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hdf5.cpp
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hdf5.cpp
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#include "stdafx.h"
#include "hdf5.hpp"
#include "util.hpp"
namespace {
void _read_header(H5::DataSet & ds, watplot::HDF5::Header & header) {
using namespace H5;
using namespace watplot;
// parse all header attributes
for (int i = 1; i < ds.getNumAttrs(); ++i) {
Attribute attr = ds.openAttribute(i);
const std::string & kwd = attr.getName();
char dtype = consts::HEADER_KEYWORD_TYPES.at(kwd);
IntType inttype = attr.getIntType();
FloatType flttype = attr.getFloatType();
StrType strtype = attr.getStrType();
H5std_string order_string;
H5T_order_t order = inttype.getOrder(order_string);
switch (dtype) {
case 'l':
{
int data;
attr.read(inttype, &data);
if (kwd == "telescope_id") header.telescope_id = data;
else if (kwd == "machine_id") header.machine_id = data;
else if (kwd == "data_type") header.data_type = data;
else if (kwd == "barycentric") header.barycentric = data != 0;
else if (kwd == "pulsarcentric") header.pulsarcentric = data != 0;
else if (kwd == "nbits") header.nbits = data;
else if (kwd == "nsamples") header.nsamples = data;
else if (kwd == "nchans") header.nchans = data;
else if (kwd == "nifs") header.nifs = data;
else if (kwd == "nbeams") header.nbeams = data;
else header.ibeam = data; // ibeam
}
break;
case 'd':
{
double data;
attr.read(flttype, &data);
if (kwd == "az_start") header.az_start = data;
else if (kwd == "za_start") header.za_start = data;
else if (kwd == "tstart") header.tstart = data;
else if (kwd == "tsamp") header.tsamp = data;
else if (kwd == "fch1") header.fch1 = data;
else if (kwd == "foff") header.foff = data;
else if (kwd == "refdm") header.refdm = data;
else header.period = data; // period
}
break;
case 's':
{
std::string data;
attr.read(flttype, data);
if (kwd == "rawdatafile") header.rawdatafile = data;
else header.source_name = data; // source_name
}
break;
case 'a':
{
double raw, data;
attr.read(flttype, (char*)& raw);
data = util::double_to_angle(raw);
if (kwd == "src_raj") header.src_raj = data;
else header.src_dej = data; // src_dej
}
break;
default:
std::cerr << "Unsupported header keyword: " << kwd << "\n";
std::exit(2);
}
}
}
}
namespace watplot {
const std::string HDF5::FILE_FORMAT_NAME = "HDF5";
const std::string HDF5::DATASET_SUBSET_NAME = "data";
void HDF5::_load(const std::string & path) {
H5::H5File file = H5::H5File(path, H5F_ACC_RDONLY);
H5::DataSet dataset = file.openDataSet(DATASET_SUBSET_NAME);
data_size_bytes = dataset.getStorageSize();
_read_header(dataset, header);
H5::DataSpace dataspace = dataset.getSpace();
hsize_t dims_out[3];
dataspace.getSimpleExtentDims(dims_out, NULL);
nints = dims_out[0];
if (header.nbits != 8 && header.nbits != 16 && header.nbits != 32 && header.nbits != 64) {
std::cerr << "Error: Unsupported data width: " << header.nbits << " (only 8, 16, 32 bit data supported)\n";
std::exit(4);
}
}
void HDF5::_view(const cv::Rect2d & rect, Eigen::MatrixXd & out, int64_t t_lo, int64_t t_hi, int64_t t_step,
int64_t f_lo, int64_t f_hi, int64_t f_step) const {
// load the data int64_to bins
H5::H5File file = H5::H5File(file_path, H5F_ACC_RDONLY);
H5::DataSet dataset = file.openDataSet(DATASET_SUBSET_NAME);
int64_t out_hi = (f_hi - f_lo) / f_step;
//int64_t out_wid = (t_hi - t_lo) / t_step;
int64_t maxf = min(f_hi, header.nchans), maxt = min(t_hi, nints);
int64_t nbytes = (header.nbits / 8);
H5::DataSpace dataspace = dataset.getSpace();
hsize_t offset[3] = { hsize_t(t_lo), 0, hsize_t(f_lo) };
hsize_t stride[3] = { hsize_t(t_step), 1, hsize_t(f_step) };
hsize_t count[3] = { hsize_t(maxt - t_lo) / stride[0], 1, hsize_t(maxf - f_lo) / stride[2] };
dataspace.selectHyperslab(H5S_SELECT_SET, count, offset, stride);
hsize_t mem_count[2] = { count[0], count[2] };
H5::DataSpace memspace(2, mem_count);
std::cerr << "HDF5-view: Reading data...\n";
if (nbytes == 4) {
Eigen::MatrixXf buf(count[2], count[0]);
dataset.read(buf.data(), H5::PredType::NATIVE_FLOAT, memspace, dataspace);
std::cerr << "HDF5-view: Copying from buffer...\n";
for (int64_t i = out.cols() - 2; i > 0; --i) {
for (int64_t j = out.rows() - 2; j > 0; --j) {
out(j, i) = static_cast<double>(buf(j - 1, i - 1));
}
}
}
else if (nbytes == 8) {
Eigen::MatrixXd buf(count[2], count[0]);
dataset.read(buf.data(), H5::PredType::NATIVE_DOUBLE, memspace, dataspace);
std::cerr << "HDF5-view: Copying from buffer...\n";
for (int64_t i = out.cols() - 2; i > 0; --i) {
for (int64_t j = out.rows() - 2; j > 0; --j) {
out(j, i) = buf(j - 1, i - 1);
}
}
}
else if (nbytes == 2) {
Eigen::Matrix<uint16_t, Eigen::Dynamic, 1> buf(count[2], count[0]);
dataset.read(buf.data(), H5::PredType::NATIVE_UINT16, memspace, dataspace);
std::cerr << "HDF5-view: Copying from buffer...\n";
for (int64_t i = out.cols() - 2; i > 0; --i) {
for (int64_t j = out.rows() - 2; j > 0; --j) {
out(j, i) = static_cast<double>(buf(j - 1, i - 1));
}
}
}
else if (nbytes == 1) {
Eigen::Matrix<uint16_t, Eigen::Dynamic, 1> buf(count[2], count[0]);
dataset.read(buf.data(), H5::PredType::NATIVE_UINT8, memspace, dataspace);
std::cerr << "HDF5-view: Copying from buffer...\n";
for (int64_t i = out.cols() - 2; i > 0; --i) {
for (int64_t j = out.rows() - 2; j > 0; --j) {
out(j, i) = static_cast<double>(buf(j - 1, i - 1));
}
}
}
out *= static_cast<double>(t_step * f_step);
out.row(0).setZero();
out.col(0).setZero();
out.row(out.rows() - 1).setZero();
out.col(out.cols() - 1).setZero();
std::cerr << "HDF5-view: 100% loaded, processing data in memory...\n";
}
}