This one below generates the datasets with the dimensions posted, as well as the names(path); once the datasets are ready; we are scanning the root group for all datasets, keeping RANK 1 as outlined in my_callback(...) function. Shamelessly passed std::vector<std::string>* op_data acts along to skim off the dataset names of interest.
Then on it is straight forward: double IO loop pushes the data blocks of given size onto data accumulating all measurements we are interested.
The verification is to print out 3.14 barely missing PI day – Enjoy!
note: H5CPP RAII mechanism reduces code complexity, and increases readability, reliability… here is the HDF5 file, if I read your spec correctly: scope.h5 (20.0 KB)
hyperslab selection requires H5D_CHUNKED dataset layout.
/* Copyright (c) 2022 vargaconsulting, Toronto,ON Canada */
#define FMT_HEADER_ONLY
#include <armadillo>
#include <h5cpp/all>
#include <cstddef>
#include <fmt/core.h>
// our callback funciton
herr_t my_callback(hid_t group, const char* name, const H5L_info_t* info, void* op_data){
h5::ds_t ds{H5Dopen(group, name, H5P_DEFAULT)}; // H5CPP with CAPI
h5::sp_t file_space{H5Dget_space(ds)}; // H5CPP RAII
// we are not interested in other than rank 1 data (vector)
if( H5Sget_simple_extent_ndims(file_space) != 1) return 0;
//H5Dread(ds, mem_type, mem_space, file_space, h5::default_dxpl, payload.data());
using T = std::vector<std::string>;
T* names = static_cast<T*>(op_data);
names->push_back(name);
return 0;
}
//
// typedef herr_t (*H5L_iterate_t)(hid_t group, const char *name, const H5L_info_t *info, void *op_data);
int main(){
h5::fd_t fd = h5::create("scope.h5",H5F_ACC_TRUNC); // and a file
// BEGIN SETUP
size_t n=100000, m=502;
std::vector orientation {"horiz","trig","vert"};
std::vector type{"offset","scale"};
for (size_t ch=1; ch<=8; ch++){
// this one is your samples
h5::create<double>(fd, fmt::format("ch{}_samples", ch),
h5::current_dims{n,m}, h5::max_dims{n, H5S_UNLIMITED}, h5::chunk{1,512});
// and here are your datasets with fake data
for(auto o : orientation) for(auto t:type)
h5::create<double>(fd, fmt::format("ch{}_{}_{}", ch, o, t),
h5::current_dims{n}, h5::chunk{512}|h5::fill_value<double>(3.14));
}
// END SETUP
// SOLUTION
std::vector<std::vector<double>> data;
std::vector<std::string> index;
// H5CPP is designed to mix CAPI code with H5CPP templates:
h5::gr_t group_id{H5Gopen(fd, "/", 0)}; // becomes an H5CPP managed resource (RAII)
hsize_t idx =0;
H5Literate(group_id, H5_INDEX_NAME, H5_ITER_NATIVE, &idx, &my_callback, &index);
// we have all the names, check it out:
for(auto path: index)
data.push_back( // following reads in an std::vector<double> with size h5::count{..}
h5::read<std::vector<double>>(fd, path, h5::count{123}));
// verification, we should see `3.14` since we just passed PI day!
for(auto i:data) for( auto j:i)
std::cout << j <<" ";
std::cout <<std::endl;
}
