void DCAttribute::writeAttribute(const char* name, const hid_t type, hid_t parent,
uint32_t ndims, const Dimensions dims, const void* src)
throw (DCException)
{
hid_t attr = -1;
if (H5Aexists(parent, name))
attr = H5Aopen(parent, name, H5P_DEFAULT);
else
{
hid_t dsp;
if( ndims == 1 && dims.getScalarSize() == 1 )
dsp = H5Screate(H5S_SCALAR);
else
dsp = H5Screate_simple( ndims, dims.getPointer(), dims.getPointer() );
attr = H5Acreate(parent, name, type, dsp, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(dsp);
}
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened or created"));
if (H5Awrite(attr, type, src) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be written"));
}
H5Aclose(attr);
}
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;
}
size_t DCDataSet::getDataTypeSize()
throw (DCException)
{
if (!opened)
throw DCException(getExceptionString("getDataTypeSize: dataset is not opened"));
size_t size = H5Tget_size(this->datatype);
if (size == 0)
throw DCException(getExceptionString("getDataTypeSize: could not get size of datatype"));
return size;
}
H5Handle DCGroup::open(H5Handle base, std::string path)
throw (DCException)
{
H5Handle newHandle;
if (checkExistence && !H5Lexists(base, path.c_str(), H5P_DEFAULT))
throw DCException(getExceptionString("Failed to open group", path));
newHandle = H5Gopen(base, path.c_str(), H5P_DEFAULT);
if (newHandle < 0)
throw DCException(getExceptionString("Failed to open group", path));
handles.push_back(newHandle);
return newHandle;
}
bool DCDataSet::open(hid_t group)
throw (DCException)
{
if (checkExistence && !H5Lexists(group, name.c_str(), H5P_LINK_ACCESS_DEFAULT))
return false;
dataset = H5Dopen(group, name.c_str(), H5P_DATASET_ACCESS_DEFAULT);
if (dataset < 0)
throw DCException(getExceptionString("open: Failed to open dataset"));
datatype = H5Dget_type(dataset);
if (datatype < 0)
{
H5Dclose(dataset);
throw DCException(getExceptionString("open: Failed to get type of dataset"));
}
dataspace = H5Dget_space(dataset);
if (dataspace < 0)
{
H5Dclose(dataset);
throw DCException(getExceptionString("open: Failed to open dataspace"));
}
int dims_result = H5Sget_simple_extent_ndims(dataspace);
if (dims_result < 0)
{
close();
throw DCException(getExceptionString("open: Failed to get dimensions"));
}
ndims = dims_result;
getLogicalSize().set(1, 1, 1);
if (H5Sget_simple_extent_dims(dataspace, getLogicalSize().getPointer(), NULL) < 0)
{
close();
throw DCException(getExceptionString("open: Failed to get sizes"));
}
getLogicalSize().swapDims(ndims);
opened = true;
return true;
}
hid_t DCDataSet::getDataSpace()
throw (DCException)
{
if (!opened)
throw DCException(getExceptionString("getDataSpace: dataset is not opened"));
return dataspace;
}
void DCDataSet::close()
throw (DCException)
{
opened = false;
isReference = false;
if (H5Dclose(dataset) < 0 || H5Sclose(dataspace) < 0)
throw DCException(getExceptionString("close: Failed to close dataset"));
}
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);
}
H5Handle DCGroup::create(H5Handle base, std::string path)
throw (DCException)
{
bool mustCreate = false;
H5Handle currentHandle = base;
char c_path[path.size() + 1];
strcpy(c_path, path.c_str());
char *token = strtok(c_path, "/");
while (token)
{
if (mustCreate || !H5Lexists(currentHandle, token, H5P_DEFAULT))
{
H5Handle newHandle = H5Gcreate(currentHandle, token, H5P_LINK_CREATE_DEFAULT,
H5P_GROUP_CREATE_DEFAULT, H5P_GROUP_ACCESS_DEFAULT);
if (newHandle < 0)
throw DCException(getExceptionString("Failed to create group", path));
currentHandle = newHandle;
mustCreate = true;
} else
{
currentHandle = H5Gopen(currentHandle, token, H5P_DEFAULT);
if (currentHandle < 0)
{
if (checkExistence)
throw DCException(getExceptionString("Failed to create group", path));
currentHandle = H5Gcreate(currentHandle, token, H5P_LINK_CREATE_DEFAULT,
H5P_GROUP_CREATE_DEFAULT, H5P_GROUP_ACCESS_DEFAULT);
if (currentHandle < 0)
throw DCException(getExceptionString("Failed to create group", path));
mustCreate = true;
}
}
handles.push_back(currentHandle);
token = strtok(NULL, "/");
}
return currentHandle;
}
void DCDataSet::setCompression()
throw (DCException)
{
if (this->compression && getPhysicalSize().getScalarSize() != 0)
{
// shuffling reorders bytes for better compression
// set gzip compression level (1=lowest - 9=highest)
if (H5Pset_shuffle(this->dsetProperties) < 0 ||
H5Pset_deflate(this->dsetProperties, 1) < 0)
throw DCException(getExceptionString("setCompression: Failed to set compression"));
}
}
void DCGroup::close()
throw (DCException)
{
for (HandlesList::const_reverse_iterator iter = handles.rbegin();
iter != handles.rend(); ++iter)
{
if (H5Gclose(*iter) < 0)
throw DCException(getExceptionString("Failed to close group", ""));
}
handles.clear();
}
void DCDataSet::createReference(hid_t refGroup,
hid_t srcGroup,
DCDataSet &srcDataSet)
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(srcDataSet.getLogicalSize());
this->ndims = srcDataSet.getNDims();
if (H5Rcreate(®ionRef, srcGroup, srcDataSet.getName().c_str(), H5R_OBJECT, -1) < 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_OBJ,
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_OBJ, H5S_ALL, H5S_ALL,
dsetWriteProperties, ®ionRef) < 0)
throw DCException(getExceptionString("createReference: failed to write reference"));
isReference = true;
opened = true;
}
void DCAttribute::readAttribute(const char* name, hid_t parent, void* dst)
throw (DCException)
{
hid_t attr = H5Aopen(parent, name, H5P_DEFAULT);
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened for reading"));
hid_t attr_type = H5Aget_type(attr);
if (attr_type < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Could not get type of attribute"));
}
if (H5Aread(attr, attr_type, dst) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be read"));
}
H5Aclose(attr);
}
void DCAttribute::writeAttribute(const char* name, const hid_t type, hid_t parent, const void* src)
throw (DCException)
{
hid_t attr = -1;
if (H5Aexists(parent, name))
attr = H5Aopen(parent, name, H5P_DEFAULT);
else
{
hid_t dsp = H5Screate(H5S_SCALAR);
attr = H5Acreate(parent, name, type, dsp, H5P_DEFAULT, H5P_DEFAULT);
H5Sclose(dsp);
}
if (attr < 0)
throw DCException(getExceptionString(name, "Attribute could not be opened or created"));
if (H5Awrite(attr, type, src) < 0)
{
H5Aclose(attr);
throw DCException(getExceptionString(name, "Attribute could not be written"));
}
H5Aclose(attr);
}
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::setChunking(size_t typeSize)
throw (DCException)
{
if (getPhysicalSize().getScalarSize() != 0)
{
// get chunking dimensions
hsize_t chunk_dims[ndims];
DCHelper::getOptimalChunkDims(getPhysicalSize().getPointer(), ndims,
typeSize, chunk_dims);
if (H5Pset_chunk(this->dsetProperties, ndims, chunk_dims) < 0)
{
for (size_t i = 0; i < ndims; ++i)
{
log_msg(1, "chunk_dims[%llu] = %llu",
(long long unsigned) i, (long long unsigned) (chunk_dims[i]));
}
throw DCException(getExceptionString("setChunking: Failed to set chunking"));
}
}
}
DCDataType DCDataSet::getDCDataType() throw (DCException)
{
if (!opened)
throw DCException(getExceptionString("getDCDataType: dataset is not opened"));
DCDataType result = DCDT_UNKNOWN;
H5T_class_t type_class = H5Tget_class(datatype);
size_t type_size = H5Tget_size(datatype);
H5T_sign_t type_signed = H5Tget_sign(datatype);
if (type_class == H5T_INTEGER)
{
if (type_signed == H5T_SGN_NONE)
{
if (type_size == sizeof (uint64_t))
result = DCDT_UINT64;
else
result = DCDT_UINT32;
} else
{
if (type_size == sizeof (int64_t))
result = DCDT_INT64;
else
result = DCDT_INT32;
}
} else
if (type_class == H5T_FLOAT)
{
// float or double
if (type_size == sizeof (float))
result = DCDT_FLOAT32;
else
if (type_size == sizeof (double))
result = DCDT_FLOAT64;
}
return result;
}
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());
}
/**
* Fetch the last exception from the JVM, if any. Clear it to
* continue processing
*
* @return the exception's descriptio,if any. Else ""
*/
String JavaBinderyImpl::getException()
{
return getExceptionString(env);
}
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));
}
