InitGridWithPixel.hpp

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//
// Created by jstark on 2019-11-07.
//
#ifndef IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
#define IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP
 
#include <iostream>
#include <typeinfo>
#include <cmath>
#include <sys/stat.h>
 
#include "Vector/vector_dist.hpp"
#include "Grid/grid_dist_id.hpp"
#include "data_type/aggregate.hpp"
#include "Decomposition/CartDecomposition.hpp"
 
#include "level_set/redistancing_Sussman/HelpFunctionsForGrid.hpp"
typedef signed char BYTE;
 
inline bool exists_test (const std::string& name) {
    struct stat buffer;
    return (stat (name.c_str(), &buffer) == 0);
}
 
 
 
std::vector<int> get_size(const std::string & path_to_file)
{
    std::vector<int> stack_dimst_1d;
    //  check if file exists and stream input csv file
    if(!exists_test(path_to_file)){
        std::cout << "------------------------------------------------------------------------" << std::endl;
        std::cout << "Error: file " << path_to_file << " does not exist. Aborting..." << std::endl;
        std::cout << "------------------------------------------------------------------------" << std::endl;
        abort();
    }
    std::ifstream file(path_to_file);
 
 
    // get its size
    std::streampos fileSize;
    file.seekg(0, std::ios::end);
    fileSize = file.tellg();
    file.seekg(0, std::ios::beg);
 
    // reserve capacity
    stack_dimst_1d.reserve(fileSize);
 
    std::string field;
    while ( getline(file, field) )         // 1 field per axis
    {
        std::istringstream iss(field);
        int val;
        iss >> val;
        stack_dimst_1d.push_back(val);       // add the #pixels for current axis to the array
    }
 
    // reverse order to compensate reverse reading
    std::reverse(std::begin(stack_dimst_1d), std::end(stack_dimst_1d));
    
    return stack_dimst_1d;
}
 
 
template <size_t Phi_0, typename grid_type>
void load_pixel_onto_grid(grid_type & grid, std::string file_name, std::vector <int> & stack_dims)
{
    constexpr size_t x = 0;
    constexpr size_t y = 1;
    constexpr size_t z = 2;
    
    // check if file exists and stream input file
    if(!exists_test(file_name)){
        std::cout << "------------------------------------------------------------------------" << std::endl;
        std::cout << "Error: file " << file_name << " does not exist. Aborting..." << std::endl;
        std::cout << "------------------------------------------------------------------------" << std::endl;
        abort();
    }
    std::ifstream file_stream (file_name, std::ifstream::binary);
    
    auto & v_cl = create_vcluster();
    if (v_cl.rank() == 0)
    {
        for (int d = 0; d < grid_type::dims; d++)
        {
            std::cout << "# grid points in dimension " << d << " = "  << grid.size(d) << std::endl;
        }
    }
    
    // assign pixel values to domain. For each pixel get factor_refinement number of grid points with corresponding value
    auto dom = grid.getDomainIterator();
    std::vector<BYTE> pixel_line; // one x-line of the image stack which will be read
    
    size_t sz_img[grid_type::dims];
    for (int d = 0; d < grid_type::dims; d++)
    {
        sz_img[d] = stack_dims[d];
    }
    grid_sm<grid_type::dims,void> ginfo_image(sz_img); // in order to get the image related key later on
    
    double refinement[grid_type::dims];
    for (int d = 0; d < grid_type::dims; d++)
    {
        refinement[d] = (double) grid.size(d) / (double)stack_dims[d]; // get the factor, by which the grid resolution differs from the image stack resolution
        if (v_cl.rank() == 0) std::cout << "effective refinement in dimension " << d << " = " << refinement[d] << std::endl;
    }
    
    while(dom.isNext())
    {
        auto key = dom.get();
        auto gkey = grid.getGKey(key);
        
        // In case a patch starts within a group of nodes to which same pixel-value should be assigned, get the
        // respective rest-offset
        int rest_offset = (int) (fmod(gkey.get(0), refinement[x])); // get the remainder
        
        
        // get l as the length of one x-line of the original image stack for the specific patch on the processor
        auto & gbox       = grid.getLocalGridsInfo();
        auto & DomBox     = gbox.get(key.getSub()).Dbox;
        size_t patch_size = DomBox.getHigh(0) - DomBox.getLow(0) + 1;
    
        size_t l          = (size_t) ceil( (patch_size + rest_offset) / refinement[x]);
        
        // in case that the grid has a different resolution than the underlying image stack:
        // create a key which is used to get the offset for the file reading
        // the indices in this key are corrected by the refinement factor
        for (int d = 0; d < grid_type::dims; d++)
        {
            gkey.set_d(d, floor(gkey.get(d) / refinement[d]));
        }
        
        // the offset matches the pixel from the image stack to the corresponding current position of the iterator
        // in the grid
        size_t offset = ginfo_image.LinId(gkey);
        file_stream.seekg(offset); // jump to the correct position in the file
        
        // prepare space for the pixel values of one x-line in the original image stack
        pixel_line.resize(l);
        // stream the file and fill pixel values into pixel_line
        file_stream.read((char*) & pixel_line[0], l);
        
        // run over a whole grid-line in x and assign pixel values from pixel_line to grid nodes
        // if the grid is finer in x as the image stack, the same pixel value from pixel_line is
        // assigned refinement[x] times
        for (int k = 0; k < patch_size; ++k)
        {
            auto key = dom.get();
            // get the correct index of the pixel to be read from pixel_line by considering a potential rest-offset,
            // when the patch divides group of nodes that belong to the same pixel
            size_t i = (size_t) floor((k + rest_offset) / refinement[x]);
            grid.template get<Phi_0>(key) = (double) pixel_line[i];
            ++dom;
        }
        // now one grid line in x is finished and the iterator dom has advanced accordingly s.t. next loop continues
        // with next line, meaning that y increased by 1 (or z respectivley, when y = ymax + 1)
    }
    
    grid.template ghost_get<Phi_0>();
}
 
 
 
#endif //IMAGE_BASED_RECONSTRUCTION_GETINITIALGRID_HPP