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@dmcdougall
Forked from simleb/test.cpp
Created September 29, 2013 20:45
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#include <iostream>
#include <hdf5.h>
// Constants
const char saveFilePath[] = "test.h5";
const hsize_t ndims = 2;
const hsize_t ncols = 3;
int main()
{
// Create a hdf5 file
hid_t file = H5Fcreate(saveFilePath, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
std::cout << "- File created" << std::endl;
// Create a 2D dataspace
// The size of the first dimension is unlimited (initially 0)
// The size of the second dimension is fixed
hsize_t dims[ndims] = {0, ncols};
hsize_t max_dims[ndims] = {H5S_UNLIMITED, ncols};
hid_t file_space = H5Screate_simple(ndims, dims, max_dims);
std::cout << "- Dataspace created" << std::endl;
// Create a dataset creation property list
// The layout of the dataset have to be chunked when using unlimited dimensions
hid_t plist = H5Pcreate(H5P_DATASET_CREATE);
H5Pset_layout(plist, H5D_CHUNKED);
// The choice of the chunk size affects performances
// This is a toy example so we will choose one line
hsize_t chunk_dims[ndims] = {2, ncols};
H5Pset_chunk(plist, ndims, chunk_dims);
std::cout << "- Property list created" << std::endl;
// Create the dataset 'dset1'
hid_t dset = H5Dcreate(file, "dset1", H5T_NATIVE_FLOAT, file_space, H5P_DEFAULT, plist, H5P_DEFAULT);
std::cout << "- Dataset 'dset1' created" << std::endl;
// Close resources
H5Pclose(plist);
H5Sclose(file_space);
// We don't need the file dataspace anymore because when the dataset will be extended,
// we will have to grab the updated file dataspace anyway
// We will now append two buffers to the end of the datset
// The first one will be two lines long
// The second one will be three lines long
// ## First buffer
// Create 2D buffer (contigous in memory, row major order)
// We will allocate enough memory to store 3 lines, so we can reuse the buffer
hsize_t nlines = 3;
float *buffer = new float[nlines * ncols];
// Let us create an array of pointers so we can use the b[i][j] notation
// instead of buffer[i * ncols + j]
float **b = new float*[nlines];
for (hsize_t i = 0; i < nlines; ++i){
b[i] = &buffer[i * ncols];
}
// Initial values in buffer to be written in the dataset
b[0][0] = 0.1;
b[0][1] = 0.2;
b[0][2] = 0.3;
b[1][0] = 0.4;
b[1][1] = 0.5;
b[1][2] = 0.6;
// Create a memory dataspace to indicate the size of our buffer
// Remember the first buffer is only two lines long
dims[0] = 2;
dims[1] = ncols;
hid_t mem_space = H5Screate_simple(ndims, dims, NULL);
std::cout << "- Memory dataspace created" << std::endl;
// Extend dataset
// We set the initial size of the dataset to 0x3, we thus need to extend it first
// Note that we extend the dataset itself, not its dataspace
// Remember the first buffer is only two lines long
dims[0] = 2;
dims[1] = ncols;
H5Dset_extent(dset, dims);
std::cout << "- Dataset extended" << std::endl;
// Select hyperslab on file dataset
file_space = H5Dget_space(dset);
hsize_t start[2] = {0, 0};
hsize_t count[2] = {2, ncols};
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
std::cout << "- First hyperslab selected" << std::endl;
// Write buffer to dataset
// mem_space and file_space should now have the same number of elements selected
// note that buffer and &b[0][0] are equivalent
H5Dwrite(dset, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
std::cout << "- First buffer written" << std::endl;
// We can now close the file dataspace
// We could close the memory dataspace and create a new one,
// but we will simply update its size
H5Sclose(file_space);
// ## Second buffer
// New values in buffer to be appended to the dataset
b[0][0] = 1.1;
b[0][1] = 1.2;
b[0][2] = 1.3;
b[1][0] = 1.4;
b[1][1] = 1.5;
b[1][2] = 1.6;
b[2][0] = 1.7;
b[2][1] = 1.8;
b[2][2] = 1.9;
// Resize the memory dataspace to indicate the new size of our buffer
// The second buffer is three lines long
dims[0] = 3;
dims[1] = ncols;
H5Sset_extent_simple(mem_space, ndims, dims, NULL);
std::cout << "- Memory dataspace resized" << std::endl;
// Extend dataset
// Note that in this simple example, we know that 2 + 3 = 5
// In general, you could read the current extent from the file dataspace
// and add the desired number of lines to it
dims[0] = 5;
dims[1] = ncols;
H5Dset_extent(dset, dims);
std::cout << "- Dataset extended" << std::endl;
// Select hyperslab on file dataset
// Again in this simple example, we know that 0 + 2 = 2
// In general, you could read the current extent from the file dataspace
// The second buffer is three lines long
file_space = H5Dget_space(dset);
start[0] = 2;
start[1] = 0;
count[0] = 3;
count[1] = ncols;
H5Sselect_hyperslab(file_space, H5S_SELECT_SET, start, NULL, count, NULL);
std::cout << "- Second hyperslab selected" << std::endl;
// Append buffer to dataset
H5Dwrite(dset, H5T_NATIVE_FLOAT, mem_space, file_space, H5P_DEFAULT, buffer);
std::cout << "- Second buffer written" << std::endl;
// Close resources
delete[] b;
delete[] buffer;
H5Sclose(file_space);
H5Sclose(mem_space);
H5Dclose(dset);
H5Fclose(file);
std::cout << "- Resources released" << std::endl;
}
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