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#include <hdf/HDFAtom.hpp>
template <>
void HDFAtom<std::string>::Create(H5::H5Location &object, const std::string &atomName)
{
H5::StrType strType(0, H5T_VARIABLE);
hsize_t defaultDims[] = {1};
H5::DataSpace defaultDataSpace(1, defaultDims);
attribute = object.createAttribute(atomName.c_str(), strType, H5::DataSpace(H5S_SCALAR));
}
#define DEFINE_TYPED_CREATE_ATOM(T, predtype) \
template <> \
void HDFAtom<T>::TypedCreate(H5::H5Location &object, const std::string &atomName, \
H5::DataSpace &defaultDataSpace) \
{ \
attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace); \
}
DEFINE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT)
DEFINE_TYPED_CREATE_ATOM(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE)
template <>
void HDFAtom<std::vector<int> >::Write(const std::vector<int> vect)
{
hsize_t length = vect.size();
H5::DataType baseType = H5::PredType::NATIVE_INT;
H5::ArrayType arrayDataType(baseType, 1, &length);
attribute.write(arrayDataType, &((vect)[0]));
}
template <>
void HDFAtom<std::string>::Write(std::string value)
{
// H5::StrType strType(0, value.size());
H5::StrType strType(0, H5T_VARIABLE);
attribute.write(strType, std::string(value.c_str()));
}
template <>
void HDFAtom<uint64_t>::Write(uint64_t value)
{
attribute.write(H5::PredType::STD_I64LE, &value);
}
template <>
void HDFAtom<int>::Write(int value)
{
attribute.write(H5::PredType::NATIVE_INT, &value);
}
template <>
void HDFAtom<unsigned int>::Write(unsigned int value)
{
attribute.write(H5::PredType::NATIVE_INT, &value);
}
template <>
void HDFAtom<unsigned char>::Write(unsigned char value)
{
attribute.write(H5::PredType::NATIVE_UINT8, &value);
}
template <>
void HDFAtom<uint16_t>::Write(uint16_t value)
{
attribute.write(H5::PredType::NATIVE_UINT16, &value);
}
template <>
void HDFAtom<char>::Write(char value)
{
attribute.write(H5::PredType::NATIVE_INT8, &value);
}
template <>
void HDFAtom<float>::Write(float value)
{
attribute.write(H5::PredType::NATIVE_FLOAT, &value);
}
template <>
void HDFAtom<std::string>::Read(std::string &value)
{
/*
* Read in a std::string that has been stored either as an array or a
* variable length std::string. To decide which, query the
* isVariableStr() option.
*/
H5::StrType stringType = attribute.getStrType();
bool stringIsVariableLength = stringType.isVariableStr();
if (stringIsVariableLength)
attribute.read(stringType, value);
else {
hsize_t stsize = attribute.getStorageSize();
value.resize(stsize);
attribute.read(stringType, &value[0]);
if (stsize > 0 and value[stsize - 1] == '\0') {
value.resize(stsize - 1);
}
}
}
template <>
void HDFAtom<int>::Read(int &value)
{
H5::DataType intType(H5::PredType::NATIVE_INT);
attribute.read(intType, &value);
}
template <>
void HDFAtom<uint16_t>::Read(uint16_t &value)
{
H5::DataType intType(H5::PredType::NATIVE_UINT16);
attribute.read(intType, &value);
}
template <>
void HDFAtom<uint64_t>::Read(uint64_t &value)
{
H5::DataType intType(H5::PredType::STD_I64LE);
attribute.read(intType, &value);
}
template <>
void HDFAtom<unsigned int>::Read(unsigned int &value)
{
H5::DataType uintType(H5::PredType::NATIVE_UINT);
attribute.read(uintType, &value);
}
template <>
void HDFAtom<float>::Read(float &value)
{
H5::DataType type(H5::PredType::NATIVE_FLOAT);
attribute.read(type, &value);
}
template <>
void HDFAtom<std::vector<std::string> >::Read(std::vector<std::string> &values)
{
std::string value;
/*
* This attribute is an array of std::strings. They are read in by
* storing pointers to std::strings in memory controlled by HDF. To read
* the std::strings, read the pointers into a temporary array, then copy
* those std::strings to the values array. This way when the values array
* is destroyed, it will not try and get rid of space that is under
* HDF control.
*/
H5::DataSpace attributeSpace = attribute.getSpace();
hsize_t nPoints;
nPoints = attributeSpace.getSelectNpoints();
H5::DataType attrType = attribute.getDataType(); // necessary for attr.read()
// Declare and initialize std::vector of pointers to std::string attribute list.
std::vector<char *> ptrsToHDFControlledMemory;
ptrsToHDFControlledMemory.resize(nPoints);
// Copy the pointers.
attribute.read(attrType, &ptrsToHDFControlledMemory[0]);
// Copy the std::strings into memory the main program has control over.
unsigned int i;
for (i = 0; i < ptrsToHDFControlledMemory.size(); i++) {
values.push_back(ptrsToHDFControlledMemory[i]);
free(ptrsToHDFControlledMemory[i]);
}
}
// Explict instantiate classes
template class HDFAtom<int>;
template class HDFAtom<unsigned int>;
template class HDFAtom<char>;
template class HDFAtom<unsigned char>;
template class HDFAtom<uint64_t>;
template class HDFAtom<float>;
template class HDFAtom<std::string>;
template class HDFAtom<std::vector<int> >;
template class HDFAtom<std::vector<unsigned int> >;
template class HDFAtom<std::vector<std::string> >;
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