void DCDataSet::append(size_t count, size_t offset, size_t stride, const void* data)
throw (DCException)
{
log_msg(2, "DCDataSet::append");
if (!opened)
throw DCException(getExceptionString("append: Dataset has not been opened/created."));
log_msg(3, "logical_size = %s", getLogicalSize().toString().c_str());
Dimensions target_offset(getLogicalSize());
// extend size (dataspace) of existing dataset with count elements
getLogicalSize()[0] += count;
hsize_t * max_dims = new hsize_t[ndims];
for (size_t i = 0; i < ndims; ++i)
max_dims[i] = H5F_UNLIMITED;
if (H5Sset_extent_simple(dataspace, 1, getLogicalSize().getPointer(), max_dims) < 0)
throw DCException(getExceptionString("append: Failed to set new extent"));
delete[] max_dims;
max_dims = NULL;
log_msg(3, "logical_size = %s", getLogicalSize().toString().c_str());
if (H5Dset_extent(dataset, getLogicalSize().getPointer()) < 0)
throw DCException(getExceptionString("append: Failed to extend dataset"));
// select the region in the target DataSpace to write to
Dimensions dim_data(count, 1, 1);
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, target_offset.getPointer(),
NULL, dim_data.getPointer(), NULL) < 0 ||
H5Sselect_valid(dataspace) < 0)
throw DCException(getExceptionString("append: Invalid target hyperslap selection"));
// append data to the dataset.
// select the region in the source DataSpace to read from
Dimensions dim_src(offset + count * stride, 1, 1);
hid_t dsp_src = H5Screate_simple(1, dim_src.getPointer(), NULL);
if (dsp_src < 0)
throw DCException(getExceptionString("append: Failed to create src dataspace while appending"));
if (H5Sselect_hyperslab(dsp_src, H5S_SELECT_SET, Dimensions(offset, 0, 0).getPointer(),
Dimensions(stride, 1, 1).getPointer(), dim_data.getPointer(), NULL) < 0 ||
H5Sselect_valid(dsp_src) < 0)
throw DCException(getExceptionString("append: Invalid source hyperslap selection"));
if (!data || (count == 0))
{
H5Sselect_none(dataspace);
data = NULL;
}
if (H5Dwrite(dataset, this->datatype, dsp_src, dataspace, dsetWriteProperties, data) < 0)
throw DCException(getExceptionString("append: Failed to append dataset"));
H5Sclose(dsp_src);
}
int_f
nh5sselect_valid_c ( hid_t_f *space_id , int_f *flag )
{
int ret_value = 0;
hid_t c_space_id;
htri_t status;
c_space_id = *space_id;
status = H5Sselect_valid(c_space_id);
*flag = (int_f)status;
if ( status < 0 ) ret_value = -1;
return ret_value;
}
void DCDataSet::createReference(hid_t refGroup,
hid_t srcGroup,
DCDataSet &srcDataSet,
Dimensions count,
Dimensions offset,
Dimensions stride)
throw (DCException)
{
if (opened)
throw DCException(getExceptionString("createReference: dataset is already open"));
if (checkExistence && H5Lexists(refGroup, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
throw DCException(getExceptionString("createReference: this reference already exists"));
getLogicalSize().set(count);
this->ndims = srcDataSet.getNDims();
count.swapDims(this->ndims);
offset.swapDims(this->ndims);
stride.swapDims(this->ndims);
// select region hyperslab in source dataset
if (H5Sselect_hyperslab(srcDataSet.getDataSpace(), H5S_SELECT_SET,
offset.getPointer(), stride.getPointer(),
count.getPointer(), NULL) < 0 ||
H5Sselect_valid(srcDataSet.getDataSpace()) <= 0)
throw DCException(getExceptionString("createReference: failed to select hyperslap for reference"));
if (H5Rcreate(®ionRef, srcGroup, srcDataSet.getName().c_str(), H5R_DATASET_REGION,
srcDataSet.getDataSpace()) < 0)
throw DCException(getExceptionString("createReference: failed to create region reference"));
hsize_t ndims = 1;
dataspace = H5Screate_simple(1, &ndims, NULL);
if (dataspace < 0)
throw DCException(getExceptionString("createReference: failed to create dataspace for reference"));
dataset = H5Dcreate(refGroup, name.c_str(), H5T_STD_REF_DSETREG,
dataspace, H5P_DEFAULT, dsetProperties, H5P_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("createReference: failed to create dataset for reference"));
if (H5Dwrite(dataset, H5T_STD_REF_DSETREG, H5S_ALL, H5S_ALL,
dsetWriteProperties, ®ionRef) < 0)
throw DCException(getExceptionString("createReference: failed to write reference"));
isReference = true;
opened = true;
}
void DCDataSet::write(Dimensions srcBuffer, Dimensions srcStride,
Dimensions srcOffset, Dimensions srcData,
Dimensions dstOffset, const void* data)
throw (DCException)
{
log_msg(2, "DCDataSet::write (%s)", name.c_str());
if (!opened)
throw DCException(getExceptionString("write: Dataset has not been opened/created"));
log_msg(3,
" ndims = %llu\n"
" logical_size = %s\n"
" physical_size = %s\n"
" src_buffer = %s\n"
" src_stride = %s\n"
" src_data = %s\n"
" src_offset = %s\n"
" dst_offset = %s\n",
(long long unsigned) ndims,
getLogicalSize().toString().c_str(),
getPhysicalSize().toString().c_str(),
srcBuffer.toString().c_str(),
srcStride.toString().c_str(),
srcData.toString().c_str(),
srcOffset.toString().c_str(),
dstOffset.toString().c_str());
// swap dimensions if necessary
srcBuffer.swapDims(ndims);
srcStride.swapDims(ndims);
srcData.swapDims(ndims);
srcOffset.swapDims(ndims);
dstOffset.swapDims(ndims);
// dataspace to read from
hid_t dsp_src;
if (getLogicalSize().getScalarSize() != 0)
{
dsp_src = H5Screate_simple(ndims, srcBuffer.getPointer(), NULL);
if (dsp_src < 0)
throw DCException(getExceptionString("write: Failed to create source dataspace"));
if (H5Sselect_hyperslab(dsp_src, H5S_SELECT_SET, srcOffset.getPointer(),
srcStride.getPointer(), srcData.getPointer(), NULL) < 0 ||
H5Sselect_valid(dsp_src) <= 0)
throw DCException(getExceptionString("write: Invalid source hyperslap selection"));
if (srcData.getScalarSize() == 0)
H5Sselect_none(dsp_src);
// dataspace to write to
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, dstOffset.getPointer(),
NULL, srcData.getPointer(), NULL) < 0 ||
H5Sselect_valid(dataspace) <= 0)
throw DCException(getExceptionString("write: Invalid target hyperslap selection"));
if (!data || (srcData.getScalarSize() == 0))
{
H5Sselect_none(dataspace);
data = NULL;
}
// write data to the dataset
if (H5Dwrite(dataset, this->datatype, dsp_src, dataspace, dsetWriteProperties, data) < 0)
throw DCException(getExceptionString("write: Failed to write dataset"));
H5Sclose(dsp_src);
}
}
void DCDataSet::read(Dimensions dstBuffer,
Dimensions dstOffset,
Dimensions srcSize,
Dimensions srcOffset,
Dimensions& sizeRead,
uint32_t& srcNDims,
void* dst)
throw (DCException)
{
log_msg(2, "DCDataSet::read (%s)", name.c_str());
if (!opened)
throw DCException(getExceptionString("read: Dataset has not been opened/created"));
if (dstBuffer.getScalarSize() == 0)
dstBuffer.set(srcSize);
// dst buffer is allowed to be NULL
// in this case, only the size of the dataset is returned
// if the dataset is empty, return just its size as there is nothing to read
if ((dst != NULL) && (getNDims() > 0))
{
log_msg(3,
" ndims = %llu\n"
" logical_size = %s\n"
" physical_size = %s\n"
" dstBuffer = %s\n"
" dstOffset = %s\n"
" srcSize = %s\n"
" srcOffset = %s\n",
(long long unsigned) ndims,
getLogicalSize().toString().c_str(),
getPhysicalSize().toString().c_str(),
dstBuffer.toString().c_str(),
dstOffset.toString().c_str(),
srcSize.toString().c_str(),
srcOffset.toString().c_str());
dstBuffer.swapDims(ndims);
dstOffset.swapDims(ndims);
srcSize.swapDims(ndims);
srcOffset.swapDims(ndims);
hid_t dst_dataspace = H5Screate_simple(ndims, dstBuffer.getPointer(), NULL);
if (dst_dataspace < 0)
throw DCException(getExceptionString("read: Failed to create target dataspace"));
if (H5Sselect_hyperslab(dst_dataspace, H5S_SELECT_SET, dstOffset.getPointer(), NULL,
srcSize.getPointer(), NULL) < 0 ||
H5Sselect_valid(dst_dataspace) <= 0)
throw DCException(getExceptionString("read: Target dataspace hyperslab selection is not valid!"));
if (H5Sselect_hyperslab(dataspace, H5S_SELECT_SET, srcOffset.getPointer(), NULL,
srcSize.getPointer(), NULL) < 0 ||
H5Sselect_valid(dataspace) <= 0)
throw DCException(getExceptionString("read: Source dataspace hyperslab selection is not valid!"));
if (srcSize.getScalarSize() == 0)
H5Sselect_none(dataspace);
if (H5Dread(dataset, this->datatype, dst_dataspace, dataspace, dsetReadProperties, dst) < 0)
throw DCException(getExceptionString("read: Failed to read dataset"));
H5Sclose(dst_dataspace);
srcSize.swapDims(ndims);
}
// swap dimensions if necessary
sizeRead.set(srcSize);
srcNDims = this->ndims;
log_msg(3, " returns ndims = %llu", (long long unsigned) ndims);
log_msg(3, " returns sizeRead = %s", sizeRead.toString().c_str());
}
int read_amuse_hdf5_dataset(hid_t group_id,
char *datasetname,
int itype,
int maxtypes,
int npartoftype[maxtypes],
int ncol,
int isrequired[ncol],
int *j)
{
hid_t dataset_id, dataspace_id, memspace_id;
herr_t status;
herr_t HDF5_error = -1;
int ierr = 0;
char name[256];
if (!checkfordataset(group_id,datasetname)) { ierr = 1; return ierr; }
#if H5_VERSION_GE(1,8,0)
dataset_id = H5Dopen2(group_id,datasetname,H5P_DEFAULT);
#else
dataset_id = H5Dopen(group_id,datasetname);
#endif
dataspace_id = H5Dget_space(dataset_id);
int rank = get_rank(dataspace_id);
int k, flag;
/* do nothing if none of the columns are required */
flag = 0;
for (k=0;k<rank;k++) {
if (isrequired[k]) flag = 1;
}
if (!flag) {
if (debug) printf("DEBUG: skipping %s : not required\n",datasetname);
H5Dclose(dataset_id);
return 0;
}
if (debug) printf("DEBUG: got %s rank %i \n",datasetname,rank);
/* make a temporary array to put each column as we read it */
hsize_t nparttmp[1];
nparttmp[0] = npartoftype[itype];
memspace_id = H5Screate_simple(1,nparttmp,NULL);
double *temp = 0;
temp = malloc(npartoftype[itype]*sizeof(double));
if (rank==1) {
*j = *j + 1;
/* read column from file */
H5Dread(dataset_id,H5T_NATIVE_DOUBLE,memspace_id,dataspace_id,H5P_DEFAULT,temp);
/* call Fortran back, sending values in temp array to fill into the main splash dat array */
read_amuse_hdf5_data_fromc(j,&npartoftype[itype],temp,&itype);
strcpy(name,datasetname);
set_blocklabel(j,name);
} else {
hsize_t offset[2], count[2];
for (k=1;k<=rank;k++) {
*j = *j + 1;
count[0] = npartoftype[itype];
count[1] = 1;
offset[0] = 0;
offset[1] = k-1; /* rank */
status = H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, offset, NULL, count, NULL);
if (status == HDF5_error) { printf("ERROR creating hyperslab \n"); ierr = 4; }
if (!H5Sselect_valid(dataspace_id)) { printf("ERROR selecting hyperslab \n"); ierr = 5; }
/* read column from file */
if (isrequired[*j]) {
H5Dread(dataset_id,H5T_NATIVE_DOUBLE,memspace_id,dataspace_id,H5P_DEFAULT,temp);
/* call Fortran back, sending values in temp array to fill into the main splash dat array */
read_amuse_hdf5_data_fromc(j,&npartoftype[itype],temp,&itype);
}
strcpy(name,datasetname);
set_blocklabel(j,name);
}
}
free(temp);
status = H5Sclose(dataspace_id);
if (status == HDF5_error) { printf("ERROR closing dataspace \n"); ierr = 4; }
H5Dclose(dataset_id);
if (status == HDF5_error) { printf("ERROR closing dataset \n"); ierr = 7; }
return ierr;
}
