void
WriteStringsT( hid_t iParent,
const std::string &iAttrName,
size_t iNumStrings,
const StringT *iStrings )
{
// Validate
ABCA_ASSERT( iNumStrings > 0, "Degenerate num strings in WriteStringsT" );
ABCA_ASSERT( iStrings, "Degenerate strings buffer in WriteStringsT" );
// Compact the strings.
std::vector<CharT> charBuffer;
CompactStrings( iStrings, iNumStrings, charBuffer );
// Create the dataspace.
size_t len = charBuffer.size();
assert( len >= iNumStrings );
Dimensions dims( len );
HDimensions hdims( dims );
hid_t dspaceId = H5Screate_simple( hdims.rank(), hdims.rootPtr(), NULL );
DspaceCloser dspaceCloser( dspaceId );
ABCA_ASSERT( dspaceId >= 0,
"WriteStringsT() Failed in dataspace constructor" );
// Create the attribute.
WriteDataToAttr( iParent, dspaceId, iAttrName,
GetFileDtype<CharT>(), GetNativeDtype<CharT>(),
( const void * )&charBuffer.front() );
// That's it!
}
//-*****************************************************************************
static void getDatatypeArrayDims( hid_t iDtype, Dimensions &dims )
{
ABCA_ASSERT( iDtype >= 0, "Invalid datatype in getDatatypeArrayDims" );
int ndims = H5Tget_array_ndims( iDtype );
ABCA_ASSERT( ndims > 0,
"getDatatypeArrayDims() H5Tget_array_ndims failed" );
HDimensions hdims( ( size_t )ndims );
ndims = H5Tget_array_dims2( iDtype, hdims.rootPtr() );
ABCA_ASSERT( ndims > 0,
"getDatatypeArrayDims() H5Tget_array_dims failed" );
ABCA_ASSERT( ndims == hdims.rank(),
"getDatatypeArrayDims() inconsistent ranks" );
dims = hdims;
}
//-*****************************************************************************
void
WriteSmallArray( hid_t iParent,
const std::string &iAttrName,
hid_t iFileType,
hid_t iNativeType,
size_t iNumVals,
const void *iData )
{
Dimensions dims( iNumVals );
HDimensions hdims( dims );
size_t npoints = hdims.numPoints();
ABCA_ASSERT( npoints > 0,
"Cannot create degenerate dataspace" );
hid_t dspaceId = H5Screate_simple( hdims.rank(), hdims.rootPtr(), NULL );
DspaceCloser dspaceCloser( dspaceId );
WriteDataToAttr( iParent, dspaceId, iAttrName, iFileType, iNativeType,
iData );
}
//-*****************************************************************************
//-*****************************************************************************
// GZIP COMPRESSION FOR DATASETS
//-*****************************************************************************
//-*****************************************************************************
hid_t DsetGzipCreatePlist( const Dimensions &dims, int level )
{
herr_t status;
hid_t ID = H5Pcreate( H5P_DATASET_CREATE );
ABCA_ASSERT( ID >= 0,
"DsetGzipCreatePlist: H5Pcreate failed" );
// Chunking.
HDimensions hdims( dims );
status = H5Pset_chunk( ID, hdims.rank(), hdims.rootPtr() );
ABCA_ASSERT( status >= 0,
"DsetGzipCreatePlist: "
"H5Pset_chunk() failed" );
level = level < 0 ? 0 : level > 9 ? 9 : level;
status = H5Pset_deflate( ID, ( unsigned int )level );
ABCA_ASSERT( status >= 0,
"DsetGzipCreatePlist: "
"H5Pset_link_creation_order() failed" );
return ID;
}
void
WriteStringT( hid_t iParent,
const std::string &iAttrName,
const StringT &iString )
{
// Verify that no NULL characters have been hidden in the string.
CharT NullChar = ( CharT )0;
ABCA_ASSERT( iString.find( NullChar ) == StringT::npos,
"Illegal NULL character found in string in WriteStringT" );
// Create the dataspace.
size_t len = iString.length();
Dimensions dims( len + 1 );
HDimensions hdims( dims );
size_t npoints = hdims.numPoints();
ABCA_ASSERT( npoints > 0,
"Cannot create degenerate dataspace" );
hid_t dspaceId = H5Screate_simple( hdims.rank(), hdims.rootPtr(), NULL );
DspaceCloser dspaceCloser( dspaceId );
// Get the data.
const CharT *data;
if ( len == 0 )
{
data = &NullChar;
}
else
{
data = iString.c_str();
}
// Write into it.
WriteDataToAttr( iParent, dspaceId, iAttrName,
GetFileDtype<CharT>(), GetNativeDtype<CharT>(),
( const void * )data );
}
WrittenArraySampleIDPtr
WriteStringArrayT( WrittenArraySampleMap &iMap,
hid_t iGroup,
const std::string &iName,
const AbcA::ArraySample &iSamp,
const AbcA::ArraySample::Key &iKey,
int iCompressionLevel )
{
// because strings are packed together, always write out the dimensions
Dimensions dims = iSamp.getDimensions();
ABCA_ASSERT( dims.rank() > 0,
"String type can not have a rank-0 array sample" );
std::string dimsName = iName + ".dims";
WriteDimensions( iGroup, dimsName, dims );
// See whether or not we've already stored this.
WrittenArraySampleIDPtr writeID = iMap.find( iKey );
if ( writeID )
{
CopyWrittenArray( iGroup, iName, writeID );
return writeID;
}
// Okay, need to actually store it.
// It will be a dataset with an internal attribute for storing
// the hash id.
bool hasData = dims.numPoints() > 0;
hid_t dspaceId = -1;
Dimensions wdims; // Used to store the "fake" dimensions.
std::vector<CharT> charBuffer;
// Get the dimensions, validate sample size.
if ( hasData )
{
size_t extent = iSamp.getDataType().getExtent();
size_t numStrings = dims.numPoints() * extent;
ABCA_ASSERT( dims.rank() > 0 && numStrings > 0,
"Degenerate array sample in WriteStringArrayT" );
// Get the data out of the array sample.
const StringT *strings =
reinterpret_cast<const StringT *>( iSamp.getData() );
ABCA_ASSERT( strings,
"Degenerate strings in WriteStringArrayT" );
// Compact the strings in the string array.
CompactStrings( strings, numStrings, charBuffer );
// Create the dataspace.
size_t len = charBuffer.size();
assert( len >= numStrings );
wdims = Dimensions( len );
HDimensions hdims( wdims );
dspaceId = H5Screate_simple( hdims.rank(),
hdims.rootPtr(), NULL );
}
else
{
dspaceId = H5Screate( H5S_NULL );
}
ABCA_ASSERT( dspaceId >= 0,
"WriteStringsT() Failed in dataspace constructor" );
DspaceCloser dspaceCloser( dspaceId );
hid_t dsetId = -1;
if ( iCompressionLevel >= 0 && hasData )
{
// Make a compression plist
hid_t zipPlist = DsetGzipCreatePlist( wdims,
iCompressionLevel > 9 ? 9 : iCompressionLevel );
PlistCloser plistCloser( zipPlist );
//std::cout << "Creating compressed data set named: "
// << iName << " in group named: " << iGroup.name()
// << std::endl;
// Make the dataset.
dsetId = H5Dcreate2( iGroup, iName.c_str(), GetFileDtype<CharT>(),
dspaceId, H5P_DEFAULT, zipPlist, H5P_DEFAULT );
}
else
{
//std::cout << "Creating uncompressed data set named: "
// << iName << " in group named: " << iGroup.name()
// << std::endl;
dsetId = H5Dcreate2( iGroup, iName.c_str(), GetFileDtype<CharT>(),
dspaceId, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT );
}
DsetCloser dsetCloser(dsetId);
ABCA_ASSERT( dsetId >= 0,
"WriteArray() Failed in dataset constructor" );
// Write the data.
if ( hasData )
{
H5Dwrite( dsetId, GetNativeDtype<CharT>(), H5S_ALL,
H5S_ALL, H5P_DEFAULT, &charBuffer.front() );
}
// Write the key
WriteKey( dsetId, "key", iKey );
writeID.reset( new WrittenArraySampleID( iKey, dsetId ) );
iMap.store( writeID );
// Return the reference.
return writeID;
}
