/*
 *  shapeModel.cpp
 *  
 *
 *  Created by Brian Patenaude on 23/06/2008.
 *  Copyright 2008 University of Oxford All rights reserved.
 *
 */
/*  Part of FSL - FMRIB's Software Library
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#include "shapeModel.h"
#include <iostream>
#include <string>
#include <sstream>
#include <fstream>
#include <stdio.h>
//#include <vector>
 #include "newmat.h"
 #include "newmatap.h"
#include "fslvtkio/fslvtkio.h"
#include "first_lib/first_newmat_vec.h"
#include <cmath>
#include <algorithm>
#include "math.h"
using namespace std;
using namespace NEWMAT;
using namespace FIRST_LIB;
using namespace fslvtkio;
namespace SHAPE_MODEL_NAME{
	
	shapeModel::shapeModel()
	{
	
	}
	shapeModel::shapeModel( const vector<float> & mshape, const vector< vector<float> > & modesshape, const vector<float> & se, \
							const vector<float> & ishape, const vector< vector<float> > & modesint, const vector<float> & ie, \
							const int & M, const vector<float> & errs)
{
		smean=mshape;
		smodes=modesshape;
		seigs=se;
		sqrtseigs=se;

		for (vector<float>::iterator i=sqrtseigs.begin();i!=sqrtseigs.end();i++)
			*i = sqrt(*i);
		sqrtseigsi=sqrtseigs;


		imean=ishape;
		imodes=modesint;
		ieigs=ie;
		NumberOfSubjects=M;
		Errs=errs;
		USE_COND=false;
		MODE_FOUND=false;
		mode=0;
	STORE_REG_XFM=true;
		
}

shapeModel::shapeModel( const vector<float> & mshape, const vector< vector<float> > & modesshape, const vector<float> & se, \
						const vector<float> & ishape, const vector< vector<float> > & modesint, const vector< vector<float> > & Iprec, const vector<float> & ie,\
						const int & M, const vector<float> & errs, const vector< vector<unsigned int> > & cellsin, const vector<int> & vlabels )
{
	labels=vlabels;
	smean=mshape;
	smodes=modesshape;
	seigs=se;
	sqrtseigs=se;
	
	for (vector<float>::iterator i=sqrtseigs.begin();i!=sqrtseigs.end();i++)
		*i = sqrt(*i);
	sqrtseigsi=sqrtseigs;
	imean=ishape;
	imodes=modesint;
	i_precision=Iprec;
	ieigs=ie;
	NumberOfSubjects=M;
	Errs=errs;
	cells=cellsin;
	USE_COND=false;
	MODE_FOUND=false;
	mode=0;
	STORE_REG_XFM=true;

	//keeps tracks of neighbourin triangles
	for (unsigned int i=0; i<static_cast<unsigned int>(smean.size()/3); i++)
	{
		vector<unsigned int> inds;
		int count=0;
		for ( vector< vector<unsigned int> >::iterator j=cells.begin(); j!=cells.end();j++,count++)
		{
			for ( vector<unsigned int>::iterator k= j->begin(); k!=j->end();k++)
			{
				if ((*k)==i)
				{
					inds.push_back(count); 
					break;
				}
			}
		}
		localTri.push_back(inds);
	}
	
	
}

shapeModel::shapeModel( const vector<float> & mshape, const vector< vector<float> > & modesshape, const vector<float> & se, \
						const vector<float> & ishape, const vector< vector<float> > & modesint, const vector<float> & ie, \
						const int & M, const vector<float> & errs, const vector<short> & vmaskin)
{
	smean=mshape;
	smodes=modesshape;
	seigs=se;
	imean=ishape;
	imodes=modesint;
	ieigs=ie;
	NumberOfSubjects=M;
	Errs=errs;
	stmask=vmaskin;
	MODE_FOUND=false;
	mode=0;
	STORE_REG_XFM=true;

}
	void shapeModel::printLabel( const unsigned int & i) const 
	{ cout<<"get labvel "<< labels.at(i) <<endl;}
	
	
//	int shapeModel::getLabel( const unsigned int & i) const 
//	{ cout<<"get labvel "<< labels.at(i) <<endl; return labels.at(i); }


std::vector<float> shapeModel::getDeformedGrid( const std::vector<float>  & vars ) const 
{

	std::vector<float> newshape=smean;
	std::vector<float>::const_iterator sqrtseigs_i=sqrtseigs.begin();
	std::vector< std::vector<float> >::const_iterator smodes_i = smodes.begin();
	for (std::vector<float>::const_iterator vars_i=vars.begin(); vars_i!=vars.end(); vars_i++,sqrtseigs_i++, smodes_i++)
	{
		std::vector<float>::iterator new_i=newshape.begin();
		for (std::vector<float>::const_iterator smodes_j= smodes_i->begin(); smodes_j!= smodes_i->end(); smodes_j++,new_i++)
			*new_i += (*vars_i) * (*sqrtseigs_i) * (*smodes_j);//* 
	}
	
	return newshape;
}

vector<float> shapeModel::getDeformedIGrid( const vector<float> & vars) const {

	vector<float> varsnew=vars;//getOrigSpaceBvars(vars);
	vector<float> newigrid=imean;
	for (unsigned int i=0; i< varsnew.size();i++){
		for (unsigned int j=0; j< imean.size(); j++){
		  newigrid.at(j)+=varsnew.at(i)*sqrtseigs.at(i)*imodes.at(i).at(j);
		}
	}
	return newigrid;
}

	vector< vector<float> > shapeModel::registerModeVectors( const vector< vector<float> >& vmodes, const vector< vector<float> >& flirtmat )
	{
		vector< vector<float> > reg_modes = vmodes;
		for (unsigned int i=0; i<vmodes.size();i++){
			for (unsigned int j=0; j<vmodes.at(0).size();j+=3){
				//exclude translation from mode of variation so that it is compatible with implementation	
				float x= flirtmat.at(0).at(0)*vmodes.at(i).at(j)  + flirtmat.at(0).at(1)*vmodes.at(i).at(j+1) + flirtmat.at(0).at(2)*vmodes.at(i).at(j+2);// +  flirtmat.at(0).at(3);
				float y= flirtmat.at(1).at(0)*vmodes.at(i).at(j)  + flirtmat.at(1).at(1)*vmodes.at(i).at(j+1) + flirtmat.at(1).at(2)*vmodes.at(i).at(j+2) ;//+  flirtmat.at(1).at(3);
				float z= flirtmat.at(2).at(0)*vmodes.at(i).at(j)  + flirtmat.at(2).at(1)*vmodes.at(i).at(j+1) + flirtmat.at(2).at(2)*vmodes.at(i).at(j+2) ;//+  flirtmat.at(2).at(3);
				
				 reg_modes.at(i).at(j)=x;
				 reg_modes.at(i).at(j+1)=y;
				 reg_modes.at(i).at(j+2)=z;	
			}
			
		}
		return reg_modes;
	}
	
	void shapeModel::registerModel(const vector< vector<float> > & flirtmat)
	{
		//start by registering mesh 
		float f_11= flirtmat.at(0).at(0);
		float f_12= flirtmat.at(0).at(1);
		float f_13= flirtmat.at(0).at(2);
		float f_14= flirtmat.at(0).at(3);
		float f_21= flirtmat.at(1).at(0);
		float f_22= flirtmat.at(1).at(1);
		float f_23= flirtmat.at(1).at(2);
		float f_24= flirtmat.at(1).at(3);
		float f_31= flirtmat.at(2).at(0);
		float f_32= flirtmat.at(2).at(1);
		float f_33= flirtmat.at(2).at(2);
		float f_34= flirtmat.at(2).at(3);
		//assumes last line is 0 0 0 1
		for (vector<float>::iterator i=smean.begin();i!=smean.end();i+=3)
		{
			float x= f_11 * (*i)  + f_12 * (*(i+1)) + f_13 * (*(i+2)) +  f_14;
			float y= f_21 * (*i)  + f_22 * (*(i+1)) + f_23 * (*(i+2)) +  f_24;
			float z= f_31 * (*i)  + f_32 * (*(i+1)) + f_33 * (*(i+2)) +  f_34;
		
			(*i)=x;
			(*(i+1))=y;
			(*(i+2))=z;				
		}
		
		vector< vector<float> > smodesAinv;
		//Matrix M_smodes_mni= first_newmat_vector::vectorOfVectorsToMatrix<float>(smodes);
		Matrix M_smodesPre= first_newmat_vector::vectorOfVectorsToMatrix<float>(smodes).t();
		smodes=registerModeVectors(smodes,flirtmat);
		
		Matrix M_smodes= first_newmat_vector::vectorOfVectorsToMatrix<float>(smodes).t();

			Matrix U,U2,V;
			DiagonalMatrix D,D2;
		Matrix Mfmat(3,3);
		for (int i=0;i<3;i++)
		{
			for (int j=0;j<3;j++)
			{
				Mfmat.element(i,j)=flirtmat.at(i).at(j);
				cout<<flirtmat.at(i).at(j)<<" ";
			}
			cout<<endl;
		}

		Mfmat=Mfmat.i();

		//invert an transpose
		Matrix A(M_smodes.Nrows(),M_smodes.Nrows());
		A=0;
		for (int i=0;i<A.Nrows()/3;i++)
			A.SubMatrix(3*i+1, 3*(i+1),3*i+1, 3*(i+1))=Mfmat; 
		
		
		if (STORE_REG_XFM)
		{
			u_xfm = first_newmat_vector:: matrixToVectorOfVectors<float>(M_smodesPre.t()*A);
			d_xfm=sqrtseigs;
		}
		
			SVD(M_smodes,D,U,V);
			DiagonalMatrix Eigs= first_newmat_vector::vectorToDiagonalMatrix(seigs);
			
			//DiagonalMatrix SqrtEigs= first_newmat_vector::vectorToDiagonalMatrix(sqrtseigs);
			SVD(D*V.t()*Eigs*V*D,D2,U2);

//		cout<<"st ore reg xfm "<<A.Nrows()<<" "<<A.Ncols()<<" "<<M_smodes.Nrows()<<" "<<M_smodes.Ncols()<<endl;
	
		
		
			smodes= first_newmat_vector::matrixToVector<float>((U*U2).SubMatrix(1,U.Nrows(),1,D2.Nrows()));
			vector<float> veigs, vsqrt_eigs;
			for (unsigned int i=0;i<static_cast<unsigned int>(D2.Nrows());i++)//static_cast<unsigned int>(D2.Nrows());i++)
			{
				veigs.push_back(D2.element(i));
				vsqrt_eigs.push_back(sqrt(D2.element(i)));
			}			
			seigs=veigs;
			sqrtseigs=vsqrt_eigs;

		
	

		
		
		Matrix M_imodes= first_newmat_vector::vectorOfVectorsToMatrix<float>(imodes).t();

//		cout<<"Transform imodes "<<M_imodes.Nrows()<<" "<<M_imodes.Ncols()<<" "<<M_smodes.Nrows()<<" "<<M_smodes.Ncols()<<A.Nrows()<<" "<<A.Ncols()<<endl;
		Matrix C=M_smodesPre.t()*A;
//		cout<<"Transform imodes "<<M_imodes.Nrows()<<" "<<M_imodes.Ncols()<<" "<<M_smodes.Nrows()<<" "<<M_smodes.Ncols()<<A.Nrows()<<" "<<A.Ncols()<<endl;

		C=C*U;
//cout<<"Transform imodes "<<M_imodes.Nrows()<<" "<<M_imodes.Ncols()<<" "<<M_smodes.Nrows()<<" "<<M_smodes.Ncols()<<A.Nrows()<<" "<<A.Ncols()<<endl;
//		cout<<"Transform imodes "<<M_imodes.Nrows()<<" "<<M_imodes.Ncols()<<" "<<M_smodes.Nrows()<<" "<<M_smodes.Ncols()<<A.Nrows()<<" "<<A.Ncols()<<endl;

		imodes= first_newmat_vector::matrixToVector<float>((M_imodes*C*U2));
			
		cout<<"NEw done imodes transform"<<endl;
 

	}
	std::vector<float> shapeModel::getOrigSpaceBvars(const std::vector<float> & bvars ) const
	{
		vector<float> bvars_orig;
		if (STORE_REG_XFM)
		{	
			DiagonalMatrix D2=first_newmat_vector::vectorToDiagonalMatrix(sqrtseigs);
			DiagonalMatrix D=first_newmat_vector::vectorToDiagonalMatrix(d_xfm);
			Matrix UU2 = first_newmat_vector::vectorOfVectorsToMatrix<float>(u_xfm);
			Matrix M_smodes= first_newmat_vector::vectorOfVectorsToMatrix<float>(smodes).t();
			/*
			
			cout<<"Smodes2 "<<UU2.Ncols()<<endl;
			for (int i=0;i<UU2.Ncols();i++)
			{
				cout<<UU2.element(0,i)<<" ";
				cout<<endl;
			}
			
		*/	
			
			ColumnVector Mbvars(D.Nrows()); 
			int count=0;
			Mbvars=0;
			for (vector<float>::const_iterator i=bvars.begin();i!=bvars.end();i++,count++)
				Mbvars.element(count)=*i;
			
			cout<<"D "<<endl;//<<"di"<<endl<<endl;
	//		for (int i=0;i<D.Nrows();i++)
	//		{
			//	if (abs(D.element(i)) < 1e-10)
		//			D.element(i)=0;
		//		else 
	//			cout<<"pre "<<i<<" "<<D.element(i)<<" "<<1/D.element(i)<<endl;
//
//					D.element(i)=1/sqrt(D.element(i));
//				cout<<i<<" "<<D.element(i)<<" "<<1/D.element(i)<<endl;
//			}
			cout<<UU2.Nrows()<<" "<<UU2.Ncols()<<" "<<M_smodes.Nrows()<<" "<<M_smodes.Ncols()<<endl;
			ColumnVector MbvarsOrg = D.i()*UU2*M_smodes*D2*Mbvars;
			
			for (int i=0;i<MbvarsOrg.Nrows();i++)
				bvars_orig.push_back(MbvarsOrg.element(i));
			
		}
		return bvars_orig;
	}
	
	
	shapeModel* shapeModel::loadAndCreateShapeModel( const string & modelname, const bool & verbose)
	{
		
		if (verbose) cout<<"read model"<<endl;
		fslvtkIO* fmodel = new fslvtkIO(modelname,static_cast<fslvtkIO::DataType>(0));
		if (verbose) cout<<"done reading model"<<endl;
		const int Npts=fmodel->getPointsAsMatrix().Nrows();
		
		
		if (verbose) cout<<"setting up shape/appearance model"<<endl;
		
		//load mean shape into vector
		vector<float> Smean;
		Matrix* Pts = new Matrix;
		*Pts=fmodel->getPointsAsMatrix();
		
		if (verbose) cout<<"The shape has "<<Npts<<" vertices."<<endl;
		for (int i=0;i< Npts ; i++){
			Smean.push_back(Pts->element(i,0));
			Smean.push_back(Pts->element(i,1));
			Smean.push_back(Pts->element(i,2));
		}   
		Pts->ReleaseAndDelete();
		
		//read polygon data
		vector< vector<unsigned int > > polygons = first_newmat_vector::matrixToVector<unsigned int>(fmodel->getPolygons().t());
		
		//process shape modes and conditional intensity mean modes
		Matrix SmodesM;
		Matrix ImodesM;
		
		
		SmodesM=first_newmat_vector::unwrapMatrix(fmodel->getField("mode0"));
		ImodesM=first_newmat_vector::unwrapMatrix(fmodel->getField("Imode0"));
		unsigned int M = static_cast<unsigned int>(fmodel->getField("numSubjects").element(0,0));
		if (verbose) cout<<"The model was constructed from "<<M<<" training subjects."<<endl;
		
		unsigned int AllModes=M;
		
		for (unsigned int i =1; i<AllModes;i++)
		{
			stringstream ss;
			ss<<i;
			string mode;
			ss>>mode;
			SmodesM=SmodesM | first_newmat_vector::unwrapMatrix(fmodel->getField("mode"+mode));
			ImodesM=ImodesM | first_newmat_vector::unwrapMatrix(fmodel->getField("Imode"+mode));
			
		}
		if (verbose) cout<<AllModes<<" modes of variation are retained."<<endl;
		
		
		vector< vector<float > > Smodes = first_newmat_vector::matrixToVector<float>(SmodesM);
		vector< vector<float > > Imodes = first_newmat_vector::matrixToVector<float>(ImodesM);
		ImodesM.Release();
		SmodesM.Release();
		
		
		//process rest of information, including intensity variance
		vector< vector<float > > Iprec = first_newmat_vector::matrixToVector<float>(fmodel->getField("iCondPrec0").t());
		vector<float > Errs =  first_newmat_vector::vectorToVector<float>(fmodel->getField("ErrPriors0"));
		vector<float > se =  first_newmat_vector::vectorToVector<float>(fmodel->getField("eigenValues"), AllModes);
		vector<float > ie =  first_newmat_vector::vectorToVector<float>(fmodel->getField("iCondEigs0"));
		vector<float > Imean =  first_newmat_vector::vectorToVector<float>(first_newmat_vector::unwrapMatrix(fmodel->getField("Imean")));
		vector<int> labels =  first_newmat_vector::vectorToVector<int>(fmodel->getField("labels"));
		
		
		
		//have read in all data and store in local structures, now delete the reader.
		delete fmodel;
		cout<<"create shapeModel "<<endl;
		//create shape model
		shapeModel* model1 = new shapeModel(Smean, Smodes, se, Imean, Imodes,Iprec, ie, M,Errs,polygons,labels);
		cout<<"done creating shapeModel "<<endl;
		
		return model1;
		
	}
	
	
}