void Sporulation::SporeGen(Img& I, double *weather, double rate){
//unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
//std::default_random_engine generator(seed);
int height = I.getHeight();
int width = I.getWidth();
if(!sp){
sp = (int **)CPLMalloc(sizeof(int *) * height);
int *stream = (int *)CPLMalloc(sizeof(int)*width*height);
for(int i=0;i<height;i++){
sp[i] = &stream[i*width];
}
}
for(int i=0;i<height;i++){
for(int j=0;j<width;j++){
if(I.data[i][j]>0){
double lambda = rate * weather[i*width+j];
int sum=0;
poisson_distribution<int> distribution(lambda);
for(int k=0;k<I.data[i][j];k++){
sum += distribution(generator);
}
sp[i][j] = sum;
}
}
}
}
void Sporulation::SporeSpreadDisp(Img& S_umca, Img& S_oaks, Img& I_umca, Img& I_oaks, Img& lvtree_rast,
Rtype rtype, double *weather, double scale1, int kappa, Direction wdir,
double scale2,double gamma){
//unsigned seed = std::chrono::system_clock::now().time_since_epoch().count();
//std::default_random_engine generator(seed);
std::cauchy_distribution<double> distribution_cauchy_one(0.0,scale1);
std::cauchy_distribution<double> distribution_cauchy_two(0.0,scale2);
std::bernoulli_distribution distribution_bern(gamma);
std::uniform_real_distribution<double> distribution_uniform(0.0,1.0);
int height = S_umca.getHeight();
int width = S_umca.getWidth();
int w_e_res = S_umca.getWEResolution();
int n_s_res = S_umca.getNSResolution();
double dist=0;
double theta = 0;
if(!sp){
cerr << "The spore matrix is empty!" << endl;
return;
}
for(int i=0;i<height;i++){
for(int j=0;j<width;j++){
if(sp[i][j]>0){
for(int k=0;k<sp[i][j];k++){
// generate the distance from cauchy distribution or cauchy mixture distribution
if(rtype == CAUCHY){
dist = abs(distribution_cauchy_one(generator));
}else if(rtype == CAUCHY_MIX){
if(gamma >= 1 || gamma <= 0){
cerr << "The parameter gamma must be in the range (0~1)" << endl;
return;
}
// use bernoulli distribution to act as the sampling with prob(gamma,1-gamma)
if(distribution_bern(generator))
dist = abs(distribution_cauchy_one(generator));
else
dist = abs(distribution_cauchy_two(generator));
}else{
cerr << "The paramter Rtype muse be set as either CAUCHY OR CAUCHY_MIX" << endl;
exit(EXIT_FAILURE);
}
if(wdir == NO){
kappa = 0;
}
theta = vonmisesvariate(wdir*PI/180,kappa);
int row = i - round(dist*cos(theta) / n_s_res);
int col = j + round(dist*sin(theta) / w_e_res);
if(row<0 || row>=height) continue;
if(col<0 || col>= width) continue;
if(row == i && col == j){
if(S_umca.data[row][col] >0 || S_oaks.data[row][col] >0){
double prob = (double)(S_umca.data[row][col]+S_oaks.data[row][col]) / lvtree_rast.data[row][col];
double U = distribution_uniform(generator);
prob = prob*weather[row*width+col];
// if U < prob, then one host will become infected
if(U<prob){
double prob_S_umca = (double)(S_umca.data[row][col]) / (
S_umca.data[row][col]+S_oaks.data[row][col]);
double prob_S_oaks = (double)(S_oaks.data[row][col]) / (
S_umca.data[row][col]+S_oaks.data[row][col]);
std::bernoulli_distribution distribution_bern_prob(prob_S_umca);
if(distribution_bern_prob(generator)){
I_umca.data[row][col] +=1;
S_umca.data[row][col] -=1;
}else{
I_oaks.data[row][col] +=1;
S_oaks.data[row][col] -=1;
}
}
}
}else{
if(S_umca.data[row][col]>0){
double prob_S_umca = (double)(S_umca.data[row][col]) / lvtree_rast.data[row][col];
double U = distribution_uniform(generator);
prob_S_umca *= weather[row*width+col];
if(U<prob_S_umca){
I_umca.data[row][col] +=1;
S_umca.data[row][col] -=1;
}
}
}
}
}
}
}
}