int main(int argc, char**argv)
{
// parse command line ----------------------------------------------
po::options_description general_opt ( "Allowed options are: " );
general_opt.add_options()
( "help,h", "display this message." )
( "input,i", po::value<std::string>(), "Input vol file." )
( "output,o", po::value<string>(),"Output filename." );
bool parseOK=true;
po::variables_map vm;
try{
po::store(po::parse_command_line(argc, argv, general_opt), vm);
}catch(const std::exception& ex){
parseOK=false;
trace.info()<< "Error checking program options: "<< ex.what()<< endl;
}
po::notify ( vm );
if ( !parseOK || vm.count ( "help" ) ||argc<=1 )
{
trace.info() << "Add a border of one voxel with value 0 around a vol file."<<std::endl
<< std::endl << "Basic usage: "<<std::endl
<< "\tvolAddBorder --input <volFileName> --o <volOutputFileName> "<<std::endl
<< general_opt << "\n";
return 0;
}
//Parse options
if ( ! ( vm.count ( "input" ) ) ) missingParam ( "--input" );
std::string filename = vm["input"].as<std::string>();
if ( ! ( vm.count ( "output" ) ) ) missingParam ( "--output" );
std::string outputFileName = vm["output"].as<std::string>();
typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> MyImageC;
MyImageC imageC = VolReader< MyImageC >::importVol ( filename );
MyImageC outputImage( Z3i::Domain( imageC.domain().lowerBound() - Vector().diagonal(1),
imageC.domain().upperBound() + Vector().diagonal(1)));
//Fast Copy
for(MyImageC::Domain::ConstIterator it = imageC.domain().begin(),
itend = imageC.domain().end(); it != itend; ++it)
outputImage.setValue( *it , imageC(*it));
typedef GrayscaleColorMap<unsigned char> Gray;
bool res = VolWriter< MyImageC , Gray>::exportVol(outputFileName, outputImage, 0, 255);
if (res) return 0; else return 1;
}
int main(int argc, char**argv)
{
// parse command line ----------------------------------------------
po::options_description general_opt ( "Allowed options are: " );
general_opt.add_options()
( "help,h", "display this message." )
( "input,i", po::value<std::string>(), "Input vol file." )
( "output,o", po::value<string>(),"Output filename." );
po::variables_map vm;
po::store ( po::parse_command_line ( argc, argv, general_opt ), vm );
po::notify ( vm );
if ( vm.count ( "help" ) ||argc<=1 )
{
trace.info() << "Brutally sub sample a vol file (division by 2 in each direction)."<<std::endl
<< std::endl << "Basic usage: "<<std::endl
<< "\tvolSubSample --input <volFileName> --o <volOutputFileName> "<<std::endl
<< general_opt << "\n";
return 0;
}
//Parse options
if ( ! ( vm.count ( "input" ) ) ) missingParam ( "--input" );
std::string filename = vm["input"].as<std::string>();
if ( ! ( vm.count ( "output" ) ) ) missingParam ( "--output" );
std::string outputFileName = vm["output"].as<std::string>();
trace.beginBlock("Loading file");
typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> MyImageC;
MyImageC imageC = VolReader< MyImageC >::importVol ( filename );
MyImageC outputImage( Z3i::Domain( imageC.domain().lowerBound() - Vector().diagonal(1),
(imageC.domain().upperBound()-imageC.domain().lowerBound())/Vector().diagonal(2) + Vector().diagonal(1)));
trace.endBlock();
unsigned int cpt=0;
unsigned int maxS = imageC.domain().size();
Point subvector = Vector().diagonal(2);
trace.beginBlock("Down-scaling the volume...");
//Fast Copy
for(MyImageC::Domain::ConstIterator it = imageC.domain().begin(),
itend = imageC.domain().end(); it != itend; ++it)
{
trace.info() << cpt;
trace.progressBar( cpt, maxS);
cpt++;
outputImage.setValue( *it/subvector , imageC(*it));
}
trace.endBlock();
typedef GrayscaleColorMap<unsigned char> Gray;
bool res = VolWriter< MyImageC , Gray>::exportVol(outputFileName, outputImage, 0, 255);
if (res) return 0; else return 1;
}
int main(int argc, char**argv)
{
// parse command line ----------------------------------------------
po::options_description general_opt ( "Allowed options are: " );
general_opt.add_options()
( "help,h", "display this message." )
( "input,i", po::value<std::string>(), "Input vol file." )
( "output,o", po::value<string>(),"Output filename." )
("function,f", po::value<string>()->default_value("mean"), "Function used to the down-sampling: {none,max, min, mean}" );
po::variables_map vm;
po::store ( po::parse_command_line ( argc, argv, general_opt ), vm );
po::notify ( vm );
if ( vm.count ( "help" ) ||argc<=1 )
{
trace.info() << "Brutally sub sample a vol file (division by 2 in each direction)."<<std::endl
<< std::endl << "Basic usage: "<<std::endl
<< "\tvolSubSample --input <volFileName> --o <volOutputFileName> "<<std::endl
<< general_opt << "\n";
return 0;
}
//Parse options
if ( ! ( vm.count ( "input" ) ) ) missingParam ( "--input" );
std::string filename = vm["input"].as<std::string>();
std::string function = vm["function"].as<std::string>();
if ( ! ( vm.count ( "output" ) ) ) missingParam ( "--output" );
std::string outputFileName = vm["output"].as<std::string>();
trace.beginBlock("Loading file");
typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> MyImageC;
MyImageC imageC = VolReader< MyImageC >::importVol ( filename );
MyImageC outputImage( Z3i::Domain( imageC.domain().lowerBound(),
(imageC.domain().upperBound()-imageC.domain().lowerBound())/Vector().diagonal(2)));
trace.endBlock();
Point subvector = Vector().diagonal(2);
Point p;
unsigned char val;
trace.beginBlock("Down-scaling the volume...");
trace.info()<<"Function= "<<function<<std::endl;
trace.info() << outputImage.domain() << std::endl;
//Fast Copy
if (function == "none")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
p = (*it) * 2;
outputImage.setValue( *it , imageC( p ));
}
else
if (function == "max")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = maxVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val );
}
else
if (function == "min")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = minVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val);
}
else
if (function == "mean")
for(MyImageC::Domain::ConstIterator it = outputImage.domain().begin(),
itend = outputImage.domain().end(); it != itend; ++it)
{
val = meanVal<unsigned char, MyImageC, Point>(imageC, *it, imageC.domain());
outputImage.setValue( *it , val );
}
else
trace.error() << "Bad function !"<<std::endl;
trace.endBlock();
trace.beginBlock("Exporting...");
bool res = VolWriter< MyImageC>::exportVol(outputFileName, outputImage);
trace.endBlock();
if (res) return 0; else return 1;
}
int main(int argc, char**argv)
{
// parse command line ----------------------------------------------
po::options_description general_opt ( "Allowed options are: " );
general_opt.add_options()
( "help,h", "display this message." )
( "input,i", po::value<std::string>(), "Input vol file." )
("thresholdMin,m", po::value<int>()->default_value(0), "threshold min (excluded) to define binary shape" )
("thresholdMax,M", po::value<int>()->default_value(255), "threshold max (included) to define binary shape" );
bool parseOK=true;
po::variables_map vm;
try{
po::store(po::parse_command_line(argc, argv, general_opt), vm);
}catch(const std::exception& ex){
parseOK=false;
trace.info()<< "Error checking program options: "<< ex.what()<< endl;
}
po::notify ( vm );
if (!parseOK || vm.count ( "help" ) ||argc<=1 )
{
trace.info() << "Compute the Euleur Characteristic of a vol to a 8-bit raw file. The vol file is first binarized using interval [m,M[ thresholds and the Eucler characteristic is given from the cubical complex"<<std::endl
<< std::endl << "Basic usage: "<<std::endl
<< "\eulerCharacteristic --input <volFileName> -m <minlevel> -M <maxlevel> "<<std::endl
<< general_opt << "\n";
return 0;
}
//Parse options
if ( ! ( vm.count ( "input" ) ) ) missingParam ( "--input" );
std::string filename = vm["input"].as<std::string>();
int thresholdMin = vm["thresholdMin"].as<int>();
int thresholdMax = vm["thresholdMax"].as<int>();
//Importing the Vol
trace.beginBlock("Loading the vol file");
typedef ImageContainerBySTLVector<Z3i::Domain, unsigned char> MyImageC;
MyImageC imageC = VolReader< MyImageC >::importVol ( filename );
trace.info()<<imageC<<std::endl;
trace.endBlock();
//Constructing the cubical complex
trace.beginBlock("Construting the cubical complex");
KSpace::CellSet myCellSet;
KSpace ks;
bool space_ok = ks.init( imageC.domain().lowerBound(), imageC.domain().upperBound(), true );
if (!space_ok)
{
trace.error() << "Error in the Khamisky space construction."<<std::endl;
return 2;
}
functors::IntervalForegroundPredicate<MyImageC> interval(imageC, thresholdMin,thresholdMax);
for(MyImageC::Domain::ConstIterator it =imageC.domain().begin(), itend= imageC.domain().end();
it != itend; ++it)
{
if (interval( *it ))
{
Domain dom( 2*(*it), 2*(*it) + Point::diagonal(2));
for(Domain::ConstIterator itdom = dom.begin(), itdomend = dom.end(); itdom != itdomend; ++itdom)
myCellSet.insert( ks.uCell( *itdom) );
}
}
trace.info() << "Got "<< myCellSet.size()<< " cells"<<std::endl;
trace.endBlock();
trace.beginBlock("Computing the characteristics");
std::vector<int> cells(4,0);
for(KSpace::CellSet::const_iterator it = myCellSet.begin(), itend = myCellSet.end(); it !=itend; ++it)
cells[ ks.uDim(*it) ] ++;
trace.info() << "Got "<< cells[0]<< " pointels "<<cells[1]<<" linels "<< cells[2]<<" surfels and "<<cells[3]<<" bells"<<std::endl;
trace.endBlock();
trace.info() << "Volumetric Euler Characteristic = "<<cells[0] - cells[1] + cells[2] - cells[3]<<std::endl;
return 0;
}