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Merge pull request #71 from bergolho/master
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Add new scripts/New ToRORd model variant/New option to save the Purkinje on the Ensight save mesh function
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@rsachetto
rsachetto authored Jun 10, 2024
2 parents 708f28a + cd6a2d3 commit 201b6f7
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Showing 25 changed files with 3,593 additions and 149 deletions.
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -186,6 +186,7 @@ sync_local.sh
sync_outputs.sh
private_configs/
private_parameter_sets/
private_src/
/src/domains_library/custom_mesh_info_data.h
retired_code/
*.gcno
Expand All @@ -199,3 +200,4 @@ VV_49900.dat
*.build_type*
/ecg.txt
__pycache__/
backup/
0 ...le_mesh_with_ToRORd_Land_endo_mid_epi.ini → ...figs/cable_mesh_with_ToRORd_Land_endo.ini
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2 changes: 1 addition & 1 deletion example_configs/cable_mesh_with_ToRORd_fkatp_endo_mid_epi.ini
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Expand Up @@ -76,4 +76,4 @@ x_limit = 500.0
main_function=stim_if_x_less_than

[extra_data]
main_function=set_extra_data_mixed_torord_fkatp_epi_mid_endo
main_function=set_extra_data_mixed_torord_fkatp_epi_mid_endo
4 changes: 4 additions & 0 deletions scripts/error_calculator/main.cpp
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Expand Up @@ -71,6 +71,10 @@ int main (int argc, char *argv[])
cerr << "[-] ERROR! The number of cells are different" << endl;
exit(EXIT_FAILURE);
}
else
{
cout << "[+] Cell number are equal " << total_num_cells_1 << " " << total_num_cells_2 << endl;
}

vtkSmartPointer<vtkFloatArray> array_1 =
vtkFloatArray::SafeDownCast(unstructured_grid_1->GetCellData()->GetArray(array_name.c_str()));
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62 changes: 35 additions & 27 deletions scripts/evaluateBenchmarkCV/main.cpp
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
// Author: Lucas Berg
// ------------------------------------------------------------------------------------
// Author: Lucas Berg, Julia Camps and Jenny Wang
// Script to evaluate the conductivities calibrated using the 'tuneCV' on a 3D wedge.
// ------------------------------------------------------------------------------------

#include <iostream>
#include <string>
Expand Down Expand Up @@ -27,8 +30,12 @@

using namespace std;

double* calculate_conduction_velocity_from_benchmark_simulation ()
{
// Change your MonoAlg3D path here:
// ----------------------------------------------------------
const char MONOALG_PATH[500] = "/home/berg/Github/MonoAlg3D_C";
// ----------------------------------------------------------

double* calculate_conduction_velocity_from_benchmark_simulation () {
string filename = "outputs/benchmark/tissue_activation_time_map_pulse_it_0.vtu";

// Read all the data from the file
Expand Down Expand Up @@ -93,8 +100,7 @@ double* calculate_conduction_velocity_from_benchmark_simulation ()
double cv_y = -1.0;
double cv_z = -1.0;

if(array)
{
if(array) {

double delta_lat_x = (array->GetValue(cellId_x_1) - array->GetValue(cellId_x_0)); // ms
double delta_lat_y = (array->GetValue(cellId_y_1) - array->GetValue(cellId_y_0)); // ms
Expand All @@ -109,8 +115,7 @@ double* calculate_conduction_velocity_from_benchmark_simulation ()
cv_y = (delta_s_y / delta_lat_y)*0.001; // {m/s}
cv_z = (delta_s_z / delta_lat_z)*0.001; // {m/s}
}
else
{
else {
cerr << "[!] ERROR! No Scalar_value found for the points!" << endl;
exit(EXIT_FAILURE);
}
Expand All @@ -126,31 +131,33 @@ double* calculate_conduction_velocity_from_benchmark_simulation ()
// TODO: Maybe pass a pre-configured config file as an input parameter with the cellular model setup that the user will use
void write_configuration_file (const double sigma_x, const double sigma_y, const double sigma_z)
{
FILE *file = fopen("/home/Julia/MonoAlg3D_C/scripts/evaluateBenchmarkCV/configs/benchmark.ini","w+");
char filename[500];
sprintf(filename,"%s/scripts/evaluateBenchmarkCV/configs/benchmark.ini",MONOALG_PATH);
FILE *file = fopen(filename,"w+");

fprintf(file,"[main]\n");
fprintf(file,"num_threads=6\n");
fprintf(file,"dt_pde=0.01\n");
fprintf(file,"simulation_time=50.0\n"); // CAREFUL DON'T USE A VALUE THAT'S TOO SMALL!
fprintf(file,"simulation_time=100.0\n"); // CAREFUL DON'T USE A VALUE THAT'S TOO SMALL!
fprintf(file,"abort_on_no_activity=false\n");
fprintf(file,"use_adaptivity=false\n");
fprintf(file,"quiet=true\n");
fprintf(file,"\n");

fprintf(file,"[update_monodomain]\n");
fprintf(file,"main_function=update_monodomain_default\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_update_monodomain.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_update_monodomain.so\n",MONOALG_PATH);
fprintf(file,"\n");

// For saving the LATs in a format that can be read for calculating the CVs
fprintf(file,"[save_result]\n");
fprintf(file,"print_rate=1\n");
fprintf(file,"output_dir=/home/Julia/MonoAlg3D_C/scripts/evaluateBenchmarkCV/outputs/benchmark\n");
fprintf(file,"output_dir=%s/scripts/evaluateBenchmarkCV/outputs/benchmark\n",MONOALG_PATH);
fprintf(file,"save_pvd=true\n");
fprintf(file,"file_prefix=V\n");
fprintf(file,"save_activation_time=true\n");
fprintf(file,"save_apd=false\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_save_mesh_purkinje.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_save_mesh_purkinje.so\n",MONOALG_PATH);
fprintf(file,"main_function=save_tissue_with_activation_times\n");
fprintf(file,"init_function=init_save_tissue_with_activation_times\n");
fprintf(file,"end_function=end_save_tissue_with_activation_times\n");
Expand All @@ -161,10 +168,10 @@ void write_configuration_file (const double sigma_x, const double sigma_y, const
// For saving the VMs for debugging
fprintf(file,"[save_result]\n");
fprintf(file,"print_rate=100\n");
fprintf(file,"output_dir=/home/Julia/MonoAlg3D_C/scripts/evaluateBenchmarkCV/outputs/benchmark\n");
fprintf(file,"output_dir=%s/scripts/evaluateBenchmarkCV/outputs/benchmark\n",MONOALG_PATH);
fprintf(file,"add_timestamp=false\n");
fprintf(file,"binary=true\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_save_mesh.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_save_mesh.so\n",MONOALG_PATH);
fprintf(file,"main_function=save_as_ensight\n");
fprintf(file,"remove_older_simulation=true\n");
fprintf(file,"\n");
Expand All @@ -175,7 +182,7 @@ void write_configuration_file (const double sigma_x, const double sigma_y, const
fprintf(file,"sigma_x=%g\n",sigma_x);
fprintf(file,"sigma_y=%g\n",sigma_y);
fprintf(file,"sigma_z=%g\n",sigma_z);
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_matrix_assembly.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_matrix_assembly.so\n",MONOALG_PATH);
fprintf(file,"main_function=homogeneous_sigma_assembly_matrix\n");
fprintf(file,"\n");

Expand All @@ -184,7 +191,7 @@ void write_configuration_file (const double sigma_x, const double sigma_y, const
fprintf(file,"use_preconditioner=no\n");
fprintf(file,"use_gpu=yes\n");
fprintf(file,"max_iterations=200\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_linear_system_solver.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_linear_system_solver.so\n",MONOALG_PATH);
fprintf(file,"init_function=init_conjugate_gradient\n");
fprintf(file,"end_function=end_conjugate_gradient\n");
fprintf(file,"main_function=conjugate_gradient\n");
Expand All @@ -194,7 +201,7 @@ void write_configuration_file (const double sigma_x, const double sigma_y, const
fprintf(file,"name=N-Version Benchmark\n");
fprintf(file,"start_discretization=500.0\n");
fprintf(file,"maximum_discretization=500.0\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_domains.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_domains.so\n",MONOALG_PATH);
fprintf(file,"main_function=initialize_grid_with_benchmark_mesh\n");
fprintf(file,"side_length_x=20000\n");
fprintf(file,"side_length_y=10000\n");
Expand All @@ -205,7 +212,7 @@ void write_configuration_file (const double sigma_x, const double sigma_y, const
fprintf(file,"dt=0.01\n");
fprintf(file,"use_gpu=yes\n");
fprintf(file,"gpu_id=0\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libToRORd_fkatp_mixed_endo_mid_epi.so\n");
fprintf(file,"library_file=%s/shared_libs/libToRORd_fkatp_mixed_endo_mid_epi_GKsGKrtjca_adjustments.so\n",MONOALG_PATH);
fprintf(file,"\n");

fprintf(file,"[stim_benchmark]\n");
Expand All @@ -219,26 +226,25 @@ void write_configuration_file (const double sigma_x, const double sigma_y, const
fprintf(file, "min_z = 0.0\n");
fprintf(file, "max_z = 3000.0\n");
fprintf(file,"main_function=stim_x_y_z_limits\n");
fprintf(file,"library_file=/home/Julia/MonoAlg3D_C/shared_libs/libdefault_stimuli.so\n");
fprintf(file,"library_file=%s/shared_libs/libdefault_stimuli.so\n",MONOALG_PATH);
fprintf(file,"\n");

fclose(file);
}

int main (int argc, char *argv[])
{
if (argc-1 != 6)
{
int main (int argc, char *argv[]) {
if (argc-1 != 6) {
cerr << "=============================================================================" << endl;
cerr << "Usage:> " << argv[0] << " <target_cv_x>" << " <target_cv_y>" << " <target_cv_z>" << \
" <sigma_x>" << " <sigma_y>" << " <sigma_z>" << endl;
cerr << "=============================================================================" << endl;
cerr << "<target_CV> = Target conduction velocity in m/s" << endl;
cerr << "<sigma> = Target conductivity in mS/um" << endl;
cerr << "=============================================================================" << endl;
cerr << "Example:" << endl;
cerr << argv[1] << " 0.67 (Longitudinal normal direction ventricle)" << endl;
cerr << argv[2] << " 0.33 (Transversal normal direction ventricle)" << endl;
cerr << argv[3] << " 0.17 (Sheet normal direction ventricle)" << endl;
cerr << argv[1] << " 0.65 (Longitudinal direction ventricle)" << endl;
cerr << argv[2] << " 0.39 (Transversal direction ventricle)" << endl;
cerr << argv[3] << " 0.48 (Normal direction ventricle)" << endl;
cerr << "=============================================================================" << endl;

exit(EXIT_FAILURE);
Expand All @@ -255,7 +261,9 @@ int main (int argc, char *argv[])
write_configuration_file(sigma_x, sigma_y, sigma_z);

// Run the simulation
system("/home/Julia/MonoAlg3D_C/bin/MonoAlg3D -c /home/Julia/MonoAlg3D_C/scripts/evaluateBenchmarkCV/configs/benchmark.ini");
char command[500];
sprintf(command,"%s/bin/MonoAlg3D -c %s/scripts/evaluateBenchmarkCV/configs/benchmark.ini",MONOALG_PATH,MONOALG_PATH);
system(command);

double* cv;
cv = calculate_conduction_velocity_from_benchmark_simulation();
Expand Down
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