//-*****************************************************************************
// Get the dimensions directly off of the dataspace on the dataset
// This isn't suitable for string and wstring
void
ReadDataSetDimensions( hid_t iParent,
const std::string &iName,
hsize_t iExtent,
Dimensions &oDims )
{
// 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 );
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 );
oDims.setRank(1);
oDims[0] = hdim / iExtent;
}
else
{
oDims.setRank(1);
oDims[0] = 0;
}
}
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();
}
int_f
nh5sget_simple_extent_type_c ( hid_t_f *space_id , int_f *classtype)
{
int ret_value = 0;
hid_t c_space_id;
H5S_class_t c_classtype;
c_space_id = *space_id;
c_classtype = H5Sget_simple_extent_type(c_space_id);
if ( c_classtype < 0 ) ret_value = -1;
*classtype = c_classtype;
/*
if (c_classtype == H5S_SCALAR) *classtype = H5S_SCALAR_F;
if (c_classtype == H5S_SIMPLE) *classtype = H5S_SIMPLE_F;
*/
return ret_value;
}
static herr_t
trav_attr(hid_t
#ifndef H5TRAV_PRINT_SPACE
UNUSED
#endif /* H5TRAV_PRINT_SPACE */
obj, const char *attr_name, const H5A_info_t UNUSED *ainfo, void *op_data)
{
char *buf;
buf = (char*)op_data;
if((strlen(buf)==1) && (*buf=='/'))
printf(" %-10s %s%s", "attribute", buf, attr_name);
else
printf(" %-10s %s/%s", "attribute", buf, attr_name);
#ifdef H5TRAV_PRINT_SPACE
if(trav_verbosity < 2) {
#endif
printf("\n");
#ifdef H5TRAV_PRINT_SPACE
}
else {
hid_t attr = -1;
hid_t space = -1;
hsize_t size[H5S_MAX_RANK];
int ndims;
int i;
H5S_class_t space_type;
if((attr = H5Aopen(obj, attr_name, H5P_DEFAULT))) {
space = H5Aget_space(attr);
/* Data space */
ndims = H5Sget_simple_extent_dims(space, size, NULL);
space_type = H5Sget_simple_extent_type(space);
switch(space_type) {
case H5S_SCALAR:
/* scalar dataspace */
printf(" scalar\n");
break;
case H5S_SIMPLE:
/* simple dataspace */
printf(" {");
for (i=0; i<ndims; i++) {
printf("%s" HSIZE_T_FORMAT, i?", ":"", size[i]);
}
printf("}\n");
break;
case H5S_NULL:
/* null dataspace */
printf(" null\n");
break;
default:
/* Unknown dataspace type */
printf(" unknown\n");
break;
} /* end switch */
H5Sclose(space);
H5Aclose(attr);
}
}
#endif
return(0);
}
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;
}
static int
find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid, size_t *maxlen)
{
hid_t datasetid = 0, spaceid = 0;
NC_VAR_INFO_T *var;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int d, dataset_ndims = 0;
int retval = NC_NOERR;
*maxlen = 0;
/* Find this var. */
for (var = grp->var; var; var = var->l.next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
/* If the var hasn't been created yet, its size is 0. */
if (!var->created)
{
*maxlen = 0;
}
else
{
/* Get the number of records in the dataset. */
if ((retval = nc4_open_var_grp2(grp, var->varid, &datasetid)))
BAIL(retval);
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
/* If it's a scalar dataset, it has length one. */
if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
{
*maxlen = (var->dimids && var->dimids[0] == dimid) ? 1 : 0;
}
else
{
/* Check to make sure ndims is right, then get the len of each
dim in the space. */
if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
if (dataset_ndims != var->ndims)
BAIL(NC_EHDFERR);
if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
h5dimlen, h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
LOG((5, "find_var_dim_max_length: varid %d len %d max: %d",
varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
for (d=0; d<dataset_ndims; d++) {
if (var->dimids[d] == dimid) {
*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
}
}
}
}
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (h5dimlen) free(h5dimlen);
if (h5dimlenmax) free(h5dimlenmax);
return retval;
}
//-*****************************************************************************
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;
}
