m->fprintf = local_fprintf;
m->free = local_free;
/* Make sure the right XML subtree was sent. */
g_assert (strcmp (scew_element_name (params), MODEL_NAME) == 0);
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "setting production types");
#endif
local_data->production_types = herds->production_type_names;
local_data->production_type =
naadsm_read_prodtype_attribute (params, "production-type", herds->production_type_names);
e = scew_element_by_name (params, "latent-period");
g_assert (e != NULL);
local_data->latent_period = PAR_get_PDF (e);
e = scew_element_by_name (params, "infectious-subclinical-period");
g_assert (e != NULL);
local_data->infectious_subclinical_period = PAR_get_PDF (e);
e = scew_element_by_name (params, "infectious-clinical-period");
g_assert (e != NULL);
local_data->infectious_clinical_period = PAR_get_PDF (e);
e = scew_element_by_name (params, "immunity-period");
g_assert (e != NULL);
local_data->immunity_period = PAR_get_PDF (e);
e = scew_element_by_name (params, "prevalence");
if (e != NULL)
/**
* Adds a set of parameters to an airborne spread model.
*/
void
set_params (struct ergadm_model_t_ *self, scew_element * params)
{
local_data_t *local_data;
gboolean *from_production_type, *to_production_type;
unsigned int nprod_types, i, j;
param_block_t *param_block;
scew_element const *e;
gboolean success;
gboolean use_rtree;
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- ENTER set_params (%s)", MODEL_NAME);
#endif
/* Make sure the right XML subtree was sent. */
g_assert (strcmp (scew_element_name (params), MODEL_NAME) == 0);
local_data = (local_data_t *) (self->model_data);
/* Find out which to-from production type combinations these parameters apply
* to. */
from_production_type =
ergadm_read_prodtype_attribute (params, "from-production-type", local_data->production_types);
to_production_type =
ergadm_read_prodtype_attribute (params, "to-production-type", local_data->production_types);
nprod_types = local_data->production_types->len;
for (i = 0; i < nprod_types; i++)
if (from_production_type[i] == TRUE)
for (j = 0; j < nprod_types; j++)
if (to_production_type[j] == TRUE)
{
/* If necessary, create a row in the 2D array for this from-
* production type. */
if (local_data->param_block[i] == NULL)
local_data->param_block[i] = g_new0 (param_block_t *, nprod_types);
/* Create a parameter block for this to-from production type
* combination, or overwrite the existing one. */
param_block = local_data->param_block[i][j];
if (param_block == NULL)
{
param_block = g_new (param_block_t, 1);
local_data->param_block[i][j] = param_block;
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG,
"setting parameters for %s -> %s",
(char *) g_ptr_array_index (local_data->production_types, i),
(char *) g_ptr_array_index (local_data->production_types, j));
#endif
}
else
{
g_warning ("overwriting previous parameters for %s -> %s",
(char *) g_ptr_array_index (local_data->production_types, i),
(char *) g_ptr_array_index (local_data->production_types, j));
}
e = scew_element_by_name (params, "prob-spread-1km");
param_block->prob_spread_1km = PAR_get_probability (e, &success);
if (success == FALSE)
{
g_warning ("setting probability of spread at 1 km to 0");
param_block->prob_spread_1km = 0;
}
e = scew_element_by_name (params, "wind-direction-start");
param_block->wind_dir_start = PAR_get_angle (e, &success);
if (success == FALSE)
{
g_warning ("setting start of wind direction range to 0");
param_block->wind_dir_start = 0;
}
/* Force the angle into the range [0,360). */
while (param_block->wind_dir_start < 0)
param_block->wind_dir_start += 360;
while (param_block->wind_dir_start >= 360)
param_block->wind_dir_start -= 360;
e = scew_element_by_name (params, "wind-direction-end");
param_block->wind_dir_end = PAR_get_angle (e, &success);
if (success == FALSE)
{
g_warning ("setting end of wind direction range to 360");
param_block->wind_dir_end = 360;
}
/* Force the angle into the range [0,360]. */
while (param_block->wind_dir_end < 0)
param_block->wind_dir_end += 360;
while (param_block->wind_dir_end > 360)
param_block->wind_dir_end -= 360;
/* Note that start > end is allowed. See the header comment. */
param_block->wind_range_crosses_0 =
(param_block->wind_dir_start > param_block->wind_dir_end);
/* Setting both start and end to 0 seems like a sensible way to
* turn off airborne spread, but headings close to north will
* "sneak through" this restriction because we allow a little
* wiggle room for rounding errors. If the user tries this,
* instead set prob-spread-1km=0. */
if (param_block->wind_dir_start == 0 && param_block->wind_dir_end == 0)
param_block->prob_spread_1km = 0;
e = scew_element_by_name (params, "max-spread");
param_block->max_spread = PAR_get_length (e, &success);
if (success == FALSE)
{
g_warning ("setting maximum distance of spread to 0");
param_block->max_spread = 0;
}
/* The maximum spread distance cannot be negative. */
if (param_block->max_spread < 0)
{
g_warning ("maximum distance of spread cannot be negative, setting to 0");
param_block->max_spread = 0;
}
/* Setting the maximum spread distance to 0 seems like a sensible
* way to turn off airborne spread, but max-spread <= 1 doesn't
* make sense in the formula. If the user tries this, instead set
* max-spread=2, prob-spread-1km=0. */
if (param_block->max_spread <= 1)
{
param_block->max_spread = 2;
param_block->prob_spread_1km = 0;
}
e = scew_element_by_name (params, "delay");
if (e != NULL)
{
param_block->delay = PAR_get_PDF (e);
}
else
param_block->delay = PDF_new_point_dist (0);
/* Keep track of the maximum distance of spread from each
* production type. This determines whether we will use the R-tree
* index when looking for herds to spread infection to. */
if (param_block->max_spread > local_data->max_spread[i])
{
local_data->max_spread[i] = param_block->max_spread;
/* Use the following heuristic to decide whether to use the
* R-tree index in searches: if the ratio of the diameter of
* circle of maximum spread to the short axis of the oriented
* bounding rectangle around the herds is <= 0.25, use the
* R-tree. */
if (local_data->short_axis_length > 0)
{
use_rtree = (param_block->max_spread * 2 / local_data->short_axis_length) <= 0.25;
}
else
{
use_rtree = FALSE;
}
#if defined(USE_RTREE) && USE_RTREE == 0
/* For debugging purposes, you can #define USE_RTREE to 0 to never
* use the spatial index, or 1 to always use it. */
use_rtree = FALSE;
#endif
local_data->use_rtree_index[i] = use_rtree;
}
}
g_free (from_production_type);
g_free (to_production_type);
#if DEBUG
g_log (G_LOG_DOMAIN, G_LOG_LEVEL_DEBUG, "----- EXIT set_params (%s)", MODEL_NAME);
#endif
return;
}
