C++ Volume::YMin方法代码示例

int main(int argc,char *argv[])
{
  VolMagick::Volume v;
  VolMagick::readVolumeFile(v,argv[1]);

  UniformGrid ugrid(1,1,1);
  ugrid.importVolume(v);
  Point min,max;
  min.x=v.XMin();
  min.y=v.YMin();
  min.z=v.ZMin();
  max.x=v.XMax();
  max.y=v.YMax();
  max.z=v.ZMax();

//generateGridFile(min,max,v.XDim(),v.YDim(),v.ZDim());

  Mesh *mesh=new Mesh();

  float iso_val=atof(argv[2]);

  Mesher mesher;

  mesher.setGrid((Grid &)(ugrid));
  mesher.setMesh(mesh);

  mesher.generateMesh(iso_val);

 // mesh->correctNormals();
  mesher.saveMesh(string(argv[3]),&v);
  delete mesh;
  
  return 0;
}

int main(int argc, char **argv)
{
  if(argc < 6)
    {
      std:: cerr << 
	"Usage: " << argv[0] << 

	
	"  <first volume>  <second volume> < threshold> <output volume left> <output volume masked> \n";
	std::cerr<<"second volume (son) is subset of first volume (mother), threshold is in [0,255], output masked is the volume in first volume with > threshold in the second volume. output volume left is the first volume - output volume masked. " << std::endl;

      return 1;
    }

  try
    {
      VolMagick::Volume inputVol;

      VolMagick::Volume inputVol2;

      
      
      VolMagick::readVolumeFile(inputVol,argv[1]); ///first argument is input volume
      
      VolMagick::readVolumeFile(inputVol2, argv[2]); /// second argument is mask volume
      
	  float threshold = atof(argv[3]);


	  VolMagick::Volume  outputLeft;
	  VolMagick::Volume  outputMasked;

      if(!inputVol2.boundingBox().isWithin(inputVol.boundingBox()) )
	  	throw VolMagick::SubVolumeOutOfBounds("The mask volume bounding box must be within the mother volume's bounding box.");



      outputLeft.voxelType(inputVol.voxelType());
      outputLeft.dimension(inputVol.dimension());
      outputLeft.boundingBox(inputVol.boundingBox());
      
      outputMasked.voxelType(inputVol.voxelType());
      outputMasked.dimension(inputVol.dimension());
      outputMasked.boundingBox(inputVol.boundingBox());
    
   

	  float x, y, z;
	  float fvalue;
	  float minvalue = (float)inputVol2.min();
	  float maxvalue = (float)inputVol2.max();

 	  for( int kz = 0; kz<inputVol.ZDim(); kz++)
	  {
	  	for( int jy = 0; jy<inputVol.YDim(); jy++)
	    {
			for( int ix = 0; ix<inputVol.XDim(); ix++)
		   	{
		     	z = inputVol.ZMin() + kz*inputVol.ZSpan();
			 	y = inputVol.YMin() + jy*inputVol.YSpan();
				x = inputVol.XMin() + ix*inputVol.XSpan();
				if((z >= (float)inputVol2.ZMin()) && (z <= (float)inputVol2.ZMax()) && ( y >=(float)inputVol2.YMin()) && (y <= (float)inputVol2.YMax()) &&(x >= (float)inputVol2.XMin()) && (x <= (float)inputVol2.XMax()) )
				{
				  fvalue = 255.0*(inputVol2.interpolate(x,y,z)-minvalue)/(maxvalue-minvalue);
				  if(fvalue > threshold)
				  {
				  	outputMasked(ix,jy,kz, inputVol(ix,jy,kz));
					outputLeft(ix,jy,kz, inputVol.min());
				  }	  
				  else
				  {
				  	outputMasked(ix,jy,kz, inputVol.min());
					outputLeft(ix,jy,kz, inputVol(ix,jy,kz));
				  }
				}
				else
				{
					outputMasked(ix,jy,kz, inputVol.min());
					outputLeft(ix,jy,kz, inputVol(ix,jy,kz));
				}
		     }		   
		  }	
		}



	VolMagick::createVolumeFile(outputLeft, argv[4]);
	VolMagick::createVolumeFile(outputMasked, argv[5]);

  
    std::cout<<"done!"<<std::endl;


    }

  catch(VolMagick::Exception &e)
    {
      std:: cerr << e.what() << std::endl;
    }
  catch(std::exception &e)
//.........这里部分代码省略.........

int main(int argc, char **argv)
{
  if(argc != 6)
    {
      cerr << "Usage: " << argv[0] << " <input Original volume file> <input cutvolume> <input seed file ><Rotate Num> <output seed file>" << endl;
      return 1;
    }

  try
    {
      VolMagickOpStatus status;
      VolMagick::setDefaultMessenger(&status);

      VolMagick::Volume inputVol;
	  VolMagick::VolumeFileInfo inputVol2info;

      VolMagick::readVolumeFile(inputVol, argv[1]);
	  inputVol2info.read(argv[2]);
	//  fstream fs;
//	  fs.open(argv[3]);

	  ifstream fs;
	  fs.open(argv[3], ios::in);
	  readUntilNewline(fs);
	  readUntilNewline(fs);
	  readUntilNewline(fs);

	  string s1, s2;

	  int seeda, seedb, seedc;
	  int Num = atoi(argv[4]);


	 float cx = (inputVol.XMin()+inputVol.XMax())*0.5;
	 float cy = (inputVol.YMin() + inputVol.YMax())*0.5;
	 
	 int ni, nj, nk;
	 float x, y;
    
         vector<vector<int> > seed(Num);
	  // vector <int>  seed[Num];
  
	 float x0, y0, z0;
	 
	while(fs>>s1>>seedb>>seedc>>s2){
  		seeda = atoi(s1.erase(0,7).c_str());
	//	cout<<seeda<< " "<< seedb<<" " <<seedc<<" " <<endl;
	    x0 = inputVol2info.XMin() + seeda * inputVol2info.XSpan();
		y0 = inputVol2info.YMin() + seedb * inputVol2info.YSpan();
	    z0 = inputVol2info.ZMin() + seedc * inputVol2info.ZSpan();


		 for(int num=0; num<Num; num ++)
		 {	
	 	 	float  nx = cos(2.0*Pi*(float)num/(float)Num)*(x0-cx) - sin(2.0*Pi*(float)num/(float)Num)*(y0-cy) + cx;
			float  ny = sin(2.0*Pi*(float)num/(float)Num)*(x0-cx) + cos(2.0*Pi*(float)num/(float)Num)*(y0-cy) + cy;
			ni = (int)((nx-inputVol.XMin())/inputVol.XSpan()+0.5);
			nj = (int)((ny-inputVol.YMin())/inputVol.YSpan()+0.5);
            nk = (int)((z0-inputVol.ZMin())/inputVol.ZSpan()+0.5);
			if(ni>=inputVol.XDim()||nj >= inputVol.YDim()|| nk >= inputVol.ZDim()|| ni<0 || nj <0 || nk <0) continue;
			else
			{
			   seed[num].push_back(ni);
			   seed[num].push_back(nj);
			   seed[num].push_back(nk);
			}
		 }
	  }
	  fs.close();

	  fstream fs1;
	  fs1.open(argv[5], ios::out);
	  fs1<<"<!DOCTYPE pointclassdoc>"<<endl;
	  fs1<<"<pointclassdoc>" <<endl;

	  string str[13]={"ffff00", "ff0000","00ff00","ff00ff","0000ff","ff5500","336699", "00ffff", "c0c0c0","800000", "800080", "808000", "008080"};
	  
	  if(Num>13) cout<<"You need add more colors." <<endl;
	  for(int num=0; num< Num; num++)
	  {
	  	 fs1<<" <pointclass timestep=\"0\" name=\"Class "<<num<<"\" color="<<"\"#"<<str[num]<<"\" variable=\"0\" >"<<endl;
		 for(int j = 0; j < seed[num].size()/3; j++)
		  fs1<<"  <point>" <<seed[num][3*j] <<" "<< seed[num][3*j+1] <<" "<<seed[num][3*j+2]<<"</point>"<<endl;
		 fs1<<" </pointclass>"<<endl;
	  }
	  fs1<<"</pointclassdoc>"<<endl;

	  fs1.close();

     cout<<"done !" <<endl;

	}
  catch(VolMagick::Exception &e)
    {
      cerr << e.what() << endl;
    }
  catch(std::exception &e)
    {
      cerr << e.what() << endl;
    }
//.........这里部分代码省略.........

int main(int argc, char **argv)
{
    if(argc < 3)
    {
        std:: cerr <<
                   "Usage: " << argv[0] <<


                   "  <first volume>  <output volume>.   \n";

        return 1;
    }

    try
    {
        VolMagick::Volume inputVol;


        VolMagick::Volume outputVol;

        VolMagick::readVolumeFile(inputVol,argv[1]); ///first argument is input volume

        VolMagick::VolumeFileInfo volinfo1;
        volinfo1.read(argv[1]);
        std::cout << volinfo1.filename() << ":" <<std::endl;


        std::cout<<"minVol1 , maxVol1: "<<volinfo1.min()<<" "<<volinfo1.max()<<std::endl;;


        VolMagick::BoundingBox bbox;
        bbox.minx = inputVol.XMin();
        bbox.maxx = inputVol.XMax();
        bbox.miny = inputVol.YMin();
        bbox.maxy = inputVol.YMax();
        bbox.minz = 2.0*inputVol.ZMin() - inputVol.ZMax();
        bbox.maxz = inputVol.ZMax();

        VolMagick::Dimension dim;
        dim.xdim = inputVol.XDim();
        dim.ydim = inputVol.YDim();
        dim.zdim = (int)((bbox.maxz -bbox.minz)/inputVol.ZSpan())+1;


//	 cout<<bbox.minz <<" " << bbox.maxz<<" "<< bbox.maxy <<endl;
//	 cout<<dim.zdim <<" " << dim.ydim << endl;

        outputVol.voxelType(inputVol.voxelType());
        outputVol.dimension(dim);
        outputVol.boundingBox(bbox);





        for( int kz = 0; kz<outputVol.ZDim()/2; kz++)
            for( int jy = 0; jy<inputVol.YDim(); jy++)
                for( int ix = 0; ix<inputVol.XDim(); ix++)
                    outputVol(ix, jy, kz, inputVol(inputVol.XDim()-1-ix, inputVol.YDim()-1-jy, inputVol.ZDim()-1-kz));

        for( int kz=outputVol.ZDim()/2; kz < outputVol.ZDim(); kz++)
            for( int jy = 0; jy<inputVol.YDim(); jy++)
                for( int ix = 0; ix<inputVol.XDim(); ix++)
                    outputVol(ix, jy, kz, inputVol(ix, jy, kz+1-inputVol.ZDim()));








        VolMagick::createVolumeFile(outputVol, argv[2]);


        cout<<"done!"<<endl;

    }

    catch(VolMagick::Exception &e)
    {
        std:: cerr << e.what() << std::endl;
    }
    catch(std::exception &e)
    {
        std::cerr << e.what() << std::endl;
    }

    return 0;
}

VolMagick::Volume signedDistanceFunction(const boost::shared_ptr<Geometry>& geom,
					 const VolMagick::Dimension& dim,
					 const VolMagick::BoundingBox& bbox)
{
  int dimx = dim[0], dimy = dim[1], dimz = dim[2];

  // read the annotated input file and
  Mesh mesh;
  cerr << "Reading input mesh ";
  read_labeled_mesh(mesh, geom);
  cerr << "done." << endl;

  // build a bounding box around the input and store the
  // origin, span etc.
  //  vector<double> bbox;
  //  construct_bbox(mesh, bbox);
  VolMagick::BoundingBox box(bbox);
  if(box.isNull())
    {
      geom->GetReadyToDrawWire(); //make sure we have calculated extents for this geometry already
      box[0] = geom->m_Min[0];
      box[1] = geom->m_Min[1];
      box[2] = geom->m_Min[2];
      box[3] = geom->m_Max[0];
      box[4] = geom->m_Max[1];
      box[5] = geom->m_Max[2];
    }

  // construct a kd-tree of all the non-isolated mesh_vertices.
  vector<VECTOR3> points;
  vector<Point> pts;
  for(int i = 0; i < mesh.get_nv(); i ++)
  {
     if( mesh.vert_list[i].iso() ) continue;
     Point p = mesh.vert_list[i].point();
     pts.push_back(p);
     points.push_back(VECTOR3(CGAL::to_double(p.x()),
                              CGAL::to_double(p.y()),
                              CGAL::to_double(p.z())));
  }
  KdTree kd_tree(points, 20);
  kd_tree.setNOfNeighbours(1);

  // Now perform a reconstruction to build a tetrahedralized solid
  // with in-out marked.
  Triangulation triang;
  recon(pts, triang);

  // assign weight to each triangle.
  vector<double> weights;
  // assign_sdf_weight(mesh, weights); // comment out for uniform weight.

  VolMagick::Volume vol;

  cerr << "SDF " << endl;
  try
    {
      vol.dimension(VolMagick::Dimension(dimx,dimy,dimz));
      vol.voxelType(VolMagick::Float);
      vol.boundingBox(box);

      for(unsigned int k=0; k<vol.ZDim(); k++)
      {
	for(unsigned int j=0; j<vol.YDim(); j++)
        {
	  for(unsigned int i=0; i<vol.XDim(); i++)
	    {
              double x = vol.XMin() + i*vol.XSpan();
              double y = vol.YMin() + j*vol.YSpan();
              double z = vol.ZMin() + k*vol.ZSpan();
              double fn_val = sdf(Point(x,y,z), mesh, weights, kd_tree, triang);
	      vol(i,j,k, fn_val);
	    }
        }
	fprintf(stderr,
		"%5.2f %%\r",
		(float(k)/float(vol.ZDim()-1))*100.0);
      }

      vol.desc("multi_sdf");
    }
  catch(VolMagick::Exception &e)
    {
      cerr << e.what() << endl;
    }
  catch(std::exception &e)
    {
      cerr << e.what() << endl;
    }

  cerr << endl << "done." << endl;

  return vol;
}

int main(int argc, char **argv) {
  // Initialize log4cplus
  std::ifstream testfile("log4cplus.properties");
  if (testfile) {
    testfile.close();
    log4cplus::PropertyConfigurator::doConfigure("log4cplus.properties");
  }
  else {
    log4cplus::BasicConfigurator::doConfigure();
  }

  if(argc < 9) {
    std::cerr << "Usage: " << argv[0] << " <first volume>" <<
	"<xmin> <ymin> <zmin> <xmax> <ymax> <zmax>  <output volume> \n";
    return 1;
  }

  try {
    VolMagick::Volume inputVol;
    VolMagick::readVolumeFile(inputVol,argv[1]); ///first argument is input volume
	
    VolMagick::Volume  outputVol;
	
    VolMagick::VolumeFileInfo volinfo1;
    volinfo1.read(argv[1]);
    std::cout << volinfo1.filename() << ":" <<std::endl;

    std::cout << "minVol1 , maxVol1: " << volinfo1.min() << " " << 
        volinfo1.max() << std::endl;;
 
    float span[3];
    span[0]=inputVol.XSpan(); 
    span[1]=inputVol.YSpan(); 
    span[2]=inputVol.ZSpan();
	
    VolMagick::BoundingBox bbox;
    bbox.minx = atof(argv[2]);
    bbox.miny = atof(argv[3]);
    bbox.minz = atof(argv[4]);
    bbox.maxx = atof(argv[5]);
    bbox.maxy = atof(argv[6]);
    bbox.maxz = atof(argv[7]);
	
    VolMagick::Dimension dim;
    dim.xdim = (int) ((bbox.maxx-bbox.minx)/ span[0])+1;
    dim.ydim = (int) ((bbox.maxy-bbox.miny)/ span[1])+1;
    dim.zdim = (int) ((bbox.maxz-bbox.minz)/ span[2])+1;

    bbox.maxx = bbox.minx + (dim.xdim-1)*span[0];
    bbox.maxy = bbox.miny + (dim.ydim-1)*span[1];
    bbox.maxz = bbox.minz + (dim.zdim-1)*span[2];
 	
    outputVol.voxelType(inputVol.voxelType());
    outputVol.dimension(dim);
    outputVol.boundingBox(bbox);
      
    float temp;
    int i, j, k;
    int xsh = (int)((bbox.minx - inputVol.XMin())/span[0]);
    int ysh = (int)((bbox.miny - inputVol.YMin())/span[1]);
    int zsh = (int)((bbox.minz - inputVol.ZMin())/span[2]);

    for( int kz = 0; kz<outputVol.ZDim(); kz++) {
      for( int jy = 0; jy<outputVol.YDim(); jy++) {
        for( int ix = 0; ix<outputVol.XDim(); ix++) {
          i = ix + xsh;
          j = jy + ysh;
          k = kz + zsh;
          if (i<0 || i >= inputVol.XDim()|| j<0 || j>= inputVol.YDim() || k <0 || k>=inputVol.ZDim()) {
            outputVol(ix, jy, kz, 0.0);
          } else {
            outputVol(ix,jy,kz, inputVol(i,j,k));
          }
        }
      }
    }
    std::cout << "creating volume file..." << std::endl;
    VolMagick::createVolumeFile(outputVol, argv[8]);
    std::cout << "done!" << std::endl;
  } catch(VolMagick::Exception &e) {
    std:: cerr << e.what() << std::endl;
  } catch(std::exception &e) {
    std::cerr << e.what() << std::endl;
  }

  return 0;
}

int main(int argc, char **argv)
{
  if(argc < 3)
    {
      std:: cerr << 
	"Usage: " << argv[0] << 

	
	"  <first volume>  <output volume> [ bool 0/1 ].   \n"; 
	cerr<<"bool 1 keeps the original volume, bool 0 only the reflection, default 0."  << endl;

      return 1;
    }

  try
    {
      VolMagick::Volume inputVol;

      
      VolMagick::Volume outputVol;

      VolMagick::readVolumeFile(inputVol,argv[1]); ///first argument is input volume
      
      VolMagick::VolumeFileInfo volinfo1;
      volinfo1.read(argv[1]);
      std::cout << volinfo1.filename() << ":" <<std::endl;

       
      std::cout<<"minVol1 , maxVol1: "<<volinfo1.min()<<" "<<volinfo1.max()<<std::endl;;

  
      VolMagick::BoundingBox bbox;
	  bbox.minx = inputVol.XMin();
	  bbox.maxx = inputVol.XMax();
	  bbox.miny = inputVol.YMin();
	  bbox.maxy = inputVol.YMax();
	  bbox.minz = inputVol.ZMin();
	  bbox.maxz = inputVol.ZMax();

	  VolMagick::Dimension dim;
	  dim.xdim = inputVol.XDim();
	  dim.ydim = inputVol.YDim();
	  dim.zdim = inputVol.ZDim();


//	 cout<<bbox.minz <<" " << bbox.maxz<<" "<< bbox.maxy <<endl;
//	 cout<<dim.zdim <<" " << dim.ydim << endl;
      
      outputVol.voxelType(inputVol.voxelType());
      outputVol.dimension(dim);
      outputVol.boundingBox(bbox);

	
      
   
      //Works for GroEL4.2
      for( int kz = 0; kz<outputVol.ZDim(); kz++)
	   for( int jy = 0; jy<inputVol.YDim(); jy++)
	      for( int ix = 0; ix<inputVol.XDim(); ix++)
		       {
			        float temp=0.0;
					if(inputVol.ZDim() >= kz && inputVol.ZDim() - kz < inputVol.ZDim()
					&& inputVol.YDim() >= jy && inputVol.YDim() - jy < inputVol.YDim() )
					temp = inputVol(ix, inputVol.YDim()-jy, inputVol.ZDim()-kz);
	  				outputVol(ix, jy, kz, temp);
			   }	
	 
	 if(argc==4 && atoi(argv[3])== 1)
	 {
      for( int kz = 0; kz<inputVol.ZDim(); kz++)
	   for( int jy = 0; jy<inputVol.YDim(); jy++)
	      for( int ix = 0; ix<inputVol.XDim(); ix++)
		       {
			   		outputVol(ix, jy, kz, outputVol(ix,jy,kz)+inputVol(ix,jy,kz));
			   }		  
	 }
		  
			  
		 
	      

      VolMagick::createVolumeFile(outputVol, argv[2]);


      cout<<"done!"<<endl;

    }

  catch(VolMagick::Exception &e)
    {
      std:: cerr << e.what() << std::endl;
    }
  catch(std::exception &e)
    {
      std::cerr << e.what() << std::endl;
    }

  return 0;
}