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#include <hdf/BufferedHDFArray.hpp>
/*
*
* Implementation of a 1-D array for IO from an HDF array.
* This is templated, but specialized for a few data types, so that
* the HDF data types do not need to be specified by anybody.
*
* Two examples of the usage of this class follow:
*
* HDFArray<int> nElemArray;
* nElemArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/NumEvent");
* nElemArray.Read(i, i+1, &nElem);
*
* HDFArray<unsigned char> qualArray;
* qualArray.Initialize(hdfFile, "PulseData/BaseCalls/QualityValue");
* qualArray.Read(cur, cur + nElem, qual);
*
*/
//
// Type specializations for some standard types. Use the macro for
// vanilla specializations (that only require the HDF type ID to be
// specified).
//
#define DEFINE_TYPED_READ_ARRAY(T, Pred) \
template <> \
void BufferedHDFArray<T>::Read(DSLength start, DSLength end, T *dest) \
{ \
Read(start, end, Pred, dest); \
}
DEFINE_TYPED_READ_ARRAY(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_READ_ARRAY(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_READ_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_READ_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_READ_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_READ_ARRAY(float, H5::PredType::NATIVE_FLOAT)
DEFINE_TYPED_READ_ARRAY(char *, H5::PredType::C_S1)
#define DEFINE_TYPED_READ_DATASET(T, Pred) \
template <> \
void BufferedHDFArray<T>::ReadDataset(std::vector<T> &dest) \
{ \
dest.resize(arrayLength); \
Read(0, arrayLength, Pred, &dest[0]); \
}
DEFINE_TYPED_READ_DATASET(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_READ_DATASET(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_READ_DATASET(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_READ_DATASET(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_READ_DATASET(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_READ_DATASET(float, H5::PredType::NATIVE_FLOAT)
DEFINE_TYPED_READ_DATASET(char *, H5::PredType::C_S1)
#define DEFINE_TYPED_CREATE_ARRAY(T, Pred) \
template <> \
void BufferedHDFArray<T>::TypedCreate(H5::DataSpace &fileSpace, H5::DSetCreatPropList &cparms) \
{ \
T zero; \
zero = 0; \
cparms.setFillValue(Pred, &zero); \
dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \
}
DEFINE_TYPED_CREATE_ARRAY(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_CREATE_ARRAY(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_CREATE_ARRAY(char *, H5::StrType(0, H5T_VARIABLE))
DEFINE_TYPED_CREATE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_CREATE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_CREATE_ARRAY(float, H5::PredType::NATIVE_FLOAT)
DEFINE_TYPED_CREATE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
template <>
void BufferedHDFArray<std::string>::TypedCreate(H5::DataSpace &space, H5::DSetCreatPropList &cparms)
{
H5::StrType varStrType(0, H5T_VARIABLE);
dataset = container->createDataSet(datasetName.c_str(), varStrType, space, cparms);
}
#define DEFINE_TYPED_WRITE_ARRAY(T, Pred) \
template <> \
void BufferedHDFArray<T>::TypedWrite(const T *data, const H5::DataSpace &memorySpace, \
const H5::DataSpace &fileSpace) \
{ \
dataset.write(data, Pred, memorySpace, fileSpace); \
}
DEFINE_TYPED_WRITE_ARRAY(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_WRITE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_WRITE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_WRITE_ARRAY(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_WRITE_ARRAY(float, H5::PredType::NATIVE_FLOAT)
DEFINE_TYPED_WRITE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_WRITE_ARRAY(char *, H5::StrType(0, H5T_VARIABLE))
DEFINE_TYPED_WRITE_ARRAY(std::string, H5::StrType(0, H5T_VARIABLE))
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