#include "polymake/client.h"
#include "polymake/Array.h"
#include "polymake/topaz/complex_tools.h"
#include "polymake/SparseMatrix.h"
#include "polymake/Smith_normal_form.h"
#include "polymake/SparseVector.h"
#include "polymake/topaz/Filtration.h"
#include "polymake/integer_linalg.h"
#include "polymake/list"
#include <string>
#include <sstream>

namespace polymake{ namespace topaz{

template<typename Matrix_type>
class PersistentHomology{

typedef typename Matrix_type::value_type Coeff;
typedef SparseVector<Coeff> Chain;
typedef pm::ensure_features<Array<Cell>, pm::cons<pm::end_sensitive, pm::indexed> >::const_iterator filtIter;

private:
const Filtration<Matrix_type> & F;
int dim;
Array<bool> marked;
Array<std::pair<int, Chain> > T;

public:
PersistentHomology(const Filtration<Matrix_type> & F_in) : F(F_in), dim(F.dim()) {
	int n_cells = F.n_cells();
	marked = Array<bool>(n_cells);
	T = Array<std::pair<int, Chain> > (n_cells); //zero as first pair value means empty. that's ok, as the zeroth filtration entry is always a point and thus has empty bd and does not get an entry in T.
}


Chain remove_pivot_rows(int j){
	Chain d = F.bd(j);

	for(typename pm::ensure_features<Chain, pm::cons<pm::end_sensitive, pm::indexed> >::iterator m = ensure(d, (pm::cons<pm::end_sensitive, pm::indexed>*)0).begin(); !m.at_end();){
		if(!marked[m.index()]) d.erase(m++); //remove unmarked cells
		else ++m;
	}

	while (!d.empty()){
		int i = indices(d).back(); //maximal index
		if(!T[i].first) break;
		Chain t = T[i].second;
		Coeff q = t[i];
		Coeff qq = d[i];
		d -= qq*(inv(q)*t); //TODO this differs from what's in the paper. they don't multiply with qq. why?
	}
	return d;
}

public:
Array<std::list<std::pair<int, int> > > compute_intervals(){
	Array<std::list<std::pair<int,int> > > L(dim+1);

	for (filtIter c = F.get_iter(); !c.at_end(); ++c) {
		int j = c.index();
		Chain d = remove_pivot_rows(j);
		if(d.empty()) marked[j] = true;
		else{
			int i = indices(d).back(); //maximal index
			int k = F[i].dim;
			T[i].first = j;
			T[i].second = d;
			int a = F[i].deg;
			int b = (*c).deg;
			if(a<b) //skip empty intervals
				L[k].push_back(std::pair<int,int>(a,b));
		}
	}

	for (filtIter c = F.get_iter(); !c.at_end(); ++c) {
		int j = c.index();
		if(marked[j] && !T[j].first){
			L[(*c).dim].push_back(std::pair<int,int>((*c).deg,-1));
		}
	}

	return L;
}

};

template<typename MatrixType>
typename std::enable_if<pm::is_field<typename MatrixType::value_type>::value, Array<std::list<std::pair<int, int> > >>::type //for field coefficients
persistent_homology(Filtration<MatrixType> F){

	PersistentHomology<MatrixType> P(F);
	return P.compute_intervals();

}

// using snf for nullspace and span computation for performance reasons
template<typename MatrixType>
SparseMatrix<typename MatrixType::value_type> rowspan_snf(MatrixType M_in){
	SmithNormalForm<typename MatrixType::value_type> S = smith_normal_form(M_in);
	return (S.form.minor(All,sequence(0,S.rank)))*((S.right_companion).minor(sequence(0,S.rank),All));
}

template<typename MatrixType>
SparseMatrix<typename MatrixType::value_type> null_space_snf(MatrixType M_in){
	SmithNormalForm<typename MatrixType::value_type> S = smith_normal_form(M_in,1);
	return (S.left_companion).minor(range(S.rank,S.left_companion.rows()-1),All);
}

template<typename MatrixType>
typename std::enable_if<std::numeric_limits<typename MatrixType::value_type>::is_integer, //for integer coefficients
         std::pair<SparseMatrix<typename MatrixType::value_type> ,
                   std::list< std::pair<typename MatrixType::value_type, SparseMatrix<typename MatrixType::value_type> > > > >::type
//less verbose: pair< SparseMatrix<Coeff>, list<pair< Coeff, SparseMatrix<Coeff>>>>
persistent_homology(Filtration<MatrixType> F, int i, int p, int k){

	typedef typename MatrixType::value_type Coeff;
	typedef SparseMatrix<Coeff> Generators;//the _rows_ of this matrix represent a generating set
	typedef std::list<std::pair<Coeff, Generators> > Torsion;//torsion coefficient and generating set of the corresponding torsion module

	pm::MatrixMinor<MatrixType&, const Set<int>&, const Set<int>& > M = F.boundary_matrix(k,i);

	if(!M.rows()) return std::pair<Generators, Torsion>(); //Z empty.

	Generators Z;
	if(k==0) Z = unit_matrix<Coeff>(M.rows()); //1-cells always have empty boundary
	else Z = null_space_snf<MatrixType>((M)); //ker(d_k)

	if(!Z.rows()) return std::pair<Generators, Torsion>(); //Z empty

	pm::MatrixMinor<MatrixType&, const Set<int>&, const Set<int>& >  M2 = F.boundary_matrix(k+1,i+p);


	Set<int> simpl_p = M2.get_subset(int_constant<2>());
	Set<int> frame = simpl_p - M.get_subset(int_constant<1>()); //indices of k-simplices present int frame i+p, but not yet in frame i

	//embedding: insert zero cols for cells missing in Z, i.e. not yet there in frame i.
	ListMatrix<SparseVector<Coeff> > ZZlist(0,Z.cols());
	int j=0;
	int maxindex = simpl_p.back();
	for(typename Entire<Cols<SparseMatrix<Coeff> > >::const_iterator c = entire(cols(Z)); maxindex>=j; ++j){
		if(frame.contains(j)) ZZlist /= zero_vector<Coeff>(Z.rows());//cell only present in B
		else if(!c.at_end() && simpl_p.contains(j)){//cell present in both
			ZZlist /= *c; ++c;
		}
	}
	SparseMatrix<Coeff> ZZ(T(ZZlist));

	if(!M2.rows()) return std::pair<Generators, Torsion>(ZZ,Torsion()); //B empty

	SparseMatrix<Coeff> B =  rowspan_snf<MatrixType>(M2); //im(d_k+1)

	if(!B.rows()) return std::pair<Generators, Torsion>(ZZ,Torsion()); //B empty

	Generators U = null_space_snf<MatrixType>((ZZ/B)).minor(All,sequence(0,Z.rows()));
	//U*ZZ is a basis of the intersection. U is thus the relation matrix for the persistence module relative to ZZ

	if(!U.rows()) return std::pair<Generators, Torsion>(ZZ,Torsion()); //intersection empty

	SmithNormalForm<Coeff> SNF4 = smith_normal_form(U);

	//find a basis for torsional part: rows of left companion corresponding to non-zero non-one diagonal entries
	Generators R = (SNF4.right_companion)*ZZ;
	Torsion tor;
	int r = SNF4.rank;
	for(typename Entire<std::list<std::pair<Coeff,int> > >::const_reverse_iterator t=pm::rentire(SNF4.torsion);!t.at_end();++t){
		int mult = (*t).second;
		std::pair<Coeff, Generators> p((*t).first,R.minor(sequence(r-mult,mult),All));
		tor.push_front(p);
		r-=mult;
	}

	//basis for the non-torsional part...
	Generators free;
	int prank = Z.rows() - SNF4.rank;
	if(prank>0) free = R.minor(sequence(SNF4.rank,prank),All);


	return std::pair<Generators, Torsion>(free, tor);

}

UserFunctionTemplate4perl("# @category Other"
				  "# Given a Filtration and three indices i,p and k, this computes the p-persistent k-th homology group of the i-th frame of the filtration for coefficients from any PID. Returns a basis for the free part and a list of torsion coefficients with bases."
				 "# @param Filtration<MatrixType> F"
				 "# @param Int i the filtration frame"
				 "# @param Int p the number of frames to consider"
				 "# @param Int k the dimension in which to compute"
				 "# @tparam MatrixType type of boundary matrices"
				"# @return Pair<SparseMatrix<Coeff>, List< Pair<Coeff, SparseMatrix<Coeff> > > >",
                   "persistent_homology<MatrixType>($$$$)");

UserFunctionTemplate4perl("# @category Other"
				  "# Given a Filtration, this computes its persistence barcodes in all dimension, using the algorithm described in the 2005 paper 'Computing Persistent Homology' by Afra Zomorodian and Gunnar Carlsson. It only works for field coefficients."
				 "# @param Filtration<MatrixType> F"
				 "# @tparam MatrixType type of the boundary matrices"
                  "# @return Array<List<Pair<int, int> > >",
                   "persistent_homology<MatrixType>($)");

}}
