DGtal: dgtalCalculus-geodesic.cpp File Reference

#include <iostream>
#include <string>
#include <DGtal/base/Common.h>
#include <DGtal/helpers/StdDefs.h>
#include <DGtal/helpers/Shortcuts.h>
#include <DGtal/helpers/ShortcutsGeometry.h>
#include <DGtal/shapes/SurfaceMesh.h>
#include <DGtal/geometry/surfaces/DigitalSurfaceRegularization.h>
#include <DGtal/dec/PolygonalCalculus.h>
#include <DGtal/dec/GeodesicsInHeat.h>
#include <polyscope/polyscope.h>
#include <polyscope/surface_mesh.h>
#include <polyscope/point_cloud.h>
#include "ConfigExamples.h"
#include <Eigen/Dense>
#include <Eigen/Sparse>

Include dependency graph for dgtalCalculus-geodesic.cpp:

Go to the source code of this file.

Typedefs
typedef Shortcuts< Z3i::KSpace >	SH3

typedef ShortcutsGeometry< Z3i::KSpace >	SHG3

typedef SurfaceMesh< RealPoint, RealVector >	SurfMesh

typedef SurfMesh::Face	Face

typedef SurfMesh::Vertex	Vertex

typedef PolygonalCalculus< SH3::RealPoint, SH3::RealVector >	PolyCalculus

Functions
void	precompute ()

std::vector< std::pair< size_t, int > >	source2count (GeodesicsInHeat< PolyCalculus >::Vector &source)

void	addSource ()

void	clearSources ()

void	computeGeodesics ()

void	myCallback ()

int	main ()

Variables
polyscope::SurfaceMesh *	psMesh

polyscope::SurfaceMesh *	psMeshReg

SurfMesh	surfmesh

SurfMesh	surfmeshReg

float	dt = 2.0

CountedPtr< SH3::BinaryImage >	binary_image

CountedPtr< SH3::DigitalSurface >	surface

GeodesicsInHeat< PolyCalculus > *	heat

PolyCalculus *	calculus

GeodesicsInHeat< PolyCalculus > *	heatReg

PolyCalculus *	calculusReg

SHG3::RealVectors	iinormals

int	sourceVertexId =0

float	radiusII = 3.0

bool	skipReg = true

bool	useProjectedCalculus = true

bool	isPrecomputed =false

Detailed Description

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Author: David Coeurjolly (david.nosp@m..coe.nosp@m.urjol.nosp@m.ly@l.nosp@m.iris..nosp@m.cnrs.nosp@m..fr ) Laboratoire d'InfoRmatique en Image et Systemes d'information - LIRIS (CNRS, UMR 5205), CNRS, France

Date: 2021/09/02

This file is part of the DGtal library.

Definition in file dgtalCalculus-geodesic.cpp.

Typedef Documentation

◆ Face

typedef SurfMesh::Face Face

Definition at line 55 of file dgtalCalculus-geodesic.cpp.

◆ PolyCalculus

typedef PolygonalCalculus<SH3::RealPoint,SH3::RealVector> PolyCalculus

Definition at line 57 of file dgtalCalculus-geodesic.cpp.

◆ SH3

typedef Shortcuts<Z3i::KSpace> SH3

Definition at line 51 of file dgtalCalculus-geodesic.cpp.

◆ SHG3

typedef ShortcutsGeometry<Z3i::KSpace> SHG3

Definition at line 52 of file dgtalCalculus-geodesic.cpp.

◆ SurfMesh

typedef SurfaceMesh< RealPoint, RealVector > SurfMesh

Definition at line 54 of file dgtalCalculus-geodesic.cpp.

◆ Vertex

typedef SurfMesh::Vertex Vertex

Definition at line 56 of file dgtalCalculus-geodesic.cpp.

Function Documentation

◆ addSource()

void addSource ( )

Definition at line 128 of file dgtalCalculus-geodesic.cpp.

 {
   auto pos =rand() % surfmesh.nbVertices();
   heat->addSource( pos );
   GeodesicsInHeat<PolyCalculus>::Vector source = heat->source();
   psMesh->addVertexCountQuantity("Sources", source2count(source));
  
   if (!skipReg)
   {
     heatReg->addSource( pos );
     GeodesicsInHeat<PolyCalculus>::Vector source = heatReg->source();
     psMeshReg->addVertexCountQuantity("Sources", source2count(source));
   }
 }

References heat, heatReg, DGtal::SurfaceMesh< TRealPoint, TRealVector >::nbVertices(), psMesh, psMeshReg, skipReg, source2count(), and surfmesh.

Referenced by myCallback().

◆ clearSources()

void clearSources ( )

Definition at line 143 of file dgtalCalculus-geodesic.cpp.

 {
   heat->clearSource();
   psMesh->addVertexScalarQuantity("source", heat->source());
 }

References heat, and psMesh.

Referenced by myCallback().

◆ computeGeodesics()

void computeGeodesics ( )

Definition at line 149 of file dgtalCalculus-geodesic.cpp.

 {
   heat->addSource( sourceVertexId ); //Forcing one seed (for screenshots)
   GeodesicsInHeat<PolyCalculus>::Vector source = heat->source();
   psMesh->addVertexCountQuantity("Sources", source2count(source));
   GeodesicsInHeat<PolyCalculus>::Vector dist = heat->compute();
   psMesh->addVertexDistanceQuantity("geodesic", dist);
  
   if (!skipReg)
   {
     heatReg->addSource( sourceVertexId ); //Forcing one seed (for screenshots)371672
     GeodesicsInHeat<PolyCalculus>::Vector sourceReg = heatReg->source();
     psMeshReg->addVertexCountQuantity("Sources", source2count(sourceReg));
     GeodesicsInHeat<PolyCalculus>::Vector dist = heatReg->compute();
     psMeshReg->addVertexDistanceQuantity("geodesic", dist);
   }
 }

References heat, heatReg, psMesh, psMeshReg, skipReg, source2count(), and sourceVertexId.

Referenced by myCallback().

◆ main()

int main ( void )

Definition at line 213 of file dgtalCalculus-geodesic.cpp.

 {
   auto params = SH3::defaultParameters() | SHG3::defaultParameters() |  SHG3::parametersGeometryEstimation();
   params("surfaceComponents", "All");
   params("r-radius", (double) radiusII);
   std::string filename = examplesPath + std::string("/samples/bunny-128.vol");
   binary_image         = SH3::makeBinaryImage(filename, params );
   auto K               = SH3::getKSpace( binary_image, params );
   surface              = SH3::makeDigitalSurface( binary_image, K, params );
   auto primalSurface   = SH3::makePrimalSurfaceMesh(surface);
   
   //Need to convert the faces
   std::vector<std::vector<SH3::SurfaceMesh::Vertex>> faces;
   std::vector<RealPoint> positions;
   
   for(auto face= 0 ; face < primalSurface->nbFaces(); ++face)
     faces.push_back(primalSurface->incidentVertices( face ));
   
   //Recasting to vector of vertices
   positions = primalSurface->positions();
  
   surfmesh = SurfMesh(positions.begin(),
                       positions.end(),
                       faces.begin(),
                       faces.end());
   std::cout << surfmesh << std::endl;
   std::cout<<"number of non-manifold Edges = " << surfmesh.computeNonManifoldEdges().size()<<std::endl;
   
   //Construction of a regularized surface
   DigitalSurfaceRegularization<SH3::DigitalSurface> regul(surface);
   regul.init();
   regul.attachConvolvedTrivialNormalVectors(params);
   regul.regularize();
   auto regularizedPosition = regul.getRegularizedPositions();
  
   surfmeshReg = SurfMesh(regularizedPosition.begin(),
                       regularizedPosition.end(),
                       faces.begin(),
                       faces.end());
   
   // Initialize polyscope
   polyscope::init();
  
   psMesh = polyscope::registerSurfaceMesh("digital surface", positions, faces);
   psMeshReg = polyscope::registerSurfaceMesh("regularized surface", regularizedPosition, faces);
   psMeshReg->setEnabled(false);
  
   // Set the callback function
   polyscope::state::userCallback = myCallback;
   polyscope::show();
   return EXIT_SUCCESS;
 }

References DGtal::DigitalSurfaceRegularization< TDigitalSurface >::attachConvolvedTrivialNormalVectors(), binary_image, DGtal::SurfaceMesh< TRealPoint, TRealVector >::computeNonManifoldEdges(), DGtal::DigitalSurfaceRegularization< TDigitalSurface >::getRegularizedPositions(), DGtal::DigitalSurfaceRegularization< TDigitalSurface >::init(), init(), K, myCallback(), psMesh, psMeshReg, radiusII, DGtal::DigitalSurfaceRegularization< TDigitalSurface >::regularize(), surface, surfmesh, and surfmeshReg.

◆ myCallback()

void myCallback ( )

Definition at line 168 of file dgtalCalculus-geodesic.cpp.

 {
   ImGui::SliderFloat("dt", &dt, 0.,4.);
   ImGui::SliderFloat("ii radius for normal vector estimation", &radiusII , 0.,10.);
   ImGui::Checkbox("Skip regularization", &skipReg);
   ImGui::Checkbox("Using projection", &useProjectedCalculus);
   ImGui::InputInt("Index of the first source vertex", &sourceVertexId);
   
   
   if(ImGui::Button("Precomputation (required if you change parameters)"))
   {
     precompute();
     isPrecomputed=true;
   }
   ImGui::Separator();
   if(ImGui::Button("Add a random source"))
   {
     if (!isPrecomputed)
     {
       precompute();
       isPrecomputed=true;
     }
     addSource();
   }
   if(ImGui::Button("Clear sources"))
   {
     if (!isPrecomputed)
     {
       precompute();
       isPrecomputed=true;
     }
     clearSources();
   }
   
   if(ImGui::Button("Compute geodesic"))
   {
     if (!isPrecomputed)
     {
       precompute();
       isPrecomputed=true;
     }
     computeGeodesics();
   }
 }

References addSource(), clearSources(), computeGeodesics(), dt, isPrecomputed, precompute(), radiusII, skipReg, sourceVertexId, and useProjectedCalculus.

Referenced by main().

◆ precompute()

void precompute ( )

Definition at line 83 of file dgtalCalculus-geodesic.cpp.

 {
   
   if (!useProjectedCalculus)
     calculus = new PolyCalculus(surfmesh);
   else
   {
     //Using the projection embedder
     auto params2 = SH3::defaultParameters() | SHG3::defaultParameters() |  SHG3::parametersGeometryEstimation();
     params2("r-radius", (double) radiusII);
     auto surfels   = SH3::getSurfelRange( surface, params2 );
     iinormals = SHG3::getIINormalVectors(binary_image, surfels,params2);
     trace.info()<<iinormals.size()<<std::endl;
     psMesh->addFaceVectorQuantity("II normals", iinormals);
     
     calculus = new PolyCalculus(surfmesh);
     functors::EmbedderFromNormalVectors<Z3i::RealPoint, Z3i::RealVector> embedderFromNormals(iinormals,surfmesh);
     calculus->setEmbedder( embedderFromNormals );
   }
   
   heat = new GeodesicsInHeat<PolyCalculus>(calculus);
   
   if (!skipReg)
   {
     calculusReg = new PolyCalculus(surfmeshReg);
     heatReg = new GeodesicsInHeat<PolyCalculus>(calculusReg);
   }
   trace.beginBlock("Init solvers");
   heat->init(dt);
   if (!skipReg)
     heatReg->init(dt);
   trace.endBlock();
 }

References DGtal::Trace::beginBlock(), binary_image, calculus, calculusReg, dt, DGtal::Trace::endBlock(), heat, heatReg, iinormals, DGtal::Trace::info(), psMesh, radiusII, DGtal::PolygonalCalculus< TRealPoint, TRealVector >::setEmbedder(), skipReg, surface, surfmesh, surfmeshReg, DGtal::trace, and useProjectedCalculus.

Referenced by myCallback().

◆ source2count()

std::vector<std::pair<size_t,int> > source2count ( GeodesicsInHeat< PolyCalculus >::Vector & source )

Definition at line 117 of file dgtalCalculus-geodesic.cpp.

 {
   std::vector<std::pair<size_t,int>> counts;
   for(auto i=0; i< source.size(); ++i)
   {
     if (source(i)!=0.0)
       counts.push_back(std::pair<size_t,int>(i,1));
   }
   return counts;
 }