void computeEstimation
( const po::variables_map& vm, //< command-line parameters
const KSpace& K, //< cellular grid space
const ImplicitShape& shape, //< implicit shape "ground truth"
const Surface& surface, //< digital surface approximating shape
Estimator& estimator ) //< an initialized estimator
{
typedef typename Surface::ConstIterator ConstIterator;
typedef typename Surface::Surfel Surfel;
typedef typename Estimator::Quantity Quantity;
typedef double Scalar;
typedef DepthFirstVisitor< Surface > Visitor;
typedef GraphVisitorRange< Visitor > VisitorRange;
typedef typename VisitorRange::ConstIterator VisitorConstIterator;
std::string fname = vm[ "output" ].as<std::string>();
string nameEstimator = vm[ "estimator" ].as<string>();
trace.beginBlock( "Computing " + nameEstimator + " estimations." );
CountedPtr<VisitorRange> range( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
std::vector<Quantity> n_estimations;
estimator.eval( range->begin(), range->end(), std::back_inserter( n_estimations ) );
trace.info() << "- nb estimations = " << n_estimations.size() << std::endl;
trace.endBlock();
trace.beginBlock( "Computing areas." );
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
double area_est = 0.0; // normal integration with absolute value.
unsigned int i = 0;
for ( typename VisitorRange::ConstIterator it = range->begin(), itE = range->end();
it != itE; ++it, ++i )
{
Surfel s = *it;
Dimension k = K.sOrthDir( s );
area_est += abs( n_estimations[ i ][ k ] );
}
double h = vm["gridstep"].as<double>();
trace.info() << setprecision(10) << "- Area_est " << ( area_est * h * h ) << std::endl;
std::ostringstream area_sstr;
area_sstr << fname << "-" << nameEstimator << "-area-" << h << ".txt";
std::ofstream area_output( area_sstr.str().c_str() );
area_output << "# Area estimation by digital surface integration." << std::endl;
area_output << "# X: " << nameEstimator << std::endl;
area_output << "# h Area[X] nb_surf" << std::endl;
area_output << setprecision(10) << h
<< " " << ( area_est * h * h )
<< " " << i << std::endl;
area_output.close();
trace.endBlock();
}
int main( int argc, char** argv )
{
//! [greedy-plane-segmentation-ex3-parseCommandLine]
trace.info() << "Segments the surface at given threshold within given volume into digital planes of rational width num/den." << std::endl;
// Setting default options: ----------------------------------------------
// input file used:
string inputFilename = examplesPath + "samples/Al.100.vol" ;
trace.info() << "input file used " << inputFilename << std::endl;
// parameter threshold
unsigned int threshold = 0;
trace.info() << "the value that defines the isosurface in the image (an integer between 0 and 255)= " << threshold<< std::endl;
// parameter widthNum
unsigned int widthNum = 1;
trace.info() << "the numerator of the rational width (a non-null integer) =" << widthNum<< std::endl;
// parameter widthDen
unsigned int widthDen = 1;
trace.info() << "the denominator of the rational width (a non-null integer)= " << widthDen<< std::endl;
//! [greedy-plane-segmentation-ex3-parseCommandLine]
//! [greedy-plane-segmentation-ex3-loadVolume]
QApplication application(argc,argv);
typedef ImageSelector < Domain, int>::Type Image;
Image image = VolReader<Image>::importVol(inputFilename);
DigitalSet set3d (image.domain());
SetFromImage<DigitalSet>::append<Image>(set3d, image, threshold,255);
//! [greedy-plane-segmentation-ex3-loadVolume]
//! [greedy-plane-segmentation-ex3-makeSurface]
trace.beginBlock( "Set up digital surface." );
// We initializes the cellular grid space used for defining the
// digital surface.
KSpace ks;
bool ok = ks.init( set3d.domain().lowerBound(),
set3d.domain().upperBound(), true );
if ( ! ok ) std::cerr << "[KSpace.init] Failed." << std::endl;
SurfelAdjacency<KSpace::dimension> surfAdj( true ); // interior in all directions.
MyDigitalSurfaceContainer* ptrSurfContainer =
new MyDigitalSurfaceContainer( ks, set3d, surfAdj );
MyDigitalSurface digSurf( ptrSurfContainer ); // acquired
trace.endBlock();
//! [greedy-plane-segmentation-ex3-makeSurface]
//! [greedy-plane-segmentation-ex3-segment]
Point p;
Dimension axis;
unsigned int j = 0;
unsigned int nb = digSurf.size();
// First pass to find biggest planes.
trace.beginBlock( "1) Segmentation first pass. Computes all planes so as to sort vertices by the plane size." );
std::map<Vertex,unsigned int> v2size;
NaivePlaneComputer planeComputer;
std::priority_queue<VertexSize> Q;
std::vector<Point> layer;
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
{
if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb );
Vertex v = *it;
axis = ks.sOrthDir( v );
planeComputer.init( axis, 500, widthNum, widthDen );
// The visitor takes care of all the breadth-first traversal.
Visitor visitor( digSurf, v );
layer.clear();
Visitor::Size currentSize = visitor.current().second;
while ( ! visitor.finished() )
{
Visitor::Node node = visitor.current();
v = node.first;
axis = ks.sOrthDir( v );
p = ks.sCoords( ks.sDirectIncident( v, axis ) );
if ( node.second != currentSize )
{
// std::cerr << "Layer " << currentSize << ", size=" << layer.size() << std::endl;
bool isExtended = planeComputer.extend( layer.begin(), layer.end() );
if ( ! isExtended )
break;
layer.clear();
currentSize = node.second;
}
layer.push_back( p );
visitor.expand();
}
// std::cerr << v << " -> " << planeComputer.size() << std::endl;
Q.push( VertexSize( v, planeComputer.size() ) );
}
trace.endBlock();
trace.beginBlock( "2) Segmentation second pass. Visits vertices from the one with biggest plane to the one with smallest plane." );
std::set<Vertex> processedVertices;
std::map<Vertex,SegmentedPlane*> v2plane;
std::vector<SegmentedPlane*> segmentedPlanes;
j = 0;
while ( ! Q.empty() )
{
if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb );
Vertex v = Q.top().v;
Q.pop();
if ( processedVertices.find( v ) != processedVertices.end() ) // already in set
continue; // process to next vertex
SegmentedPlane* ptrSegment = new SegmentedPlane;
segmentedPlanes.push_back( ptrSegment ); // to delete them afterwards.
axis = ks.sOrthDir( v );
ptrSegment->plane.init( axis, 500, widthNum, widthDen );
// The visitor takes care of all the breadth-first traversal.
Visitor visitor( digSurf, v );
while ( ! visitor.finished() )
{
Visitor::Node node = visitor.current();
v = node.first;
if ( processedVertices.find( v ) == processedVertices.end() )
{ // Vertex is not in processedVertices
axis = ks.sOrthDir( v );
p = ks.sCoords( ks.sDirectIncident( v, axis ) );
bool isExtended = ptrSegment->plane.extend( p );
if ( isExtended )
{ // surfel is in plane.
processedVertices.insert( v );
v2plane[ v ] = ptrSegment;
visitor.expand();
}
else // surfel is not in plane and should not be used in the visit.
visitor.ignore();
}
else // surfel is already in some plane.
visitor.ignore();
}
// Assign random color for each plane.
ptrSegment->color = Color( rand() % 256, rand() % 256, rand() % 256, 255 );
}
trace.endBlock();
//! [greedy-plane-segmentation-ex3-segment]
//! [greedy-plane-segmentation-ex3-visualization]
Viewer3D<> viewer( ks );
viewer.show();
Color col( 255, 255, 120 );
for ( std::map<Vertex,SegmentedPlane*>::const_iterator
it = v2plane.begin(), itE = v2plane.end();
it != itE; ++it )
{
viewer << CustomColors3D( it->second->color, it->second->color );
viewer << ks.unsigns( it->first );
}
viewer << Viewer3D<>::updateDisplay;
//! [greedy-plane-segmentation-ex3-visualization]
//! [greedy-plane-segmentation-ex3-freeMemory]
for ( std::vector<SegmentedPlane*>::iterator
it = segmentedPlanes.begin(), itE = segmentedPlanes.end();
it != itE; ++it )
delete *it;
segmentedPlanes.clear();
v2plane.clear();
//! [greedy-plane-segmentation-ex3-freeMemory]
return application.exec();
}
int main( int argc, char** argv )
{
//! [greedy-plane-segmentation-parseCommandLine]
// parse command line ----------------------------------------------
po::options_description general_opt("Allowed options are: ");
general_opt.add_options()
("help,h", "display this message")
("input-file,i", po::value<std::string>()->default_value( examplesPath + "samples/Al.100.vol" ), "the volume file (.vol)" )
("threshold,t", po::value<unsigned int>()->default_value(1), "the value that defines the isosurface in the image (an integer between 0 and 255)." )
("width-num,w", po::value<unsigned int>()->default_value(1), "the numerator of the rational width (a non-null integer)." )
("width-den,d", po::value<unsigned int>()->default_value(1), "the denominator of the rational width (a non-null integer)." );
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 ) )
{
std::cout << "Usage: " << argv[0]
<< " [-i <fileName.vol>] [-t <threshold>] [-w <num>] [-d <den>]" << std::endl
<< "Segments the surface at given threshold within given volume into digital planes of rational width num/den." << std::endl
<< general_opt << std::endl;
return 0;
}
string inputFilename = vm["input-file"].as<std::string>();
unsigned int threshold = vm["threshold"].as<unsigned int>();
unsigned int widthNum = vm["width-num"].as<unsigned int>();
unsigned int widthDen = vm["width-den"].as<unsigned int>();
//! [greedy-plane-segmentation-parseCommandLine]
//! [greedy-plane-segmentation-loadVolume]
QApplication application(argc,argv);
typedef ImageSelector < Domain, int>::Type Image;
Image image = VolReader<Image>::importVol(inputFilename);
DigitalSet set3d (image.domain());
SetFromImage<DigitalSet>::append<Image>(set3d, image, threshold,255);
//! [greedy-plane-segmentation-loadVolume]
//! [greedy-plane-segmentation-makeSurface]
trace.beginBlock( "Set up digital surface." );
// We initializes the cellular grid space used for defining the
// digital surface.
KSpace ks;
bool ok = ks.init( set3d.domain().lowerBound(),
set3d.domain().upperBound(), true );
if ( ! ok ) std::cerr << "[KSpace.init] Failed." << std::endl;
SurfelAdjacency<KSpace::dimension> surfAdj( true ); // interior in all directions.
MyDigitalSurfaceContainer* ptrSurfContainer =
new MyDigitalSurfaceContainer( ks, set3d, surfAdj );
MyDigitalSurface digSurf( ptrSurfContainer ); // acquired
trace.endBlock();
//! [greedy-plane-segmentation-makeSurface]
//! [greedy-plane-segmentation-segment]
trace.beginBlock( "Segment into planes." );
std::set<Vertex> processedVertices;
std::vector<SegmentedPlane*> segmentedPlanes;
std::map<Vertex,SegmentedPlane*> v2plane;
Point p;
Dimension axis;
unsigned int j = 0;
unsigned int nb = digSurf.size();
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
{
if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb );
Vertex v = *it;
if ( processedVertices.find( v ) != processedVertices.end() ) // already in set
continue; // process to next vertex
SegmentedPlane* ptrSegment = new SegmentedPlane;
segmentedPlanes.push_back( ptrSegment ); // to delete them afterwards.
axis = ks.sOrthDir( v );
ptrSegment->plane.init( axis, 500, widthNum, widthDen );
// The visitor takes care of all the breadth-first traversal.
Visitor visitor( digSurf, v );
while ( ! visitor.finished() )
{
Visitor::Node node = visitor.current();
v = node.first;
if ( processedVertices.find( v ) == processedVertices.end() )
{ // Vertex is not in processedVertices
axis = ks.sOrthDir( v );
p = ks.sCoords( ks.sDirectIncident( v, axis ) );
bool isExtended = ptrSegment->plane.extend( p );
if ( isExtended )
{ // surfel is in plane.
processedVertices.insert( v );
v2plane[ v ] = ptrSegment;
visitor.expand();
}
else // surfel is not in plane and should not be used in the visit.
visitor.ignore();
}
else // surfel is already in some plane.
visitor.ignore();
}
// Assign random color for each plane.
ptrSegment->color = Color( random() % 256, random() % 256, random() % 256, 255 );
}
trace.endBlock();
//! [greedy-plane-segmentation-segment]
//! [greedy-plane-segmentation-visualization]
Viewer3D viewer;
viewer.show();
for ( std::map<Vertex,SegmentedPlane*>::const_iterator
it = v2plane.begin(), itE = v2plane.end();
it != itE; ++it )
{
viewer << CustomColors3D( it->second->color, it->second->color );
viewer << ks.unsigns( it->first );
}
viewer << Display3D::updateDisplay;
//! [greedy-plane-segmentation-visualization]
//! [greedy-plane-segmentation-freeMemory]
for ( std::vector<SegmentedPlane*>::iterator
it = segmentedPlanes.begin(), itE = segmentedPlanes.end();
it != itE; ++it )
delete *it;
segmentedPlanes.clear();
v2plane.clear();
//! [greedy-plane-segmentation-freeMemory]
return application.exec();
}
int main( int argc, char** argv )
{
typedef SpaceND<3,int> Space;
typedef KhalimskySpaceND<3,int> KSpace;
typedef HyperRectDomain<Space> Domain;
typedef ImageSelector<Domain, unsigned char>::Type Image;
typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;
// 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>(), "vol file (.vol) , pgm3d (.p3d or .pgm3d, pgm (with 3 dims)) file or sdp (sequence of discrete points)" )
("output,o", po::value<std::string>(), "output obj file (.obj)" )
("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" )
#ifdef WITH_ITK
("dicomMin", po::value<int>()->default_value(-1000), "set minimum density threshold on Hounsfield scale")
("dicomMax", po::value<int>()->default_value(3000), "set maximum density threshold on Hounsfield scale")
#endif
("mode", po::value<std::string>()->default_value("BDRY"), "set mode for display: INNER: inner voxels, OUTER: outer voxels, BDRY: surfels (default), CLOSURE: surfels with linels and pointels.")
("normalization,n", "Normalization so that the geometry fits in [-1/2,1/2]^3") ;
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)
{
std::cout << "Usage: " << argv[0] << " -i [input] -o [output]\n"
<< "Export the boundary of a volume file to OBJ format. The mode specifies if you wish to see surface elements (BDRY), the inner voxels (INNER) or the outer voxels (OUTER) that touch the boundary."<< endl
<< general_opt << "\n";
return 0;
}
if(! vm.count("input"))
{
trace.error() << " The file name was defined" << endl;
return 0;
}
if(! vm.count("output"))
{
trace.error() << " The output filename was defined" << endl;
return 0;
}
string inputFilename = vm["input"].as<std::string>();
int thresholdMin = vm["thresholdMin"].as<int>();
int thresholdMax = vm["thresholdMax"].as<int>();
string mode = vm["mode"].as<string>();
bool normalization = false;
if (vm.count("normalization"))
normalization = true;
string extension = inputFilename.substr(inputFilename.find_last_of(".") + 1);
if(extension!="vol" && extension != "p3d" && extension != "pgm3D" && extension != "pgm3d" && extension != "sdp" && extension != "pgm"
#ifdef WITH_ITK
&& extension !="dcm"
#endif
){
trace.info() << "File extension not recognized: "<< extension << std::endl;
return 0;
}
if(extension=="vol" || extension=="pgm3d" || extension=="pgm3D"
#ifdef WITH_ITK
|| extension =="dcm"
#endif
){
trace.beginBlock( "Loading image into memory." );
#ifdef WITH_ITK
int dicomMin = vm["dicomMin"].as<int>();
int dicomMax = vm["dicomMax"].as<int>();
typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
Image image = extension == "dcm" ? DicomReader< Image, RescalFCT >::importDicom( inputFilename,
RescalFCT(dicomMin,
dicomMax,
0, 255) ) :
GenericReader<Image>::import( inputFilename );
#else
Image image = GenericReader<Image>::import (inputFilename );
#endif
trace.info() << "Image loaded: "<<image<< std::endl;
trace.endBlock();
trace.beginBlock( "Construct the Khalimsky space from the image domain." );
Domain domain = image.domain();
KSpace ks;
bool space_ok = ks.init( domain.lowerBound(), domain.upperBound(), true );
if (!space_ok)
{
trace.error() << "Error in the Khamisky space construction."<<std::endl;
return 2;
}
trace.endBlock();
trace.beginBlock( "Wrapping a digital set around image. " );
typedef functors::IntervalForegroundPredicate<Image> ThresholdedImage;
ThresholdedImage thresholdedImage( image, thresholdMin, thresholdMax );
trace.endBlock();
trace.beginBlock( "Extracting boundary by scanning the space. " );
typedef KSpace::SurfelSet SurfelSet;
typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
MySurfelAdjacency surfAdj( true ); // interior in all directions.
MySetOfSurfels theSetOfSurfels( ks, surfAdj );
Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(),
ks, thresholdedImage,
domain.lowerBound(),
domain.upperBound() );
MyDigitalSurface digSurf( theSetOfSurfels );
trace.info() << "Digital surface has " << digSurf.size() << " surfels."
<< std::endl;
trace.endBlock();
trace.beginBlock( "Exporting everything." );
Board3D<Space,KSpace> board(ks);
board << SetMode3D( ks.unsigns( *digSurf.begin() ).className(), "Basic" );
typedef MyDigitalSurface::ConstIterator ConstIterator;
if ( mode == "BDRY" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
board << ks.unsigns( *it );
else if ( mode == "INNER" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
board << ks.sCoords( ks.sDirectIncident( *it, ks.sOrthDir( *it ) ) );
else if ( mode == "OUTER" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
board << ks.sCoords( ks.sIndirectIncident( *it, ks.sOrthDir( *it ) ) );
else if (mode == "CLOSURE")
{
std::set<KSpace::Cell> container;
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
{
container.insert( ks.unsigns( *it ) );
KSpace::SCells oneNeig = ks.sLowerIncident(*it);
//Processing linels
for(KSpace::SCells::ConstIterator itt = oneNeig.begin(), ittend = oneNeig.end(); itt != ittend; ++itt)
{
container.insert( ks.unsigns( *itt) );
KSpace::SCells oneNeig2 = ks.sLowerIncident(*itt);
//Processing pointels
for(KSpace::SCells::ConstIterator ittt = oneNeig2.begin(), itttend = oneNeig2.end(); ittt != itttend; ++ittt)
container.insert( ks.unsigns(*ittt) );
}
}
trace.info()<< "Exporting "<< container.size() << " cells"<<std::endl;
for(auto cell: container)
board << cell;
}
string outputFilename = vm["output"].as<std::string>();
board.saveOBJ(outputFilename, normalization);
trace.endBlock();
}
return 0;
}
bool testSurfelAdjacency()
{
typedef typename KSpace::Integer Integer;
typedef typename KSpace::Cell Cell;
typedef typename KSpace::SCell SCell;
typedef typename KSpace::Point Point;
typedef typename KSpace::DirIterator DirIterator;
typedef typename KSpace::Cells Cells;
typedef typename KSpace::SCells SCells;
unsigned int nbok = 0;
unsigned int nb = 0;
trace.beginBlock ( "Testing block KSpace instantiation and scan ..." );
KSpace K;
int xlow[ 4 ] = { -3, -3, -3, -3 };
int xhigh[ 4 ] = { 5, 3, 3, 3 };
Point low( xlow );
Point high( xhigh );
bool space_ok = K.init( low, high, true );
nbok += space_ok ? 1 : 0;
nb++;
trace.info() << "(" << nbok << "/" << nb << ") "
<< "K.init( low, high )" << std::endl;
trace.info() << "K.dim()=" << K.dimension << endl;
trace.endBlock();
trace.beginBlock ( "Testing surfel adjacency ..." );
SurfelAdjacency<KSpace::dimension> SAdj( true );
for ( Dimension i = 0; i < K.dimension; ++i )
for ( Dimension j = 0; j < K.dimension; ++j )
if ( i != j )
trace.info() << "(" << i << "," << j << ")="
<< ( SAdj.getAdjacency( i, j ) ? "i2e" : "e2i" );
trace.info() << endl;
trace.endBlock();
int spel[ 4 ] = { 1, 1, 1, 1 }; // pixel
Point kp( spel );
SCell sspel = K.sCell( kp, K.POS );
trace.beginBlock ( "Testing surfel directness ..." );
for ( Dimension k = 0; k < K.dimension; ++k )
{
SCell surfel = K.sIncident( sspel, k, true );
SCell innerspel = K.sDirectIncident( surfel, K.sOrthDir( surfel ) );
trace.info() << "spel=" << sspel << " surfel=" << surfel
<< " innerspel=" << innerspel << endl;
nbok += sspel == innerspel ? 1 : 0;
nb++;
trace.info() << "(" << nbok << "/" << nb << ") "
<< "spel == innerspel" << std::endl;
surfel = K.sIncident( sspel, k, false );
innerspel = K.sDirectIncident( surfel, K.sOrthDir( surfel ) );
trace.info() << "spel=" << sspel << " surfel=" << surfel
<< " innerspel=" << innerspel << endl;
nbok += sspel == innerspel ? 1 : 0;
nb++;
trace.info() << "(" << nbok << "/" << nb << ") "
<< "spel == innerspel" << std::endl;
}
trace.endBlock();
SurfelNeighborhood<KSpace> SN;
trace.beginBlock ( "Testing surfel neighborhood ..." );
SCell surfel = K.sIncident( sspel, 0, false );
SN.init( &K, &SAdj, surfel );
trace.info() << "surfel =" << surfel << endl;
trace.info() << "follower1(+)=" << SN.follower1( 1, true ) << endl;
trace.info() << "follower2(+)=" << SN.follower2( 1, true ) << endl;
trace.info() << "follower3(+)=" << SN.follower3( 1, true ) << endl;
trace.info() << "follower1(-)=" << SN.follower1( 1, false ) << endl;
trace.info() << "follower2(-)=" << SN.follower2( 1, false ) << endl;
trace.info() << "follower3(-)=" << SN.follower3( 1, false ) << endl;
trace.endBlock();
trace.beginBlock ( "Testing surface tracking ..." );
typedef SpaceND< KSpace::dimension, Integer > Space;
typedef HyperRectDomain<Space> Domain;
typedef typename DigitalSetSelector< Domain, BIG_DS+HIGH_BEL_DS >::Type DigitalSet;
Domain domain( low, high );
DigitalSet shape_set( domain );
SetPredicate<DigitalSet> shape_set_predicate( shape_set );
int center[ 4 ] = { 1, 0, 0, 0 }; // pixel
Point pcenter( center );
Shapes<Domain>::addNorm1Ball( shape_set, pcenter, 1 );
trace.info() << "surfel = " << surfel << endl;
SCell other1, other2;
SN.getAdjacentOnDigitalSet( other1, shape_set, 1, K.sDirect( surfel, 1 ) );
SN.getAdjacentOnDigitalSet( other2, shape_set, 1, !K.sDirect( surfel, 1 ) );
trace.info() << "directNext = " << other1 << endl;
trace.info() << "indirectNext= " << other2 << endl;
std::set<SCell> bdry;
// surfel = Surfaces<KSpace>::findABel( K, shape_set );
Surfaces<KSpace>::trackBoundary( bdry,
K, SAdj, shape_set_predicate, surfel );
trace.info() << "tracking finished, size=" << bdry.size()
<< ", should be " << 2*K.dimension*(2*K.dimension-1) << endl;
nbok += bdry.size() == ( 2*K.dimension*(2*K.dimension-1) ) ? 1 : 0;
nb++;
trace.info() << "(" << nbok << "/" << nb << ") "
<< "bdry.size() == ( 2*K.dimension*(2*K.dimension-1) )"
<< std::endl;
std::set<SCell> bdry_direct;
Surfaces<KSpace>::trackClosedBoundary( bdry_direct,
K, SAdj, shape_set_predicate, surfel );
trace.info() << "fast direct tracking finished, size=" << bdry_direct.size()
<< ", should be " << 2*K.dimension*(2*K.dimension-1) << endl;
nbok += bdry_direct.size() == ( 2*K.dimension*(2*K.dimension-1) ) ? 1 : 0;
nb++;
trace.info() << "(" << nbok << "/" << nb << ") "
<< "bdry_direct.size() == ( 2*K.dimension*(2*K.dimension-1) )"
<< std::endl;
trace.endBlock();
if ( K.dimension == 2 )
{
Board2D board;
board.setUnit( LibBoard::Board::UCentimeter );
board << SetMode( domain.className(), "Paving" )
<< domain;
for ( typename std::set<SCell>::const_iterator it = bdry_direct.begin(),
it_end = bdry_direct.end(); it != it_end; ++it )
board << *it;
board.saveEPS( "cells-2.eps" );
board.saveSVG( "cells-2.svg" );
}
return nbok == nb;
}
int main( int argc, char** argv )
{
typedef SpaceND<3,int> Space;
typedef KhalimskySpaceND<3,int> KSpace;
typedef HyperRectDomain<Space> Domain;
typedef ImageSelector<Domain, unsigned char>::Type Image;
typedef DigitalSetSelector< Domain, BIG_DS+HIGH_BEL_DS >::Type DigitalSet;
typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;
// 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>(), "vol file (.vol) , pgm3d (.p3d or .pgm3d, pgm (with 3 dims)) file or sdp (sequence of discrete points)" )
("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" )
#ifdef WITH_ITK
("dicomMin", po::value<int>()->default_value(-1000), "set minimum density threshold on Hounsfield scale")
("dicomMax", po::value<int>()->default_value(3000), "set maximum density threshold on Hounsfield scale")
#endif
("mode", po::value<std::string>()->default_value("INNER"), "set mode for display: INNER: inner voxels, OUTER: outer voxels, BDRY: surfels") ;
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)
{
std::cout << "Usage: " << argv[0] << " -i [input]\n"
<< "Display the boundary of a volume file by using QGLviewer. The mode specifies if you wish to see surface elements (BDRY), the inner voxels (INNER) or the outer voxels (OUTER) that touch the boundary."<< endl
<< general_opt << "\n";
return 0;
}
if(! vm.count("input"))
{
trace.error() << " The file name was defined" << endl;
return 0;
}
string inputFilename = vm["input"].as<std::string>();
int thresholdMin = vm["thresholdMin"].as<int>();
int thresholdMax = vm["thresholdMax"].as<int>();
string mode = vm["mode"].as<string>();
QApplication application(argc,argv);
string extension = inputFilename.substr(inputFilename.find_last_of(".") + 1);
if(extension!="vol" && extension != "p3d" && extension != "pgm3D" && extension != "pgm3d" && extension != "sdp" && extension != "pgm"
#ifdef WITH_ITK
&& extension !="dcm"
#endif
){
trace.info() << "File extension not recognized: "<< extension << std::endl;
return 0;
}
if(extension=="vol" || extension=="pgm3d" || extension=="pgm3D"
#ifdef WITH_ITK
|| extension =="dcm"
#endif
){
trace.beginBlock( "Loading image into memory." );
#ifdef WITH_ITK
int dicomMin = vm["dicomMin"].as<int>();
int dicomMax = vm["dicomMax"].as<int>();
typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
Image image = extension == "dcm" ? DicomReader< Image, RescalFCT >::importDicom( inputFilename,
RescalFCT(dicomMin,
dicomMax,
0, 255) ) :
GenericReader<Image>::import( inputFilename );
#else
Image image = GenericReader<Image>::import (inputFilename );
#endif
trace.info() << "Image loaded: "<<image<< std::endl;
trace.endBlock();
//! [3dVolBoundaryViewer-KSpace]
trace.beginBlock( "Construct the Khalimsky space from the image domain." );
Domain domain = image.domain();
KSpace ks;
bool space_ok = ks.init( domain.lowerBound(), domain.upperBound(), true );
if (!space_ok)
{
trace.error() << "Error in the Khamisky space construction."<<std::endl;
return 2;
}
trace.endBlock();
//! [3dVolBoundaryViewer-KSpace]
//! [3dVolBoundaryViewer-Set3D]
trace.beginBlock( "Wrapping a digital set around image. " );
typedef functors::IntervalForegroundPredicate<Image> ThresholdedImage;
ThresholdedImage thresholdedImage( image, thresholdMin, thresholdMax );
trace.endBlock();
//! [3dVolBoundaryViewer-Set3D]
//! [3dVolBoundaryViewer-ExtractingSurface]
trace.beginBlock( "Extracting boundary by scanning the space. " );
typedef KSpace::SurfelSet SurfelSet;
typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
MySurfelAdjacency surfAdj( true ); // interior in all directions.
MySetOfSurfels theSetOfSurfels( ks, surfAdj );
Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(),
ks, thresholdedImage,
domain.lowerBound(),
domain.upperBound() );
MyDigitalSurface digSurf( theSetOfSurfels );
trace.info() << "Digital surface has " << digSurf.size() << " surfels."
<< std::endl;
trace.endBlock();
//! [3dVolBoundaryViewer-ExtractingSurface]
//! [3dVolBoundaryViewer-ViewingSurface]
trace.beginBlock( "Displaying everything. " );
Viewer3D<Space,KSpace> viewer(ks);
viewer.setWindowTitle("Simple boundary of volume Viewer");
viewer.show();
typedef MyDigitalSurface::ConstIterator ConstIterator;
if ( mode == "BDRY" ){
viewer << SetMode3D(ks.unsigns( *(digSurf.begin()) ).className(), "Basic");
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
viewer << ks.unsigns( *it );
}else if ( mode == "INNER" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
viewer << ks.sCoords( ks.sDirectIncident( *it, ks.sOrthDir( *it ) ) );
else if ( mode == "OUTER" )
for ( ConstIterator it = digSurf.begin(), itE = digSurf.end(); it != itE; ++it )
viewer << ks.sCoords( ks.sIndirectIncident( *it, ks.sOrthDir( *it ) ) );
else{
trace.error() << "Warning display mode (" << mode << ") not implemented." << std::endl;
trace.error() << "The display will be empty." << std::endl;
}
viewer << Viewer3D<>::updateDisplay;
trace.endBlock();
return application.exec();
}
return 0;
}
int main( int argc, char** argv )
{
QApplication application(argc,argv);
string inputFilename = argc > 1 ? argv[ 1 ] : examplesPath+"/samples/Al.100.vol";
int threshold = argc > 2 ? atoi( argv[ 2 ] ) : 0;
int widthNum = argc > 3 ? atoi( argv[ 3 ] ) : 2;
int widthDen = argc > 4 ? atoi( argv[ 4 ] ) : 1;
//! [polyhedralizer-readVol]
trace.beginBlock( "Reading vol file into an image." );
typedef ImageContainerBySTLVector< Domain, int> Image;
Image image = VolReader<Image>::importVol(inputFilename);
typedef functors::SimpleThresholdForegroundPredicate<Image> DigitalObject;
DigitalObject digitalObject( image, threshold );
trace.endBlock();
//! [polyhedralizer-readVol]
//! [polyhedralizer-KSpace]
trace.beginBlock( "Construct the Khalimsky space from the image domain." );
KSpace ks;
bool space_ok = ks.init( image.domain().lowerBound(), image.domain().upperBound(), true );
if (!space_ok)
{
trace.error() << "Error in the Khamisky space construction."<<endl;
return 2;
}
trace.endBlock();
//! [polyhedralizer-KSpace]
//! [polyhedralizer-SurfelAdjacency]
typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;
MySurfelAdjacency surfAdj( false ); // exterior in all directions.
//! [polyhedralizer-SurfelAdjacency]
//! [polyhedralizer-ExtractingSurface]
trace.beginBlock( "Extracting boundary by tracking the surface. " );
typedef KSpace::Surfel Surfel;
Surfel start_surfel = Surfaces<KSpace>::findABel( ks, digitalObject, 100000 );
typedef ImplicitDigitalSurface< KSpace, DigitalObject > MyContainer;
typedef DigitalSurface< MyContainer > MyDigitalSurface;
typedef MyDigitalSurface::ConstIterator ConstIterator;
MyContainer container( ks, digitalObject, surfAdj, start_surfel );
MyDigitalSurface digSurf( container );
trace.info() << "Digital surface has " << digSurf.size() << " surfels."
<< endl;
trace.endBlock();
//! [polyhedralizer-ExtractingSurface]
//! [polyhedralizer-ComputingPlaneSize]
// First pass to find biggest planes.
trace.beginBlock( "Decomposition first pass. Computes all planes so as to sort vertices by the plane size." );
typedef BreadthFirstVisitor<MyDigitalSurface> Visitor;
typedef ChordGenericNaivePlaneComputer<Z3,Z3::Point, DGtal::int64_t> NaivePlaneComputer;
map<Surfel,unsigned int> v2size;
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
v2size[ *it ] = 0;
int j = 0;
int nb = digSurf.size();
NaivePlaneComputer planeComputer;
vector<Point> layer;
vector<Surfel> layer_surfel;
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
{
if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb );
Surfel v = *it;
planeComputer.init( widthNum, widthDen );
// The visitor takes care of all the breadth-first traversal.
Visitor visitor( digSurf, v );
layer.clear();
layer_surfel.clear();
Visitor::Size currentSize = visitor.current().second;
while ( ! visitor.finished() )
{
Visitor::Node node = visitor.current();
v = node.first;
int axis = ks.sOrthDir( v );
Point p = ks.sCoords( ks.sDirectIncident( v, axis ) );
if ( node.second != currentSize )
{
bool isExtended = planeComputer.extend( layer.begin(), layer.end() );
if ( isExtended )
{
for ( vector<Surfel>::const_iterator it_layer = layer_surfel.begin(),
it_layer_end = layer_surfel.end(); it_layer != it_layer_end; ++it_layer )
{
++v2size[ *it_layer ];
}
layer_surfel.clear();
layer.clear();
currentSize = node.second;
}
else
break;
}
layer_surfel.push_back( v );
layer.push_back( p );
visitor.expand();
}
}
// Prepare queue
typedef PairSorted2nd<Surfel,int> SurfelWeight;
priority_queue<SurfelWeight> Q;
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
Q.push( SurfelWeight( *it, v2size[ *it ] ) );
trace.endBlock();
//! [polyhedralizer-ComputingPlaneSize]
//! [polyhedralizer-segment]
// Segmentation into planes
trace.beginBlock( "Decomposition second pass. Visits vertices from the one with biggest plane to the one with smallest plane." );
typedef Triple<NaivePlaneComputer, Color, pair<RealVector,double> > RoundPlane;
set<Surfel> processedVertices;
vector<RoundPlane*> roundPlanes;
map<Surfel,RoundPlane*> v2plane;
j = 0;
while ( ! Q.empty() )
{
if ( ( (++j) % 50 == 0 ) || ( j == nb ) ) trace.progressBar( j, nb );
Surfel v = Q.top().first;
Q.pop();
if ( processedVertices.find( v ) != processedVertices.end() ) // already in set
continue; // process to next vertex
RoundPlane* ptrRoundPlane = new RoundPlane;
roundPlanes.push_back( ptrRoundPlane ); // to delete them afterwards.
v2plane[ v ] = ptrRoundPlane;
ptrRoundPlane->first.init( widthNum, widthDen );
ptrRoundPlane->third = make_pair( RealVector::zero, 0.0 );
// The visitor takes care of all the breadth-first traversal.
Visitor visitor( digSurf, v );
layer.clear();
layer_surfel.clear();
Visitor::Size currentSize = visitor.current().second;
while ( ! visitor.finished() )
{
Visitor::Node node = visitor.current();
v = node.first;
Dimension axis = ks.sOrthDir( v );
Point p = ks.sCoords( ks.sDirectIncident( v, axis ) );
if ( node.second != currentSize )
{
bool isExtended = ptrRoundPlane->first.extend( layer.begin(), layer.end() );
if ( isExtended )
{
for ( vector<Surfel>::const_iterator it_layer = layer_surfel.begin(),
it_layer_end = layer_surfel.end(); it_layer != it_layer_end; ++it_layer )
{
Surfel s = *it_layer;
processedVertices.insert( s );
if ( v2plane.find( s ) == v2plane.end() )
v2plane[ s ] = ptrRoundPlane;
}
layer.clear();
layer_surfel.clear();
currentSize = node.second;
}
else break;
}
layer_surfel.push_back( v );
layer.push_back( p );
if ( processedVertices.find( v ) != processedVertices.end() )
// surfel is already in some plane.
visitor.ignore();
else
visitor.expand();
}
if ( visitor.finished() )
{
for ( vector<Surfel>::const_iterator it_layer = layer_surfel.begin(),
it_layer_end = layer_surfel.end(); it_layer != it_layer_end; ++it_layer )
{
Surfel s = *it_layer;
processedVertices.insert( s );
if ( v2plane.find( s ) == v2plane.end() )
v2plane[ s ] = ptrRoundPlane;
}
}
// Assign random color for each plane.
ptrRoundPlane->second = Color( rand() % 192 + 64, rand() % 192 + 64, rand() % 192 + 64, 255 );
}
trace.endBlock();
//! [polyhedralizer-segment]
//! [polyhedralizer-lsf]
for ( vector<RoundPlane*>::iterator
it = roundPlanes.begin(), itE = roundPlanes.end();
it != itE; ++it )
{
NaivePlaneComputer& computer = (*it)->first;
RealVector normal;
double mu = LSF( normal, computer.begin(), computer.end() );
(*it)->third = make_pair( normal, mu );
}
//! [polyhedralizer-lsf]
//! [polyhedralizer-projection]
map<Surfel, RealPoint> coordinates;
for ( map<Surfel,RoundPlane*>::const_iterator
it = v2plane.begin(), itE = v2plane.end();
it != itE; ++it )
{
Surfel v = it->first;
RoundPlane* rplane = it->second;
Point p = ks.sKCoords( v );
RealPoint rp( (double)p[ 0 ]/2.0, (double)p[ 1 ]/2.0, (double)p[ 2 ]/2.0 );
double mu = rplane->third.second;
RealVector normal = rplane->third.first;
double lambda = mu - rp.dot( normal );
coordinates[ v ] = rp + lambda*normal;
}
typedef vector<Surfel> SurfelRange;
map<Surfel, RealPoint> new_coordinates;
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
{
Surfel s = *it;
SurfelRange neighbors;
back_insert_iterator<SurfelRange> writeIt = back_inserter( neighbors );
digSurf.writeNeighbors( writeIt, *it );
RealPoint x = RealPoint::zero;
for ( SurfelRange::const_iterator its = neighbors.begin(), itsE = neighbors.end();
its != itsE; ++its )
x += coordinates[ *its ];
new_coordinates[ s ] = x / neighbors.size();
}
//! [polyhedralizer-projection]
//! [polyhedralizer-MakeMesh]
typedef unsigned int Number;
typedef Mesh<RealPoint> MyMesh;
typedef MyMesh::MeshFace MeshFace;
typedef MyDigitalSurface::FaceSet FaceSet;
typedef MyDigitalSurface::VertexRange VertexRange;
map<Surfel, Number> index; // Numbers all vertices.
Number nbv = 0;
MyMesh polyhedron( true );
// Insert all projected surfels as vertices of the polyhedral surface.
for ( ConstIterator it = digSurf.begin(), itE= digSurf.end(); it != itE; ++it )
{
polyhedron.addVertex( new_coordinates[ *it ] );
index[ *it ] = nbv++;
}
// Define faces of the mesh. Outputs closed faces.
FaceSet faces = digSurf.allClosedFaces();
for ( typename FaceSet::const_iterator itf = faces.begin(), itf_end = faces.end();
itf != itf_end; ++itf )
{
MeshFace mface( itf->nbVertices );
VertexRange vtcs = digSurf.verticesAroundFace( *itf );
int i = 0;
for ( typename VertexRange::const_iterator itv = vtcs.begin(), itv_end = vtcs.end();
itv != itv_end; ++itv )
{
mface[ i++ ] = index[ *itv ];
}
polyhedron.addFace( mface, Color( 255, 243, 150, 255 ) );
}
//! [polyhedralizer-MakeMesh]
//! [polyhedralizer-visualization]
typedef Viewer3D<Space,KSpace> MyViewer3D;
MyViewer3D viewer( ks );
viewer.show();
bool isOK = polyhedron >> "test.off";
bool isOK2 = polyhedron >> "test.obj";
viewer << polyhedron;
viewer << MyViewer3D::updateDisplay;
application.exec();
//! [polyhedralizer-visualization]
//! [polyhedralizer-freeMemory]
for ( vector<RoundPlane*>::iterator
it = roundPlanes.begin(), itE = roundPlanes.end();
it != itE; ++it )
delete *it;
//! [polyhedralizer-freeMemory]
if (isOK && isOK2)
return 0;
else
return 1;
}
