Posts Tagged ‘segmentation’

Mex wrapper for graph segmentation

Thursday, May 4th, 2017

I wrote a small mex wrapper for the graph segmentation part of the “Graph Based Image Segmentation” code. Most of the previously matlab implementations/wrappers worked on images. I want to apply this to geometry so I needed access to the graph segmentation directly. Here’s the wrapper (soon to be part of gptoolbox):

// mexopts = gptoolbox_mexopts('Static',false,'Debug',true);
// mex('segment_graph.cpp',mexopts{:});
#ifdef MEX
#  include <mex.h>
#  include <igl/C_STR.h>
#  include <igl/matlab/mexErrMsgTxt.h>
#  undef assert
#  define assert( isOK ) ( (isOK) ? (void)0 : (void) ::mexErrMsgTxt(C_STR(__FILE__<<":"<<__LINE__<<": failed assertion `"<<#isOK<<"'"<<std::endl) ) )
#include "segment-graph.h"
#include <igl/matlab/mexErrMsgTxt.h>
#include <igl/matlab/parse_rhs.h>
#include <igl/unique.h>
#include <igl/matlab/prepare_lhs.h>
#include <igl/matlab/requires_arg.h>
#include <igl/matlab/validate_arg.h>
#include <igl/matlab/MexStream.h>
#include <Eigen/Sparse>
void mexFunction(
 int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
  using namespace igl::matlab;
  using namespace Eigen;
  using namespace std;
  igl::matlab::MexStream mout;        
  std::streambuf *outbuf = std::cout.rdbuf(&mout);

  mexErrMsgTxt(nrhs>0,"Too few inputs");
  mexErrMsgTxt(mxIsSparse(prhs[0]),"Matrix should be sparse");
  const mxArray * mx_data = prhs[0];
  const int m = mxGetM(mx_data);
  const int n = mxGetN(mx_data);
  mexErrMsgTxt(n == mxGetM(prhs[0]), "Matrix should be square");
  assert(mxGetNumberOfDimensions(mx_data) == 2);
  // TODO: It should be possible to directly load the data into the sparse
  // matrix without going through the triplets
  // Copy data immediately
  double * pr = mxGetPr(mx_data);
  mwIndex * ir = mxGetIr(mx_data);
  mwIndex * jc = mxGetJc(mx_data);
  const int num_edges = mxGetNzmax(mx_data);
  edge * edges = new edge[num_edges];
  int k = 0;
  for(int j=0; j<n;j++)
    // Iterate over inside
      //cout<<ir[k]<<" "<<j<<" "<<pr[k]<<endl;
      edges[k].a = ir[k];
      edges[k].b = j;
      edges[k].w = pr[k];

  // defaults 
  int min_size = 0;
  // Threshold 
  int c = sqrt((double)n);
    int i = 1;
      mexErrMsgTxt(mxIsChar(prhs[i]),"Parameter names should be strings");
      // Cast to char
      const char * name = mxArrayToString(prhs[i]);
      if(strcmp("Threshold",name) == 0)
        c = (double)*mxGetPr(prhs[++i]);
      }else if(strcmp("MinSize",name) == 0)
        min_size = (int)((double)*mxGetPr(prhs[++i]));

  universe *u = segment_graph(n, num_edges, edges, c);

  // post process small components
  for (int i = 0; i < num_edges; i++) {
    int a = u->find(edges[i].a);
    int b = u->find(edges[i].b);
    if ((a != b) && ((u->size(a) < min_size) || (u->size(b) < min_size)))
      u->join(a, b);

    case 1:
      plhs[0] = mxCreateDoubleMatrix(m,1, mxREAL);
      Eigen::VectorXi C(m);
      for(int i = 0;i<m;i++)
        C(i) = u->find(i);
      Eigen::VectorXi uC,I,J;
    default: break;

  delete[] edges;
  delete u;

It takes the graph as a sparse matrix and outputs the component ids:

C = segment_graph(A);

GPU implementation of Generalized Winding Numbers

Friday, August 16th, 2013

Martin Bisson has implemented our paper “Robust Inside/Outside Segmentation via Generalized Winding Numbers” on the GPU. Since the computation is embarrassingly parallel even a straightforward implementation on the GPU shows huge performance gains. Check out a demo of his implementation for voxelization in this video:

Voxelization using generalized winding numbers from Martin Bisson on Vimeo.

Robust Inside-Outside Segmentation using Generalized Winding Numbers project page

Wednesday, April 10th, 2013

100 Armadillos animated in real time.

My colleagues, Ladislav Kavan, Olga Sorkine, and I have just submitted the camera ready version of paper “Robust Inside-Outside Segmentation using Generalized Winding Numbers” to be presented at ACM SIGGRAPH 2013. I’ve put up a Robust Inside-Outside Segmentation using Generalized Winding Numbers page where you can find the preprint version of the article, videos and more to come.


Solid shapes in computer graphics are often represented with boundary descriptions, e.g. triangle meshes, but animation, physically-based simulation, and geometry processing are more realistic and accurate when explicit volume representations are available. Tetrahedral meshes which exactly contain (interpolate) the input boundary description are desirable but difficult to construct for a large class of input meshes. Character meshes and CAD models are often composed of many connected components with numerous self-intersections, non-manifold pieces, and open boundaries, precluding existing meshing algorithms. We propose an automatic algorithm handling all of these issues, resulting in a compact discretization of the input’s inner volume. We only require reasonably consistent orientation of the input triangle mesh. By generalizing the winding number for arbitrary triangle meshes, we define a function that is a perfect segmentation for watertight input and is well-behaved otherwise. This function guides a graphcut segmentation of a constrained Delaunay tessellation (CDT), providing a minimal description that meets the boundary exactly and may be fed as input to existing tools to achieve element quality. We highlight our robustness on a number of examples and show applications of solving PDEs, volumetric texturing and elastic simulation.

Update: The accompanying video (with narration)