1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
|
#include <hdf/BufferedHDF2DArray.hpp>
/*
*
* Implementation of a 2-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 somebody when reading.
*
* Currently no support exists for reading non-contiguous blocks of data, and
* the main intended use is to read in increments of rows.
int main(int argc, char* argv[]) {
if (argc < 1) {
std::cout << "usage: testHDFReading hdfFile" << std::endl;
exit(EXIT_SUCCESS);
}
std::string hdfFileName = argv[1];
H5File hdfFile;
hdfFile.openFile(hdfFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
BufferedHDF2DArray<uint16_t> xyArray;
xyArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/HoleXY");
DSLength curX = 0;
xyArray.Read(curX, curX + 1, 0, 2, holeXY);
or, to read a row:
xyArray.Read(curX, curX+1, holeXY);
*/
DSLength GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName)
{
HDFData tmpDataset;
tmpDataset.InitializeDataset(parentGroup, datasetName);
H5::DataSpace dataspace = tmpDataset.dataset.getSpace();
DSLength nDims = dataspace.getSimpleExtentNdims();
dataspace.close();
tmpDataset.dataset.close();
return nDims;
}
#define DEFINE_TYPED_WRITE_ROW(T, Pred) \
template <> \
void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, \
const H5::DataSpace &fileSpace) \
{ \
dataset.write(data, Pred, memorySpace, fileSpace); \
}
DEFINE_TYPED_WRITE_ROW(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_WRITE_ROW(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_WRITE_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_WRITE_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_WRITE_ROW(int16_t, H5::PredType::NATIVE_INT16)
DEFINE_TYPED_WRITE_ROW(float, H5::PredType::NATIVE_FLOAT)
#define DEFINE_TYPED_READ_ROW(T, Pred) \
template <> \
void BufferedHDF2DArray<T>::Read(DSLength startX, DSLength endX, DSLength startY, \
DSLength endY, T *dest) \
{ \
Read(startX, endX, startY, endY, Pred, dest); \
}
DEFINE_TYPED_READ_ROW(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_READ_ROW(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_READ_ROW(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_READ_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_READ_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_READ_ROW(int16_t, H5::PredType::NATIVE_INT16)
DEFINE_TYPED_READ_ROW(float, H5::PredType::NATIVE_FLOAT)
#define DEFINE_TYPED_CREATE_ROW(T, Pred) \
template <> \
void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace &fileSpace, \
H5::DSetCreatPropList &cparms) \
{ \
dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \
}
DEFINE_TYPED_CREATE_ROW(int, H5::PredType::NATIVE_INT)
DEFINE_TYPED_CREATE_ROW(unsigned int, H5::PredType::NATIVE_UINT)
DEFINE_TYPED_CREATE_ROW(char, H5::PredType::NATIVE_INT8)
DEFINE_TYPED_CREATE_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
DEFINE_TYPED_CREATE_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
DEFINE_TYPED_CREATE_ROW(int16_t, H5::PredType::NATIVE_INT16)
DEFINE_TYPED_CREATE_ROW(float, H5::PredType::NATIVE_FLOAT)
|
