void dssLength() {
typedef DGtal::ImageContainerBySTLVector< DGtal::Z2i::Domain, unsigned char> Image;
std::string filename = examplesPath + "contourS.pgm";
Image image = DGtal::PGMReader<Image>::importPGM(filename);
typedef DGtal::functors::IntervalThresholder<Image::Value> Binarizer;
Binarizer b(1, 135);
DGtal::functors::PointFunctorPredicate<Image, Binarizer> predicate(image, b);
DGtal::Z2i::KSpace ks;
ks.init( image.domain().lowerBound(), image.domain().upperBound(), true );
DGtal::SurfelAdjacency<2> sAdj(true);
std::vector< std::vector< DGtal::Z2i::SCell > > contours;
DGtal::Surfaces<DGtal::Z2i::KSpace>::extractAll2DSCellContours(contours, ks, sAdj, predicate);
DGtal::Z2i::Curve c;
c.initFromSCellsVector( contours.at(1) );
typedef DGtal::Z2i::Curve::PointsRange Range;
Range r = c.getPointsRange();
DGtal::DSSLengthEstimator< Range::ConstCirculator > DSSlength;
DSSlength.init(1, r.c(), r.c());
DGtal::trace.info() << "Length: " << DSSlength.eval() << std::endl;
}
void
estimateGeometry(Shape& s,
const double& h,
const Range& r,
std::vector<Point>& points,
std::vector<Point>& tangents,
std::vector<Quantity>& curvatures) {
typedef typename Range::ConstIterator ConstIterator;
for (ConstIterator i = r.begin(); i != r.end(); ++i) {
Point p( *i );
p *= h;
points.push_back(p);
}
typedef typename Range::ConstCirculator ConstCirculator;
typedef ParametricShapeTangentFunctor< Shape > TangentFunctor;
TrueLocalEstimatorOnPoints< ConstCirculator, Shape, TangentFunctor >
trueTangentEstimator;
trueTangentEstimator.attach(&s);
trueTangentEstimator.init( h, r.c(), r.c());
trueTangentEstimator.eval(r.c(), r.c(), std::back_inserter(tangents) );
typedef ParametricShapeCurvatureFunctor< Shape > CurvatureFunctor;
TrueLocalEstimatorOnPoints< ConstCirculator, Shape, CurvatureFunctor >
trueCurvatureEstimator;
trueCurvatureEstimator.attach(&s);
trueCurvatureEstimator.init( h, r.c(), r.c());
trueCurvatureEstimator.eval(r.c(), r.c(), std::back_inserter(curvatures) );
}
/**
* Test
*
*/
bool testFP(string filename)
{
trace.info() << endl;
trace.info() << "Reading GridCurve from " << filename << endl;
ifstream instream; // input stream
instream.open (filename.c_str(), ifstream::in);
//range of points
typedef int Coordinate;
typedef KhalimskySpaceND<2,Coordinate> Kspace; //space
GridCurve<Kspace> c; //building grid curve
c.initFromVectorStream(instream);
typedef GridCurve<Kspace >::PointsRange Range;//range
Range r = c.getPointsRange();//building range
typedef Range::ConstIterator ConstIterator;//constIterator
//faithful polyon
trace.info() << "Building FP (process digital curve as";
trace.info() << ( (c.isClosed())?"closed":"open" ) << ")" << endl;
bool res = true;
if (c.isClosed())
{
typedef FP<Range::ConstCirculator,Coordinate,4> FP;
FP theFP( r.c(), r.c() );
res = theFP.isValid();
}
else
{
typedef FP<Range::ConstIterator,Coordinate,4> FP;
FP theFP( r.begin(), r.end() );
res = theFP.isValid();
}
return res;
}
/**
* Applying test on a given data file
*
*/
bool testEval(string filename)
{
trace.info() << endl;
trace.info() << "Reading GridCurve from " << filename << endl;
ifstream instream; // input stream
instream.open (filename.c_str(), ifstream::in);
typedef KhalimskySpaceND<2> Kspace; //space
GridCurve<Kspace> c; //building grid curve
c.initFromVectorStream(instream);
typedef GridCurve<Kspace >::PointsRange Range;//range
Range r = c.getPointsRange();//building range
trace.info() << "Building Estimator (process range as";
trace.info() << ( (c.isClosed())?"closed":"open" ) << ")" << endl;
if (c.isClosed())
return test(r.c(), r.c());
else
return test(r.begin(), r.end());
}
bool testRange(const Range &aRange)
{
trace.info() << endl;
trace.info() << "Testing Range (" << aRange.size() << " elts)" << endl;
typedef typename IteratorCirculatorTraits<typename Range::ConstIterator>::Value Value;
std::vector<Value> v1,v2,v3,v4;
{
trace.info() << "Forward" << endl;
typename Range::ConstIterator i = aRange.begin();
typename Range::ConstIterator end = aRange.end();
for ( ; i != end; ++i) {
//cout << *i << endl;
v1.push_back(*i);
}
}
{
trace.info() << "Backward" << endl;
typename Range::ConstReverseIterator i = aRange.rbegin();
typename Range::ConstReverseIterator end = aRange.rend();
for ( ; i != end; ++i) {
//cout << *i << endl;
v2.push_back(*i);
}
}
{
trace.info() << "Circulator" << endl;
typename Range::ConstCirculator c = aRange.c();
typename Range::ConstCirculator cend = aRange.c();
if (isNotEmpty(c,cend))
{
do
{
//cout << *c << endl;
v3.push_back(*c);
c++;
} while (c!=cend);
}
}
{
trace.info() << "Reverse Circulator" << endl;
typename Range::ConstReverseCirculator c = aRange.rc();
typename Range::ConstReverseCirculator cend = aRange.rc();
if (isNotEmpty(c,cend))
{
do
{
//cout << *c << endl;
v4.push_back(*c);
c++;
} while (c!=cend);
}
}
return ( std::equal(v1.begin(),v1.end(),v3.begin())
&& std::equal(v2.begin(),v2.end(),v4.begin())
&& std::equal(v1.begin(),v1.end(),v2.rbegin())
&& std::equal(v3.begin(),v3.end(),v4.rbegin()) );
}
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 FreemanChain file name")
("SDP", po::value<std::string>(), "Import a contour as a Sequence of Discrete Points (SDP format)")
("SFP", po::value<std::string>(), "Import a contour as a Sequence of Floating Points (SFP format)")
("drawContourPoint", po::value<double>(), "<size> display contour points as disk of radius <size>")
("fillContour", "fill the contours with default color (gray)")
("lineWidth", po::value<double>()->default_value(1.0), "Define the linewidth of the contour (SDP format)")
("drawPointOfIndex", po::value<int>(), "<index> Draw the contour point of index <index> (default 0) ")
("pointSize", po::value<double>()->default_value(2.0), "<size> Set the display point size of the point displayed by drawPointofIndex option (default 2.0) ")
("noXFIGHeader", " to exclude xfig header in the resulting output stream (no effect with option -outputFile).")
("withProcessing", po::value<std::string>(), "Processing (used only when the input is a Freeman chain (--input)):\n\t DSS segmentation {DSS}\n\t Maximal segments {MS}\n\t Faithful Polygon {FP}\n\t Minimum Length Polygon {MLP}")
("outputFile,o", po::value<std::string>(), " <filename> save output file automatically according the file format extension.")
("outputStreamEPS", " specify eps for output stream format.")
("outputStreamSVG", " specify svg for output stream format.")
("outputStreamFIG", " specify fig for output stream format.")
("invertYaxis", " invertYaxis invert the Y axis for display contours (used only with --SDP)")
("backgroundImage", po::value<std::string>(), "backgroundImage <filename> : display image as background ")
("alphaBG", po::value<double>(), "alphaBG <value> 0-1.0 to display the background image in transparency (default 1.0), (transparency works only if cairo is available)")
("scale", po::value<double>(), "scale <value> 1: normal; >1 : larger ; <1 lower resolutions )");
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()<< std::endl;
}
po::notify(vm);
if(!parseOK||vm.count("help")||argc<=1 || (!(vm.count("input")) && !(vm.count("SDP")) && !(vm.count("SFP"))&&
!(vm.count("backgroundImage")) ) )
{
trace.info()<< "Display discrete contours. " <<std::endl << "Basic usage: "<<std::endl
<< "\t displayContours [options] --input <fileName> "<<std::endl
<< general_opt << "\n";
return 0;
}
double lineWidth= vm["lineWidth"].as<double>();
bool filled = vm.count("fillContour");
double scale=1.0;
if(vm.count("scale")) {
scale = vm["scale"].as<double>();
}
Board2D aBoard;
aBoard.setUnit (0.05*scale, LibBoard::Board::UCentimeter);
double alpha=1.0;
if(vm.count("alphaBG")) {
alpha = vm["alphaBG"].as<double>();
}
if(vm.count("backgroundImage")) {
std::string imageName = vm["backgroundImage"].as<std::string>();
typedef ImageSelector<Z2i::Domain, unsigned char>::Type Image;
Image img = DGtal::GenericReader<Image>::import( imageName );
Z2i::Point ptInf = img.domain().lowerBound();
Z2i::Point ptSup = img.domain().upperBound();
unsigned int width = abs(ptSup[0]-ptInf[0]+1);
unsigned int height = abs(ptSup[1]-ptInf[1]+1);
aBoard.drawImage(imageName, 0-0.5,height-0.5, width, height, -1, alpha );
}
if(vm.count("input")) {
std::string fileName = vm["input"].as<std::string>();
std::vector< FreemanChain<int> > vectFc = PointListReader< Z2i::Point>:: getFreemanChainsFromFile<int> (fileName);
aBoard << CustomStyle( vectFc.at(0).className(),
new CustomColors( Color::Red , filled? Color::Gray: Color::None ) );
aBoard.setLineWidth (lineWidth);
for(unsigned int i=0; i<vectFc.size(); i++) {
aBoard << vectFc.at(i) ;
if(vm.count("drawPointOfIndex")) {
int index = vm["drawPointOfIndex"].as<int>();
double size = vm["pointSize"].as<double>();
aBoard.setPenColor(Color::Blue);
aBoard.fillCircle((double)(vectFc.at(i).getPoint(index)[0]), (double)(vectFc.at(i).getPoint(index)[1]), size);
}
if(vm.count("withProcessing")) {
std::string processingName = vm["withProcessing"].as<std::string>();
std::vector<Z2i::Point> vPts(vectFc.at(i).size()+1);
copy ( vectFc.at(i).begin(), vectFc.at(i).end(), vPts.begin() );
bool isClosed;
if ( vPts.at(0) == vPts.at(vPts.size()-1) ) {
isClosed = true;
vPts.pop_back();
} else isClosed = false;
if (processingName == "DSS") {
typedef ArithmeticalDSSComputer<std::vector<Z2i::Point>::iterator,int,4> DSS4;
typedef GreedySegmentation<DSS4> Decomposition4;
DSS4 computer;
Decomposition4 theDecomposition( vPts.begin(),vPts.end(),computer );
//for each segment
std::string className;
for ( Decomposition4::SegmentComputerIterator it = theDecomposition.begin();
it != theDecomposition.end(); ++it )
{
DSS4::Primitive segment(it->primitive());
aBoard << SetMode( segment.className(), "BoundingBox" );
className = segment.className() + "/BoundingBox";
aBoard << CustomStyle( className,
new CustomPenColor( DGtal::Color::Gray ) );
aBoard << segment; // draw each segment
}
} else if (processingName == "MS") {
typedef ArithmeticalDSSComputer<std::vector<Z2i::Point>::iterator,int,4> DSS4;
typedef SaturatedSegmentation<DSS4> Decomposition4;
//Segmentation
DSS4 computer;
Decomposition4 theDecomposition( vPts.begin(),vPts.end(),computer );
//for each segment
std::string className;
for ( Decomposition4::SegmentComputerIterator it = theDecomposition.begin();
it != theDecomposition.end(); ++it )
{
DSS4::Primitive segment(it->primitive());
aBoard << SetMode( segment.className(), "BoundingBox" );
className = segment.className() + "/BoundingBox";
aBoard << CustomStyle( className,
new CustomPenColor( DGtal::Color::Gray ) );
aBoard << segment; // draw each segment
}
} else if (processingName == "FP") {
typedef FP<std::vector<Z2i::Point>::iterator,int,4> FP;
FP theFP( vPts.begin(),vPts.end() );
aBoard << CustomStyle( theFP.className(),
new CustomPenColor( DGtal::Color::Black ) );
aBoard << theFP;
} else if (processingName == "MLP") {
typedef FP<std::vector<Z2i::Point>::iterator,int,4> FP;
FP theFP( vPts.begin(),vPts.end() );
std::vector<FP::RealPoint> v( theFP.size() );
theFP.copyMLP( v.begin() );
//polyline to draw
std::vector<LibBoard::Point> polyline;
std::vector<FP::RealPoint>::const_iterator it = v.begin();
for ( ; it != v.end(); ++it) {
FP::RealPoint p = (*it);
polyline.push_back(LibBoard::Point(p[0],p[1]));
}
if (isClosed) {
FP::RealPoint p = (*v.begin());
polyline.push_back(LibBoard::Point(p[0],p[1]));
}
aBoard.setPenColor(DGtal::Color::Black);
aBoard.drawPolyline(polyline);
} else if (processingName == "MDCA") {
typedef KhalimskySpaceND<2,int> KSpace;
typedef GridCurve<KSpace> Curve;
Curve curve; //grid curve
curve.initFromPointsVector( vPts );
typedef Curve::IncidentPointsRange Range; //range
Range r = curve.getIncidentPointsRange(); //range
typedef Range::ConstCirculator ConstCirculator; //iterator
typedef StabbingCircleComputer<ConstCirculator> SegmentComputer; //segment computer
//typedef GeometricalDCA<ConstIterator> SegmentComputer; //segment computer
typedef SaturatedSegmentation<SegmentComputer> Segmentation;
//Segmentation theSegmentation( r.begin(), r.end(), SegmentComputer() );
Segmentation theSegmentation( r.c(), r.c(), SegmentComputer() );
theSegmentation.setMode("Last");
// board << curve;
Segmentation::SegmentComputerIterator it = theSegmentation.begin();
Segmentation::SegmentComputerIterator itEnd = theSegmentation.end();
Board2D otherBoard;
otherBoard.setPenColor(DGtal::Color::Black);
otherBoard << curve;
for ( ; it != itEnd; ++it ) {
aBoard << SetMode(SegmentComputer().className(), "") << (*it);
otherBoard << SetMode(SegmentComputer().className(), "") << (*it);
}
otherBoard.saveSVG("mdca.svg", Board2D::BoundingBox, 5000 );
}
}
}
}
if(vm.count("SDP") || vm.count("SFP")) {
bool drawPoints= vm.count("drawContourPoint");
bool invertYaxis = vm.count("invertYaxis");
double pointSize=1.0;
if(drawPoints) {
pointSize = vm["drawContourPoint"].as<double>();
}
std::vector<LibBoard::Point> contourPt;
if(vm.count("SDP")) {
std::string fileName = vm["SDP"].as<std::string>();
std::vector< Z2i::Point > contour =
PointListReader< Z2i::Point >::getPointsFromFile(fileName);
for(unsigned int j=0; j<contour.size(); j++) {
LibBoard::Point pt((double)(contour.at(j)[0]),
(invertYaxis? (double)(-contour.at(j)[1]+contour.at(0)[1]):(double)(contour.at(j)[1])));
contourPt.push_back(pt);
if(drawPoints) {
aBoard.fillCircle(pt.x, pt.y, pointSize);
}
}
}
if(vm.count("SFP")) {
std::string fileName = vm["SFP"].as<std::string>();
std::vector< PointVector<2,double> > contour =
PointListReader< PointVector<2,double> >::getPointsFromFile(fileName);
for(unsigned int j=0; j<contour.size(); j++) {
LibBoard::Point pt((double)(contour.at(j)[0]),
(invertYaxis? (double)(-contour.at(j)[1]+contour.at(0)[1]):(double)(contour.at(j)[1])));
contourPt.push_back(pt);
if(drawPoints) {
aBoard.fillCircle(pt.x, pt.y, pointSize);
}
}
}
aBoard.setPenColor(Color::Red);
aBoard.setFillColor(Color::Gray);
aBoard.setLineStyle (LibBoard::Shape::SolidStyle );
aBoard.setLineWidth (lineWidth);
if(!filled) {
aBoard.drawPolyline(contourPt);
} else {
aBoard.fillPolyline(contourPt);
}
if(vm.count("drawPointOfIndex")) {
int index = vm["drawPointOfIndex"].as<int>();
double size = vm["pointSize"].as<double>();
aBoard.fillCircle((double)(contourPt.at(index).x), (double)(contourPt.at(index).y), size);
}
}
if(vm.count("outputFile")) {
std::string outputFileName= vm["outputFile"].as<std::string>();
std::string extension = outputFileName.substr(outputFileName.find_last_of(".") + 1);
if(extension=="svg") {
aBoard.saveSVG(outputFileName.c_str());
}
#ifdef WITH_CAIRO
else if (extension=="eps") {
aBoard.saveCairo(outputFileName.c_str(),Board2D::CairoEPS );
} else if (extension=="pdf") {
aBoard.saveCairo(outputFileName.c_str(),Board2D::CairoPDF );
} else if (extension=="png") {
aBoard.saveCairo(outputFileName.c_str(),Board2D::CairoPNG );
}
#endif
else if(extension=="eps") {
aBoard.saveEPS(outputFileName.c_str());
} else if(extension=="fig") {
aBoard.saveFIG(outputFileName.c_str(),LibBoard::Board::BoundingBox, 10.0, !vm.count("noXFIGHeader") );
}
}
if (vm.count("outputStreamSVG")) {
aBoard.saveSVG(std::cout);
} else if (vm.count("outputStreamFIG")) {
aBoard.saveFIG(std::cout, LibBoard::Board::BoundingBox, 10.0, !vm.count("noXFIGHeader"));
} else if (vm.count("outputStreamEPS")) {
aBoard.saveEPS(std::cout);
}
}
bool
estimatorOnShapeDigitization( const string& name,
Shape & aShape,
const RealPoint& low, const RealPoint& up,
double h )
{
using namespace Z2i;
trace.beginBlock ( ( "Curvature estimation on digitization of "
+ name ). c_str() );
// Creates a digitizer on the window (low, up).
GaussDigitizer<Space,Shape> dig;
dig.attach( aShape ); // attaches the shape.
dig.init( low, up, h );
// The domain size is given by the digitizer
// according to the window and the step.
Domain domain = dig.getDomain();
// Create cellular space
KSpace K;
bool ok = K.init( dig.getLowerBound(), dig.getUpperBound(), true );
if ( ! ok )
{
std::cerr << "[estimatorOnShapeDigitization]"
<< " error in creating KSpace." << std::endl;
}
else
try {
// Extracts shape boundary
SurfelAdjacency<KSpace::dimension> SAdj( true );
SCell bel = Surfaces<KSpace>::findABel( K, dig, 10000 );
// Getting the consecutive surfels of the 2D boundary
std::vector<Point> points;
Surfaces<KSpace>::track2DBoundaryPoints( points, K, SAdj, dig, bel );
// Create GridCurve
GridCurve<KSpace> gridcurve( K );
gridcurve.initFromVector( points );
// Create range of incident points
typedef GridCurve<KSpace>::IncidentPointsRange Range;
typedef Range::ConstIterator ClassicIterator;
typedef Range::ConstCirculator CircularIterator;
Range r = gridcurve.getIncidentPointsRange();//building range
// Estimation
std::vector<double> estimations;
if (gridcurve.isOpen())
{
typedef StabbingCircleComputer<ClassicIterator> SegmentComputer;
typedef CurvatureFromDCAEstimator<SegmentComputer> SCEstimator;
typedef MostCenteredMaximalSegmentEstimator<SegmentComputer,SCEstimator> CurvatureEstimator;
SegmentComputer sc;
SCEstimator sce;
CurvatureEstimator estimator(sc, sce);
std::cout << "# open grid curve" << endl;
estimator.init( h, r.begin(), r.end() );
estimator.eval( r.begin(), r.end(), std::back_inserter(estimations) );
}
else
{
typedef StabbingCircleComputer<CircularIterator> SegmentComputer;
typedef CurvatureFromDCAEstimator<SegmentComputer> SCEstimator;
typedef MostCenteredMaximalSegmentEstimator<SegmentComputer,SCEstimator> CurvatureEstimator;
SegmentComputer sc;
SCEstimator sce;
CurvatureEstimator estimator(sc, sce);
std::cout << "# closed grid curve" << endl;
estimator.init( h, r.c(), r.c() );
estimator.eval( r.c(), r.c(), std::back_inserter(estimations) );
}
// Print (standard output)
std::cout << "# idx kappa" << endl;
unsigned int i = 0;
for ( ClassicIterator it = r.begin(), ite = r.end();
it != ite; ++it, ++i )
{
std::cout << i << " " << estimations.at(i) << std::endl;
}
}
catch ( InputException e )
{
std::cerr << "[estimatorOnShapeDigitization]"
<< " error in finding a bel." << std::endl;
ok = false;
}
trace.emphase() << ( ok ? "Passed." : "Error." ) << endl;
trace.endBlock();
return ok;
}
