CPLErr HDF5Dataset::CreateMetadata( HDF5GroupObjects *poH5Object, int nType)
{
hid_t hGroupID; /* identifier of group */
hid_t hDatasetID;
int nbAttrs;
herr_t ret;
HDF5Dataset *poDS;
if( !poH5Object->pszPath )
return CE_None;
poDS = this;
poH5CurrentObject = poH5Object;
nbAttrs = poH5Object->nbAttrs;
if( poH5Object->pszPath == NULL || EQUAL(poH5Object->pszPath, "" ) )
return CE_None;
switch( nType ) {
case H5G_GROUP:
hGroupID = H5Gopen( hHDF5, poH5Object->pszPath );
if( nbAttrs > 0 ) {
ret = H5Aiterate( hGroupID, NULL,
HDF5AttrIterate, (void *)poDS );
ret = H5Gclose( hGroupID );
}
break;
case H5G_DATASET:
hDatasetID = H5Dopen(hHDF5, poH5Object->pszPath );
if( nbAttrs > 0 ) {
ret = H5Aiterate( hDatasetID, NULL,
HDF5AttrIterate, (void *)poDS );
ret = H5Dclose( hDatasetID );
}
break;
default:
break;
}
return CE_None;
}
static int find_objs(hid_t group, const char *name, void *op_data)
{
hid_t obj;
H5G_stat_t statbuf;
unsigned int idx = 0;
int status;
h5item *parent = (h5item *)op_data;
h5item *item = (h5item *)malloc(sizeof(h5item));
h5item *itm;
item->item_type = 0;
item->name=strcpy(malloc(strlen(name)+1),name);
item->child = 0;
item->brother = 0;
item->parent = parent;
item->obj = 0;
item->attribute = 0;
if (parent->child == NULL)
{
parent->child = item;
}
else
{
for (itm = parent->child; itm->brother; itm = itm->brother);
itm->brother = item;
}
if (parent->child == item)
/* H5Aiterate(group,&idx,find_attr,(void *)item); */
H5Aiterate(group,NULL,find_attr,(void *)item);
// H5Aiterate(group,&idx,find_attr,(void *)0);
H5Gget_objinfo(group, name, 1, &statbuf);
item->item_type = statbuf.type;
switch (statbuf.type) {
case H5G_GROUP:
if ((obj = H5Gopen(group, name)) >= 0) {
H5Giterate(obj, ".", NULL, find_objs, (void *)item);
H5Gclose (obj);
}
break;
case H5G_DATASET:
if ((obj = H5Dopen (group, name)) >= 0) {
item->obj = obj;
/* H5Aiterate(obj,&idx,find_attr,(void *)item); */
H5Aiterate(obj,&idx,find_attr,(void *)item);
}
break;
}
return 0;
}
int VsFilter::visitDataset(hid_t locId, const char* name, void* opdata) {
RECURSION_DATA* data = static_cast< RECURSION_DATA* >(opdata);
VsGroup* parent = static_cast< VsGroup*>(data->parent);
VsRegistry* registry = data->registry;
VsLog::debugLog() << "VsFilter::visitDataset: node '" << name
<<"' is a dataset." << std::endl;
hid_t datasetId = H5Dopen(locId, name, H5P_DEFAULT);
VsDataset* newDataset = new VsDataset(registry, parent, name, datasetId);
//If unable to get a handle to the hdf5 object, we just drop the object
//But return 0 to continue iterating over objects
if (datasetId < 0) {
VsLog::errorLog() <<"VsFilter::visitDataset() - Unable to open dataset with name " <<name <<std::endl;
VsLog::errorLog() <<"VsFilter::visitDataset() - This object and all children will be dropped." <<std::endl;
return 0;
}
RECURSION_DATA nextLevelData;
nextLevelData.registry = registry;
nextLevelData.parent = newDataset;
// Recurse over attributes
H5Aiterate(datasetId, H5_INDEX_NAME, H5_ITER_INC, NULL, visitAttrib, &nextLevelData);
VsLog::debugLog() <<"VsFilter::visitDataset: Returning." <<std::endl;
return 0;
}
static int readIntAttribute_v1(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
herr_t status;
hsize_t n = 0;
int iVal = -1;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name_v1, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen_by_name(_iDatasetId, ".", _pstName, H5P_DEFAULT, H5P_DEFAULT);
if (iAttributeId < 0)
{
return -1;
}
status = H5Aread(iAttributeId, H5T_NATIVE_INT, &iVal);
if (status < 0)
{
return -1;
}
status = H5Aclose(iAttributeId);
if (status < 0)
{
return -1;
}
}
return iVal;
}
/****************************************************************
**
** Aiterate(): Attribute set iteration routine.
**
****************************************************************/
PyObject *Aiterate(hid_t loc_id) {
hsize_t i = 0;
PyObject *attrlist; /* List where the attrnames are put */
attrlist = PyList_New(0);
H5Aiterate(loc_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &i,
(H5A_operator_t)aitercb, (void *)attrlist);
return attrlist;
}
int _CheckAttrFC(int loc_id, const char *name, void *strname)
{
int iTempValue;
H5G_stat_t statbuf;
hid_t hDatasetID;
H5Gget_objinfo((hid_t)loc_id, name, 0, &statbuf);
hDatasetID = H5Dopen(loc_id, name);
iTempValue=H5Aiterate(hDatasetID,NULL, _GetValue, strname );
H5Dclose(hDatasetID);
return iTempValue;
}
void H5Dataset::ls(std::vector<std::string> & name, std::vector<std::string> & type) const
{
herr_t err;
OpDataGetLs opdata(const_cast<H5Dataset *>(this), &name, &type);
hsize_t idx = 0;
err = H5Aiterate(dataset, H5_INDEX_NAME, H5_ITER_INC, &idx, H5Object::getLsAttributes, &opdata);
if (err < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot list dataset attributes."));
}
}
CPLErr HDF5Dataset::CreateMetadata( HDF5GroupObjects *poH5Object, int nType)
{
if( !poH5Object->pszPath )
return CE_None;
poH5CurrentObject = poH5Object;
if( poH5Object->pszPath == nullptr || EQUAL(poH5Object->pszPath, "") )
return CE_None;
HDF5Dataset *const poDS = this;
const int nbAttrs = poH5Object->nbAttrs;
switch( nType )
{
case H5G_GROUP:
if( nbAttrs > 0 )
{
// Identifier of group.
const hid_t l_hGroupID = H5Gopen(hHDF5, poH5Object->pszPath);
H5Aiterate(l_hGroupID, nullptr, HDF5AttrIterate, poDS);
H5Gclose(l_hGroupID);
}
break;
case H5G_DATASET:
if( nbAttrs > 0 )
{
const hid_t hDatasetID = H5Dopen(hHDF5, poH5Object->pszPath);
H5Aiterate(hDatasetID, nullptr, HDF5AttrIterate, poDS);
H5Dclose(hDatasetID);
}
break;
default:
break;
}
return CE_None;
}
int VsFilter::visitGroup(hid_t locId, const char* name, void* opdata) {
RECURSION_DATA* data = static_cast< RECURSION_DATA* >(opdata);
VsGroup* parent = static_cast< VsGroup*> (data->parent);
VsRegistry* registry = data->registry;
VsLog::debugLog() << "VsFilter::visitGroup: node '" << name
<< "' is a group." << std::endl;
if (std::string(name) == "..")
{
VsLog::debugLog() << "VsFilter::visitGroup: skipping group '..'" << std::endl;
return 0;
}
hid_t groupId = H5Gopen(locId, name, H5P_DEFAULT);
//If unable to get a handle to the hdf5 object, we just drop the object
//But return 0 to continue iterating over objects
if (groupId < 0) {
VsLog::errorLog() <<"VsFilter::visitGroup() - Unable to open group with name " <<name <<std::endl;
VsLog::errorLog() <<"VsFilter::visitGroup() - This object and all children will be dropped." <<std::endl;
return 0;
}
VsGroup* newGroup = new VsGroup(registry, parent, name, groupId);
RECURSION_DATA nextLevelData;
nextLevelData.registry = registry;
nextLevelData.parent = newGroup;
// Recurse over all attributes of the group
VsLog::debugLog() <<"VsFilter::visitGroup(): Recursing on attributes of group " <<newGroup->getFullName() <<std::endl;
H5Aiterate(groupId, H5_INDEX_NAME, H5_ITER_INC, NULL, visitAttrib, &nextLevelData);
// Recurse to examine child groups
VsLog::debugLog() <<"VsFilter::visitGroup(): Recursing on children of group " <<newGroup->getFullName() <<std::endl;
H5Literate(groupId, H5_INDEX_NAME, H5_ITER_INC, NULL, visitLinks, &nextLevelData);
// Not needed because the newly declared VsGroup takes ownership of the id
// And will do the H5GClose when it is deleted
// H5Gclose(groupId);
VsLog::debugLog() <<"VsFilter::visitGroup(): Returning." <<std::endl;
return 0;
}
/*
** WARNING : this function returns an allocated value that must be freed.
*/
static char* readAttribute_v1(int _iDatasetId, const char *_pstName)
{
hid_t iAttributeId;
hid_t iFileType, memtype, iSpace;
herr_t status;
hsize_t dims[1];
hsize_t n = 0;
size_t iDim;
char *pstValue = NULL;
if (H5Aiterate(_iDatasetId, H5_INDEX_NAME, H5_ITER_NATIVE, &n, find_attr_by_name_v1, (void *)_pstName) > 0)
{
iAttributeId = H5Aopen_by_name(_iDatasetId, ".", _pstName, H5P_DEFAULT, H5P_DEFAULT);
if (iAttributeId < 0)
{
return NULL;
}
/*
* Get the datatype and its size.
*/
iFileType = H5Aget_type(iAttributeId);
iDim = H5Tget_size(iFileType);
iDim++; /* Make room for null terminator */
/*
* Get dataspace and allocate memory for read buffer. This is a
* two dimensional attribute so the dynamic allocation must be done
* in steps.
*/
iSpace = H5Aget_space(iAttributeId);
if (iSpace < 0)
{
return NULL;
}
status = H5Sget_simple_extent_dims(iSpace, dims, NULL);
if (status < 0)
{
return NULL;
}
/*
* Allocate space for string data.
*/
pstValue = (char *)MALLOC((size_t) ((dims[0] * iDim + 1) * sizeof(char)));
/*
* Create the memory datatype.
*/
memtype = H5Tcopy(H5T_C_S1);
status = H5Tset_size(memtype, iDim);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
/*
* Read the data.
*/
status = H5Aread(iAttributeId, memtype, pstValue);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Tclose(memtype);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Sclose(iSpace);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Tclose(iFileType);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
status = H5Aclose(iAttributeId);
if (status < 0)
{
FREE(pstValue);
return NULL;
}
}
return pstValue;
}
