// Sequential blob analysis 
// Reads parallel simulation data and performs connectivity analysis
// and averaging on a blob-by-blob basis
// James E. McClure 2014

#include <iostream>
#include <math.h>
#include "common/Communication.h"
#include "analysis/analysis.h"
#include "analysis/SubPhase.h"


std::shared_ptr<Database> loadInputs( int nprocs )
{
	//auto db = std::make_shared<Database>( "Domain.in" );
	auto db = std::make_shared<Database>();
	db->putScalar<int>( "BC", 0 );
	db->putVector<int>( "nproc", { 1, 1, 1 } );
	db->putVector<int>( "n", { 100, 100, 100 } );
	db->putScalar<int>( "nspheres", 1 );
	db->putVector<double>( "L", { 1, 1, 1 } );
	return db;
}


int main(int argc, char **argv)
{
	// Initialize MPI
        Utilities::startup( argc, argv );
	Utilities::MPI comm( MPI_COMM_WORLD );
        int rank = comm.getRank();
        int nprocs = comm.getSize();
	{ // Limit scope so variables that contain communicators will free before MPI_Finialize

		if ( rank==0 ) {
			printf("-----------------------------------------------------------\n");
			printf("Unit test for torus (Euler-Poincarie characteristic) \n");
			printf("-----------------------------------------------------------\n");
		}

		//.......................................................................
		// Reading the domain information file
		//.......................................................................
		int i,j,k,n;

		// Load inputs
		auto db = loadInputs( nprocs );
		int Nx = db->getVector<int>( "n" )[0];
		int Ny = db->getVector<int>( "n" )[1];
		int Nz = db->getVector<int>( "n" )[2];
		int nprocx = db->getVector<int>( "nproc" )[0];
		int nprocy = db->getVector<int>( "nproc" )[1];
		int nprocz = db->getVector<int>( "nproc" )[2];

		if (rank==0){
			printf("********************************************************\n");
			printf("Sub-domain size = %i x %i x %i\n",Nx,Ny,Nz);
			printf("********************************************************\n");
		}

		// Get the rank info
		auto Dm = std::make_shared<Domain>(db,comm);
		auto Averages = std::make_shared<SubPhase>(Dm);
		Nx += 2;
		Ny += 2;
		Nz += 2;
		//.......................................................................
		for ( k=1;k<Nz-1;k++){
			for ( j=1;j<Ny-1;j++){
				for ( i=1;i<Nx-1;i++){
					n = k*Nx*Ny+j*Nx+i;
					Dm->id[n] = 1;
				}
			}
		}
		//.......................................................................
		Dm->CommInit(); // Initialize communications for domains
		//.......................................................................

		//.......................................................................
		// Assign the phase ID field based and the signed distance
		//.......................................................................
		double R1,R2;
		double CX,CY,CZ; //CY1,CY2;
		CX=Nx*nprocx*0.5;
		CY=Ny*nprocy*0.5;
		CZ=Nz*nprocz*0.5;
		R1 = Nx*nprocx*0.2; // middle radius
		R2 = Nx*nprocx*0.1; // donut thickness
		//
		//CY1=Nx*nprocx*0.5+R1;
		//CY2=Ny*nprocy*0.5-R1;

		double x,y,z;
		if (rank==0) printf("Initializing the system \n");
		for ( k=1;k<Nz-1;k++){
			for ( j=1;j<Ny-1;j++){
				for ( i=1;i<Nx-1;i++){
					n = k*Nx*Ny+j*Nx+i;

					// global position relative to center
					x = Dm->iproc()*Nx+i - CX;
					y = Dm->jproc()*Ny+j - CY;
					z = Dm->kproc()*Nz+k - CZ;

					// Shrink the sphere sizes by two voxels to make sure they don't touch
					Averages->SDs(i,j,k) = 100.0;
					//..............................................................................
					// Single torus
					Averages->Phi(i,j,k) = sqrt((sqrt(x*x+y*y) - R1)*(sqrt(x*x+y*y) - R1) + z*z) - R2;
					// Double torus
					/*		y = Dm->jproc()*Ny+j - CY1;
				//z = Dm->kproc()*Nz+k - CZ +R1;
				Averages->Phi(i,j,k) = sqrt((sqrt(x*x+y*y) - R1)*(sqrt(x*x+y*y) - R1) + z*z) - R2;

				y = Dm->jproc()*Ny+j - CY2;
				//z = Dm->kproc()*Nz+k - CZ-R1;
				Averages->Phi(i,j,k) = min(Averages->Phi(i,j,k),
						sqrt((sqrt(x*x+y*y) - R1)*(sqrt(x*x+y*y) - R1) + z*z) - R2);
					 *///..............................................................................

					//Averages->Phi(i,j,k) = - Averages->Phi(i,j,k);
					if (Averages->Phi(i,j,k) > 0.0){
						Dm->id[n] = 2;
					}
					else{
						Dm->id[n] = 1;
					}
				}
			}
		}

		if (rank==0) printf("Aggregating labels \n");

		Averages->AggregateLabels("phase_id.raw");
		// Averages->Reduce();

	} // Limit scope so variables that contain communicators will free before MPI_Finialize
        Utilities::shutdown();
	return 0;  
}