void
ReadStringsT( hid_t iParent,
const std::string &iAttrName,
size_t iNumStrings,
StringT *oStrings )
{
ABCA_ASSERT( iParent >= 0, "Invalid parent in ReadStringsT" );
// Open the attribute.
hid_t attrId = H5Aopen( iParent, iAttrName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( attrId >= 0,
"Couldn't open attribute named: " << iAttrName );
AttrCloser attrCloser( attrId );
// Checking code.
{
hid_t attrFtype = H5Aget_type( attrId );
DtypeCloser dtypeCloser( attrFtype );
hid_t nativeDtype = GetNativeDtype<CharT>();
ABCA_ASSERT( H5Tget_class( attrFtype ) ==
H5Tget_class( nativeDtype ) &&
H5Tget_sign( attrFtype ) ==
H5Tget_sign( nativeDtype ),
"Invalid datatype for stringT" );
}
hid_t attrSpace = H5Aget_space( attrId );
ABCA_ASSERT( attrSpace >= 0,
"Couldn't get dataspace for attribute: " << iAttrName );
DspaceCloser dspaceCloser( attrSpace );
hssize_t numPoints = H5Sget_simple_extent_npoints( attrSpace );
ABCA_ASSERT( numPoints > 0,
"Degenerate string dimensions in ReadStringsT" );
// Create temporary char storage buffer.
std::vector<CharT> charStorage( ( size_t )( 1 + numPoints ),
( CharT )0 );
// Read into it.
herr_t status = H5Aread( attrId, GetNativeDtype<CharT>(),
( void * )&charStorage.front() );
ABCA_ASSERT( status >= 0, "Couldn't read from attribute: " << iAttrName );
// Extract 'em.
ExtractStrings( oStrings, ( const CharT * )&charStorage.front(),
1 + numPoints, iNumStrings );
}
void
ReadStringT<std::string,char>( hid_t iParent,
const std::string &iAttrName,
std::string &oString )
{
ABCA_ASSERT( iParent >= 0, "Invalid parent in ReadStringT" );
// Open the attribute.
hid_t attrId = H5Aopen( iParent, iAttrName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( attrId >= 0,
"Couldn't open attribute named: " << iAttrName );
AttrCloser attrCloser( attrId );
// Checking code.
hid_t attrFtype = H5Aget_type( attrId );
DtypeCloser dtypeCloser( attrFtype );
ssize_t numChars = H5Tget_size( attrFtype );
ABCA_ASSERT( numChars >= 0,
"ReadStringT() H5Aget_size() failed" );
// Read and check space
{
hid_t attrSpace = H5Aget_space( attrId );
ABCA_ASSERT( attrSpace >= 0,
"Couldn't get dataspace for attribute: " << iAttrName );
DspaceCloser dspaceCloser( attrSpace );
H5S_class_t attrSpaceClass = H5Sget_simple_extent_type( attrSpace );
ABCA_ASSERT( attrSpaceClass == H5S_SCALAR,
"Tried to read non-scalar attribute: " << iAttrName
<< " as scalar" );
}
// Create temporary char storage buffer.
std::vector<char> charStorage( ( size_t )( 1 + numChars ),
( char )0 );
// Read into it.
herr_t status = H5Aread( attrId, attrFtype,
( void * )&charStorage.front() );
ABCA_ASSERT( status >= 0, "Couldn't read from attribute: " << iAttrName );
// Return it.
oString = ( const char * )&charStorage.front();
}
void
WriteStringT<std::string,char>( hid_t iParent,
const std::string &iAttrName,
const std::string &iString )
{
// Verify that no NULL characters have been hidden in the string.
const char NullChar = ( char )0;
ABCA_ASSERT( iString.find( NullChar ) == std::string::npos,
"Illegal NULL character found in string in WriteStringT" );
size_t len = iString.length();
if ( len < 1 ) { len = 1; }
hid_t dtypeId = H5Tcopy( H5T_C_S1 );
DtypeCloser dtypeCloser( dtypeId );
H5Tset_size( dtypeId, len );
hid_t dspaceId = H5Screate( H5S_SCALAR );
DspaceCloser dspaceCloser( dspaceId );
WriteDataToAttr( iParent, dspaceId, iAttrName,
dtypeId, dtypeId, ( const void * )iString.c_str() );
}
static AbcA::ArraySamplePtr
ReadStringArrayT( AbcA::ReadArraySampleCachePtr iCache,
hid_t iParent,
const std::string &iName,
const AbcA::DataType &iDataType )
{
assert( iDataType.getExtent() > 0 );
// Open the data set.
hid_t dsetId = H5Dopen( iParent, iName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( dsetId >= 0, "Cannot open dataset: " << iName );
DsetCloser dsetCloser( dsetId );
// Read the digest, if there's a cache.
AbcA::ArraySample::Key key;
bool foundDigest = ReadKey( dsetId, "key", key );
// If we found a digest and there's a cache, see
// if we're in there, and return it if so.
if ( foundDigest && iCache )
{
AbcA::ReadArraySampleID found = iCache->find( key );
if ( found )
{
AbcA::ArraySamplePtr ret = found.getSample();
assert( ret );
if ( ret->getDataType() != iDataType )
{
ABCA_THROW( "ERROR: Read data type for dset: " << iName
<< ": " << ret->getDataType()
<< " does not match expected data type: "
<< iDataType );
}
// Got it!
return ret;
}
}
// Okay, we haven't found it in a cache.
// Read the data type.
// Checking code.
{
hid_t dsetFtype = H5Dget_type( dsetId );
DtypeCloser dtypeCloser( dsetFtype );
hid_t nativeDtype = GetNativeDtype<CharT>();
ABCA_ASSERT( H5Tget_class( dsetFtype ) ==
H5Tget_class( nativeDtype ) &&
H5Tget_sign( dsetFtype ) ==
H5Tget_sign( nativeDtype )
// CJH They can now be different
// sizes, because wchar_t is sometimes 16-bit,
// but we always store 32 bit.
// && H5Tget_size( dsetFtype ) ==
//H5Tget_size( nativeDtype ),
, "Invalid datatype for stringT" );
}
// String array datatypes require a "dimensions" to be stored
// externally, since the strings themselves are stored in a compacted
// array of rank 1.
// This is an attribute called "dims" that lives in the dset itself.
Dimensions realDims;
ReadDimensions( dsetId, "dims", realDims );
ABCA_ASSERT( realDims.rank() > 0,
"Degenerate rank in Dataset read" );
// Read the data space.
hid_t dspaceId = H5Dget_space( dsetId );
ABCA_ASSERT( dspaceId >= 0, "Could not get dataspace for dataSet: "
<< iName );
DspaceCloser dspaceCloser( dspaceId );
AbcA::ArraySamplePtr ret;
H5S_class_t dspaceClass = H5Sget_simple_extent_type( dspaceId );
if ( dspaceClass == H5S_SIMPLE )
{
ABCA_ASSERT( realDims.numPoints() > 0,
"Degenerate dims in Dataset read" );
size_t totalNumStrings = realDims.numPoints() * iDataType.getExtent();
// Get the dimensions
Dimensions dims;
int rank = H5Sget_simple_extent_ndims( dspaceId );
ABCA_ASSERT( rank == realDims.rank(),
"H5Sget_simple_extent_ndims() failed." );
HDimensions hdims;
hdims.setRank( rank );
rank = H5Sget_simple_extent_dims( dspaceId, hdims.rootPtr(), NULL );
ABCA_ASSERT( rank == hdims.rank(),
"H5Sget_simple_extent_dims() "
"found inconsistent ranks."
<< std::endl
<< "Expecting rank: " << hdims.rank()
<< " instead was: " << rank );
dims = hdims;
ABCA_ASSERT( dims.numPoints() > 0,
"Degenerate dims in Dataset read" );
// Create temporary char storage buffer.
size_t totalNumChars = dims.numPoints() + 1;
std::vector<CharT> charStorage( totalNumChars, ( CharT )0 );
// Read into it.
herr_t status = H5Dread( dsetId, GetNativeDtype<CharT>(),
H5S_ALL, H5S_ALL, H5P_DEFAULT,
( void * )&charStorage.front() );
ABCA_ASSERT( status >= 0,
"Could not read string array from data set. Weird." );
// Make an appropriately dimensionalized (and manageable)
// array of strings using the ArraySamples.
ret = AbcA::AllocateArraySample( iDataType,
realDims );
StringT *strings = reinterpret_cast<StringT*>(
const_cast<void*>( ret->getData() ) );
assert( strings != NULL );
// This part is hard. We have to go through the one dimensional
// array extracting each string.
ExtractStrings<StringT,CharT>( strings,
( const CharT * )&charStorage.front(),
totalNumChars,
totalNumStrings );
}
else if ( dspaceClass == H5S_NULL )
{
// Num points should be zero here.
ABCA_ASSERT( realDims.numPoints() == 0,
"Expecting zero points in dimensions" );
ret = AbcA::AllocateArraySample( iDataType, realDims );
}
else
{
ABCA_THROW( "Unexpected scalar dataspace encountered." );
}
// Store if there is a cache.
if ( foundDigest && iCache )
{
AbcA::ReadArraySampleID stored = iCache->store( key, ret );
if ( stored )
{
return stored.getSample();
}
}
// Otherwise, just leave! ArraySamplePtr returned by AllocateArraySample
// already has fancy-dan deleter built in.
// I REALLY LOVE SMART PTRS.
return ret;
}
//-*****************************************************************************
void
ReadArray( void * iIntoLocation,
hid_t iParent,
const std::string &iName,
const AbcA::DataType &iDataType,
hid_t iType )
{
// Dispatch string stuff.
if ( iDataType.getPod() == kStringPOD )
{
return ReadStringArray( iIntoLocation, iParent, iName, iDataType );
}
else if ( iDataType.getPod() == kWstringPOD )
{
return ReadWstringArray( iIntoLocation, iParent, iName, iDataType );
}
assert( iDataType.getPod() != kStringPOD &&
iDataType.getPod() != kWstringPOD );
// Open the data set.
hid_t dsetId = H5Dopen( iParent, iName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( dsetId >= 0, "Cannot open dataset: " << iName );
DsetCloser dsetCloser( dsetId );
// Read the data space.
hid_t dspaceId = H5Dget_space( dsetId );
ABCA_ASSERT( dspaceId >= 0, "Could not get dataspace for dataSet: "
<< iName );
DspaceCloser dspaceCloser( dspaceId );
// Read the data type.
hid_t dtypeId = H5Dget_type( dsetId );
ABCA_ASSERT( dtypeId >= 0, "Could not get datatype for dataSet: "
<< iName );
DtypeCloser dtypeCloser( dtypeId );
H5S_class_t dspaceClass = H5Sget_simple_extent_type( dspaceId );
if ( dspaceClass == H5S_SIMPLE )
{
// Get the dimensions
int rank = H5Sget_simple_extent_ndims( dspaceId );
ABCA_ASSERT( rank == 1,
"H5Sget_simple_extent_ndims() must be 1." );
hsize_t hdim = 0;
rank = H5Sget_simple_extent_dims( dspaceId, &hdim, NULL );
ABCA_ASSERT( hdim > 0,
"Degenerate dims in Dataset read" );
// And... read into it.
herr_t status = H5Dread( dsetId, iType,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
iIntoLocation );
ABCA_ASSERT( status >= 0, "H5Dread() failed." );
}
else if ( dspaceClass != H5S_NULL )
{
ABCA_THROW( "Unexpected scalar dataspace encountered." );
}
}
//-*****************************************************************************
AbcA::ArraySamplePtr
ReadArray( AbcA::ReadArraySampleCachePtr iCache,
hid_t iParent,
const std::string &iName,
const AbcA::DataType &iDataType,
hid_t iFileType,
hid_t iNativeType )
{
// Dispatch string stuff.
if ( iDataType.getPod() == kStringPOD )
{
return ReadStringArray( iCache, iParent, iName, iDataType );
}
else if ( iDataType.getPod() == kWstringPOD )
{
return ReadWstringArray( iCache, iParent, iName, iDataType );
}
assert( iDataType.getPod() != kStringPOD &&
iDataType.getPod() != kWstringPOD );
// Open the data set.
hid_t dsetId = H5Dopen( iParent, iName.c_str(), H5P_DEFAULT );
ABCA_ASSERT( dsetId >= 0, "Cannot open dataset: " << iName );
DsetCloser dsetCloser( dsetId );
// Read the data space.
hid_t dspaceId = H5Dget_space( dsetId );
ABCA_ASSERT( dspaceId >= 0, "Could not get dataspace for dataSet: "
<< iName );
DspaceCloser dspaceCloser( dspaceId );
AbcA::ArraySample::Key key;
bool foundDigest = false;
// if we are caching, get the key and see if it is being used
if ( iCache )
{
key.origPOD = iDataType.getPod();
key.readPOD = key.origPOD;
key.numBytes = Util::PODNumBytes( key.readPOD ) *
H5Sget_simple_extent_npoints( dspaceId );
foundDigest = ReadKey( dsetId, "key", key );
AbcA::ReadArraySampleID found = iCache->find( key );
if ( found )
{
AbcA::ArraySamplePtr ret = found.getSample();
assert( ret );
if ( ret->getDataType().getPod() != iDataType.getPod() )
{
ABCA_THROW( "ERROR: Read data type for dset: " << iName
<< ": " << ret->getDataType()
<< " does not match expected data type: "
<< iDataType );
}
// Got it!
return ret;
}
}
// Okay, we haven't found it in a cache.
// Read the data type.
hid_t dtypeId = H5Dget_type( dsetId );
ABCA_ASSERT( dtypeId >= 0, "Could not get datatype for dataSet: "
<< iName );
DtypeCloser dtypeCloser( dtypeId );
ABCA_ASSERT( EquivalentDatatypes( iFileType, dtypeId ),
"File DataType clash for array dataset: "
<< iName );
AbcA::ArraySamplePtr ret;
H5S_class_t dspaceClass = H5Sget_simple_extent_type( dspaceId );
if ( dspaceClass == H5S_SIMPLE )
{
// Get the dimensions
int rank = H5Sget_simple_extent_ndims( dspaceId );
ABCA_ASSERT( rank == 1,
"H5Sget_simple_extent_ndims() must be 1." );
hsize_t hdim = 0;
rank = H5Sget_simple_extent_dims( dspaceId, &hdim, NULL );
Dimensions dims;
std::string dimName = iName + ".dims";
if ( H5Aexists( iParent, dimName.c_str() ) )
{
ReadDimensions( iParent, dimName, dims );
}
else
{
dims.setRank(1);
dims[0] = hdim / iDataType.getExtent();
}
ABCA_ASSERT( dims.numPoints() > 0,
"Degenerate dims in Dataset read" );
// Create a buffer into which we shall read.
ret = AbcA::AllocateArraySample( iDataType, dims );
assert( ret->getData() );
// And... read into it.
herr_t status = H5Dread( dsetId, iNativeType,
H5S_ALL, H5S_ALL, H5P_DEFAULT,
const_cast<void*>( ret->getData() ) );
ABCA_ASSERT( status >= 0, "H5Dread() failed." );
}
else if ( dspaceClass == H5S_NULL )
{
Dimensions dims;
std::string dimName = iName + ".dims";
if ( H5Aexists( iParent, dimName.c_str() ) )
{
ReadDimensions( iParent, dimName, dims );
ABCA_ASSERT( dims.rank() > 0,
"Degenerate rank in Dataset read" );
// Num points should be zero here.
ABCA_ASSERT( dims.numPoints() == 0,
"Expecting zero points in dimensions" );
}
else
{
dims.setRank(1);
dims[0] = 0;
}
ret = AbcA::AllocateArraySample( iDataType, dims );
}
else
{
ABCA_THROW( "Unexpected scalar dataspace encountered." );
}
// Store if there is a cache.
if ( foundDigest && iCache )
{
AbcA::ReadArraySampleID stored = iCache->store( key, ret );
if ( stored )
{
return stored.getSample();
}
}
// Otherwise, just leave! ArraySamplePtr returned by AllocateArraySample
// already has fancy-dan deleter built in.
// I REALLY LOVE SMART PTRS.
return ret;
}
