inline typename boost::enable_if<boost::is_same<T, std::string>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
}
catch (H5::AttributeIException const&) {
throw;
}
if (!has_scalar_space(attr)) {
throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
}
H5::DataType tid = attr.getDataType();
std::string value;
if (!tid.isVariableStr()) {
// read fixed-size string, allocate space in advance and let the HDF5
// library take care about NULLTERM and NULLPAD strings
value.resize(tid.getSize(), std::string::value_type());
attr.read(tid, &*value.begin());
}
else {
// read variable-length string, memory will be allocated by HDF5 C
// library and must be freed by us
char *c_str;
if (H5Aread(attr.getId(), tid.getId(), &c_str) < 0) {
throw H5::AttributeIException("Attribute::read", "H5Aread failed");
}
value = c_str; // copy '\0'-terminated string
free(c_str);
}
return value;
}
std::string hdfutil::ReadString (const H5::CommonFG& group, const std::string & dsname) {
const H5::DataSet & dataset = group.openDataSet(dsname);
try {
H5::DataType type = dataset.getDataType();
std::string retval;
retval.resize(type.getSize());
dataset.read(&retval[0], dataset.getStrType());
return retval;
} catch (H5::Exception e) {
std::string error = "Unable to ReadString.";// + dsname;
throw std::runtime_error(error.c_str());
}
}
DataSet DataSet::create(const H5::CommonFG &parent,
const std::string &name,
const H5::DataType &fileType,
const NDSize &size,
const NDSize &maxsize,
const NDSize &chunks,
bool max_size_unlimited,
bool guess_chunks)
{
H5::DataSpace space;
if (size) {
if (maxsize) {
space = DataSpace::create(size, maxsize);
} else {
space = DataSpace::create(size, max_size_unlimited);
}
}
H5::DSetCreatPropList plcreate = H5::DSetCreatPropList::DEFAULT;
if (chunks) {
int rank = static_cast<int>(chunks.size());
plcreate.setChunk(rank, chunks.data());
} else if (guess_chunks) {
NDSize guessedChunks = DataSet::guessChunking(size, fileType.getSize());
plcreate.setChunk(static_cast<int>(guessedChunks.size()), guessedChunks.data());
}
H5::DataSet dset = parent.createDataSet(name, fileType, space);
return DataSet(dset);
}
inline typename boost::enable_if<boost::mpl::and_<
is_vector<T>
, boost::is_same<typename T::value_type, std::string>
>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
}
catch (H5::AttributeIException const&) {
throw;
}
H5::DataSpace ds(attr.getSpace());
if (!ds.isSimple()) {
throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
}
size_t size = ds.getSimpleExtentNpoints();
H5::DataType tid = attr.getDataType();
if (tid.isVariableStr()) {
throw error("reading non-scalar attribute of variable-length strings not supported");
}
size_t str_len = tid.getSize();
// read to contiguous buffer and copy to std::vector
std::vector<char> buffer(str_len * size);
attr.read(tid, &*buffer.begin());
T value;
value.reserve(size);
char const* s = buffer.data();
for (size_t i = 0; i < size; ++i, s += str_len) {
size_t len = strnlen(s, str_len); // strings of str_len size are not '\0'-terminated
value.push_back(std::string(s, len)); // copy len bytes from buffer
}
return value;
}
/**
* @param variable
* @param vattribute
* @return
*/
Attribute HDF5FileReader::getVariableAttribute(const std::string& variable, const std::string& vattribute)
{
//first, check the vAttributes map
// std::cout<<"Checking variable attributes map\n";
boost::unordered_map<std::string, boost::unordered_map< std::string, Attribute> >::iterator iter =
vAttributes.find(variable);
if (iter != vAttributes.end())
{
boost::unordered_map< std::string, Attribute>::iterator iter2 = vAttributes[variable].find(vattribute);
if (iter2 != vAttributes[variable].end())
{
return (*iter2).second;
}
}
// std::cout<<"Attribute not loaded, opening Variables group\n";
H5::Group group = this->current_file->openGroup("Variables");
// std::cout<<"Group opened. Creating memory for H5::DataSet\n";
H5::DataSet * dataset = new H5::DataSet(group.openDataSet(variable));
// std::cout<<"creating h5attribute for variable\n";
H5::Attribute h5attribute = dataset->openAttribute(vattribute); //changed from group.openAttribute(vattribute);
// std::cout<<"attribute opened, obtaining data type\n";
H5::DataType dataType = h5attribute.getDataType();
Attribute attribute;
// std::cerr<<"Retrieving Variable attribute info:"<<std::endl;
if (dataType.getClass() == H5T_STRING)
{
// std::cout<<"String type variable attribute\n";
std::string attributeValue = "NULL";
h5attribute.read(dataType, &attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "attributeBuffer: " << attributeBuffer << endl;
attribute.setAttributeValue(attributeValue);
//return attribute;
} else if (dataType.getClass() == H5T_INTEGER) //shouldn't this be H5T_INT or something?
{
// std::cout<<"Int type variable attribute\n";
//int attributeValue = 0.f;
int attributeBuffer;// = new int[1];
h5attribute.read(dataType, &attributeBuffer);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
attribute.setAttributeValue(attributeBuffer);
//return attribute;
} else if (dataType.getClass() == H5T_FLOAT)//CDF_FLOAT
{
// std::cout<<"Float type variable attribute\n";
//int attributeValue = 0.f;
float attributeValue;// = new int[1];
h5attribute.read(dataType, &attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
attribute.setAttributeValue(attributeValue);
//return attribute;
}
//cout << "added: " << i << " name: " << attribute.getAttributeName() << endl;
//std::cout << "Attribute: " << attribute.toString() << std::endl;
(vAttributes[variable])[vattribute] = attribute;
return attribute;
}
/**
* @param attribute
* @return
*/
Attribute HDF5FileReader::getGlobalAttribute(const std::string& attribute)
{
//first, check if the attribute has already been requested. If so, return stored value
boost::unordered_map<std::string, Attribute>::iterator iter = gAttributes.find(attribute);
if (iter != gAttributes.end())
return (*iter).second;
// std::cout << "after search in getGlobalAttribute(const std::string& attribute)" << std::endl;
// std::cout << "attribute: " << attribute << std::endl;
H5::Group group = this->current_file->openGroup("/");
H5::Attribute h5attribute = group.openAttribute(attribute);
long attrNum = h5attribute.getId();
H5::DataType dataType = h5attribute.getDataType();
// std::cout << "attrNum after attribute: " << attrNum << std::endl;
Attribute current_attribute;
if (attrNum < 0)
{
std::cout << "attrNum: " << attrNum << " returned for " << attribute << std::endl;
}
else
{
// std::cout << "attribute: " << attribute << " attribute number: " << attrNum << std::endl;
// std::cout << "attempting to get attribute without using attribute number\n";
if (dataType.getClass() == H5T_STRING)
{
std::string attributeValue = "NULL";
h5attribute.read(dataType, attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
current_attribute.setAttributeName(attributeName);
//std::cout << "name: '" << attributeName << "' string attributeBuffer: '" << attributeValue << "'"<< std::endl;
current_attribute.setAttributeValue(attributeValue);
gAttributeByID[(int)attrNum] = current_attribute;
gAttributes[current_attribute.getAttributeName()] = current_attribute;
//return attribute;
} else if (dataType.getClass() == H5T_INTEGER)
{
//int attributeValue = 0.f;
int attributeBuffer;// = new int[1];
h5attribute.read(dataType, &attributeBuffer);
std::string attributeName = "";
attributeName = h5attribute.getName();
current_attribute.setAttributeName(attributeName);
//std::cout << "int attributeBuffer: '" << attributeBuffer << "'"<< std::endl;
current_attribute.setAttributeValue(attributeBuffer);
gAttributeByID[(int)attrNum] = current_attribute;
gAttributes[current_attribute.getAttributeName()] = current_attribute;
//return attribute;
} else if (dataType.getClass() == H5T_FLOAT)//CDF_FLOAT
{
//int attributeValue = 0.f;
float attributeValue;// = new int[1];
h5attribute.read(dataType, &attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
current_attribute.setAttributeName(attributeName);
//std::cout << "float attributeBuffer: '" << attributeValue << "'"<< std::endl;
current_attribute.setAttributeValue(attributeValue);
gAttributeByID[(int)attrNum] = current_attribute;
gAttributes[current_attribute.getAttributeName()] = current_attribute;
//return attribute;
}
}//gAttributes[attribute] = current_attribute;
return current_attribute;
// return Attribute();
}
/**
* @param i The attribute number
* @return
*/
Attribute HDF5FileReader::getGlobalAttribute(long i)
{
std::cerr << "entered " << BOOST_CURRENT_FUNCTION << " i = " << (int)i << std::endl;
H5::Group group = this->current_file->openGroup("/");
std::cout<< "group assigned\n";
H5::Attribute h5attribute = group.openAttribute((unsigned int)i);
std::cout<< "attribute opened\n";
H5::DataType dataType = h5attribute.getDataType();
std::cout<< "dataType retrieved\n";
Attribute attribute;
std::cout << "checking dataType"<<std::endl;
if (dataType.getClass() == H5T_STRING)
{
std::string attributeValue = "NULL";
h5attribute.read(dataType, attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "name: '" << attributeName << "' string attributeBuffer: '" << attributeValue << "'"<< std::endl;
attribute.setAttributeValue(attributeValue);
gAttributeByID[i] = attribute;
gAttributes[attribute.getAttributeName()] = attribute;
//return attribute;
} else if (dataType.getClass() == H5T_INTEGER)
{
//int attributeValue = 0.f;
int attributeBuffer;// = new int[1];
h5attribute.read(dataType, &attributeBuffer);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "int attributeBuffer: '" << attributeBuffer << "'"<< std::endl;
attribute.setAttributeValue(attributeBuffer);
gAttributeByID[i] = attribute;
gAttributes[attribute.getAttributeName()] = attribute;
//return attribute;
} else if (dataType.getClass() == H5T_FLOAT)//CDF_FLOAT
{
//int attributeValue = 0.f;
float attributeValue;// = new int[1];
h5attribute.read(dataType, &attributeValue);
std::string attributeName = "";
attributeName = h5attribute.getName();
attribute.setAttributeName(attributeName);
//std::cout << "float attributeBuffer: '" << attributeValue << "'"<< std::endl;
attribute.setAttributeValue(attributeValue);
gAttributeByID[i] = attribute;
gAttributes[attribute.getAttributeName()] = attribute;
//return attribute;
}
//std::cout << "added: " << i << " name: '" << attribute.getAttributeName() << "'" << endl;
//std::cout << "Attribute: " << attribute.toString() << std::endl;
return attribute;
}
void ossim_hdf5::printAttribute( const H5::Attribute& attr,
const std::string& prefix,
std::ostream& out )
{
std::string name = attr.getName();
H5::DataType type = attr.getDataType();
H5T_class_t typeClass = attr.getTypeClass();
size_t size = type.getSize();
std::string value; // Initialized below.
if ( ( typeClass == H5T_INTEGER ) || ( typeClass == H5T_FLOAT ) )
{
H5::IntType intType = attr.getIntType();
ossimScalarType scalar = ossim_hdf5::getScalarType( intType.getId() );
ossimByteOrder order = ossim_hdf5::getByteOrder( &attr );
ossimEndian* endian = 0;
if ( ( size > 1 ) && ( order != ossim::byteOrder() ) )
{
endian = new ossimEndian(); // If set used as flag to byte swap.
}
if ( typeClass == H5T_INTEGER )
{
switch ( scalar )
{
case OSSIM_UINT8:
{
if ( size == 1 )
{
ossim_uint8 i;
attr.read( type, (void*)&i );
value = ossimString::toString( ossim_int32(i) ).string();
}
break;
}
case OSSIM_SINT8:
{
if ( size == 1 )
{
ossim_sint8 i;
attr.read( type, (void*)&i );
value = ossimString::toString( ossim_int32(i) ).string();
}
break;
}
case OSSIM_UINT16:
{
if ( size == 2 )
{
ossim_uint16 i;
attr.read( type, (void*)&i );
if ( endian )
{
endian->swap( i );
}
value = ossimString::toString( i ).string();
}
break;
}
case OSSIM_SINT16:
{
if ( size == 2 )
{
ossim_sint16 i;
attr.read( type, (void*)&i );
if ( endian )
{
endian->swap( i );
}
value = ossimString::toString( i ).string();
}
break;
}
case OSSIM_UINT32:
{
if ( size == 4 )
{
ossim_uint32 i;
attr.read( type, (void*)&i );
if ( endian )
{
endian->swap( i );
}
value = ossimString::toString( i ).string();
}
break;
}
case OSSIM_SINT32:
{
if ( size == 4 )
{
ossim_sint32 i;
attr.read( type, (void*)&i );
if ( endian )
{
endian->swap( i );
}
value = ossimString::toString( i ).string();
}
break;
}
case OSSIM_UINT64:
{
if ( size == 8 )
{
ossim_uint64 i;
attr.read( type, (void*)&i );
if ( endian )
{
endian->swap( i );
}
value = ossimString::toString( i ).string();
}
break;
}
case OSSIM_SINT64:
{
if ( size == 8 )
{
ossim_sint32 i;
attr.read( type, (void*)&i );
if ( endian )
{
endian->swap( i );
}
value = ossimString::toString( i ).string();
}
break;
}
default:
break;
}
}
else if ( typeClass == H5T_FLOAT )
{
if ( scalar == OSSIM_FLOAT32 )
{
if ( size == 4 )
{
ossim_float32 f;
attr.read( type, (void*)&f );
if ( endian )
{
endian->swap( f );
}
value = ossimString::toString( f ).string();
}
}
if ( scalar == OSSIM_FLOAT64 )
{
if ( size == 8 )
{
ossim_float64 f;
attr.read( type, (void*)&f );
if ( endian )
{
endian->swap( f );
}
value = ossimString::toString( f ).string();
}
}
}
if ( endian )
{
delete endian;
endian = 0;
}
}
else if ( typeClass == H5T_STRING )
{
attr.read( type, value );
}
else
{
ossimNotify(ossimNotifyLevel_DEBUG)
<< "ossimH5Util::printAttribute WARN: Unhandled type class: " << typeClass
<< std::endl;
}
out << prefix << "." << name << ": " << value << std::endl;
} // End: ossim_hdf5::printAttribute
void ossimH5ImageDataset::getTileBuf(void* buffer, const ossimIrect& rect, ossim_uint32 band)
{
static const char MODULE[] = "ossimH5ImageDataset::getTileBuf";
if ( m_dataset )
{
try
{
// Shift rectangle by the sub image offse (if any) from the m_validRect.
ossimIrect irect = rect + m_validRect.ul();
//--
// Turn off the auto-printing when failure occurs so that we can
// handle the errors appropriately
//---
// H5::Exception::dontPrint();
// NOTE: rank == array dimensions in hdf5 documentation lingo.
// Get dataspace of the dataset.
H5::DataSpace imageDataSpace = m_dataset->getSpace();
// Number of dimensions of the input dataspace.:
const ossim_int32 IN_DIM_COUNT = imageDataSpace.getSimpleExtentNdims();
// Native type:
H5::DataType dataType = m_dataset->getDataType();
std::vector<hsize_t> inputCount(IN_DIM_COUNT);
std::vector<hsize_t> inputOffset(IN_DIM_COUNT);
if ( IN_DIM_COUNT == 2 )
{
inputOffset[0] = irect.ul().y;
inputOffset[1] = irect.ul().x;
inputCount[0] = irect.height();
inputCount[1] = irect.width();
}
else
{
inputOffset[0] = band;
inputOffset[1] = irect.ul().y;
inputOffset[2] = irect.ul().x;
inputCount[0] = 1;
inputCount[1] = irect.height();
inputCount[2] = irect.width();
}
// Define hyperslab in the dataset; implicitly giving strike strike and block NULL.
imageDataSpace.selectHyperslab( H5S_SELECT_SET,
&inputCount.front(),
&inputOffset.front() );
// Output dataspace dimensions.
const ossim_int32 OUT_DIM_COUNT = 3;
std::vector<hsize_t> outputCount(OUT_DIM_COUNT);
outputCount[0] = 1; // single band
outputCount[1] = irect.height(); // lines
outputCount[2] = irect.width(); // samples
// Output dataspace offset.
std::vector<hsize_t> outputOffset(OUT_DIM_COUNT);
outputOffset[0] = 0;
outputOffset[1] = 0;
outputOffset[2] = 0;
// Output dataspace.
H5::DataSpace bufferDataSpace( OUT_DIM_COUNT, &outputCount.front());
bufferDataSpace.selectHyperslab( H5S_SELECT_SET,
&outputCount.front(),
&outputOffset.front() );
// Read data from file into the buffer.
m_dataset->read( buffer, dataType, bufferDataSpace, imageDataSpace );
if ( m_endian )
{
// If the m_endian pointer is initialized(not zero) swap the bytes.
m_endian->swap( m_scalar, buffer, irect.area() );
}
// Cleanup:
bufferDataSpace.close();
dataType.close();
imageDataSpace.close();
// memSpace.close();
// dataType.close();
// dataSpace.close();
}
catch( const H5::FileIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::FileIException!" << std::endl;
error.printError();
}
// catch failure caused by the DataSet operations
catch( const H5::DataSetIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::DataSetIException!" << std::endl;
error.printError();
}
// catch failure caused by the DataSpace operations
catch( const H5::DataSpaceIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::DataSpaceIException!" << std::endl;
error.printError();
}
// catch failure caused by the DataSpace operations
catch( const H5::DataTypeIException& error )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught H5::DataTypeIException!" << std::endl;
error.printError();
}
catch( ... )
{
ossimNotify(ossimNotifyLevel_WARN)
<< MODULE << " caught unknown exception !" << std::endl;
}
} // Matches: if ( m_dataset )
} // End: ossimH5ImageDataset::getTileBuf
