Add 'custom_functions' files

src/domains_library/custom_functions.c

@@ -0,0 +1,136 @@
+//
+// Created by bergolho and jennyhelyanwe on 03/06/24.
+//
+
+#include "domain_helpers.h"
+
+#include "../3dparty/sds/sds.h"
+#include "../3dparty/stb_ds.h"
+#include "../config/domain_config.h"
+#include "../config_helpers/config_helpers.h"
+#include "../libraries_common/common_data_structures.h"
+#include "../logger/logger.h"
+#include "../utils/stop_watch.h"
+#include "../utils/utils.h"
+#include <assert.h>
+#include <time.h>
+
+#include "mesh_info_data.h"
+#include "custom_mesh_info_data.h"
+
+#include <float.h>
+#include <unistd.h>
+
+SET_CUSTOM_DATA_FOR_MESH(set_custom_data_for_dti_mesh_with_dense_and_sparse_regions_twave) {
+
+    INITIALIZE_DTI_MESH_INFO(cell);
+
+    // Ruben mesh labels (transmuralityLabels): 1=ENDO, 2=MID, 3=EPI
+    // Dense/Sparse regions (DenseSparseRegion): 1=NORMAL, 2=DENSE, 3=SPARSE
+    // Cellular model labels: 0=ENDO, 1=MID, 2=EPI, 3=DENSE, 4=SPARSE
+    DTI_MESH_TRANSMURALITY(cell) = custom_data[0];
+    DTI_MESH_TRANSMURALITY_LABELS(cell) = custom_data[1]-1;
+    DTI_MESH_BASE_APEX_HETEROGENEITY(cell) = custom_data[2];
+    DTI_MESH_FAST_ENDO(cell) = (int)custom_data[3];
+
+    cell->sigma.fibers.f[0] = custom_data[5];
+    cell->sigma.fibers.f[1] = custom_data[6];
+    cell->sigma.fibers.f[2] = custom_data[7];
+
+    cell->sigma.fibers.s[0] = custom_data[8];
+    cell->sigma.fibers.s[1] = custom_data[9];
+    cell->sigma.fibers.s[2] = custom_data[10];
+
+    cell->sigma.fibers.n[0] = custom_data[11];
+    cell->sigma.fibers.n[1] = custom_data[12];
+    cell->sigma.fibers.n[2] = custom_data[13];
+
+    DTI_MESH_SCALE_FACTOR_IKS(cell) = custom_data[14];
+}
+
+// Domain function to load the ALG file
+// Works with all DTI meshes (T-wave personalisation) - Fiber orientation, transmurality, dense/sparse regions 
+// and scale factor for IKs (resolution = 500um)
+SET_SPATIAL_DOMAIN(initialize_grid_with_dti_mesh_with_dense_and_sparse_regions_twave) {
+
+    char *mesh_file = NULL;
+    GET_PARAMETER_STRING_VALUE_OR_REPORT_ERROR(mesh_file, config, "mesh_file");
+
+    real_cpu start_h = 500.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real_cpu, start_h, config, "original_discretization");
+
+    real_cpu desired_h = 500.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real_cpu, desired_h, config, "desired_discretization");
+
+    assert(the_grid);
+
+    log_info("DTI Mesh with discretization: %lf\n", desired_h);
+
+    uint32_t num_volumes = 0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(uint32_t, num_volumes, config, "num_volumes");
+
+    // ALG mesh column config:
+    // center_x, center_y, center_z, dx, dy, dz, transmurality, transmurality_label, base_to_apex, dense_sparse_region_tag, fibrotic, fx, fy, fz, sx, sy, sz, nx, ny, nz, sf_IKs  
+    uint32_t num_extra_fields = 15;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(uint32_t, num_extra_fields, config, "num_extra_fields");
+
+    int num_loaded = set_custom_mesh_from_file(the_grid, mesh_file, num_volumes, start_h, num_extra_fields, set_custom_data_for_dti_mesh_with_dense_and_sparse_regions_twave);
+
+    log_info("Read %d volumes from file (expected %d): %s\n", num_loaded, num_volumes, mesh_file);
+
+    int num_refs_remaining = (int)(start_h / desired_h) - 1;
+
+    if(num_refs_remaining > 0) {
+        refine_grid(the_grid, num_refs_remaining);
+    }
+
+    the_grid->start_discretization = SAME_POINT3D(desired_h);
+
+    free(mesh_file);
+
+    return num_loaded;
+}
+
+SET_SPATIAL_DOMAIN(initialize_grid_with_dti_mesh_with_dense_and_sparse_regions_twave_mesh_number) {
+
+	char *mesh_directory = NULL;
+	GET_PARAMETER_STRING_VALUE_OR_REPORT_ERROR(mesh_directory, config, "mesh_directory");
+	int mesh_number = 0;
+	GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(int, mesh_number, config, "mesh_number");
+
+    real_cpu start_h = 500.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real_cpu, start_h, config, "original_discretization");
+
+    real_cpu desired_h = 500.0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(real_cpu, desired_h, config, "desired_discretization");
+
+    assert(the_grid);
+
+    log_info("DTI Mesh with discretization: %lf\n", desired_h);
+
+	char mesh_file[500];
+	sprintf(mesh_file,"%s/%d.alg", mesh_directory, mesh_number);
+    uint32_t num_volumes = 0;
+    GET_PARAMETER_NUMERIC_VALUE_OR_REPORT_ERROR(uint32_t, num_volumes, config, "num_volumes");
+
+    // ALG mesh column config:
+    // center_x, center_y, center_z, dx, dy, dz, transmurality, transmurality_label, base_to_apex, dense_sparse_region_tag, fibrotic, fx, fy, fz, sx, sy, sz, nx, ny, nz, sf_IKs  
+    uint32_t num_extra_fields = 15;
+    GET_PARAMETER_NUMERIC_VALUE_OR_USE_DEFAULT(uint32_t, num_extra_fields, config, "num_extra_fields");
+
+    int num_loaded = set_custom_mesh_from_file(the_grid, mesh_file, num_volumes, start_h, num_extra_fields, set_custom_data_for_dti_mesh_with_dense_and_sparse_regions_twave);
+
+    log_info("Read %d volumes from file (expected %d): %s\n", num_loaded, num_volumes, mesh_file);
+
+    int num_refs_remaining = (int)(start_h / desired_h) - 1;
+
+    if(num_refs_remaining > 0) {
+        refine_grid(the_grid, num_refs_remaining);
+    }
+
+    the_grid->start_discretization = SAME_POINT3D(desired_h);
+
+    free(mesh_file);
+
+    return num_loaded;
+}

src/domains_library/custom_mesh_info_data.h

@@ -0,0 +1,9 @@
+#ifndef __CUSTOM_MESH_INFO_DATA_H
+#define __CUSTOM_MESH_INFO_DATA_H 
+
+#include <stdbool.h>
+#include "../common_types/common_types.h"
+
+
+
+#endif /* __CUSTOM_MESH_INFO_DATA_H */

src/extra_data_library/custom_functions.c

@@ -0,0 +1,40 @@
+//
+// Created by bergolho and jennyhelyanwe on 03/06/24.
+//
+
+#include <unistd.h>
+
+#include "../config/extra_data_config.h"
+#include "../config_helpers/config_helpers.h"
+#include "../libraries_common/common_data_structures.h"
+#include "../domains_library/mesh_info_data.h"
+#include "../domains_library/custom_mesh_info_data.h"
+#include "../logger/logger.h"
+#include "helper_functions.h"
+
+// Extra data function to configure the transmurality and IKs scaling factor
+// Works with all DTI meshes - Extra data function to load the ToRORd cellular model with modifications
+// Function used for the T-wave personalisation paper.
+SET_EXTRA_DATA(set_extra_data_for_dti_mesh_twave_with_torord_gksgkrtjca) {
+
+	uint32_t num_active_cells = the_grid->num_active_cells;
+	struct cell_node ** ac = the_grid->active_cells;
+
+	struct extra_data_for_torord_gksgkrtjca_twave *extra_data = NULL;
+	extra_data = set_common_torord_gksgkrtjca_twave_data(config, num_active_cells);		// ToRORd used for T-wave personalisation
+
+	// Ruben mesh labels (transmuralityLabels): 1=ENDO, 2=MID, 3=EPI
+    // Dense/Sparse regions (DenseSparseRegion): 1=NORMAL, 2=DENSE, 3=SPARSE
+    // Cellular model labels: 0=ENDO, 1=MID, 2=EPI, 3=DENSE, 4=SPARSE
+	OMP(parallel for)
+	for (int i = 0; i < num_active_cells; i++) {
+		real tag = DTI_MESH_TRANSMURALITY_LABELS(ac[i]);
+        real sf_IKs = DTI_MESH_SCALE_FACTOR_IKS(ac[i]);
+		extra_data->transmurality[i] = tag;
+        extra_data->sf_IKs[i] = sf_IKs;
+	}
+
+	SET_EXTRA_DATA_SIZE(sizeof(struct extra_data_for_torord_gksgkrtjca_twave));
+
+	return (void*)extra_data;
+}