src/tools/lvr2_hdf5togeotiff/Main.cpp

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#include "lvr2/io/HDF5IO.hpp"

#include <boost/range/iterator_range.hpp>
#include <boost/foreach.hpp>
#include <boost/filesystem.hpp>

#include <string>
#include <fstream>

#include <sys/stat.h>

#include "lvr2/io/GeoTIFFIO.hpp"
#include "Options.hpp"


using namespace lvr2;

int processConversion(std::string input_filename,
        std::string position_code, std::string output_filename, size_t min_channel, size_t max_channel)
{
    /*------------------- HDF5 INPUT ------------------------*/
    HDF5IO hdf5(input_filename, false);
    std::vector<size_t> dim;

    // extract radiometric data
    std::string groupname = "raw/spectral/position_" + position_code;
    std::string datasetname = "spectral";
    boost::shared_array<uint16_t> spectrals = hdf5.getArray<uint16_t>(groupname, datasetname, dim);

    // extract array dimension information
    size_t num_channels = dim[0];
    size_t num_rows = dim[1];
    size_t num_cols = dim[2];

    // set upper boundary
    if(num_channels < max_channel)
    {
        std::cout << "The dataset has only " << num_channels << " channels. Using this as upper boundary." << std::endl;
        max_channel = num_channels;
    }
    num_channels = max_channel - min_channel;

    GeoTIFFIO gtifio(output_filename, num_cols, num_rows, num_channels);

    /*--------------- FILE CONVERSION --------------------*/
    // for each channel create a cv::Mat containing the spectral intensity data for the channel ...
    for(size_t channel = 0; channel < num_channels; channel++)
    {
        cv::Mat *mat = new cv::Mat(num_rows, num_cols, CV_16UC1);
        for(size_t row = 0; row < num_rows; row++)
        {
            for(size_t col = 0; col < num_cols; col++)
            {
                mat->at<uint16_t>(row, col) = spectrals.get()[(channel + min_channel) * num_cols * num_rows + row * num_cols + col];
            }
        }
        // ... and write it to the output GeoTIFF file
        int ret = gtifio.writeBand(mat, channel + 1);
        delete mat;
        if (ret != 0)
        {
            return ret;
        }
    }
    return 0;
}

int main(int argc, char**argv)
{
    hdf5togeotiff::Options options(argc, argv);

    /*--------------- GET PROGRAM OPTIONS --------------------*/

    boost::filesystem::path input_filename(options.getH5File());
    std::string input_extension = boost::filesystem::extension(input_filename);

    boost::filesystem::path output_filename(options.getGTIFFFile());
    std::string  output_extension = boost::filesystem::extension(output_filename);
    
    size_t min_channel = options.getMinChannel();
    size_t max_channel = options.getMaxChannel();

    std::string position_code = options.getPositionCode();

    /*---------------- PREPARE CONVERSION -------------------*/

    boost::filesystem::path output_dir = output_filename.parent_path();
    if (output_dir != "" && !boost::filesystem::exists(output_dir))
    {
        boost::filesystem::create_directory(output_dir);
    }

    std::cout << "Starting conversion..." <<  std::endl;
    if (processConversion(input_filename.string(), position_code, output_filename.string(), min_channel, max_channel) < 0)
    {
        std::cout << "An Error occurred during conversion." << std::endl;
    }

    return 0;
}