/*
* Class: hdf_hdf5lib_H5
* Method: H5Rget_region
* Signature: (JI[B)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5__1H5Rget_1region(JNIEnv *env, jclass clss, jlong dataset, jint ref_type, jbyteArray ref)
{
hid_t retVal = -1;
jboolean isCopy;
jbyte *refP;
if (ref_type != H5R_DATASET_REGION) {
h5badArgument( env, "H5Rget_region: bad ref_type ");
} /* end if */
else if (ref == NULL) {
h5nullArgument( env, "H5Rget_region: ref is NULL");
} /* end if */
else if ( ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
h5badArgument( env, "H5Rget_region: region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
} /* end if */
else {
refP = (jbyte*)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy);
if (refP == NULL) {
h5JNIFatalError(env, "H5Rget_region: ref not pinned");
} /* end if */
else {
retVal = H5Rget_region((hid_t)dataset, (H5R_type_t)ref_type, refP);
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
if (retVal < 0)
h5libraryError(env);
} /* end else */
} /* end else */
return (jlong)retVal;
} /* end Java_hdf_hdf5lib_H5__1H5Rget_1region */
//--------------------------------------------------------------------------
// Function: H5Object::p_get_region (protected)
// Purpose Retrieves a dataspace with the region pointed to selected.
// Parameters
// ref_type - IN: Type of reference to get region of - default
// to H5R_DATASET_REGION
// ref - IN: Reference to get region of
// Return Dataspace id
// Exception H5::IdComponentException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
hid_t H5Object::p_get_region(void *ref, H5R_type_t ref_type) const
{
hid_t space_id = H5Rget_region(getId(), ref_type, ref);
if (space_id < 0)
{
throw IdComponentException("", "H5Rget_region failed");
}
return(space_id);
}
//--------------------------------------------------------------------------
// Function: H5Location::getRegion
///\brief Retrieves a dataspace with the region pointed to selected.
///\param ref - IN: Reference to get region of
///\param ref_type - IN: Type of reference to get region of - default
// to H5R_DATASET_REGION
///\return DataSpace object
///\exception H5::ReferenceException
// Programmer Binh-Minh Ribler - May, 2004
//--------------------------------------------------------------------------
DataSpace H5Location::getRegion(void *ref, H5R_type_t ref_type) const
{
hid_t space_id = H5Rget_region(getId(), ref_type, ref);
if (space_id < 0)
{
throw ReferenceException(inMemFunc("getRegion"), "H5Rget_region failed");
}
try {
DataSpace dataspace(space_id);
return(dataspace);
}
catch (DataSpaceIException E) {
throw ReferenceException(inMemFunc("getRegion"), E.getDetailMsg());
}
}
/*----------------------------------------------------------------------------
* Name: h5rget_region_region_object_c
* Purpose: Call H5Rget_region to dereference dataspace region
* Inputs: dset_id - dataset identifier
* ref - reference to the dataset region
* Outputs: space_id - dereferenced dataset dataspace identifier
* Returns: 0 on success, -1 on failure
* Programmer: Elena Pourmal
* Wednesday, December 1, 1999
* Modifications:
*---------------------------------------------------------------------------*/
int_f
nh5rget_region_region_c (hid_t_f *dset_id, int_f *ref, hid_t_f *space_id)
{
int ret_value = -1;
hid_t c_dset_id;
hid_t c_space_id;
hdset_reg_ref_t ref_c;
HDmemcpy (&ref_c, ref, H5R_DSET_REG_REF_BUF_SIZE);
/*
* Call H5Rget_region function.
*/
c_dset_id = *dset_id;
c_space_id = H5Rget_region(c_dset_id, H5R_DATASET_REGION, &ref_c);
if(c_space_id < 0) return ret_value;
*space_id = (hid_t_f)c_space_id;
ret_value = 0;
return ret_value;
}
int do_copy_refobjs(hid_t fidin,
hid_t fidout,
trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
hid_t grp_in=(-1); /* read group ID */
hid_t grp_out=(-1); /* write group ID */
hid_t dset_in=(-1); /* read dataset ID */
hid_t dset_out=(-1); /* write dataset ID */
hid_t type_in=(-1); /* named type ID */
hid_t dcpl_id=(-1); /* dataset creation property list ID */
hid_t space_id=(-1); /* space ID */
hid_t ftype_id=(-1); /* file data type ID */
hid_t mtype_id=(-1); /* memory data type ID */
size_t msize; /* memory size of memory type */
hsize_t nelmts; /* number of elements in dataset */
int rank; /* rank of dataset */
hsize_t dims[H5S_MAX_RANK]; /* dimensions of dataset */
unsigned int i, j;
int k;
/*-------------------------------------------------------------------------
* browse
*-------------------------------------------------------------------------
*/
for ( i = 0; i < travt->nobjs; i++)
{
switch ( travt->objs[i].type )
{
/*-------------------------------------------------------------------------
* H5G_GROUP
*-------------------------------------------------------------------------
*/
case H5G_GROUP:
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if ((grp_out=H5Gopen(fidout,travt->objs[i].name))<0)
goto error;
if((grp_in = H5Gopen (fidin,travt->objs[i].name))<0)
goto error;
if (copy_refs_attr(grp_in,grp_out,options,travt,fidout)<0)
goto error;
if (H5Gclose(grp_out)<0)
goto error;
if (H5Gclose(grp_in)<0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++)
{
H5Glink(fidout,
H5G_LINK_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name);
}
}
break;
/*-------------------------------------------------------------------------
* H5G_DATASET
*-------------------------------------------------------------------------
*/
case H5G_DATASET:
if ((dset_in=H5Dopen(fidin,travt->objs[i].name))<0)
goto error;
if ((space_id=H5Dget_space(dset_in))<0)
goto error;
if ((ftype_id=H5Dget_type (dset_in))<0)
goto error;
if ((dcpl_id=H5Dget_create_plist(dset_in))<0)
goto error;
if ( (rank=H5Sget_simple_extent_ndims(space_id))<0)
goto error;
if ( H5Sget_simple_extent_dims(space_id,dims,NULL)<0)
goto error;
nelmts=1;
for (k=0; k<rank; k++)
nelmts*=dims[k];
if ((mtype_id=h5tools_get_native_type(ftype_id))<0)
goto error;
if ((msize=H5Tget_size(mtype_id))==0)
goto error;
/*-------------------------------------------------------------------------
* check if the dataset creation property list has filters that
* are not registered in the current configuration
* 1) the external filters GZIP and SZIP might not be available
* 2) the internal filters might be turned off
*-------------------------------------------------------------------------
*/
if (h5tools_canreadf((NULL),dcpl_id)==1)
{
/*-------------------------------------------------------------------------
* test for a valid output dataset
*-------------------------------------------------------------------------
*/
dset_out = FAIL;
/*-------------------------------------------------------------------------
* object references are a special case
* we cannot just copy the buffers, but instead we recreate the reference
*-------------------------------------------------------------------------
*/
if (H5Tequal(mtype_id, H5T_STD_REF_OBJ))
{
H5G_obj_t1 obj_type;
hid_t refobj_id;
hobj_ref_t *refbuf=NULL; /* buffer for object references */
hobj_ref_t *buf=NULL;
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(dset_in,H5R_OBJECT,buf))<0)
goto error;
refbuf=HDcalloc((unsigned)nelmts,msize);
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(dset_in,H5R_OBJECT,&buf[u]))<0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
/* create the reference, -1 parameter for objects */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_OBJECT,-1)<0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
}
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
if (nelmts) {
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
goto error;
}
if (buf)
free(buf);
if (refbuf)
free(refbuf);
}/*H5T_STD_REF_OBJ*/
/*-------------------------------------------------------------------------
* dataset region references
*-------------------------------------------------------------------------
*/
else if (H5Tequal(mtype_id, H5T_STD_REF_DSETREG))
{
H5G_obj_t1 obj_type;
hid_t refobj_id;
hdset_reg_ref_t *refbuf=NULL; /* input buffer for region references */
hdset_reg_ref_t *buf=NULL; /* output buffer */
const char* refname;
unsigned u;
/*-------------------------------------------------------------------------
* read input to memory
*-------------------------------------------------------------------------
*/
if (nelmts)
{
buf=(void *) HDmalloc((unsigned)(nelmts*msize));
if ( buf==NULL){
printf( "cannot read into memory\n" );
goto error;
}
if (H5Dread(dset_in,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,buf)<0)
goto error;
if ((obj_type = H5Rget_obj_type(dset_in,H5R_DATASET_REGION,buf))<0)
goto error;
/*-------------------------------------------------------------------------
* create output
*-------------------------------------------------------------------------
*/
refbuf=HDcalloc(sizeof(hdset_reg_ref_t),(size_t)nelmts); /*init to zero */
if ( refbuf==NULL){
printf( "cannot allocate memory\n" );
goto error;
}
for ( u=0; u<nelmts; u++)
{
H5E_BEGIN_TRY {
if ((refobj_id = H5Rdereference(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
continue;
} H5E_END_TRY;
/* get the name. a valid name could only occur in the
second traversal of the file */
if ((refname=MapIdToName(refobj_id,travt))!=NULL)
{
hid_t region_id; /* region id of the referenced dataset */
if ((region_id = H5Rget_region(dset_in,H5R_DATASET_REGION,&buf[u]))<0)
goto error;
/* create the reference, we need the space_id */
if (H5Rcreate(&refbuf[u],fidout,refname,H5R_DATASET_REGION,region_id)<0)
goto error;
if (H5Sclose(region_id)<0)
goto error;
if(options->verbose)
{
printf(FORMAT_OBJ,"dset",travt->objs[i].name );
printf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
}
}/*refname*/
close_obj(obj_type,refobj_id);
}/* u */
}/*nelmts*/
/*-------------------------------------------------------------------------
* create/write dataset/close
*-------------------------------------------------------------------------
*/
if ((dset_out=H5Dcreate(fidout,travt->objs[i].name,mtype_id,space_id,dcpl_id))<0)
goto error;
if (nelmts) {
if (H5Dwrite(dset_out,mtype_id,H5S_ALL,H5S_ALL,H5P_DEFAULT,refbuf)<0)
goto error;
}
if (buf)
free(buf);
if (refbuf)
free(refbuf);
} /* H5T_STD_REF_DSETREG */
/*-------------------------------------------------------------------------
* not references, open previously created object in 1st traversal
*-------------------------------------------------------------------------
*/
else
{
if ((dset_out=H5Dopen(fidout,travt->objs[i].name))<0)
goto error;
}
assert(dset_out!=FAIL);
/*-------------------------------------------------------------------------
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
if (copy_refs_attr(dset_in,dset_out,options,travt,fidout)<0)
goto error;
/*-------------------------------------------------------------------------
* check for hard links
*-------------------------------------------------------------------------
*/
if (travt->objs[i].nlinks)
{
for ( j=0; j<travt->objs[i].nlinks; j++){
H5Glink(fidout,
H5G_LINK_HARD,
travt->objs[i].name,
travt->objs[i].links[j].new_name);
}
}
if (H5Dclose(dset_out)<0)
goto error;
}/*can_read*/
int
main(void)
{
hid_t fid1; /* HDF5 File IDs */
hid_t dset1, /* Dataset ID */
dset2; /* Dereferenced dataset ID */
hid_t sid1, /* Dataspace ID #1 */
sid2; /* Dataspace ID #2 */
hsize_t * coords; /* Coordinate buffer */
hsize_t low[SPACE2_RANK]; /* Selection bounds */
hsize_t high[SPACE2_RANK]; /* Selection bounds */
hdset_reg_ref_t *rbuf; /* buffer to to read disk */
int *drbuf; /* Buffer for reading numeric data from disk */
int i, j; /* counting variables */
herr_t ret; /* Generic return value */
/* Output message about test being performed */
/* Allocate write & read buffers */
rbuf=malloc(sizeof(hdset_reg_ref_t)*SPACE1_DIM1);
drbuf=calloc(sizeof(int),SPACE2_DIM1*SPACE2_DIM2);
/* Open the file */
fid1 = H5Fopen(FILE2, H5F_ACC_RDWR, H5P_DEFAULT);
/* Open the dataset */
dset1=H5Dopen(fid1,"/Dataset1");
/* Read selection from disk */
ret=H5Dread(dset1,H5T_STD_REF_DSETREG,H5S_ALL,H5S_ALL,H5P_DEFAULT,rbuf);
/* Try to open objects */
dset2 = H5Rdereference(dset1,H5R_DATASET_REGION,&rbuf[0]);
/* Check information in referenced dataset */
sid1 = H5Dget_space(dset2);
ret=H5Sget_simple_extent_npoints(sid1);
printf(" Number of elements in the dataset is : %d\n",ret);
/* Read from disk */
ret=H5Dread(dset2,H5T_NATIVE_INT,H5S_ALL,H5S_ALL,H5P_DEFAULT,drbuf);
for(i=0; i<SPACE2_DIM1; i++) {
for (j=0; j<SPACE2_DIM2; j++) printf (" %d ", drbuf[i*SPACE2_DIM2+j]);
printf("\n"); }
/* Get the hyperslab selection */
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[0]);
/* Verify correct hyperslab selected */
ret = H5Sget_select_npoints(sid2);
printf(" Number of elements in the hyperslab is : %d \n", ret);
ret = H5Sget_select_hyper_nblocks(sid2);
coords=malloc(ret*SPACE2_RANK*sizeof(hsize_t)*2); /* allocate space for the hyperslab blocks */
ret = H5Sget_select_hyper_blocklist(sid2,0,ret,coords);
printf(" Hyperslab coordinates are : \n");
printf (" ( %lu , %lu ) ( %lu , %lu ) \n", \
(unsigned long)coords[0],(unsigned long)coords[1],(unsigned long)coords[2],(unsigned long)coords[3]);
free(coords);
ret = H5Sget_select_bounds(sid2,low,high);
/* Close region space */
ret = H5Sclose(sid2);
/* Get the element selection */
sid2=H5Rget_region(dset1,H5R_DATASET_REGION,&rbuf[1]);
/* Verify correct elements selected */
ret = H5Sget_select_elem_npoints(sid2);
printf(" Number of selected elements is : %d\n", ret);
/* Allocate space for the element points */
coords= malloc(ret*SPACE2_RANK*sizeof(hsize_t));
ret = H5Sget_select_elem_pointlist(sid2,0,ret,coords);
printf(" Coordinates of selected elements are : \n");
for (i=0; i<2*NPOINTS; i=i+2)
printf(" ( %lu , %lu ) \n", (unsigned long)coords[i],(unsigned long)coords[i+1]);
free(coords);
ret = H5Sget_select_bounds(sid2,low,high);
/* Close region space */
ret = H5Sclose(sid2);
/* Close first space */
ret = H5Sclose(sid1);
/* Close dereferenced Dataset */
ret = H5Dclose(dset2);
/* Close Dataset */
ret = H5Dclose(dset1);
/* Close file */
ret = H5Fclose(fid1);
/* Free memory buffers */
free(rbuf);
free(drbuf);
return 0;
}
int
main (void)
{
hid_t file, space, memspace, dset, dset2, attr;
/* Handles */
herr_t status;
hsize_t dims[1] = {DIM0},
dims2[2] = {DS2DIM0, DS2DIM1},
coords[4][2] = { {0, 1},
{2, 11},
{1, 0},
{2, 4} },
start[2] = {0, 0},
stride[2] = {2, 11},
count[2] = {2, 2},
block[2] = {1, 3};
hssize_t npoints;
hdset_reg_ref_t wdata[DIM0], /* Write buffer */
*rdata; /* Read buffer */
ssize_t size;
char wdata2[DS2DIM0][DS2DIM1] = {"The quick brown",
"fox jumps over ",
"the 5 lazy dogs"},
*rdata2,
*name;
int ndims,
i;
/*
* Create a new file using the default properties.
*/
file = H5Fcreate (FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a dataset with character data.
*/
space = H5Screate_simple (2, dims2, NULL);
dset2 = H5Dcreate (file, DATASET2, H5T_STD_I8LE, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Dwrite (dset2, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, H5P_DEFAULT,
wdata2);
/*
* Create reference to a list of elements in dset2.
*/
status = H5Sselect_elements (space, H5S_SELECT_SET, 4, coords[0]);
status = H5Rcreate (&wdata[0], file, DATASET2, H5R_DATASET_REGION, space);
/*
* Create reference to a hyperslab in dset2, close dataspace.
*/
status = H5Sselect_hyperslab (space, H5S_SELECT_SET, start, stride, count,
block);
status = H5Rcreate (&wdata[1], file, DATASET2, H5R_DATASET_REGION, space);
status = H5Sclose (space);
/*
* Create dataset with a null dataspace to serve as the parent for
* the attribute.
*/
space = H5Screate (H5S_NULL);
dset = H5Dcreate (file, DATASET, H5T_STD_I32LE, space, H5P_DEFAULT,
H5P_DEFAULT, H5P_DEFAULT);
status = H5Sclose (space);
/*
* Create dataspace. Setting maximum size to NULL sets the maximum
* size to be the current size.
*/
space = H5Screate_simple (1, dims, NULL);
/*
* Create the attribute and write the region references to it.
*/
attr = H5Acreate (dset, ATTRIBUTE, H5T_STD_REF_DSETREG, space, H5P_DEFAULT,
H5P_DEFAULT);
status = H5Awrite (attr, H5T_STD_REF_DSETREG, wdata);
/*
* Close and release resources.
*/
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Dclose (dset2);
status = H5Sclose (space);
status = H5Fclose (file);
/*
* Now we begin the read section of this example. Here we assume
* the attribute has the same name and rank, but can have any size.
* Therefore we must allocate a new array to read in data using
* malloc().
*/
/*
* Open file, dataset, and attribute.
*/
file = H5Fopen (FILE, H5F_ACC_RDONLY, H5P_DEFAULT);
dset = H5Dopen (file, DATASET, H5P_DEFAULT);
attr = H5Aopen (dset, ATTRIBUTE, H5P_DEFAULT);
/*
* Get dataspace and allocate memory for read buffer.
*/
space = H5Aget_space (attr);
ndims = H5Sget_simple_extent_dims (space, dims, NULL);
rdata = (hdset_reg_ref_t *) malloc (dims[0] * sizeof (hdset_reg_ref_t));
status = H5Sclose (space);
/*
* Read the data.
*/
status = H5Aread (attr, H5T_STD_REF_DSETREG, rdata);
/*
* Output the data to the screen.
*/
for (i=0; i<dims[0]; i++) {
printf ("%s[%d]:\n ->", ATTRIBUTE, i);
/*
* Open the referenced object, retrieve its region as a
* dataspace selection.
*/
dset2 = H5Rdereference (dset, H5P_DEFAULT, H5R_DATASET_REGION, &rdata[i]);
space = H5Rget_region (dset, H5R_DATASET_REGION, &rdata[i]);
/*
* Get the length of the object's name, allocate space, then
* retrieve the name.
*/
size = 1 + H5Iget_name (dset2, NULL, 0);
name = (char *) malloc (size);
size = H5Iget_name (dset2, name, size);
/*
* Allocate space for the read buffer. We will only allocate
* enough space for the selection, plus a null terminator. The
* read buffer will be 1-dimensional.
*/
npoints = H5Sget_select_npoints (space);
rdata2 = (char *) malloc (npoints + 1);
/*
* Read the dataset region, and add a null terminator so we can
* print it as a string.
*/
memspace = H5Screate_simple (1, (hsize_t *) &npoints, NULL);
status = H5Dread (dset2, H5T_NATIVE_CHAR, memspace, space, H5P_DEFAULT,
rdata2);
rdata2[npoints] = '\0';
/*
* Print the name and region data, close and release resources.
*/
printf (" %s: %s\n", name, rdata2);
free (rdata2);
free (name);
status = H5Sclose (space);
status = H5Sclose (memspace);
status = H5Dclose (dset2);
}
/*
* Close and release resources.
*/
free (rdata);
status = H5Aclose (attr);
status = H5Dclose (dset);
status = H5Fclose (file);
return 0;
}
void H5ReferenceData::printData(std::ostream & os, const unsigned int pos, const unsigned int indentLevel) const
{
char * cdata = static_cast<char *>(data) + offset + pos * (stride ? stride : dataSize);
void ** ref = &(((void **)cdata)[0]);
hid_t file = getFile().getH5Id();
hid_t obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);
if (obj < 0)
{
os << "NULL";
return;
}
ssize_t size = H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, 0, 0);
char * name = 0;
H5O_info_t info;
if (size != -1)
{
name = new char[size + 1];
H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, name, size + 1);
if (datasetReference == H5R_OBJECT)
{
H5Oget_info(obj, &info);
H5Oclose(obj);
switch (info.type)
{
case H5O_TYPE_GROUP:
os << "GROUP ";
break;
case H5O_TYPE_DATASET:
os << "DATASET ";
break;
case H5O_TYPE_NAMED_DATATYPE:
os << "DATATYPE ";
break;
case H5O_TYPE_UNKNOWN:
default:
if (size != -1)
{
delete[] name;
}
throw H5Exception(__LINE__, __FILE__, _("Unknown HDF5 object"));
}
os << (haddr_t)(*ref) << " " << name;
}
else
{
hid_t space = H5Rget_region(file, H5R_DATASET_REGION, ref);
hssize_t npoints = H5Sget_select_elem_npoints(space);
hsize_t ndims = H5Sget_simple_extent_dims(space, 0, 0);
H5Oclose(obj);
os << "DATASET " << name << " {";
if (npoints >= 0)
{
const hsize_t N = ndims * npoints;
hsize_t * buf = new hsize_t[N];
herr_t err = H5Sget_select_elem_pointlist(space, 0, npoints, buf);
for (hssize_t i = 0; i < (hssize_t)N; i += ndims)
{
os << "(";
for (unsigned int j = 0; j < ndims - 1; j++)
{
os << buf[i + j] << ",";
}
os << buf[i + ndims - 1] << ")";
if (i != N - ndims)
{
os << ", ";
}
else
{
os << "}";
}
}
delete[] buf;
}
else
{
hssize_t nblocks = H5Sget_select_hyper_nblocks(space);
if (nblocks >= 0)
{
const hsize_t N = 2 * ndims * nblocks;
hsize_t * buf = new hsize_t[N];
herr_t err = H5Sget_select_hyper_blocklist(space, 0, nblocks, buf);
for (hssize_t i = 0; i < (hssize_t)N; i += 2 * ndims)
{
os << "(";
for (unsigned int j = 0; j < ndims - 1; j++)
{
os << buf[i + j] << ",";
}
os << buf[i + ndims - 1] << ")-(";
for (unsigned int j = 0; j < ndims - 1; j++)
{
os << buf[i + ndims + j] << ",";
}
os << buf[i + 2 * ndims - 1] << ")";
if (i != N - 2 * ndims)
{
os << ", ";
}
else
{
os << "}";
}
}
delete[] buf;
}
}
H5Sclose(space);
}
delete[] name;
}
}
int main(void)
{
hid_t file_id; /* file identifier */
hid_t space_id; /* dataspace identifiers */
hid_t spacer_id;
hid_t dsetv_id; /*dataset identifiers*/
hid_t dsetr_id;
hsize_t dims[2] = {2,9};
hsize_t dimsr[1] = {2};
int rank = 2;
int rankr =1;
herr_t status;
hdset_reg_ref_t ref[2];
hdset_reg_ref_t ref_out[2];
int data[2][9] = {{1,1,2,3,3,4,5,5,6},{1,2,2,3,4,4,5,6,6}};
int data_out[2][9] = {{0,0,0,0,0,0,0,0,0},{0,0,0,0,0,0,0,0,0}};
hsize_t start[2];
hsize_t count[2];
hsize_t coord[2][3] = {{0, 0, 1}, {6, 0, 8}};
unsigned num_points = 3;
int i, j;
size_t name_size1, name_size2;
char buf1[10], buf2[10];
/*
* Create file with default file access and file creation properties.
*/
file_id = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create dataspace for datasets.
*/
space_id = H5Screate_simple(rank, dims, NULL);
spacer_id = H5Screate_simple(rankr, dimsr, NULL);
/*
* Create integer dataset.
*/
dsetv_id = H5Dcreate2(file_id, dsetnamev, H5T_NATIVE_INT, space_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Write data to the dataset.
*/
status = H5Dwrite(dsetv_id, H5T_NATIVE_INT, H5S_ALL , H5S_ALL, H5P_DEFAULT,data);
status = H5Dclose(dsetv_id);
/*
* Dataset with references.
*/
dsetr_id = H5Dcreate2(file_id, dsetnamer, H5T_STD_REF_DSETREG, spacer_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
/*
* Create a reference to the hyperslab.
*/
start[0] = 0;
start[1] = 3;
count[0] = 2;
count[1] = 3;
status = H5Sselect_hyperslab(space_id, H5S_SELECT_SET, start, NULL, count, NULL);
status = H5Rcreate(&ref[0], file_id, dsetnamev, H5R_DATASET_REGION, space_id);
/*
* Create a reference to elements selection.
*/
status = H5Sselect_none(space_id);
status = H5Sselect_elements(space_id, H5S_SELECT_SET, num_points, (const hsize_t *)coord);
status = H5Rcreate(&ref[1], file_id, dsetnamev, H5R_DATASET_REGION, space_id);
/*
* Write dataset with the references.
*/
status = H5Dwrite(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL, H5P_DEFAULT,ref);
/*
* Close all objects.
*/
status = H5Sclose(space_id);
status = H5Sclose(spacer_id);
status = H5Dclose(dsetr_id);
status = H5Fclose(file_id);
/*
* Reopen the file to read selections back.
*/
file_id = H5Fopen(filename, H5F_ACC_RDWR, H5P_DEFAULT);
/*
* Reopen the dataset with object references and read references
* to the buffer.
*/
dsetr_id = H5Dopen2(file_id, dsetnamer, H5P_DEFAULT);
status = H5Dread(dsetr_id, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
H5P_DEFAULT, ref_out);
/*
* Dereference the first reference.
*/
dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[0]);
/*
* Get name of the dataset the first region reference points to
* using H5Rget_name
*/
name_size1 = H5Rget_name(dsetr_id, H5R_DATASET_REGION, &ref_out[0], (char*)buf1, 10);
printf(" Dataset's name (returned by H5Rget_name) the reference points to is %s, name length is %d\n", buf1, (int)name_size1);
/*
* Get name of the dataset the first region reference points to
* using H5Iget_name
*/
name_size2 = H5Iget_name(dsetv_id, (char*)buf2, 10);
printf(" Dataset's name (returned by H5Iget_name) the reference points to is %s, name length is %d\n", buf2, (int)name_size2);
space_id = H5Rget_region(dsetr_id, H5R_DATASET_REGION,&ref_out[0]);
/*
* Read and display hyperslab selection from the dataset.
*/
status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
H5P_DEFAULT, data_out);
printf("Selected hyperslab: ");
for (i = 0; i <= 1; i++)
{
printf("\n");
for (j = 0; j <= 8; j++)
printf("%d ", data_out[i][j]);
}
printf("\n");
/*
* Close dataspace and the dataset.
*/
status = H5Sclose(space_id);
status = H5Dclose(dsetv_id);
/*
* Initialize data_out array again to get point selection.
*/
for (i = 0; i <= 1; i++)
for (j = 0; j <= 8; j++)
data_out[i][j] = 0;
/*
* Dereference the second reference.
*/
dsetv_id = H5Rdereference2(dsetr_id, H5P_DEFAULT, H5R_DATASET_REGION, &ref_out[1]);
space_id = H5Rget_region(dsetv_id, H5R_DATASET_REGION,&ref_out[1]);
/*
* Read selected data from the dataset.
*/
status = H5Dread(dsetv_id, H5T_NATIVE_INT, H5S_ALL, space_id,
H5P_DEFAULT, data_out);
printf("Selected points: ");
for (i = 0; i <= 1; i++)
{
printf("\n");
for (j = 0; j <= 8; j++)
printf("%d ", data_out[i][j]);
}
printf("\n");
/*
* Close dataspace and the dataset.
*/
status = H5Sclose(space_id);
status = H5Dclose(dsetv_id);
status = H5Dclose(dsetr_id);
status = H5Fclose(file_id);
return 0;
}
