CellAtlasUtils.hpp

Go to the documentation of this file.

#ifndef CellAtlasUtils_H
#define CellAtlasUtils_H
 
#include <Process.hpp> // for vvGraph, forall, ... 
#include <GraphUtils.hpp> // for neighborhoodGraph
 
#include <ImageData.hpp>
#include <Triangulate.hpp> // calcNearestPointOnBezierLine
 
using namespace std;
 
// CellAtlasUtils contains typedefs and class-independent helper-functions for the CellAtlas AddOn
namespace mgx 
{
 
typedef std::map<int, std::vector<vertex> > labelVertexMap;
 
typedef std::pair<int, std::vector<vertex> > labelVertexVecPair;
 
//typedef std::map<int, Point3d> labelPosMap;
//typedef std::map<int, double> labelDataMap;
//typedef std::map<int, bool> labelBoolMap;
 
// typedef Vector<3, vertex> tri;
// typedef std::vector<tri> triVector;
 
typedef std::pair<int, int> IntInt;
//typedef std::map<int, triVector> labelTriMap;
 
typedef std::map<int,std::map<int,double> > cellMorphLandscape;
 
typedef std::map <int, std::vector<int> > intToVec;
 
typedef std::map<Point2i, double> P2iDMap;
typedef std::pair<Point2i, double> P2iDPair;
typedef std::pair<IntInt, double> IntIntDouPair;
 
 
 
  //bool neighborhoodGraphLocal(const vvGraph& S, double tolerance, RootCellProcessing& cellAtlasData);
  bool neighborhoodGraphLocal(const vvGraph& S, double tolerance, std::map<int, double>& cellWallArea, std::map<IntInt, double>& wallArea, std::map<int, double>& outsideWallArea);
 
  int findSelectedLabel(const vvGraph& S);
 
  bool findTwoSelectedLabels(const vvGraph& S, int& label1, int& label2);
 
 
  bool pointInCone(Point3d axisVec, Point3d& coneTop, Point3d& coneBase, double coneAngle, Point3d& pointToTest);
 
  double gauss1D(double x, double muX, double sigmaX);
 
 
 
 
  
  // TODO documentation
 
 
 
  double calcCircumferential(Point3d dirRadRef, Point3d dirLongRef, Point3d cellCenter, Point3d cellOnLong);
 
  Point3d inPrimCoord(double radiant, Point3d dirRadRef, Point3d dirLongRef);
 
 
 
    // finds min and max value of a map
  void findMinMax(std::map<int,double>& map, double& min, double& max);
 
 
 
 
void differentialOfBezierGrid(std::vector<std::vector<Point3d> >& bezierGrid, Point2i& p, Point3d& diffU, Point3d& diffV);
 
 
  double cartesianToOrganCoordsLong(Point3d cartesianCoords, std::map<int, Point3d>& bMap, Point3d& closestPoint);
 
 
 
}
 
#endif