Laboratoire RDP » Biophysics Team » lsm3d

/*

Level-set Method to detect tissue contour (exterior shape)

- Sequential -

      Copyright 2016 ENS de Lyon

       File author(s):

           Typhaine Moreau, Annamaria Kiss <annamaria.kiss@ens-lyon.fr.fr>

       See accompanying file LICENSE.txt

To compile

 g++ -o contour_init contour_init.cpp -O2 -L/usr/X11R6/lib -lm -lpthread -lX11 -l:libtiff.so.5

 Need CImg.h and lsm_lib.h

To execute

 ./contour_init img t_up t_down smooth

 img : grayscale image of cells, .inr or .inr.gz

 t_up,t_down : linear threshold value (inr)

 smooth : amount of gaussian blur to apply to the image

*/

#include <iostream>

#include <math.h>

#include <sstream>

#include <vector>

#include <fstream>

#include "lsm_lib.h"

using namespace cimg_library;

using namespace std;

//------------------------------------------------------------------------------

//Main

//------------------------------------------------------------------------------

int main (int argc, char* argv[])

{

  clock_t begin=clock();

  if(argc!=5)

    {

      cout<<"!! wrong number of arguments"<<endl;

      cout<<"Usage : contour_init img t_up t_down smooth"<<endl;

      cout<<"Examples for parameter values:"<<endl;

      cout<<"------------------------------"<<endl;

      cout<<"img : grayscale image of cells, (.inr or .inr.gz)"<<endl;

      cout<<"Upper threshold : t_up = 20"<<endl;

      cout<<"Down threshold : t_down = 5"<<endl;

      cout<<"Gaussian filter : smooth = 1 (0, if image already filtered)"<<endl;

      return 0;

    }

  //ckeck filename and read image

  string filename=argv[1];

  float tailleVoxel[3] = {0};// resolution initialisation

  CImg<float> img=imread(filename, tailleVoxel);

  //--------------------------------------------Parameters

  //linear threshold and smoothing

  int t_up=atoi(argv[2]);

  int t_down=atoi(argv[3]);

  float smooth=atof(argv[4]);

  //-------------------------------------------Names and directories

  //new name with arguments

  string ar2=argv[2];

  string ar3=argv[3];

  string ar4=argv[4];

  string insert="_initial"+ar2+"-"+ar3+"s"+ar4;

  filename.insert(filename.size()-4,insert);

  //-----------------------------------------Image Pre-processing

  //smooth image

  img.blur(smooth);

  //-------------------------------------------Initialization

  //initialize level-set

  CImg<unsigned char> segmented=threshold_linear_alongZ(img,t_up,t_down);

  int s=imsave(filename, tailleVoxel, segmented);

  return 0;

}