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)
{
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;
}
return 0;
}
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;
}
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;
}