multispot5_headless.cc

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#include <tag/printf.h>
#undef make_tuple

#include <tr1/tuple>
#include <algorithm>
#include <climits>
#include <iomanip>
#include <map>
#include <cvd/image_io.h>
#include <cvd/image_convert.h>
#include <cvd/morphology.h>
#include <cvd/connected_components.h>
#include <cvd/draw.h>
#include <cvd/vector_image_ref.h>

#include <gvars3/instances.h>

#include "storm_imagery.h"
#include "multispot5.h"
#include "multispot5_place_choice.h"
#include "utility.h"

using namespace std;
using namespace std::tr1;
using namespace CVD;
using namespace GVars3;
using namespace TooN;



vector<vector<ImageRef> > get_regions(const SubImage<double>& log_ratios)
{
    gvar3<double> radius("radius", 0, 1);

    //Set the liklihood ratio threshold/spot density prior
    //same thing.
    double threshold = GV3::get<double>("threshold", 0, -1);
    int edge = GV3::get<int>("edge", 0, -1);


    //Threshold image
    Image<byte> thresholded(log_ratios.size(), 0);
    for(int r=0; r < thresholded.size().y; r++)
        for(int c=0; c < min(thresholded.size().x, edge); c++)
            thresholded[r][c] = 255 * (log_ratios[r][c] > threshold);
    
    //Dilate
    Image<byte> dilated = morphology(thresholded, getDisc(*radius), Morphology::BinaryDilate<byte>());

    transform(dilated.begin(), dilated.end(), dilated.begin(), bind1st(multiplies<int>(), 255));
    
    //Connected components of dilated image
    vector<ImageRef> fg;
    for(int r=0; r < thresholded.size().y; r++)
        for(int c=0; c < min(thresholded.size().x, edge); c++)
            if(dilated[r][c])
                fg.push_back(ImageRef(c, r));

    vector<vector<ImageRef> > regions;
    connected_components(fg, regions);

    return regions;
}

void mmain(int argc, char** argv)
{
    GUI.LoadFile("multispot5.cfg");
    int lastarg = GUI.parseArguments(argc, argv);
    if(lastarg >= argc)
    {   
        cerr << "Specify the images to load\n";
        exit(1);
    }
    vector<string> files(argv + lastarg, argv + argc);
    
    //Save this now since the de-checkpointing code will kl0bber it 
    //when it reloads the gvars
    string save_spots_file = GV3::get<string>("save_spots", "", -1);

    string checkpoint_file = GV3::get<string>("load_checkpoint", "", 1);

    if(checkpoint_file != "")
    {
        //Load and de-checkpointing
        ifstream chk;
        open_or_die(chk, checkpoint_file);
        
        StateParameters p;

        try{
            p = parse_log_file(chk);
        }
        catch(LogFileParseError e)
        {
            cerr << "SI TEH FUX0R11ONEone!oneleven: " << e.what << endl;
            exit(1);
        }
        
        vector<Image<float> > ims = load_and_normalize_images(files);

        //Restore kl0bbered variable
        GV3::get<string>("save_spots") = save_spots_file;
        
        ofstream save_spots;
        open_or_die(save_spots, save_spots_file);
        
        fit_spots_new(ims, p, save_spots, *null_graphics());

    }
     
    vector<Image<float> > ims = load_and_normalize_images(files);

    //Load the log_ratios image.
    //We will use this as a starting point for searching for spots.
    Image<double> log_ratios;
    try
    {
        log_ratios = img_load(GV3::get<string>("log_ratios", "", -1));
    }
    catch(Exceptions::All e)
    {
        cerr << "Error loading " << GV3::get<string>("log_ratios", "") << ": " << e.what << endl;
        exit(1);
    }
    
    
    gvar3<int> cluster_to_show("cluster_to_show", 0, -1);
    gvar3<int> use_largest("use_largest", 0, 1);

    vector<vector<ImageRef> > regions;

    regions = get_regions(log_ratios);
    if(regions.size() == 0)
    {
        cerr << "There are no regions!\n";

        ofstream save_spots;
        open_or_die(save_spots, save_spots_file);
        save_spots << "NOREGIONS\n";

        exit(1);
    }
    
    if(*use_largest && !regions.empty())
    {
        *cluster_to_show=0;
        for(unsigned int i=1; i < regions.size(); i++)
            if(regions[i].size() > regions[*cluster_to_show].size())
                *cluster_to_show = i;
                
    }
    else
        *cluster_to_show = max(min(*cluster_to_show, (int)regions.size() - 1), 0);

    
    auto_ptr<FitSpotsGraphics> gr = null_graphics();
    place_and_fit_spots(ims, regions[*cluster_to_show], log_ratios, save_spots_file, *gr);
}

    
int main(int argc, char** argv)
{
    try{
        mmain(argc, argv);
    }
    catch(Exceptions::All e)
    {
        cerr << "Fatal error: " << e.what << endl;
    }
}