H5Object & H5ReferenceData::getData(const unsigned int size, const unsigned int * index) const
{
char * cdata = static_cast<char *>(data) + offset;
void ** ref = 0;
unsigned int pos = 0;
unsigned int cumprod = 1;
H5O_info_t info;
H5Object * hobj;
hid_t obj;
hid_t file;
ssize_t ssize;
char * name = 0;
std::string _name;
for (unsigned int i = 0; i < size; i++)
{
pos += cumprod * index[i];
}
if (pos >= totalSize)
{
throw H5Exception(__LINE__, __FILE__, _("Invalid index."));
}
cdata += pos * (stride ? stride : dataSize);
file = getFile().getH5Id();
ref = &(((void **)cdata)[0]);
obj = H5Rdereference(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref);
if (obj < 0)
{
throw H5Exception(__LINE__, __FILE__, _("Cannot open object at the given position."));
}
ssize = H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, 0, 0);
name = new char[ssize + 1];
H5Rget_name(file, datasetReference ? H5R_DATASET_REGION : H5R_OBJECT, ref, name, ssize + 1);
_name = std::string(name);
delete[] name;
H5Oget_info(obj, &info);
switch (info.type)
{
case H5O_TYPE_GROUP:
hobj = new H5Group(getParent(), obj, _name);
break;
case H5O_TYPE_DATASET:
hobj = new H5Dataset(getParent(), obj, _name);
break;
case H5O_TYPE_NAMED_DATATYPE:
hobj = new H5Type(getParent(), obj, _name);
break;
case H5O_TYPE_UNKNOWN:
default:
H5Oclose(obj);
throw H5Exception(__LINE__, __FILE__, _("Unknown HDF5 object"));
}
return *hobj;
}
/*
* Class: hdf_hdf5lib_H5
* Method: H5Rget_name
* Signature: (JI[B[Ljava/lang/String;J)J
*/
JNIEXPORT jlong JNICALL
Java_hdf_hdf5lib_H5_H5Rget_1name(JNIEnv *env, jclass clss, jlong loc_id, jint ref_type, jbyteArray ref, jobjectArray name, jlong size)
{
jlong ret_val = -1;
jbyte *refP;
jboolean isCopy;
char *aName = NULL;
jstring str;
size_t bs;
bs = (size_t)size;
if (bs <= 0) {
h5badArgument(env, "H5Rget_name: size <= 0");
} /* end if */
else if (ref == NULL) {
h5nullArgument(env, "H5Rget_name: ref is NULL");
} /* end else if */
else {
if ((ref_type == H5R_OBJECT) && ENVPTR->GetArrayLength(ENVPAR ref) != H5R_OBJ_REF_BUF_SIZE) {
h5badArgument(env, "H5Rget_name: obj ref input array != H5R_OBJ_REF_BUF_SIZE");
} /* end if */
else if ((ref_type == H5R_DATASET_REGION)
&& ENVPTR->GetArrayLength(ENVPAR ref) != H5R_DSET_REG_REF_BUF_SIZE) {
h5badArgument(env, "H5Rget_name: region ref input array != H5R_DSET_REG_REF_BUF_SIZE");
} /* end else if */
else {
refP = (jbyte *)ENVPTR->GetByteArrayElements(ENVPAR ref, &isCopy);
if (refP == NULL) {
h5JNIFatalError(env, "H5Rget_name: ref not pinned");
} /* end if */
else {
aName = (char*)HDmalloc(sizeof(char)*bs);
if (aName == NULL) {
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
h5outOfMemory(env, "H5Rget_name: malloc failed");
} /* end if */
else {
ret_val = (jlong)H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refP, aName, bs) ;
ENVPTR->ReleaseByteArrayElements(ENVPAR ref, refP, JNI_ABORT);
if (ret_val < 0) {
HDfree(aName);
h5libraryError(env);
} /* end if */
else {
str = ENVPTR->NewStringUTF(ENVPAR aName);
ENVPTR->SetObjectArrayElement(ENVPAR name, 0, str);
HDfree(aName);
} /* end else */
} /* end else */
} /* end else */
} /* end else */
} /* end else */
return ret_val;
} /* end Java_hdf_hdf5lib_H5_H5Rget_1name */
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;
}
