/*
 * 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"
#include "analysis/TwoPhase.h"
#include "analysis/eikonal.h"

inline void MeanFilter(DoubleArray &Mesh){
	for (int k=1; k<(int)Mesh.size(2)-1; k++){
		for (int j=1; j<(int)Mesh.size(1)-1; j++){
			for (int i=1; i<(int)Mesh.size(0)-1; i++){
				double sum;
				sum=Mesh(i,j,k)+Mesh(i+1,j,k)+Mesh(i-1,j,k)+Mesh(i,j+1,k)+Mesh(i,j-1,k)+
						+Mesh(i,j,k+1)+Mesh(i,j,k-1);
				Mesh(i,j,k) = sum/7.0;
			}
		}
	}
}


double ReadFromBlock( char *ID, int iproc, int jproc, int kproc, int Nx, int Ny, int Nz){

	int x,y,z,i,j,k;
	// Get the list of blocks that contain the local rank
	int b0x =iproc*(Nx-2)/1024;
	int b0y =jproc*(Ny-2)/1024;
	int b0z =kproc*(Nz-2)/1024;
	int Bx =(iproc+1)*(Nx-2)/1024+1;
	int By =(jproc+1)*(Ny-2)/1024+1;
	int Bz =(kproc+1)*(Nz-2)/1024+1;

	// arrays to hold the strings 
    char LocalRankFilename[40];
    char sx[2];
    char sy[2];
    char sz[2];
    char tmpstr[10];
    
	// array to store ids read from block
	char *id;
	id = new char [1024*1024*1024];

	for (int bz=b0z; bz<Bz; bz++){
		for (int by=b0y; by<By; by++){
			for (int bx=b0x; bx<Bx; bx++){
				sprintf(sx,"%d",bx);
				sprintf(sy,"%d",by);
				sprintf(sz,"%d",bz);
				sprintf(LocalRankFilename,"%s%s%s%s%s%s%s","a2_x",sx,"_y",sy,"_z",sz,".gbd");
				//sprintf(LocalRankFilename,"%s%s%s%s%s%s%s","dis_",sx,"x_",sy,"y_",sz,"z.gbd");
				//printf("Reading file: %s \n", LocalRankFilename);
				//fflush(stdout);
				
				// Read the file
				size_t readID;
				FILE *IDFILE = fopen(LocalRankFilename,"rb");
				readID=fread(id,1,1024*1024*1024,IDFILE);
				fclose(IDFILE);
				//printf("Loading data ... \n");
				
				// loop over global index
				for ( k=0;k<Nz;k++){
					for ( j=0;j<Ny;j++){
						for ( i=0;i<Nx;i++){
							//  id for this process relative to current block
							x = iproc*(Nx-2) + i - 1 - 1024*bx;
							y = jproc*(Ny-2) + j - 1 - 1024*by;
							z = kproc*(Nz-2) + k - 1 - 1024*bz;
							if (!(x<0) && !(y<0) && !(z<0) && x < 1024  && y < 1024  && z < 1024){
							  //char value=id[z*1024*1024 + y*1024 + x];
							  char value=0;
								  // check porespace nodes
								if (id[z*1024*1024 + y*1024 + x] < 215)	value = 1;
								// set the ID
								ID[k*Nx*Ny + j*Nx + i] = value;
							}
						}
					}
				}
			}
		}
	}

	// Compute porosity 
	uint64_t count=0;
	for (k=1; k<Nz-1; k++){
		for (j=1; j<Ny-1; j++){
			for (i=1; i<Nx-1; i++){
				if (ID[k*Nx*Ny+j*Nx+i] == 1) count++; 
			}
		}
	}
	double porosity = double(count)/double((Nx-2)*(Ny-2)*(Nz-2));
	return porosity;
	/*printf("Porosity is %f \n",double(count)/double(NX*NY*NZ));

	printf("Done getting data -- writing main file \n");
	FILE *OUT = fopen("FullData.raw","wb");
	fwrite(ID,1,N,OUT);
	fclose(OUT);
	printf("Completed! \n");
	 */
}



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 Nx,Ny,Nz;
		int i,j,k,n;
		int BC=0;
		//  char fluidValue,solidValue;
		int MAXTIME=1000;
		int READ_FROM_BLOCK=0;
		if (argc > 1){
			MAXTIME=atoi(argv[1]);
		}
		if (argc > 2){
			READ_FROM_BLOCK=atoi(argv[2]);			
		}

		std::vector<char> solidValues;
		std::vector<char> nwpValues;
		std::string line;

		if (rank==0){
			ifstream domain("Domain.in");
			domain >> nprocx;
			domain >> nprocy;
			domain >> nprocz;
			domain >> nx;
			domain >> ny;
			domain >> nz;
			domain >> nspheres;
			domain >> Lx;
			domain >> Ly;
			domain >> Lz;

		}
		MPI_Barrier(comm);
		// Computational domain
		MPI_Bcast(&nx,1,MPI_INT,0,comm);
		MPI_Bcast(&ny,1,MPI_INT,0,comm);
		MPI_Bcast(&nz,1,MPI_INT,0,comm);
		MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
		MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
		MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
		MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
		MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
		MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
		MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
		//.................................................
		MPI_Barrier(comm);

		// 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);
			fflush(stdout);

		}
		if ( nprocs < nprocx*nprocy*nprocz ){
			ERROR("Insufficient number of processors");
		}

		char LocalRankFilename[40];

		int N = (nx+2)*(ny+2)*(nz+2);
		Domain Dm(nx,ny,nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
		for (n=0; n<N; n++) Dm.id[n]=1;
		Dm.CommInit(comm);
		nx+=2; ny+=2; nz+=2;

		// Read the phase ID
		double porosity;
		sprintf(LocalRankFilename,"ID.%05i",rank);
		if (READ_FROM_BLOCK == 0){
			size_t readID;
			FILE *ID = fopen(LocalRankFilename,"rb");
			readID=fread(Dm.id,1,N,ID);
			if (readID != size_t(N)) printf("lbpm_segmented_pp: Error reading ID \n");
			fclose(ID);
		}
		else{
			// Read from the large block and write the local ID file
			if (rank==0) printf("Reading ID file from blocks \n");
			fflush(stdout);
			porosity = ReadFromBlock(Dm.id,Dm.iproc,Dm.jproc,Dm.kproc,nx,ny,nz);
			
			MPI_Barrier(MPI_COMM_WORLD);
			if (rank==0) printf("Writing local ID files (poros=%f) \n",porosity);
			fflush(stdout);
			FILE *ID = fopen(LocalRankFilename,"wb");
			fwrite(Dm.id,1,N,ID);
			fclose(ID);
			if (rank==0) printf("Succeeded! \n");
			fflush(stdout);

		}

		// Initialize the domain and communication
		char *id;
		id = new char [N];
		TwoPhase Averages(Dm);
		//	DoubleArray Distance(nx,ny,nz);
		//	DoubleArray Phase(nx,ny,nz);

		int count = 0;
		// Solve for the position of the solid phase
		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;
					// Initialize the solid phase
					if (Dm.id[n] == 0)	id[n] = 0;
					else		      	id[n] = 1;
				}
			}
		}
		// Initialize the signed distance function
		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;
					// Initialize distance to +/- 1
					Averages.SDs(i,j,k) = 2.0*double(id[n])-1.0;
				}
			}
		}
		MeanFilter(Averages.SDs);

		double LocalVar, TotalVar;
		if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
		int Maxtime=10*max(max(Dm.Nx*Dm.nprocx,Dm.Ny*Dm.nprocy),Dm.Nz*Dm.nprocz);
		Maxtime=min(Maxtime,MAXTIME);
		LocalVar = Eikonal(Averages.SDs,id,Dm,Maxtime);

		MPI_Allreduce(&LocalVar,&TotalVar,1,MPI_DOUBLE,MPI_SUM,comm);
		TotalVar /= nprocs;
		if (rank==0) printf("Final variation in signed distance function %f \n",TotalVar);

		sprintf(LocalRankFilename,"SignDist.%05i",rank);
		FILE *DIST = fopen(LocalRankFilename,"wb");
		fwrite(Averages.SDs.data(),8,N,DIST);
		fclose(DIST);

	}
	MPI_Barrier(comm);
	MPI_Finalize();
	return 0;

}