csv_mesh.cc

/*    Copyright (C) 2012 University of Oxford  */

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#include "csv_mesh.h"

using namespace fslsurface_name;
using namespace mesh;


//////// CSVMESH
// 1: ascii, 2:vtk, 3: gii, -1: unknown
int  meshFileType(const string& filename){
  if(filename.size()<=5){return -1;}
  string last_3 = filename.substr(filename.size()-3, 3);
  if( last_3 == ".gz" ){
    last_3 = filename.substr(filename.size()-6, 3);
    if( last_3 == "gii" ) {return CSV_GIFTI;}
  }

  if( last_3 == "gii" ) {return CSV_GIFTI;}

  ifstream f(filename.c_str());
  //reading the header
  string header;
  getline(f, header);
  {
    string::size_type pos = header.find("# vtk DataFile Version 3.0");
    if (pos!= string::npos) {
      f.close();
      return CSV_VTK;
    }
  }
  {
    string::size_type pos = header.find("#!ascii");
    if (pos != string::npos) {
      f.close();
      return CSV_ASCII;
    }
  }
  return -1;
}
bool meshExists(const string& filename){
  int type = meshFileType(filename);
  if(type>0){return true;}
  return false;
}

void CsvMesh::load(const string& filename){
  int type=meshFileType(filename);
  if(type==CSV_ASCII){
    load_ascii(filename);
  }
  else if(type==CSV_VTK){
    load_vtk(filename);
  }
  else if(type==CSV_GIFTI){
    // cerr<<" GIFTI format not yet supported"<<endl;exit(1);
   load_gifti(filename);
  }
  else{
    cerr<<"CsvMesh::load:error reading file: "<<filename<<"  ... Unknown format"<<endl;
    exit(1);
  }
  
}

void CsvMesh::load_gifti(const string& filename) {

  fslSurface<float,unsigned int> surf;
  read_surface(surf,filename);        
  
  _points.clear();
  _pvalues.clear();
  unsigned int count=0;
  for ( vector< vertex<float> >::iterator  i= surf.vbegin(); i!= surf.vend();++i,++count){
    CsvMpoint m(i->x, i->y, i->z, count);
    _points.push_back(m);
    _pvalues.push_back(0);
  }            
  count=0;
  _triangles.clear();
  for ( vector<unsigned int>::const_iterator i = surf.const_facebegin(); i != surf.const_faceend(); i+=3,++count){
    CsvMpoint m1 = get_point(*i);    
    CsvMpoint m2 = get_point(*(i+1));
    CsvMpoint m3 = get_point(*(i+2));
    
    CsvTriangle t(m1,m2,m3,count);
    //_triangles.push_back(t);    
    push_triangle(t);
  }        

  reset_pvalues();
  count = 0;
  if (surf.getNumberOfScalarData()>0) {
    for ( vector<float>::const_iterator i= surf.const_scbegin(0); i!= surf.const_scend(0);++i,++count){
      set_pvalue(count,*i);
    }
  }

}

void CsvMesh::load_vtk(const string& filename) {
  clear();
  ifstream f(filename.c_str());
  if (f.is_open())
    {	
      //reading the header
      string header;
      getline(f, header);
      string::size_type pos = header.find("# vtk DataFile Version 3.0");
      if (pos == string::npos) {
	cerr<<"CsvMesh::load_vtk:error in the header"<<endl;exit(1);
      }
      getline(f,header);
      getline(f,header);
      getline(f,header);
      int NVertices, NFaces;
      f>>header>>NVertices>>header;	  
      //reading the points
      for (int i=0; i<NVertices; i++)
	{
	  double x, y, z;
	  f>>x>>y>>z;
	  CsvMpoint m(x,y,z,i);
	  _points.push_back(m);
	  _pvalues.push_back(0);
	}
      f>>header>>NFaces>>header;
      //reading the triangles
      for (int i=0; i<NFaces; i++)
	{
	  int p0, p1, p2;
	  int j;
	  f>>j>>p0>>p1>>p2;
	  CsvTriangle t(get_point(p0), get_point(p1), get_point(p2),i);
	  push_triangle(t);
	  _tvalues.push_back(0);
	}
      f>>header>>header;
      f>>header>>header>>header;
      f>>header>>header;
      //reading the values
      for (int i=0; i<NVertices; i++)
	{
	  int val;
	  f>>val;	      
	  set_pvalue(i,val);
	}      	  
      f.close();
    }
  else {cout<<"CsvMesh::error opening file: "<<filename<<endl; exit(1);}
}

void CsvMesh::load_ascii(const string& filename) { //load a freesurfer ascii mesh
  clear();

  ifstream f(filename.c_str());
  if (f.is_open())
    {	
      //reading the header
      string header;
      getline(f, header);
      string::size_type pos = header.find("#!ascii");
      if (pos == string::npos) {
	cerr<<"CsvMesh::load_ascii:error in the header"<<endl;exit(1);
      }

      //reading the size of the mesh
      int NVertices, NFaces;
      f>>NVertices>>NFaces;
      //reading the points
      for (int i=0; i<NVertices; i++)
	{
	  double x, y, z;
	  float val;
	  f>>x>>y>>z>>val;
	  CsvMpoint m(x, y, z, i);
	  _points.push_back(m);
	  _pvalues.push_back(val);
	}      
      //reading the triangles
      for (int i=0; i<NFaces; i++)
	{
	  int p0, p1, p2;
	  float val;
	  f>>p0>>p1>>p2>>val;
	  CsvTriangle t(get_point(p0), get_point(p1), get_point(p2),i);
	  push_triangle(t);
	  _tvalues.push_back(val);
	}
      f.close();
    }
  else {cout<<"CsvMesh::load_ascii:error opening file: "<<filename<<endl; exit(1);}
 
}

void CsvMesh::save(const string& filename, const int& type)const{
  switch(type)
    {
    case CSV_ASCII:
      save_ascii(filename);break;
    case CSV_VTK:
      save_vtk(filename);break;
    default:
      save_gifti(filename,type);break;
    }
}
void CsvMesh::save_gifti(const string& s,const int& type)const{
  string filename(s);
  string last_3 = filename.substr(filename.size()-3, 3);
  if( last_3 != "gii" ){
    if(last_3 != ".gz"){
      filename=filename+".gii";
    }
  }
  
  fslSurface<float,unsigned int> surf;
  string subtype = filename.substr(filename.size()-8, 4);

  if(subtype == "surf"){
    surf.setVertices(getPointsAsVectors());
    surf.setFaces(getTrianglesAsVectors());
  }
  else if(subtype == "func"){
    surf.insertScalars(getValuesAsVectors(),0,"MyScalars");
  }
  else{
    surf.setVertices(getPointsAsVectors());
    surf.setFaces(getTrianglesAsVectors());
    surf.insertScalars(getValuesAsVectors(),0,"MyScalars");
  }

  writeGIFTI(surf,filename,type);
}
void CsvMesh::save_vtk(const string& s)const{
  string filename(s);
  string last_3 = filename.substr(filename.size()-3, 3);
  if( last_3 != "vtk" ){
    filename=filename+".vtk";
  }
  
  ofstream flot(filename.c_str());
  if(flot.is_open()){
    flot<<"# vtk DataFile Version 3.0"<<endl
	<<"surface file"<<endl
	<<"ASCII"<<endl
	<<"DATASET POLYDATA"<<endl
	<<"POINTS ";
    flot<<_points.size()<<"  float"<<endl;
    
    for (unsigned int i =0; i<_points.size();i++)  { 
      //	flot.precision(6);
      flot<<_points[i].get_coord().X<<" "
	  <<_points[i].get_coord().Y<<" "
	  <<_points[i].get_coord().Z<<endl;
#ifdef PPC64
      if ((n++ % 20) == 0) flot.flush();
#endif
    }
    flot<<"POLYGONS "<<_triangles.size()<<" "<<_triangles.size()*4<<endl;
    for ( unsigned int i=0; i<_triangles.size(); i++) 
      flot<<"3 "
	  <<_triangles[i].get_vertice(0).get_no()<<" "
	  <<_triangles[i].get_vertice(1).get_no()<<" "
	  <<_triangles[i].get_vertice(2).get_no()<<" "<<endl;
#ifdef PPC64
    if ((n++ % 20) == 0) flot.flush();
#endif
  }
  else{
    cerr<<"Csv::save_vtk:error opening file "<<filename<<" for writing"<<endl;
    exit(1);
  }


}
void CsvMesh::save_ascii(const string& s)const{
  string filename(s);
  string last_3 = filename.substr(filename.size()-3, 3);
  if( last_3 != "asc" ){filename=filename+".asc";}
  
  ofstream f(filename.c_str());
  stringstream flot;
  if (f.is_open())
    {
      int ptcount(0), tricount(0);
      for(unsigned int i=0;i<_points.size();i++){
	flot<<_points[i].get_coord().X<<" "
 	    <<_points[i].get_coord().Y<<" "
 	    <<_points[i].get_coord().Z<<" "
 	    <<_pvalues[i]<<endl; 	  
	ptcount++;
      }
      for(unsigned int i=0;i<_triangles.size();i++){
	flot<<_triangles[i].get_vertice(0).get_no()<<" "
	    <<_triangles[i].get_vertice(1).get_no()<<" "
	    <<_triangles[i].get_vertice(2).get_no()<<" "<<0<<endl;
	tricount++;
      }
      f<<"#!ascii from CsvMesh"<<endl;
      f<<ptcount<<" "<<tricount<<endl<<flot.str();
      f.close();
    }
  else cerr<<"CsvMesh::save_ascii:error opening file for writing: "<<s<<endl;

}



// ostream& operator <<(ostream& flot,const Mesh & m){
//   m.stream_mesh(flot,1);
//   return flot;
// }


void CsvMesh::push_triangle(const CsvTriangle& t){
  _triangles.push_back(t);
  for(int i=0;i<3;i++){
    _points[t.get_vertice(i).get_no()].push_triangle(t.get_no());
  }
}


const bool operator ==(const CsvMpoint &p2, const CsvMpoint &p1){
  return (fabs(p1.get_coord().X- p2.get_coord().X)<1e-8 && fabs(p1.get_coord().Y - p2.get_coord().Y)<1e-8 && fabs(p1.get_coord().Z - p2.get_coord().Z)<1e-8);
}
const bool operator ==(const CsvMpoint &p2, const Pt &p1){
  return (fabs(p1.X- p2.get_coord().X)<1e-3 && fabs(p1.Y - p2.get_coord().Y)<1e-3 && fabs(p1.Z - p2.get_coord().Z)<1e-3);
}

const Vec operator -(const CsvMpoint&p1, const CsvMpoint &p2){
  return Vec (p1.get_coord().X - p2.get_coord().X,p1.get_coord().Y - p2.get_coord().Y,p1.get_coord().Z - p2.get_coord().Z );
}

const Vec operator -(const Pt&p1, const CsvMpoint &p2){
  return Vec (p1.X - p2.get_coord().X,p1.Y - p2.get_coord().Y,p1.Z - p2.get_coord().Z );
}

const Vec operator -(const CsvMpoint&p1, const Pt &p2){
  return Vec (p1.get_coord().X - p2.X,p1.get_coord().Y - p2.Y,p1.get_coord().Z - p2.Z );
}

const Vec operator -(const ColumnVector& p1, const CsvMpoint& p2){
  return Vec (p1(1)-p2.get_coord().X,p1(2)-p2.get_coord().Y,p1(3)-p2.get_coord().Z);
}
const Vec operator -(const ColumnVector& p1, const Vec& p2){
  return Vec (p1(1)-p2.X,p1(2)-p2.Y,p1(3)-p2.Z);
}
const Vec operator -(const Vec& p1, const CsvMpoint &p2){
  return Vec(p1.X-p2.get_coord().X,p1.Y-p2.get_coord().Y,p1.Z-p2.get_coord().Z);
}
// calculate on what side of a surface a step goes to
// a step here always starts at a vertex (vertind)
// the sign corresponds to the sign of the dot-product with the 
// normal to te closest tile
int CsvMesh::step_sign(const int& vertind,const Vec& step)const{
  int trid;
  float d=0,dmin=0;
  for(int i=0;i<_points[vertind].ntriangles();i++){
    trid=_points[vertind].get_trID(i);    
    d=(_triangles[trid].normal()|step);
    if(i==0||(fabs(d)<fabs(dmin))){dmin=d;}
  }
  return (dmin>0?1:-1);
}


bool CsvTriangle::isinside(const Vec& x)const{
  Vec v0,v1,v2;
  v0=_vertice[2]-_vertice[0];
  v1=_vertice[1]-_vertice[0];
  v2=x-_vertice[0];
  double dot00=v0|v0;
  double dot01=v0|v1;
  double dot02=v0|v2;
  double dot11=v1|v1;
  double dot12=v1|v2;
  double invDenom = 1 / (dot00 * dot11 - dot01 * dot01);
  double u = (dot11 * dot02 - dot01 * dot12) * invDenom;
  double v = (dot00 * dot12 - dot01 * dot02) * invDenom;

  // Check if point is in triangle
  return (u > 0) && (v > 0) && (u + v < 1);

}

double CsvTriangle::dist_to_point(const Vec& x0)const{
  double d;
  Vec x1(_vertice[0].get_coord().X,_vertice[0].get_coord().Y,_vertice[0].get_coord().Z);
  Vec x2(_vertice[1].get_coord().X,_vertice[1].get_coord().Y,_vertice[1].get_coord().Z);
  Vec x3(_vertice[2].get_coord().X,_vertice[2].get_coord().Y,_vertice[2].get_coord().Z);
  Vec u;
  double dmin=1000000;
  // test edges
  u=x2-x1;
  if( ((x0-x1)|u)>0 && ((x0-x2)|u)<0 ){
    d=(((x0-x1)*(x0-x2)).norm()/(x2-x1).norm());
    if(d<dmin)dmin=d;
  }
  u=x3-x1;
  if( ((x0-x1)|u)>0 && ((x0-x3)|u)<0 ){
    d=(((x0-x1)*(x0-x3)).norm()/(x3-x1).norm());  
    if(d<dmin)dmin=d;
  }
  u=x3-x2;
  if( ((x0-x2)|u)>0 && ((x0-x3)|u)<0 ){
   d=(((x0-x2)*(x0-x3)).norm()/(x3-x2).norm());
   if(d<dmin)dmin=d;
  }
  
  d=(x0-x1).norm();if(d<dmin)dmin=d;
  d=(x0-x2).norm();if(d<dmin)dmin=d;
  d=(x0-x3).norm();if(d<dmin)dmin=d;
  return dmin;
}

  // Saad
  // algorithm from:
  // http://softsurfer.com/Archive/algorithm_0105/algorithm_0105.htm#intersect_RayTriangle()

  const bool CsvTriangle::intersect(const vector<Pt> & p) const {
    Vec    u,v,n;   // triangle vectors
    Vec    dir,w0,w; // ray vectors
    double r, a, b;              // params to calc ray-plane intersect

    // check if point is one the vertices
    for(int ii=0;ii<=2;ii++){
      if((_vertice[ii])==p[0])return true;
      if((_vertice[ii])==p[1])return true;
    }

    // get triangle edge vectors and plane normal
    u = _vertice[1]-_vertice[0];
    v = _vertice[2]-_vertice[0];
    n = u*v;             // cross product
    if (n.norm()==0) // triangle is degenerate
      return false;                 
    

    dir = p[1]-p[0];             // ray direction vector
    w0 = p[0]-_vertice[0];
    a = -(n|w0)/n.norm()/w0.norm();
    b = (n|dir)/n.norm()/dir.norm();
    if (fabs(b) < 0.001) { // ray is parallel to triangle plane
      if (fabs(a) < 0.001)                 // ray lies in triangle plane
	return true;
      else return false;             // ray disjoint from plane
    }
    
    // get intersect point of ray with triangle plane
    r = a / b;
    if (r < 0.0)                   // ray goes away from triangle
      return false;                  // => no intersect
    
    // for a segment, also test if (r > 1.0) => no intersect
    Pt I;
    I = p[0] + r * dir;           // intersect point of ray and plane
    
    // is I inside T?
    double    uu, uv, vv, wu, wv, D;
    uu = (u|u);
    uv = (u|v);
    vv = (v|v);
    w = I - _vertice[0];
    wu = (w|u);
    wv = (w|v);
    D = uv * uv - uu * vv;
    
    // get and test parametric coords
    double s, t;
    s = (uv * wv - vv * wu) / D;
    if (s < 0.0 || s > 1.0)        // I is outside T
      return false;
    t = (uv * wu - uu * wv) / D;
    if (t < 0.0 || (s + t) > 1.0)  // I is outside T
      return false;
    
    return true;                      // I is in T
    
  }
  

  const bool CsvTriangle::intersect(const vector<Pt> & p,int& ind) const {
    Vec    u,v,n;   // triangle vectors
    Vec    dir,w0,w; // ray vectors
    double r, a, b;              // params to calc ray-plane intersect

    // check if point is one the vertices
    for(int ii=0;ii<=2;ii++){
      if((_vertice[ii])==p[0]){ind=ii;return true;}
      if((_vertice[ii])==p[1]){ind=ii;return true;}
    }

    // get triangle edge vectors and plane normal
    u = _vertice[1]-_vertice[0];
    v = _vertice[2]-_vertice[0];
    n = u*v;             // cross product
    if (n.norm()==0) // triangle is degenerate
      return false;                 
    

    dir = p[1]-p[0];             // ray direction vector
    w0 = p[0]-_vertice[0];
    a = -(n|w0);
    b = (n|dir);
    if (fabs(b) < 0.001) { // ray is parallel to triangle plane
      if (fabs(a) < 0.001)                 // ray lies in triangle plane
	{ind=0;return true;}
      else return false;             // ray disjoint from plane
    }
    
    // get intersect point of ray with triangle plane
    r = a / b;
    if (r < 0.0)                   // ray goes away from triangle
      return false;                  // => no intersect
    
    // for a segment, also test if (r > 1.0) => no intersect
    Pt I;
    I = p[0] + r * dir;           // intersect point of ray and plane
    
    // is I inside T?
    double    uu, uv, vv, wu, wv, D;
    uu = (u|u);
    uv = (u|v);
    vv = (v|v);
    w = I - _vertice[0];
    wu = (w|u);
    wv = (w|v);
    D = uv * uv - uu * vv;
    
    // get and test parametric coords
    double s, t;
    s = (uv * wv - vv * wu) / D;
    if (s < 0.0 || s > 1.0)        // I is outside T
      return false;
    t = (uv * wu - uu * wv) / D;
    if (t < 0.0 || (s + t) > 1.0)  // I is outside T
      return false;

    // which vertex is closest to where the segment intersects?
    float x=uu-2*wu,y=vv-2*wv;
    if( x<0 ){
      if( x<y ) ind=1;
      else ind=2;
    }
    else{
      if( y<0 ) ind=2;
      else ind=0;
    }
    
    return true;                      // I is in T
    
  }