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Commit 2f53aa26 authored by Andreas Gattringer's avatar Andreas Gattringer
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butterflies: implement and debug dispersal (random walks)

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src/modules/butterflies/butterflies_dispersal.c
+ 1
− 0
View file @ 2f53aa26
......@@ -12,5 +12,6 @@ void add_dispersed_eggs(struct cats_configuration *conf, struct cats_grid *grid,
//struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
const int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
assert(eggs >= 0);
data->eggs[row][col] += eggs;
}
\ No newline at end of file
src/modules/butterflies/butterflies_main.c
+ 11
− 2
View file @ 2f53aa26
......@@ -51,16 +51,25 @@ void load_butterflies_species_params(struct cats_configuration *conf, struct cat
load_conf_vital_rate(&data->butterfly_egg_to_adult_survival, conf, ini, section_name, param);
//bool _get_int32_config_value(const struct cats_ini *ini, const char *section, const char *key, bool required, int32_t *value);
int32_t rw_max;
cats_dt_rates female_percentage;
load_conf_value(true, ini, section_name, "butterflies random walk steps maximum", &rw_max);
load_conf_value(true, ini, section_name, "butterflies random walk steps maximum", &data->animal_dispersal_max_radius);
if (data->animal_dispersal_max_radius <= 0) {
log_message(LOG_ERROR, "butterflies random walk steps maximum must be > 0, is %d", data->animal_dispersal_max_radius);
exit_cats(EXIT_FAILURE);
}
load_conf_value(true, ini, section_name, "butterflies female fraction", &female_percentage);
data->generations_max = (int32_t) ceill(data->butterfly_generations.max_rate);
param->plant_dispersal_max_radius = data->animal_dispersal_max_radius;
if (! data->actions_added) {
add_actions(conf);
data->actions_added = true;
}
}
......
src/modules/butterflies/butterflies_main.h
+ 4
− 0
View file @ 2f53aa26
......@@ -13,8 +13,12 @@ struct grid_data_butterflies {
};
#define BF_DEBUG_ROW 4319
#define BF_DEBUG_COL 10502
struct conf_data_butterflies {
// fixme -> move to grid data;
int32_t generations_max;
int32_t current_generation;
int32_t animal_dispersal_max_radius; ///< maximal flight/dispersal distance
......
src/modules/butterflies/butterflies_populations.c
+ 25
− 5
View file @ 2f53aa26
......@@ -23,22 +23,42 @@ void butterflies_cell_maturation(struct cats_grid *grid, struct cats_thread_info
const int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
int32_t local_max_generation = (int32_t) ceilf(data->generations[row][col]);
if (data->generation_current > local_max_generation ) return;
if (data->eggs[row][col] == 0) return;
if (data->eggs[row][col] < 0) {
log_message(LOG_ERROR, "Number of eggs < 0: row %d col %d: %f", row, col, data->eggs[row][col]);
exit(EXIT_FAILURE);
}
float proportion = 1.0f;
if (data->generation_current == local_max_generation && (float) local_max_generation > proportion) {
proportion = data->generations[row][col] - (float) local_max_generation;
}
proportion = (float) local_max_generation- data->generations[row][col];
}
assert(proportion >= 0);
assert(proportion <= 1.0);
if (data->eggs[row][col] == 0) return; // FIXME MOVE UP
assert (conf->grid_count == 1);
float eggs = proportion * data->eggs[row][col];
if (eggs > data->eggs[row][col]) {
log_message(LOG_ERROR, "Removing more eggs than present: %d %d: %f/%f", row, col, data->eggs[row][col], eggs);
exit(EXIT_FAILURE);
}
data->eggs[row][col] -= eggs;
assert(data->eggs[row][col] >= 0);
cats_dt_rates maturation_rate = calculate_rate(&module_conf->butterfly_egg_to_adult_survival, NAN, &grid->param, grid, row, col, NULL);
cats_dt_population K = get_carrying_capacity(grid, row, col);
cats_dt_population adults = poisson_population_capped(ts->rng, eggs * proportion * maturation_rate, K);
set_population_ignore_cc(grid, row, col, adults);
/*
if (adults >0 ) {
printf("adults %d %d: %d\n", row, col, adults);
}*/
set_population(grid, row, col, adults);
}
src/modules/butterflies/butterfly_actions.c
+ 111
− 13
View file @ 2f53aa26
......@@ -7,9 +7,14 @@
#include "butterflies_main.h"
#include "inline_overlays.h"
#include "butterflies_populations.h"
#include "inline_population.h"
#include "random_walk.h"
#include "butterflies_inline.h"
#include "grids/grid_wrapper.h"
#include "grids/gdal_save.h"
#include "paths/output_paths.h"
#include "paths/paths.h"
#include "populations/population.h"
#include "inline_population.h"
enum action_status action_butterfly_stats_reset(struct cats_grid *grid, struct cats_configuration *conf)
......@@ -28,7 +33,7 @@ void grid_butterflies_maturation(struct cats_grid *grid, struct cats_thread_info
const cats_dt_coord end_col = ts->area.end_col;
ts->temp = 0;
for (cats_dt_coord row = start_row; row < end_row; row++) {
for (cats_dt_coord col = start_col; col < end_col; col++) {
......@@ -36,10 +41,11 @@ void grid_butterflies_maturation(struct cats_grid *grid, struct cats_thread_info
|| cell_excluded_by_generation(grid, row, col)) {
continue;
}
butterflies_cell_maturation(grid, ts, row, col, false);
}
}
}
......@@ -52,22 +58,25 @@ void grid_butterflies_dispersal(struct cats_grid *grid, struct cats_thread_info
const cats_dt_coord start_col = ts->area.start_col;
const cats_dt_coord end_col = ts->area.end_col;
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
const int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
// struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
//const int module_id = CATS_MODULE_ID;
//struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
ts->temp = 0;
ts->temp1 = 0;
ts->temp2 = 0;
for (cats_dt_coord row = start_row; row < end_row; row++) {
for (cats_dt_coord col = start_col; col < end_col; col++) {
if (cell_excluded_by_overlay(conf, row, col)
|| data->generation_current > (int32_t) ceilf(data->generations[row][col])) {
|| cell_excluded_by_generation(grid, row, col)) {
continue;
}
butterflies_random_walk()
butterflies_random_walk(grid, ts, row, col, false);
}
}
// if (ts->temp) printf("thread %d: %ld random walks (%ld cells) avg %f\n", ts->id, ts->temp, ts->temp1, (float) ts->temp / (float) ts->temp1);
}
......@@ -94,6 +103,46 @@ enum action_status action_butterflies_maturation(struct cats_grid *grid, struct
return ACTION_RUN;
}
char *get_butterfly_population_filename(struct cats_configuration *conf, struct cats_grid *grid)
{
assert(grid != NULL);
assert(conf != NULL);
assert(conf->grid_count == 1);
int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
struct string_array *path = get_output_directory(conf, "butterfly-adults"); // FIXME MAKE DIRECTORY
char *extension = get_extension(conf, "adults");
struct string_array *name = standard_output_file_name(conf, NULL, NULL, NULL);
string_array_add_int(name, data->generation_current, "g%03d");
char *filename = assemble_filename(path, name, "_", extension);
free_string_array(&path);
free_string_array(&name);
free(extension);
return filename;
}
enum action_status action_butterflies_save_grid(struct cats_grid *grid, struct cats_configuration *conf)
{
int32_t id = grid->id;
char *filename = get_butterfly_population_filename(conf, grid);
struct grid_wrapper data = gridwrapper(grid->population, grid->dimension);
save_grid_to_gdal(&data, GDT_Int32, conf, filename, conf->param[id].species_name);
free(filename);
return ACTION_RUN;
}
enum action_status action_butterflies_kill_adults(struct cats_grid *grid, struct cats_configuration *conf)
{
......@@ -105,6 +154,8 @@ enum action_status action_butterflies_kill_adults(struct cats_grid *grid, struct
enum action_status action_butterflies_dispersal(struct cats_grid *grid, struct cats_configuration *conf)
{
threaded_action(&grid_butterflies_dispersal, grid, conf, TS_DISPERSAL);
return ACTION_RUN;
}
......@@ -151,6 +202,7 @@ void grid_update_generations(struct cats_grid *grid, struct cats_thread_info *ts
}
cats_dt_rates gen = calculate_rate(rate, 0, conf->param, grid, row, col, NULL);
data->generations[row][col] = (float) gen;
//printf("GENERATIONS::thread %03d:: %d %d %f\n", ts->id ,row, col, (float) gen);
}
}
......@@ -159,15 +211,47 @@ void grid_update_generations(struct cats_grid *grid, struct cats_thread_info *ts
enum action_status action_butterfly_update_generations(struct cats_grid *grid, struct cats_configuration *conf)
{
struct conf_data_butterflies *data = CATS_MODULE_DATA;
int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
data->generation_current = module_conf->generations_max;
log_message(LOG_IMPORTANT, "resetting generation to %d", module_conf->generations_max);
if (grid->param.initial_population.adjusted == false) {
if (grid->param.initial_population.set_to_cc == true) increase_initial_population_to_cc(grid, conf);
if (grid->param.initial_population.suitability_threshold > 0.0) {
prune_initial_population_under_threshold(conf, grid);
}
grid->param.initial_population.adjusted = true;
}
threaded_action(&grid_update_generations, grid, conf, TS_DEFAULT);
return ACTION_RUN;
}
enum action_status action_update_generation(struct cats_grid *grid, struct cats_configuration *conf)
enum action_status action_finish_generation(struct cats_grid *grid, struct cats_configuration *conf)
{
struct conf_data_butterflies *data = CATS_MODULE_DATA;
int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
data->generation_current--;
log_message(LOG_IMPORTANT, "Setting generation to %d\n", data->generation_current);
assert(data->generation_current >= 0);
// struct conf_data_butterflies *data = CATS_MODULE_DATA;
return ACTION_RUN;
}
enum action_status action_start_generation(struct cats_grid *grid, struct cats_configuration *conf)
{
int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
log_message(LOG_IMPORTANT, "Starting generation to %d\n", data->generation_current);
assert(data->generation_current >= 0);
// struct conf_data_butterflies *data = CATS_MODULE_DATA;
return ACTION_RUN;
}
......@@ -186,17 +270,27 @@ void add_butterfly_generation_action(struct cats_configuration *conf, action_fun
void add_actions(struct cats_configuration *conf)
{
struct conf_data_butterflies *data = CATS_MODULE_DATA;
printf("MAXIMUM GENERATIONS %d\n", data->generations_max);
register_action_function(conf, action_butterfly_stats_reset, "butterfly_action_reset_stats",
"resetting butterfly statistics");
register_action_function(conf, action_butterfly_update_generations, "butterfly_action_update_generations",
"update generations");
register_action_function(conf, action_finish_generation, "action_finish_generation",
"update generation");
register_action_function(conf, action_start_generation, "action_start_generation",
"start generation");
register_action_function(conf, action_butterflies_maturation, "butterfly_action_egg_to_adult",
"transition eggs to adults");
register_action_function(conf, action_butterflies_dispersal, "butterfly_action_dispersal", "egg dispersal");
register_action_function(conf, action_butterflies_kill_adults, "butterfly_kill_adults", "kill adults");
register_action_function(conf, action_butterflies_save_grid, "action_butterflies_save_grid", "output");
list_actions_full(conf);
......@@ -204,12 +298,16 @@ void add_actions(struct cats_configuration *conf)
append_action_by_name(conf, "action_load_environments", ALL_STAGES, "environment update", module_name);
append_action_by_name(conf, "action_overlay_update", ALL_STAGES, "overlay update", module_name);
append_action(conf, action_butterfly_update_generations, ALL_STAGES, "update generations", module_name);
for (int32_t generation = data->generations_max; generation > 0; generation--) {
add_butterfly_generation_action(conf, action_update_generation, "update generation", generation);
add_butterfly_generation_action(conf, action_start_generation, "start generation", generation);
add_butterfly_generation_action(conf, action_butterflies_maturation, "transition eggs to adults",
generation);
add_butterfly_generation_action(conf, action_butterflies_dispersal, "dispersal", generation);
add_butterfly_generation_action(conf, action_butterflies_save_grid, "output", generation);
add_butterfly_generation_action(conf, action_butterflies_kill_adults, "kill adults", generation);
add_butterfly_generation_action(conf, action_finish_generation, "finish generation", generation);
}
}
\ No newline at end of file
src/modules/butterflies/random_walk.c
+ 56
− 18
View file @ 2f53aa26
......@@ -39,44 +39,52 @@ static inline bool suitable_for_egg_laying(const struct cats_configuration *conf
if (conf->overlays.overlay[OL_HABITAT_TYPE_CC].enabled) {
double multiplier = conf->overlays.habitat_cc->data[row][col];
if (multiplier < 1.0) { return false; }
if (multiplier < 0.0) { return false; }
}
return true;
}
void single_random_walk(struct cats_thread_info *ts, struct cats_grid *grid, cats_dt_coord source_row, cats_dt_coord source_col, int32_t eggs)
static void inline single_random_walk(struct cats_thread_info *ts, struct cats_grid *grid, cats_dt_coord source_row, cats_dt_coord source_col, int32_t eggs, int32_t rw_num)
{
const struct cats_configuration *conf = ts->conf;
const int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
double max_distance = 0;
cats_dt_coord max_steps = 10;
double distance = 0;
int32_t eggs_left = eggs;
cats_dt_coord max_steps = module_conf->animal_dispersal_max_radius;
//double max_distance = 0;
//double distance = 0;
cats_dt_coord steps = 0;
bool done = false;
cats_dt_coord row = source_row;
cats_dt_coord col = source_col;
int32_t deposition_count = 0;
/*
if (row == BF_DEBUG_ROW && col == BF_DEBUG_COL ) {
printf("rw,run,row,col,step,deposit,eggs_left,thread_id\n");
printf("rw,%d,%d,%d,%d,%d,%d,%d\n", rw_num, row, col, 0, 0, eggs_left,ts->id);
}
*/
while (! done) {
bool accepted = false;
//bool accepted = false;
unsigned long int direction = gsl_rng_uniform_int(ts->rng, N_DIRECTIONS);
cats_dt_coord *offsets = DIRECTION_OFFSETS[direction];
cats_dt_coord row_offset = offsets[0];
cats_dt_coord col_offset = offsets[1];
assert(row_offset >= -1 && row_offset <= 1);
assert(col_offset >= -1 && col_offset <= 1);
row += row_offset;
col += col_offset;
if (row >= grid->dimension.rows || row < 0 || col >= grid->dimension.cols || col < 0) {
//printf("out of bounds %d %d - %d %d\n", row, col, grid->dimension.rows, grid->dimension.cols);
return; // we escaped the simulation extent and got lost
}
steps++;
/*
double this_distance = sqrt((row_offset * row_offset) + (col_offset * col_offset));
if (distance + this_distance <= max_distance) {
accepted = true;
......@@ -85,17 +93,34 @@ void single_random_walk(struct cats_thread_info *ts, struct cats_grid *grid, cat
accepted = false;
done = true;
}
if (!accepted) return;
*/
int32_t eggs_to_deposit = 0;
if (suitable_for_egg_laying(conf, grid, row, col)) {
int32_t eggs_to_deposit= (int32_t) ceilf((float) eggs/(float) deposition_count);
data->eggs[row][col] += (float) eggs_to_deposit;
deposition_count++;
eggs_to_deposit = (int32_t) ceilf((float) eggs_left/(2.0f));
assert(eggs_to_deposit >= 0);
if (eggs_to_deposit > eggs_left) {
eggs_to_deposit = eggs_left;
}
eggs_left -= eggs_to_deposit;
data->eggs[row][col] += (float) eggs_to_deposit;
if (steps >= max_steps) done = true;
steps += 1;
}
/*
if (source_row == BF_DEBUG_ROW && source_col == BF_DEBUG_COL ) {
printf("rw,%d,%d,%d,%d,%d,%d,%d\n", rw_num, row, col, steps, eggs_to_deposit,eggs_left,ts->id);
}
*/
if (steps >= max_steps || eggs_left == 0) done = true;
}
//printf("rw,%d,%d,%d,%d,%d,%d,%d\n", rw_num, row, col, steps, 0,eggs_left,ts->id);
fflush(stdout);
assert(eggs_left >= 0);
}
......@@ -105,14 +130,27 @@ void butterflies_random_walk(struct cats_grid *grid, struct cats_thread_info *ts
if (check_exclusion
&& (cell_excluded_by_overlay(conf, row, col) ||cell_excluded_by_generation(grid, row, col))) return;
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
const int module_id = CATS_MODULE_ID;
struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
// struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
// const int module_id = CATS_MODULE_ID;
// struct grid_data_butterflies *data = grid->grid_modules[module_id].module_data;
int32_t population = get_adult_population(grid, row, col);
int32_t dispersing_population = population;
int32_t eggs = 0;
struct conf_data_butterflies *module_conf = CATS_MODULE_DATA;
cats_dt_population N = get_adult_population(grid, row, col);
cats_dt_rates eggs = calculate_rate(&module_conf->eggs_per_female, N, &grid->param, grid, row, col, NULL);
int32_t e = (int32_t) ceill(eggs);
assert(e >= 0);
if (e == 0) return;
if (dispersing_population > 0) ts->temp1++;
if (dispersing_population == 0) return;
for (int32_t p = 0; p < dispersing_population; p++) {
single_random_walk(ts, grid, row, col, eggs);
single_random_walk(ts, grid, row, col, e, p);
ts->temp++;
}
//exit_cats(EXIT_SUCCESS);
}
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