void model_parameters::preliminary_calculations(void)
{
#if defined(USE_ADPVM)
admaster_slave_variable_interface(*this);
#endif
// get the data out of the columns of the data matrix
landings=column(data,1);
biomass=column(data,2);
// calculate observed surplus production (Pobs)
for(int i=1;i<=nobs-1;i++)
{
Pobs(i)=biomass(i+1)-biomass(i)+landings(i);
}
// set starting values
lnMSY=log(0.6*max(Pobs));
lnK=log(max(biomass));
n=2;
}
void model_parameters::calc_residuals(void)
{
for(int j=1;j<=nobs-1;j++)
{
Ppred(j)=zMSY*((biomass(j)/K) - pow(biomass(j)/K,n));
}
epsilon=Pobs-Ppred;
sig=sqrt(norm2(epsilon)/(nobs-1));
SSQ=norm2(epsilon);
}
int main(int argc, char *argv[])
{
int nrows, ncols;
int row, col;
struct GModule *module;
struct Option *input1, *input2, *input3, *input4, *input5, *input6;
struct Option *output1;
struct History history; /*metadata */
struct Colors colors;
char *result1; /*output raster name */
int infd_fpar, infd_luf, infd_lat;
int infd_doy, infd_tsw, infd_wa;
int outfd1;
char *fpar, *luf, *lat, *doy, *tsw, *wa;
void *inrast_fpar, *inrast_luf, *inrast_lat;
void *inrast_doy, *inrast_tsw, *inrast_wa;
DCELL * outrast1;
CELL val1, val2;
/************************************/
G_gisinit(argv[0]);
module = G_define_module();
G_add_keyword(_("imagery"));
G_add_keyword(_("biomass"));
G_add_keyword(_("fpar"));
G_add_keyword(_("yield"));
module->description =
_("Computes biomass growth, precursor of crop yield calculation.");
/* Define the different options */
input1 = G_define_standard_option(G_OPT_R_INPUT);
input1->key = "fpar";
input1->description = _("Name of fPAR raster map");
input2 = G_define_standard_option(G_OPT_R_INPUT);
input2->key = "lightuseefficiency";
input2->description =
_("Name of light use efficiency raster map (UZB:cotton=1.9)");
input3 = G_define_standard_option(G_OPT_R_INPUT);
input3->key = "latitude";
input3->description = _("Name of degree latitude raster map [dd.ddd]");
input4 = G_define_standard_option(G_OPT_R_INPUT);
input4->key = "dayofyear";
input4->description = _("Name of Day of Year raster map [1-366]");
input5 = G_define_standard_option(G_OPT_R_INPUT);
input5->key = "transmissivitysingleway";
input5->description =
_("Name of single-way transmissivity raster map [0.0-1.0]");
input6 = G_define_standard_option(G_OPT_R_INPUT);
input6->key = "wateravailability";
input6->description =
_("Value of water availability raster map [0.0-1.0]");
output1 = G_define_standard_option(G_OPT_R_OUTPUT);
output1->description =
_("Name for output daily biomass growth raster map [kg/ha/d]");
/********************/
if (G_parser(argc, argv))
exit(EXIT_FAILURE);
fpar = input1->answer;
luf = input2->answer;
lat = input3->answer;
doy = input4->answer;
tsw = input5->answer;
wa = input6->answer;
result1 = output1->answer;
/***************************************************/
infd_fpar = Rast_open_old(fpar, "");
inrast_fpar = Rast_allocate_d_buf();
infd_luf = Rast_open_old(luf, "");
inrast_luf = Rast_allocate_d_buf();
infd_lat = Rast_open_old(lat, "");
inrast_lat = Rast_allocate_d_buf();
infd_doy = Rast_open_old(doy, "");
inrast_doy = Rast_allocate_d_buf();
infd_tsw = Rast_open_old(tsw, "");
inrast_tsw = Rast_allocate_d_buf();
infd_wa = Rast_open_old(wa, "");
inrast_wa = Rast_allocate_d_buf();
nrows = Rast_window_rows();
ncols = Rast_window_cols();
outrast1 = Rast_allocate_d_buf();
/* Create New raster files */
outfd1 = Rast_open_new(result1, DCELL_TYPE);
/* Process pixels */
for (row = 0; row < nrows; row++)
{
DCELL d;
DCELL d_fpar;
DCELL d_luf;
DCELL d_lat;
DCELL d_doy;
DCELL d_tsw;
DCELL d_solar;
DCELL d_wa;
G_percent(row, nrows, 2);
/* read input maps */
Rast_get_d_row(infd_fpar, inrast_fpar, row);
Rast_get_d_row(infd_luf,inrast_luf,row);
Rast_get_d_row(infd_lat, inrast_lat, row);
Rast_get_d_row(infd_doy, inrast_doy, row);
Rast_get_d_row(infd_tsw, inrast_tsw, row);
Rast_get_d_row(infd_wa,inrast_wa,row);
/*process the data */
for (col = 0; col < ncols; col++)
{
d_fpar = ((DCELL *) inrast_fpar)[col];
d_luf = ((DCELL *) inrast_luf)[col];
d_lat = ((DCELL *) inrast_lat)[col];
d_doy = ((DCELL *) inrast_doy)[col];
d_tsw = ((DCELL *) inrast_tsw)[col];
d_wa = ((DCELL *) inrast_wa)[col];
if (Rast_is_d_null_value(&d_fpar) ||
Rast_is_d_null_value(&d_luf) ||
Rast_is_d_null_value(&d_lat) ||
Rast_is_d_null_value(&d_doy) ||
Rast_is_d_null_value(&d_tsw) ||
Rast_is_d_null_value(&d_wa))
Rast_set_d_null_value(&outrast1[col], 1);
else {
d_solar = solar_day(d_lat, d_doy, d_tsw);
d = biomass(d_fpar,d_solar,d_wa,d_luf);
outrast1[col] = d;
}
}
Rast_put_d_row(outfd1, outrast1);
}
/* Color table for biomass */
Rast_init_colors(&colors);
val1 = 0;
val2 = 1;
Rast_add_c_color_rule(&val1, 0, 0, 0, &val2, 255, 255, 255, &colors);
G_free(inrast_fpar);
G_free(inrast_luf);
G_free(inrast_lat);
G_free(inrast_doy);
G_free(inrast_tsw);
G_free(inrast_wa);
G_free(outrast1);
Rast_close(infd_fpar);
Rast_close(infd_luf);
Rast_close(infd_lat);
Rast_close(infd_doy);
Rast_close(infd_tsw);
Rast_close(infd_wa);
Rast_close(outfd1);
Rast_short_history(result1, "raster", &history);
Rast_command_history(&history);
Rast_write_history(result1, &history);
exit(EXIT_SUCCESS);
}
std::vector<double> biomass(Graph *graph, double *fpar, int *dbg, int *included)
{
if(*dbg)Rprintf("biomass[");
int target_type;
int i,j,k,n=0,m,dbg0;
double a1[2], vtemp;
std::vector<double> value;
value.clear();
if(*dbg)Rprintf("(type=%i, mean=%i)",(int)fpar[0], (int) fpar[1]);
if((int)fpar[0]==0)
{
dbg0 = *dbg;
*dbg = 0;
a1[1] = fpar[1];
for(i=0;i< graph->pp->getNtypes();i++)
{
if(graph->typeIncluded.at(i))
{
a1[0] = (double) graph->pp->getTypevec(&i);
value.push_back(biomass(graph, a1, dbg ,included).at(0));
}
}
*dbg = dbg0;
}
else // target type given
{
target_type = (int) fpar[0];
value.push_back(0.0);
// double ko = 99;
double vi;
for(i=0;i< (int)graph->nodelist.size() ;i++)
if(included[i] && graph->pp->getT(&i) == target_type)
{
//Rprintf("%f", graph->pp->getMass(&i));
vi = 0.0;
m = graph->nodelist[i].size();
if(m>0)
{
n++;
for(j=0;j<m;j++)
{
k = graph->nodelist[i][j]-1;
vi = vi + graph->pp->getMass(&k);
}
if(fpar[1]>0) // if mean version
{
vi = vi/(double)m;
//graph->pp->setMass2(&i, &vtemp);
}
//else graph->pp->setMass2(&i, &vi);
value.at(0) = value.at(0) + vi;//graph->pp->getMass2(&i);
}
// graph->pp->setMass2(&i, &ko);
//Rprintf(" - %f\n", graph->pp->getMass(&i));
}
if(n>0) value.at(0) = value.at(0)/(double)n;
}
if(*dbg)Rprintf("]");
return value;
}
