csv_mesh.h

/*    Copyright (C) 2012 University of Oxford  */

/*  Part of FSL - FMRIB's Software Library
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    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
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#if !defined (CSV_MESH_H)
#define CSV_MESH_H


#define CSV_ASCII 5
#define CSV_VTK   6
#define CSV_GIFTI 7

#include <stdio.h>
#include "meshclass/point.h"
#include "meshclass/mpoint.h"
#include "miscmaths/miscmaths.h"
#include "utils/tracer_plus.h"
#include "fslsurface/fslsurfaceio.h"
#include "fslsurface/fslsurface.h"


using namespace fslsurface_name;
using namespace std;
using namespace MISCMATHS;
using namespace mesh;
using namespace Utilities;

int  meshFileType(const string& filename);
bool meshExists(const string& filename);


class CsvMpoint {

public:

	CsvMpoint(double x, double y, double z, int counter):_no(counter){
		_coord=Pt(x, y, z);
	}
	CsvMpoint(const Pt p, int counter,float val=0):_no(counter){
		_coord=p;
	}
	~CsvMpoint(){}
	CsvMpoint(const CsvMpoint &p):_coord(p._coord),_no(p._no),_trID(p._trID){
		*this=p;
	}
	CsvMpoint& operator=(const CsvMpoint& p){
		_coord=p._coord;
		_no=p._no;
		_trID=p._trID;
		return(*this);
	}

	const Pt&    get_coord() const         {return _coord;}
	void         set_coord(const Pt& coord){_coord=coord;}
	inline int          get_no() const            {return _no;}
	void         push_triangle(const int& i){_trID.push_back(i);}
	int          ntriangles()const{return (int)_trID.size();}
	int          get_trID(const int i)const{return _trID[i];}

private:
	Pt                  _coord;
	int                 _no;
	vector<int>         _trID;
};

class CsvTriangle {
private:
	vector<CsvMpoint> _vertice;
	int               _no;

public:
	CsvTriangle(){}
	CsvTriangle(const CsvMpoint& p1,const CsvMpoint& p2,const CsvMpoint& p3,int no):_no(no){
		_vertice.push_back(p1);
		_vertice.push_back(p2);
		_vertice.push_back(p3);
	}
	~CsvTriangle(){}
	CsvTriangle(const CsvTriangle &t):_vertice(t._vertice),_no(t._no){
		*this=t;
	}
	CsvTriangle& operator=(const CsvTriangle& t){
		_vertice=t._vertice;_no=t._no;return *this;
	}

	Vec  centroid() const{
		Vec p ((_vertice[0].get_coord().X +_vertice[1].get_coord().X +_vertice[2].get_coord().X)/3,
				(_vertice[0].get_coord().Y +_vertice[1].get_coord().Y +_vertice[2].get_coord().Y)/3,
				(_vertice[0].get_coord().Z +_vertice[1].get_coord().Z +_vertice[2].get_coord().Z)/3);

		return p;
	}
	Vec normal()const{
		Vec result=(_vertice[2].get_coord()-_vertice[0].get_coord())*(_vertice[1].get_coord()-_vertice[0].get_coord());
		result.normalize();
		return result;
	}
	bool isinside(const Vec& x)const;
	double dist_to_point(const Vec& x0)const;


	inline const CsvMpoint& get_vertice(const int& i) const{return _vertice[i];}
	const bool intersect(const vector<Pt> & p)const;          // checks if a segment intersects the triangle
	const bool intersect(const vector<Pt> & p,int& ind)const; // checks if a segment intersects the triangle+gives the index of the closest vertex
	inline int get_no()const{return _no;}
};


const bool operator ==(const CsvMpoint &p2, const CsvMpoint &p1);
const bool operator ==(const CsvMpoint &p2, const Pt &p1);

const Vec operator -(const CsvMpoint&p1, const CsvMpoint &p2);
const Vec operator -(const Pt&p1, const CsvMpoint &p2);
const Vec operator -(const CsvMpoint&p1, const Pt &p2);
const Vec operator -(const ColumnVector& p1, const CsvMpoint &p2);
const Vec operator -(const ColumnVector& p1, const Vec &p2);
const Vec operator -(const Vec& p1, const CsvMpoint &p2);


class CsvMesh {

public:
	vector<CsvMpoint>   _points;
	vector<CsvTriangle> _triangles;
	vector<float>       _pvalues;
	vector<float>       _tvalues;


	CsvMesh(){}
	~CsvMesh(){}
	CsvMesh(const CsvMesh &m):_points(m._points),_triangles(m._triangles),_pvalues(m._pvalues),_tvalues(m._tvalues){
		*this=m;
	}
	CsvMesh& operator=(const CsvMesh& m){
		_points=m._points;
		_triangles=m._triangles;
		_pvalues=m._pvalues;
		_tvalues=m._tvalues;
		return(*this);
	}

	void        clear(){
		_points.clear();_triangles.clear();_pvalues.clear();_tvalues.clear();
	}

	int   nvertices() const{return (int)_points.size();}
	int   ntriangles() const{return (int)_triangles.size();}
	inline const CsvMpoint&    get_point(const int& n)const{return _points[n];}
	inline const CsvTriangle&  get_triangle(const int& n)const{return _triangles[n];}
	bool triangle_intersect(const vector<Pt>& segment,const int& triid)const{
		return( _triangles[triid].intersect(segment) );
	}
	bool triangle_intersect(const vector<Pt>& segment,const int& triid, int& ind)const{
		return( _triangles[triid].intersect(segment,ind) );
	}

	float get_pvalue(const int& i)const{return _pvalues[i];}
	float get_tvalue(const int& i)const{return _tvalues[i];}
	void set_pvalue(const int& i,const float& val){_pvalues[i]=val;}
	void set_tvalue(const int& i,const float& val){_tvalues[i]=val;}
	void set_pvalues(const vector<int>& ids,const float& val){
		for(unsigned int i=0;i<ids.size();i++){_pvalues[ids[i]]=val;}
	}
	void set_pvalues(const ColumnVector& vals){
		if(vals.Nrows()!=(int)_points.size()){
			cerr<<"CsvMesh::set_pvalues:incompatible number of scalars"<<endl;
			exit(1);
		}
		for(int i=1;i<=vals.Nrows();i++)
			_pvalues[i-1]=vals(i);
	}
	void set_pvalues(const float& val){
		for(unsigned int i=0;i<_pvalues.size();i++)
			_pvalues[i]=val;
	}

	vector< float > getPointsAsVectors()const{
		vector< float > ret;
		for(int i=0;i<nvertices();i++){
			ret.push_back( get_point(i).get_coord().X );
			ret.push_back( get_point(i).get_coord().Y );
			ret.push_back( get_point(i).get_coord().Z );
		}
		return ret;
	}
	vector< float > getValuesAsVectors()const{
		vector< float > ret;
		for(int i=0;i<nvertices();i++){
			ret.push_back( get_pvalue(i) );
		}
		return ret;
	}
	vector< vector<unsigned int> > getTrianglesAsVectors()const{
		vector< vector<unsigned int> > ret;
		for(int i=0;i<ntriangles();i++){
			vector<unsigned int> tmp(3);
			tmp[0]=(unsigned int)_triangles[i].get_vertice(0).get_no();
			tmp[1]=(unsigned int)_triangles[i].get_vertice(1).get_no();
			tmp[2]=(unsigned int)_triangles[i].get_vertice(2).get_no();
			ret.push_back(tmp);
		}
		return ret;
	}

	void reset_pvalues(){
		_pvalues.clear();
		for(unsigned int i=0;i<_points.size();i++)
			_pvalues.push_back(0);
	}
	void reset_tvalues(){
		_tvalues.clear();
		for(unsigned int i=0;i<_triangles.size();i++)
			_tvalues.push_back(0);
	}

	void push_triangle(const CsvTriangle& t);
	Vec  local_normal(const int& pt)const{
		Vec v(0,0,0);
		for(int i=0;i<_points[pt].ntriangles();i++){
			v+=_triangles[ _points[pt].get_trID(i) ].normal();
		}
		v.normalize();
		return v;
	}

	int step_sign(const int& vertind,const Vec& step)const;

	void load(const string& filename);
	void load_gifti(const string& filename);
	void load_ascii(const string& filename);
	void load_vtk(const string& filename);

	void save(const string& filename, const int& type=GIFTI_ENCODING_B64GZ)const;
	void save_ascii(const string& s)const;
	void save_gifti(const string& s,const int& type=GIFTI_ENCODING_B64GZ)const;
	void save_vtk(const string& s)const;


	void print(const string& filename){
		ofstream fs(filename.c_str());
		fs<<_points.size()<<" vertices"<<endl;
		for(unsigned int i=0;i<_points.size();i++){
			fs<<_points[i].get_coord().X<<" "
					<<_points[i].get_coord().Y<<" "
					<<_points[i].get_coord().Z<<endl;
		}
		fs<<_triangles.size()<<" triangles"<<endl;
		for(unsigned int i=0;i<_triangles.size();i++){
			fs<<_triangles[i].get_vertice(0).get_no()<<" "
					<<_triangles[i].get_vertice(1).get_no()<<" "
					<<_triangles[i].get_vertice(2).get_no()<<endl;
		}
		fs<<_pvalues.size()<<" scalars"<<endl;
		for(unsigned int i=0;i<_pvalues.size();i++){
			if(_pvalues[i]!=0){fs<<_pvalues[i]<<endl;}
		}
		fs.close();
	}

	//  ostream& operator <<(ostream& flot);
};



#endif