int write_pa_v2(int hue, int sat, int val, int cont)
{
struct msmfb_mdp_pp pp;
memset(&pp, 0, sizeof(struct msmfb_mdp_pp));
pp.op = mdp_op_pa_v2_cfg;
pp.data.pa_v2_cfg_data.block = MDP_LOGICAL_BLOCK_DISP_0;
pp.data.pa_v2_cfg_data.pa_v2_data.flags =
MDP_PP_OPS_WRITE | MDP_PP_OPS_ENABLE;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_HUE_ENABLE;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_HUE_MASK;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_SAT_ENABLE;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_SAT_MASK;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_VAL_ENABLE;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_VAL_MASK;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_CONT_ENABLE;
pp.data.pa_v2_cfg_data.pa_v2_data.flags |= MDP_PP_PA_CONT_MASK;
pp.data.pa_v2_cfg_data.pa_v2_data.global_hue_adj = hue;
pp.data.pa_v2_cfg_data.pa_v2_data.global_sat_adj = sat;
pp.data.pa_v2_cfg_data.pa_v2_data.global_val_adj = val;
pp.data.pa_v2_cfg_data.pa_v2_data.global_cont_adj = cont;
write_pp(&pp);
return 0;
}
int write_pcc(int red, int green, int blue, int invert)
{
struct msmfb_mdp_pp pp;
memset(&pp, 0, sizeof(struct msmfb_mdp_pp));
pp.op = mdp_op_pcc_cfg;
pp.data.pcc_cfg_data.block = MDP_LOGICAL_BLOCK_DISP_0;
pp.data.pcc_cfg_data.ops = MDP_PP_OPS_WRITE | MDP_PP_OPS_ENABLE;
pp.data.pcc_cfg_data.r.r = red * 128;
pp.data.pcc_cfg_data.g.g = green * 128;
pp.data.pcc_cfg_data.b.b = blue * 128;
if (invert) {
pp.data.pcc_cfg_data.r.c = pp.data.pcc_cfg_data.g.c =
pp.data.pcc_cfg_data.b.c = 0x7ff8;
pp.data.pcc_cfg_data.r.r |= (0xffff << 16);
pp.data.pcc_cfg_data.g.g |= (0xffff << 16);
pp.data.pcc_cfg_data.b.b |= (0xffff << 16);
}
write_pp(&pp);
return 0;
}
int write_pa(int hue, int sat, int val, int cont)
{
struct msmfb_mdp_pp pp;
memset(&pp, 0, sizeof(struct msmfb_mdp_pp));
pp.op = mdp_op_pa_cfg;
pp.data.pa_cfg_data.block = MDP_LOGICAL_BLOCK_DISP_0;
pp.data.pa_cfg_data.pa_data.flags = MDP_PP_OPS_WRITE | MDP_PP_OPS_ENABLE;
pp.data.pa_cfg_data.pa_data.hue_adj = hue;
pp.data.pa_cfg_data.pa_data.sat_adj = sat;
pp.data.pa_cfg_data.pa_data.val_adj = val;
pp.data.pa_cfg_data.pa_data.cont_adj = cont;
write_pp(&pp);
return 0;
}
int main(int argc,char *argv[])
{
// decode arguments
args(argc,argv);
inits();
if(run_type==6)
to_year=2010;
// Read in Data //
cout<< "Reading Data\n";
read_data();
// Set initial Params //
cout<< "Initiallizing...\n";
init_state();
init_t();
calc_state();
if(fixed_d != 0) //run traf_mat once and only once (for faster prototyping)
{
calc_traf();
/* _vbc_vec<float> Uj(1,n_lakes);
for(int j=1;j<=n_lakes;j++)
{
Uj(j) = 0;
for(int i=1;i<=n_sources;i++)
{
Uj(j) += sources(i).Gij(j) * sources(i).Oi;
}
cout << Uj(j) << "\t" << 1-exp(- pow(0.001 * Uj(j), 1 ) ) << "\n";
}
*/
calc_traf_mat();
calc_pp();
}
ofstream ll_("output/ll_test.dat");
if(FALSE)
{
calc_traf();
calc_traf_mat();
calc_pp(); //!!
int tmp_t;
for(int lake=1;lake<=n_lakes;lake++)
{
if(lakes(lake).invaded == 0 && lakes(lake).last_abs == 0 )
{
for(int t=from_year;t<=to_year+2;t++)
{
// sample_t();
tmp_t=t_vec(lake);
t_vec(lake)=t;
calc_state();
calc_pp();
cout << lake << "\t" << t <<endl;
ll_ << lake << "\t" << t <<"\t"<<l_hood()<<endl;
}
t_vec(lake)=tmp_t;
}
}
}
if(FALSE) // likelihood profile of d and e //if init_t is random, MLE d=e=0 (no effect of distance or size: CHECK)
{
d_par=-1;
e_par=0;
for(int i=0;i<=60;i++)
{
d_par=d_par+0.1;
e_par=0;
for(int j=0;j<=10;j++)
{
e_par=e_par + 0.1;
calc_traf();
calc_traf_mat();
calc_pp();
ll_ << d_par << "\t" << e_par << "\t" << l_hood()<< endl;
cout << d_par <<"\t"<< e_par << "\t" << l_hood()<< endl;
}
}
}
if(FALSE) //likelihood profile of alpha
{
chem_pars(1)=0;
for(int i=0;i<=1000;i++)
{
chem_pars(1)+=0.0001;
ll_ << chem_pars(1) << "\t" << l_hood()<< endl;
}
}
//Just sim under the true alpha to see the t_vec distribution
// to compare with sim_dat.R
if(FALSE)
{
for(int lake_index=1;lake_index<=n_lakes;lake_index++)
{
lakes(lake_index).discovered=0;
lakes(lake_index).last_abs=0;
}
for(int i=1;i<=1000;i++)
{
sim_spread();
write_t();
}
}
/// SEEDS ///
//i d e c B_o NAUT KKUT MGUT
//8394 1.06513 0.531416 0.000125572 -13.713 0.00405104 -0.00475339 0.0038181
// CAUT PPUT1 SIO3UR DOC COLTR ALKTI ALKT
//0.00403173 0.0571088 1.28896 -0.31447 -0.00654376 0.0621327 -0.000480646
// PH COND25 SECCHI.DEPTH NA
//0.00852002 0.00335544 0.0995729 -380.192
//0.407766 1.44137 0.417034 -10.8476 0.708086 -0.0150081 -0.404532 -0.512538 0.689779 0.43177-0.584563 -0.224491 0.786624 1.0269 0.868935 -0.0982729 0.37267
chem_pars(1)=-10;
chem_pars(2)=0.7;
chem_pars(3)=-0.01; //-2:1 MLE ~0
chem_pars(4)=-0.38; //-1.5:1.5 MLE ~0
chem_pars(5)=-0.5; //-0.4:0.2 MLE ~0
chem_pars(6)=0.68; //0:0.1 MLE 0.05 ***
chem_pars(7)=0.43; //-0.4:0.2 MLE ~1.3 ****
chem_pars(8)=-0.58; //-0.7:0.1 MLE ~-0.31 ****
chem_pars(9)=-0.22; //-0.4:0.2 MLE ~-0.01 **
chem_pars(10)=0.78; //-0.1:0.1 MLE ~0.06 *
chem_pars(11)=1.02; //-0.16:0.1 MLE ~0
chem_pars(12)=0.85; //-0.2:0.2 MLE ~0
chem_pars(13)=-0.09; //-0.04:0.01 MLE ~0
chem_pars(14)=0.37; //-0.3:0.3 MLE ~0.1
int test_ch=14;
d_par=1.54;
//float bb = l_hood();
if(ll)
{
float tmplhood;
for(int i=1;i<=20;i++)
{
cerr << i << "\n";
//chem_pars(test_ch)=chem_pars(test_ch)+0.0013;
d_par=d_par+0.05;
calc_traf();
cerr << "A" << "\n";
calc_traf_mat();
cerr << "B" << "\n";
sim_spread();
cerr << "C" << "\n";
//write_t();
tmplhood = l_hood();
cerr << "D" << "\n";
ll_ << chem_pars(test_ch) << "\t" << tmplhood << "\n";
cout << d_par << "\t" << tmplhood << "\n";
}
}
ll_.close();
cout << "# sampled\t" << n_sampled << "\n";
if(run_type==1)
{
// FIT ON TRAF_PARS & SPREAD PARS ONLY (NO ENV) //
// need a likelihood function wrapper to call l_hood() multiple times and average the result
// to smooth out stochastic surface.
// BOOTSTRAP RESAMPLING OF DATA (SAMPLED LAKES) TO GENERATE CI //
float garbage=l_hood();
int n_reps = 1000;
ofstream par_file;
int n_pars; //13 env + intercept + d,c,gamma
_vbc_vec<float> params1;
_vbc_vec<float> dat1;
_vbc_vec<float> MLE_params;
if(!env)
{
if(sim)
par_file.open("sims/gb_output/pred_pars.tab");
else
par_file.open("output/pred_pars.tab");
n_pars=4; // d,c,gamma,alpha
params1.redim(1,n_pars);
dat1.redim(1,n_pars);
MLE_params.redim(1,n_pars);
params1(1)=1.27;
params1(2)=1.48;
params1(3)=0.0000489;
params1(4)=0.00105;
}else{
if(sim)
par_file.open("sims/gb_output/pred_parsENV.tab");
else
par_file.open("output/pred_parsENV.tab");
n_pars=18; //13 env + intercept + d,e,c,gamma
params1.redim(1,n_pars);
dat1.redim(1,n_pars);
MLE_params.redim(1,n_pars);
params1(1)=1.79;
params1(2)=2;
params1(3)=0.69;
params1(4)=0.0000489;
/// SEEDS ///
params1(5)=-6.2;
params1(6)=0.014;
params1(7)=-0.08; //-2:1 MLE ~0
params1(8)=0.15; //-1.5:1.5 MLE ~0
params1(9)=0.21; //-0.4:0.2 MLE ~0
params1(10)=0.03; //0:0.1 MLE 0.05 ***
params1(11)=-0.13; //-0.4:0.2 MLE ~1.3 ****
params1(12)=-0.43; //-0.7:0.1 MLE ~-0.31 ****
params1(13)=-0.007; //-0.4:0.2 MLE ~-0.01 **
params1(14)=0.056; //-0.1:0.1 MLE ~0.06 *
params1(15)=0.0087; //-0.16:0.1 MLE ~0
params1(16)=0.081; //-0.2:0.2 MLE ~0
params1(17)=-0.015; //-0.04:0.01 MLE ~0
params1(18)=0.013; //-0.3:0.3 MLE ~0.1
}
_vbc_vec<int> tmp_index_sampled;
tmp_index_sampled = sampled_index;
if(boot)
{
ofstream boot_file;
if(sim)
boot_file.open("sims/gb_output/boot_lakes.tab");
else
boot_file.open("output/boot_lakes.tab");
for(int i=1;i<=n_reps;i++)
{
//Bootstrap resample //
sampled_index = sample_w_replace(tmp_index_sampled);
for(int j=1;j<=n_sampled;j++)
boot_file << sampled_index(j) << "\t";
boot_file << "\n";
boot_file.flush();
// --- //
simplex::clsSimplex<float> gertzen_rep;
//gertzen_rep.set_param_small(1e-3);
gertzen_rep.start(&dat1,¶ms1, &MLE_l_hood,n_pars, 1e-2);
gertzen_rep.getParams(&MLE_params);
cout << "\n\nMLE "<< i << " of " << n_reps << "\n\n";
for(int p=1;p<=n_pars;p++)
par_file << MLE_params(p) <<"\t";
par_file << "\n";
par_file.flush();
}
boot_file.close();
}else{
simplex::clsSimplex<float> gertzen_rep;
//gertzen_rep.set_param_small(1e-3);
gertzen_rep.start(&dat1,¶ms1, &MLE_l_hood,n_pars, 1e-2);
gertzen_rep.getParams(&MLE_params);
cout << "\n\nMLE\n";
for(int p=1;p<=n_pars;p++)
par_file << MLE_params(p) <<"\t";
par_file << "\n";
par_file.flush();
// Print out distribution of alpha values at MLE
ofstream alphas_file;
alphas_file.open("output/alphas.tab",std::fstream::app);
for(int i=1;i<=n_lakes;i++)
{
alphas_file << calc_alpha(i) << "\n";
}
alphas_file.close();
}
par_file.close();
}
if(run_type==2)
{
//MCMC lib
string mcmc_file("output/lib.mcmc");
if(env)
{
_vbc_vec<float> params(1,4+n_chem_var);
_vbc_vec<float> prop_width(1,4+n_chem_var,1,4+n_chem_var);
prop_width(1)=0.05;
prop_width(2)=0.05;
prop_width(3)=0.05;
params(1)=0.4;
params(2)=1.4;
params(3)=0.42;
for(int i=1;i<=n_chem_var+1;i++)
{
prop_width(i+3)=0.0001;
params(i+3)=chem_pars(i);
}
prop_width(4)=0.1;
_vbc_vec<float> prop_sigma;
prop_sigma = diag(prop_width);
// Print out prop_sigma
for(int i=1;i<=n_chem_var+4;i++)
{
for(int j=1;j<=n_chem_var+4;j++)
cout << prop_sigma(i,j) << " | ";
cout << "\n";
}
mcmcMD::run_mcmc(params,
prop_sigma,
&likelihood_wrapperMCMC_MD,
&prior_MD,
&restrict_MCMC_MD,
50000,
50,
1,
mcmc_file.c_str(),
true,
true,
true,
500,
4);
}else
{
/// No env.
_vbc_vec<float> params(1,4);
_vbc_vec<float> prop_width(1,4,1,4);
prop_width(1)=0.05;
prop_width(2)=0.05;
prop_width(3)=0.000001;
prop_width(4)=0.00001;
params(1)=1.27;
params(2)=1.48;
params(3)=0.0000489;
params(4)=0.00105;
_vbc_vec<float> prop_sigma;
prop_sigma = diag(prop_width);
// Print out prop_sigma
for(int i=1;i<=4;i++)
{
for(int j=1;j<=4;j++)
cout << prop_sigma(i,j) << " | ";
cout << "\n";
}
mcmcMD::run_mcmc(params,
prop_sigma,
&likelihood_wrapperMCMC_MD,
&prior_MD,
&restrict_MCMC_MD,
500000,
1,
1,
mcmc_file.c_str(),
true,
true,
true,
500,
5);
}
/* mcmcMD::run_mcmc(pms,
props,
&like,
&prior,
&restrictions,
500000,
1,
100,
file_name.c_str(),
TRUE,
TRUE,
1000);
*/
}
/// Sim from posterior ///
if(run_type==3)
sim_spread_posterior();
/// Traf tests ////
if(run_type==4)
{
ofstream traf_ll_file("output/traf_ll.dat");
d_par=1.54;
e_par=2;
c_par=0.8;
calc_traf();
calc_traf_mat();
calc_pp();
sim_spread();
cout << l_hood() <<"\n";
/*
for(int i=1;i<=70;i++)
{
e_par=e_par+0.05;
cout << e_par << "\t";
calc_traf();
calc_traf_mat();
calc_pp();
sim_spread();
traf_ll_file << e_par << "\t" << l_hood() << "\n";
cout << l_hood() <<"\t";
sim_spread();
traf_ll_file << e_par << "\t" << l_hood() << "\n";
cout << l_hood() <<"\t";
sim_spread();
traf_ll_file << e_par << "\t" << l_hood() << "\n";
cout << l_hood() <<"\n";
traf_ll_file << e_par << "\t" << l_hood() << "\n";
}
for(int i=1;i<=10;i++)
{
e_par=e_par+0.2;
c_par=0.8;
calc_traf();
calc_traf_mat();
calc_pp();
for(int j = 1;j<=10;j++)
{
c_par=c_par+0.2;
glb_alpha=0; //from MLE
for(int k=1;k<=500;k++)
{
glb_alpha=glb_alpha+0.00001;
sim_spread();
sim_spread();
sim_spread();
cout << e_par << "\t" << c_par << "\t" << glb_alpha << "\t" << l_hood() << "\n";
traf_ll_file << e_par << "\t" << c_par << "\t" << glb_alpha << "\t" << l_hood() << "\n";
}
}
}
*/
traf_ll_file.close();
calc_pp();
write_pp();
write_inv_stat();
}
/// Holdout sets for internal AUC ////
if(run_type==5)
{
int n_pars=4;
_vbc_vec<float>params1(1,n_pars);
// Read parameters values from file //
ifstream pred_pars;
if(sim)
pred_pars.open("sims/gb_output/pred_pars.tab");
else
pred_pars.open("output/pred_pars.tab");
for(int j=1;j<=n_pars;j++)
pred_pars >> params1(j);
pred_pars.close();
// -- //
d_par=params1(1);
e_par = 1;
c_par=params1(2);
gamma_par=params1(3);
glb_alpha=params1(4);
calc_traf();
calc_traf_mat();
//write_traf_mat();
//Sub-sample a holdout set from sampled lakes (pre-2010)
int n_sub_sampled = 100,choose_from=0;
_vbc_vec<int> index_2006_big(1,n_lakes);
for(int i = 1; i<=n_lakes;i++)
{
if( (lakes(i).last_abs==2006 || lakes(i).discovered == 2006) )
{
choose_from += 1;
index_2006_big(choose_from)=i;
}
}
_vbc_vec<int> index_2006(1,choose_from);
for(int i = 1; i<=choose_from;i++)
index_2006(i)=index_2006_big(i);
ofstream prop_holdout_file;
prop_holdout_file.open("output/holdout_sim_props.csv");
ofstream holdout_inv_file("output/holdout2006_data_status.csv");
_vbc_vec<int> holdout_inv_status(1,n_sub_sampled);
_vbc_vec<int> indicies_holdout(1,n_sub_sampled);
_vbc_vec<int> tmp_discovered(1,n_sub_sampled);
_vbc_vec<int> tmp_last_abs(1,n_sub_sampled);
cout << "Total 2006 lakes to choose from " << choose_from << "\n";
for(int rep=1;rep<=50;rep++)
{
indicies_holdout = sample_wo_replace(index_2006,n_sub_sampled);
//Record the year_discovered of holdoutset
for(int i = 1; i<=n_sub_sampled;i++)
{
if(lakes(indicies_holdout(i)).discovered == 2006)
holdout_inv_status(i) = 1;
else
holdout_inv_status(i) = 0;
//write year discovered
if(i == n_sub_sampled)
holdout_inv_file << holdout_inv_status(i) << "\n";
else
holdout_inv_file << holdout_inv_status(i) << ",";
//save last_abs and discoved
tmp_discovered(i) = lakes(indicies_holdout(i)).discovered;
tmp_last_abs(i) = lakes(indicies_holdout(i)).last_abs;
//remove year discovered
lakes(indicies_holdout(i)).discovered = 0;
lakes(indicies_holdout(i)).last_abs = 0;
}
//SIM SPREAD
_vbc_vec<float> prop_holdout_invaded(1,n_sub_sampled);
for(int i=1;i<=n_sub_sampled;i++)
prop_holdout_invaded(i) = 0;
int n_sims=1000;
for(int s=1; s<= n_sims; s++)
{
sim_spread();
for(int i=1;i<=n_sub_sampled;i++)
{
if(t_vec(indicies_holdout(i)) <= 2006)
prop_holdout_invaded(i) += 1;
}
}
//write prop inv
for(int i=1;i<=n_sub_sampled;i++)
{
prop_holdout_invaded(i) = prop_holdout_invaded(i)/n_sims;
if(i < n_sub_sampled)
prop_holdout_file << prop_holdout_invaded(i) << ",";
else
prop_holdout_file << prop_holdout_invaded(i) << "\n";
//reset last_abs and discoved
lakes(indicies_holdout(i)).discovered = tmp_discovered(i);
lakes(indicies_holdout(i)).last_abs = tmp_last_abs(i);
}
}
holdout_inv_file.close();
prop_holdout_file.close();
}