med_err _MEDsoftlinkDel(const med_idt id,
const char * const softlinkname,
med_bool linkmustexist
) {
med_err _ret=-1;
H5L_info_t _linkinfo;
if ( H5Lget_info( id, softlinkname, &_linkinfo, H5P_DEFAULT ) >= 0 ) {
if ( _linkinfo.type == H5L_TYPE_SOFT ) {
if ( H5Ldelete(id,softlinkname,H5P_DEFAULT) < 0 ) {
MED_ERR_(_ret,MED_ERR_DELETE,MED_ERR_LINK,softlinkname);
goto ERROR;
}
} else if (linkmustexist) {
MED_ERR_(_ret,MED_ERR_UNRECOGNIZED,MED_ERR_LINK,softlinkname);
goto ERROR;
}
} else if (linkmustexist) {
MED_ERR_(_ret,MED_ERR_OPEN,MED_ERR_LINK,softlinkname);
goto ERROR;
}
_ret=0;
ERROR:
return _ret;
}
int luaC_h5_open_group(lua_State *L)
{
const char *gname = luaL_checkstring(L, 1);
const char *mode = luaL_checkstring(L, 2);
hid_t grp = 0;
if (PresentFile < 0) {
luaL_error(L, "need an open file to open group\n");
}
else if (strcmp(mode, "w") == 0) {
if (H5Lexists(PresentFile, gname, H5P_DEFAULT)) {
H5Ldelete(PresentFile, gname, H5P_DEFAULT);
}
grp = H5Gcreate(PresentFile, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (strcmp(mode, "r+") == 0) {
if (H5Lexists(PresentFile, gname, H5P_DEFAULT)) {
grp = H5Gopen(PresentFile, gname, H5P_DEFAULT);
}
else {
grp = H5Gcreate(PresentFile, gname, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
}
else {
luaL_error(L, "invalid group access mode '%s'\n", mode);
}
lua_pushnumber(L, grp);
return 1;
}
//--------------------------------------------------------------------------
// Function: CommonFG::unlink
///\brief Removes the specified name at this location.
///\param name - IN: Name of the object to be removed
///\exception H5::FileIException or H5::GroupIException
// Programmer Binh-Minh Ribler - 2000
// Modification
// 2007: QAK modified to use H5L APIs - BMR
//--------------------------------------------------------------------------
void CommonFG::unlink( const char* name ) const
{
herr_t ret_value = H5Ldelete( getLocId(), name, H5P_DEFAULT );
if( ret_value < 0 )
{
throwException("unlink", "H5Ldelete failed");
}
}
char HDocument::deleteObject(const std::string & path, hid_t parentId)
{
if(parentId == 0) parentId = fFileId;
if(H5Ldelete(parentId, path.c_str(), H5P_DEFAULT) < 0) {
fCurrentError = eDeleteFailure;
return 0;
}
return 1;
}
void DCDataSet::create(const CollectionType& colType,
hid_t group, const Dimensions size, uint32_t ndims, bool compression)
throw (DCException)
{
log_msg(2, "DCDataSet::create (%s, size %s)", name.c_str(), size.toString().c_str());
if (opened)
throw DCException(getExceptionString("create: dataset is already open"));
// if the dataset already exists, remove/unlink it
// note that this won't free the memory occupied by this
// dataset, however, there currently is no function to delete
// a dataset
if (!checkExistence || (checkExistence && H5Lexists(group, name.c_str(), H5P_LINK_ACCESS_DEFAULT)))
H5Ldelete(group, name.c_str(), H5P_LINK_ACCESS_DEFAULT);
this->ndims = ndims;
this->compression = compression;
this->datatype = colType.getDataType();
getLogicalSize().set(size);
setChunking(colType.getSize());
setCompression();
if (getPhysicalSize().getScalarSize() != 0)
{
hsize_t *max_dims = new hsize_t[ndims];
for (size_t i = 0; i < ndims; ++i)
max_dims[i] = H5F_UNLIMITED;
dataspace = H5Screate_simple(ndims, getPhysicalSize().getPointer(), max_dims);
delete[] max_dims;
max_dims = NULL;
} else
dataspace = H5Screate(H5S_NULL);
if (dataspace < 0)
throw DCException(getExceptionString("create: Failed to create dataspace"));
// create the new dataset
dataset = H5Dcreate(group, this->name.c_str(), this->datatype, dataspace,
H5P_DEFAULT, dsetProperties, H5P_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("create: Failed to create dataset"));
isReference = false;
opened = true;
}
//------------------------------------------------------------------------------
xdm::RefPtr< DatasetIdentifier > createDatasetIdentifier(
const DatasetParameters& parameters ) {
// check if the dataset already exists within the given parent
htri_t exists = H5Lexists(
parameters.parent,
parameters.name.c_str(),
H5P_DEFAULT );
if ( exists ) {
if ( parameters.mode == xdm::Dataset::kCreate ) {
// the dataset exists and a create was requested, delete the existing one
H5Ldelete( parameters.parent, parameters.name.c_str(), H5P_DEFAULT );
} else {
// read or modify access, open and return the existing dataset
return openExistingDataset( parameters );
}
}
// the dataset doesn't exist. Read only access is an error.
if ( parameters.mode == xdm::Dataset::kRead ) {
XDM_THROW( xdm::DatasetNotFound( parameters.name ) );
}
// Determine the dataset access properties based off chunking and compression
// parameters.
xdm::RefPtr< PListIdentifier > createPList( new PListIdentifier( H5P_DEFAULT ) );
if ( parameters.chunked ) {
createPList->reset( H5Pcreate( H5P_DATASET_CREATE ) );
setupChunks( createPList->get(), parameters.chunkSize, parameters.dataspace );
// Chunking is enabled, so check for compression and enable it if possible.
if ( parameters.compress ) {
setupCompression( createPList->get(), parameters.compressionLevel );
}
}
// the mode is create or modify. In both cases we want to create it if it
// doesn't yet exist. It is safe to create the dataset here because we deleted
// the dataset earlier if it existed.
hid_t datasetId = H5Dcreate(
parameters.parent,
parameters.name.c_str(),
parameters.type,
parameters.dataspace,
H5P_DEFAULT,
createPList->get(),
H5P_DEFAULT );
return xdm::RefPtr< DatasetIdentifier >( new DatasetIdentifier( datasetId ) );
}
hdf5dataset::hdf5dataset(hdf5file &hfile, const std::string &name, hid_t type_id, hid_t space_id, bool overwrite): _type_id(type_id), _hfile(hfile), _name(name)
{
hfile.touch_group_recursive(name);
bool exists = H5Lexists(_hfile.handle(), name.c_str(), H5P_DEFAULT);
if(exists && overwrite)
H5Ldelete(_hfile.handle(), name.c_str(), H5P_DEFAULT);
else if(exists && !overwrite)
throw std::runtime_error("Dataset already exists (" + _hfile.filename() + ") in file (" + name + ")");
_dataset_id = H5Dcreate(hfile.handle(), name.c_str(), type_id, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
_own_type_id = false;
if(_dataset_id < 0)
throw std::runtime_error("Error creating or opening dataset (" + _hfile.filename() + ") in file (" + name + ")");
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Ldelete
* Signature: (JLjava/lang/String;J)V
*/
JNIEXPORT void JNICALL
Java_hdf_hdf5lib_H5_H5Ldelete
(JNIEnv *env, jclass clss, jlong loc_id, jstring name, jlong access_id)
{
herr_t status = -1;
const char *lName;
PIN_JAVA_STRING(name, lName);
if (lName != NULL) {
status = H5Ldelete((hid_t)loc_id, lName, (hid_t)access_id);
UNPIN_JAVA_STRING(name, lName);
if (status < 0)
h5libraryError(env);
}
} /* end Java_hdf_hdf5lib_H5_H5Ldelete */
HDF5Err
HDF5Group::deleteSubtree(HDF5Id group_id, const char *group_name,
const H5L_info_t *NK_UNUSED_PARAM(group_info),
void *NK_UNUSED_PARAM(op_data))
{
// open the child group
HDF5Group child_group;
child_group.open(group_id, String(group_name));
// iterate over the group's children
HDF5Size iter_index = 0;
H5Literate(child_group.id(), H5_INDEX_CRT_ORDER, H5_ITER_NATIVE,
&iter_index, deleteSubtree, NULL);
// close the child group
child_group.close();
// delete the link
H5Ldelete(group_id, group_name, H5P_DEFAULT);
return 0;
}
int
datErase(const HDSLoc *locator, const char *name_str, int *status) {
char groupstr[DAT__SZNAM+1];
char cleanname[DAT__SZNAM+1];
if (*status != SAI__OK) return *status;
/* Validate input locator. */
dat1ValidateLocator( "datErase", 1, locator, 0, status );
/* containing locator must refer to a group */
if (locator->group_id <= 0) {
*status = DAT__OBJIN;
emsRep("datErase_1", "Input object is not a structure",
status);
return *status;
}
/* Parent group for error reporting */
datName( locator, groupstr, status);
/* Ensure the name is cleaned up before we use it */
dau1CheckName( name_str, 1, cleanname, sizeof(cleanname), status );
CALLHDFQ( H5Ldelete( locator->group_id, cleanname, H5P_DEFAULT ));
/* Remove the handle for the erased component and all sub-components */
dat1EraseHandle( locator->handle, cleanname, status );
CLEANUP:
if (*status != SAI__OK) {
emsRepf("datErase_2", "Error deleting component %s in group %s",
status, name_str, groupstr);
}
return *status;
}
void LocID::deleteLink(std::string name, hid_t plist) {
HErr res = H5Ldelete(hid, name.c_str(), plist);
res.check("LocIDL::deleteLink: Could not delete link: " + name);
}
void hdf5_h5l_delete(value loc_v, value lapl_v, value name_v)
{
CAMLparam3(loc_v, lapl_v, name_v);
raise_if_fail(H5Ldelete(Hid_val(loc_v), String_val(name_v), H5P_opt_val(lapl_v)));
CAMLreturn0;
}
void MAJ_236_300_champs(med_idt fid)
{
med_err lret,ret;
/* med_idt _datagroup=0; */
med_field_type typcha;
char nomcha [MED_NAME_SIZE+1]="";
char _meshname [MED_NAME_SIZE+1]="";
char _dtunit [MED_SNAME_SIZE+1]="";
char *comp= NULL, *unit= NULL;
med_int ncomp,ncha;
med_int _ncstp=0;
med_bool _local=MED_FALSE;
htri_t _datasetexist;
char _pathi[MED_TAILLE_CHA+1+MED_NAME_SIZE+1]=MED_CHA;
char _pathf[MED_TAILLE_CHA+2+MED_NAME_SIZE+1]="/CHA_/";
char _pathtmp[MED_TAILLE_CHA+3]="/CHA__/";
int i,j;
char nomlien[MED_NAME_SIZE+1]="";
char * lien = NULL;
med_int nln,nval;
med_int _nloc,_intgeotype,_sdim;
char _pathloc[MED_TAILLE_GAUSS+MED_NAME_SIZE+1]=MED_GAUSS;
med_int _npar,_numdt,_numit;
char _pathpari[MED_TAILLE_NUM_DATA+MED_NAME_SIZE+1+2*MED_MAX_PARA+1+1]=MED_NUM_DATA;
char _pathparf[MED_TAILLE_NUM_DATA+MED_NAME_SIZE+1+2*MED_MAX_PARA+1+1]=MED_NUM_DATA;
int _pathparlen;
med_size _n=0;
char _cpstnamei[2*MED_MAX_PARA+1]="";
char _cpstnamef[2*MED_MAX_PARA+1]="";
char _uniname[MED_SNAME_SIZE+1]="";
/* hid_t _lac_plist_id; */
hid_t _lcp_plist_id;
hid_t _ocp_plist_id;
med_bool _createunt = MED_TRUE;
MAJ_version_num(fid,2,3,6);
/* MAJ des varaibles scalaires */
_npar = MEDnParameter(fid);
if (_npar > 0) {
fprintf(stdout," >>> Normalisation des paramètres scalaires\n");
_pathparf[MED_TAILLE_NUM_DATA-2]='_';
/* _lac_plist_id = H5Pcreate( H5P_LINK_ACCESS ); */
_ocp_plist_id = H5Pcreate( H5P_OBJECT_COPY );
_lcp_plist_id = H5Pcreate( H5P_LINK_CREATE );
H5Pset_create_intermediate_group( _lcp_plist_id, 1 );
H5Pset_copy_object( _ocp_plist_id, H5O_COPY_SHALLOW_HIERARCHY_FLAG);
}
for (i=0 ; i < _npar ; i++ ) {
MED_ERR_EXIT_IF (_MEDobjectGetName(fid, _pathpari ,i, &_pathpari[MED_TAILLE_NUM_DATA]) < 0,
MED_ERR_ACCESS,MED_ERR_DATAGROUP,_pathpari);
strcpy(&_pathparf[MED_TAILLE_NUM_DATA],&_pathpari[MED_TAILLE_NUM_DATA]);
/* SSCRUTE(_pathparf); */
/* SSCRUTE(_pathpari); */
/*Copie le group avec ses attributs et les objets de premier niveau.*/
ret = H5Ocopy(fid,_pathpari,fid,_pathparf,_ocp_plist_id,_lcp_plist_id);
/* ret = H5Lcopy(fid,_pathpari,fid,_pathparf,_lcp_plist_id,_lac_plist_id); */
EXIT_IF(ret < 0,"Copie du datagroup",_pathpari);
_pathparlen=strlen(_pathpari);
_pathpari[_pathparlen]='/';_pathparf[_pathparlen]='/';
++_pathparlen;
_pathpari[_pathparlen]='\0';_pathparf[_pathparlen]='\0';
/* SSCRUTE(_pathparf); */
/* SSCRUTE(_pathpari); */
ret =_MEDnObjects(fid,_pathpari, &_n);
MED_ERR_EXIT_IF( (ret == (MED_ERR_COUNT + MED_ERR_DATAGROUP)), MED_ERR_COUNT,MED_ERR_PARAMETER,_pathpari);
for (j=0 ; j < _n ; ++j ) {
MED_ERR_EXIT_IF (_MEDobjectGetName(fid, _pathpari ,j, &_pathpari[_pathparlen]) < 0,
MED_ERR_ACCESS,MED_ERR_DATAGROUP,_pathpari);
MED_ERR_EXIT_IF (_MEDattributeNumRdByName(fid,_pathpari,MED_NOM_NOR,
MED_INTERNAL_INT,(unsigned char * const ) &_numit) < 0,
MED_ERR_READ,MED_ERR_ATTRIBUTE,MED_NOM_NOR);
MED_ERR_EXIT_IF (_MEDattributeNumRdByName(fid,_pathpari,MED_NOM_NDT,
MED_INTERNAL_INT,(unsigned char * const ) &_numdt) < 0,
MED_ERR_READ,MED_ERR_ATTRIBUTE,MED_NOM_NDT);
MED_ERR_EXIT_IF (_MEDattributeStringRdByName(fid,_pathpari,MED_NOM_UNI,
MED_SNAME_SIZE,_uniname) < 0,
MED_ERR_READ,MED_ERR_ATTRIBUTE,MED_NOM_NDT);
_MEDgetComputationStepName(MED_SORT_DTIT,_numdt,_numit,&_pathparf[_pathparlen]);
/* strcat(_pathpari,"/"); */
/* strcat(_pathparf,"/"); */
/* SSCRUTE(_pathparf); */
/* SSCRUTE(_pathpari); */
/* ret = H5Ocopy(fid,_pathpari,fid,_pathparf,_ocp_plist_id,_lcp_plist_id); */
/* ret = H5Lcopy(fid,_pathpari,fid,_pathparf,_lcp_plist_id,_lac_plist_id); */
/* H5Eprint1(stderr); */
/* EXIT_IF(ret < 0,"Copie d'une étape de calcul du paramètre scalaire ",_pathpari); */
/*On modifie temporairement _pathpari pour pointer dans _pathparf*/
_pathpari[MED_TAILLE_NUM_DATA-2]='_';
/* SSCRUTE(_pathparf); */
/* SSCRUTE(_pathpari); */
ret = H5Gmove(fid, _pathpari, _pathparf );
EXIT_IF(ret < 0,"Renommage de l'étape de calcul",_pathpari);
_pathpari[MED_TAILLE_NUM_DATA-2]='A';
MED_ERR_EXIT_IF(H5Adelete_by_name( fid, _pathparf, MED_NOM_UNI, H5P_DEFAULT ) < 0,
MED_ERR_DELETE,MED_ERR_ATTRIBUTE,_pathparf);
_pathparf[_pathparlen]='\0';
_pathpari[_pathparlen]='\0';
if ( _createunt ) {
MED_ERR_EXIT_IF (_MEDattributeStringWrByName(fid,_pathparf,MED_NOM_UNT, MED_SNAME_SIZE,_uniname) < 0,
MED_ERR_WRITE,MED_ERR_ATTRIBUTE,MED_NOM_UNT);
_createunt = MED_FALSE;
}
}
_createunt = MED_TRUE;
_pathpari[MED_TAILLE_NUM_DATA]='\0';
}
if ( _npar > 0 ) {
_pathpari[MED_TAILLE_NUM_DATA]='\0';
_pathparf[MED_TAILLE_NUM_DATA]='\0';
MED_ERR_EXIT_IF ( H5Ldelete(fid,_pathpari,H5P_DEFAULT) < 0 ,
MED_ERR_DELETE,MED_ERR_LINK,_pathpari);
ret = H5Gmove(fid, _pathparf, _pathpari );
EXIT_IF(ret < 0,"Renommage du group de paramètres scalaires",_pathparf);
}
/* MAJ des localisations */
_nloc = MEDnLocalization(fid);
/* ISCRUTE(_nloc); */
if (_nloc > 0)
fprintf(stdout," >>> Normalisation des localisations des points d'intégration\n");
for (i=0 ; i < _nloc ; i++ ) {
/* SSCRUTE(_pathloc); */
MED_ERR_EXIT_IF (_MEDobjectGetName(fid, _pathloc ,i, &_pathloc[MED_TAILLE_GAUSS]) < 0,
MED_ERR_ACCESS,MED_ERR_DATAGROUP,_pathloc);
/* SSCRUTE(_pathloc); */
MED_ERR_EXIT_IF (_MEDattributeNumRdByName(fid,_pathloc,MED_NOM_GEO,
MED_INTERNAL_INT,(unsigned char * const ) &_intgeotype) < 0,
MED_ERR_READ,MED_ERR_ATTRIBUTE,MED_NOM_GEO);
_sdim = (_intgeotype/100);
MED_ERR_EXIT_IF (_MEDattributeNumWrByName(fid,_pathloc,MED_NOM_DIM,
MED_INTERNAL_INT,(const unsigned char * const) &_sdim) < 0,
MED_ERR_WRITE,MED_ERR_ATTRIBUTE,MED_NOM_DIM);
MED_ERR_EXIT_IF ( _MEDattributeStringWrByName(fid,_pathloc,MED_NOM_INM,MED_NAME_SIZE,"") < 0,
MED_ERR_WRITE,MED_ERR_ATTRIBUTE,MED_NOM_INM);
_pathloc[MED_TAILLE_GAUSS]='\0';
}
/* MAJ des liens */
nln = MEDnLink(fid);
if (nln > 0)
fprintf(stdout," >>> Normalisation des liens\n");
for (i=1 ; i <= nln ; i++ ) {
ret = MEDlinkInfo(fid, i, nomlien, &nval);
EXIT_IF(ret,"Erreur a la demande d'information sur le lien",NULL);
/* printf("\t- Lien n°%i de nom |%s| et de taille "IFORMAT"\n",i,nomlien,nval); */
lien = (char *) malloc((nval+1)*sizeof(char));
EXIT_IF(lien == NULL,NULL,NULL);
ret = MEDlinkRd(fid, nomlien, lien );
EXIT_IF(ret,"Erreur a la lecture du lien : ",nomlien);
MAJ_version_num(fid,3,0,8);
ret = MED30linkWr(fid,nomlien,lien);
EXIT_IF(ret,"Erreur a l'écrtiure du lien : ",nomlien);
MAJ_version_num(fid,2,3,6);
lien[nval] = '\0';
/* printf("\t\t|%s|\n\n",lien); */
free(lien);
}
/* combien de champs dans le fichier */
ncha = MEDnField(fid);
EXIT_IF(ncha < 0,"lors de la lecture du nombre de champs",NULL);
/* MAJ des champs */
for (i =0;i<ncha;i++) {
lret = 0;
/* Lecture du nombre de composantes */
ncomp = MEDfieldnComponent(fid,i+1);
if (ncomp < 0) {
MESSAGE("Erreur à la lecture du nombre de composantes : "); ISCRUTE(ncomp);
exit(1);
}
/* Lecture du type du champ, des noms des composantes et du nom de l'unité*/
comp = (char*) malloc(ncomp*MED_SNAME_SIZE+1);
EXIT_IF(comp == NULL,NULL,NULL);
unit = (char*) malloc(ncomp*MED_SNAME_SIZE+1);
EXIT_IF(unit == NULL,NULL,NULL);
/* ret = MED231champInfoEtRen(fid,i+1,nomcha,&typcha,comp,unit,ncomp); */
ret = MEDfieldInfo(fid,i+1,nomcha,_meshname,&_local,&typcha,comp,unit,_dtunit,&_ncstp);
MED_ERR_EXIT_IF(ret,MED_ERR_ACCESS,MED_ERR_FIELD,nomcha);
/* creation du champ destination */
MAJ_version_num(fid,3,0,8);
EXIT_IF( H5Gmove(fid, _pathi, _pathtmp ) < 0,"Switch to ",_pathtmp);
_datasetexist=H5Lexists( fid, _pathf, H5P_DEFAULT );
if (_datasetexist ) { EXIT_IF( (H5Gmove(fid, _pathf, _pathi ) < 0) ,"Switch to ",_pathi); }
MED_ERR_EXIT_IF( MEDfieldCr(fid,nomcha,typcha,ncomp,comp,unit,_dtunit,_meshname ) < 0,
MED_ERR_CREATE,MED_ERR_FIELD,_pathf);
EXIT_IF( H5Gmove(fid, _pathi , _pathf ) < 0,"Switch to ",_pathf);
EXIT_IF( H5Gmove(fid, _pathtmp, _pathi ) < 0,"Switch to ",_pathi);
MAJ_version_num(fid,2,3,6);
free(comp);
free(unit);
lret = MAJ_236_300_fieldOnEntity( fid, nomcha, _meshname, typcha, ncomp, MED_NODE,_ncstp, _pathi, _pathf);
if (lret != 0) {
MESSAGE("Erreur à la lecture des champs aux noeuds "); exit(1);
}
lret = MAJ_236_300_fieldOnEntity( fid, nomcha, _meshname, typcha, ncomp, MED_CELL,_ncstp, _pathi, _pathf);
if (lret != 0) {
MESSAGE("Erreur à la lecture des champs aux mailles "); exit(1);
}
lret = MAJ_236_300_fieldOnEntity( fid, nomcha, _meshname, typcha, ncomp, MED_DESCENDING_FACE,_ncstp, _pathi, _pathf);
if (lret != 0) {
MESSAGE("Erreur à la lecture des champs aux faces "); exit(1);
}
lret = MAJ_236_300_fieldOnEntity( fid, nomcha, _meshname, typcha, ncomp, MED_DESCENDING_EDGE,_ncstp, _pathi, _pathf);
if (lret != 0) {
MESSAGE("Erreur à la lecture des champs aux aretes "); exit(1);
}
lret = MAJ_236_300_fieldOnEntity( fid, nomcha, _meshname, typcha, ncomp, MED_NODE_ELEMENT,_ncstp, _pathi, _pathf);
if (lret != 0) {
MESSAGE("Erreur à la lecture des champs aux aretes "); exit(1);
}
}
_datasetexist=H5Lexists( fid, _pathf, H5P_DEFAULT );
if (_datasetexist ) {
EXIT_IF( (H5Ldelete(fid,_pathi, H5P_DEFAULT) < 0) ,"Delete ",_pathi);
EXIT_IF( (H5Gmove(fid, _pathf, _pathi ) < 0) ,"Switch to ",_pathf);
}
}
/****************************************************************
**
** test_vl_rewrite(): Test basic VL string code.
** Tests I/O on VL strings when lots of objects in the file
** have been linked/unlinked.
**
****************************************************************/
static void test_vl_rewrite(void)
{
hid_t file1, file2; /* File IDs */
hid_t type; /* VL string datatype ID */
hid_t space; /* Scalar dataspace */
char name[256]; /* Buffer for names & data */
int i; /* Local index variable */
herr_t ret; /* Generic return value */
/* Create the VL string datatype */
type = H5Tcopy(H5T_C_S1);
CHECK(type, FAIL, "H5Tcopy");
ret = H5Tset_size(type, H5T_VARIABLE);
CHECK(ret, FAIL, "H5Tset_size");
/* Create the scalar dataspace */
space = H5Screate(H5S_SCALAR);
CHECK(space, FAIL, "H5Screate");
/* Open the files */
file1 = H5Fcreate(DATAFILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(file1, FAIL, "H5Fcreate");
file2 = H5Fcreate(DATAFILE2, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
CHECK(file1, FAIL, "H5Fcreate");
/* Create in file 1 */
for(i=0; i<REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
write_scalar_dset(file1, type, space, name, name);
}
/* Effectively copy data from file 1 to 2 */
for(i=0; i<REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
read_scalar_dset(file1, type, space, name, name);
write_scalar_dset(file2, type, space, name, name);
}
/* Read back from file 2 */
for(i = 0; i < REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
read_scalar_dset(file2, type, space, name, name);
} /* end for */
/* Remove from file 2. */
for(i = 0; i < REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
ret = H5Ldelete(file2, name, H5P_DEFAULT);
CHECK(ret, FAIL, "H5Ldelete");
} /* end for */
/* Effectively copy from file 1 to file 2 */
for(i = 0; i < REWRITE_NDATASETS; i++) {
sprintf(name, "/set_%d", i);
read_scalar_dset(file1, type, space, name, name);
write_scalar_dset(file2, type, space, name, name);
} /* end for */
/* Close everything */
ret = H5Tclose(type);
CHECK(ret, FAIL, "H5Tclose");
ret = H5Sclose(space);
CHECK(ret, FAIL, "H5Sclose");
ret = H5Fclose(file1);
CHECK(ret, FAIL, "H5Fclose");
ret = H5Fclose(file2);
CHECK(ret, FAIL, "H5Fclose");
return;
} /* end test_vl_rewrite() */
int main (void)
{
hid_t file;
hid_t grp;
hid_t dataset, dataspace;
hid_t plist;
herr_t status;
hsize_t dims[2];
hsize_t cdims[2];
int idx_f, idx_g;
/*
* Create a file.
*/
file = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a group in the file.
*/
grp = H5Gcreate(file, "/Data", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataset "Compressed Data" in the group using absolute
* name. Dataset creation property list is modified to use
* GZIP compression with the compression effort set to 6.
* Note that compression can be used only when dataset is chunked.
*/
dims[0] = 1000;
dims[1] = 20;
cdims[0] = 20;
cdims[1] = 20;
dataspace = H5Screate_simple(RANK, dims, NULL);
plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_chunk(plist, 2, cdims);
H5Pset_deflate( plist, 6);
dataset = H5Dcreate(file, "/Data/Compressed_Data", H5T_NATIVE_INT,
dataspace, H5P_DEFAULT, plist, H5P_DEFAULT);
/*
* Close the first dataset .
*/
H5Sclose(dataspace);
H5Dclose(dataset);
/*
* Create the second dataset.
*/
dims[0] = 500;
dims[1] = 20;
dataspace = H5Screate_simple(RANK, dims, NULL);
dataset = H5Dcreate(file, "/Data/Float_Data", H5T_NATIVE_FLOAT,
dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
*Close the second dataset and file.
*/
H5Sclose(dataspace);
H5Dclose(dataset);
H5Pclose(plist);
H5Gclose(grp);
H5Fclose(file);
/*
* Now reopen the file and group in the file.
*/
file = H5Fopen(H5FILE_NAME, H5F_ACC_RDWR, H5P_DEFAULT);
grp = H5Gopen(file, "Data", H5P_DEFAULT);
/*
* Access "Compressed_Data" dataset in the group.
*/
dataset = H5Dopen(grp, "Compressed_Data", H5P_DEFAULT);
if( dataset < 0) printf(" Dataset 'Compressed-Data' is not found. \n");
printf("\"/Data/Compressed_Data\" dataset is open \n");
/*
* Close the dataset.
*/
status = H5Dclose(dataset);
/*
* Create hard link to the Data group.
*/
status = H5Lcreate_hard(file, "Data", H5L_SAME_LOC, "Data_new", H5P_DEFAULT, H5P_DEFAULT);
/*
* We can access "Compressed_Data" dataset using created
* hard link "Data_new".
*/
dataset = H5Dopen(file, "/Data_new/Compressed_Data", H5P_DEFAULT);
if( dataset < 0) printf(" Dataset is not found. \n");
printf("\"/Data_new/Compressed_Data\" dataset is open \n");
/*
* Close the dataset.
*/
status = H5Dclose(dataset);
/*
* Use iterator to see the names of the objects in the root group.
*/
idx_f = H5Literate(file, H5_INDEX_NAME, H5_ITER_INC, NULL, file_info, NULL);
/*
* Unlink name "Data" and use iterator to see the names
* of the objects in the file root direvtory.
*/
if(H5Ldelete(file, "Data", H5P_DEFAULT) < 0)
printf(" H5Ldelete failed \n");
else
printf("\"Data\" is unlinked \n");
idx_f = H5Literate(file, H5_INDEX_NAME, H5_ITER_INC, NULL, file_info, NULL);
/*
* Use iterator to see the names of the objects in the group
* /Data_new.
*/
idx_g = H5Literate_by_name(grp, "/Data_new", H5_INDEX_NAME, H5_ITER_INC, NULL, group_info, NULL, H5P_DEFAULT);
/*
* Close the file.
*/
H5Gclose(grp);
H5Fclose(file);
return 0;
}
int main(void)
{
hid_t fil,spc,set;
hid_t cs6, cmp, fix;
hid_t cmp1, cmp2, cmp3;
hid_t plist;
hid_t array_dt;
hsize_t dim[2];
hsize_t cdim[4];
char string5[5];
float fok[2] = {1234., 2341.};
float fnok[2] = {5678., 6785.};
float *fptr;
char *data;
char *mname;
int result = 0;
printf("%-70s", "Testing alignment in compound datatypes");
strcpy(string5, "Hi!");
HDunlink(fname);
fil = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
if (fil < 0) {
puts("*FAILED*");
return 1;
}
H5E_BEGIN_TRY {
H5Ldelete(fil, setname, H5P_DEFAULT);
} H5E_END_TRY;
cs6 = H5Tcopy(H5T_C_S1);
H5Tset_size(cs6, sizeof(string5));
H5Tset_strpad(cs6, H5T_STR_NULLPAD);
cmp = H5Tcreate(H5T_COMPOUND, sizeof(fok) + sizeof(string5) + sizeof(fnok));
H5Tinsert(cmp, "Awkward length", 0, cs6);
cdim[0] = sizeof(fok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp, "Ok", sizeof(string5), array_dt);
H5Tclose(array_dt);
cdim[0] = sizeof(fnok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp, "Not Ok", sizeof(fok) + sizeof(string5), array_dt);
H5Tclose(array_dt);
fix=h5tools_get_native_type(cmp);
cmp1 = H5Tcreate(H5T_COMPOUND, sizeof(fok));
cdim[0] = sizeof(fok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp1, "Ok", 0, array_dt);
H5Tclose(array_dt);
cmp2 = H5Tcreate(H5T_COMPOUND, sizeof(string5));
H5Tinsert(cmp2, "Awkward length", 0, cs6);
cmp3 = H5Tcreate(H5T_COMPOUND, sizeof(fnok));
cdim[0] = sizeof(fnok) / sizeof(float);
array_dt = H5Tarray_create2(H5T_NATIVE_FLOAT, 1, cdim);
H5Tinsert(cmp3, "Not Ok", 0, array_dt);
H5Tclose(array_dt);
plist = H5Pcreate(H5P_DATASET_XFER);
H5Pset_preserve(plist, 1);
/*
* Create a small dataset, and write data into it we write each field
* in turn so that we are avoid alignment issues at this point
*/
dim[0] = 1;
spc = H5Screate_simple(1, dim, NULL);
set = H5Dcreate2(fil, setname, cmp, spc, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dwrite(set, cmp1, spc, H5S_ALL, plist, fok);
H5Dwrite(set, cmp2, spc, H5S_ALL, plist, string5);
H5Dwrite(set, cmp3, spc, H5S_ALL, plist, fnok);
H5Dclose(set);
/* Now open the set, and read it back in */
data = malloc(H5Tget_size(fix));
if(!data) {
perror("malloc() failed");
abort();
}
set = H5Dopen2(fil, setname, H5P_DEFAULT);
H5Dread(set, fix, spc, H5S_ALL, H5P_DEFAULT, data);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
if(fok[0] != fptr[0] || fok[1] != fptr[1]
|| fnok[0] != fptr[2] || fnok[1] != fptr[3]) {
result = 1;
printf("%14s (%2d) %6s = %s\n",
mname = H5Tget_member_name(fix, 0), (int)H5Tget_member_offset(fix,0),
string5, (char *)(data + H5Tget_member_offset(fix, 0)));
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
printf("Data comparison:\n"
"%14s (%2d) %6f = %f\n"
" %6f = %f\n",
mname = H5Tget_member_name(fix, 1), (int)H5Tget_member_offset(fix,1),
fok[0], fptr[0],
fok[1], fptr[1]);
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 2));
printf("%14s (%2d) %6f = %f\n"
" %6f = %6f\n",
mname = H5Tget_member_name(fix, 2), (int)H5Tget_member_offset(fix,2),
fnok[0], fptr[0],
fnok[1], fptr[1]);
free(mname);
fptr = (float *)(data + H5Tget_member_offset(fix, 1));
printf("\n"
"Short circuit\n"
" %6f = %f\n"
" %6f = %f\n"
" %6f = %f\n"
" %6f = %f\n",
fok[0], fptr[0],
fok[1], fptr[1],
fnok[0], fptr[2],
fnok[1], fptr[3]);
puts("*FAILED*");
} else {
puts(" PASSED");
}
free(data);
H5Sclose(spc);
H5Tclose(cmp);
H5Tclose(cmp1);
H5Tclose(cmp2);
H5Tclose(cmp3);
H5Pclose(plist);
H5Fclose(fil);
HDunlink(fname);
fflush(stdout);
return result;
}
void DCGroup::remove(H5Handle base, std::string path)
throw (DCException)
{
if (H5Ldelete(base, path.c_str(), H5P_LINK_ACCESS_DEFAULT) < 0)
throw DCException(getExceptionString("failed to remove group", path));
}
static void hard_link_example(void)
{
hid_t file_id;
hid_t group_id;
H5L_info_t li;
/* Define the link class that we'll use to register "user-defined hard
* links" using the callbacks we defined above.
* A link class can have NULL for any callback except its traverse
* callback.
*/
const H5L_class_t UD_hard_class[1] = {{
H5L_LINK_CLASS_T_VERS, /* Version number for this struct.
* This field is always H5L_LINK_CLASS_T_VERS */
(H5L_type_t)UD_HARD_CLASS, /* Link class id number. This can be any
* value between H5L_TYPE_UD_MIN (64) and
* H5L_TYPE_MAX (255). It should be a
* value that isn't already being used by
* another kind of link. We'll use 66. */
"UD_hard_link", /* Link class name for debugging */
UD_hard_create, /* Creation callback */
NULL, /* Move callback */
NULL, /* Copy callback */
UD_hard_traverse, /* The actual traversal function */
UD_hard_delete, /* Deletion callback */
NULL /* Query callback */
}};
/* First, create a file and an object within the file for the link to
* point to.
*/
file_id = H5Fcreate(HARD_LINK_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
group_id = H5Gcreate2(file_id, TARGET_GROUP, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Gclose(group_id);
/* This is how we create a normal hard link to the group. This
* creates a second "name" for the group.
*/
H5Lcreate_hard(file_id, TARGET_GROUP, file_id, HARD_LINK_NAME, H5P_DEFAULT, H5P_DEFAULT);
/* To do the same thing using a user-defined link, we first have to
* register the link class we defined.
*/
H5Lregister(UD_hard_class);
/* Since hard links link by object address, we'll need to retrieve
* the target group's address. We do this by calling H5Lget_info
* on a hard link to the object.
*/
H5Lget_info(file_id, TARGET_GROUP, &li, H5P_DEFAULT);
/* Now create a user-defined link. We give it the group's address
* as its udata.
*/
H5Lcreate_ud(file_id, UD_HARD_LINK_NAME, (H5L_type_t)UD_HARD_CLASS, &(li.u.address),
sizeof(li.u.address), H5P_DEFAULT, H5P_DEFAULT);
/* The UD hard link has now incremented the group's reference count
* like a normal hard link would. This means that we can unlink the
* other two links to that group and it won't be deleted until the
* UD hard link is deleted.
*/
H5Ldelete(file_id, TARGET_GROUP, H5P_DEFAULT);
H5Ldelete(file_id, HARD_LINK_NAME, H5P_DEFAULT);
/* The group is still accessible through the UD hard link. If this were
* a soft link instead, the object would have been deleted when the last
* hard link to it was unlinked. */
group_id = H5Gopen2(file_id, UD_HARD_LINK_NAME, H5P_DEFAULT);
/* The group is now open normally. Don't forget to close it! */
H5Gclose(group_id);
/* Removing the user-defined hard link will delete the group. */
H5Ldelete(file_id, UD_HARD_LINK_NAME, H5P_DEFAULT);
H5Fclose(file_id);
}
/** Delete a child */
void unlink(std::string const & name) {
h5e::check_error(H5Ldelete(_self, name.c_str(), H5P_DEFAULT));
}
