0) {
dims[0] = (hsize_t)n;
sid = H5Screate_simple(1, dims, NULL);
H5Dvlen_reclaim(tid, sid, H5P_DEFAULT, strs);
H5Sclose(sid);
HDfree(strs);
h5JNIFatalError(env, "H5AreadVL_str: failed to read variable length strings");
} /* end if */
else {
for (i=0; i < n; i++) {
jstr = ENVPTR->NewStringUTF(ENVPAR strs[i]);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
H5free_memory (strs[i]);
} /* end for */
/*
for repeatedly reading a dataset with a large number of strs (e.g., 1,000,000 strings,
H5Dvlen_reclaim() may crash on Windows because the Java GC will not be able to collect
free space in time. Instead, use "H5free_memory(strs[i])" above to free individual strings
after it is done.
H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, strs);
*/
HDfree(strs);
} /* end else */
} /* end else */
return status;
} /* end H5AreadVL_str */
std::string HdfAttribute::readString() const
{
char name[HDF_MAX_NAME];
hid_t datatype = H5Tcopy( H5T_C_S1 );
H5Tset_size( datatype, HDF_MAX_NAME );
herr_t status = H5Aread( d->id, datatype, name );
if ( status < 0 )
{
//MDAL::debug("Failed to read data!");
return std::string();
}
H5Tclose( datatype );
return std::string( name );
}
/*----------------------------------------------------------------------------
* Name: h5aread_c
* Purpose: Call H5Aread to read an attribute
* Inputs: dset_id - dataset identifier
* mem_type_id - memory datatype identifier
* dims - array to store dimensions sizes of buf; used only
* by Fortran routine.
* Outputs: buf - data buffer
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Thursday, August 12, 1999
* Modifications: dims paramete added.
* April 4, 2001
* Added nh5aread_integer(real,double)_s,1-7 functions to eliminate
* complains about wrong parameters types in h5awrite_c function
* called by Fortran routines.
* October 9, 2006 EIP
*---------------------------------------------------------------------------*/
int_f
nh5aread_c (hid_t_f *attr_id, hid_t_f *mem_type_id, void *buf, void UNUSED * dims)
{
int_f ret_value=0; /* Return value */
/*
* Call H5Aread function.
*/
if (H5Aread((hid_t)*attr_id, (hid_t)*mem_type_id, buf) < 0)
HGOTO_DONE(FAIL);
done:
return ret_value;
}
