/*
 * Pre-processor to generate signed distance function from segmented data
 * segmented data should be stored in a raw binary file as 1-byte integer (type char)
 * will output distance functions for phases
 */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <iostream>
#include <fstream>
#include <sstream>
#include "common/Array.h"
#include "common/Domain.h"


//*************************************************************************
// Morpohological drainage pre-processor 
//   Generate states on primary drainage using morphological approach
//   Signed distance function is used to determine fluid configuration
//*************************************************************************
inline void PackID(int *list, int count, char *sendbuf, char *ID){
	// Fill in the phase ID values from neighboring processors
	// This packs up the values that need to be sent from one processor to another
	int idx,n;

	for (idx=0; idx<count; idx++){
		n = list[idx];
		sendbuf[idx] = ID[n];
	}
}
//***************************************************************************************

inline void UnpackID(int *list, int count, char *recvbuf, char *ID){
	// Fill in the phase ID values from neighboring processors
	// This unpacks the values once they have been recieved from neighbors
	int idx,n;

	for (idx=0; idx<count; idx++){
		n = list[idx];
		ID[n] = recvbuf[idx];
	}
}

//***************************************************************************************


int main(int argc, char **argv)
{
	// Initialize MPI
	int rank, nprocs;
	MPI_Init(&argc,&argv);
    MPI_Comm comm = MPI_COMM_WORLD;
	MPI_Comm_rank(comm,&rank);
	MPI_Comm_size(comm,&nprocs);

	//.......................................................................
	// Reading the domain information file
	//.......................................................................
	int nprocx, nprocy, nprocz, nx, ny, nz, nspheres;
	double Lx, Ly, Lz;
	int i,j,k,n;
	int BC=0;

	string filename;
	if (argc > 1){
		filename=argv[1];
	}
	else ERROR("No input database provided\n");
	// read the input database 
	auto db = std::make_shared<Database>( filename );
	auto domain_db = db->getDatabase( "Domain" );

	// Read domain parameters
	auto L = domain_db->getVector<double>( "L" );
	auto size = domain_db->getVector<int>( "n" );
	auto nproc = domain_db->getVector<int>( "nproc" );
	double SW = domain_db->getScalar<double>( "Sw" );
	
	nx = size[0];
	ny = size[1];
	nz = size[2];
	nprocx = nproc[0];
	nprocy = nproc[1];
	nprocz = nproc[2];

	// Check that the number of processors >= the number of ranks
	if ( rank==0 ) {
		printf("Number of MPI ranks required: %i \n", nprocx*nprocy*nprocz);
		printf("Number of MPI ranks used: %i \n", nprocs);
		printf("Full domain size: %i x %i x %i  \n",nx*nprocx,ny*nprocy,nz*nprocz);
	}
	if ( nprocs < nprocx*nprocy*nprocz ){
		ERROR("Insufficient number of processors");
	}

	char LocalRankFilename[40];

	int BoundaryCondition=1;
	Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BoundaryCondition);

	nx+=2; ny+=2; nz+=2;
	int N = nx*ny*nz;
	char *id;
	id = new char[N];


	// Define communication sub-domain -- everywhere
	for (int k=0; k<nz; k++){
		for (int j=0; j<ny; j++){
			for (int i=0; i<nx; i++){
				n = k*nx*ny+j*nx+i;
				Dm.id[n] = 1;
			}
		}
	}

	Dm.CommInit();

	int xdim,ydim,zdim;
	xdim=Dm.Nx-2;
	ydim=Dm.Ny-2;
	zdim=Dm.Nz-2;
	fillHalo<double> fillData(Dm.Comm, Dm.rank_info,{xdim,ydim,zdim},{1,1,1},0,1);

	DoubleArray SignDist(nx,ny,nz);
	// Read the signed distance from file
	sprintf(LocalRankFilename,"SignDist.%05i",rank);
	FILE *DIST = fopen(LocalRankFilename,"rb");
	size_t ReadSignDist;
	ReadSignDist=fread(SignDist.data(),8,N,DIST);
	if (ReadSignDist != size_t(N)) printf("lbpm_morphdrain_pp: Error reading signed distance function (rank=%i)\n",rank);
	fclose(DIST);

	fillData.fill(SignDist);

	sprintf(LocalRankFilename,"ID.%05i",rank);
	size_t readID;
	FILE *IDFILE = fopen(LocalRankFilename,"rb");
	if (IDFILE==NULL) ERROR("Error opening file: ID.xxxxx");
	readID=fread(id,1,N,IDFILE);
	if (readID != size_t(N)) printf("lbpm_segmented_pp: Error reading ID (rank=%i) \n",rank);
	fclose(IDFILE);

	
	Dm.CommInit();
	int iproc = Dm.iproc();
	int jproc = Dm.jproc();
	int kproc = Dm.kproc();

	// Generate the NWP configuration
	//if (rank==0) printf("Performing morphological drainage with critical radius %f \n", Rcrit);
	if (rank==0) printf("Performing morphological drainage with target saturation %f \n", SW);
	//	GenerateResidual(id,nx,ny,nz,Saturation);

	// Communication buffers
	char *sendID_x, *sendID_y, *sendID_z, *sendID_X, *sendID_Y, *sendID_Z;
	char *sendID_xy, *sendID_yz, *sendID_xz, *sendID_Xy, *sendID_Yz, *sendID_xZ;
	char *sendID_xY, *sendID_yZ, *sendID_Xz, *sendID_XY, *sendID_YZ, *sendID_XZ;
	char *recvID_x, *recvID_y, *recvID_z, *recvID_X, *recvID_Y, *recvID_Z;
	char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
	char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
	// send buffers
	sendID_x = new char [Dm.sendCount_x];
	sendID_y = new char [Dm.sendCount_y];
	sendID_z = new char [Dm.sendCount_z];
	sendID_X = new char [Dm.sendCount_X];
	sendID_Y = new char [Dm.sendCount_Y];
	sendID_Z = new char [Dm.sendCount_Z];
	sendID_xy = new char [Dm.sendCount_xy];
	sendID_yz = new char [Dm.sendCount_yz];
	sendID_xz = new char [Dm.sendCount_xz];
	sendID_Xy = new char [Dm.sendCount_Xy];
	sendID_Yz = new char [Dm.sendCount_Yz];
	sendID_xZ = new char [Dm.sendCount_xZ];
	sendID_xY = new char [Dm.sendCount_xY];
	sendID_yZ = new char [Dm.sendCount_yZ];
	sendID_Xz = new char [Dm.sendCount_Xz];
	sendID_XY = new char [Dm.sendCount_XY];
	sendID_YZ = new char [Dm.sendCount_YZ];
	sendID_XZ = new char [Dm.sendCount_XZ];
	//......................................................................................
	// recv buffers
	recvID_x = new char [Dm.recvCount_x];
	recvID_y = new char [Dm.recvCount_y];
	recvID_z = new char [Dm.recvCount_z];
	recvID_X = new char [Dm.recvCount_X];
	recvID_Y = new char [Dm.recvCount_Y];
	recvID_Z = new char [Dm.recvCount_Z];
	recvID_xy = new char [Dm.recvCount_xy];
	recvID_yz = new char [Dm.recvCount_yz];
	recvID_xz = new char [Dm.recvCount_xz];
	recvID_Xy = new char [Dm.recvCount_Xy];
	recvID_xZ = new char [Dm.recvCount_xZ];
	recvID_xY = new char [Dm.recvCount_xY];
	recvID_yZ = new char [Dm.recvCount_yZ];
	recvID_Yz = new char [Dm.recvCount_Yz];
	recvID_Xz = new char [Dm.recvCount_Xz];
	recvID_XY = new char [Dm.recvCount_XY];
	recvID_YZ = new char [Dm.recvCount_YZ];
	recvID_XZ = new char [Dm.recvCount_XZ];
	//......................................................................................
	int sendtag,recvtag;
	sendtag = recvtag = 7;

	int x,y,z;
	int ii,jj,kk;
	int Nx = nx;
	int Ny = ny;
	int Nz = nz;
	double GlobalNumber = 1.f;

	double count,countGlobal,totalGlobal;
	count = 0.f;
	for (int k=0; k<nz; k++){
		for (int j=0; j<ny; j++){
			for (int i=0; i<nx; i++){
				n = k*nx*ny+j*nx+i;
				if (SignDist(i,j,k) < 0.0)  id[n] = 0;
				else{
					// initially saturated with wetting phase
					id[n] = 2;
					count+=1.0;
				}
			}
		}
	}
	// total Global is the number of nodes in the pore-space
	MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,comm);
	double porosity=totalGlobal/(double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2));
	if (rank==0) printf("Media Porosity: %f \n",porosity);


	double radius,Rcrit_new;
	radius = 0.0;
	// Layer the inlet with NWP
	if (kproc == 0){
		for(j=0; j<Ny; j++){
			for(i=0; i<Nx; i++){
				n = j*nx+i;
				//				n = nx*ny + j*nx+i;
			        id[n]=1;
			        if (SignDist(i,j,0) > radius){
			        	radius=SignDist(i,j,0);
			        }
			}
		}
	}

	MPI_Allreduce(&radius,&Rcrit_new,1,MPI_DOUBLE,MPI_MAX,comm);

	if (rank==0) printf("Starting morhpological drainage with critical radius = %f \n",Rcrit_new);

	int imin,jmin,kmin,imax,jmax,kmax;

	// Decrease the critical radius until the target saturation is met
	double deltaR=0.01; // amount to change the radius in voxel units
    double Rcrit_old;
	double sw_old=1.0; // initial WP saturation set to one
	double sw_new=1.0; // initial WP saturation set to one
    double sw_diff_old = 1.0;
    double sw_diff_new = 1.0;
   
	while (sw_new > SW && Rcrit_new > 0.99){
        
        Rcrit_old = Rcrit_new;
		Rcrit_new -= deltaR*Rcrit_old;// decrease critical radius
        sw_old = sw_new;
        sw_diff_old = sw_diff_new;

        int Window=round(Rcrit_new);
		GlobalNumber = 1.0;

		while (GlobalNumber > 0){

		  //if (rank==0) printf("GlobalNumber=%f \n",GlobalNumber);
			double LocalNumber=GlobalNumber=0.f;
			for(k=0; k<Nz; k++){
				for(j=0; j<Ny; j++){
					for(i=0; i<Nx; i++){
						n = k*nx*ny + j*nx+i;
						if (id[n] == 1 && SignDist(i,j,k) > Rcrit_new){
							// loop over the window and update
							imin=max(1,i-Window);
							jmin=max(1,j-Window);
							kmin=max(1,k-Window);
							imax=min(Nx-1,i+Window);
							jmax=min(Ny-1,j+Window);
							kmax=min(Nz-1,k+Window);
							for (kk=kmin; kk<kmax; kk++){
								for (jj=jmin; jj<jmax; jj++){
									for (ii=imin; ii<imax; ii++){
										int nn = kk*nx*ny+jj*nx+ii;
										double dsq = double((ii-i)*(ii-i)+(jj-j)*(jj-j)+(kk-k)*(kk-k));
										if (id[nn] == 2 && dsq <= Rcrit_new*Rcrit_new){
											LocalNumber+=1.0;
											id[nn]=1;
										}
									}
								}
							}
						}
						// move on
					}
				}
			}


			// Pack and send the updated ID values
			PackID(Dm.sendList_x, Dm.sendCount_x ,sendID_x, id);
			PackID(Dm.sendList_X, Dm.sendCount_X ,sendID_X, id);
			PackID(Dm.sendList_y, Dm.sendCount_y ,sendID_y, id);
			PackID(Dm.sendList_Y, Dm.sendCount_Y ,sendID_Y, id);
			PackID(Dm.sendList_z, Dm.sendCount_z ,sendID_z, id);
			PackID(Dm.sendList_Z, Dm.sendCount_Z ,sendID_Z, id);
			PackID(Dm.sendList_xy, Dm.sendCount_xy ,sendID_xy, id);
			PackID(Dm.sendList_Xy, Dm.sendCount_Xy ,sendID_Xy, id);
			PackID(Dm.sendList_xY, Dm.sendCount_xY ,sendID_xY, id);
			PackID(Dm.sendList_XY, Dm.sendCount_XY ,sendID_XY, id);
			PackID(Dm.sendList_xz, Dm.sendCount_xz ,sendID_xz, id);
			PackID(Dm.sendList_Xz, Dm.sendCount_Xz ,sendID_Xz, id);
			PackID(Dm.sendList_xZ, Dm.sendCount_xZ ,sendID_xZ, id);
			PackID(Dm.sendList_XZ, Dm.sendCount_XZ ,sendID_XZ, id);
			PackID(Dm.sendList_yz, Dm.sendCount_yz ,sendID_yz, id);
			PackID(Dm.sendList_Yz, Dm.sendCount_Yz ,sendID_Yz, id);
			PackID(Dm.sendList_yZ, Dm.sendCount_yZ ,sendID_yZ, id);
			PackID(Dm.sendList_YZ, Dm.sendCount_YZ ,sendID_YZ, id);
			//......................................................................................
			MPI_Sendrecv(sendID_x,Dm.sendCount_x,MPI_CHAR,Dm.rank_x(),sendtag,
					recvID_X,Dm.recvCount_X,MPI_CHAR,Dm.rank_X(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_X,Dm.sendCount_X,MPI_CHAR,Dm.rank_X(),sendtag,
					recvID_x,Dm.recvCount_x,MPI_CHAR,Dm.rank_x(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_y,Dm.sendCount_y,MPI_CHAR,Dm.rank_y(),sendtag,
					recvID_Y,Dm.recvCount_Y,MPI_CHAR,Dm.rank_Y(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_Y,Dm.sendCount_Y,MPI_CHAR,Dm.rank_Y(),sendtag,
					recvID_y,Dm.recvCount_y,MPI_CHAR,Dm.rank_y(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_z,Dm.sendCount_z,MPI_CHAR,Dm.rank_z(),sendtag,
					recvID_Z,Dm.recvCount_Z,MPI_CHAR,Dm.rank_Z(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_Z,Dm.sendCount_Z,MPI_CHAR,Dm.rank_Z(),sendtag,
					recvID_z,Dm.recvCount_z,MPI_CHAR,Dm.rank_z(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_xy,Dm.sendCount_xy,MPI_CHAR,Dm.rank_xy(),sendtag,
					recvID_XY,Dm.recvCount_XY,MPI_CHAR,Dm.rank_XY(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_XY,Dm.sendCount_XY,MPI_CHAR,Dm.rank_XY(),sendtag,
					recvID_xy,Dm.recvCount_xy,MPI_CHAR,Dm.rank_xy(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_Xy,Dm.sendCount_Xy,MPI_CHAR,Dm.rank_Xy(),sendtag,
					recvID_xY,Dm.recvCount_xY,MPI_CHAR,Dm.rank_xY(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_xY,Dm.sendCount_xY,MPI_CHAR,Dm.rank_xY(),sendtag,
					recvID_Xy,Dm.recvCount_Xy,MPI_CHAR,Dm.rank_Xy(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_xz,Dm.sendCount_xz,MPI_CHAR,Dm.rank_xz(),sendtag,
					recvID_XZ,Dm.recvCount_XZ,MPI_CHAR,Dm.rank_XZ(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_XZ,Dm.sendCount_XZ,MPI_CHAR,Dm.rank_XZ(),sendtag,
					recvID_xz,Dm.recvCount_xz,MPI_CHAR,Dm.rank_xz(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_Xz,Dm.sendCount_Xz,MPI_CHAR,Dm.rank_Xz(),sendtag,
					recvID_xZ,Dm.recvCount_xZ,MPI_CHAR,Dm.rank_xZ(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_xZ,Dm.sendCount_xZ,MPI_CHAR,Dm.rank_xZ(),sendtag,
					recvID_Xz,Dm.recvCount_Xz,MPI_CHAR,Dm.rank_Xz(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_yz,Dm.sendCount_yz,MPI_CHAR,Dm.rank_yz(),sendtag,
					recvID_YZ,Dm.recvCount_YZ,MPI_CHAR,Dm.rank_YZ(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_YZ,Dm.sendCount_YZ,MPI_CHAR,Dm.rank_YZ(),sendtag,
					recvID_yz,Dm.recvCount_yz,MPI_CHAR,Dm.rank_yz(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_Yz,Dm.sendCount_Yz,MPI_CHAR,Dm.rank_Yz(),sendtag,
					recvID_yZ,Dm.recvCount_yZ,MPI_CHAR,Dm.rank_yZ(),recvtag,comm,MPI_STATUS_IGNORE);
			MPI_Sendrecv(sendID_yZ,Dm.sendCount_yZ,MPI_CHAR,Dm.rank_yZ(),sendtag,
					recvID_Yz,Dm.recvCount_Yz,MPI_CHAR,Dm.rank_Yz(),recvtag,comm,MPI_STATUS_IGNORE);

			UnpackID(Dm.recvList_x, Dm.recvCount_x ,recvID_x, id);
			UnpackID(Dm.recvList_X, Dm.recvCount_X ,recvID_X, id);
			UnpackID(Dm.recvList_y, Dm.recvCount_y ,recvID_y, id);
			UnpackID(Dm.recvList_Y, Dm.recvCount_Y ,recvID_Y, id);
			UnpackID(Dm.recvList_z, Dm.recvCount_z ,recvID_z, id);
			UnpackID(Dm.recvList_Z, Dm.recvCount_Z ,recvID_Z, id);
			UnpackID(Dm.recvList_xy, Dm.recvCount_xy ,recvID_xy, id);
			UnpackID(Dm.recvList_Xy, Dm.recvCount_Xy ,recvID_Xy, id);
			UnpackID(Dm.recvList_xY, Dm.recvCount_xY ,recvID_xY, id);
			UnpackID(Dm.recvList_XY, Dm.recvCount_XY ,recvID_XY, id);
			UnpackID(Dm.recvList_xz, Dm.recvCount_xz ,recvID_xz, id);
			UnpackID(Dm.recvList_Xz, Dm.recvCount_Xz ,recvID_Xz, id);
			UnpackID(Dm.recvList_xZ, Dm.recvCount_xZ ,recvID_xZ, id);
			UnpackID(Dm.recvList_XZ, Dm.recvCount_XZ ,recvID_XZ, id);
			UnpackID(Dm.recvList_yz, Dm.recvCount_yz ,recvID_yz, id);
			UnpackID(Dm.recvList_Yz, Dm.recvCount_Yz ,recvID_Yz, id);
			UnpackID(Dm.recvList_yZ, Dm.recvCount_yZ ,recvID_yZ, id);
			UnpackID(Dm.recvList_YZ, Dm.recvCount_YZ ,recvID_YZ, id);
			//......................................................................................

			MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,comm);

			// Layer the inlet with NWP
			if (kproc == 0){
				for(j=0; j<Ny; j++){
					for(i=0; i<Nx; i++){
						n = j*nx+i;
						//				n = nx*ny + j*nx+i;
						id[n]=1;
					}
				}
			}

			// Layer the outlet with WP
			if (kproc == nprocz-1){
				for(j=0; j<Ny; j++){
					for(i=0; i<Nx; i++){
						n = (nz-1)*nx*ny+j*nx+i;
						//				n = nx*ny + j*nx+i;
						id[n]=2;
					}
				}
			}

		}

		count = 1.f;
		for (int k=1; k<Nz-1; k++){
			for (int j=1; j<Ny-1; j++){
				for (int i=1; i<Nx-1; i++){
					n=k*Nx*Ny+j*Nx+i;
					if (id[n] == 2){
						count+=1.0;
					}
				}
			}
		}
		MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,comm);
		sw_new= countGlobal/totalGlobal;
        sw_diff_new = abs(sw_new-SW);
//        if (rank==0){
//            printf("Final saturation=%f\n",sw_new);
//            printf("Final critical radius=%f\n",Rcrit_new);
//
//        }
	}

    if (sw_diff_new<sw_diff_old){
        if (rank==0){
            printf("Final saturation=%f\n",sw_new);
            printf("Final critical radius=%f\n",Rcrit_new);

        }
    }
    else{
        if (rank==0){
            printf("Final saturation=%f\n",sw_old);
            printf("Final critical radius=%f\n",Rcrit_old);

        }
    }

	sprintf(LocalRankFilename,"ID.%05i",rank);
	FILE *ID = fopen(LocalRankFilename,"wb");
	fwrite(id,1,N,ID);
	fclose(ID);

	MPI_Barrier(comm);
	MPI_Finalize();
}