#define _USE_MATH_DEFINES
#include "math.h"
#include <stdlib.h>
#include <stdio.h>
#include <locale.h>
#include <time.h>
#include <stdbool.h>

#define Node_count 5*5*2 // должно быть таким, что бы из этого числа, разделенного на два, извлекался корень
#define Node_count_half Node_count / 2
#define Node_wire_width (int)sqrt(Node_count_half)

#define Equations_per_node 4
#define Equations_count Node_count * Equations_per_node

double f[Equations_count];
double f_diff[Equations_count];

double C_m  =   1; // muF/cm^2
double g_K  =  35; // mS/cm^2
double g_Na =  40; // mS/cm^2
double g_L  = 0.3; // mS/cm^2
double E_K  = -77; // mV
double E_Na =  55; // mV
double E_L  = -65; // mV

double g_syn = 0.08; // 0.1 // 0.04 // 0.2
double k_syn = 0.2; // 0.2
double E_syn[Node_count];

double I_app[Node_count];

/*const double sigma_G  = 0.0;
const double sigma_GN = 0.0;
const double sigma_N  = 1.0;*/

double** A;
double** B;
double*  C;
double** sigma;
double tau[Node_count][Node_count];

#define tau_min  2 // ms
#define tau_max 12 // ms

#define ms_to_step 200 // (0.001 / dt) !!! Don't forget !!!

#define Max_delay tau_max * ms_to_step
double V_old_array[Node_count][Max_delay];

const double Freq = 1300; // Hz
const double Min_magintude = -0.00; // pA
const double Max_magintude =  0.1; // pA
const double Duration = 0.001; // sec

double Meander_start_from_zero[Node_count];
double Meander_width[Node_count];
double Meander_height[Node_count];
double Meander_interval[Node_count];
double last_meander_end[Node_count];

double I_stim(int i, double t)
{
	if (t < Meander_start_from_zero[i])
		return 0;

	t -= Meander_start_from_zero[i];
	t = fmod(t, Meander_width[i] + Meander_interval[i]);

	return t < Meander_width[i] ? Meander_height[i] : 0;
}

double V(int i)
{
	return f[i * 4];
}

void SetV(int i, double value)
{
	f[i * 4] = value;
}

double m(int i)
{
	return f[i * 4 + 1];
}

void Setm(int i, double value)
{
	f[i * 4 + 1] = value;
}

double n(int i)
{
	return f[i * 4 + 2];
}

void Setn(int i, double value)
{
	f[i * 4 + 2] = value;
}

double h(int i)
{
	return f[i * 4 + 3];
}

void Seth(int i, double value)
{
	f[i * 4 + 3] = value;
}

double V_old(int i, int delay)
{
	return V_old_array[i][Max_delay - 1 - delay];
}

int RandomI(int min, int max)
{
	return ((double)rand() / (RAND_MAX - 1)) * (max - min) + min;
}

double RandomD(double min, double max)
{
	return ((double)rand() / RAND_MAX) * (max - min) + min;
}

double alpha_m(double* f, int i)
{
	return 0.182 * (V(i) + 35) / (1 - exp(-(V(i) + 35) / 9));
}

double beta_m(double* f, int i)
{
	return -0.124 * (V(i) + 35) / (1 - exp((V(i) + 35) / 9));
}

double alpha_n(double* f, int i)
{
	return 0.02 * (V(i) - 25) / (1 - exp(-(V(i) - 25) / 9));
}

double beta_n(double* f, int i)
{
	return -0.002 * (V(i) - 25) / (1 - exp((V(i) - 25) / 9));
}

double alpha_h(double* f, int i)
{
	return 0.25 * exp(-(V(i) + 90) / 12);
}

double beta_h(double* f, int i)
{
	return 0.25 * exp((V(i) + 62) / 6) / exp((V(i) + 90) / 12);
}

double HodgkinHuxley(int i, double* f, double t)
{
	int in = i / 4;
	int il = i % 4;

	switch (il)
	{
	  case 0:
	  {
		  double sum = 0;
			//double ee = 0;
			//double Vold = 0;

		  /*for (int j = 0; j < Node_count; j++)
		  {
			  //sum += A[in][j] * g_syn * (V(in) - V(j));
			  sum += A[in][j] * g_syn * (V(in) - E_syn[in]) / (1 + exp(-V_old(j, tau[in][j]) / k_syn));
		  }*/

		  /*for (int j = 0; j < C[in]; j++)
		  {
		    sum += sigma[in][(int)B[in][j]] * (V((int)B[in][j]) - V(in));
		  }*/

		  for (int j = 0; j < C[in]; j++)
		  {
		    //sum += g_syn * (V((int)B[in][j]) - V(in)); // устаревшая часть, нужна для проверки разностной схемы
				//sum += A[in][j] * g_syn * (V(in) - E_syn[in]) / (1 + exp(-V_old((int)B[in][j]) / k_syn)); // устаревшая часть
        sum += A[in][(int)B[in][j]] * g_syn * (V(in) - E_syn[in]) / (1 + exp(-V_old((int)B[in][j], tau[in][(int)B[in][j]]) / k_syn));

				//Vold = V_old((int)B[in][j], tau[in][(int)B[in][j]]);
				//ee = exp(-V_old((int)B[in][j], tau[in][(int)B[in][j]]) / k_syn);
				//printf("i = %d\t V_old = %f\t exp = %f\n", in, Vold, ee);
		  }
		  //printf("i = %d\t sum = %f\n", in, sum);

		  return 1000 * ((g_Na * pow(m(in), 3) * h(in) * (E_Na - V(in)) + g_K * n(in) * (E_K - V(in)) + g_L * (E_L - V(in)) + I_app[in] + I_stim(in, t) + sum ) / C_m); // V
	  }

	  case 1:
	  {
		  return 1000 * (alpha_m(f, in) * (1 - m(in)) - beta_m(f, in) * m(in)); // m
	  }

	  case 2:
	  {
		  return 1000 * (alpha_n(f, in) * (1 - n(in)) - beta_n(f, in) * n(in)); // n
	  }

	  case 3:
	  {
		  return 1000 * (alpha_h(f, in) * (1 - h(in)) - beta_h(f, in) * h(in)); // h
	  }
	}

	return 0;
}

void RungeKutta(double t, double dt, double* f, double* f_next)
{
	double k[Equations_count][4];

	// k1
	for (int i = 0; i < Equations_count; i++)
		k[i][0] = HodgkinHuxley(i, f, t) * dt;

	double phi_k1[Equations_count];
	for (int i = 0; i < Equations_count; i++)
		phi_k1[i] = f[i] + k[i][0] / 2;

	// k2
	for (int i = 0; i < Equations_count; i++)
		k[i][1] = HodgkinHuxley(i, phi_k1, t) * dt;

	double phi_k2[Equations_count];
	for (int i = 0; i < Equations_count; i++)
		phi_k2[i] = f[i] + k[i][1] / 2;

	// k3
	for (int i = 0; i < Equations_count; i++)
		k[i][2] = HodgkinHuxley(i, phi_k2, t) * dt;

	double phi_k3[Equations_count];
	for (int i = 0; i < Equations_count; i++)
		phi_k3[i] = f[i] + k[i][2] / 2;

	// k4
	for (int i = 0; i < Equations_count; i++)
		k[i][3] = HodgkinHuxley(i, phi_k3, t) * dt;

	for (int i = 0; i < Equations_count; i++)
		f_next[i] = f[i] + (k[i][0] + 2 * k[i][1] + 2 * k[i][2] + k[i][3]) / 6;
}

void CopyArray(double* source, double* target, int N)
{
	for (int i = 0; i < N; i++)
		target[i] = source[i];
}

bool Approximately(double a, double b)
{
	if (a < 0)
		a = -a;

	if (b < 0)
		b = -b;

	return a - b <= 0.000001;
}

// http://preshing.com/20111007/how-to-generate-random-timings-for-a-poisson-process/
double nextTime(double rateParameter)
{
	return -log(1.0 - (double)rand() / (RAND_MAX)) / rateParameter;
}

void GenerateRandomMeander(int i, double min_start_time)
{
	double offset = nextTime(Freq);

	if (offset < 0)
	{
		int a = 0;
	}

	Meander_start_from_zero[i] = min_start_time + offset;
	Meander_width[i] = Duration;
	Meander_height[i] = RandomD(Min_magintude, Max_magintude);
}

void FillAMatrixZero()
{
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < Node_count; j++)
		{
			A[i][j] = 0;
		}
	}
}

void FillBCMatrix()
{
	for (int i = 0; i < Node_count; i++)
	{
		int bIndex = 0;
		C[i] = 0;
		for (int j = 0; j < Node_count; j++)
		{
			if (A[i][j] == 1)
			{
				B[i][bIndex] = j;
				bIndex++;
				C[i]++;
			}
		}
	}
}

/*void FillSigmaMatrix()
{
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < Node_count; j++)
		{
			if ((i >= 0 && i < Node_count_half) && (j >= 0 || j < Node_count_half))
			{
				sigma[i][j] = sigma_G;
			}
			if ((((i >= Node_count_half && i < Node_count) && (j >= 0 && j < Node_count_half)) || ((i >= 0 && i < Node_count_half) && (j >= Node_count_half && j < Node_count))))
			{
				sigma[i][j] = sigma_GN;
			}
			if ((i >= Node_count_half && i < Node_count) && (j >= Node_count_half && j < Node_count))
			{
				sigma[i][j] = sigma_N;
			}
		}
	}
}*/

void FillRandomMatrix()
{
	double p_links = 0.2; // 0.2
	//for (int k = 0; k < 2 * Node_count_half; k++)
	for (int k = 0; k < p_links * Node_count_half * (Node_count_half - 1); k++)
	{
		int i, j;

		do
		{
			i = RandomI(Node_count_half, Node_count);
			j = RandomI(Node_count_half, Node_count);
		} while ((i == j) || (A[i][j] == 1));

		A[i][j] = 1;
		//A[j][i] = 1;
	}
}

void FillVOldFromCurrent()
{
	for (int i = 0; i < Node_count; i++)
		for (int j = 0; j < Max_delay; j++)
			V_old_array[i][j] = V(i);
}

void UpdateVOld()
{
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 1; j < Max_delay; j++)
			V_old_array[i][j - 1] = V_old_array[i][j];

		V_old_array[i][Max_delay - 1] = V(i);
	}
}

/*void FillFullTauMatrix()
{
for (int i = 0; i < Node_count; i++)
{
for (int j = 0; j < Node_count; j++)
{
if (i < Node_count_half || j < Node_count_half)
{
tau[i][j] = 0;
continue;
}

int i_neuron = i - Node_count_half;
int j_neuron = j - Node_count_half;

int i_wire_x = i_neuron / Node_wire_width;
int i_wire_y = i_neuron % Node_wire_width;

int j_wire_x = j_neuron / Node_wire_width;
int j_wire_y = j_neuron % Node_wire_width;

double distance_max = sqrt(2.) * (Node_wire_width - 1);
double distance = sqrt((i_wire_x - j_wire_x) * (i_wire_x - j_wire_x) + (i_wire_y - j_wire_y) * (i_wire_y - j_wire_y));

tau[i][j] = (tau_min + distance / (distance_max) * (tau_max - tau_min)) * ms_to_step;
}
}
}*/

void FillTauMatrix()
{
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < Node_count; j++)
		{
			if (i < Node_count_half || j < Node_count_half || i == j || A[i][j] == 0)
			{
				tau[i][j] = 0;
				continue;
			}

			int i_neuron = i - Node_count_half;
			int j_neuron = j - Node_count_half;

			int i_wire_x = i_neuron / Node_wire_width;
			int i_wire_y = i_neuron % Node_wire_width;

			int j_wire_x = j_neuron / Node_wire_width;
			int j_wire_y = j_neuron % Node_wire_width;

			double distance_max = sqrt(2.) * (Node_wire_width - 1);
			double distance = sqrt((i_wire_x - j_wire_x) * (i_wire_x - j_wire_x) + (i_wire_y - j_wire_y) * (i_wire_y - j_wire_y));

			double t = (distance - 1) / (distance_max - 1);
			tau[i][j] = (tau_min + t * (tau_max - tau_min)) * ms_to_step;
		}
	}
}

int main(int argc, char *argv[])
{
	FILE *fp0;
	//FILE *fp_Ca;
	//FILE *fp_IP3;
	//FILE *fp_z;
	//FILE *fp_G;
	FILE *fp_I_stim;
	FILE *fp_V;
	FILE *fp_m;
	FILE *fp_n;
	FILE *fp_h;
	FILE *fp_V_spikes;
	srand(time(NULL));

	//for (int i = 0; i < Node_count; i++)
	//	V_old_length[i] = 0;

	A = malloc(Node_count * sizeof(double));
	for (int i = 0; i < Node_count; i++)
		A[i] = malloc(Node_count * sizeof(double));

	B = malloc(Node_count * sizeof(double));
	for (int i = 0; i < Node_count; i++)
		B[i] = malloc(Node_count * sizeof(double));

	C = malloc(Node_count * sizeof(double));

	sigma = malloc(Node_count * sizeof(double));
	for (int i = 0; i < Node_count; i++)
		sigma[i] = malloc(Node_count * sizeof(double));

	FillAMatrixZero();
	FillRandomMatrix();
	FillBCMatrix();
	//FillSigmaMatrix();
	FillTauMatrix();

	fp0 = fopen("A.txt", "w+");
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < Node_count; j++)
		{
			fprintf(fp0, "%d\t", (int)A[i][j]);
		}
		fprintf(fp0, "\n");
	}
	fclose(fp0);

	fp0 = fopen("tau.txt", "w+");
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < Node_count; j++)
		{
			fprintf(fp0, "%f\t", tau[i][j] / ms_to_step);
		}
		fprintf(fp0, "\n");
	}
	fclose(fp0);

	//Пишем в файл число связей у каждого осциллятора в четвертом квадранте
	fp0 = fopen("links.txt", "w+");
	for (int i = Node_count_half; i < Node_count; i++)
	{
		int links_count = 0;
		for (int j = Node_count_half; j < Node_count; j++)
		{
			if (A[i][j] == 1)
			{
				links_count++;
			}
		}
		fprintf(fp0, "%d\n", (int)links_count);

	}
	fclose(fp0);

	//setlocale(LC_NUMERIC, "French_Canada.1252");
	fp0 = fopen("test_Poisson.txt", "w+");
	for (int i = 0; i < 10000; i++)
		fprintf(fp0, "%f\n", nextTime(Freq));
	fclose(fp0);

	fp0 = fopen("B.txt", "w+");
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < C[i]; j++)
		{
			fprintf(fp0, "%d\t", (int)B[i][j]);
		}
		fprintf(fp0, "\n");
	}
	fclose(fp0);

	fp0 = fopen("C.txt", "w+");
	for (int i = 0; i < Node_count; i++)
	{
		fprintf(fp0, "%d\n", (int)C[i]);
	}
	fclose(fp0);

	/*fp0 = fopen("sigma.txt", "w+");
	for (int i = 0; i < Node_count; i++)
	{
		for (int j = 0; j < Node_count; j++)
		{
			fprintf(fp0, "%f\t", sigma[i][j]);
		}
		fprintf(fp0, "\n");
	}
	fclose(fp0);*/

	// Initial values
	/*for (int i = 0; i < Equations_count; i++)
	{
	f[i] = 0;
	}

	for (int i = 0; i < Equations_count; i++)
	{
	I_app[i] = RandomD(9, 40);
	}*/

	double percent_stable_state = 0.40; // 0.40

	double V0 = -58.7085;
	double m0 =  0.0953;
	double n0 =  0.000913;
	double h0 =  0.3662;

	double V1 =  14.8409;
	double m1 =  0.9174;
	double n1 =  0.0140;
	double h1 =  0.0539;

	for (int i = 0; i < Node_count; i++) // init array for all neurons
	{
		SetV(i, 0); // V
		Setm(i, 0); // m
		Setn(i, 0); // n
		Seth(i, 0); // h
	}
	for (int i = Node_count_half; i < Node_count; i++) // init only neuron nodes
	{
		double random = RandomD(0, 1);

		SetV(i, random < percent_stable_state ? V0 : V1); // V
		Setm(i, random < percent_stable_state ? m0 : m1); // m
		Setn(i, random < percent_stable_state ? n0 : n1); // n
		Seth(i, random < percent_stable_state ? h0 : h1); // h
	}

	for (int i = 0; i < Node_count_half; i++)
	{
		I_app[i] = 0; // init for 1st half array
	}

	for (int i = Node_count_half; i < Node_count; i++)
	{
		I_app[i] = 0.8; // init for neurons; Bifurcation point: I_app = 0.82; I_app_up = 1.04
	}

	double percent_excitable = 0.8; // 0.8
	double E_syn0 =  0;
	double E_syn1 = -90;

	for (int i = 0; i < Node_count; i++)
	{
		E_syn[i] = 0; // init for neurons all array
	}

	for (int i = Node_count_half; i < Node_count; i++)
	{
		double random = RandomD(0, 1);
		E_syn[i] = random < percent_excitable ? E_syn0 : E_syn1;
		//printf("i = %d\t E_syn = %f\n", i, E_syn[i]);
	}

	for (int i = 0; i < Node_count; i++)
	{
		GenerateRandomMeander(i, 0);
		last_meander_end[i] = Meander_start_from_zero[i] + Duration;
	}

	const double t_start = 0;
	const double t_max   = 40.0; // 100 msec = 0.1 sec
	const double dt      = 0.000005; // 0.01 msec = 0.00001 sec; 1 msec = 0.001 sec

	double t = t_start;

	//fp0 = fopen("results.txt", "w+");
	//setlocale(LC_NUMERIC, "French_Canada.1252");

	clock_t start_rk4, end_rk4;
	start_rk4 = clock();
	int lastPercent = -1;

	FillVOldFromCurrent();

	//fp_Ca  = fopen("results_Ca.txt", "w+");
	//fp_IP3 = fopen("results_IP3.txt", "w+");
	//fp_z   = fopen("results_z.txt", "w+");
	//fp_G   = fopen("results_G.txt", "w+");
	fp_I_stim = fopen("results_I_stim.txt", "w+");
	fp_V = fopen("results_V.txt", "w+");
	fp_m = fopen("results_m.txt", "w+");
	fp_n = fopen("results_n.txt", "w+");
	fp_h = fopen("results_h.txt", "w+");
	fp_V_spikes = fopen("results_V_spikes.txt", "w+");

	while (t < t_max || Approximately(t, t_max))
	{
		//fprintf(fp_Ca, "%f\t", t);
		//fprintf(fp_IP3, "%f\t", t);
		//fprintf(fp_z, "%f\t", t);
		//fprintf(fp_G, "%f\t", t);
		fprintf(fp_I_stim, "%f\t", t);
		fprintf(fp_V, "%f\t", t);
		fprintf(fp_m, "%f\t", t);
		fprintf(fp_n, "%f\t", t);
		fprintf(fp_h, "%f\t", t);
		fprintf(fp_V_spikes, "%f\t", t);

		for (int i = 0; i < Node_count; i++)
		{
			if (t > last_meander_end[i])
			{
				GenerateRandomMeander(i, t);
				last_meander_end[i] = Meander_start_from_zero[i] + Duration;
			}

			fprintf(fp_I_stim, "%f\t", I_stim(i, t));
		}
		fprintf(fp_I_stim, "\n");

		// Зашито на будущее
		//for (int i = 0; i < Equations_count; i += 8)
		//	fprintf(fp_Ca, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // Ca

		//for (int i = 1; i < Equations_count; i += 8)
		//	fprintf(fp_IP3, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // IP3

		//for (int i = 2; i < Equations_count; i += 8)
		//	fprintf(fp_z, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // z

		//for (int i = 3; i < Equations_count; i += 8)
		//	fprintf(fp_G, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // G

		for (int i = 0; i < Equations_count; i += 4)
			fprintf(fp_V, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // V

		for (int i = 1; i < Equations_count; i += 4)
			fprintf(fp_m, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // m

		for (int i = 2; i < Equations_count; i += 4)
			fprintf(fp_n, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // n

		for (int i = 3; i < Equations_count; i += 4)
			fprintf(fp_h, i == Equations_count - 1 ? "%f" : "%f\t", f[i]); // h

    //fprintf(fp_Ca, "\n");
    //fprintf(fp_IP3, "\n");
    //fprintf(fp_z, "\n");
    //fprintf(fp_G, "\n");
		fprintf(fp_V, "\n");
		fprintf(fp_m, "\n");
		fprintf(fp_n, "\n");
		fprintf(fp_h, "\n");

		double f_next[Equations_count];

		RungeKutta(t, dt, f, f_next);

		for (int i = 0; i < Equations_count; i += 4)
    {
      double diff = f_next[i] - f[i];

      fprintf(fp_V_spikes, i == Equations_count - 1 ? "%d" : "%d\t", diff < 0 && f_diff[i] > 0 && f[i] > 0 ? 1 : 0);

      f_diff[i] = diff;
    }

    fprintf(fp_V_spikes, "\n");

		CopyArray(f_next, f, Equations_count);

		t += dt;

		int percent = (int)(100 * (t - t_start) / (t_max - t_start));
		if (percent != lastPercent)
		{
			printf("Progress: %d%%\n", percent);
			lastPercent = percent;
		}

		//printf("V(24) = %f\t V_old(24) = %f\n", f[24*4], V_old(24));
		UpdateVOld();
	}

	//fclose(fp_Ca);
	//fclose(fp_IP3);
	//fclose(fp_z);
	//fclose(fp_G);
	fclose(fp_I_stim);
	fclose(fp_V);
	fclose(fp_m);
	fclose(fp_n);
	fclose(fp_h);
	fclose(fp_V_spikes);

	end_rk4 = clock();
	double extime_rk4 = (double)(end_rk4 - start_rk4) / CLOCKS_PER_SEC;
	int minutes = (int)extime_rk4 / 60;
	int seconds = (int)extime_rk4 % 60;
	printf("\nExecution time is: %d minutes %d seconds\n ", minutes, seconds);

	fp0 = fopen("time_exec.txt", "w+");
	fprintf(fp0, "%f\n", extime_rk4);
	fclose(fp0);

	for (int i = 0; i < Node_count; i++)
		free(A[i]);
	free(A);

	for (int i = 0; i < Node_count; i++)
		free(B[i]);
	free(B);

	for (int i = 0; i < Node_count; i++)
		free(sigma[i]);
	free(sigma);

	free(C);
}