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 /*

  #

  #  File        : use_skeleton.cpp

  #                ( C++ source file )

  #

  #  Description : Example of use for the CImg plugin 'plugins/skeleton.h'.

  #                This file is a part of the CImg Library project.

  #                ( http://cimg.sourceforge.net )

  #

  #  Copyright   : Francois-Xavier Dupe

  #                ( http://www.greyc.ensicaen.fr/~fdupe/ )

  #

  #  License     : CeCILL v2.0

  #                ( http://www.cecill.info/licences/Licence_CeCILL_V2-en.html )

  #

  #  This software is governed by the CeCILL  license under French law and

  #  abiding by the rules of distribution of free software.  You can  use,

  #  modify and/ or redistribute the software under the terms of the CeCILL

  #  license as circulated by CEA, CNRS and INRIA at the following URL

  #  "http://www.cecill.info".

  #

  #  As a counterpart to the access to the source code and rights to copy,

  #  modify and redistribute granted by the license, users are provided only

  #  with a limited warranty  and the software's author,  the holder of the

  #  economic rights,  and the successive licensors  have only  limited

  #  liability.

  #

  #  In this respect, the user's attention is drawn to the risks associated

  #  with loading,  using,  modifying and/or developing or reproducing the

  #  software by the user in light of its specific status of free software,

  #  that may mean  that it is complicated to manipulate,  and  that  also

  #  therefore means  that it is reserved for developers  and  experienced

  #  professionals having in-depth computer knowledge. Users are therefore

  #  encouraged to load and test the software's suitability as regards their

  #  requirements in conditions enabling the security of their systems and/or

  #  data to be ensured and,  more generally, to use and operate it in the

  #  same conditions as regards security.

  #

  #  The fact that you are presently reading this means that you have had

  #  knowledge of the CeCILL license and that you accept its terms.

  #

 */

 #include <queue>

 #define cimg_plugin "plugins/skeleton.h"

 #include "../CImg.h"

 using namespace cimg_library;

 #ifndef cimg_imagepath

 #define cimg_imagepath "img/"

 #endif

 int main (int argc, char **argv) {

   cimg_usage("Compute the skeleton of a shape, using Hamilton-Jacobi equations");

   // Read command line arguments

   cimg_help("Input/Output options\n"

             "--------------------");

   const char* file_i = cimg_option("-i",cimg_imagepath "milla.bmp","Input (black&white) image");

   const int median = cimg_option("-median",0,"Apply median filter");

   const bool invert = cimg_option("-inv",false,"Invert image values");

   const char* file_o = cimg_option("-o",(char*)0,"Output skeleton image");

   const bool display = cimg_option("-visu",true,"Display results");

   cimg_help("Skeleton computation parameters\n"

             "-------------------------------");

   const float thresh = cimg_option("-t",-0.3f,"Threshold");

   const bool curve = cimg_option("-curve",false,"Create medial curve");

   cimg_help("Torsello correction parameters\n"

             "------------------------------");

   const bool correction = cimg_option("-corr",false,"Torsello correction");

   const float dlt1 = 2;

   const float dlt2 = cimg_option("-dlt",1.0f,"Discrete step");

   cimg_help("Sampling parameters\n"

             "-------------------");

   const float sX = cimg_option("-sizeX",1.0f,"X-Size of the pixel/voxel");

   const float sY = cimg_option("-sizeY",1.0f,"Y-Size of the pixel/voxel");

   const float sZ = cimg_option("-sizeZ",1.0f,"Z-Size of the pixel/voxel");

   // Load the image (forcing it to be scalar with 2 values { 0,1 }).

   CImg<unsigned int> image0(file_i), image = image0.get_pointwise_norm().quantize(2).normalize(0,1);

   if (median) image.blur_median(median);

   if (invert) (image-=1)*=-1;

   if (display) (image0.get_normalize(0,255)<<image.get_normalize(0,255)).display("Input image - Binary image");

   // Compute distance map.

   CImgList<float> visu;

   CImg<float> distance = image.get_distance(0,sX,sY,sZ);

   if (display) visu.insert(distance);

   // Compute the gradient of the distance function, and the flux (divergence) of the gradient field.

   const CImgList<float> grad = distance.get_gradient("xyz");

   CImg<float> flux = image.get_flux(grad,sY,sZ);

   if (display) visu.insert(flux);

   // Use the Torsello correction of the flux if necessary.

   if (correction) {

     CImg<float>

       logdensity = image.get_logdensity(distance,grad,flux,dlt1),

       nflux = image.get_corrected_flux(logdensity,grad,flux,dlt2);

     if (display) visu.insert(logdensity).insert(nflux);

     flux = nflux;

   }

   if (visu) {

     cimglist_apply(visu,normalize)(0,255);

     visu.display(visu.size==2?"Distance function - Flux":"Distance function - Flux - Log-density - Corrected flux");

   }

   // Compute the skeleton

   const CImg<unsigned int> skel = image.get_skeleton(flux,distance,curve,thresh);

   if (display) {

     (image0.resize(-100,-100,1,3)*=0.7f).get_shared_channel(1)|=skel*255.0;

     image0.draw_image(0,0,0,0,image*255.0,0.5f).display("Image + Skeleton");

   }

   // Save output image if necessary.

   if (file_o) skel.save(file_o);

   return 0;

 }