void HDFWalkerIOEngine::readAll(hid_t grp, const char* name, Communicate* comm)
{
int mynode=comm->rank();
int nprocs=comm->size();
vector<int> woffset(nprocs+1,0);
const int RANK = 3;
hsize_t offset[]={1,1,1};
hsize_t gcount[RANK],count[RANK];
hsize_t stride[]={1,1,1};
hid_t dataset = H5Dopen(grp,name);
hid_t dataspace = H5Dget_space(dataset);
int rank_n = H5Sget_simple_extent_ndims(dataspace);
int status_n = H5Sget_simple_extent_dims(dataspace, gcount, NULL);
//assign offsets and size
FairDivideLow(gcount[0],nprocs,woffset);
offset[0]=woffset[mynode]; offset[1] = 0; offset[2] = 0;
count[0]=woffset[mynode+1]-woffset[mynode];
count[1]=gcount[1];
count[2]=gcount[2];
app_log() << " Initial walker distribution: ";
std::copy(woffset.begin(),woffset.end(),ostream_iterator<int>(app_log()," "));
app_log() << endl;
vector<MCWalkerConfiguration::PosType> posIn(count[0]*count[1]);
hid_t memspace = H5Screate_simple(RANK, count, NULL);
herr_t status = H5Sselect_hyperslab(dataspace,H5S_SELECT_SET, offset,NULL,count,NULL);
#if defined(H5_HAVE_PARALLEL)
xfer_plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(xfer_plist,H5FD_MPIO_COLLECTIVE);
#else
xfer_plist = H5P_DEFAULT;
#endif
hid_t type_id=get_h5_datatype(posIn[0][0]);
status = H5Dread(dataset, type_id, memspace, dataspace, xfer_plist, &(posIn[0][0]));
H5Sclose(dataspace);
H5Sclose(memspace);
H5Dclose(dataset);
#if defined(H5_HAVE_PARALLEL)
H5Pclose(xfer_plist);
#endif
int curWalker = W.getActiveWalkers();
if(curWalker) {
W.createWalkers(count[0]);
} else {
W.resize(count[0],count[1]);
}
MCWalkerConfiguration::iterator it = W.begin()+curWalker;
int ii=0;
for(int iw=0; iw<count[0]; iw++) {
//std::copy(Post_temp[iw],Post_temp[iw+1], (*it)->R.begin());
for(int iat=0; iat < count[1]; iat++,ii++){
(*it)->R(iat) = posIn[ii];
}
++it;
}
}
bool ReadHDF5file(char* filename, char* fieldname, dtype** outArray, int* dims)
{
#ifdef _HDF5_H
// Open the file
hid_t file_id;
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
//? file_id = H5Fopen(filename,H5F_ACC_RDONLY,faplist_id);
if(file_id < 0){
printf("ERROR: Could not open file %s\n",filename);
return false;
}
// Open the dataset
hid_t dataset_id;
hid_t dataspace_id;
dataset_id = H5Dopen1(file_id, fieldname);
if(dataset_id < 0){
printf("ERROR: Could not open the data field %s\n",fieldname);
return false;
}
dataspace_id = H5Dget_space(dataset_id);
// Test if 2D data
int ndims;
ndims = H5Sget_simple_extent_ndims(dataspace_id);
// Get dimensions of data set (nx, ny, nn)
hsize_t* dimsl = new hsize_t[ndims];
H5Sget_simple_extent_dims(dataspace_id,dimsl,NULL);
for(int i = 0;(i<ndims&&i<3);i++)
dims[i] = dimsl[ndims-1-i]; //!!!!!!!! NOT SURE
size_t nn = 1;
for(int i = 0;i<ndims;i++)
nn *= dimsl[i];
// Create space for the new data
dtype* data = *outArray;
if (data!=NULL) delete data;//free(data);
*outArray = new dtype[nn];
data = *outArray;
hid_t datatype_id;
H5T_class_t dataclass;
size_t size;
datatype_id = H5Dget_type(dataset_id);
dataclass = H5Tget_class(datatype_id);
size = H5Tget_size(datatype_id);
int rrr = sizeof(int);
if(dataclass == H5T_FLOAT){
if (size == sizeof(float)) {
float* buffer = (float *) calloc(nn, sizeof(float));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(double)) {
double* buffer = (double *) calloc(nn, sizeof(double));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown floating point type, size=%i\n",(int) size);
return false;
}
}
else if(dataclass == H5T_INTEGER){
if (size == sizeof(short)) {
short* buffer = (short*) calloc(nn, sizeof(short));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(int)) {
int* buffer = (int *) calloc(nn, sizeof(int));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(long)) {
long* buffer = (long *) calloc(nn, sizeof(long));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown integer type, size=%i\n",(int) size);
return false;
}
}
else {
printf("2dData::readHDF5: unknown HDF5 data type\n");
return false;
}
// Close and cleanup
H5Dclose(dataset_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
return true;
#endif
return false;
}
herr_t HDF5CreateGroupObjs(hid_t hHDF5, const char *pszObjName,
void *poHObjParent)
{
hid_t hGroupID; /* identifier of group */
hid_t hDatasetID; /* identifier of dataset */
hsize_t nbObjs=0; /* number of objects in a group */
int nbAttrs=0; /* number of attributes in object */
unsigned idx;
int n_dims;
H5G_stat_t oStatbuf;
hsize_t *dims=NULL;
hsize_t *maxdims=NULL;
hid_t datatype;
hid_t dataspace;
hid_t native;
HDF5GroupObjects *poHchild;
HDF5GroupObjects *poHparent;
poHparent = ( HDF5GroupObjects * ) poHObjParent;
poHchild=poHparent->poHchild;
if( H5Gget_objinfo( hHDF5, pszObjName, FALSE, &oStatbuf ) < 0 )
return -1;
/* -------------------------------------------------------------------- */
/* Look for next child */
/* -------------------------------------------------------------------- */
for( idx=0; idx < poHparent->nbObjs; idx++ ) {
if( poHchild->pszName == NULL ) break;
poHchild++;
}
if( idx == poHparent->nbObjs )
return -1; // all children parsed
/* -------------------------------------------------------------------- */
/* Save child information */
/* -------------------------------------------------------------------- */
poHchild->pszName = CPLStrdup( pszObjName );
poHchild->nType = oStatbuf.type;
poHchild->nIndex = idx;
poHchild->poHparent = poHparent;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
poHchild->objno[0] = oStatbuf.objno[0];
poHchild->objno[1] = oStatbuf.objno[1];
if( poHchild->pszPath == NULL ) {
poHchild->pszPath = CreatePath( poHchild );
}
if( poHparent->pszPath == NULL ) {
poHparent->pszPath = CreatePath( poHparent );
}
switch ( oStatbuf.type )
{
case H5G_LINK:
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = NULL;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
break;
case H5G_GROUP:
if( ( hGroupID = H5Gopen( hHDF5, pszObjName ) ) == -1 ) {
printf( "Error: unable to access \"%s\" group.\n",
pszObjName );
return -1;
}
nbAttrs = H5Aget_num_attrs( hGroupID );
H5Gget_num_objs( hGroupID, &nbObjs );
poHchild->nbAttrs= nbAttrs;
poHchild->nbObjs = (int) nbObjs;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
if( nbObjs > 0 ) {
poHchild->poHchild =( HDF5GroupObjects * )
CPLCalloc( (int)nbObjs, sizeof( HDF5GroupObjects ) );
memset( poHchild->poHchild, 0,
(size_t) (sizeof( HDF5GroupObjects ) * nbObjs) );
}
else
poHchild->poHchild = NULL;
if( !HDF5GroupCheckDuplicate( poHparent, oStatbuf.objno ) )
H5Giterate( hHDF5, pszObjName, NULL,
HDF5CreateGroupObjs, (void*) poHchild );
else
CPLDebug( "HDF5", "avoiding link looping on node '%s'.",
pszObjName );
H5Gclose( hGroupID );
break;
case H5G_DATASET:
if( ( hDatasetID = H5Dopen( hHDF5, pszObjName ) ) == -1 ) {
printf( "Error: unable to access \"%s\" dataset.\n",
pszObjName );
return -1;
}
nbAttrs = H5Aget_num_attrs( hDatasetID );
datatype = H5Dget_type( hDatasetID );
dataspace = H5Dget_space( hDatasetID );
n_dims = H5Sget_simple_extent_ndims( dataspace );
native = H5Tget_native_type( datatype, H5T_DIR_ASCEND );
if( n_dims > 0 ) {
dims = (hsize_t *) CPLCalloc( n_dims,sizeof( hsize_t ) );
maxdims = (hsize_t *) CPLCalloc( n_dims,sizeof( hsize_t ) );
}
H5Sget_simple_extent_dims( dataspace, dims, maxdims );
if( maxdims != NULL )
CPLFree( maxdims );
if( n_dims > 0 ) {
poHchild->nRank = n_dims; // rank of the array
poHchild->paDims = dims; // dimmension of the array.
poHchild->HDatatype = datatype; // HDF5 datatype
}
else {
poHchild->nRank = -1;
poHchild->paDims = NULL;
poHchild->HDatatype = 0;
}
poHchild->nbAttrs = nbAttrs;
poHchild->nbObjs = 0;
poHchild->poHchild = NULL;
poHchild->native = native;
H5Tclose( datatype );
H5Sclose( dataspace );
H5Dclose( hDatasetID );
break;
case H5G_TYPE:
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = NULL;
poHchild->nRank = 0;
poHchild->paDims = 0;
poHchild->HDatatype = 0;
break;
default:
break;
}
return 0;
}
/* Given a varid, find its shape. For unlimited dimensions, return
the current number of records. */
static int
find_var_shape_grp(NC_GRP_INFO_T *grp, int varid, int *ndims,
int *dimid, size_t *dimlen)
{
hid_t datasetid = 0, spaceid = 0;
NC_VAR_INFO_T *var;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int d, dataset_ndims = 0;
int retval = NC_NOERR;
/* Find this var. */
for (var = grp->var; var; var = var->next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
/* Get the dimids and the ndims for this var. */
if (ndims)
*ndims = var->ndims;
if (dimid)
for (d = 0; d < var->ndims; d++)
dimid[d] = var->dimids[d];
if (dimlen)
{
/* If the var hasn't been created yet, its size is 0. */
if (!var->created)
{
for (d = 0; d < var->ndims; d++)
dimlen[d] = 0;
}
else
{
/* Get the number of records in the dataset. */
if ((retval = nc4_open_var_grp2(grp, var->varid, &datasetid)))
BAIL(retval);
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
/* If it's a scalar dataset, it has length one. */
if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
{
dimlen[0] = 1;
}
else
{
/* Check to make sure ndims is right, then get the len of each
dim in the space. */
if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
if (ndims && dataset_ndims != *ndims)
BAIL(NC_EHDFERR);
if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
h5dimlen, h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
LOG((5, "find_var_shape_nc: varid %d len %d max: %d",
varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
for (d=0; d<dataset_ndims; d++)
dimlen[d] = h5dimlen[d];
}
}
}
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (h5dimlen) free(h5dimlen);
if (h5dimlenmax) free(h5dimlenmax);
return retval;
}
int RD_verify_dataset(hid_t file_id, const char *dset_name, int ndims,
int *dims, hid_t dtype, int dims_known)
{
hid_t dset_id, dspc_id, dtyp_id;
herr_t err;
/* data sizes */
hsize_t *this_dims;
int i;
/* get dataset */
dset_id = H5Dopen2(file_id, dset_name, H5P_DEFAULT);
if (!RD_ID_ISVALID(dset_id)) return RD_ERROR_DSETNOTVALID;
/* get dataspace */
dspc_id = H5Dget_space(dset_id);
if (!RD_ID_ISVALID(dspc_id)) return RD_ERROR_DSPACENOTVALID;
/* check number of dimensions */
if (H5Sget_simple_extent_ndims(dspc_id) != ndims)
return RD_ERROR_DSETBADNDIMS;
/* get dimensions */
this_dims = malloc(sizeof(*this_dims)*ndims);
if (H5Sget_simple_extent_dims(dspc_id, this_dims, NULL) < 0)
return RD_ERROR_DSETBADDIMS;
/* copy into or check agains dims */
if (dims_known) {
for (i=0; i<ndims; i++) {
if (dims[i] != (int)(this_dims[i]))
return RD_ERROR_DSETBADDIMS;
}
} else {
for (i=0; i<ndims; i++) {
dims[i] = (int)(this_dims[i]);
}
}
/* clean up */
free(this_dims);
/* close dataspace */
err = H5Sclose(dspc_id);
if (err < 0) return RD_ERROR_DSPACENOTVALID;
/* get datatype */
dtyp_id = H5Dget_type(dset_id);
if (!RD_ID_ISVALID(dtyp_id)) return RD_ERROR_DTYPENOTVALID;
if (H5Tequal(dtyp_id, dtype) <= 0) return RD_ERROR_DTYPENOTVALID;
/* close dataset */
err = H5Tclose(dtyp_id);
if (err < 0) return RD_ERROR_DTYPENOTVALID;
/* close dataset */
err = H5Dclose(dset_id);
if (err < 0) return RD_ERROR_DSETNOTVALID;
return 0;
}
static herr_t
trav_attr(hid_t
#ifndef H5TRAV_PRINT_SPACE
H5_ATTR_UNUSED
#endif /* H5TRAV_PRINT_SPACE */
obj, const char *attr_name, const H5A_info_t H5_ATTR_UNUSED *ainfo, void *_op_data)
{
trav_path_op_data_t *op_data = (trav_path_op_data_t *)_op_data;
const char *buf = op_data->path;
if((strlen(buf)==1) && (*buf=='/'))
printf(" %-10s %s%s", "attribute", buf, attr_name);
else
printf(" %-10s %s/%s", "attribute", buf, attr_name);
#ifdef H5TRAV_PRINT_SPACE
if(trav_verbosity < 2) {
#endif
printf("\n");
#ifdef H5TRAV_PRINT_SPACE
}
else {
hid_t attr = -1;
hid_t space = -1;
hsize_t size[H5S_MAX_RANK];
int ndims;
int i;
H5S_class_t space_type;
if((attr = H5Aopen(obj, attr_name, H5P_DEFAULT))) {
space = H5Aget_space(attr);
/* Data space */
ndims = H5Sget_simple_extent_dims(space, size, NULL);
space_type = H5Sget_simple_extent_type(space);
switch(space_type) {
case H5S_SCALAR:
/* scalar dataspace */
printf(" scalar\n");
break;
case H5S_SIMPLE:
/* simple dataspace */
printf(" {");
for (i = 0; i < ndims; i++) {
printf("%s" HSIZE_T_FORMAT, i?", ":"", size[i]);
}
printf("}\n");
break;
case H5S_NULL:
/* null dataspace */
printf(" null\n");
break;
default:
/* Unknown dataspace type */
printf(" unknown\n");
break;
} /* end switch */
H5Sclose(space);
H5Aclose(attr);
}
}
#endif
return(0);
}
int arma_H5Sget_simple_extent_dims(hid_t space_id, hsize_t* dims, hsize_t* maxdims)
{
return H5Sget_simple_extent_dims(space_id, dims, maxdims);
}
bool Hdf5Dataset::getMultimap(MultiMap &mMap)
{
hsize_t dims_out[2], count[2], offset[2];
hid_t dataspace = H5Dget_space(this->poses_dataset_); /* dataspace handle */
int rank = H5Sget_simple_extent_ndims(dataspace);
herr_t status_n = H5Sget_simple_extent_dims(dataspace, dims_out, NULL);
herr_t status;
int chunk_size, chunk_itr;
if (dims_out[0] % 10)
{
chunk_itr = 11;
}
else
{
chunk_itr = 10;
}
chunk_size = (dims_out[0] / 10);
offset[0] = 0;
for (int it = 0; it < chunk_itr; it++)
{
offset[1] = 0;
if ((dims_out[0] - (chunk_size * it)) / chunk_size != 0)
{
count[0] = chunk_size;
offset[0] = chunk_size * it;
}
else
{
count[0] = (dims_out[0] - (chunk_size * it));
offset[0] = count[0];
}
count[1] = 10;
double data_out[count[0]][count[1]];
status = H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, offset, NULL, count, NULL);
hsize_t dimsm[2];
dimsm[0] = count[0];
dimsm[1] = count[1];
hid_t memspace;
memspace = H5Screate_simple(RANK_OUT, dimsm, NULL);
status = H5Dread(this->poses_dataset_, H5T_NATIVE_DOUBLE, memspace, dataspace, H5P_DEFAULT, data_out);
for(int i=0; i<count[0]; i++)
{
std::vector<double> sphere_center(3);
std::vector<double> Poses(7);
for(int j=0; j<3;j++)
{
sphere_center[j] = data_out[i][j];
}
for(int k=3;k<10; k++)
{
Poses[k-3] = data_out[i][k];
}
mMap.insert(std::make_pair(sphere_center, Poses));
}
}
return 0;
}
void Hdf5DataReader::CommonConstructor()
{
if (!mDirectory.IsDir() || !mDirectory.Exists())
{
EXCEPTION("Directory does not exist: " + mDirectory.GetAbsolutePath());
}
std::string file_name = mDirectory.GetAbsolutePath() + mBaseName + ".h5";
FileFinder h5_file(file_name, RelativeTo::Absolute);
if (!h5_file.Exists())
{
EXCEPTION("Hdf5DataReader could not open " + file_name + " , as it does not exist.");
}
// Open the file and the main dataset
mFileId = H5Fopen(file_name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
if (mFileId <= 0)
{
EXCEPTION("Hdf5DataReader could not open " << file_name <<
" , H5Fopen error code = " << mFileId);
}
mVariablesDatasetId = H5Dopen(mFileId, mDatasetName.c_str(), H5P_DEFAULT);
SetMainDatasetRawChunkCache();
if (mVariablesDatasetId <= 0)
{
H5Fclose(mFileId);
EXCEPTION("Hdf5DataReader opened " << file_name << " but could not find the dataset '" <<
mDatasetName.c_str() << "', H5Dopen error code = " << mVariablesDatasetId);
}
hid_t variables_dataspace = H5Dget_space(mVariablesDatasetId);
mVariablesDatasetRank = H5Sget_simple_extent_ndims(variables_dataspace);
// Get the dataset/dataspace dimensions
hsize_t dataset_max_sizes[AbstractHdf5Access::DATASET_DIMS];
H5Sget_simple_extent_dims(variables_dataspace, mDatasetDims, dataset_max_sizes);
for (unsigned i=1; i<AbstractHdf5Access::DATASET_DIMS; i++) // Zero is excluded since it may be unlimited
{
assert(mDatasetDims[i] == dataset_max_sizes[i]);
}
// Check if an unlimited dimension has been defined
if (dataset_max_sizes[0] == H5S_UNLIMITED)
{
// 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 this class.
// - if this dataset is missing we look for simply "Time" to remain backwards compatible with Releases <= 3.1
SetUnlimitedDatasetId();
hid_t timestep_dataspace = H5Dget_space(mUnlimitedDatasetId);
// Get the dataset/dataspace dimensions
H5Sget_simple_extent_dims(timestep_dataspace, &mNumberTimesteps, NULL);
}
// Get the attribute where the name of the variables are stored
hid_t attribute_id = H5Aopen_name(mVariablesDatasetId, "Variable Details");
// Get attribute datatype, dataspace, rank, and dimensions
hid_t attribute_type = H5Aget_type(attribute_id);
hid_t attribute_space = H5Aget_space(attribute_id);
hsize_t attr_dataspace_dim;
H5Sget_simple_extent_dims(attribute_space, &attr_dataspace_dim, NULL);
unsigned num_columns = H5Sget_simple_extent_npoints(attribute_space);
char* string_array = (char *)malloc(sizeof(char)*MAX_STRING_SIZE*(int)num_columns);
H5Aread(attribute_id, attribute_type, string_array);
// Loop over column names and store them.
for (unsigned index=0; index < num_columns; index++)
{
// Read the string from the raw vector
std::string column_name_unit(&string_array[MAX_STRING_SIZE*index]);
// Find beginning of unit definition.
size_t name_length = column_name_unit.find('(');
size_t unit_length = column_name_unit.find(')') - name_length - 1;
std::string column_name = column_name_unit.substr(0, name_length);
std::string column_unit = column_name_unit.substr(name_length+1, unit_length);
mVariableNames.push_back(column_name);
mVariableToColumnIndex[column_name] = index;
mVariableToUnit[column_name] = column_unit;
}
// Release all the identifiers
H5Tclose(attribute_type);
H5Sclose(attribute_space);
H5Aclose(attribute_id);
// Free allocated memory
free(string_array);
// Find out if it's incomplete data
H5E_BEGIN_TRY //Supress HDF5 error if the IsDataComplete name isn't there
{
attribute_id = H5Aopen_name(mVariablesDatasetId, "IsDataComplete");
}
H5E_END_TRY;
if (attribute_id < 0)
{
// This is in the old format (before we added the IsDataComplete attribute).
// Just quit (leaving a nasty hdf5 error).
return;
}
attribute_type = H5Aget_type(attribute_id);
attribute_space = H5Aget_space(attribute_id);
unsigned is_data_complete;
H5Aread(attribute_id, H5T_NATIVE_UINT, &is_data_complete);
// Release all the identifiers
H5Tclose(attribute_type);
H5Sclose(attribute_space);
H5Aclose(attribute_id);
mIsDataComplete = (is_data_complete == 1) ? true : false;
if (is_data_complete)
{
return;
}
// Incomplete data
// Read the vector thing
attribute_id = H5Aopen_name(mVariablesDatasetId, "NodeMap");
attribute_type = H5Aget_type(attribute_id);
attribute_space = H5Aget_space(attribute_id);
// Get the dataset/dataspace dimensions
unsigned num_node_indices = H5Sget_simple_extent_npoints(attribute_space);
// Read data from hyperslab in the file into the hyperslab in memory
mIncompleteNodeIndices.clear();
mIncompleteNodeIndices.resize(num_node_indices);
H5Aread(attribute_id, H5T_NATIVE_UINT, &mIncompleteNodeIndices[0]);
H5Tclose(attribute_type);
H5Sclose(attribute_space);
H5Aclose(attribute_id);
}
herr_t H5IMget_palette_info( hid_t loc_id,
const char *image_name,
int pal_number,
hsize_t *pal_dims )
{
hid_t did;
int has_pal;
hid_t atid=-1;
hid_t aid;
hid_t asid=-1;
hssize_t n_refs;
hsize_t dim_ref;
hobj_ref_t *refbuf; /* buffer to read references */
hid_t pal_id;
hid_t pal_space_id;
hsize_t pal_maxdims[2];
/* Open the dataset. */
if((did = H5Dopen2(loc_id, image_name, H5P_DEFAULT)) < 0)
return -1;
/* Try to find the attribute "PALETTE" on the >>image<< dataset */
has_pal = H5IM_find_palette(did);
if(has_pal == 1)
{
if((aid = H5Aopen(did, "PALETTE", H5P_DEFAULT)) < 0)
goto out;
if((atid = H5Aget_type(aid)) < 0)
goto out;
if(H5Tget_class(atid) < 0)
goto out;
/* Get the reference(s) */
if((asid = H5Aget_space(aid)) < 0)
goto out;
n_refs = H5Sget_simple_extent_npoints(asid);
dim_ref = n_refs;
refbuf = (hobj_ref_t*)malloc( sizeof(hobj_ref_t) * (int)dim_ref );
if ( H5Aread( aid, atid, refbuf ) < 0)
goto out;
/* Get the actual palette */
if ( (pal_id = H5Rdereference( did, H5R_OBJECT, &refbuf[pal_number] )) < 0)
goto out;
if ( (pal_space_id = H5Dget_space( pal_id )) < 0)
goto out;
if ( H5Sget_simple_extent_ndims( pal_space_id ) < 0)
goto out;
if ( H5Sget_simple_extent_dims( pal_space_id, pal_dims, pal_maxdims ) < 0)
goto out;
/* close */
if (H5Dclose(pal_id)<0)
goto out;
if ( H5Sclose( pal_space_id ) < 0)
goto out;
if ( H5Sclose( asid ) < 0)
goto out;
if ( H5Tclose( atid ) < 0)
goto out;
if ( H5Aclose( aid ) < 0)
goto out;
free( refbuf );
}
/* Close the image dataset. */
if ( H5Dclose( did ) < 0)
return -1;
return 0;
out:
H5Dclose( did );
H5Sclose( asid );
H5Tclose( atid );
H5Aclose( aid );
return -1;
}
/*-------------------------------------------------------------------------
* Function: check_file
*
* Purpose: Part 2 of a two-part H5Fflush() test.
*
* Return: Success: 0
*
* Failure: 1
*
* Programmer: Leon Arber
* Sept. 26, 2006.
*
*-------------------------------------------------------------------------
*/
static int
check_file(char* name, hid_t fapl)
{
hid_t file, space, dset, groups, grp, plist;
hsize_t ds_size[2];
double error;
hsize_t i, j;
plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE);
if((file = H5Fopen(name, H5F_ACC_RDONLY, fapl)) < 0) goto error;
/* Open the dataset */
if((dset = H5Dopen2(file, "dset", H5P_DEFAULT)) < 0) goto error;
if((space = H5Dget_space(dset)) < 0) goto error;
if(H5Sget_simple_extent_dims(space, ds_size, NULL) < 0) goto error;
assert(100==ds_size[0] && 100==ds_size[1]);
/* Read some data */
if (H5Dread(dset, H5T_NATIVE_DOUBLE, space, space, plist,
the_data) < 0) goto error;
for (i=0; i<ds_size[0]; i++) {
for (j=0; j<ds_size[1]; j++) {
/*
* The extra cast in the following statement is a bug workaround
* for the Win32 version 5.0 compiler.
* 1998-11-06 ptl
*/
error = fabs(the_data[i][j]-(double)(hssize_t)i/((hssize_t)j+1));
if (error>0.0001) {
H5_FAILED();
printf(" dset[%lu][%lu] = %g\n",
(unsigned long)i, (unsigned long)j, the_data[i][j]);
printf(" should be %g\n",
(double)(hssize_t)i/(hssize_t)(j+1));
goto error;
}
}
}
/* Open some groups */
if((groups = H5Gopen2(file, "some_groups", H5P_DEFAULT)) < 0) goto error;
for(i = 0; i < 100; i++) {
sprintf(name, "grp%02u", (unsigned)i);
if((grp = H5Gopen2(groups, name, H5P_DEFAULT)) < 0) goto error;
if(H5Gclose(grp) < 0) goto error;
}
if(H5Gclose(groups) < 0) goto error;
if(H5Dclose(dset) < 0) goto error;
if(H5Fclose(file) < 0) goto error;
if(H5Pclose(plist) < 0) goto error;
if(H5Sclose(space) < 0) goto error;
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(plist);
H5Gclose(groups);
H5Dclose(dset);
H5Fclose(file);
H5Sclose(space);
} H5E_END_TRY;
return 1;
}
herr_t H5IMget_image_info( hid_t loc_id,
const char *dset_name,
hsize_t *width,
hsize_t *height,
hsize_t *planes,
char *interlace,
hssize_t *npals )
{
hid_t did;
hid_t sid;
hsize_t dims[IMAGE24_RANK];
hid_t aid;
hid_t asid;
hid_t atid;
H5T_class_t aclass;
int has_pal;
int has_attr;
/*assume initially we have no palettes attached*/
*npals = 0;
/* Open the dataset. */
if((did = H5Dopen2(loc_id, dset_name, H5P_DEFAULT)) < 0)
return -1;
/* Try to find the attribute "INTERLACE_MODE" on the >>image<< dataset */
has_attr = H5LT_find_attribute(did, "INTERLACE_MODE");
/* It exists, get it */
if(has_attr == 1)
{
if((aid = H5Aopen(did, "INTERLACE_MODE", H5P_DEFAULT)) < 0)
goto out;
if((atid = H5Aget_type(aid)) < 0)
goto out;
if(H5Aread(aid, atid, interlace) < 0)
goto out;
if(H5Tclose(atid) < 0)
goto out;
if(H5Aclose(aid) < 0)
goto out;
}
/* Get the dataspace handle */
if ( (sid = H5Dget_space( did )) < 0)
goto out;
/* Get dimensions */
if ( H5Sget_simple_extent_dims( sid, dims, NULL) < 0)
goto out;
/* Initialize the image dimensions */
if ( has_attr == 1 )
/* This is a 24 bit image */
{
if ( strcmp( interlace, "INTERLACE_PIXEL" ) == 0 )
{
/* Number of color planes is defined as the third dimension */
*height = dims[0];
*width = dims[1];
*planes = dims[2];
}
else
if ( strcmp( interlace, "INTERLACE_PLANE" ) == 0 )
{
/* Number of color planes is defined as the first dimension */
*planes = dims[0];
*height = dims[1];
*width = dims[2];
}
else return -1;
}
else
/* This is a 8 bit image */
{
*height = dims[0];
*width = dims[1];
*planes = 1;
}
/* Close */
if ( H5Sclose( sid ) < 0)
goto out;
/* Get number of palettes */
/* Try to find the attribute "PALETTE" on the >>image<< dataset */
has_pal = H5IM_find_palette(did);
if(has_pal == 1)
{
if((aid = H5Aopen(did, "PALETTE", H5P_DEFAULT)) < 0)
goto out;
if((atid = H5Aget_type(aid)) < 0)
goto out;
if((aclass = H5Tget_class(atid)) < 0)
goto out;
/* Check if it is really a reference */
if(aclass == H5T_REFERENCE)
{
/* Get the reference(s) */
if ( (asid = H5Aget_space( aid )) < 0)
goto out;
*npals = H5Sget_simple_extent_npoints( asid );
if ( H5Sclose( asid ) < 0)
goto out;
} /* H5T_REFERENCE */
if ( H5Tclose( atid ) < 0)
goto out;
/* Close the attribute. */
if ( H5Aclose( aid ) < 0)
goto out;
}
/* End access to the dataset and release resources used by it. */
if ( H5Dclose( did ) < 0)
goto out;
return 0;
out:
H5Dclose( did );
H5Aclose( aid );
H5Sclose( asid );
H5Tclose( atid );
return -1;
}
void XFLASH_File::Open_HDF5_Chombo(void)
{
hid_t handle = (hid_t)m_iFile_Handle;
unsigned int nRefineLevels, numVariables, dim;
unsigned int n_rBlocks ;
hsize_t nB;
hid_t gid, dspace, dset, attrib, varNameType;
herr_t status;
char component_name[MAX_STRING_LENGTH];
char level_name[MAX_STRING_LENGTH];
char tmpVarName[FR_VAR_STRING_SIZE + 1];
hid_t tmpType;
// float dx;
// int *buf;
int idx_bbox;
unsigned int i, j, k;
/*prepare file struct*/
// nodetype=NULL;
/*We are not going to use these. But sfocu code checks for them so make them
* trivially zero*/
for( i=0; i < FR_MDIM; i++)
m_uiBlock_Dimensions[i] =0;
m_eFormat = FMT_HDF5_CHOMBO;
/*get total number of refinement level*/
attrib= H5Aopen_name( handle, "num_levels");
status= H5Aread(attrib, H5T_NATIVE_INT, (void *)&nRefineLevels);
H5Aclose(attrib);
m_uiNum_Levels = nRefineLevels;
/*Dimensions*/
gid= H5Gopen(handle, "Chombo_global");
attrib= H5Aopen_name( gid, "SpaceDim");
status= H5Aread(attrib, H5T_NATIVE_INT, (void *)&dim);
H5Aclose(attrib);
m_uiNum_Dimensions = dim;
H5Gclose(gid);
/*number of components*/
attrib= H5Aopen_name( handle, "num_components");
status= H5Aread(attrib, H5T_NATIVE_INT, (void *)&numVariables);
H5Aclose(attrib);
m_uiNum_Vars = numVariables;
/*Get component names*/
varNameType = H5Tcopy(H5T_C_S1);
H5Tset_size(varNameType, 4);
tmpVarName[FR_VAR_STRING_SIZE ] ='\0';
m_lpszVar_Names = new char *[numVariables];
m_lpeVar_Types = new XFLASH_VAR_TYPE [numVariables];
for(i=0; i < numVariables; i++)
{
sprintf(component_name,"component_%d", i);
attrib= H5Aopen_name( handle, component_name);
status= H5Aread(attrib, varNameType, (void *)tmpVarName);
H5Aclose(attrib);
int iLen = strlen(tmpVarName) + 1;
if (iLen > FR_VAR_STRING_SIZE)
iLen = FR_VAR_STRING_SIZE;
m_lpszVar_Names[i] = new char[iLen];
strncpy(m_lpszVar_Names[i], (char *)tmpVarName, FR_VAR_STRING_SIZE);
m_lpszVar_Names[i][iLen - 1] = 0;
m_lpeVar_Types[i] = VT_UNK;
}
H5Tclose(varNameType);
/* Get Total Number of Blocks, refine level for each Block */
m_uiNum_Blocks = 0;
m_lpuiBlocks_Per_Refine_Level = new unsigned int [nRefineLevels];
idx_bbox=0;
int * buf=NULL;
unsigned int uiBufSize = 0;
for(i =0; i < nRefineLevels; i++)
{
sprintf(level_name, "level_%d", i);
gid= H5Gopen(handle, level_name);
dset= H5Dopen(gid, "boxes");
dspace = H5Dget_space(dset);
status = H5Sget_simple_extent_dims(dspace, &nB, NULL);
n_rBlocks = (int)nB;
// int block0 = m_uiNum_Blocks;
m_uiNum_Blocks += n_rBlocks;
m_lpuiBlocks_Per_Refine_Level[i] = n_rBlocks;
/*get bounding box for all the blocks on this refine level */
/*
attrib= H5Aopen_name( gid, "dx");
status= H5Aread(attrib, H5T_NATIVE_FLOAT, (void *)&dx);
H5Aclose(attrib);
*/
unsigned int uiSize = n_rBlocks * (2 * dim + PADSIZE / 4);
if (uiSize > uiBufSize)
{
if (buf)
delete [] buf;
buf = new int [uiSize];
uiBufSize = uiSize;
}
tmpType= H5Dget_type(dset);
status= H5Dread(dset, tmpType, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf);
H5Tclose(tmpType);
m_lpdBlock_Bounding_Box = new double [m_uiNum_Blocks * 2 * dim];
/*unroll struct into the out->bbox double array*/
for(j = 0; j < n_rBlocks; j++)
{
for(k=0; k < (dim *2); k++)
{
m_lpdBlock_Bounding_Box[idx_bbox++] = (*buf);
buf++;
}
buf += (PADSIZE/sizeof(int));
}
buf = NULL;
/***clean up************/
H5Sclose(dspace);
H5Dclose(dset);
H5Gclose(gid);
}
if (buf)
delete [] buf;
/*All Chombo blocks are LEAF blocks*/
m_lpeBlock_Node_Type = new int[m_uiNum_Blocks];
for(j=0; j < m_uiNum_Blocks; j++)
m_lpeBlock_Node_Type[j]= FR_LEAF_NODE;
/* Fill size and coords array. This data set is redundant so we will fill it with zeros so that it trivially
* passes some checks in the sameblock() function from the old sfocu code for
* compatibility
*/
m_lpdBlock_Coords = new double [m_uiNum_Blocks * m_uiNum_Dimensions];
m_lpdBlock_Size = new double [m_uiNum_Blocks * m_uiNum_Dimensions];
for(j=0; j < (m_uiNum_Blocks * m_uiNum_Dimensions ); j++)
{
m_lpdBlock_Coords[j] = 0.;
m_lpdBlock_Size[j] = 0.;
}
/* Fill lref array */
int idx_lref =0;
m_lpiRefinement_Levels = new int [m_uiNum_Blocks];
for(j = 0; j < m_uiNum_Levels; j++)
{
for(k=0; k < m_lpuiBlocks_Per_Refine_Level[j]; k++)
m_lpiRefinement_Levels[idx_lref++] = j;
}
}
int extractfromh5(struct param par, std::string vTmpFile)
{
hid_t vH5File = -1;
hid_t vH5Dataset = -1;
hid_t vH5Datatype = -1;
hid_t vH5Dataspace = -1;
hid_t vH5OPAQUETypeId = -1;
std::string cpath, cname;
std::string pathi = (std::string) par.pathi;
std::string conti = (std::string) par.conti;
std::string grupi = (std::string) par.grupi;
std::string filei = (std::string) par.filei;
cpath = pathi + "/" + conti;
cname = grupi + "/" + filei;
/* Open an existing file. */
vH5File = H5Fopen(cpath.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
CHKRTN(vH5File < 0, FILEERR);
/* Open an existing dataset. */
vH5Dataset = H5Dopen(vH5File, cname.c_str(), H5P_DEFAULT);
vH5Datatype = H5Dget_type(vH5Dataset);
vH5Dataspace = H5Dget_space(vH5Dataset);
// TODO: The rank is hardcoded to 1 (which is sufficient
// for openBIS), but it would be more generic to code
// for a dynamic rank!
const int rank = H5Sget_simple_extent_ndims(vH5Dataspace);
if (rank != 1) {
if (vH5OPAQUETypeId >= 0) H5Tclose(vH5OPAQUETypeId);
if (vH5Datatype >= 0) H5Tclose(vH5Datatype);
if (vH5Dataspace >= 0) H5Sclose(vH5Dataspace);
if (vH5Dataset >= 0) H5Dclose(vH5Dataset);
if (vH5File >= 0) H5Fclose(vH5File);
CHKRTNMSG((rank != 1), "Data space rank is not '1' as expected");
}
hsize_t vH5DataspaceDims[1];
H5Sget_simple_extent_dims(vH5Dataspace, vH5DataspaceDims, NULL);
// Define the memory dataspace.
hid_t memspace = H5Screate_simple(1, vH5DataspaceDims, NULL);
// allocate memory for the dataset:
std::vector<char> vDataSet(vH5DataspaceDims[0]);
if (vDataSet.size() != vH5DataspaceDims[0]) {
fprintf(stderr, "Could not reserve memory");
if (vH5OPAQUETypeId >= 0) H5Tclose(vH5OPAQUETypeId);
if (vH5Datatype >= 0) H5Tclose(vH5Datatype);
if (vH5Dataspace >= 0) H5Sclose(vH5Dataspace);
if (vH5Dataset >= 0) H5Dclose(vH5Dataset);
if (vH5File >= 0) H5Fclose(vH5File);
return -1;
}
//hid_t vH5OPAQUETypeId = H5Tcreate(H5T_OPAQUE, 1);
hid_t vDataTypeId = H5Dget_type(vH5Dataset);
vH5OPAQUETypeId = H5Tget_native_type(vDataTypeId, H5T_DIR_ASCEND);
// read the data from the dataset/dataspace:
herr_t readstatus = H5Dread(vH5Dataset, vH5OPAQUETypeId, memspace, vH5Dataspace, H5P_DEFAULT, &vDataSet[0]);
if (readstatus < 0) {
fprintf(stderr, "Failed to read dataset from file");
if (vH5OPAQUETypeId >= 0) H5Tclose(vH5OPAQUETypeId);
if (vH5Datatype >= 0) H5Tclose(vH5Datatype);
if (vH5Dataspace >= 0) H5Sclose(vH5Dataspace);
if (vH5Dataset >= 0) H5Dclose(vH5Dataset);
if (vH5File >= 0) H5Fclose(vH5File);
return -1;
}
if (!writefile(vTmpFile, vDataSet)) {
fprintf(stderr, "Failed to write dataset to new file");
if (vH5OPAQUETypeId >= 0) H5Tclose(vH5OPAQUETypeId);
if (vH5Datatype >= 0) H5Tclose(vH5Datatype);
if (vH5Dataspace >= 0) H5Sclose(vH5Dataspace);
if (vH5Dataset >= 0) H5Dclose(vH5Dataset);
if (vH5File >= 0) H5Fclose(vH5File);
return -1;
}
return 0;
}
int
rec_scan_group(hid_t grpid)
{
hid_t spaceid, datasetid = 0, child_grpid;
hsize_t num_obj, i;
int obj_class;
char obj_name[STR_LEN + 1];
htri_t is_scale;
int num_scales;
hsize_t dims[MAX_DIMS], max_dims[MAX_DIMS];
int ndims, d;
/* Loop through datasets to find variables. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, STR_LEN) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n",
obj_class, obj_name);*/
/* Deal with groups and datasets, ignore the rest. */
switch(obj_class)
{
case H5G_GROUP:
if ((child_grpid = H5Gopen(grpid, obj_name)) < 0) ERR;
if (rec_scan_group(child_grpid)) ERR;
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen(grpid, obj_name)) < 0) ERR;
/*printf("\nobj_name %s\n", obj_name);*/
/* Get the dimensions of this dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
if (ndims > MAX_DIMS) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/*printf("dimension scale! Hoorah for the Pirate King!\n");*/
}
else
{
int visitor_data = 0;
/* Here's how to get the number of scales attached
* to the dataset's dimension 0. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor,
&visitor_data) < 0) ERR;
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
printf("found a type!\n");
break;
case H5G_LINK:
printf("found a link! Yikes!\n");
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
return 0;
}
bool GH5_FetchAttribute( hid_t loc_id, const char *pszAttrName,
double &dfResult, bool bReportError )
{
hid_t hAttr = H5Aopen_name( loc_id, pszAttrName );
dfResult = 0.0;
if( hAttr < 0 )
{
if( bReportError )
CPLError( CE_Failure, CPLE_AppDefined,
"Attempt to read attribute %s failed, not found.",
pszAttrName );
return false;
}
hid_t hAttrTypeID = H5Aget_type( hAttr );
hid_t hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
/* -------------------------------------------------------------------- */
/* Confirm that we have a single element value. */
/* -------------------------------------------------------------------- */
hid_t hAttrSpace = H5Aget_space( hAttr );
hsize_t anSize[64];
int nAttrDims = H5Sget_simple_extent_dims( hAttrSpace, anSize, NULL );
int i, nAttrElements = 1;
for( i=0; i < nAttrDims; i++ ) {
nAttrElements *= (int) anSize[i];
}
if( nAttrElements != 1 )
{
if( bReportError )
CPLError( CE_Failure, CPLE_AppDefined,
"Attempt to read attribute %s failed, count=%d, not 1.",
pszAttrName, nAttrElements );
H5Sclose( hAttrSpace );
H5Tclose( hAttrNativeType );
H5Tclose( hAttrTypeID );
H5Aclose( hAttr );
return false;
}
/* -------------------------------------------------------------------- */
/* Read the value. */
/* -------------------------------------------------------------------- */
void *buf = (void *)CPLMalloc( H5Tget_size( hAttrNativeType ));
H5Aread( hAttr, hAttrNativeType, buf );
/* -------------------------------------------------------------------- */
/* Translate to double. */
/* -------------------------------------------------------------------- */
if( H5Tequal( H5T_NATIVE_INT, hAttrNativeType ) )
dfResult = *((int *) buf);
else if( H5Tequal( H5T_NATIVE_FLOAT, hAttrNativeType ) )
dfResult = *((float *) buf);
else if( H5Tequal( H5T_NATIVE_DOUBLE, hAttrNativeType ) )
dfResult = *((double *) buf);
else
{
if( bReportError )
CPLError( CE_Failure, CPLE_AppDefined,
"Attribute %s of unsupported type for conversion to double.",
pszAttrName );
CPLFree( buf );
H5Sclose( hAttrSpace );
H5Tclose( hAttrNativeType );
H5Tclose( hAttrTypeID );
H5Aclose( hAttr );
return false;
}
CPLFree( buf );
H5Sclose( hAttrSpace );
H5Tclose( hAttrNativeType );
H5Tclose( hAttrTypeID );
H5Aclose( hAttr );
return true;
}
/*
* Append planes, each of (1,2*chunksize,2*chunksize) to the dataset.
* In other words, 4 chunks are appended to the dataset at a time.
* Fill each plane with the plane number and then write it at the nth plane.
* Increase the plane number and repeat till the end of dataset, when it
* reaches chunksize long. End product is a (2*chunksize)^3 cube.
*
* Return: 0 succeed; -1 fail.
*/
static int
write_file(void)
{
hid_t fid; /* File ID for new HDF5 file */
hid_t dsid; /* dataset ID */
hid_t fapl; /* File access property list */
hid_t dcpl; /* Dataset creation property list */
char *name;
UC_CTYPE *buffer, *bufptr; /* data buffer */
hsize_t cz=chunksize_g; /* Chunk size */
hid_t f_sid; /* dataset file space id */
hid_t m_sid; /* memory space id */
int rank; /* rank */
hsize_t chunk_dims[3]; /* Chunk dimensions */
hsize_t dims[3]; /* Dataspace dimensions */
hsize_t memdims[3]; /* Memory space dimensions */
hsize_t start[3] = {0,0,0}, count[3]; /* Hyperslab selection values */
hbool_t disabled; /* Object's disabled status */
hsize_t i, j, k;
name = filename_g;
/* Open the file */
if((fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
return -1;
if(use_swmr_g)
if(H5Pset_libver_bounds(fapl, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0)
return -1;
if((fid = H5Fopen(name, H5F_ACC_RDWR | (use_swmr_g ? H5F_ACC_SWMR_WRITE : 0), fapl)) < 0){
fprintf(stderr, "H5Fopen failed\n");
return -1;
}
/* Open the dataset of the program name */
if((dsid = H5Dopen2(fid, progname_g, H5P_DEFAULT)) < 0){
fprintf(stderr, "H5Dopen2 failed\n");
return -1;
}
/* Disabled mdc flushed for the dataset */
if(H5Odisable_mdc_flushes(dsid) < 0) {
fprintf(stderr, "H5Odisable_mdc_flushes failed\n");
return -1;
}
/* Get mdc disabled status of the dataset */
if(H5Oare_mdc_flushes_disabled(dsid, &disabled) < 0) {
fprintf(stderr, "H5Oare_mdc_flushes_disabled failed\n");
return -1;
} else if(disabled)
printf("Dataset has disabled mdc flushes.\n");
else
printf("Dataset should have disabled its mdc flushes.\n");
/* Find chunksize used */
if ((dcpl = H5Dget_create_plist(dsid)) < 0){
fprintf(stderr, "H5Dget_create_plist failed\n");
return -1;
}
if (H5D_CHUNKED != H5Pget_layout(dcpl)){
fprintf(stderr, "storage layout is not chunked\n");
return -1;
}
if ((rank = H5Pget_chunk(dcpl, 3, chunk_dims)) != 3){
fprintf(stderr, "storage rank is not 3\n");
return -1;
}
/* verify chunk_dims against set paramenters */
if (chunk_dims[0]!= chunkdims_g[0] || chunk_dims[1] != cz || chunk_dims[2] != cz){
fprintf(stderr, "chunk size is not as expected. Got dims=(%llu,%llu,%llu)\n",
(unsigned long long)chunk_dims[0], (unsigned long long)chunk_dims[1],
(unsigned long long)chunk_dims[2]);
return -1;
}
/* allocate space for data buffer 1 X dims[1] X dims[2] of UC_CTYPE */
memdims[0]=1;
memdims[1] = dims_g[1];
memdims[2] = dims_g[2];
if ((buffer=(UC_CTYPE*)HDmalloc((size_t)memdims[1]*(size_t)memdims[2]*sizeof(UC_CTYPE)))==NULL) {
fprintf(stderr, "malloc: failed\n");
return -1;
};
/*
* Get dataset rank and dimension.
*/
f_sid = H5Dget_space(dsid); /* Get filespace handle first. */
rank = H5Sget_simple_extent_ndims(f_sid);
if (rank != UC_RANK){
fprintf(stderr, "rank(%d) of dataset does not match\n", rank);
return -1;
}
if (H5Sget_simple_extent_dims(f_sid, dims, NULL) < 0){
fprintf(stderr, "H5Sget_simple_extent_dims got error\n");
return -1;
}
printf("dataset rank %d, dimensions %llu x %llu x %llu\n",
rank, (unsigned long long)(dims[0]), (unsigned long long)(dims[1]),
(unsigned long long)(dims[2]));
/* verify that file space dims are as expected and are consistent with memory space dims */
if (dims[0] != 0 || dims[1] != memdims[1] || dims[2] != memdims[2]){
fprintf(stderr, "dataset is not empty. Got dims=(%llu,%llu,%llu)\n",
(unsigned long long)dims[0], (unsigned long long)dims[1],
(unsigned long long)dims[2]);
return -1;
}
/* setup mem-space for buffer */
if ((m_sid=H5Screate_simple(rank, memdims, NULL))<0){
fprintf(stderr, "H5Screate_simple for memory failed\n");
return -1;
};
/* write planes */
count[0]=1;
count[1]=dims[1];
count[2]=dims[2];
for (i=0; i<nplanes_g; i++){
/* fill buffer with value i+1 */
bufptr = buffer;
for (j=0; j<dims[1]; j++)
for (k=0; k<dims[2]; k++)
*bufptr++ = i;
/* extend the dataset by one for new plane */
dims[0]=i+1;
if(H5Dset_extent(dsid, dims) < 0){
fprintf(stderr, "H5Dset_extent failed\n");
return -1;
}
/* Get the dataset's dataspace */
if((f_sid = H5Dget_space(dsid)) < 0){
fprintf(stderr, "H5Dset_extent failed\n");
return -1;
}
start[0]=i;
/* Choose the next plane to write */
if(H5Sselect_hyperslab(f_sid, H5S_SELECT_SET, start, NULL, count, NULL) < 0){
fprintf(stderr, "Failed H5Sselect_hyperslab\n");
return -1;
}
/* Write plane to the dataset */
if(H5Dwrite(dsid, UC_DATATYPE, m_sid, f_sid, H5P_DEFAULT, buffer) < 0){
fprintf(stderr, "Failed H5Dwrite\n");
return -1;
}
/* Flush the dataset for every "chunkplanes_g" planes */
if(!((i + 1) % (hsize_t)chunkplanes_g)) {
if(H5Dflush(dsid) < 0) {
fprintf(stderr, "Failed to H5Dflush dataset\n");
return -1;
}
}
}
if(H5Dflush(dsid) < 0) {
fprintf(stderr, "Failed to H5Dflush dataset\n");
return -1;
}
/* Enable mdc flushes for the dataset */
/* Closing the dataset later will enable mdc flushes automatically if this is not done */
if(disabled)
if(H5Oenable_mdc_flushes(dsid) < 0) {
fprintf(stderr, "Failed to H5Oenable_mdc_flushes\n");
return -1;
}
/* Done writing. Free/Close all resources including data file */
HDfree(buffer);
if(H5Dclose(dsid) < 0){
fprintf(stderr, "Failed to close datasete\n");
return -1;
}
if(H5Sclose(m_sid) < 0){
fprintf(stderr, "Failed to close memory space\n");
return -1;
}
if(H5Sclose(f_sid) < 0){
fprintf(stderr, "Failed to close file space\n");
return -1;
}
if(H5Pclose(fapl) < 0){
fprintf(stderr, "Failed to property list\n");
return -1;
}
if(H5Fclose(fid) < 0){
fprintf(stderr, "Failed to close file id\n");
return -1;
}
return 0;
} /* write_file() */
int
main()
{
printf("\n*** Checking HDF5 dimscales some more.\n");
printf("*** Creating a file with one var with one dimension scale...");
{
hid_t fileid, spaceid, datasetid, dimscaleid, cparmsid;
hsize_t dims[NDIMS] = {DIM1_LEN}, maxdims[NDIMS] = {H5S_UNLIMITED};
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the space that will be used both for the dimscale and
* the 1D dataset that will attach it. */
if ((spaceid = H5Screate_simple(NDIMS, dims, maxdims)) < 0) ERR;
/* Modify dataset creation properties, i.e. enable chunking. */
dims[0] = 1;
if ((cparmsid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(cparmsid, NDIMS, dims) < 0) ERR;
/* Create our dimension scale, as an unlimited dataset. */
if ((dimscaleid = H5Dcreate(fileid, DIMSCALE_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(dimscaleid, NAME_ATTRIBUTE) < 0) ERR;
/* Create a variable which uses it. */
if ((datasetid = H5Dcreate(fileid, VAR1_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(datasetid, dimscaleid, 0) < 0) ERR;
if (H5DSset_label(datasetid, 0, DIMSCALE_LABEL) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(dimscaleid) < 0 ||
H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, one dimscale file can be read...");
{
hid_t fileid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
char dimscale_name[NC_MAX_NAME+1];
htri_t is_scale;
char label[NC_MAX_NAME+1];
int num_scales;
hsize_t dims[1], maxdims[1];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj, vars_dimscale_obj;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n",
obj_class, obj_name);*/
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* This should be an unlimited dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if (maxdims[0] != H5S_UNLIMITED) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale && strcmp(obj_name, DIMSCALE_NAME)) ERR;
if (is_scale)
{
/* A dimscale comes with a NAME attribute, in
* addition to its real name. */
if (H5DSget_scale_name(datasetid, dimscale_name, NC_MAX_NAME) < 0) ERR;
if (strcmp(dimscale_name, NAME_ATTRIBUTE)) ERR;
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj.fileno[0] = statbuf.fileno[0];
dimscale_obj.objno[0] = statbuf.objno[0];
dimscale_obj.fileno[1] = statbuf.fileno[1];
dimscale_obj.objno[1] = statbuf.objno[1];
/*printf("statbuf.fileno = %d statbuf.objno = %d\n",
statbuf.fileno, statbuf.objno);*/
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
if (H5DSiterate_scales(datasetid, 0, NULL, alien_visitor,
&vars_dimscale_obj) < 0) ERR;
/*printf("vars_dimscale_obj.fileno = %d vars_dimscale_obj.objno = %d\n",
vars_dimscale_obj.fileno, vars_dimscale_obj.objno);*/
if (vars_dimscale_obj.fileno[0] != dimscale_obj.fileno[0] ||
vars_dimscale_obj.objno[0] != dimscale_obj.objno[0] ||
vars_dimscale_obj.fileno[1] != dimscale_obj.fileno[1] ||
vars_dimscale_obj.objno[1] != dimscale_obj.objno[1]) ERR;
/* There's also a label for dimension 0. */
if (H5DSget_label(datasetid, 0, label, NC_MAX_NAME) < 0) ERR;
/*printf("found non-scale dataset %s, label %s\n", obj_name, label);*/
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Sclose(spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with one var with two dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define DIMS_2 2
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME "pres"
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS_2];
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_2, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate(fileid, PRES_NAME, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking that one var, two dimscales file can be read...");
{
#define NDIMS2 2
hid_t fileid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t dims[NDIMS2], maxdims[NDIMS2];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[2], vars_dimscale_obj[2];
int dimscale_cnt = 0;
int d, ndims;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
if (ndims > NDIMS2) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with one var with two unlimited dimension scales...");
{
#define U1_LEN 3
#define U2_LEN 2
#define DIMS2 2
#define U1_NAME "u1"
#define U2_NAME "u2"
#define VNAME "v1"
hid_t fapl_id, fcpl_id, grpid, plistid, plistid2;
hid_t fileid, lat_spaceid, lon_spaceid, pres_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid;
hsize_t dims[DIMS2], maxdims[DIMS2], chunksize[DIMS2] = {10, 10};
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[2], vars_dimscale_obj[2];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = 0;
maxdims[0] = H5S_UNLIMITED;
if ((lat_spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
if ((lon_spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = 0;
dims[1] = 0;
maxdims[0] = H5S_UNLIMITED;
maxdims[1] = H5S_UNLIMITED;
if ((pres_spaceid = H5Screate_simple(DIMS2, dims, maxdims)) < 0) ERR;
/* Set up the dataset creation property list for the two dimensions. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid, 1, chunksize) < 0) ERR;
if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate(grpid, U1_NAME, H5T_NATIVE_INT,
lat_spaceid, plistid)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate(grpid, U2_NAME, H5T_NATIVE_INT,
lon_spaceid, plistid)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
/* Set up the dataset creation property list for the variable. */
if ((plistid2 = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(plistid2, DIMS2, chunksize) < 0) ERR;
if (H5Pset_attr_creation_order(plistid2, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0) ERR;
/* Create a variable which uses these two dimscales. */
if ((pres_datasetid = H5Dcreate(grpid, VNAME, H5T_NATIVE_DOUBLE, pres_spaceid,
plistid2)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
/* Close down the show. */
if (H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Pclose(plistid) < 0 ||
H5Pclose(plistid2) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
/*Get the type (i.e. group, dataset, etc.), and the name of
the object. */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(grpid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Check the dimension lengths. */
{
hid_t spaceid1;
hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2];
int dataset_ndims;
/* Check U1. */
if ((datasetid = H5Dopen1(grpid, U1_NAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 1 || h5dimlen[0] != 0 || h5dimlenmax[0] != H5S_UNLIMITED) ERR;
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
/* Check U2. */
if ((datasetid = H5Dopen1(grpid, U2_NAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 1 || h5dimlen[0] != 0 || h5dimlenmax[0] != H5S_UNLIMITED) ERR;
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
/* Check V1. */
if ((datasetid = H5Dopen1(grpid, VNAME)) < 0) ERR;
if ((spaceid1 = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid1, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 0 || h5dimlen[1] != 0 ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* All done. */
if (H5Dclose(datasetid) ||
H5Sclose(spaceid1)) ERR;
}
/* Write two hyperslabs. */
{
#define NUM_VALS 3
hid_t file_spaceid, mem_spaceid;
hsize_t h5dimlen[DIMS2], h5dimlenmax[DIMS2], xtend_size[DIMS2] = {1, NUM_VALS};
hsize_t start[DIMS2] = {0, 0};
hsize_t count[DIMS2] = {1, NUM_VALS};
double value[NUM_VALS];
int dataset_ndims;
int i;
/* Set up phony data. */
for (i = 0; i < NUM_VALS; i++)
value[i] = (float)i;
/* Open the dataset, check its dimlens. */
if ((datasetid = H5Dopen1(grpid, VNAME)) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 0 || h5dimlen[1] != 0 ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Extend the size of the dataset. */
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
/* Check the size. */
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 1 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Set up the file and memory spaces. */
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0) ERR;
if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
/* Write a slice of data. */
if (H5Dwrite(datasetid, H5T_NATIVE_DOUBLE, mem_spaceid, file_spaceid,
H5P_DEFAULT, value) < 0)
/* Check the size. */
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 1 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* Extend the size of the dataset for the second slice. */
xtend_size[0]++;
if (H5Dextend(datasetid, xtend_size) < 0) ERR;
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
/* Set up the file and memory spaces for a second slice. */
start[0]++;
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0) ERR;
if ((mem_spaceid = H5Screate_simple(DIMS2, count, NULL)) < 0) ERR;
/* Write a second slice of data. */
if (H5Dwrite(datasetid, H5T_NATIVE_DOUBLE, mem_spaceid, file_spaceid,
H5P_DEFAULT, value) < 0)
/* Check the size again. */
if ((file_spaceid = H5Dget_space(datasetid)) < 0) ERR;
if ((dataset_ndims = H5Sget_simple_extent_dims(file_spaceid, h5dimlen,
h5dimlenmax)) < 0) ERR;
if (dataset_ndims != 2 || h5dimlen[0] != 2 || h5dimlen[1] != NUM_VALS ||
h5dimlenmax[0] != H5S_UNLIMITED || h5dimlenmax[1] != H5S_UNLIMITED) ERR;
/* All done. */
if (H5Dclose(datasetid) ||
H5Sclose(mem_spaceid) ||
H5Sclose(file_spaceid)) ERR;
}
/* Close up the shop. */
if (H5Sclose(spaceid)) ERR;
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking dimension scales with attached dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define TIME_LEN 5
#define LEN_LEN 10
#define DIMS_3 3
#define NUM_DIMSCALES1 4
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME1 "z_pres"
#define TIME_NAME "time"
#define LEN_NAME "u_len"
hid_t fileid, lat_spaceid, lon_spaceid, time_spaceid, pres_spaceid, len_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid, time_dimscaleid, len_dimscaleid;
hid_t fapl_id, fcpl_id;
hsize_t dims[DIMS_3];
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t maxdims[DIMS_3];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[NUM_DIMSCALES1], vars_dimscale_obj[NUM_DIMSCALES1];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = TIME_LEN;
if ((time_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LEN_LEN;
if ((len_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
dims[2] = TIME_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_3, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
if ((time_dimscaleid = H5Dcreate1(fileid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(time_dimscaleid, NULL) < 0) ERR;
if ((len_dimscaleid = H5Dcreate1(fileid, LEN_NAME, H5T_NATIVE_INT,
len_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(len_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these three dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME1, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, time_dimscaleid, 2) < 0) ERR;
/* Attach a dimscale to a dimscale. Unfortunately, HDF5 does not
* allow this. Woe is me. */
/*if (H5DSattach_scale(time_dimscaleid, len_dimscaleid, 0) < 0) ERR;*/
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(time_dimscaleid) < 0 ||
H5Dclose(len_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(time_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Sclose(len_spaceid) < 0 ||
H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking cration ordering of datasets which are also dimension scales...");
{
#define LAT_LEN 3
#define LON_LEN 2
#define TIME_LEN 5
#define LEN_LEN 10
#define DIMS_3 3
#define NUM_DIMSCALES2 4
#define LAT_NAME "lat"
#define LON_NAME "lon"
#define PRES_NAME1 "z_pres"
#define TIME_NAME "time"
#define LEN_NAME "u_len"
hid_t fileid, lat_spaceid, lon_spaceid, time_spaceid, pres_spaceid, len_spaceid;
hid_t pres_datasetid, lat_dimscaleid, lon_dimscaleid, time_dimscaleid, len_dimscaleid;
hid_t fapl_id, fcpl_id;
hsize_t dims[DIMS_3];
hid_t spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[NC_MAX_NAME + 1];
htri_t is_scale;
int num_scales;
hsize_t maxdims[DIMS_3];
H5G_stat_t statbuf;
HDF5_OBJID_T dimscale_obj[NUM_DIMSCALES2], vars_dimscale_obj[NUM_DIMSCALES2];
int dimscale_cnt = 0;
int d, ndims;
/* Create file access and create property lists. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
/* Set latest_format in access propertly list. This ensures that
* the latest, greatest, HDF5 versions are used in the file. */
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST, H5F_LIBVER_LATEST) < 0) ERR;
/* Set H5P_CRT_ORDER_TRACKED in the creation property list. This
* turns on HDF5 creation ordering in the file. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0) ERR;
/* Create file. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
/* Create the spaces that will be used for the dimscales. */
dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = TIME_LEN;
if ((time_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
dims[0] = LEN_LEN;
if ((len_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
/* Create the space for the dataset. */
dims[0] = LAT_LEN;
dims[1] = LON_LEN;
dims[2] = TIME_LEN;
if ((pres_spaceid = H5Screate_simple(DIMS_3, dims, dims)) < 0) ERR;
/* Create our dimension scales. */
if ((lat_dimscaleid = H5Dcreate1(fileid, LAT_NAME, H5T_NATIVE_INT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_dimscaleid, NULL) < 0) ERR;
if ((lon_dimscaleid = H5Dcreate1(fileid, LON_NAME, H5T_NATIVE_INT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_dimscaleid, NULL) < 0) ERR;
if ((time_dimscaleid = H5Dcreate1(fileid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(time_dimscaleid, NULL) < 0) ERR;
if ((len_dimscaleid = H5Dcreate1(fileid, LEN_NAME, H5T_NATIVE_INT,
len_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(len_dimscaleid, NULL) < 0) ERR;
/* Create a variable which uses these three dimscales. */
if ((pres_datasetid = H5Dcreate1(fileid, PRES_NAME1, H5T_NATIVE_FLOAT,
pres_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lat_dimscaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, lon_dimscaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_datasetid, time_dimscaleid, 2) < 0) ERR;
/* Attach a dimscale to a dimscale. Unfortunately, HDF5 does not
* allow this. Woe is me. */
/*if (H5DSattach_scale(time_dimscaleid, len_dimscaleid, 0) < 0) ERR;*/
/* Fold up our tents. */
if (H5Dclose(lat_dimscaleid) < 0 ||
H5Dclose(lon_dimscaleid) < 0 ||
H5Dclose(time_dimscaleid) < 0 ||
H5Dclose(len_dimscaleid) < 0 ||
H5Dclose(pres_datasetid) < 0 ||
H5Sclose(lat_spaceid) < 0 ||
H5Sclose(lon_spaceid) < 0 ||
H5Sclose(time_spaceid) < 0 ||
H5Sclose(pres_spaceid) < 0 ||
H5Sclose(len_spaceid) < 0 ||
H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Open the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
/* Loop through objects in the root group. */
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(fileid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(fileid, i, obj_name, NC_MAX_NAME) < 0) ERR;
/* printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", */
/* obj_class, obj_name); */
/* Deal with object based on its obj_class. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen1(fileid, obj_name)) < 0) ERR;
/* Get space info. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if ((ndims = H5Sget_simple_extent_ndims(spaceid)) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
/* fileno and objno uniquely identify an object and a
* HDF5 file. */
if (H5Gget_objinfo(datasetid, ".", 1, &statbuf) < 0) ERR;
dimscale_obj[dimscale_cnt].fileno[0] = statbuf.fileno[0];
dimscale_obj[dimscale_cnt].objno[0] = statbuf.objno[0];
dimscale_obj[dimscale_cnt].fileno[1] = statbuf.fileno[1];
dimscale_obj[dimscale_cnt].objno[1] = statbuf.objno[1];
/* printf("dimscale_obj[%d].fileno = %d dimscale_obj[%d].objno = %d\n", */
/* dimscale_cnt, dimscale_obj[dimscale_cnt].fileno, dimscale_cnt, */
/* dimscale_obj[dimscale_cnt].objno); */
dimscale_cnt++;
}
else
{
/* Here's how to get the number of scales attached
* to the dataset's dimension 0 and 1. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
if ((num_scales = H5DSget_num_scales(datasetid, 1)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
for (d = 0; d < ndims; d++)
{
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor2,
&(vars_dimscale_obj[d])) < 0) ERR;
/* Verify that the object ids passed from the
* alien_visitor2 function match the ones we found
* for the lat and lon datasets. */
if (vars_dimscale_obj[d].fileno[0] != dimscale_obj[d].fileno[0] ||
vars_dimscale_obj[d].objno[0] != dimscale_obj[d].objno[0]) ERR;
if (vars_dimscale_obj[d].fileno[1] != dimscale_obj[d].fileno[1] ||
vars_dimscale_obj[d].objno[1] != dimscale_obj[d].objno[1]) ERR;
}
}
if (H5Dclose(datasetid) < 0) ERR;
if (H5Sclose(spaceid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
int ImageBase::readHDF5(size_t select_img)
{
bool isStack = false;
H5infoProvider provider = getProvider(fhdf5); // Provider name
int errCode = 0;
hid_t dataset; /* Dataset and datatype identifiers */
hid_t filespace;
hsize_t dims[4]; // We are not going to support more than 4 dimensions, at this moment.
hsize_t nobjEman;
hid_t cparms;
int rank;
String dsname = filename.getBlockName();
// Setting default dataset name
if (dsname.empty())
{
dsname = provider.second;
switch (provider.first)
{
case EMAN: // Images in stack are stored in separated groups
hid_t grpid;
grpid = H5Gopen(fhdf5,"/MDF/images/", H5P_DEFAULT);
/*herr_t err = */
H5Gget_num_objs(grpid, &nobjEman);
dsname = formatString(dsname.c_str(), IMG_INDEX(select_img));
H5Gclose(grpid);
break;
default:
break;
}
}
else
{
switch (provider.first)
{
case EMAN: // Images in stack are stored in separated groups
nobjEman=1;
break;
default:
break;
}
}
dataset = H5Dopen2(fhdf5, dsname.c_str(), H5P_DEFAULT);
if( dataset < 0)
REPORT_ERROR(ERR_IO_NOTEXIST, formatString("readHDF5: Dataset '%s' not found",dsname.c_str()));
cparms = H5Dget_create_plist(dataset); /* Get properties handle first. */
// Get dataset rank and dimension.
filespace = H5Dget_space(dataset); /* Get filespace handle first. */
// rank = H5Sget_simple_extent_ndims(filespace);
rank = H5Sget_simple_extent_dims(filespace, dims, NULL);
// Offset only set when it is possible to access to data directly
offset = (H5D_CONTIGUOUS == H5Pget_layout(cparms))? H5Dget_offset(dataset) : 0;
// status = H5Dread(dataset, tid, H5S_ALL, H5S_ALL, H5P_DEFAULT, bm_out);
hid_t h5datatype = H5Dget_type(dataset);
// Reading byte order
switch(H5Tget_order(h5datatype))
{
case H5T_ORDER_ERROR:
REPORT_ERROR(ERR_IO, "readHDF5: error reading endianness.");
break;
case H5T_ORDER_LE:
swap = IsBigEndian();
break;
case H5T_ORDER_BE:
swap = IsLittleEndian();
break;
default:
REPORT_ERROR(ERR_IO, "readHDF5: unknown endianness type, maybe mixed types.");
break;
}
DataType datatype = datatypeH5(h5datatype);
MDMainHeader.setValue(MDL_DATATYPE,(int) datatype);
// Setting isStack depending on provider
switch (provider.first)
{
case MISTRAL: // rank 3 arrays are stacks
isStack = true;
break;
// case EMAN: // Images in stack are stored in separated groups
default:
break;
}
ArrayDim aDim;
size_t nDimFile;
aDim.xdim = dims[rank-1];
aDim.ydim = (rank>1)?dims[rank-2]:1;
aDim.zdim = (rank>3 || (rank==3 && !isStack))?dims[rank-3]:1;
if ( provider.first == EMAN )
nDimFile = nobjEman;
else
nDimFile = ( rank<3 || !isStack )?1:dims[0] ;
if (select_img > nDimFile)
REPORT_ERROR(ERR_INDEX_OUTOFBOUNDS, formatString("readHDF5 (%s): Image number %lu exceeds stack size %lu", filename.c_str(), select_img, nDimFile));
aDim.ndim = replaceNsize = (select_img == ALL_IMAGES)? nDimFile :1 ;
setDimensions(aDim);
//Read header only
if(dataMode == HEADER || (dataMode == _HEADER_ALL && aDim.ndim > 1))
return errCode;
// EMAN stores each image in a separate dataset
if ( provider.first == EMAN )
select_img = 1;
size_t imgStart = IMG_INDEX(select_img);
size_t imgEnd = (select_img != ALL_IMAGES) ? imgStart + 1 : aDim.ndim;
MD.clear();
MD.resize(imgEnd - imgStart,MDL::emptyHeader);
if (dataMode < DATA) // Don't read data if not necessary but read the header
return errCode;
if ( H5Pget_layout(cparms) == H5D_CONTIGUOUS ) //We can read it directly
readData(fimg, select_img, datatype, 0);
else // We read it by hyperslabs
{
// Allocate memory for image data (Assume xdim, ydim, zdim and ndim are already set
//if memory already allocated use it (no resize allowed)
mdaBase->coreAllocateReuse();
hid_t memspace;
hsize_t offset[4]; // Hyperslab offset in the file
hsize_t count[4]; // Size of the hyperslab in the file
// Define the offset and count of the hyperslab to be read.
switch (rank)
{
case 4:
count[0] = 1;
case 3:
// if (stack)
count[rank-3] = aDim.zdim;
offset[rank-2] = 0;
case 2:
count[rank-2] = aDim.ydim;
offset[rank-2] = 0;
break;
}
count[rank-1] = aDim.xdim;
offset[rank-1] = 0;
aDim.xdim = dims[rank-1];
aDim.ydim = (rank>1)?dims[rank-2]:1;
aDim.zdim = (rank == 4)?dims[1]:1;
// size_t nDimFile = (rank>2)?dims[0]:1 ;
// Define the memory space to read a hyperslab.
memspace = H5Screate_simple(rank,count,NULL);
size_t data = (size_t) this->mdaBase->getArrayPointer();
size_t pad = aDim.zyxdim*gettypesize(myT());
for (size_t idx = imgStart, imN = 0; idx < imgEnd; ++idx, ++imN)
{
// Set the offset of the hyperslab to be read
offset[0] = idx;
if ( H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset, NULL,
count, NULL) < 0 )
REPORT_ERROR(ERR_IO_NOREAD, formatString("readHDF5: Error selecting hyperslab %d from filename %s",
imgStart, filename.c_str()));
// movePointerTo(ALL_SLICES,imN);
// Read
if ( H5Dread(dataset, H5Datatype(myT()), memspace, filespace,
H5P_DEFAULT, (void*)(data + pad*imN)) < 0 )
REPORT_ERROR(ERR_IO_NOREAD,formatString("readHDF5: Error reading hyperslab %d from filename %s",
imgStart, filename.c_str()));
}
H5Sclose(memspace);
}
H5Pclose(cparms);
H5Sclose(filespace);
H5Dclose(dataset);
return errCode;
}
//-*****************************************************************************
AbcA::ArraySamplePtr
ReadArray( AbcA::ReadArraySampleCachePtr iCache,
hid_t iParent,
const std::string &iName,
const AbcA::DataType &iDataType,
hid_t iFileType,
hid_t iNativeType )
{
// Dispatch string stuff.
if ( iDataType.getPod() == kStringPOD )
{
return ReadStringArray( iCache, iParent, iName, iDataType );
}
else if ( iDataType.getPod() == kWstringPOD )
{
return ReadWstringArray( iCache, iParent, iName, iDataType );
}
assert( iDataType.getPod() != kStringPOD &&
iDataType.getPod() != kWstringPOD );
// Open the data set.
hid_t dsetId = H5Dopen( iParent, iName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( dsetId >= 0, "Cannot open dataset: " << iName );
DsetCloser dsetCloser( dsetId );
// Read the data space.
hid_t dspaceId = H5Dget_space( dsetId );
ABCA_ASSERT( dspaceId >= 0, "Could not get dataspace for dataSet: "
<< iName );
DspaceCloser dspaceCloser( dspaceId );
AbcA::ArraySample::Key key;
bool foundDigest = false;
// if we are caching, get the key and see if it is being used
if ( iCache )
{
key.origPOD = iDataType.getPod();
key.readPOD = key.origPOD;
key.numBytes = Util::PODNumBytes( key.readPOD ) *
H5Sget_simple_extent_npoints( dspaceId );
foundDigest = ReadKey( dsetId, "key", key );
AbcA::ReadArraySampleID found = iCache->find( key );
if ( found )
{
AbcA::ArraySamplePtr ret = found.getSample();
assert( ret );
if ( ret->getDataType().getPod() != iDataType.getPod() )
{
ABCA_THROW( "ERROR: Read data type for dset: " << iName
<< ": " << ret->getDataType()
<< " does not match expected data type: "
<< iDataType );
}
// Got it!
return ret;
}
}
// Okay, we haven't found it in a cache.
// Read the data type.
hid_t dtypeId = H5Dget_type( dsetId );
ABCA_ASSERT( dtypeId >= 0, "Could not get datatype for dataSet: "
<< iName );
DtypeCloser dtypeCloser( dtypeId );
ABCA_ASSERT( EquivalentDatatypes( iFileType, dtypeId ),
"File DataType clash for array dataset: "
<< iName );
AbcA::ArraySamplePtr ret;
H5S_class_t dspaceClass = H5Sget_simple_extent_type( dspaceId );
if ( dspaceClass == H5S_SIMPLE )
{
// Get the dimensions
int rank = H5Sget_simple_extent_ndims( dspaceId );
ABCA_ASSERT( rank == 1,
"H5Sget_simple_extent_ndims() must be 1." );
hsize_t hdim = 0;
rank = H5Sget_simple_extent_dims( dspaceId, &hdim, NULL );
Dimensions dims;
std::string dimName = iName + ".dims";
if ( H5Aexists( iParent, dimName.c_str() ) )
{
ReadDimensions( iParent, dimName, dims );
}
else
{
dims.setRank(1);
dims[0] = hdim / iDataType.getExtent();
}
ABCA_ASSERT( dims.numPoints() > 0,
"Degenerate dims in Dataset read" );
// Create a buffer into which we shall read.
ret = AbcA::AllocateArraySample( iDataType, dims );
assert( ret->getData() );
// And... read into it.
herr_t status = H5Dread( dsetId, iNativeType,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
const_cast<void*>( ret->getData() ) );
ABCA_ASSERT( status >= 0, "H5Dread() failed." );
}
else if ( dspaceClass == H5S_NULL )
{
Dimensions dims;
std::string dimName = iName + ".dims";
if ( H5Aexists( iParent, dimName.c_str() ) )
{
ReadDimensions( iParent, dimName, dims );
ABCA_ASSERT( dims.rank() > 0,
"Degenerate rank in Dataset read" );
// Num points should be zero here.
ABCA_ASSERT( dims.numPoints() == 0,
"Expecting zero points in dimensions" );
}
else
{
dims.setRank(1);
dims[0] = 0;
}
ret = AbcA::AllocateArraySample( iDataType, dims );
}
else
{
ABCA_THROW( "Unexpected scalar dataspace encountered." );
}
// Store if there is a cache.
if ( foundDigest && iCache )
{
AbcA::ReadArraySampleID stored = iCache->store( key, ret );
if ( stored )
{
return stored.getSample();
}
}
// Otherwise, just leave! ArraySamplePtr returned by AllocateArraySample
// already has fancy-dan deleter built in.
// I REALLY LOVE SMART PTRS.
return ret;
}
int
main (void)
{
hid_t vfile, file, src_space, mem_space, vspace,
vdset, dset; /* Handles */
hid_t dcpl;
herr_t status;
hsize_t vdsdims[3] = {4*DIM0_1, VDSDIM1, VDSDIM2},
vdsdims_max[3] = {VDSDIM0, VDSDIM1, VDSDIM2},
dims[3] = {DIM0_1, DIM1, DIM2},
extdims[3] = {2*DIM0_1, DIM1, DIM2},
chunk_dims[3] = {DIM0_1, DIM1, DIM2},
dims_max[3] = {DIM0, DIM1, DIM2},
vdsdims_out[3],
vdsdims_max_out[3],
start[3], /* Hyperslab parameters */
stride[3],
count[3],
src_count[3],
block[3];
hsize_t start_out[3], /* Hyperslab parameter out */
stride_out[3],
count_out[3],
block_out[3];
int i, j, k;
H5D_layout_t layout; /* Storage layout */
size_t num_map; /* Number of mappings */
ssize_t len; /* Length of the string; also a return value */
char *filename;
char *dsetname;
int wdata[DIM0_1*DIM1*DIM2];
int rdata[80][10][10];
int a_rdata[20][10][10];
/*
* Create source files and datasets. This step is optional.
*/
for (i=0; i < PLANE_STRIDE; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0_1*DIM1*DIM2; j++) wdata[j] = i+1;
/*
* Create the source files and datasets. Write data to each dataset and
* close all resources.
*/
file = H5Fcreate (SRC_FILE[i], H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
src_space = H5Screate_simple (RANK, dims, dims_max);
dcpl = H5Pcreate(H5P_DATASET_CREATE);
status = H5Pset_chunk (dcpl, RANK, chunk_dims);
dset = H5Dcreate2 (file, SRC_DATASET[i], H5T_NATIVE_INT, src_space, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata);
status = H5Sclose (src_space);
status = H5Pclose (dcpl);
status = H5Dclose (dset);
status = H5Fclose (file);
}
vfile = H5Fcreate (VFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/* Create VDS dataspace. */
vspace = H5Screate_simple (RANK, vdsdims, vdsdims_max);
/* Create dataspaces for the source dataset. */
src_space = H5Screate_simple (RANK, dims, dims_max);
/* Create VDS creation property */
dcpl = H5Pcreate (H5P_DATASET_CREATE);
/* Initialize hyperslab values */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = PLANE_STRIDE; /* we will select every fifth plane in VDS */
stride[1] = 1;
stride[2] = 1;
count[0] = H5S_UNLIMITED;
count[1] = 1;
count[2] = 1;
src_count[0] = H5S_UNLIMITED;
src_count[1] = 1;
src_count[2] = 1;
block[0] = 1;
block[1] = DIM1;
block[2] = DIM2;
/*
* Build the mappings
*
*/
status = H5Sselect_hyperslab (src_space, H5S_SELECT_SET, start, NULL, src_count, block);
for (i=0; i < PLANE_STRIDE; i++) {
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
status = H5Pset_virtual (dcpl, vspace, SRC_FILE[i], SRC_DATASET[i], src_space);
start[0]++;
}
H5Sselect_none(vspace);
/* Create a virtual dataset */
vdset = H5Dcreate2 (vfile, DATASET, H5T_NATIVE_INT, vspace, H5P_DEFAULT,
dcpl, H5P_DEFAULT);
status = H5Sclose (vspace);
status = H5Sclose (src_space);
status = H5Pclose (dcpl);
/* Let's get space of the VDS and its dimension; we should get 40x10x10 */
vspace = H5Dget_space (vdset);
H5Sget_simple_extent_dims (vspace, vdsdims_out, vdsdims_max_out);
printf ("VDS dimensions first time \n");
printf (" Current: ");
for (i=0; i<RANK; i++)
printf (" %d ", (int)vdsdims_out[i]);
printf ("\n");
/* Let's add data to the source datasets and check new dimensions for VDS */
for (i=0; i < PLANE_STRIDE; i++) {
/*
* Initialize data for i-th source dataset.
*/
for (j = 0; j < DIM0_1*DIM1*DIM2; j++) wdata[j] = 10*(i+1);
/*
* Create the source files and datasets. Write data to each dataset and
* close all resources.
*/
file = H5Fopen (SRC_FILE[i], H5F_ACC_RDWR, H5P_DEFAULT);
dset = H5Dopen2 (file, SRC_DATASET[i], H5P_DEFAULT);
status = H5Dset_extent (dset, extdims);
src_space = H5Dget_space (dset);
start[0] = DIM0_1;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = 1;
block[0] = DIM0_1;
block[1] = DIM1;
block[2] = DIM2;
mem_space = H5Screate_simple(RANK, dims, NULL);
status = H5Sselect_hyperslab (src_space, H5S_SELECT_SET, start, NULL, count, block);
status = H5Dwrite (dset, H5T_NATIVE_INT, mem_space, src_space, H5P_DEFAULT,
wdata);
status = H5Sclose (src_space);
status = H5Dclose (dset);
status = H5Fclose (file);
}
status = H5Dclose (vdset);
status = H5Fclose (vfile);
/*
* Now we begin the read section of this example.
*/
/*
* Open file and dataset using the default properties.
*/
vfile = H5Fopen (VFILE, H5F_ACC_RDONLY, H5P_DEFAULT);
vdset = H5Dopen2 (vfile, DATASET, H5P_DEFAULT);
/*
* Get creation property list and mapping properties.
*/
dcpl = H5Dget_create_plist (vdset);
/*
* Get storage layout.
*/
layout = H5Pget_layout (dcpl);
if (H5D_VIRTUAL == layout)
printf(" Dataset has a virtual layout \n");
else
printf(" Wrong layout found \n");
/*
* Find number of mappings.
*/
status = H5Pget_virtual_count (dcpl, &num_map);
printf(" Number of mappings is %lu\n", (unsigned long)num_map);
/*
* Get mapping parameters for each mapping.
*/
for (i = 0; i < (int)num_map; i++) {
printf(" Mapping %d \n", i);
printf(" Selection in the virtual dataset \n");
/* Get selection in the virttual dataset */
vspace = H5Pget_virtual_vspace (dcpl, (size_t)i);
if (H5Sget_select_type(vspace) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(vspace)) {
status = H5Sget_regular_hyperslab (vspace, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
/* Get source file name */
len = H5Pget_virtual_filename (dcpl, (size_t)i, NULL, 0);
filename = (char *)malloc((size_t)len*sizeof(char)+1);
H5Pget_virtual_filename (dcpl, (size_t)i, filename, len+1);
printf(" Source filename %s\n", filename);
/* Get source dataset name */
len = H5Pget_virtual_dsetname (dcpl, (size_t)i, NULL, 0);
dsetname = (char *)malloc((size_t)len*sizeof(char)+1);
H5Pget_virtual_dsetname (dcpl, (size_t)i, dsetname, len+1);
printf(" Source dataset name %s\n", dsetname);
/* Get selection in the source dataset */
printf(" Selection in the source dataset \n");
src_space = H5Pget_virtual_srcspace (dcpl, (size_t)i);
if (H5Sget_select_type(src_space) == H5S_SEL_HYPERSLABS) {
if (H5Sis_regular_hyperslab(src_space)) {
status = H5Sget_regular_hyperslab (src_space, start_out, stride_out, count_out, block_out);
printf(" start = [%llu, %llu, %llu] \n", (unsigned long long)start_out[0], (unsigned long long)start_out[1], (unsigned long long)start_out[2]);
printf(" stride = [%llu, %llu, %llu] \n", (unsigned long long)stride_out[0], (unsigned long long)stride_out[1], (unsigned long long)stride_out[2]);
printf(" count = [%llu, %llu, %llu] \n", (unsigned long long)count_out[0], (unsigned long long)count_out[1], (unsigned long long)count_out[2]);
printf(" block = [%llu, %llu, %llu] \n", (unsigned long long)block_out[0], (unsigned long long)block_out[1], (unsigned long long)block_out[2]);
}
}
H5Sclose(vspace);
H5Sclose(src_space);
free(filename);
free(dsetname);
}
/*
* Read data from VDS.
*/
vspace = H5Dget_space (vdset);
H5Sget_simple_extent_dims (vspace, vdsdims_out, vdsdims_max_out);
printf ("VDS dimensions second time \n");
printf (" Current: ");
for (i=0; i<RANK; i++)
printf (" %d ", (int)vdsdims_out[i]);
printf ("\n");
/* Read all VDS data */
/* EIP We should be able to do it by using H5S_ALL instead of making selection
* or using H5Sselect_all from vspace.
*/
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = 1;
count[2] = 1;
block[0] = vdsdims_out[0];
block[1] = vdsdims_out[1];
block[2] = vdsdims_out[2];
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, NULL, count, block);
mem_space = H5Screate_simple(RANK, vdsdims_out, NULL);
status = H5Dread (vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT,
rdata);
printf (" All data: \n");
for (i=0; i < (int)vdsdims_out[0]; i++) {
for (j=0; j < (int)vdsdims_out[1]; j++) {
printf ("(%d, %d, 0)", i, j);
for (k=0; k < (int)vdsdims_out[2]; k++)
printf (" %d ", rdata[i][j][k]);
printf ("\n");
}
}
/* Read VDS, but only data mapeed to dataset a.h5 */
start[0] = 0;
start[1] = 0;
start[2] = 0;
stride[0] = PLANE_STRIDE;
stride[1] = 1;
stride[2] = 1;
count[0] = 2*DIM0_1;
count[1] = 1;
count[2] = 1;
block[0] = 1;
block[1] = vdsdims_out[1];
block[2] = vdsdims_out[2];
dims[0] = 2*DIM0_1;
status = H5Sselect_hyperslab (vspace, H5S_SELECT_SET, start, stride, count, block);
mem_space = H5Screate_simple(RANK, dims, NULL);
status = H5Dread (vdset, H5T_NATIVE_INT, mem_space, vspace, H5P_DEFAULT,
a_rdata);
printf (" All data: \n");
for (i=0; i < 2*DIM0_1; i++) {
for (j=0; j < (int)vdsdims_out[1]; j++) {
printf ("(%d, %d, 0)", i, j);
for (k=0; k < (int)vdsdims_out[2]; k++)
printf (" %d ", a_rdata[i][j][k]);
printf ("\n");
}
}
/*
* Close and release resources.
*/
status = H5Sclose(mem_space);
status = H5Pclose (dcpl);
status = H5Dclose (vdset);
status = H5Fclose (vfile);
return 0;
}
//-*****************************************************************************
void
ReadArray( void * iIntoLocation,
hid_t iParent,
const std::string &iName,
const AbcA::DataType &iDataType,
hid_t iType )
{
// Dispatch string stuff.
if ( iDataType.getPod() == kStringPOD )
{
return ReadStringArray( iIntoLocation, iParent, iName, iDataType );
}
else if ( iDataType.getPod() == kWstringPOD )
{
return ReadWstringArray( iIntoLocation, iParent, iName, iDataType );
}
assert( iDataType.getPod() != kStringPOD &&
iDataType.getPod() != kWstringPOD );
// Open the data set.
hid_t dsetId = H5Dopen( iParent, iName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( dsetId >= 0, "Cannot open dataset: " << iName );
DsetCloser dsetCloser( dsetId );
// Read the data space.
hid_t dspaceId = H5Dget_space( dsetId );
ABCA_ASSERT( dspaceId >= 0, "Could not get dataspace for dataSet: "
<< iName );
DspaceCloser dspaceCloser( dspaceId );
// Read the data type.
hid_t dtypeId = H5Dget_type( dsetId );
ABCA_ASSERT( dtypeId >= 0, "Could not get datatype for dataSet: "
<< iName );
DtypeCloser dtypeCloser( dtypeId );
H5S_class_t dspaceClass = H5Sget_simple_extent_type( dspaceId );
if ( dspaceClass == H5S_SIMPLE )
{
// Get the dimensions
int rank = H5Sget_simple_extent_ndims( dspaceId );
ABCA_ASSERT( rank == 1,
"H5Sget_simple_extent_ndims() must be 1." );
hsize_t hdim = 0;
rank = H5Sget_simple_extent_dims( dspaceId, &hdim, NULL );
ABCA_ASSERT( hdim > 0,
"Degenerate dims in Dataset read" );
// And... read into it.
herr_t status = H5Dread( dsetId, iType,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
iIntoLocation );
ABCA_ASSERT( status >= 0, "H5Dread() failed." );
}
else if ( dspaceClass != H5S_NULL )
{
ABCA_THROW( "Unexpected scalar dataspace encountered." );
}
}
GDALDataset *HDF5ImageDataset::Open( GDALOpenInfo * poOpenInfo )
{
int i;
HDF5ImageDataset *poDS;
char szFilename[2048];
if(!EQUALN( poOpenInfo->pszFilename, "HDF5:", 5 ) ||
strlen(poOpenInfo->pszFilename) > sizeof(szFilename) - 3 )
return NULL;
/* -------------------------------------------------------------------- */
/* Confirm the requested access is supported. */
/* -------------------------------------------------------------------- */
if( poOpenInfo->eAccess == GA_Update )
{
CPLError( CE_Failure, CPLE_NotSupported,
"The HDF5ImageDataset driver does not support update access to existing"
" datasets.\n" );
return NULL;
}
poDS = new HDF5ImageDataset();
/* -------------------------------------------------------------------- */
/* Create a corresponding GDALDataset. */
/* -------------------------------------------------------------------- */
/* printf("poOpenInfo->pszFilename %s\n",poOpenInfo->pszFilename); */
char **papszName =
CSLTokenizeString2( poOpenInfo->pszFilename,
":", CSLT_HONOURSTRINGS|CSLT_PRESERVEESCAPES );
if( !((CSLCount(papszName) == 3) || (CSLCount(papszName) == 4)) )
{
CSLDestroy(papszName);
delete poDS;
return NULL;
}
poDS->SetDescription( poOpenInfo->pszFilename );
/* -------------------------------------------------------------------- */
/* Check for drive name in windows HDF5:"D:\... */
/* -------------------------------------------------------------------- */
strcpy(szFilename, papszName[1]);
if( strlen(papszName[1]) == 1 && papszName[3] != NULL )
{
strcat(szFilename, ":");
strcat(szFilename, papszName[2]);
poDS->SetSubdatasetName( papszName[3] );
}
else
poDS->SetSubdatasetName( papszName[2] );
CSLDestroy(papszName);
papszName = NULL;
if( !H5Fis_hdf5(szFilename) ) {
delete poDS;
return NULL;
}
poDS->SetPhysicalFilename( szFilename );
/* -------------------------------------------------------------------- */
/* Try opening the dataset. */
/* -------------------------------------------------------------------- */
poDS->hHDF5 = H5Fopen(szFilename,
H5F_ACC_RDONLY,
H5P_DEFAULT );
if( poDS->hHDF5 < 0 )
{
delete poDS;
return NULL;
}
poDS->hGroupID = H5Gopen( poDS->hHDF5, "/" );
if( poDS->hGroupID < 0 )
{
poDS->bIsHDFEOS=false;
delete poDS;
return NULL;
}
/* -------------------------------------------------------------------- */
/* THIS IS AN HDF5 FILE */
/* -------------------------------------------------------------------- */
poDS->bIsHDFEOS=TRUE;
poDS->ReadGlobalAttributes( FALSE );
/* -------------------------------------------------------------------- */
/* Create HDF5 Data Hierarchy in a link list */
/* -------------------------------------------------------------------- */
poDS->poH5Objects =
poDS->HDF5FindDatasetObjectsbyPath( poDS->poH5RootGroup,
(char *)poDS->GetSubdatasetName() );
if( poDS->poH5Objects == NULL ) {
delete poDS;
return NULL;
}
/* -------------------------------------------------------------------- */
/* Retrieve HDF5 data information */
/* -------------------------------------------------------------------- */
poDS->dataset_id = H5Dopen( poDS->hHDF5,poDS->poH5Objects->pszPath );
poDS->dataspace_id = H5Dget_space( poDS->dataset_id );
poDS->ndims = H5Sget_simple_extent_ndims( poDS->dataspace_id );
poDS->dims = (hsize_t*)CPLCalloc( poDS->ndims, sizeof(hsize_t) );
poDS->maxdims = (hsize_t*)CPLCalloc( poDS->ndims, sizeof(hsize_t) );
poDS->dimensions = H5Sget_simple_extent_dims( poDS->dataspace_id,
poDS->dims,
poDS->maxdims );
poDS->datatype = H5Dget_type( poDS->dataset_id );
poDS->clas = H5Tget_class( poDS->datatype );
poDS->size = H5Tget_size( poDS->datatype );
poDS->address = H5Dget_offset( poDS->dataset_id );
poDS->native = H5Tget_native_type( poDS->datatype, H5T_DIR_ASCEND );
poDS->nRasterYSize=(int)poDS->dims[poDS->ndims-2]; // Y
poDS->nRasterXSize=(int)poDS->dims[poDS->ndims-1]; // X alway last
poDS->nBands=1;
if( poDS->ndims == 3 ) poDS->nBands=(int) poDS->dims[0];
for( i = 1; i <= poDS->nBands; i++ ) {
HDF5ImageRasterBand *poBand =
new HDF5ImageRasterBand( poDS, i,
poDS->GetDataType( poDS->native ) );
poDS->SetBand( i, poBand );
if( poBand->bNoDataSet )
poBand->SetNoDataValue( 255 );
}
// CSK code in IdentifyProductType() and CreateProjections()
// uses dataset metadata.
poDS->SetMetadata( poDS->papszMetadata );
// Check if the hdf5 is a well known product type
poDS->IdentifyProductType();
poDS->CreateProjections( );
/* -------------------------------------------------------------------- */
/* Setup/check for pam .aux.xml. */
/* -------------------------------------------------------------------- */
poDS->TryLoadXML();
/* -------------------------------------------------------------------- */
/* Setup overviews. */
/* -------------------------------------------------------------------- */
poDS->oOvManager.Initialize( poDS, ":::VIRTUAL:::" );
return( poDS );
}
/// @todo extend to Wegdes (aka Prisms)
void SalomeIO::read(const std::string& name, vector < vector < double> > &coords, const double Lref, std::vector<bool> &type_elem_flag) {
Mesh& mesh = GetMesh();
mesh.SetLevel(0);
hsize_t dims[2];
// compute number of menus ===============
hid_t file_id = H5Fopen(name.c_str(),H5F_ACC_RDWR, H5P_DEFAULT);
hid_t gid = H5Gopen(file_id,mesh_ensemble.c_str(),H5P_DEFAULT);
hsize_t n_menus;
hid_t status= H5Gget_num_objs(gid, &n_menus); // number of menus
if(status !=0) { std::cout << "Number of mesh menus not found"; abort(); }
// compute number of groups and number of meshes ===============
std::vector<std::string> mesh_menus;
std::vector<std::string> group_menus;
unsigned n_groups = 0;
unsigned n_meshes = 0;
for (unsigned j=0; j<n_menus; j++) {
char * menu_names_j = new char[max_length];
H5Gget_objname_by_idx(gid,j,menu_names_j,max_length); ///@deprecated see the HDF doc to replace this
std::string tempj(menu_names_j);
if (tempj.substr(0,5).compare("Group") == 0) {
n_groups++;
group_menus.push_back(tempj);
}
else if (tempj.substr(0,4).compare("Mesh") == 0) {
n_meshes++;
mesh_menus.push_back(tempj);
}
}
// compute number of groups and number of meshes ===============
unsigned int n_elements_b_bb = 0;
// meshes ========================
for (unsigned j=0; j< n_meshes; j++) {
std::string tempj = mesh_menus[j];
// dimension ===============
/// @todo this determination of the dimension from the mesh file would not work with a 2D mesh embedded in 3D
std::string my_mesh_name_dir = mesh_ensemble + "/" + tempj + "/" + aux_zeroone + "/" + elem_list + "/"; ///@todo here we have to loop
hsize_t n_fem_type;
hid_t gid = H5Gopen(file_id,my_mesh_name_dir.c_str(),H5P_DEFAULT);
hid_t status0 = H5Gget_num_objs(gid, &n_fem_type);
if(status0 !=0) {std::cout << "SalomeIO::read_fem_type: H5Gget_num_objs not found"; abort();}
FindDimension(gid,tempj,n_fem_type);
H5Gclose(gid);
if (mesh.GetDimension() != n_fem_type) { std::cout << "Mismatch between dimension and number of element types" << std::endl; abort(); }
// fem type ===============
std::vector<std::string> el_fe_type(mesh.GetDimension());
ReadFE(file_id,el_fe_type, n_fem_type, my_mesh_name_dir);
// // read NODAL COORDINATES **************** C
std::string coord_dataset = mesh_ensemble + "/" + tempj + "/" + aux_zeroone + "/" + node_list + "/" + coord_list + "/"; ///@todo here we have to loop
hid_t dtset = H5Dopen(file_id,coord_dataset.c_str(),H5P_DEFAULT);
// SET NUMBER OF NODES
hid_t filespace = H5Dget_space(dtset); /* Get filespace handle first. */
hid_t status = H5Sget_simple_extent_dims(filespace, dims, NULL);
if(status ==0) std::cerr << "SalomeIO::read dims not found";
// reading xyz_med
unsigned int n_nodes = dims[0]/mesh.GetDimension();
double *xyz_med = new double[dims[0]];
std::cout << " Number of nodes in med file " << n_nodes << " " << std::endl;
mesh.SetNumberOfNodes(n_nodes);
// SET NODE COORDINATES
coords[0].resize(n_nodes);
coords[1].resize(n_nodes);
coords[2].resize(n_nodes);
status=H5Dread(dtset,H5T_NATIVE_DOUBLE,H5S_ALL,H5S_ALL,H5P_DEFAULT,xyz_med);
H5Dclose(dtset);
if (mesh.GetDimension()==3) {
for (unsigned j=0; j<n_nodes; j++) {
coords[0][j] = xyz_med[j]/Lref;
coords[1][j] = xyz_med[j+n_nodes]/Lref;
coords[2][j] = xyz_med[j+2*n_nodes]/Lref;
}
}
else if (mesh.GetDimension()==2) {
for (unsigned j=0; j<n_nodes; j++) {
coords[0][j] = xyz_med[j]/Lref;
coords[1][j] = xyz_med[j+n_nodes]/Lref;
coords[2][j] = 0.;
}
}
else if (mesh.GetDimension()==1) {
for (unsigned j=0; j<n_nodes; j++) {
coords[0][j] = xyz_med[j]/Lref;
coords[1][j] = 0.;
coords[2][j] = 0.;
}
}
delete[] xyz_med;
// // end read NODAL COORDINATES ************* C
// // read ELEMENT/cell ******************** B
std::string node_name_dir = my_mesh_name_dir + el_fe_type[mesh.GetDimension()-1] + "/" + connectivity;
hid_t dtset2 = H5Dopen(file_id,node_name_dir.c_str(),H5P_DEFAULT);
filespace = H5Dget_space(dtset2);
status = H5Sget_simple_extent_dims(filespace, dims, NULL);
if(status ==0) {std::cerr << "SalomeIO::read dims not found"; abort();}
// DETERMINE NUMBER OF NODES PER ELEMENT
unsigned Node_el = FindElemNodes( el_fe_type[mesh.GetDimension()-1] );
const int dim_conn = dims[0];
unsigned int n_elements = dim_conn/Node_el;
// SET NUMBER OF ELEMENTS
mesh.SetNumberOfElements(n_elements);
int * conn_map = new int[dim_conn];
std::cout << " Number of elements in med file " << n_elements << std::endl;
status=H5Dread(dtset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,conn_map);
if(status !=0) {std::cout << "SalomeIO::read: connectivity not found"; abort();}
H5Dclose(dtset2);
mesh.el = new elem(n_elements); ///@todo check where this is going to be deleted
// BOUNDARY (and BOUNDARY of the BOUNDARY in 3D) =========================
for (unsigned i=0; i < mesh.GetDimension()-1; i++) {
hsize_t dims_i[2];
std::string node_name_dir_i = my_mesh_name_dir + el_fe_type[i] + "/" + dofobj_indices;
hid_t dtset_i = H5Dopen(file_id,node_name_dir_i.c_str(),H5P_DEFAULT);
filespace = H5Dget_space(dtset_i);
hid_t status = H5Sget_simple_extent_dims(filespace, dims_i, NULL);
if(status ==0) { std::cerr << "SalomeIO::read dims not found"; abort(); }
n_elements_b_bb += dims_i[0];
H5Dclose(dtset_i);
}
// BOUNDARY =========================
for (unsigned iel=0; iel<n_elements; iel++) {
mesh.el->SetElementGroup(iel,1);
unsigned nve = Node_el; /// @todo this is only one element type
if (nve==27) {
type_elem_flag[0]=type_elem_flag[3]=true;
mesh.el->AddToElementNumber(1,"Hex");
mesh.el->SetElementType(iel,HEX);
} else if (nve==10) {
type_elem_flag[1]=type_elem_flag[4]=true;
mesh.el->AddToElementNumber(1,"Tet");
mesh.el->SetElementType(iel,TET);
} else if (nve==18) {
type_elem_flag[2]=type_elem_flag[3]=type_elem_flag[4]=true;
mesh.el->AddToElementNumber(1,"Wedge");
mesh.el->SetElementType(iel,WEDGE);
} else if (nve==9) {
type_elem_flag[3]=true;
mesh.el->AddToElementNumber(1,"Quad");
mesh.el->SetElementType(iel,QUAD);
}
else if (nve==6 && mesh.GetDimension()==2) {
type_elem_flag[4]=true;
mesh.el->AddToElementNumber(1,"Triangle");
mesh.el->SetElementType(iel,TRI);
}
else if (nve==3 && mesh.GetDimension()==1) {
mesh.el->AddToElementNumber(1,"Line");
mesh.el->SetElementType(iel,LINE);
} else {
std::cout<<"Error! Invalid element type in reading File!"<<std::endl;
std::cout<<"Error! Use a second order discretization"<<std::endl;
exit(0);
}
for (unsigned i=0; i<nve; i++) {
unsigned inode = SalomeToFemusVertexIndex[mesh.el->GetElementType(iel)][i];
mesh.el->SetElementDofIndex(iel,inode,conn_map[iel+i*n_elements] - 1u);
}
}
// // end read ELEMENT/CELL **************** B
// clean
delete [] conn_map;
} //end meshes
mesh.el->SetElementGroupNumber(n_groups);
// read GROUP **************** E
//we assume that these are VOLUME groups
//in general, I'd say that a group can only have ONE element type (should study the possibility of hybrid mesh)
for (unsigned j=0; j<n_groups; j++) {
const uint n_fe_types_for_groups = 1; // so far we have this assumption
std::string tempj = group_menus[j];
std::string my_mesh_name_dir = mesh_ensemble + "/" + tempj + "/" + aux_zeroone + "/" + elem_list + "/"; ///@todo here we have to loop
/// @todo check the underscores according to our naming standard
// strip the first number to get the group number
// strip the second number to get the group material
int gr_name = atoi(tempj.substr(6,1).c_str());
int gr_mat = atoi(tempj.substr(8,1).c_str());
std::vector<std::string> el_fe_type(mesh.GetDimension());
ReadFE(file_id, el_fe_type, n_fe_types_for_groups, my_mesh_name_dir);
std::string group_dataset = mesh_ensemble + "/" + tempj + "/" + aux_zeroone + "/" + elem_list + "/" + el_fe_type[mesh.GetDimension()-1] + "/" + dofobj_indices; ///@todo here we have to loop
hid_t dtset = H5Dopen(file_id,group_dataset.c_str(),H5P_DEFAULT);
hid_t filespace = H5Dget_space(dtset);
hid_t status = H5Sget_simple_extent_dims(filespace, dims, NULL);
int * elem_indices = new int[dims[0]];
status=H5Dread(dtset,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,elem_indices);
for (unsigned i=0; i < dims[0]; i++) {
mesh.el->SetElementGroup(elem_indices[i] -1 - n_elements_b_bb, gr_name);
mesh.el->SetElementMaterial(elem_indices[i] -1 - n_elements_b_bb ,gr_mat);
}
H5Dclose(dtset);
delete [] elem_indices;
}
// // end read GROUP **************** E
status = H5Fclose(file_id);
//loop over volume elements
//extract faces
//
// unsigned nbcd;
// // read boundary **************** D
// inf.open(name.c_str());
// if (!inf) {
// std::cout<<"Generic-mesh file "<< name << " cannot read boudary\n";
// exit(0);
// }
// for (unsigned k=0; k<nbcd; k++) {
// while (str2.compare("CONDITIONS") != 0) inf >> str2;
// inf >> str2;
// int value;
// unsigned nface;
// inf >>value>>str2>>nface>>str2>>str2;
// value=-value-1;
// for (unsigned i=0; i<nface; i++) {
// unsigned iel,iface;
// inf>>iel>>str2>>iface;
// iel--;
// iface=SalomeIO::SalomeToFemusFaceIndex[mesh.el->GetElementType(iel)][iface-1u];
// mesh.el->SetFaceElementIndex(iel,iface,value);
// }
// inf >> str2;
// if (str2.compare("ENDOFSECTION") != 0) {
// std::cout<<"error boundary data mesh"<<std::endl;
// exit(0);
// }
// }
// inf.close();
// // end read boundary **************** D
}
void cData2d::readHDF5(char* filename, char* fieldname){
// Open the file
hid_t file_id;
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if(file_id < 0){
printf("ERROR: Could not open file %s\n",filename);
return;
}
// Open the dataset
hid_t dataset_id;
hid_t dataspace_id;
dataset_id = H5Dopen1(file_id, fieldname);
dataspace_id = H5Dget_space(dataset_id);
// Test if 2D data
int ndims;
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if(ndims != 2) {
printf("2dData::readHDF5: Not 2D data set, ndims=%i\n",ndims);
exit(0);
}
// Get dimensions of data set (nx, ny, nn)
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dataspace_id,dims,NULL);
ny = dims[0];
nx = dims[1];
nn = 1;
for(int i = 0;i<ndims;i++)
nn *= dims[i];
// Create space for the new data
free(data); data = NULL;
data = (tData2d *) calloc(nn, sizeof(tData2d));
// Read in data after setting up a temporary buffer of the appropriate variable type
// Somehow this works best when split out accordint to different data types
// Fix into general form later
hid_t datatype_id;
H5T_class_t dataclass;
size_t size;
datatype_id = H5Dget_type(dataset_id);
dataclass = H5Tget_class(datatype_id);
size = H5Tget_size(datatype_id);
if(dataclass == H5T_FLOAT){
if (size == sizeof(float)) {
float* buffer = (float *) calloc(nn, sizeof(float));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(double)) {
double* buffer = (double *) calloc(nn, sizeof(double));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown floating point type, size=%i\n",(int) size);
return;
}
}
else if(dataclass == H5T_INTEGER){
if (size == sizeof(char)) {
char* buffer = (char*) calloc(nn, sizeof(char));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(short)) {
short* buffer = (short*) calloc(nn, sizeof(short));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(int)) {
int* buffer = (int *) calloc(nn, sizeof(int));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else if (size == sizeof(long)) {
long* buffer = (long *) calloc(nn, sizeof(long));
H5Dread(dataset_id, datatype_id, H5S_ALL,H5S_ALL, H5P_DEFAULT, buffer);
for(long i=0; i<nn; i++)
data[i] = buffer[i];
free(buffer);
}
else {
printf("2dData::readHDF5: unknown integer type, size=%lu\n",size);
exit(1);
}
}
else {
printf("2dData::readHDF5: unknown HDF5 data type\n");
return;
}
// Close and cleanup
H5Dclose(dataset_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
}
int
main(void)
{
hid_t fid = -1; /* HDF5 file ID */
hid_t did = -1; /* dataset ID */
hid_t msid = -1; /* memory dataspace ID */
hid_t fsid = -1; /* file dataspace ID */
hsize_t start[RANK]; /* hyperslab start point */
int n_elements = 0; /* size of buffer (elements) */
size_t size = 0; /* size of buffer (bytes) */
int *buffer = NULL; /* data buffer */
int n_dims = -1; /* # dimensions in dataset */
hsize_t dims[RANK]; /* current size of dataset */
hsize_t max_dims[RANK]; /* max size of dataset */
/* Open the VDS file and dataset */
if((fid = H5Fopen(VDS_FILE_NAME, H5F_ACC_RDONLY | H5F_ACC_SWMR_READ, H5P_DEFAULT)) < 0)
TEST_ERROR
if((did = H5Dopen2(fid, VDS_DSET_NAME, H5P_DEFAULT)) < 0)
TEST_ERROR
/* Create the read buffer */
n_elements = VDS_PLANE[1] * VDS_PLANE[2];
size = n_elements * sizeof(int);
if(NULL == (buffer = (int *)HDmalloc(size)))
TEST_ERROR
/* Create memory dataspace */
if((msid = H5Screate_simple(RANK, VDS_PLANE, NULL)) < 0)
TEST_ERROR
/* Read data until the dataset is full (via the writer) */
do {
/* Refresh metadata */
if(H5Drefresh(did) < 0)
TEST_ERROR
/* Get the dataset dimensions */
if((fsid = H5Dget_space(did)) < 0)
TEST_ERROR
if(H5Sget_simple_extent_dims(fsid, dims, max_dims) < 0)
TEST_ERROR
/* Check the reported size of the VDS */
if((n_dims = H5Sget_simple_extent_ndims(fsid)) < 0)
TEST_ERROR
if(n_dims != RANK)
TEST_ERROR
if(H5Sget_simple_extent_dims(fsid, dims, max_dims) < 0)
TEST_ERROR
/* NOTE: Don't care what dims[0] is. */
if(dims[1] != FULL_HEIGHT)
TEST_ERROR
if(dims[2] != WIDTH)
TEST_ERROR
if(max_dims[0] != H5S_UNLIMITED)
TEST_ERROR
if(max_dims[1] != FULL_HEIGHT)
TEST_ERROR
if(max_dims[2] != WIDTH)
TEST_ERROR
/* Continue if there's nothing to read */
if(0 == dims[0]) {
if(H5Sclose(fsid) < 0)
TEST_ERROR
continue;
}
/* Read a plane from the VDS */
/* At this time, we just make sure we can read planes without errors. */
start[0] = dims[0] - 1;
start[1] = 0;
start[2] = 0;
if(H5Sselect_hyperslab(fsid, H5S_SELECT_SET, start, NULL, VDS_PLANE, NULL) < 0)
TEST_ERROR
if(H5Dread(did, H5T_NATIVE_INT, msid, fsid, H5P_DEFAULT, buffer) < 0)
TEST_ERROR
if(H5Sclose(fsid) < 0)
TEST_ERROR
} while (dims[0] < N_PLANES_TO_WRITE);
/* Close file and dataset */
if(H5Sclose(msid) < 0)
TEST_ERROR
if(H5Dclose(did) < 0)
TEST_ERROR
if(H5Fclose(fid) < 0)
TEST_ERROR
HDfree(buffer);
HDfprintf(stderr, "SWMR reader exited successfully\n");
return EXIT_SUCCESS;
error:
H5E_BEGIN_TRY {
if(fid >= 0)
(void)H5Fclose(fid);
if(did >= 0)
(void)H5Dclose(did);
if(msid >= 0)
(void)H5Sclose(msid);
if(fsid >= 0)
(void)H5Sclose(fsid);
if(buffer != NULL)
HDfree(buffer);
} H5E_END_TRY
HDfprintf(stderr, "ERROR: SWMR reader exited with errors\n");
return EXIT_FAILURE;
} /* end main */
/**
* Reads an array of double attributes from the HDF5 metadata.
* It reads the attributes directly on it's binary form directly,
* thus avoiding string conversions.
*
* Important: It allocates the memory for the attributes internally,
* so the caller must free the returned array after using it.
* @param pszAttrName Name of the attribute to be read.
* the attribute name must be the form:
* root attribute name
* SUBDATASET/subdataset attribute name
* @param pdfValues pointer wich will store the array of doubles read.
* @param nLen it stores the length of the array read. If NULL it doesn't
* inform the lenght of the array.
* @return CPLErr CE_None in case of success, CE_Failure in case of failure
*/
CPLErr HDF5Dataset::HDF5ReadDoubleAttr(const char* pszAttrFullPath,
double **pdfValues,int *nLen)
{
CPLErr retVal = CE_Failure;
hid_t hAttrID=-1;
hid_t hAttrTypeID=-1;
hid_t hAttrNativeType=-1;
hid_t hAttrSpace=-1;
hid_t hObjAttrID=-1;
hsize_t nSize[64];
unsigned int nAttrElmts;
hsize_t i;
unsigned int nAttrDims;
size_t nSlashPos;
CPLString osAttrFullPath(pszAttrFullPath);
CPLString osObjName;
CPLString osAttrName;
//Search for the last "/" in order to get the
//Path to the attribute
nSlashPos = osAttrFullPath.find_last_of("/");
//If objects name have been found
if(nSlashPos != CPLString::npos )
{
//Split Object name (dataset, group)
osObjName = osAttrFullPath.substr(0,nSlashPos);
//Split attribute name
osAttrName = osAttrFullPath.substr(nSlashPos+1);
}
else
{
//By default the group is root, and
//the attribute is the full path
osObjName = "/";
osAttrName = pszAttrFullPath;
}
hObjAttrID = H5Oopen( hHDF5, osObjName.c_str(),H5P_DEFAULT);
if(hObjAttrID < 0)
{
CPLError( CE_Failure, CPLE_OpenFailed,
"Object %s could not be opened\n", pszAttrFullPath);
retVal = CE_Failure;
}
else
{
//Open attribute handler by name, from the object handler opened
//earlier
hAttrID = H5Aopen_name( hObjAttrID, osAttrName.c_str());
//Check for errors opening the attribute
if(hAttrID <0)
{
CPLError( CE_Failure, CPLE_OpenFailed,
"Attribute %s could not be opened\n", pszAttrFullPath);
retVal = CE_Failure;
}
else
{
hAttrTypeID = H5Aget_type( hAttrID );
hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
hAttrSpace = H5Aget_space( hAttrID );
nAttrDims = H5Sget_simple_extent_dims( hAttrSpace, nSize, NULL );
if( !H5Tequal( H5T_NATIVE_DOUBLE, hAttrNativeType ) )
{
CPLError( CE_Failure, CPLE_OpenFailed,
"Attribute %s is not of type double\n", pszAttrFullPath);
retVal = CE_Failure;
}
else
{
//Get the ammount of elements
nAttrElmts = 1;
for( i=0; i < nAttrDims; i++ )
{
//For multidimensional attributes
nAttrElmts *= nSize[i];
}
if(nLen != NULL)
*nLen = nAttrElmts;
(*pdfValues) = (double *) CPLMalloc(nAttrElmts*sizeof(double));
//Read the attribute contents
if(H5Aread( hAttrID, hAttrNativeType, *pdfValues )<0)
{
CPLError( CE_Failure, CPLE_OpenFailed,
"Attribute %s could not be opened\n",
pszAttrFullPath);
retVal = CE_Failure;
}
else
{
retVal = CE_None;
}
}
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Sclose(hAttrSpace);
H5Aclose(hAttrID);
}
H5Oclose(hObjAttrID);
}
return retVal;
}
int
main()
{
printf("\n*** Checking HDF5 dimension scales.\n");
#define GRP_NAME "simple_scales"
#define DIMSCALE_NAME "dimscale"
#define NAME_ATTRIBUTE "Billy-Bob"
#define VAR1_NAME "var1"
#define VAR2_NAME "var2"
#define VAR3_NAME "var3"
#define DIM1_LEN 3
#define DIM2_LEN 2
#define FIFTIES_SONG "Mamma said they'll be days like this. They'll be days like this, my mamma said."
printf("*** Creating simple dimension scales file...");
{
hid_t fileid, grpid, dimscaleid;
hid_t dimscale_spaceid, var1_spaceid, var3_spaceid;
hid_t var1_datasetid, var2_datasetid, var3_datasetid;
hsize_t dims[2] = {DIM1_LEN, DIM2_LEN};
hsize_t dimscale_dims[1] = {DIM1_LEN};
/* Open file and create group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, GRP_NAME, 0)) < 0) ERR;
/* Create our dimension scale. Use the built-in NAME attribute
* on the dimscale. */
if ((dimscale_spaceid = H5Screate_simple(1, dimscale_dims,
dimscale_dims)) < 0) ERR;
if ((dimscaleid = H5Dcreate(grpid, DIMSCALE_NAME, H5T_NATIVE_INT,
dimscale_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(dimscaleid, NAME_ATTRIBUTE) < 0) ERR;
/* Create a 1D variable which uses the dimscale. Attach a label
* to this scale. */
if ((var1_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
if ((var1_datasetid = H5Dcreate(grpid, VAR1_NAME, H5T_NATIVE_INT,
var1_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(var1_datasetid, dimscaleid, 0) < 0) ERR;
if (H5DSset_label(var1_datasetid, 0, FIFTIES_SONG) < 0) ERR;
/* Create a 1D variabls that doesn't use the dimension scale. */
if ((var2_datasetid = H5Dcreate(grpid, VAR2_NAME, H5T_NATIVE_INT,
var1_spaceid, H5P_DEFAULT)) < 0) ERR;
/* Create a 2D dataset which uses the scale for one of its
* dimensions. */
if ((var3_spaceid = H5Screate_simple(2, dims, dims)) < 0) ERR;
if ((var3_datasetid = H5Dcreate(grpid, VAR3_NAME, H5T_NATIVE_INT,
var3_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(var3_datasetid, dimscaleid, 0) < 0) ERR;
/* Close up the shop. */
if (H5Dclose(dimscaleid) < 0 ||
H5Dclose(var1_datasetid) < 0 ||
H5Dclose(var2_datasetid) < 0 ||
H5Dclose(var3_datasetid) < 0 ||
H5Sclose(var1_spaceid) < 0 ||
H5Sclose(var3_spaceid) < 0 ||
H5Sclose(dimscale_spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* HELP! If you are reading this in the future, and time
* machines have been invented, please come back to July 10,
* 2005, the Java Java coffee shop in Lafayette, 8:00 am MST +-
* 20 minutes. Bring back some advanced weapons systems to
* destroy the sound system here, which is playing 50's rock and
* roll. Do-op, do-op, la-ma la-ma, ding dong. Save me!!! (Mind
* you, James Brown is a different story!) */
}
SUMMARIZE_ERR;
printf("*** Checking that simple dimscale file can be read...");
{
hid_t fileid, grpid, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[STR_LEN + 1];
htri_t is_scale;
int num_scales;
/* Reopen the file and group. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, GRP_NAME)) < 0) ERR;
/* Loop through datasets to find variables. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of the
* object. Confusingly, this is a different type than the type
* of a variable. This type might be better called "class" or
* "type of type" */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, STR_LEN) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", obj_class, obj_name);*/
/* Deal with groups and datasets. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/*Close the last datasetid, if one is open. */
if (datasetid > 0)
{
H5Dclose(datasetid);
}
if ((datasetid = H5Dopen(grpid, obj_name)) < 0) ERR;
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale && strcmp(obj_name, DIMSCALE_NAME)) ERR;
if (is_scale)
{
char nom_de_quincey[STR_LEN+1];
/* A dimscale comes with a NAME attribute, in
* addition to its real name. */
if (H5DSget_scale_name(datasetid, nom_de_quincey,
STR_LEN) < 0) ERR;
if (strcmp(nom_de_quincey, NAME_ATTRIBUTE)) ERR;
/*printf("found scale %s, NAME %s\n", obj_name, nom_de_quincey);*/
}
else
{
char label[STR_LEN+1];
/* Here's how to get the number of scales attached
* to the dataset. I would think that this would
* return 0 scales for a dataset that doesn't have
* scales, but instead it errors. So take an error
* to be the same as no dimension scales. */
num_scales = H5DSget_num_scales(datasetid, 0);
if (strcmp(obj_name, VAR1_NAME) == 0 && num_scales != 1) ERR;
if (strcmp(obj_name, VAR2_NAME) == 0 && num_scales > 0) ERR;
if (strcmp(obj_name, VAR3_NAME) == 0 && num_scales != 1) ERR;
/* There's also a label for dimension 0 of var1. */
if (strcmp(obj_name, VAR1_NAME) == 0)
{
if (H5DSget_label(datasetid, 0, label, STR_LEN) < 0) ERR;
if (strcmp(label, FIFTIES_SONG)) ERR;
}
}
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Dclose(datasetid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating simple dimension scales file with lots of datasets...");
#define NUM_DATASETS 500
{
hid_t fileid, grpid, dimscaleid;
hid_t dimscale_spaceid, var1_spaceid;
hid_t var1_datasetid[NUM_DATASETS];
hsize_t dims[2] = {DIM1_LEN, DIM2_LEN};
hsize_t dimscale_dims[1] = {DIM1_LEN};
char var_name[STR_LEN + 1];
int v;
/* Open file and create group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, GRP_NAME, 0)) < 0) ERR;
/* Create our dimension scale. Use the built-in NAME attribute
* on the dimscale. */
if ((dimscale_spaceid = H5Screate_simple(1, dimscale_dims,
dimscale_dims)) < 0) ERR;
if ((dimscaleid = H5Dcreate(grpid, DIMSCALE_NAME, H5T_NATIVE_INT,
dimscale_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(dimscaleid, NAME_ATTRIBUTE) < 0) ERR;
/* Create many 1D datasets which use the dimscale. */
if ((var1_spaceid = H5Screate_simple(1, dims, dims)) < 0) ERR;
for (v = 0; v < NUM_DATASETS; v++)
{
sprintf(var_name, "var_%d", v);
if ((var1_datasetid[v] = H5Dcreate(grpid, var_name, H5T_NATIVE_INT,
var1_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSattach_scale(var1_datasetid[v], dimscaleid, 0) < 0) ERR;
}
/* Close up the shop. */
for (v = 0; v < NUM_DATASETS; v++)
if (H5Dclose(var1_datasetid[v]) < 0) ERR;
if (H5Dclose(dimscaleid) < 0 ||
H5Sclose(var1_spaceid) < 0 ||
H5Sclose(dimscale_spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating a file with an unlimited dimension scale...");
{
hid_t fileid, grpid, spaceid, datasetid, dimscaleid, cparmsid;
hsize_t dims[1] = {1}, maxdims[1] = {H5S_UNLIMITED};
/* Create file and group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, GRP_NAME, 0)) < 0) ERR;
if ((spaceid = H5Screate_simple(1, dims, maxdims)) < 0) ERR;
/* Modify dataset creation properties, i.e. enable chunking */
if ((cparmsid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
if (H5Pset_chunk(cparmsid, 1, dims) < 0) ERR;
/* Create our dimension scale, as an unlimited dataset. */
if ((dimscaleid = H5Dcreate(grpid, DIMSCALE_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(dimscaleid, NAME_ATTRIBUTE) < 0) ERR;
/* Create a variable which uses it. */
if ((datasetid = H5Dcreate(grpid, VAR1_NAME, H5T_NATIVE_INT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(datasetid, dimscaleid, 0) < 0) ERR;
if (H5DSset_label(datasetid, 0, "dimension label") < 0) ERR;
/* Close up the shop. */
if (H5Dclose(dimscaleid) < 0 ||
H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
#ifdef EXTRA_TESTS
printf("*** Checking that unlimited dimscale file can be read...");
{
hid_t fileid, grpid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[STR_LEN + 1];
htri_t is_scale;
int num_scales;
hsize_t dims[1], maxdims[1];
/* Reopen the file and group. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, GRP_NAME)) < 0) ERR;
/* Loop through datasets to find variables. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, STR_LEN) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", obj_class, obj_name);*/
/* Deal with groups and datasets. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/*Close the last datasetid, if one is open. */
if (datasetid > 0)
{
H5Dclose(datasetid);
datasetid = 0;
}
/* Open the dataset. */
if ((datasetid = H5Dopen(grpid, obj_name)) < 0) ERR;
/* This should be an unlimited dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, maxdims) < 0) ERR;
if (maxdims[0] != H5S_UNLIMITED) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale && strcmp(obj_name, DIMSCALE_NAME)) ERR;
if (is_scale)
{
char nom_de_quincey[STR_LEN+1];
/* A dimscale comes with a NAME attribute, in
* addition to its real name. */
if (H5DSget_scale_name(datasetid, nom_de_quincey, STR_LEN) < 0) ERR;
/*printf("found scale %s, NAME %s\n", obj_name, nom_de_quincey);*/
}
else
{
char label[STR_LEN+1];
int visitor_data = 0;
/* Here's how to get the number of scales attached
* to the dataset's dimension 0. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn about them. */
if (H5DSiterate_scales(datasetid, 0, NULL, alien_visitor,
&visitor_data) < 0) ERR;
/* There's also a label for dimension 0. */
if (H5DSget_label(datasetid, 0, label, STR_LEN) < 0) ERR;
/*printf("found non-scale dataset %s, label %s\n", obj_name, label);*/
}
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Dclose(datasetid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating some 3D datasets using shared dimscales...");
{
#define NDIMS 3
#define TIME_DIM 0
#define LAT_DIM 1
#define LON_DIM 2
#define LAT_LEN 2
#define LON_LEN 3
#define LAT_NAME "Lat"
#define LON_NAME "Lon"
#define TIME_NAME "Time"
#define PRES_NAME "Pressure"
#define TEMP_NAME "Temperature"
hid_t fileid, grpid, lat_spaceid, lon_spaceid, time_spaceid, spaceid;
hid_t lat_scaleid, lon_scaleid, time_scaleid;
hid_t pres_dsid, temp_dsid, cparmsid;
hsize_t dims[NDIMS], max_dims[NDIMS];
/* Create file and group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gcreate(fileid, GRP_NAME, 0)) < 0) ERR;
/* Create 3 1D spaces for the 3 dimension scale datasets. Time
* starts out as size 0. It's an unlimited dimension scale. */
dims[0] = 0;
max_dims[0] = H5S_UNLIMITED;
if ((time_spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
dims[0] = LAT_LEN;
max_dims[0] = LAT_LEN;
if ((lat_spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
dims[0] = LON_LEN;
max_dims[0] = LON_LEN;
if ((lon_spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
/* Enable chunking for unlimited time scale. */
if ((cparmsid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
dims[TIME_DIM] = 1;
if (H5Pset_chunk(cparmsid, 1, dims) < 0) ERR;
/* Create our dimension scales. */
if ((time_scaleid = H5Dcreate(grpid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(time_scaleid, TIME_NAME) < 0) ERR;
if ((lat_scaleid = H5Dcreate(grpid, LAT_NAME, H5T_NATIVE_FLOAT,
lat_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lat_scaleid, LAT_NAME) < 0) ERR;
if ((lon_scaleid = H5Dcreate(grpid, LON_NAME, H5T_NATIVE_FLOAT,
lon_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(lon_scaleid, LON_NAME) < 0) ERR;
/* Create a space coresponding to these three dimensions. */
dims[TIME_DIM] = 0;
dims[LAT_DIM] = LAT_LEN;
dims[LON_DIM] = LON_LEN;
max_dims[TIME_DIM] = H5S_UNLIMITED;
max_dims[LAT_DIM] = LAT_LEN;
max_dims[LON_DIM] = LON_LEN;
if ((spaceid = H5Screate_simple(NDIMS, dims, max_dims)) < 0) ERR;
/* Create two variables which use them, and attach the dimension scales. */
dims[TIME_DIM] = 1;
if (H5Pset_chunk(cparmsid, NDIMS, dims) < 0) ERR;
if ((pres_dsid = H5Dcreate(grpid, PRES_NAME, H5T_NATIVE_FLOAT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(pres_dsid, time_scaleid, 0) < 0) ERR;
if (H5DSattach_scale(pres_dsid, lat_scaleid, 1) < 0) ERR;
if (H5DSattach_scale(pres_dsid, lon_scaleid, 2) < 0) ERR;
if (H5DSset_label(pres_dsid, TIME_DIM, TIME_NAME) < 0) ERR;
if (H5DSset_label(pres_dsid, LAT_DIM, LAT_NAME) < 0) ERR;
if (H5DSset_label(pres_dsid, LON_DIM, LON_NAME) < 0) ERR;
if ((temp_dsid = H5Dcreate(grpid, TEMP_NAME, H5T_NATIVE_FLOAT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(temp_dsid, time_scaleid, 0) < 0) ERR;
if (H5DSattach_scale(temp_dsid, lat_scaleid, 1) < 0) ERR;
if (H5DSattach_scale(temp_dsid, lon_scaleid, 2) < 0) ERR;
if (H5DSset_label(temp_dsid, TIME_DIM, TIME_NAME) < 0) ERR;
if (H5DSset_label(temp_dsid, LAT_DIM, LAT_NAME) < 0) ERR;
if (H5DSset_label(temp_dsid, LON_DIM, LON_NAME) < 0) ERR;
/* Close up the shop. */
if (H5Dclose(pres_dsid) < 0 ||
H5Dclose(temp_dsid) < 0 ||
H5Dclose(lat_scaleid) < 0 ||
H5Dclose(lon_scaleid) < 0 ||
H5Dclose(time_scaleid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking 3D datasets created with shared dimscales...");
{
hid_t fileid, grpid, spaceid = 0, datasetid = 0;
hsize_t num_obj, i;
int obj_class;
char obj_name[STR_LEN + 1];
htri_t is_scale;
int num_scales;
hsize_t dims[NDIMS], max_dims[NDIMS];
int d;
/* Reopen the file and group. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, GRP_NAME)) < 0) ERR;
/* Loop through datasets to find variables. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the type (i.e. group, dataset, etc.), and the name of
* the object. */
if ((obj_class = H5Gget_objtype_by_idx(grpid, i)) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, STR_LEN) < 0) ERR;
/*printf("\nEncountered: HDF5 object obj_class %d obj_name %s\n", obj_class, obj_name);*/
/* Deal with groups and datasets. */
switch(obj_class)
{
case H5G_GROUP:
break;
case H5G_DATASET:
/* Open the dataset. */
if ((datasetid = H5Dopen(grpid, obj_name)) < 0) ERR;
/*printf("\nobj_name %s\n", obj_name);*/
/* Get the dimensions of this dataset. */
if ((spaceid = H5Dget_space(datasetid)) < 0) ERR;
if (H5Sget_simple_extent_dims(spaceid, dims, max_dims) < 0) ERR;
/* Is this a dimscale? */
if ((is_scale = H5DSis_scale(datasetid)) < 0) ERR;
if (is_scale)
{
char nom_de_quincey[STR_LEN+1];
/* A dimscale comes with a NAME attribute, in
* addition to its real name. */
if (H5DSget_scale_name(datasetid, nom_de_quincey,
STR_LEN) < 0) ERR;
/*printf("found scale %s, NAME %s id 0x%x\n", obj_name,
nom_de_quincey, datasetid);*/
/* Check size depending on name. */
if ((!strcmp(obj_name, LAT_NAME) && dims[TIME_DIM] != LAT_LEN) ||
(!strcmp(obj_name, LON_NAME) && dims[TIME_DIM] != LON_LEN) ||
(!strcmp(obj_name, TIME_NAME) &&
max_dims[TIME_DIM] != H5S_UNLIMITED)) ERR;
}
else
{
char label[STR_LEN+1];
int visitor_data = 0;
/* SHould have these dimensions... */
if (dims[TIME_DIM] != 0 || dims[LAT_DIM] != LAT_LEN ||
dims[LON_DIM] != LON_LEN) ERR;
if (max_dims[TIME_DIM] != H5S_UNLIMITED) ERR;
/* Here's how to get the number of scales attached
* to the dataset's dimension 0. */
if ((num_scales = H5DSget_num_scales(datasetid, 0)) < 0) ERR;
if (num_scales != 1) ERR;
/* Go through all dimscales for this var and learn
* about them. What I want is the dataset id of each
* dimscale. Then... */
for (d = 0; d < NDIMS; d++)
if (H5DSiterate_scales(datasetid, d, NULL, alien_visitor,
&visitor_data) < 0) ERR;
/*printf("visitor_data: 0x%x\n", visitor_data);*/
/* There's also a label for each dimension. */
if (H5DSget_label(datasetid, 0, label, STR_LEN) < 0) ERR;
if (strcmp(label, TIME_NAME)) ERR;
if (H5DSget_label(datasetid, 1, label, STR_LEN) < 0) ERR;
if (strcmp(label, LAT_NAME)) ERR;
if (H5DSget_label(datasetid, 2, label, STR_LEN) < 0) ERR;
if (strcmp(label, LON_NAME)) ERR;
}
if (H5Dclose(datasetid) < 0) ERR;
break;
case H5G_TYPE:
break;
case H5G_LINK:
break;
default:
printf("Unknown object class %d!", obj_class);
}
}
/* Close up the shop. */
if (H5Sclose(spaceid) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Creating 3D datasets using shared dimscales in groups...");
{
#define FATHER "Adam"
#define GOOD_CHILD "Able"
#define BAD_CHILD "Cain"
#define DISTANCE_LEN 3
#define SMELLINESS_NAME "Smelliness"
#define DISTANCE_NAME "Distance"
#define TIME_NAME "Time"
#define TIME_DIM 0
#define SMELLINESS_DIM 1
#define DISTANCE_DIM 2
#define GOAT_NAME "Billy_goat_gruff"
#define CAMEL_NAME "Grumpy_the_camel"
hid_t fileid, smelliness_spaceid, distance_spaceid, time_spaceid, spaceid;
hid_t adam_grpid, able_grpid, cain_grpid;
hid_t time_scaleid, smelliness_scaleid, distance_scaleid;
hid_t goat_dsid, camel_dsid, cparmsid;
hsize_t dims[NDIMS], max_dims[NDIMS];
/* Create file and group. */
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT)) < 0) ERR;
if ((adam_grpid = H5Gcreate(fileid, FATHER, 0)) < 0) ERR;
if ((able_grpid = H5Gcreate(adam_grpid, GOOD_CHILD, 0)) < 0) ERR;
if ((cain_grpid = H5Gcreate(adam_grpid, BAD_CHILD, 0)) < 0) ERR;
/* Create 3 1D spaces for the 3 dimension scale datasets. Time
* and smelliness starts out as 0. They are unlimited dimension
* scales. */
dims[0] = 0;
max_dims[0] = H5S_UNLIMITED;
if ((time_spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
dims[0] = 0;
max_dims[0] = H5S_UNLIMITED;
if ((smelliness_spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
dims[0] = DISTANCE_LEN;
max_dims[0] = DISTANCE_LEN;
if ((distance_spaceid = H5Screate_simple(1, dims, max_dims)) < 0) ERR;
/* Enable chunking for unlimited time and smelliness scale. */
if ((cparmsid = H5Pcreate(H5P_DATASET_CREATE)) < 0) ERR;
dims[0] = 1;
if (H5Pset_chunk(cparmsid, 1, dims) < 0) ERR;
/* Create our dimension scales. */
if ((time_scaleid = H5Dcreate(adam_grpid, TIME_NAME, H5T_NATIVE_INT,
time_spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(time_scaleid, TIME_NAME) < 0) ERR;
if ((smelliness_scaleid = H5Dcreate(adam_grpid, SMELLINESS_NAME, H5T_NATIVE_FLOAT,
smelliness_spaceid, cparmsid)) < 0) ERR;
if (H5DSset_scale(smelliness_scaleid, SMELLINESS_NAME) < 0) ERR;
if ((distance_scaleid = H5Dcreate(adam_grpid, DISTANCE_NAME, H5T_NATIVE_FLOAT,
distance_spaceid, H5P_DEFAULT)) < 0) ERR;
if (H5DSset_scale(distance_scaleid, DISTANCE_NAME) < 0) ERR;
/* Create a space coresponding to these three dimensions. */
dims[TIME_DIM] = 0;
dims[SMELLINESS_DIM] = 0;
dims[DISTANCE_DIM] = DISTANCE_LEN;
max_dims[TIME_DIM] = H5S_UNLIMITED;
max_dims[SMELLINESS_DIM] = H5S_UNLIMITED;
max_dims[DISTANCE_DIM] = DISTANCE_LEN;
if ((spaceid = H5Screate_simple(NDIMS, dims, max_dims)) < 0) ERR;
/* Set up chunking for our 3D vars. */
dims[TIME_DIM] = 1;
dims[SMELLINESS_DIM] = 1;
if (H5Pset_chunk(cparmsid, NDIMS, dims) < 0) ERR;
/* Create two variables which use them, and attach the dimension scales. */
if ((goat_dsid = H5Dcreate(able_grpid, GOAT_NAME, H5T_NATIVE_FLOAT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(goat_dsid, time_scaleid, 0) < 0) ERR;
if (H5DSattach_scale(goat_dsid, smelliness_scaleid, 1) < 0) ERR;
if (H5DSattach_scale(goat_dsid, distance_scaleid, 2) < 0) ERR;
if ((camel_dsid = H5Dcreate(cain_grpid, CAMEL_NAME, H5T_NATIVE_FLOAT,
spaceid, cparmsid)) < 0) ERR;
if (H5DSattach_scale(camel_dsid, time_scaleid, 0) < 0) ERR;
if (H5DSattach_scale(camel_dsid, smelliness_scaleid, 1) < 0) ERR;
if (H5DSattach_scale(camel_dsid, distance_scaleid, 2) < 0) ERR;
/* Close up the shop. */
if (H5Dclose(goat_dsid) < 0 ||
H5Dclose(camel_dsid) < 0 ||
H5Dclose(smelliness_scaleid) < 0 ||
H5Dclose(distance_scaleid) < 0 ||
H5Dclose(time_scaleid) < 0 ||
H5Sclose(spaceid) < 0 ||
H5Gclose(cain_grpid) < 0 ||
H5Gclose(able_grpid) < 0 ||
H5Gclose(adam_grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Checking 3D datasets in groups created with shared dimscales...");
{
hid_t fileid, grpid;
/* Reopen the file and group. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, FATHER)) < 0) ERR;
/* If we can't scan the group, crash into a flaming heap of
* smoking, smoldering rubbish. */
if (rec_scan_group(grpid)) ERR;
/* Close up the shop. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
#endif
FINAL_RESULTS;
}
herr_t HDF5AttrIterate( hid_t hH5ObjID,
const char *pszAttrName,
void *pDS )
{
hid_t hAttrID;
hid_t hAttrTypeID;
hid_t hAttrNativeType;
hid_t hAttrSpace;
char *szData = NULL;
hsize_t nSize[64];
unsigned int nAttrElmts;
hsize_t nAttrSize;
hsize_t i;
void *buf = NULL;
unsigned int nAttrDims;
char **papszTokens;
HDF5Dataset *poDS;
CPLString osKey;
char *szValue = NULL;
poDS = (HDF5Dataset *) pDS;
// Convert "/" into "_" for the path component
const char* pszPath = poDS->poH5CurrentObject->pszUnderscorePath;
if(pszPath != NULL && strlen(pszPath) > 0)
{
papszTokens = CSLTokenizeString2( pszPath, "/", CSLT_HONOURSTRINGS );
for( i = 0; papszTokens != NULL && papszTokens[i] != NULL; ++i )
{
if( i != 0)
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy( papszTokens );
}
// Convert whitespaces into "_" for the attribute name component
papszTokens = CSLTokenizeString2( pszAttrName, " ",
CSLT_STRIPLEADSPACES | CSLT_STRIPENDSPACES );
for( i = 0; papszTokens != NULL && papszTokens[i] != NULL; ++i )
{
if(!osKey.empty())
osKey += '_';
osKey += papszTokens[i];
}
CSLDestroy( papszTokens );
hAttrID = H5Aopen_name( hH5ObjID, pszAttrName );
hAttrTypeID = H5Aget_type( hAttrID );
hAttrNativeType = H5Tget_native_type( hAttrTypeID, H5T_DIR_DEFAULT );
hAttrSpace = H5Aget_space( hAttrID );
nAttrDims = H5Sget_simple_extent_dims( hAttrSpace, nSize, NULL );
nAttrElmts = 1;
for( i=0; i < nAttrDims; i++ ) {
nAttrElmts *= (int) nSize[i];
}
if( H5Tget_class( hAttrNativeType ) == H5T_STRING )
{
if ( H5Tis_variable_str(hAttrNativeType) )
{
char** papszStrings;
papszStrings = (char**) CPLMalloc( nAttrElmts * sizeof(char*) );
// Read the values
H5Aread( hAttrID, hAttrNativeType, papszStrings );
// Concatenate all values as one string (separated by a space)
CPLString osVal = papszStrings[0];
for( i=1; i < nAttrElmts; i++ ) {
osVal += " ";
osVal += papszStrings[i];
}
szValue = (char*) CPLMalloc(osVal.length() + 1);
strcpy( szValue, osVal.c_str() );
H5Dvlen_reclaim( hAttrNativeType, hAttrSpace, H5P_DEFAULT,
papszStrings );
CPLFree( papszStrings );
}
else
{
nAttrSize = H5Aget_storage_size( hAttrID );
szValue = (char*) CPLMalloc((size_t) (nAttrSize+1));
H5Aread( hAttrID, hAttrNativeType, szValue );
szValue[nAttrSize] = '\0';
}
}
else {
if( nAttrElmts > 0 ) {
buf = (void *) CPLMalloc( nAttrElmts*
H5Tget_size( hAttrNativeType ));
szData = (char*) CPLMalloc( 8192 );
szValue = (char*) CPLMalloc( MAX_METADATA_LEN );
szData[0] = '\0';
szValue[0] ='\0';
H5Aread( hAttrID, hAttrNativeType, buf );
}
if( H5Tequal( H5T_NATIVE_CHAR, hAttrNativeType )
|| H5Tequal( H5T_NATIVE_SCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c ", ((char *) buf)[i]);
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UCHAR, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%c", ((char *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_SHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((short *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_USHORT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned short *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_INT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%d ", ((int *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_UINT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ud ", ((unsigned int *) buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_LONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((long *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_ULONG, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
sprintf( szData, "%ld ", ((unsigned long *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_FLOAT, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
CPLsprintf( szData, "%.8g ", ((float *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
else if( H5Tequal( H5T_NATIVE_DOUBLE, hAttrNativeType ) ) {
for( i=0; i < nAttrElmts; i++ ) {
CPLsprintf( szData, "%.15g ", ((double *)buf)[i] );
if( CPLStrlcat(szValue, szData, MAX_METADATA_LEN) >=
MAX_METADATA_LEN )
CPLError( CE_Warning, CPLE_OutOfMemory,
"Header data too long. Truncated\n");
}
}
CPLFree( buf );
}
H5Sclose(hAttrSpace);
H5Tclose(hAttrNativeType);
H5Tclose(hAttrTypeID);
H5Aclose( hAttrID );
poDS->papszMetadata = CSLSetNameValue( poDS->papszMetadata, osKey, szValue);
CPLFree( szData );
CPLFree( szValue );
return 0;
}
void readSpectrumEnergyScale(cGlobal *global, char *filename) {
char groupname[1024];
char fieldname[1024];
hid_t file_id;
hid_t datagroup_id;
hid_t dataset_id;
hid_t dataspace_id;
hid_t datatype_id;
H5T_class_t dataclass;
size_t size;
int ndims;
sprintf(groupname, "energySpectrum");
sprintf(fieldname, "runIntegratedEnergyScale");
// Check if an energy scale calibration file has been specified
if ( strcmp(filename,"") == 0 ){
printf("spectrum energy scale calibration file path was not specified\n");
printf("spectra will be output with default (0) energy scale\n");
return;
}
// Check whether file exists!
FILE* fp = fopen(filename, "r");
if (fp) // file exists
fclose(fp);
else { // file doesn't exist
printf("specified energy scale calibration file does not exist: %s\n",filename);
printf("spectra will be output with default (0) energy scale\n");
return;
}
printf("Reading energy spectrum scale calibration file:\n");
printf("\t%s\n",filename);
// Open the file
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if(file_id < 0){
printf("ERROR: Could not open file %s\n",filename);
printf("spectra will be output with default (0) energy scale\n");
return;
}
// Open the dataset
datagroup_id = H5Gopen1(file_id, groupname);
dataset_id = H5Dopen1(datagroup_id, fieldname);
dataspace_id = H5Dget_space(dataset_id);
// Test if correct dimensions / size
ndims = H5Sget_simple_extent_ndims(dataspace_id);
if(ndims != 1) {
printf("the specified file does not have the correct dimensions for energy scale calibration, ndims=%i\n",ndims);
printf("spectra will be output with default (0) energy scale\n");
return;
}
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dataspace_id,dims,NULL);
if (dims[0]!=1 || dims[1]!=(hsize_t)global->espectrumLength) {
printf("the specified file does not have the correct dimensions for energy scale calibration\n");
printf("spectra will be output with default (0) energy scale\n");
return;
}
datatype_id = H5Dget_type(dataset_id);
dataclass = H5Tget_class(datatype_id);
size = H5Tget_size(datatype_id);
double* energyscale = (double *) calloc(global->espectrumLength, sizeof(double));
H5Dread(dataset_id, datatype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, energyscale);
for(int i=0; i<global->espectrumLength; i++) {
global->espectrumScale[i] = energyscale[i];
}
free(energyscale);
// Close and cleanup
H5Dclose(dataset_id);
H5Gclose(datagroup_id);
// Cleanup stale IDs
hid_t ids[256];
int n_ids = H5Fget_obj_ids(file_id, H5F_OBJ_ALL, 256, ids);
for (long i=0; i<n_ids; i++ ) {
hid_t id;
H5I_type_t type;
id = ids[i];
type = H5Iget_type(id);
if ( type == H5I_GROUP )
H5Gclose(id);
if ( type == H5I_DATASET )
H5Dclose(id);
if ( type == H5I_DATASPACE )
H5Sclose(id);
//if ( type == H5I_DATATYPE )
// H5Dclose(id);
}
H5Fclose(file_id);
printf("energy spectrum scale calibration file read successful:\n");
return;
}
