From f94dacf1cba1e912c02d6903d61ac41d4618ecb1 Mon Sep 17 00:00:00 2001
From: Andreas Gattringer <andreas.gattringer@univie.ac.at>
Date: Wed, 19 Jul 2023 08:58:56 +0200
Subject: [PATCH] preparations for multi-scale simulations
- new functions to access input grids (overlay, environment)
these will be used to translate between input layer coordinates
and population grid coordinates
- overdue helper function to set environment values
- helper function to check to copy and verify grid dimension info
---
src/cats/CMakeLists.txt | 2 +-
src/cats/actions/setup.c | 6 +++--
src/cats/debug/debug_vital_rates.c | 6 ++---
src/cats/environment/environment.c | 14 +++++-----
src/cats/environment/environment_rasters.c | 4 +--
src/cats/grids/dimensions.c | 29 +++++++++++++++++++++
src/cats/grids/dimensions.h | 12 +++++++++
src/cats/grids/direct_access.c | 28 ++++++++++++++++++++
src/cats/grids/direct_access.h | 10 +++++++
src/cats/inline.h | 18 +++++++++----
src/cats/inline_overlays.h | 9 ++++---
src/cats/inline_population.h | 16 ++++--------
src/cats/overlays/overlay_habitat_type_cc.c | 18 +++++++++++++
src/cats/overlays/overlay_habitat_type_cc.h | 3 +++
src/cats/populations/carrying_capacity.c | 8 +++---
src/cats/vital_rates/direct_functions.c | 3 ++-
src/cats/vital_rates/glm_functions.c | 4 +--
17 files changed, 148 insertions(+), 42 deletions(-)
create mode 100644 src/cats/grids/dimensions.c
create mode 100644 src/cats/grids/dimensions.h
create mode 100644 src/cats/grids/direct_access.c
create mode 100644 src/cats/grids/direct_access.h
diff --git a/src/cats/CMakeLists.txt b/src/cats/CMakeLists.txt
index 00239ae..fb05cbc 100644
--- a/src/cats/CMakeLists.txt
+++ b/src/cats/CMakeLists.txt
@@ -39,7 +39,7 @@ include_directories(${GDAL_INCLUDE_DIR})
include_directories(${GSL_INCLUDE_DIR})
include_directories(${MPI_C_INCLUDE_PATH})
-add_library(libcats STATIC "" stats/statistics.c stats/statistics.h data/cats_global.c ../cats_windows.h test/test_ini.c test/test_ini.h debug/debug_vital_rates.c debug/debug_vital_rates.h overlays/overlay_resources.c overlays/overlay_resources.h paths/path_patterns.c paths/path_patterns.h)
+add_library(libcats STATIC "" stats/statistics.c stats/statistics.h data/cats_global.c ../cats_windows.h test/test_ini.c test/test_ini.h debug/debug_vital_rates.c debug/debug_vital_rates.h overlays/overlay_resources.c overlays/overlay_resources.h paths/path_patterns.c paths/path_patterns.h grids/dimensions.c grids/dimensions.h grids/direct_access.c grids/direct_access.h)
target_include_directories(libcats PUBLIC ".")
target_sources(libcats PRIVATE
diff --git a/src/cats/actions/setup.c b/src/cats/actions/setup.c
index d88079d..7252e60 100644
--- a/src/cats/actions/setup.c
+++ b/src/cats/actions/setup.c
@@ -37,6 +37,7 @@
#include "temporal/simulation_time.h"
#include "populations/population.h"
#include "dispersal/dispersal.h"
+#include "inline.h"
void setup_lambda_test_simulation(struct cats_configuration *conf, struct cats_grid *grid) // FIXME MAYBE MOVE
@@ -55,7 +56,7 @@ void setup_lambda_test_simulation(struct cats_configuration *conf, struct cats_g
cats_dt_coord row = 0;
cats_dt_coord col = 0;
- grid->suitability->environments[0]->current.values[row][col] = (cats_dt_environment) grid->param.OT; // FIXME -> set suitability
+ set_suitability(grid, row, col, (cats_dt_environment) grid->param.OT);
cats_dt_population target_pop = get_adult_carrying_capacity(grid, row, col) / 5;
set_population_ignore_cc(grid, row, col, target_pop);
@@ -94,7 +95,8 @@ void setup_lambda_gradient_simulation(struct cats_configuration *conf, struct ca
cats_dt_environment diff = 1.0f / ((cats_dt_environment) conf->geometry.dimension.cols - 1.0f);
for (cats_dt_coord row = 0; row < rows; row++) {
for (cats_dt_coord col = 0; col < cols; col++) {
- grid->suitability->environments[0]->current.values[row][col] = (cats_dt_environment) col * diff;
+ cats_dt_environment value = (cats_dt_environment) col * diff;
+ set_suitability(grid, row, col, value);
}
}
diff --git a/src/cats/debug/debug_vital_rates.c b/src/cats/debug/debug_vital_rates.c
index ec6f362..4e3de11 100644
--- a/src/cats/debug/debug_vital_rates.c
+++ b/src/cats/debug/debug_vital_rates.c
@@ -90,7 +90,7 @@ struct cats_grid *minimal_grid(struct cats_configuration *conf, struct cats_envi
}
-void set_suitability(struct cats_environment *env, cats_dt_environment suit)
+void debug_set_suitability(struct cats_environment *env, cats_dt_environment suit)
{
env->environments[0]->current.values[0][0] = suit;
}
@@ -138,7 +138,7 @@ static inline cats_dt_rates attempt_rate_calculation(cats_dt_environment suit, c
}
- set_suitability(grid->suitability, suit);
+ debug_set_suitability(grid->suitability, suit);
*K_suit = get_adult_carrying_capacity(grid, 0, 0);
if (N > *K_suit) return NAN;
@@ -209,7 +209,7 @@ void debug_vital_rate(struct cats_vital_rate *vr, struct cats_vital_rate *cc, st
void debug_vital_rates(struct cats_configuration *conf, const struct program_options *command_line_options)
{
struct cats_environment *env = minimal_suitability_environment();
- set_suitability(env, 0.5f);
+ debug_set_suitability(env, 0.5f);
struct cats_grid *grid = minimal_grid(conf, env);
struct cats_species_param *param = &grid->param;
set_param_values(param, 0.5, 0.25, 0.5);
diff --git a/src/cats/environment/environment.c b/src/cats/environment/environment.c
index 0f85e76..290fe3d 100644
--- a/src/cats/environment/environment.c
+++ b/src/cats/environment/environment.c
@@ -38,6 +38,7 @@
#include "environment.h"
#include "grids/gdal_load.h"
#include "environment/environment_rasters.h"
+#include "grids/dimensions.h"
#ifdef USEMPI
#include "mpi/mpi_save.h"
@@ -69,10 +70,10 @@ void interpolate_environment(const struct cats_configuration *conf,
const cats_dt_coord rows = environment->current.dimension.rows;
const cats_dt_coord cols = environment->current.dimension.cols;
- if (environment->start.dimension.rows != environment->end.dimension.rows
- || environment->start.dimension.cols != environment->end.dimension.cols
- || environment->start.dimension.rows != environment->current.dimension.rows
- || environment->start.dimension.cols != environment->current.dimension.cols) {
+ bool matching_dimensions = dimensions_match(&environment->start.dimension, &environment->end.dimension)
+ && dimensions_match(&environment->start.dimension, &environment->current.dimension);
+
+ if (!matching_dimensions) {
log_message(LOG_ERROR, "%s: dimension mismatch", __func__);
log_message(LOG_ERROR, "environment (start): %d x %d", environment->start.dimension.rows,
environment->start.dimension.cols);
@@ -149,8 +150,9 @@ load_environment_raster(struct cats_configuration *conf, struct cats_environment
}
unload_environment_raster(raster);
- raster->dimension.rows = conf->geometry.dimension.rows;
- raster->dimension.cols = conf->geometry.dimension.cols;
+
+ copy_dimensions_from_to(&conf->geometry.dimension, &raster->dimension);
+
raster->interpolation_type = type;
raster->environment_type = environment_type;
if (raster->values == NULL) {
diff --git a/src/cats/environment/environment_rasters.c b/src/cats/environment/environment_rasters.c
index e7a3a12..7abcda8 100644
--- a/src/cats/environment/environment_rasters.c
+++ b/src/cats/environment/environment_rasters.c
@@ -27,6 +27,7 @@
#include "logging.h"
#include "environment_rasters.h"
#include "environment.h"
+#include "grids/dimensions.h"
void print_raster_quick_info(struct cats_environment_raster *gr)
@@ -53,9 +54,8 @@ void create_raster_if_needed(struct cats_configuration *conf, struct cats_enviro
log_message(LOG_INFO, "\tinitializing empty grid for <%s>", get_raster_type_name_specific(raster));
log_message(LOG_DEBUG, "%s: ALLOCATING NEW GRID NOW", __func__);
raster->values = new_raw_2d_array_from_dimension(conf->geometry.dimension, sizeof(cats_dt_environment));
- raster->dimension.rows = conf->geometry.dimension.rows;
- raster->dimension.cols = conf->geometry.dimension.cols;
+ copy_dimensions_from_to(&conf->geometry.dimension, &raster->dimension);
}
diff --git a/src/cats/grids/dimensions.c b/src/cats/grids/dimensions.c
new file mode 100644
index 0000000..7445ed5
--- /dev/null
+++ b/src/cats/grids/dimensions.c
@@ -0,0 +1,29 @@
+#include <assert.h>
+#include "dimensions.h"
+
+
+void copy_dimensions_from_to(const struct cats_dimension *from, struct cats_dimension *to)
+{
+ to->rows = from->rows;
+ to->cols = from->cols;
+}
+
+
+bool valid_coordinates(const struct cats_dimension *dim, cats_dt_coord row, cats_dt_coord col)
+{
+ assert(dim != NULL);
+ assert(row >= 0 && row < dim->rows);
+ assert(col >= 0 && col < dim->cols);
+ if (row < 0 || col < 0) return false;
+ if (row >= dim->rows || col >= dim->cols) return false;
+ return true;
+}
+
+
+bool dimensions_match(const struct cats_dimension *dim1, const struct cats_dimension *dim2)
+{
+ if (dim1->rows == dim2->rows && dim1->cols == dim2->cols) {
+ return true;
+ }
+ return false;
+}
\ No newline at end of file
diff --git a/src/cats/grids/dimensions.h b/src/cats/grids/dimensions.h
new file mode 100644
index 0000000..b25912c
--- /dev/null
+++ b/src/cats/grids/dimensions.h
@@ -0,0 +1,12 @@
+#ifndef CATS_DIMENSIONS_H
+#define CATS_DIMENSIONS_H
+
+#include "memory/arrays.h"
+
+void copy_dimensions_from_to(const struct cats_dimension *from, struct cats_dimension *to);
+
+bool dimensions_match(const struct cats_dimension *dim1, const struct cats_dimension *dim2);
+
+bool valid_coordinates(const struct cats_dimension *dim, cats_dt_coord row, cats_dt_coord col);
+
+#endif //CATS_DIMENSIONS_H
diff --git a/src/cats/grids/direct_access.c b/src/cats/grids/direct_access.c
new file mode 100644
index 0000000..dfcefa1
--- /dev/null
+++ b/src/cats/grids/direct_access.c
@@ -0,0 +1,28 @@
+#include <assert.h>
+#include "direct_access.h"
+#include "dimensions.h"
+
+
+double load_input_2d_array_double(const struct cats_2d_array_double *raster, cats_dt_coord row, cats_dt_coord col)
+{
+ valid_coordinates(&raster->dimension, row, col);
+ return raster->data[row][col];
+}
+
+char load_input_2d_array_char(const struct cats_2d_array_char *raster, cats_dt_coord row, cats_dt_coord col)
+{
+ valid_coordinates(&raster->dimension, row, col);
+ return raster->data[row][col];
+}
+
+cats_dt_environment load_input_environment_raster(struct cats_environment_raster *raster, cats_dt_coord row, cats_dt_coord col)
+{
+ valid_coordinates(&raster->dimension, row, col);
+ return raster->values[row][col];
+}
+
+void set_input_environment_raster(struct cats_environment_raster *raster, cats_dt_coord row, cats_dt_coord col, cats_dt_environment value)
+{
+ valid_coordinates(&raster->dimension, row, col);
+ raster->values[row][col] = value;
+}
\ No newline at end of file
diff --git a/src/cats/grids/direct_access.h b/src/cats/grids/direct_access.h
new file mode 100644
index 0000000..147dab2
--- /dev/null
+++ b/src/cats/grids/direct_access.h
@@ -0,0 +1,10 @@
+#ifndef CATS_DIRECT_ACCESS_H
+#define CATS_DIRECT_ACCESS_H
+#include "memory/arrays.h"
+#include "environment/environment.h"
+
+double load_input_2d_array_double(const struct cats_2d_array_double *raster, cats_dt_coord row, cats_dt_coord col);
+cats_dt_environment load_input_environment_raster(struct cats_environment_raster *raster, cats_dt_coord row, cats_dt_coord col);
+void set_input_environment_raster(struct cats_environment_raster *raster, cats_dt_coord row, cats_dt_coord col, cats_dt_environment value);
+char load_input_2d_array_char(const struct cats_2d_array_char *raster, cats_dt_coord row, cats_dt_coord col);
+#endif //CATS_DIRECT_ACCESS_H
diff --git a/src/cats/inline.h b/src/cats/inline.h
index da78d77..1e3606b 100644
--- a/src/cats/inline.h
+++ b/src/cats/inline.h
@@ -42,6 +42,7 @@
#include "inline_carrying_capacity.h"
#include "inline_population.h"
#include "inline_vital_ages.h"
+#include "grids/dimensions.h"
static inline cats_dt_environment
@@ -53,7 +54,16 @@ get_suitability_from_env(const struct cats_environment *set, cats_dt_coord row,
assert(col >= 0);
assert(row < set->environments[0]->current.dimension.rows);
assert(col < set->environments[0]->current.dimension.cols);
- return set->environments[0]->current.values[row][col];
+ return load_input_environment_raster(&set->environments[0]->current, row, col);
+}
+
+
+static inline void
+set_suitability(struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col, cats_dt_environment value)
+{
+ assert(value >= 0.0f);
+ assert(value <= 1.0f);
+ set_input_environment_raster(&grid->suitability->environments[0]->current, row, col, value);
}
@@ -171,8 +181,7 @@ static inline cats_dt_environment get_suitability(const struct cats_grid *grid,
static inline double get_seed_sum(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
assert(grid != NULL && grid->juveniles != NULL);
- assert(row >= 0 && row < grid->dimension.rows);
- assert(col >= 0 && col < grid->dimension.cols);
+ assert(valid_coordinates(&grid->dimension, row, col));
const int32_t max_sp = get_vital_age(grid, VA_SEED_PERSISTENCE); //grid->param.seed_persistence;
double sum = grid->dispersed_seeds[row][col];
if (grid->seed_bank[row][col] == NULL) return sum;
@@ -187,8 +196,7 @@ static inline cats_dt_population_sum
get_juvenile_sum(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
assert(grid != NULL && grid->juveniles != NULL);
- assert(row >= 0 && row < grid->dimension.rows);
- assert(col >= 0 && col < grid->dimension.cols);
+ assert(valid_coordinates(&grid->dimension, row, col));
assert(grid->juveniles[row] != NULL);
const cats_dt_population *juveniles = grid->juveniles[row][col];
diff --git a/src/cats/inline_overlays.h b/src/cats/inline_overlays.h
index 519689e..5f73167 100644
--- a/src/cats/inline_overlays.h
+++ b/src/cats/inline_overlays.h
@@ -28,6 +28,7 @@
#include "assert.h"
#include "overlays/overlays.h"
#include "configuration/configuration.h"
+#include "grids/direct_access.h"
static inline bool
@@ -35,8 +36,7 @@ cell_excluded_by_habitat(const struct cats_configuration *config, cats_dt_coord
{
if (!config->overlays.have_overlays) return false;
if (!config->overlays.overlay[OL_HABITAT_TYPE_CC].enabled) return false;
-
- return (config->overlays.habitat_cc->data[row][col] == 0.0);
+ return (load_input_2d_array_double(config->overlays.habitat_cc, row, col) == 0.0);
}
@@ -45,11 +45,12 @@ cell_excluded_by_overlay(const struct cats_configuration *config, cats_dt_coord
{
assert(config != NULL);
- if (config->overlays.have_overlays == false || config->overlays.overlay[OL_EXCLUSION].enabled == false) return false;
+ if (config->overlays.have_overlays == false || config->overlays.overlay[OL_EXCLUSION].enabled == false)
+ return false;
assert(config->overlays.exclusion->data != NULL);
- const char value = config->overlays.exclusion->data[row][col];
+ const char value = load_input_2d_array_char(config->overlays.exclusion, row, col);
switch (value) { // NOLINT(hicpp-multiway-paths-covered)
case OL_EXCLUSION_NOT_EXCLUDED:
diff --git a/src/cats/inline_population.h b/src/cats/inline_population.h
index 933b3d0..ef61806 100644
--- a/src/cats/inline_population.h
+++ b/src/cats/inline_population.h
@@ -34,14 +34,14 @@
#include "inline_overlays.h"
#include "populations/carrying_capacity.h"
#include "populations/plant_juveniles.h"
+#include "grids/dimensions.h"
static inline cats_dt_population
get_adult_population(const struct cats_grid *grid, cats_dt_coord row, cats_dt_coord col)
{
assert(grid != NULL && grid->population != NULL);
- assert(row >= 0 && row < grid->dimension.rows);
- assert(col >= 0 && col < grid->dimension.cols);
+ assert(valid_coordinates(&grid->dimension, row, col));
assert(grid->population[row] != NULL);
assert(grid->population[row][col] >= 0);
return grid->population[row][col]; // getter
@@ -83,10 +83,7 @@ reduce_population_by(const struct cats_grid *grid, cats_dt_coord row, cats_dt_co
assert(to_reduce >= 0);
assert(grid != NULL);
assert(grid->population != NULL);
- assert(row < grid->dimension.rows);
- assert(col < grid->dimension.cols);
- assert(row >= 0);
- assert(col >= 0);
+ assert(valid_coordinates(&grid->dimension, row, col));
assert(grid->population[row] != NULL);
//cats_dt_population cc = get_carrying_capacity(grid, row, col);
@@ -105,7 +102,7 @@ set_population_ignore_cc(const struct cats_grid *grid, const cats_dt_coord row,
const cats_dt_population pop)
{
assert(grid != NULL && grid->population != NULL);
- assert(row >= 0 && row < grid->dimension.rows && col >= 0 && col < grid->dimension.cols);
+ assert(valid_coordinates(&grid->dimension, row, col));
assert(grid->population[row] != NULL);
if (pop > CATS_MAX_POPULATION || pop < 0.0) {
@@ -171,10 +168,7 @@ get_population_ts(const struct cats_grid *grid, const cats_dt_coord row, const c
{
assert(grid != NULL);
assert(grid->population != NULL);
- assert(row < grid->dimension.rows);
- assert(col < grid->dimension.cols);
- assert(row >= 0);
- assert(col >= 0);
+ assert(valid_coordinates(&grid->dimension, row, col));
assert(grid->population[row] != NULL);
cats_dt_population tmp = grid->population[row][col]; // getter
diff --git a/src/cats/overlays/overlay_habitat_type_cc.c b/src/cats/overlays/overlay_habitat_type_cc.c
index e98c258..8752843 100644
--- a/src/cats/overlays/overlay_habitat_type_cc.c
+++ b/src/cats/overlays/overlay_habitat_type_cc.c
@@ -30,6 +30,7 @@
#include "cats_csv/cats_csv.h"
#include "logging.h"
#include "memory/cats_memory.h"
+#include "grids/direct_access.h"
void cleanup_habitat_layer_cc_aux(void **data)
@@ -139,3 +140,20 @@ struct cats_2d_array_double *translate_habitat(const struct cats_2d_array_double
return result;
}
+
+
+double get_overlay_cc_multiplier(const struct cats_configuration *conf, cats_dt_coord row, cats_dt_coord col)
+{
+
+ if (!conf->overlays.overlay[OL_HABITAT_TYPE_CC].enabled) {
+ return 1.0;
+ }
+
+ double multiplier = load_input_2d_array_double(conf->overlays.habitat_cc, row, col);
+
+ if (multiplier <= 0.0) {
+ return 0.0;
+ }
+
+ return multiplier;
+}
\ No newline at end of file
diff --git a/src/cats/overlays/overlay_habitat_type_cc.h b/src/cats/overlays/overlay_habitat_type_cc.h
index c355afb..89b2997 100644
--- a/src/cats/overlays/overlay_habitat_type_cc.h
+++ b/src/cats/overlays/overlay_habitat_type_cc.h
@@ -26,6 +26,7 @@
#include <stdint.h>
#include "../../memory/arrays.h"
+#include "configuration/configuration.h"
#define MAX_HABITAT_TYPE_CODES 1024
@@ -43,4 +44,6 @@ struct cats_2d_array_double *translate_habitat(const struct cats_2d_array_double
struct habitat_layer_cc_aux *load_habitat_layer_cc_aux(const char *csv_file, double default_value);
+double get_overlay_cc_multiplier(const struct cats_configuration *conf, cats_dt_coord row, cats_dt_coord col);
+
#endif //CATS_OVERLAY_HABITAT_TYPE_CC_H
diff --git a/src/cats/populations/carrying_capacity.c b/src/cats/populations/carrying_capacity.c
index a285ee5..1e45bca 100644
--- a/src/cats/populations/carrying_capacity.c
+++ b/src/cats/populations/carrying_capacity.c
@@ -28,6 +28,7 @@
#include "plants/juveniles.h"
#include "inline_overlays.h"
#include "inline_population.h"
+#include "overlays/overlay_habitat_type_cc.h"
void
@@ -57,12 +58,9 @@ get_carrying_capacity(const struct cats_grid *grid, cats_dt_coord row, cats_dt_c
// if we have an exclusion mask AND it is set the CC is 0
if (cell_excluded_by_overlay(conf, row, col)) { return 0; }
- double multiplier = 1.0;
+ double multiplier = get_overlay_cc_multiplier(conf, row, col);
+ if (multiplier <= 0.0) { return 0; }
- if (conf->overlays.overlay[OL_HABITAT_TYPE_CC].enabled) {
- multiplier *= conf->overlays.habitat_cc->data[row][col];
- if (multiplier <= 0.0) { return 0; }
- }
cats_dt_rates cc;
diff --git a/src/cats/vital_rates/direct_functions.c b/src/cats/vital_rates/direct_functions.c
index a421048..1599ad0 100644
--- a/src/cats/vital_rates/direct_functions.c
+++ b/src/cats/vital_rates/direct_functions.c
@@ -45,7 +45,8 @@ cats_dt_rates get_direct_rate(const struct cats_vital_rate *rate_info,
log_message(LOG_ERROR, "%s: wrong environment set type for set '%s'", __func__, set->name);
exit(EXIT_FAILURE);
}
- cats_dt_rates rate = set->environments[0]->current.values[row][col] * rate_info->environment_multiplier;
+ cats_dt_environment value = load_input_environment_raster(&set->environments[0]->current, row, col);
+ cats_dt_rates rate = value * rate_info->environment_multiplier;
if (isnan(rate)) return 0.0f;
cats_dt_rates dens_multiplier = density_multiplier(density_type, N, K, rate_info->density_ts);
diff --git a/src/cats/vital_rates/glm_functions.c b/src/cats/vital_rates/glm_functions.c
index 60a9c3e..0be349a 100644
--- a/src/cats/vital_rates/glm_functions.c
+++ b/src/cats/vital_rates/glm_functions.c
@@ -45,13 +45,13 @@ cats_dt_rates get_glm(const struct cats_vital_rate *rate_info,
if (set->glm.type == GLM_QUADRATIC) {
for (int32_t i = 0; i < set->count; i++) {
- const cats_dt_rates predictor = set->environments[i]->current.values[row][col];
+ const cats_dt_rates predictor = load_input_environment_raster(&set->environments[i]->current, row, col);
result += predictor * set->glm.linear[i] + predictor * predictor * set->glm.quadratic[i];
}
} else if (set->glm.type == GLM_LINEAR) {
for (int32_t i = 0; i < set->count; i++) {
- const cats_dt_rates predictor = set->environments[i]->current.values[row][col];
+ const cats_dt_rates predictor = load_input_environment_raster(&set->environments[i]->current, row, col);
result += predictor * set->glm.linear[i];
}
} else {
--
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