int main( int argc, char** argv )
{
// for 3D display with Viewer3D
QApplication application(argc,argv);
//! [digitalSurfaceSlice-readVol]
trace.beginBlock( "Reading vol file into an image." );
typedef ImageSelector < Domain, int>::Type Image;
std::string inputFilename = examplesPath + "samples/Al.100.vol";
Image image = VolReader<Image>::importVol(inputFilename);
DigitalSet set3d (image.domain());
SetPredicate<DigitalSet> set3dPredicate( set3d );
SetFromImage<DigitalSet>::append<Image>(set3d, image,
0, 1 );
Viewer3D viewer;
viewer.show();
trace.endBlock();
//! [digitalSurfaceSlice-readVol]
//! [digitalSurfaceSlice-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."<<std::endl;
return 2;
}
trace.endBlock();
//! [digitalSurfaceSlice-KSpace]
//! [digitalSurfaceSlice-SurfelAdjacency]
typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;
MySurfelAdjacency surfAdj( true ); // interior in all directions.
//! [digitalSurfaceSlice-SurfelAdjacency]
//! [digitalSurfaceSlice-ExtractingSurface]
trace.beginBlock( "Extracting boundary by scanning the space. " );
typedef KSpace::Surfel Surfel;
typedef KSpace::SurfelSet SurfelSet;
typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
MySetOfSurfels theSetOfSurfels( ks, surfAdj );
Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(),
ks, set3dPredicate,
image.domain().lowerBound(),
image.domain().upperBound() );
MyDigitalSurface digSurf( theSetOfSurfels );
trace.info() << "Digital surface has " << digSurf.size() << " surfels."
<< std::endl;
trace.endBlock();
//! [digitalSurfaceSlice-ExtractingSurface]
//! [digitalSurfaceSlice-ExtractingSlice]
trace.beginBlock( "Extract slices." );
typedef MyDigitalSurface::DigitalSurfaceTracker MyTracker;
typedef DigitalSurface2DSlice< MyTracker > My2DSlice;
//Extract an initial boundary cell
Surfel surf = *digSurf.begin();
MyTracker* tracker1 = digSurf.container().newTracker( surf );
MyTracker* tracker2 = digSurf.container().newTracker( surf );
// Extract the bondary contour associated to the initial surfel in
// its first direction
My2DSlice slice1( tracker1, *(ks.sDirs( surf )) );
// Extract the bondary contour associated to the initial surfel in
// its second direction
My2DSlice slice2( tracker2, *++(ks.sDirs( surf )) );
delete tracker1;
delete tracker2;
trace.endBlock();
//! [digitalSurfaceSlice-ExtractingSlice]
ASSERT( slice1.start() == slice1.begin() );
ASSERT( slice1.cstart() == slice1.c() );
ASSERT( *slice1.begin() == surf );
ASSERT( *slice1.c() == surf );
ASSERT( *slice1.start() == surf );
ASSERT( *slice1.cstart() == surf );
ASSERT( *slice1.rcstart() == surf );
ASSERT( slice1.rcstart() == slice1.rc() );
ASSERT( *slice1.rc() == surf );
ASSERT( *(slice1.c()+1) == *(slice1.begin()+1) );
ASSERT( *(slice1.rc()+1) == *(slice1.rbegin()) );
//! [digitalSurfaceSlice-displayingAll]
trace.beginBlock( "Display all with QGLViewer." );
// Displaying all the surfels in transparent mode
viewer << SetMode3D( surf.className(), "Transparent");
for( MyDigitalSurface::ConstIterator it = theSetOfSurfels.begin(),
it_end = theSetOfSurfels.end(); it != it_end; ++it )
viewer<< *it;
// Displaying First surfels cut with gradient colors.;
GradientColorMap<int> cmap_grad( 0, slice1.size() );
cmap_grad.addColor( Color( 50, 50, 255 ) );
cmap_grad.addColor( Color( 255, 0, 0 ) );
cmap_grad.addColor( Color( 255, 255, 10 ) );
// Need to avoid surfel superposition (the surfel size in increased)
viewer << Viewer3D::shiftSurfelVisu;
viewer << SetMode3D( surf.className(), "");
viewer.setFillColor(Color(180, 200, 25, 255));
int d=0;
for ( My2DSlice::ConstIterator it = slice1.begin(),
it_end = slice1.end(); it != it_end; ++it )
{
Color col= cmap_grad(d);
viewer.setFillColor(Color(col.red(),col.green() ,col.blue(), 255));
viewer<< *it;
d++;
}
GradientColorMap<int> cmap_grad2( 0, slice2.size() );
cmap_grad2.addColor( Color( 50, 50, 255 ) );
cmap_grad2.addColor( Color( 255, 0, 0 ) );
cmap_grad2.addColor( Color( 255, 255, 10 ) );
d=0;
for ( My2DSlice::ConstIterator it = slice2.begin(),
it_end = slice2.end(); it != it_end; ++it )
{
Color col= cmap_grad2(d);
viewer.setFillColor(Color(col.red(),col.green() ,col.blue(), 255));
viewer<< *it;
d++;
}
// One need once again to avoid superposition.
viewer << Viewer3D::shiftSurfelVisu;
viewer.setFillColor(Color(18, 200, 25, 255));
viewer << surf ;
viewer << Viewer3D::updateDisplay;
trace.endBlock();
return application.exec();
//! [digitalSurfaceSlice-displayingAll]
}
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
TrueEstimator& true_estimator, //< "ground truth" estimator
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 ground truth." );
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
std::vector<Quantity> n_true_estimations;
true_estimator.eval( range->begin(), range->end(), std::back_inserter( n_true_estimations ) );
trace.info() << "- nb estimations = " << n_true_estimations.size() << std::endl;
trace.endBlock();
trace.beginBlock( "Correcting orientations." );
ASSERT( n_estimations.size() == n_true_estimations.size() );
for ( unsigned int i = 0; i < n_estimations.size(); ++i )
if ( n_estimations[ i ].dot( n_true_estimations[ i ] ) < 0 )
n_estimations[ i ] = -n_estimations[ i ];
trace.endBlock();
DGtal::GradientColorMap<double> grad( 0.0, 40.0 );
// 0 metallic blue, 5 light cyan, 10 light green, 15 light
// yellow, 20 yellow, 25 orange, 30 red, 35, dark red, 40- grey
grad.addColor( DGtal::Color( 128, 128, 255 ) ); // 0
grad.addColor( DGtal::Color( 128, 255, 255 ) ); // 5
grad.addColor( DGtal::Color( 128, 255, 128 ) ); // 10
grad.addColor( DGtal::Color( 255, 255, 128 ) ); // 15
grad.addColor( DGtal::Color( 255, 255, 0 ) ); // 20
grad.addColor( DGtal::Color( 255, 128, 0 ) ); // 25
grad.addColor( DGtal::Color( 255, 0, 0 ) ); // 30
grad.addColor( DGtal::Color( 128, 0, 0 ) ); // 35
grad.addColor( DGtal::Color( 128, 128, 128 ) ); // 40
if ( vm.count( "angle-deviation-stats" ) )
{
trace.beginBlock( "Computing angle deviation error stats." );
std::ostringstream adev_sstr;
adev_sstr << fname << "-" << nameEstimator << "-angle-deviation-"
<< estimator.h() << ".txt";
DGtal::Statistic<Scalar> adev_stat;
unsigned int i = 0;
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
for ( VisitorConstIterator it = range->begin(), itE = range->end(); it != itE; ++it, ++i )
{
Quantity n_est = n_estimations[ i ];
Quantity n_true_est = n_true_estimations[ i ];
Scalar angle_error = acos( n_est.dot( n_true_est ) );
adev_stat.addValue( angle_error );
}
adev_stat.terminate();
std::ofstream adev_output( adev_sstr.str().c_str() );
adev_output << "# Average error X of the absolute angle between two vector estimations." << std::endl;
adev_output << "# h L1 L2 Loo E[X] Var[X] Min[X] Max[X] Nb[X]" << std::endl;
adev_output << estimator.h()
<< " " << adev_stat.mean() // L1
<< " " << sqrt( adev_stat.unbiasedVariance()
+ adev_stat.mean()*adev_stat.mean() ) // L2
<< " " << adev_stat.max() // Loo
<< " " << adev_stat.mean() // E[X] (=L1)
<< " " << adev_stat.unbiasedVariance() // Var[X]
<< " " << adev_stat.min() // Min[X]
<< " " << adev_stat.max() // Max[X]
<< " " << adev_stat.samples() // Nb[X]
<< std::endl;
adev_output.close();
trace.endBlock();
}
if ( vm[ "export" ].as<string>() != "None" )
{
trace.beginBlock( "Exporting cell geometry." );
std::ostringstream export_sstr;
export_sstr << fname << "-" << nameEstimator << "-cells-"
<< estimator.h() << ".txt";
std::ofstream export_output( export_sstr.str().c_str() );
export_output << "# ImaGene viewer (viewSetOfSurfels) file format for displaying cells." << std::endl;
bool adev = vm[ "export" ].as<string>() == "AngleDeviation";
unsigned int i = 0;
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
for ( VisitorConstIterator it = range->begin(), itE = range->end(); it != itE; ++it, ++i )
{
Quantity n_est = n_estimations[ i ];
Quantity n_true_est = n_true_estimations[ i ];
Scalar angle_error = acos( n_est.dot( n_true_est ) )*180.0 / 3.14159625;
Surfel s = *it;
export_output
<< "CellN"
<< " " << min( 1023, max( 512+K.sKCoord( s, 0 ), 0 ) )
<< " " << min( 1023, max( 512+K.sKCoord( s, 1 ), 0 ) )
<< " " << min( 1023, max( 512+K.sKCoord( s, 2 ), 0 ) )
<< " " << K.sSign( s );
Color c = grad( 0 );
if ( adev ) c = grad( max( 0.0, min( angle_error, 40.0 ) ) );
export_output << " " << ((double) c.red() / 255.0 )
<< " " << ((double) c.green() / 255.0 )
<< " " << ((double) c.blue() / 255.0 );
export_output << " " << n_est[ 0 ] << " " << n_est[ 1 ]
<< " " << n_est[ 2 ] << std::endl;
}
export_output.close();
trace.endBlock();
}
if ( vm.count( "normals" ) )
{
trace.beginBlock( "Exporting cells normals." );
std::ostringstream export_sstr;
export_sstr << fname << "-" << nameEstimator << "-normals-"
<< estimator.h() << ".txt";
std::ofstream export_output( export_sstr.str().c_str() );
export_output << "# kx ky kz sign n_est[0] n_est[1] n_est[2] n_true[0] n_true[1] n_true[2]" << std::endl;
unsigned int i = 0;
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
for ( VisitorConstIterator it = range->begin(), itE = range->end(); it != itE; ++it, ++i )
{
Quantity n_est = n_estimations[ i ];
Quantity n_true_est = n_true_estimations[ i ];
Surfel s = *it;
export_output
<< K.sKCoord( s, 0 ) << " " << K.sKCoord( s, 1 ) << " " << K.sKCoord( s, 2 )
<< " " << K.sSign( s )
<< " " << n_est[ 0 ] << " " << n_est[ 1 ] << " " << n_est[ 2 ]
<< " " << n_true_est[ 0 ] << " " << n_true_est[ 1 ] << " " << n_true_est[ 2 ]
<< std::endl;
}
export_output.close();
trace.endBlock();
}
if ( vm.count( "noff" ) )
{
trace.beginBlock( "Exporting NOFF file." );
std::ostringstream export_sstr;
export_sstr << fname << "-" << nameEstimator << "-noff-"
<< estimator.h() << ".off";
std::ofstream export_output( export_sstr.str().c_str() );
std::map<Surfel,Quantity> normals;
unsigned int i = 0;
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
for ( VisitorConstIterator it = range->begin(), itE = range->end(); it != itE; ++it, ++i )
{
Quantity n_est = n_estimations[ i ];
normals[ *it ] = n_est;
}
CanonicSCellEmbedder<KSpace> surfelEmbedder( K );
typedef SCellEmbedderWithNormal< CanonicSCellEmbedder<KSpace> > Embedder;
Embedder embedder( surfelEmbedder, normals );
surface.exportAs3DNOFF( export_output, embedder );
export_output.close();
trace.endBlock();
}
#ifdef WITH_VISU3D_QGLVIEWER
if ( vm[ "view" ].as<string>() != "None" )
{
typedef typename KSpace::Space Space;
typedef Viewer3D<Space,KSpace> MyViewever3D;
typedef Display3DFactory<Space,KSpace> MyDisplay3DFactory;
int argc = 1;
char name[] = "Viewer";
char* argv[ 1 ];
argv[ 0 ] = name;
Surfel s;
QApplication application( argc, argv );
MyViewever3D viewer( K );
viewer.show();
viewer << SetMode3D( s.className(), "Basic" );
trace.beginBlock( "Viewing surface." );
bool adev = vm[ "view" ].as<string>() == "AngleDeviation";
unsigned int i = 0;
range = CountedPtr<VisitorRange>( new VisitorRange( new Visitor( surface, *(surface.begin()) )) );
for ( VisitorConstIterator it = range->begin(), itE = range->end(); it != itE; ++it, ++i )
{
Quantity n_est = n_estimations[ i ];
Quantity n_true_est = n_true_estimations[ i ];
Scalar angle_error = acos( n_est.dot( n_true_est ) )*180.0 / 3.14159625;
s = *it;
Color c = grad( 0 );
if ( adev ) c = grad( max( 0.0, min( angle_error, 40.0 ) ) );
viewer.setFillColor( c );
MyDisplay3DFactory::drawOrientedSurfelWithNormal( viewer, s, n_est, false );
}
trace.endBlock();
viewer << MyViewever3D::updateDisplay;
application.exec();
}
#endif
}
int main( int argc, char** argv )
{
trace.info() << "exampleGridCurve3d: the type can be changed in example source code with <gridcurve>, <inner>, <outer>, <incident> " << std::endl;
string type = "gridcurve";
//vol reading and digital set construction
trace.beginBlock( "Reading vol file into an image." );
typedef ImageSelector < Domain, int>::Type Image;
std::string inputFilename = examplesPath + "samples/cat10.vol";
Image image = VolReader<Image>::importVol(inputFilename);
DigitalSet set3d (image.domain());
setFromImage( image, DigitalSetInserter<DigitalSet>(set3d), 1);
trace.info() << set3d.size() << " voxels." << std::endl;
trace.endBlock();
//Khalimsky space construction
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."<<std::endl;
return 2;
}*/
trace.endBlock();
//digital surface construction
typedef SurfelAdjacency<KSpace::dimension> MySurfelAdjacency;
MySurfelAdjacency surfAdj( true ); // interior in all directions.
trace.beginBlock( "Extracting boundary by scanning the space. " );
typedef KSpace::Surfel Surfel;
typedef KSpace::SurfelSet SurfelSet;
typedef SetOfSurfels< KSpace, SurfelSet > MySetOfSurfels;
typedef DigitalSurface< MySetOfSurfels > MyDigitalSurface;
MySetOfSurfels theSetOfSurfels( ks, surfAdj );
Surfaces<KSpace>::sMakeBoundary( theSetOfSurfels.surfelSet(),
ks, set3d,
image.domain().lowerBound(),
image.domain().upperBound() );
MyDigitalSurface digSurf( theSetOfSurfels );
trace.info() << digSurf.size() << " surfels." << std::endl;
trace.endBlock();
//slice retrieving
trace.beginBlock( "Extracting slice and constructing a grid curve. " );
typedef MyDigitalSurface::DigitalSurfaceTracker MyTracker;
typedef DigitalSurface2DSlice< MyTracker > My2DSlice;
//Extract an initial boundary cell
Surfel surf = *digSurf.begin();
MyTracker* tracker = digSurf.container().newTracker( surf );
// Extract the bondary contour associated to the initial surfel in
// its first direction
My2DSlice slice( tracker, *(ks.sDirs( surf )) );
delete tracker;
//! [exampleGridCurve3d-Construction]
GridCurve<KSpace> gc(ks);
gc.initFromSCellsRange( slice.begin(), slice.end() );
//! [exampleGridCurve3d-Construction]
trace.endBlock();
// for 3D display with Viewer3D
QApplication application(argc,argv);
trace.beginBlock( "Display all with QGLViewer." );
Viewer3D<> viewer;
viewer.show();
// Displaying all the surfels in transparent mode
viewer << SetMode3D( surf.className(), "Transparent");
for( MyDigitalSurface::ConstIterator it = theSetOfSurfels.begin(),
it_end = theSetOfSurfels.end(); it != it_end; ++it )
viewer<< *it;
// Displaying slice
viewer << Viewer3D<>::shiftSurfelVisu;
viewer << SetMode3D( surf.className(), "");
viewer.setFillColor( Color( 50, 50, 255 ) );
if (type == "gridcurve")
{
viewer << gc;
}
else if (type == "inner")
{
viewer << gc.getInnerPointsRange();
}
else if (type == "outer")
{
viewer << gc.getOuterPointsRange();
}
else if (type == "incident")
{
viewer << gc.getIncidentPointsRange();
}
else
{
trace.info() << "Display type not known. Use option -h" << std::endl;
}
viewer << Viewer3D<>::updateDisplay;
trace.endBlock();
return application.exec();
}