int
main()
{
printf("\n*** Checking HDF5 file c0.nc.\n");
printf("*** Checking HDF5 objcts...");
{
hid_t fileid, grpid;
hsize_t num_obj, i;
char obj_name[MAX_NAME];
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* Find the variables. Read their metadata and attributes. */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i=0; i<num_obj; i++)
{
/* Get the class (i.e. group, dataset, etc.), and the name of
* the object. */
if (H5Gget_objtype_by_idx(grpid, i) < 0) ERR;
if (H5Gget_objname_by_idx(grpid, i, obj_name, MAX_NAME) < 0) ERR;
}
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
CPLErr HDF5Dataset::ReadGlobalAttributes(int bSUBDATASET)
{
HDF5GroupObjects *poRootGroup =
static_cast<HDF5GroupObjects *>(CPLCalloc(sizeof(HDF5GroupObjects), 1));
poH5RootGroup = poRootGroup;
poRootGroup->pszName = CPLStrdup("/");
poRootGroup->nType = H5G_GROUP;
poRootGroup->poHparent = nullptr;
poRootGroup->pszPath = nullptr;
poRootGroup->pszUnderscorePath = nullptr;
if( hHDF5 < 0 )
{
CPLError(CE_Failure, CPLE_AppDefined, "hHDF5 < 0!");
return CE_None;
}
H5G_stat_t oStatbuf = {{0, 0}, {0, 0}, 0, H5G_UNKNOWN, 0, 0, {0, 0, 0, 0}};
if( H5Gget_objinfo(hHDF5, "/", FALSE, &oStatbuf) < 0 )
return CE_Failure;
poRootGroup->objno[0] = oStatbuf.objno[0];
poRootGroup->objno[1] = oStatbuf.objno[1];
if( hGroupID > 0 )
H5Gclose(hGroupID);
hGroupID = H5Gopen(hHDF5, "/");
if( hGroupID < 0 )
{
CPLError(CE_Failure, CPLE_AppDefined, "hGroupId <0!");
return CE_None;
}
poRootGroup->nbAttrs = H5Aget_num_attrs(hGroupID);
H5Gget_num_objs(hGroupID, &(poRootGroup->nbObjs));
if( poRootGroup->nbObjs > 0 )
{
poRootGroup->poHchild = static_cast<HDF5GroupObjects *>(
CPLCalloc(static_cast<size_t>(poRootGroup->nbObjs),
sizeof(HDF5GroupObjects)));
H5Giterate(hGroupID, "/", nullptr, HDF5CreateGroupObjs, poRootGroup);
}
else
{
poRootGroup->poHchild = nullptr;
}
HDF5ListGroupObjects(poRootGroup, bSUBDATASET);
return CE_None;
}
int HBase::numDatas()
{
int res = 0;
hsize_t nobj;
H5Gget_num_objs(fObjectId, &nobj);
hsize_t i;
for(i = 0; i < nobj; i++) {
if(isChildData(i))
res++;
}
return res;
}
CPLErr HDF5Dataset::ReadGlobalAttributes(int bSUBDATASET)
{
HDF5GroupObjects *poRootGroup;
poRootGroup = (HDF5GroupObjects*) CPLCalloc(sizeof(HDF5GroupObjects), 1);
poH5RootGroup=poRootGroup;
poRootGroup->pszName = CPLStrdup( "/" );
poRootGroup->nType = H5G_GROUP;
poRootGroup->poHparent = NULL;
poRootGroup->pszPath = NULL;
poRootGroup->pszUnderscorePath = NULL;
if( hHDF5 < 0 ) {
printf( "hHDF5 <0!!\n" );
return CE_None;
}
H5G_stat_t oStatbuf;
if( H5Gget_objinfo( hHDF5, "/", FALSE, &oStatbuf ) < 0 )
return CE_Failure;
poRootGroup->objno[0] = oStatbuf.objno[0];
poRootGroup->objno[1] = oStatbuf.objno[1];
if( hGroupID > 0 )
H5Gclose( hGroupID );
hGroupID = H5Gopen( hHDF5, "/" );
if( hGroupID < 0 ){
printf( "hGroupID <0!!\n" );
return CE_None;
}
poRootGroup->nbAttrs = H5Aget_num_attrs( hGroupID );
H5Gget_num_objs( hGroupID, &( poRootGroup->nbObjs ) );
if( poRootGroup->nbObjs > 0 ) {
poRootGroup->poHchild = ( HDF5GroupObjects * )
CPLCalloc( poRootGroup->nbObjs,
sizeof( HDF5GroupObjects ) );
H5Giterate( hGroupID, "/", NULL,
HDF5CreateGroupObjs, (void *)poRootGroup );
}
else poRootGroup->poHchild = NULL;
HDF5ListGroupObjects( poRootGroup, bSUBDATASET );
return CE_None;
}
char HBase::hasNamedChild(const char * childName)
{
hsize_t nobj = 0;
H5Gget_num_objs(fObjectId, &nobj);
//std::cout<<"\n"<<fObjectPath<<" has "<<nobj<<"objs\n";
hsize_t i;
for(i = 0; i < nobj; i++) {
//std::cout<<getChildName(i)<<"\n";
if(getChildName(i) == childName) {
//std::cout<<"found "<<childName;
return 1;
}
}
return 0;
}
std::vector<std::string> HdfGroup::objects( H5G_obj_t type ) const
{
std::vector<std::string> lst;
hsize_t nobj;
H5Gget_num_objs( d->id, &nobj );
for ( hsize_t i = 0; i < nobj; ++i )
{
if ( type == H5G_UNKNOWN || H5Gget_objtype_by_idx( d->id, i ) == type )
{
char name[HDF_MAX_NAME];
H5Gget_objname_by_idx( d->id, i, name, ( size_t )HDF_MAX_NAME );
lst.push_back( std::string( name ) );
}
}
return lst;
}
int AMRreader::
getInfo( const char* filename )
{
debug2 << "opening AMR file " << filename << "\n";
filename_ = filename;
hid_t file_id = H5Fopen( filename, H5F_ACC_RDONLY, H5P_DEFAULT );
if( file_id<0 ) {
debug1 << "Failed to open AMR file: " << filename << ".\n";
return -1;
}
hsize_t nobjs;
herr_t err = H5Gget_num_objs( file_id, &nobjs );
debug2 << "nobjs in " << filename << " is " << nobjs << "\n";
for( hsize_t i=0; i<nobjs; i++ ) {
int type = H5Gget_objtype_by_idx( file_id, i );
if( type == H5G_GROUP ) {
char name[1000];
ssize_t l= H5Gget_objname_by_idx( file_id, i, name, 1000 );
hid_t gid = H5Gopen1( file_id, name );
if( strcmp( name, amr_grpname )==0 ) {
if( getAMRinfo( gid )!=0 ) {
debug1 << "Failed to retrieve AMR info in " << filename << "\n";
H5Gclose(gid);
return -2;
}}
else if( strcmp( name, intf_grp_name )==0 ) {
if( getIntfInfo( gid ) != 0 ) {
debug1 << "Failed to retrieve Interface info in " << filename << "\n";
return -3;
}}
else {
debug1 << "Find a unrecongnized group " << name << " in " << filename << "\n";
}
H5Gclose(gid);
}
}
H5Fclose( file_id );
return 0;
}
char HBase::hasNamedData(const char * dataName)
{
hsize_t nobj;
H5Gget_num_objs(fObjectId, &nobj);
//std::cout<<"\n"<<fObjectPath<<" has "<<nobj<<"objs\n";
hsize_t i;
for(i = 0; i < nobj; i++) {
//std::cout<<getChildName(i)<<"\n";
if(isChildData(i)) {
if(getChildName(i) == dataName) {
//std::cout<<"found "<<dataName<<"\n";;
return 1;
}
}
}
return 0;
}
bool
FWSingleOMP::put(xmlNodePtr q){
fname<<xmlrootName<<".storeConfig.h5";
c_file = H5Fopen(fname.str().c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
hsize_t numGrps = 0;
H5Gget_num_objs(c_file, &numGrps);
numSteps = static_cast<int> (numGrps)-3;
app_log()<<" Total number of steps in input file "<<numSteps<<endl;
if (weightFreq<1) weightFreq=1;
int numberDataPoints = weightLength/weightFreq;
// pointsToCalculate.resize(numberDataPoints);
// for(int i=0;i<numberDataPoints;i++) pointsToCalculate[i]=i*weightFreq;
app_log()<<" "<<numberDataPoints<<" sets of observables will be calculated each "<<weightFreq<<" steps"<<endl;
app_log()<<" Config Generations skipped for thermalization: "<<startStep<<endl;//<<" steps. At: ";
// for(int i=0;i<numberDataPoints;i++) app_log()<<pointsToCalculate[i]<<" ";
app_log()<<endl;
if (H5Fclose(c_file)>-1) c_file=-1;
return true;
}
//------------------------------------------------------------------------------
// Description:
// Finds the block index (blockIndx) within the HDF5 file associated with
// the given file index.
static bool FindBlockIndex(hid_t fileIndx, const int blockIdx, hid_t &rootIndx)
{
// retrieve the contents of the root directory to look for a group
// corresponding to the target block, if available, open that group
hsize_t numbObjs;
rootIndx = H5Gopen(fileIndx, "/");
if (rootIndx < 0)
{
vtkGenericWarningMacro("Failed to open root node of particles file");
return false;
}
bool found = false;
H5Gget_num_objs(rootIndx, &numbObjs);
for (int objIndex = 0; objIndex < static_cast < int >(numbObjs); objIndex++)
{
if (H5Gget_objtype_by_idx(rootIndx, objIndex) == H5G_GROUP)
{
int blckIndx;
char blckName[65];
H5Gget_objname_by_idx(rootIndx, objIndex, blckName, 64);
// Is this the target block?
if ((sscanf(blckName, "Grid%d", &blckIndx) == 1) &&
(blckIndx == blockIdx))
{
// located the target block
rootIndx = H5Gopen(rootIndx, blckName);
if (rootIndx < 0)
{
vtkGenericWarningMacro("Could not locate target block!\n");
}
found = true;
break;
}
} // END if group
} // END for all objects
return (found);
}
/*
* utility function which checks whether a particular dataset
* is present in the HDF5 file
*/
int checkfordataset(hid_t file_id, char *datasetname)
{
/* default is zero */
int ispresent=0;
/* get number of datasets in file */
hsize_t ndatasets[1];
H5Gget_num_objs(file_id, ndatasets);
/* loop over all datasets looking for dataset matching datasetname
set function value to true (1) if it is present */
int i;
char name[256];
for (i=0;i<(int)ndatasets[0];i++) {
H5Gget_objname_by_idx(file_id, i, name, 256);
/* printf(" dataset %s in file \n",name); */
if (strcmp(name,datasetname)==0) {
/*printf(" %s in file \n",datasetname);*/
ispresent = 1;
}
}
return ispresent;
}
std::vector<std::string> hdf5file::subelements(const std::string& path, int desired_type)
{
hid_t group_id = H5Gopen(_file_id, path.c_str(), H5P_DEFAULT);
const size_t MAX_NAME = 256;
char element_name[MAX_NAME];
hsize_t object_count;
H5Gget_num_objs(group_id, &object_count);
std::vector<std::string> result;
for(std::size_t i = 0; i < object_count; ++i)
{
int object_type = H5Gget_objtype_by_idx(group_id, i);
H5Gget_objname_by_idx(group_id, i, element_name, MAX_NAME);
if(object_type == desired_type)
result.push_back(std::string(element_name));
}
return result;
}
int
main()
{
printf("\n*** Checking HDF5 file functions.\n");
printf("*** Creating HDF5 file in the canonical netCDF-4 way...");
{
hid_t fapl_id, fcpl_id, fileid, grpid, fileid2;
hsize_t num_obj;
/* 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;
/* Set close degree. */
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
/* Create the 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;
/* Close up. */
if (H5Pclose(fapl_id) < 0 ||
H5Pclose(fcpl_id) < 0 ||
H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0)
ERR;
/* Reopen the file and check it. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, fapl_id)) < 0) ERR;
if (H5Gget_num_objs(fileid, &num_obj) < 0) ERR;
if (num_obj) ERR;
/* Open another copy of the same file. Must use the same file
* access degree or HDF5 will not open the file. */
if ((fileid2 = H5Fopen(FILE_NAME, H5F_ACC_RDWR, fapl_id)) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Fclose(fileid2) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Opening a HDF5 file with H5Literate...");
{
hid_t fapl_id, fileid, grpid;
hsize_t idx = 0;
char obj_name[STR_LEN + 1];
hsize_t num_obj;
int i;
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, CHUNK_CACHE_NELEMS, CHUNK_CACHE_SIZE,
CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
if (H5Literate(grpid, H5_INDEX_CRT_ORDER, H5_ITER_INC, &idx, op_func,
(void *)obj_name) != 1) ERR;
printf("encountered object %s\n", obj_name);
}
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
printf("*** Opening a HDF5 file in the canonical netCDF-4 way...");
{
hid_t fapl_id, fileid, grpid;
H5_index_t idx_field = H5_INDEX_CRT_ORDER;
H5O_info_t obj_info;
hsize_t num_obj;
ssize_t size;
char obj_name[STR_LEN + 1];
int i;
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, CHUNK_CACHE_NELEMS, CHUNK_CACHE_SIZE,
CHUNK_CACHE_PREEMPTION) < 0) ERR;
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* How many objects in this group? */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
for (i = 0; i < num_obj; i++)
{
if (H5Oget_info_by_idx(grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT)) ERR;
if ((size = H5Lget_name_by_idx(grpid, ".", idx_field, H5_ITER_INC, i,
NULL, 0, H5P_DEFAULT)) < 0) ERR;
if (H5Lget_name_by_idx(grpid, ".", idx_field, H5_ITER_INC, i,
obj_name, size+1, H5P_DEFAULT) < 0) ERR;
}
if (H5Gclose(grpid) < 0) ERR;
if (H5Fclose(fileid) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
int HBase::numChildren()
{
hsize_t nobj = 0;
H5Gget_num_objs(fObjectId, &nobj);
return (int)nobj;
}
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;
}
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;
}
/// @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->SetElementVertexIndex(iel,inode,conn_map[iel+i*n_elements]);
}
}
// // 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
}
int
main()
{
printf("\n*** Checking HDF5 attribute functions some more.\n");
printf("*** Creating tst_xplatform2_3.nc with HDF only...");
{
hid_t fapl_id, fcpl_id;
size_t chunk_cache_size = MY_CHUNK_CACHE_SIZE;
size_t chunk_cache_nelems = CHUNK_CACHE_NELEMS;
float chunk_cache_preemption = CHUNK_CACHE_PREEMPTION;
hid_t fileid, grpid, attid, spaceid;
hid_t s1_typeid, vlen_typeid, s3_typeid;
hid_t file_typeid1[NUM_OBJ], native_typeid1[NUM_OBJ];
hid_t file_typeid2, native_typeid2;
hsize_t num_obj;
H5O_info_t obj_info;
char obj_name[STR_LEN + 1];
hsize_t dims[1] = {ATT_LEN}; /* netcdf attributes always 1-D. */
struct s1
{
float x;
double y;
};
struct s3
{
hvl_t data[NUM_VL];
};
/* cvc stands for "Compound with Vlen of Compound." */
struct s3 cvc_out[ATT_LEN];
int i, j, k;
/* Create some output data: a struct s3 array (length ATT_LEN)
* which holds an array of vlen (length NUM_VL) of struct s1. */
for (i = 0; i < ATT_LEN; i++)
for (j = 0; j < NUM_VL; j++)
{
cvc_out[i].data[j].len = i + 1;
if (!(cvc_out[i].data[j].p = calloc(sizeof(struct s1), cvc_out[i].data[j].len))) ERR;
for (k = 0; k < cvc_out[i].data[j].len; k++)
{
((struct s1 *)cvc_out[i].data[j].p)[k].x = 42.42;
((struct s1 *)cvc_out[i].data[j].p)[k].y = 2.0;
}
}
/* Create the HDF5 file, with cache control, creation order, and
* all the timmings. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG)) ERR;
if (H5Pset_cache(fapl_id, 0, chunk_cache_nelems, chunk_cache_size,
chunk_cache_preemption) < 0) ERR;
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_LATEST,
H5F_LIBVER_LATEST) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
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;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create the compound type for struct s1. */
if ((s1_typeid = H5Tcreate(H5T_COMPOUND, sizeof(struct s1))) < 0) ERR;
if (H5Tinsert(s1_typeid, X_NAME, offsetof(struct s1, x),
H5T_NATIVE_FLOAT) < 0) ERR;
if (H5Tinsert(s1_typeid, Y_NAME, offsetof(struct s1, y),
H5T_NATIVE_DOUBLE) < 0) ERR;
if (H5Tcommit(grpid, S1_TYPE_NAME, s1_typeid) < 0) ERR;
/* Create a vlen type. Its a vlen of struct s1. */
if ((vlen_typeid = H5Tvlen_create(s1_typeid)) < 0) ERR;
if (H5Tcommit(grpid, VLEN_TYPE_NAME, vlen_typeid) < 0) ERR;
/* Create the struct s3 type, which contains the vlen. */
if ((s3_typeid = H5Tcreate(H5T_COMPOUND, sizeof(struct s3))) < 0) ERR;
if (H5Tinsert(s3_typeid, VL_NAME, offsetof(struct s3, data),
vlen_typeid) < 0) ERR;
if (H5Tcommit(grpid, S3_TYPE_NAME, s3_typeid) < 0) ERR;
/* Create an attribute of this new type. */
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
if ((attid = H5Acreate(grpid, S3_ATT_NAME, s3_typeid, spaceid,
H5P_DEFAULT)) < 0) ERR;
if (H5Awrite(attid, s3_typeid, cvc_out) < 0) ERR;
/* Close the types. */
if (H5Tclose(s1_typeid) < 0 ||
H5Tclose(vlen_typeid) < 0 ||
H5Tclose(s3_typeid) < 0) ERR;
/* Close the att. */
if (H5Aclose(attid) < 0) ERR;
/* Close the space. */
if (H5Sclose(spaceid) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* How many objects in this group? (There should be 3, the
* types. Atts don't count as objects to HDF5.) */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
if (num_obj != NUM_OBJ) ERR;
/* For each object in the group... */
for (i = 0; i < num_obj; i++)
{
/* Get the name, and make sure this is a type. */
if (H5Oget_info_by_idx(grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT) < 0) ERR;
if (H5Lget_name_by_idx(grpid, ".", H5_INDEX_NAME, H5_ITER_INC, i,
obj_name, STR_LEN + 1, H5P_DEFAULT) < 0) ERR;
if (obj_info.type != H5O_TYPE_NAMED_DATATYPE) ERR;
/* Get the typeid and native typeid. */
if ((file_typeid1[i] = H5Topen2(grpid, obj_name, H5P_DEFAULT)) < 0) ERR;
if ((native_typeid1[i] = H5Tget_native_type(file_typeid1[i],
H5T_DIR_DEFAULT)) < 0) ERR;
}
/* There is one att: open it by index. */
if ((attid = H5Aopen_idx(grpid, 0)) < 0) ERR;
/* Get file and native typeids of the att. */
if ((file_typeid2 = H5Aget_type(attid)) < 0) ERR;
if ((native_typeid2 = H5Tget_native_type(file_typeid2, H5T_DIR_DEFAULT)) < 0) ERR;
/* Close the attribute. */
if (H5Aclose(attid) < 0) ERR;
/* Close the typeids. */
for (i = 0; i < NUM_OBJ; i++)
{
if (H5Tclose(file_typeid1[i]) < 0) ERR;
if (H5Tclose(native_typeid1[i]) < 0) ERR;
}
if (H5Tclose(file_typeid2) < 0) ERR;
if (H5Tclose(native_typeid2) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Deallocate our vlens. */
for (i = 0; i < ATT_LEN; i++)
for (j = 0; j < NUM_VL; j++)
free(cvc_out[i].data[j].p);
}
SUMMARIZE_ERR;
printf("*** Checking vlen of compound file...");
{
#define NUM_OBJ_1 1
#define ATT_NAME "Poseidon"
hid_t fapl_id, fcpl_id;
hid_t fileid, grpid, attid, spaceid;
hid_t vlen_typeid;
hid_t file_typeid1[NUM_OBJ_1], native_typeid1[NUM_OBJ_1];
hid_t file_typeid2, native_typeid2;
hsize_t num_obj;
H5O_info_t obj_info;
char obj_name[STR_LEN + 1];
hsize_t dims[1] = {ATT_LEN}; /* netcdf attributes always 1-D. */
/* vc stands for "Vlen of Compound." */
hvl_t vc_out[ATT_LEN];
int i, k;
/* Create some output data: an array of vlen (length ATT_LEN) of
* int. */
for (i = 0; i < ATT_LEN; i++)
{
vc_out[i].len = i + 1;
if (!(vc_out[i].p = calloc(sizeof(int), vc_out[i].len))) ERR;
for (k = 0; k < vc_out[i].len; k++)
((int *)vc_out[i].p)[k] = 42;
}
/* Create the HDF5 file with creation order. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
if ((fcpl_id = H5Pcreate(H5P_FILE_CREATE)) < 0) ERR;
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;
if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, fcpl_id, fapl_id)) < 0) ERR;
if (H5Pclose(fapl_id) < 0) ERR;
if (H5Pclose(fcpl_id) < 0) ERR;
/* Open the root group. */
if ((grpid = H5Gopen2(fileid, "/", H5P_DEFAULT)) < 0) ERR;
/* Create a vlen type. Its a vlen of int. */
if ((vlen_typeid = H5Tvlen_create(H5T_NATIVE_INT)) < 0) ERR;
if (H5Tcommit(grpid, VLEN_TYPE_NAME, vlen_typeid) < 0) ERR;
/* Create an attribute of this new type. */
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
if ((attid = H5Acreate(grpid, ATT_NAME, vlen_typeid, spaceid,
H5P_DEFAULT)) < 0) ERR;
if (H5Awrite(attid, vlen_typeid, vc_out) < 0) ERR;
/* Close the type. */
if (H5Tclose(vlen_typeid) < 0) ERR;
/* Close the att. */
if (H5Aclose(attid) < 0) ERR;
/* Close the space. */
if (H5Sclose(spaceid) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Reopen the file. */
if ((fileid = H5Fopen(FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT)) < 0) ERR;
if ((grpid = H5Gopen(fileid, "/")) < 0) ERR;
/* How many objects in this group? (There should be 2, the
* types. Atts don't count as objects to HDF5.) */
if (H5Gget_num_objs(grpid, &num_obj) < 0) ERR;
if (num_obj != NUM_OBJ_1) ERR;
/* For each object in the group... */
for (i = 0; i < num_obj; i++)
{
/* Get the name, and make sure this is a type. */
if (H5Oget_info_by_idx(grpid, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC,
i, &obj_info, H5P_DEFAULT) < 0) ERR;
if (H5Lget_name_by_idx(grpid, ".", H5_INDEX_NAME, H5_ITER_INC, i,
obj_name, STR_LEN + 1, H5P_DEFAULT) < 0) ERR;
if (obj_info.type != H5O_TYPE_NAMED_DATATYPE) ERR;
/* Get the typeid and native typeid. */
if ((file_typeid1[i] = H5Topen2(grpid, obj_name, H5P_DEFAULT)) < 0) ERR;
if ((native_typeid1[i] = H5Tget_native_type(file_typeid1[i],
H5T_DIR_DEFAULT)) < 0) ERR;
}
/* There is one att: open it by index. */
if ((attid = H5Aopen_idx(grpid, 0)) < 0) ERR;
/* Get file and native typeids of the att. */
if ((file_typeid2 = H5Aget_type(attid)) < 0) ERR;
if ((native_typeid2 = H5Tget_native_type(file_typeid2, H5T_DIR_DEFAULT)) < 0) ERR;
/* Close the attribute. */
if (H5Aclose(attid) < 0) ERR;
/* Close the typeids. */
for (i = 0; i < NUM_OBJ_1; i++)
{
if (H5Tclose(file_typeid1[i]) < 0) ERR;
if (H5Tclose(native_typeid1[i]) < 0) ERR;
}
if (H5Tclose(file_typeid2) < 0) ERR;
if (H5Tclose(native_typeid2) < 0) ERR;
/* Close the group and file. */
if (H5Gclose(grpid) < 0 ||
H5Fclose(fileid) < 0) ERR;
/* Deallocate our vlens. */
for (i = 0; i < ATT_LEN; i++)
free(vc_out[i].p);
}
SUMMARIZE_ERR;
FINAL_RESULTS;
}
herr_t HDF5CreateGroupObjs(hid_t hHDF5, const char *pszObjName,
void *poHObjParent)
{
herr_t ret; /* error return status */
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 */
int 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;
herr_t status;
char *CreatePath( HDF5GroupObjects *poH5Object );
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 );
ret = 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 ) );
}
status = 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;
ret = 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;
}
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;
}
hsize_t H5G::getGroupCount(){
hsize_t i;
H5Gget_num_objs(classID,&i);
return i;
}
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;
}
void rdiff(const char *name, hid_t f1, hid_t f2) {
hid_t g1 = H5Gopen(f1, name, H5P_DEFAULT);
hid_t g2 = H5Gopen(f2, name, H5P_DEFAULT);
if (g1 >= 0 && g2 >= 0) {
int n1 = H5Aget_num_attrs(g1);
for (int i = 0; i < n1; i++) {
char aname[MAXNAME];
hid_t a1 = H5Aopen_idx(g1, i);
assert(H5Aget_name(a1, MAXNAME, aname) < MAXNAME);
H5Aclose(a1);
if (!H5LTfind_attribute(g2, aname)) {
printf("Only in %s[%s%s]\n", file1, name, aname);
continue;
}
int d1, d2;
H5LTget_attribute_ndims(f1, name, aname, &d1);
H5LTget_attribute_ndims(f2, name, aname, &d2);
assert(d1 <= 1 && d2 <= 1);
hsize_t dims1, dims2;
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_attribute_info(f1, name, aname, &dims1, &t1, &ts1);
H5LTget_attribute_info(f2, name, aname, &dims2, &t2, &ts2);
assert(t1 == t2);
assert(t1 == H5T_INTEGER || t1 == H5T_FLOAT || t1 == H5T_STRING);
if (t1 == H5T_INTEGER) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
int v1, v2;
H5LTget_attribute_int(f1, name, aname, &v1);
H5LTget_attribute_int(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%d %s[%s%s]=%d\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_FLOAT) {
assert(d1==0 || (dims1 == 1 && dims2 == 1));
assert(ts1 == 4 && ts2 == 4);
float v1, v2;
H5LTget_attribute_float(f1, name, aname, &v1);
H5LTget_attribute_float(f2, name, aname, &v2);
if (v1 != v2) {
printf("%s[%s%s]=%g %s[%s%s]=%g\n", file1, name, aname, v1, file2, name, aname, v2);
}
}
if (t1 == H5T_STRING) {
assert(ts1 < 256 && ts2 < 256);
char buf1[256];
char buf2[256];
H5LTget_attribute_string(f1, name, aname, buf1);
H5LTget_attribute_string(f2, name, aname, buf2);
if (strcmp(buf1, buf2)) {
printf("%s[%s%s]=%s %s[%s%s]=%s\n", file1, name, aname, buf1, file2, name, aname, buf2);
}
}
}
int n2 = H5Aget_num_attrs(g2);
for (int i = 0; i < n2; i++) {
char aname[MAXNAME];
hid_t a2 = H5Aopen_idx(g2, i);
assert(H5Aget_name(a2, MAXNAME, aname) < MAXNAME);
H5Aclose(a2);
if (!H5LTfind_attribute(g1, aname)) {
printf("Only in %s[%s%s]\n", file2, name, aname);
continue;
}
}
hsize_t nobj;
H5Gget_num_objs(g1, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g1, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g1, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g2, oname)) {
printf("Only in %s[%s%s]\n", file1, name, oname);
continue;
}
hsize_t dims1[2], dims2[2];
H5T_class_t t1, t2;
size_t ts1, ts2;
H5LTget_dataset_info(g1, oname, dims1, &t1, &ts1);
H5LTget_dataset_info(g2, oname, dims2, &t2, &ts2);
if (dims1[0] != dims2[0] || dims1[1] != dims2[1]) {
printf("%s[%s%s](%d,%d) != %s[%s%s](%d,%d)\n",
file1, name, oname, dims1[1], dims1[0],
file2, name, oname, dims2[1], dims2[0]);
continue;
}
float *data1 = malloc(dims1[0]*dims1[1]*sizeof(float));
float *data2 = malloc(dims1[0]*dims1[1]*sizeof(float));
H5LTread_dataset_float(g1, oname, data1);
H5LTread_dataset_float(g2, oname, data2);
float maxdiff = 0;
for (int i = dims1[0]*dims1[1]-1; i >= 0; i--) {
float d = data1[i] - data2[i];
if (d < 0) d = -d;
if (d > maxdiff) maxdiff = d;
}
printf("max |%s[%s%s] - %s[%s%s]| = %g\n",
file1, name, oname, file2, name, oname, maxdiff);
free(data1); free(data2);
}
H5Gget_num_objs(g2, &nobj);
for (int i = 0; i < nobj; i++) {
char oname[MAXNAME];
assert(H5Gget_objname_by_idx(g2, i, oname, MAXNAME) < MAXNAME);
int otype = H5Gget_objtype_by_idx(g2, i);
assert(otype == H5G_DATASET);
if (!H5LTfind_dataset(g1, oname)) {
printf("Only in %s[%s%s]\n", file2, name, oname);
continue;
}
}
H5Gclose(g1);
H5Gclose(g2);
} else if (g1 >= 0) {
printf("Only in %s:%s\n", file1, name);
H5Gclose(g1);
} else if (g2 >= 0) {
printf("Only in %s:%s\n", file2, name);
H5Gclose(g2);
} else {
printf("Group %s does not exist in either file.\n", name);
}
}
bool HDFWalkerInput_0_0::put(xmlNodePtr cur)
{
hid_t h_file = H5Fopen(FileName.c_str(),H5F_ACC_RDWR,H5P_DEFAULT);
hid_t h_config = H5Gopen(h_file,"config_collection");
if(h_config<0)
{
app_error() << " HDFWalkerInput_0_0::put config_collection is not found in " << FileName << "." << endl;
H5Fclose(h_file);
return false;
}
int NumSets=0;
hid_t h1=H5Dopen(h_config,"NumOfConfigurations");
if(h1>-1)
{
H5Dread(h1, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,&(NumSets));
H5Dclose(h1);
}
if(!NumSets)
{
//resolve the integer and long problem with 64bit
hsize_t nset;
H5Gget_num_objs(h_config,&nset);
NumSets=nset;
}
if(!NumSets)
{
app_error() << " HDFWalkerInput_0_0::put " << FileName << " does not contain walkers!" << endl;
H5Gclose(h_config);
H5Gclose(h_file);
return false;
}
//select the last block
int selected=NumSets-1;
typedef MCWalkerConfiguration::PosType PosType;
typedef MCWalkerConfiguration::PropertyContainer_t ProtertyContainer_t;
typedef Matrix<PosType> PosContainer_t;
int nwt = 0;
int npt = 0;
//2D array of PosTypes (x,y,z) indexed by (walker,particle)
PosContainer_t Pos_temp;
//open the group
char GrpName[128];
sprintf(GrpName,"config%04d",selected);
hid_t group_id = H5Gopen(h_config,GrpName);
HDFAttribIO<PosContainer_t> Pos_in(Pos_temp);
//read the dataset
Pos_in.read(group_id,"coord");
//close groups
H5Gclose(group_id);
H5Gclose(h_config);
H5Fclose(h_file);
/*check to see if the number of walkers and particles is consistent with W */
int nptcl = Pos_temp.cols();
nwt = Pos_temp.rows();
int curWalker = targetW.getActiveWalkers();
if(curWalker)
{
app_log() << "HDFWalkerInput_0_0::put Adding " << nwt << " walkers to " << curWalker << endl;
targetW.createWalkers(nwt);
}
else
{
app_log() << "HDFWalkerInput_0_0::put Creating " << nwt << " walkers." << endl;
targetW.resize(nwt,nptcl);
}
//assign configurations to W
int iw=0;
MCWalkerConfiguration::iterator it = targetW.begin()+curWalker;
MCWalkerConfiguration::iterator it_end = targetW.end();
while(it != it_end)
{
std::copy(Pos_temp[iw],Pos_temp[iw+1], (*it)->R.begin());
++it;
++iw;
}
return true;
}
herr_t HDF5CreateGroupObjs( hid_t hHDF5, const char *pszObjName,
void *poHObjParent)
{
HDF5GroupObjects *const poHparent =
static_cast<HDF5GroupObjects *>(poHObjParent);
HDF5GroupObjects *poHchild = poHparent->poHchild;
H5G_stat_t oStatbuf;
if( H5Gget_objinfo(hHDF5, pszObjName, FALSE, &oStatbuf) < 0 )
return -1;
// Look for next child.
unsigned idx = 0; // idx is used after the for loop.
for( ; idx < poHparent->nbObjs; idx++ )
{
if( poHchild->pszName == nullptr ) 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 = nullptr;
poHchild->HDatatype = 0;
poHchild->objno[0] = oStatbuf.objno[0];
poHchild->objno[1] = oStatbuf.objno[1];
if( poHchild->pszPath == nullptr )
{
CreatePath(poHchild);
}
if( poHparent->pszPath == nullptr )
{
CreatePath(poHparent);
}
switch( oStatbuf.type )
{
case H5G_LINK:
{
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = nullptr;
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
break;
}
case H5G_GROUP:
{
hid_t hGroupID = H5I_INVALID_HID; // Identifier of group.
if( (hGroupID = H5Gopen(hHDF5, pszObjName)) == -1)
{
CPLError(CE_Failure, CPLE_AppDefined,
"unable to access \"%s\" group.", pszObjName);
return -1;
}
// Number of attributes in object.
const int nbAttrs = H5Aget_num_attrs(hGroupID);
hsize_t nbObjs = 0; // Number of objects in a group.
H5Gget_num_objs(hGroupID, &nbObjs);
poHchild->nbAttrs = nbAttrs;
poHchild->nbObjs = static_cast<int>(nbObjs);
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
if( nbObjs > 0 )
{
poHchild->poHchild = static_cast<HDF5GroupObjects *>(
CPLCalloc(static_cast<int>(nbObjs), sizeof(HDF5GroupObjects)));
memset(poHchild->poHchild, 0,
static_cast<size_t>(sizeof(HDF5GroupObjects) * nbObjs));
}
else
{
poHchild->poHchild = nullptr;
}
if( !HDF5GroupCheckDuplicate(poHparent, oStatbuf.objno) )
H5Giterate(hHDF5, pszObjName, nullptr, HDF5CreateGroupObjs, poHchild);
else
CPLDebug("HDF5", "avoiding link looping on node '%s'.", pszObjName);
H5Gclose(hGroupID);
break;
}
case H5G_DATASET:
{
hid_t hDatasetID = H5I_INVALID_HID; // Identifier of dataset.
if( (hDatasetID = H5Dopen(hHDF5, pszObjName)) == -1)
{
CPLError(CE_Failure, CPLE_AppDefined,
"unable to access \"%s\" dataset.", pszObjName);
return -1;
}
const int nbAttrs = H5Aget_num_attrs(hDatasetID);
const hid_t datatype = H5Dget_type(hDatasetID);
const hid_t dataspace = H5Dget_space(hDatasetID);
const int n_dims = H5Sget_simple_extent_ndims(dataspace);
const hid_t native = H5Tget_native_type(datatype, H5T_DIR_ASCEND);
hsize_t *maxdims = nullptr;
hsize_t *dims = nullptr;
if( n_dims > 0 )
{
dims = static_cast<hsize_t *>(CPLCalloc(n_dims, sizeof(hsize_t)));
maxdims =
static_cast<hsize_t *>(CPLCalloc(n_dims, sizeof(hsize_t)));
}
H5Sget_simple_extent_dims(dataspace, dims, maxdims);
if( maxdims != nullptr )
CPLFree(maxdims);
if( n_dims > 0 )
{
poHchild->nRank = n_dims; // rank of the array
poHchild->paDims = dims; // dimension of the array.
poHchild->HDatatype = datatype; // HDF5 datatype
}
else
{
poHchild->nRank = -1;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
}
poHchild->nbAttrs = nbAttrs;
poHchild->nbObjs = 0;
poHchild->poHchild = nullptr;
poHchild->native = native;
H5Tclose(datatype);
H5Sclose(dataspace);
H5Dclose(hDatasetID);
break;
}
case H5G_TYPE:
{
poHchild->nbAttrs = 0;
poHchild->nbObjs = 0;
poHchild->poHchild = nullptr;
poHchild->nRank = 0;
poHchild->paDims = nullptr;
poHchild->HDatatype = 0;
break;
}
default:
break;
}
return 0;
}
void read_amuse_hdf5_data(char *filename,
int maxtypes,
int npartoftype[maxtypes],
int ncol,
int isrequired[ncol],
int *ierr)
{
hid_t file_id;
hid_t group_id, group_id1, group_id2;
herr_t status;
herr_t HDF5_error = -1;
char groupname[12];
char datasetname[256];
int i;
if (debug) printf("DEBUG: re-opening %s \n",filename);
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if (file_id == HDF5_error)
{ printf("ERROR re-opening %s \n",filename); *ierr = 1; return; }
/* open main particles group */
char *maingroup = "particles";
#if H5_VERSION_GE(1,8,0)
group_id1 = H5Gopen2(file_id,maingroup,H5P_DEFAULT);
#else
group_id1 = H5Gopen(file_id,maingroup);
#endif
if (debug) printf("DEBUG: maxtypes = %i\n",maxtypes);
/* read dataset for each particle type present in dump file */
int itype,iobjtype;
for (itype=0;itype<maxtypes;itype++) {
if (debug) printf("DEBUG: type %i npartoftype = %i\n",itype,npartoftype[itype]);
if (npartoftype[itype] > 0) {
/* If npartoftype[N] > 0 in header, look for dataset of the form 000000000N */
sprintf(groupname,"00000000%02i",itype+1);
if (debug) printf("DEBUG: opening group %s\n",groupname);
#if H5_VERSION_GE(1,8,0)
group_id = H5Gopen2(group_id1,groupname,H5P_DEFAULT);
#else
group_id = H5Gopen(group_id1,groupname);
#endif
if (group_id == HDF5_error)
{ printf("ERROR opening %s group \n",groupname); *ierr = 2; }
else {
#if H5_VERSION_GE(1,8,0)
group_id2 = H5Gopen2(group_id,"attributes",H5P_DEFAULT);
#else
group_id2 = H5Gopen(group_id,"attributes");
#endif
if (group_id2 == HDF5_error)
{ printf("ERROR opening attributes group \n"); *ierr = 2; }
else {
hsize_t ndatasets;
status = H5Gget_num_objs(group_id2, &ndatasets);
if (debug) printf("DEBUG: number of datasets = %i \n",(int)ndatasets);
int j = 0;
/* always read particle positions first */
*ierr = read_amuse_hdf5_dataset(group_id2,"x",itype,maxtypes,npartoftype,ncol,isrequired,&j);
j = 1;
*ierr = read_amuse_hdf5_dataset(group_id2,"y",itype,maxtypes,npartoftype,ncol,isrequired,&j);
j = 2;
*ierr = read_amuse_hdf5_dataset(group_id2,"z",itype,maxtypes,npartoftype,ncol,isrequired,&j);
/* read remaining datasets in the order they appear in the file */
for(i=0; i < (int)ndatasets; i++) {
status = H5Gget_objname_by_idx(group_id2, i, datasetname, 256);
iobjtype = H5Gget_objtype_by_idx(group_id2, i);
if (strcmp(datasetname,"x")&&
strcmp(datasetname,"y")&&
strcmp(datasetname,"z")&& (iobjtype == H5G_DATASET)) {
*ierr = read_amuse_hdf5_dataset(group_id2,datasetname,itype,maxtypes,npartoftype,ncol,isrequired,&j);
}
}
/* close "attributes" group */
H5Gclose(group_id2);
}
H5Gclose(group_id);
}
}
}
H5Gclose(group_id1);
status = H5Fclose( file_id );
if (status == HDF5_error) { printf("ERROR closing file \n"); *ierr = 7; }
}
void read_amuse_hdf5_header(char *filename,
int *npart,
int *ncol,
int *ndim,
int *ndimV,
double *time,
int *ierr)
{
hid_t file_id;
hid_t group_id, group_id1, group_id2;
hid_t attrib_id;
herr_t status;
herr_t HDF5_error = -1;
*ierr = 0;
*ndim = 0;
*ndimV = 0;
if (debug) printf("DEBUG: opening %s \n",filename);
file_id = H5Fopen(filename,H5F_ACC_RDONLY,H5P_DEFAULT);
if (file_id == HDF5_error)
{ printf("ERROR opening %s \n",filename); *ierr = 1; return; }
char *maingroup = "particles";
/*
* Open the "particles" dataset and read the number of particles attribute
*
*/
if (!checkfordataset(file_id,maingroup))
{
printf(" ERROR: \"%s\" dataset not found in AMUSE HDF5 file\n",maingroup);
*ierr = 2;
return;
}
#if H5_VERSION_GE(1,8,0)
group_id1 = H5Gopen2(file_id,maingroup,H5P_DEFAULT);
#else
group_id1 = H5Gopen(file_id,maingroup);
#endif
if (group_id1 == HDF5_error)
{ printf("ERROR opening %s data set \n",maingroup); *ierr = 2; return; }
#if H5_VERSION_GE(1,8,0)
group_id = H5Gopen2(group_id1,"0000000001",H5P_DEFAULT);
#else
group_id = H5Gopen(group_id1,"0000000001");
#endif
if (group_id == HDF5_error)
{ printf("ERROR opening 00000000001 data set \n"); *ierr = 2; return; }
int nattrib;
int i;
char name[256];
nattrib = H5Aget_num_attrs(group_id);
if (debug) printf("number of attributes found = %i\n",nattrib);
/*
* Read through all of the attributes in the header, so we
* can still spit out the values even if they are not used by SPLASH
*/
for(i=0; i < nattrib; i++) {
attrib_id = H5Aopen_idx(group_id,i);
ssize_t attr_status;
attr_status = H5Aget_name(attrib_id, 256, name);
hid_t type_id;
type_id = H5Aget_type(attrib_id);
/*type_class = H5Tget_native_type(type_id,H5T_DIR_ASCEND);*/
if (strcmp(name,"time")==0) {
status = H5Aread(attrib_id,H5T_NATIVE_DOUBLE,time);
} else if (strcmp(name,"number_of_particles")==0) {
status = H5Aread(attrib_id,H5T_NATIVE_INT,npart);
} else {
if (debug) printf("DEBUG: unknown attribute %s \n",name);
}
if (status==HDF5_error) {
printf(" ERROR reading attribute %s \n",name);
}
status = H5Aclose(attrib_id);
}
/*
* Now we need to get the number of data columns in the file
* (from the number of datasets in the "attributes" group)
*/
#if H5_VERSION_GE(1,8,0)
group_id2 = H5Gopen2(group_id,"attributes",H5P_DEFAULT);
#else
group_id2 = H5Gopen(group_id,"attributes");
#endif
if (group_id2 == HDF5_error)
{ printf("ERROR opening %s data set \n","attributes"); *ierr = 2; return; }
hsize_t ndatasets;
status = H5Gget_num_objs(group_id2, &ndatasets);
if (debug) printf("DEBUG: number of datasets = %i \n",(int)ndatasets);
*ncol = (int)ndatasets;
int idim;
/* check that coordinates are present in file */
idim = get_rank_by_name(group_id2,"x");
if (idim <= 0) { printf("ERROR: x positions not found\n"); *ierr = 3; }
idim = get_rank_by_name(group_id2,"y");
if (idim <= 0) { printf("ERROR: y positions not found\n"); *ierr = 3; }
idim = get_rank_by_name(group_id2,"z");
if (idim <= 0) {
printf("z positions not found, assuming file is 2D \n");
*ndim = 2;
*ndimV = 2;
} else {
*ndim = 3;
*ndimV = 3;
}
/* finish, close all open datasets and close file */
status = H5Gclose(group_id2);
if (status == HDF5_error)
{ printf("ERROR closing attributes data set \n"); *ierr = 3; return; }
status = H5Gclose(group_id);
if (status == HDF5_error)
{ printf("ERROR closing %s data set \n",maingroup); *ierr = 3; return; }
status = H5Gclose(group_id1);
if (status == HDF5_error)
{ printf("ERROR closing 0001 data set \n"); *ierr = 3; return; }
status = H5Fclose( file_id );
if (status == HDF5_error) { printf("ERROR closing file \n"); *ierr = 7; }
if (debug) printf("DEBUG: finished header read \n");
}
bool FWSingleOMP::run()
{
hdf_WGT_data.setFileName(xmlrootName);
hdf_OBS_data.setFileName(xmlrootName);
if (doWeights==1)
{
fillIDMatrix();
hdf_WGT_data.makeFile();
hdf_WGT_data.openFile();
hdf_WGT_data.addFW(0);
for (int i=0;i<Weights.size();i++) hdf_WGT_data.addStep(i,Weights[i]);
hdf_WGT_data.closeFW();
hdf_WGT_data.closeFile();
for(int ill=1;ill<weightLength;ill++)
{
transferParentsOneGeneration();
FWOneStep();
// WeightHistory.push_back(Weights);
hdf_WGT_data.openFile();
hdf_WGT_data.addFW(ill);
for (int i=0;i<Weights.size();i++) hdf_WGT_data.addStep(i,Weights[i]);
hdf_WGT_data.closeFW();
hdf_WGT_data.closeFile();
}
}
else
{
fillIDMatrix();
// find weight length from the weight file
hid_t f_file = H5Fopen(hdf_WGT_data.getFileName().c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
hsize_t numGrps = 0;
H5Gget_num_objs(f_file, &numGrps);
weightLength = static_cast<int> (numGrps)-1;
if (H5Fclose(f_file)>-1) f_file=-1;
if (verbose>0) app_log()<<" weightLength "<<weightLength<<endl;
}
if (verbose>0) app_log()<<" Done Computing Weights"<<endl;
if (doObservables==1)
{
int nprops = H.sizeOfObservables();//local energy, local potnetial and all hamiltonian elements
int FirstHamiltonian = H.startIndex();
// vector<vector<vector<RealType> > > savedValues;
int nelectrons = W[0]->R.size();
int nfloats=OHMMS_DIM*nelectrons;
// W.clearEnsemble();
makeClones(W,Psi,H);
vector<ForwardWalkingData* > FWvector;
for(int ip=0; ip<NumThreads; ip++) FWvector.push_back(new ForwardWalkingData(nelectrons));
if (myComm->rank()==0) hdf_OBS_data.makeFile();
hdf_float_data.openFile(fname.str());
for(int step=0;step<numSteps;step++)
{
hdf_float_data.setStep(step);
vector<RealType> stepObservables(walkersPerBlock[step]*(nprops+2), 0);
for(int wstep=0; wstep<walkersPerBlock[step];)
{
vector<float> ThreadsCoordinate(NumThreads*nfloats);
int nwalkthread = hdf_float_data.getFloat(wstep*nfloats, (wstep+NumThreads)*nfloats, ThreadsCoordinate) / nfloats;
// for(int j=0;j<ThreadsCoordinate.size();j++)cout<<ThreadsCoordinate[j]<<" ";
// cout<<endl;
#pragma omp parallel for
for(int ip=0; ip<nwalkthread; ip++)
{
vector<float> SINGLEcoordinate(0);
vector<float>::iterator TCB1(ThreadsCoordinate.begin()+ip*nfloats), TCB2(ThreadsCoordinate.begin()+(1+ip)*nfloats);
SINGLEcoordinate.insert(SINGLEcoordinate.begin(),TCB1,TCB2);
FWvector[ip]->fromFloat(SINGLEcoordinate);
wClones[ip]->R=FWvector[ip]->Pos;
wClones[ip]->update();
RealType logpsi(psiClones[ip]->evaluateLog(*wClones[ip]));
RealType eloc=hClones[ip]->evaluate( *wClones[ip] );
hClones[ip]->auxHevaluate(*wClones[ip]);
int indx=(wstep+ip)*(nprops+2);
stepObservables[indx]= eloc;
stepObservables[indx+1]= hClones[ip]->getLocalPotential();
for(int i=0;i<nprops;i++) stepObservables[indx+i+2] = hClones[ip]->getObservable(i) ;
}
wstep+=nwalkthread;
for(int ip=0; ip<NumThreads; ip++) wClones[ip]->resetCollectables();
}
hdf_OBS_data.openFile();
hdf_OBS_data.addStep(step, stepObservables);
hdf_OBS_data.closeFile();
// savedValues.push_back(stepObservables);
hdf_float_data.endStep();
if (verbose >1) cout<<"Done with step: "<<step<<endl;
}
}
if(doDat>=1)
{
vector<int> Dimensions(4);
hdf_WGT_data.openFile();
hdf_OBS_data.openFile();
Estimators->start(weightLength,1);
int nprops;
if (doObservables==1) nprops = H.sizeOfObservables()+2;
else
{
int Noo = hdf_OBS_data.numObsStep(0);
int Nwl = hdf_WGT_data.numWgtStep(0);
nprops = Noo/Nwl;
}
for(int ill=0;ill<weightLength;ill++)
{
Dimensions[0]=ill;
Dimensions[1]= nprops ;
Dimensions[2]=numSteps;
Dimensions[3]=startStep;
Estimators->startBlock(1);
Estimators->accumulate(hdf_OBS_data,hdf_WGT_data,Dimensions);
Estimators->stopBlock(getNumberOfSamples(ill));
}
hdf_OBS_data.closeFile();
hdf_WGT_data.closeFile();
Estimators->stop();
}
return true;
}
/* ****************************************************************************************************************************** */
int main(int argc, char *argv[]) {
hid_t fileID, dataSetID;
herr_t hErrVal;
int i;
hsize_t dims[1024], maxDims[1024];
H5T_class_t class;
char classStr[32];
hid_t dataTypeID;
size_t dataSize;
H5T_order_t order;
int rank; /* Note this is an int, not an hssize_t */
int intVal;
hid_t dataSpaceID;
hid_t rootGroupID;
hsize_t numInRootGrp, firstDataSetIdx, foundFirstDataSet;
char attrName[1024], firstDataSetName[1024];
ssize_t objectNameSize, attrNameSize;
H5G_stat_t objectStatInfo;
int numAttrs;
int curAttrIdx;
hid_t attrID;
hsize_t numDataPoints;
unsigned majnum, minnum, relnum;
/* Load the library -- not required most platforms. */
hErrVal = H5open();
mjrHDF5_chkError(hErrVal);
/* Get the library version */
hErrVal = H5get_libversion(&majnum, &minnum, &relnum);
mjrHDF5_chkError(hErrVal);
printf("Lib Version: v%lu.%lur%lu\n", (unsigned long)majnum, (unsigned long)minnum, (unsigned long)relnum);
/* Open an existing file. */
fileID = H5Fopen(TST_FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT);
mjrHDF5_chkError(fileID);
/* Get the ID for the "root" group -- every HDF5 has one */
rootGroupID = H5Gopen(fileID, "/", H5P_DEFAULT);
mjrHDF5_chkError(rootGroupID);
/* Get the number of objects in the root group. */
hErrVal = H5Gget_num_objs(rootGroupID, &numInRootGrp);
mjrHDF5_chkError(hErrVal);
printf("The root group contains %lu object%c\n", (unsigned long)numInRootGrp, (numInRootGrp==1?' ':'s'));
if(numInRootGrp < 1) {
printf("As the file contains NO objects, I have nothing left to do...\n");
exit(1);
} /* end if */
/* Find the first dataset in the root group. */
for(foundFirstDataSet=0,firstDataSetIdx=0; (!foundFirstDataSet)&&(firstDataSetIdx<numInRootGrp); firstDataSetIdx++) {
/* Get object name from the index. */
objectNameSize = H5Gget_objname_by_idx(rootGroupID, firstDataSetIdx, firstDataSetName, 1024);
mjrHDF5_chkError(objectNameSize);
if(objectNameSize == 0) { /* Need to check for zero return too */
printf("ERROR: Object with index %lu doesn't exist in root group!\n", (unsigned long)firstDataSetIdx);
exit(1);
} /* end if */
/* Now use the object name to get info about the object... */
hErrVal = H5Gget_objinfo(rootGroupID, firstDataSetName, 0, &objectStatInfo);
mjrHDF5_chkError(hErrVal);
/* If the object is a dataset, then print out some info. */
if(objectStatInfo.type == H5G_DATASET) {
printf("Object %luth (%s) is a dataset!\n", (unsigned long)firstDataSetIdx, firstDataSetName);
printf("The name of the %luth object of the root group is: %s\n", (unsigned long)firstDataSetIdx, firstDataSetName);
foundFirstDataSet = 1;
printf("Info for the %s dataset:\n", firstDataSetName);
printf(" Modify time: %lu\n", (unsigned long)objectStatInfo.mtime);
printf(" Type: %lu\n", (unsigned long)objectStatInfo.type);
printf(" Link count: %lu\n", (unsigned long)objectStatInfo.nlink);
} /* end if */
} /* end for */
/* Note: At this point index of the dataset will be: firstDataSetIdx-- */
if(!foundFirstDataSet) {
printf("ERROR: Could not find a dataset in the root group\n");
exit(1);
} /* end if */
/* Open the dataset we found -- we know it exists. */
dataSetID = H5Dopen(rootGroupID, firstDataSetName, H5P_DEFAULT);
mjrHDF5_chkError(dataSetID);
/* ****************************************************************************************************************************** */
/* Get some info regarding the TYPE of the dataset. */
dataTypeID = H5Dget_type(dataSetID);
mjrHDF5_chkError(dataTypeID);
/* Get the class of the data */
class = H5Tget_class(dataTypeID);
mjrHDF5_Tclass2str(class, classStr);
printf(" Object class: %s\n", classStr);
/* Get the size of the type */
dataSize = H5Tget_size(dataTypeID);
if(dataSize == 0) {
printf("ERROR: Failure in H5Tget_size().\n");
exit(1);
} /* end if */
printf(" Size of data type: %lu\n", (unsigned long)dataSize);
/* Get the byte order */
order = H5Tget_order(dataTypeID);
printf(" Byte Order: ");
switch(order) {
case H5T_ORDER_ERROR : printf("ERROR\n"); break;
case H5T_ORDER_LE : printf("Little Endian\n"); break;
case H5T_ORDER_BE : printf("Big Endian\n"); break;
case H5T_ORDER_VAX : printf("VAX mixed endian\n"); break;
case H5T_ORDER_MIXED : printf("Mixed endian\n"); break;
case H5T_ORDER_NONE : printf("particular order\n"); break;
} /* end switch */
/* We are done with the datatype. */
hErrVal = H5Tclose(dataTypeID);
mjrHDF5_chkError(hErrVal);
/* ****************************************************************************************************************************** */
/* Figure out the size of the dataset. */
dataSpaceID = H5Dget_space(dataSetID);
mjrHDF5_chkError(dataSpaceID);
/* Get the number of dims. */
rank = H5Sget_simple_extent_ndims(dataSpaceID);
mjrHDF5_chkError(rank);
if(rank > 1024) {
/* This can't really happen (limit is 32) */
printf("ERROR: rank too large.\n");
exit(1);
} /* end if */
/* Get the size of each dim. */
intVal = H5Sget_simple_extent_dims(dataSpaceID, dims, maxDims);
mjrHDF5_chkError(intVal);
printf(" Dataspace Rank %lu\n", (unsigned long)rank);
printf(" Dim Lengths: ");
for(i=0; i<rank; i++)
if(dims[i] == H5S_UNLIMITED) {
printf("%s ", "UNLIMITED");
} else {
printf("%ld ", (long)(dims[i]));
} /* end if/else */
printf("\n");
printf(" Max Dim Lengths: ");
for(i=0; i<rank; i++)
if(maxDims[i] == H5S_UNLIMITED) {
printf("%s ", "UNLIMITED");
} else {
printf("%ld ", (long)(maxDims[i]));
} /* end if/else */
printf("\n");
numDataPoints = H5Sget_simple_extent_npoints(dataSpaceID);
if(numDataPoints == 0) {
printf("ERROR: Call to H5Sget_simple_extent_npoints failed.\n");
exit(1);
} /* end if */
printf("Number of data points: %lu\n", (unsigned long)numDataPoints);
/* We are done with the dataSpaceID */
hErrVal = H5Sclose(dataSpaceID);
mjrHDF5_chkError(hErrVal);
/* Get the number of attributes for the dataSet. */
numAttrs = H5Aget_num_attrs(dataSetID);
mjrHDF5_chkError(numAttrs);
printf(" Number of attrs: %lu\n", (unsigned long)numAttrs);
/* If we have any attributes, we get info for them */
if(numAttrs > 0) {
printf(" Attribute info:\n");
for(curAttrIdx=0; curAttrIdx<numAttrs; curAttrIdx++) {
attrID = H5Aopen_idx(dataSetID, curAttrIdx);
mjrHDF5_chkError(attrID);
attrNameSize = H5Aget_name(attrID, 1024, attrName);
mjrHDF5_chkError(attrNameSize);
printf(" Number %3lu: ", (unsigned long)curAttrIdx);
dataTypeID = H5Aget_type(attrID);
mjrHDF5_chkError(dataTypeID);
/* Get the class for the type. */
class = H5Tget_class(dataTypeID);
mjrHDF5_Tclass2str(class, classStr);
printf(" Class: %-16s", classStr);
/* Get the size of the type */
dataSize = H5Tget_size(dataTypeID);
if(dataSize == 0) {
printf("ERROR: Failure in H5Tget_size().\n");
exit(1);
} /* end if */
printf(" Size: %3lu ", (unsigned long)dataSize);
hErrVal = H5Tclose(dataTypeID);
mjrHDF5_chkError(hErrVal);
printf(" Name: %s \n", attrName);
hErrVal = H5Aclose(attrID);
mjrHDF5_chkError(hErrVal);
} /* end for */
} /* end if */