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fix ode-energy-sample and clean/fix librr stuff #361

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ac2cf48
fix ode-energy-sample and clean/fix librr stuff
drbergman Feb 11, 2025
6d8ab2d
make sure to validate every librr model
drbergman Feb 12, 2025
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242 changes: 32 additions & 210 deletions addons/libRoadrunner/src/librr_intracellular.cpp
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21 changes: 3 additions & 18 deletions addons/libRoadrunner/src/librr_intracellular.h
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Expand Up @@ -26,47 +26,32 @@ class RoadRunnerIntracellular : public PhysiCell::Intracellular
{
private:
public:

// static long counter;

std::string sbml_filename;
// bool enabled = false;


int num_rows_result_table = 1;

// double time_step = 12;
// bool discrete_time = false;
// double time_tick = 0.5;
// double scaling = 1.0;

// std::map<std::string, double> initial_values;
std::map<std::string, double> parameters;
std::map<std::string, std::string> substrate_species;
std::map<std::string, std::string> custom_data_species;
std::map<std::string, std::string> phenotype_species;
std::map<std::string, int> species_result_column_index;

// rrc::RRHandle rrHandle = createRRInstance();
rrc::RRHandle rrHandle;
// rrc::RRHandle rrHandle;
// rrc::RRVectorPtr vptr;
rrc::RRCDataPtr result = 0; // start time, end time, and number of points

double next_librr_run = 0;
double update_time_step = 0.01;
double previous_update_time = 0.0;
double next_librr_run = 0.0;

RoadRunnerIntracellular();

RoadRunnerIntracellular(pugi::xml_node& node);

RoadRunnerIntracellular(RoadRunnerIntracellular* copy);

// rwh: review this
Intracellular* clone()
{
// return static_cast<Intracellular*>(new RoadRunnerIntracellular(this));
RoadRunnerIntracellular* clone = new RoadRunnerIntracellular(this);
clone->sbml_filename = this->sbml_filename;
clone->substrate_species = this->substrate_species;
clone->phenotype_species = this->phenotype_species;
clone->custom_data_species = this->custom_data_species;
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6 changes: 2 additions & 4 deletions core/PhysiCell_cell.cpp
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Expand Up @@ -3144,18 +3144,16 @@ Cell_Definition* initialize_cell_definition_from_pugixml( pugi::xml_node cd_node
// If it has already be copied
if (pParent != NULL && pParent->phenotype.intracellular != NULL)
{
// std::cout << "------ " << __FUNCTION__ << ": copying another\n";
pCD->phenotype.intracellular->initialize_intracellular_from_pugixml(node);
}
// Otherwise we need to create a new one
else
{
std::cout << "\n------ " << __FUNCTION__ << ": creating new RoadRunnerIntracellular\n";
RoadRunnerIntracellular* pIntra = new RoadRunnerIntracellular(node);
pCD->phenotype.intracellular = pIntra->getIntracellularModel();
pCD->phenotype.intracellular->validate_PhysiCell_tokens(pCD->phenotype);
pCD->phenotype.intracellular->validate_SBML_species();
}
pCD->phenotype.intracellular->validate_PhysiCell_tokens(pCD->phenotype);
pCD->phenotype.intracellular->validate_SBML_species();
}
#endif

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8 changes: 6 additions & 2 deletions core/PhysiCell_cell_container.cpp
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Expand Up @@ -149,12 +149,16 @@ void Cell_Container::update_all_cells(double t, double phenotype_dt_ , double me
if( (*all_cells)[i]->phenotype.intracellular != NULL && (*all_cells)[i]->phenotype.intracellular->need_update())
{
if ((*all_cells)[i]->functions.pre_update_intracellular != NULL)
(*all_cells)[i]->functions.pre_update_intracellular( (*all_cells)[i], (*all_cells)[i]->phenotype , diffusion_dt_ );
{
(*all_cells)[i]->functions.pre_update_intracellular((*all_cells)[i], (*all_cells)[i]->phenotype, diffusion_dt_);
}

(*all_cells)[i]->phenotype.intracellular->update( (*all_cells)[i], (*all_cells)[i]->phenotype , diffusion_dt_ );

if ((*all_cells)[i]->functions.post_update_intracellular != NULL)
(*all_cells)[i]->functions.post_update_intracellular( (*all_cells)[i], (*all_cells)[i]->phenotype , diffusion_dt_ );
{
(*all_cells)[i]->functions.post_update_intracellular((*all_cells)[i], (*all_cells)[i]->phenotype, diffusion_dt_);
}
}
}
}
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5 changes: 3 additions & 2 deletions sample_projects_intracellular/ode/ode_energy/config/PhysiCell_settings.xml
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Expand Up @@ -90,7 +90,8 @@
<max_time units="min">1440</max_time> <!-- 1 days * 24 h * 60 min -->
<time_units>min</time_units>
<space_units>micron</space_units>


<dt_intracellular units="min">0.01</dt_intracellular>
<dt_diffusion units="min">0.01</dt_diffusion>
<dt_mechanics units="min">0.1</dt_mechanics>
<dt_phenotype units="min">6</dt_phenotype>
Expand Down Expand Up @@ -307,7 +308,7 @@

<intracellular type="roadrunner">
<sbml_filename>./config/Toy_Metabolic_Model.xml</sbml_filename>
<intracellular_dt>0.01</intracellular_dt>
<intracellular_dt>0.1</intracellular_dt>
<map PC_substrate="oxygen" sbml_species="Oxygen"></map >
<map PC_substrate="lactate" sbml_species="Lactate"></map >
<map PC_substrate="glucose" sbml_species="Glucose"></map >
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96 changes: 41 additions & 55 deletions sample_projects_intracellular/ode/ode_energy/custom_modules/custom.cpp
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Expand Up @@ -179,80 +179,66 @@ void setup_tissue( void )
set_single_behavior( pCell , "custom:intra_lac" , parameters.doubles("initial_internal_lactate"));
set_single_behavior( pCell , "custom:intra_energy" , parameters.doubles("initial_energy"));

/* pCell->custom_data[i_Oxy_i] = parameters.doubles("initial_internal_oxygen");
pCell->custom_data[i_Glu_i] = parameters.doubles("initial_internal_glucose");
pCell->custom_data[i_Lac_i] = parameters.doubles("initial_internal_lactate");
pCell->custom_data[energy_vi] = parameters.doubles("initial_energy"); */

double cell_volume = pCell->phenotype.volume.total;

//std::cout << "oxygen custom data : " << pCell->custom_data[i_Oxy_i] << std::endl;
//std::cout << "oxygen custom data : SIGNAL" << get_single_signal( pCell, "custom:intra_oxy") << std::endl;


set_single_behavior( pCell , "custom:intra_oxy" , parameters.doubles("initial_internal_oxygen"));


pCell->phenotype.molecular.internalized_total_substrates[oxygen_substrate_index]= get_single_signal( pCell, "custom:intra_oxy") * cell_volume;
pCell->phenotype.molecular.internalized_total_substrates[glucose_substrate_index]= get_single_signal( pCell, "custom:intra_glu") * cell_volume;
pCell->phenotype.molecular.internalized_total_substrates[lactate_substrate_index]= get_single_signal( pCell, "custom:intra_lac") * cell_volume;
pCell->phenotype.intracellular->start();
(*all_cells)[i]->phenotype.intracellular->set_parameter_value("Energy",get_single_signal( pCell, "custom:intra_energy"));

pCell->phenotype.intracellular->set_parameter_value("Energy",get_single_signal( pCell, "custom:intra_energy"));

pCell->functions.pre_update_intracellular = pre_update_intracellular;
pCell->functions.post_update_intracellular = post_update_intracellular;
}

return;
}

void update_intracellular()
void pre_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt )
{
// BioFVM Indices
static int oxygen_substrate_index = microenvironment.find_density_index( "oxygen" );
static int glucose_substrate_index = microenvironment.find_density_index( "glucose" );
static int lactate_substrate_index = microenvironment.find_density_index( "lactate");

#pragma omp parallel for
for( int i=0; i < (*all_cells).size(); i++ )
{
if( (*all_cells)[i]->is_out_of_domain == false )
{
// Cell Volume
double cell_volume = (*all_cells)[i]->phenotype.volume.total;

// Get Intracellular Concentrations
double oxy_val_int = get_single_signal((*all_cells)[i], "intracellular oxygen");
double glu_val_int = get_single_signal((*all_cells)[i], "intracellular glucose");
double lac_val_int = get_single_signal((*all_cells)[i], "intracellular lactate");

// Update SBML
(*all_cells)[i]->phenotype.intracellular->set_parameter_value("Oxygen",oxy_val_int);
(*all_cells)[i]->phenotype.intracellular->set_parameter_value("Glucose",glu_val_int);
(*all_cells)[i]->phenotype.intracellular->set_parameter_value("Lactate",lac_val_int);

// SBML Simulation
(*all_cells)[i]->phenotype.intracellular->update();

// Phenotype Simulation
(*all_cells)[i]->phenotype.intracellular->update_phenotype_parameters((*all_cells)[i]->phenotype);

// Internalized Chemical Update After SBML Simulation
(*all_cells)[i]->phenotype.molecular.internalized_total_substrates[oxygen_substrate_index] = (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Oxygen") * cell_volume;
(*all_cells)[i]->phenotype.molecular.internalized_total_substrates[glucose_substrate_index] = (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Glucose") * cell_volume;
(*all_cells)[i]->phenotype.molecular.internalized_total_substrates[lactate_substrate_index] = (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Lactate") * cell_volume;


//Save custom data
set_single_behavior( (*all_cells)[i] , "custom:intra_oxy" , (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Oxygen") );
set_single_behavior( (*all_cells)[i] , "custom:intra_glu" , (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Glucose") );
set_single_behavior( (*all_cells)[i] , "custom:intra_lac" , (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Lactate") );
set_single_behavior( (*all_cells)[i] , "custom:intra_energy" , (*all_cells)[i]->phenotype.intracellular->get_parameter_value("Energy") );

}
}

// Cell Volume
double cell_volume = pCell->phenotype.volume.total;

// Get Intracellular Concentrations
double oxy_val_int = get_single_signal(pCell, "intracellular oxygen");
double glu_val_int = get_single_signal(pCell, "intracellular glucose");
double lac_val_int = get_single_signal(pCell, "intracellular lactate");

// Update SBML
pCell->phenotype.intracellular->set_parameter_value("Oxygen",oxy_val_int);
pCell->phenotype.intracellular->set_parameter_value("Glucose",glu_val_int);
pCell->phenotype.intracellular->set_parameter_value("Lactate",lac_val_int);
}

void post_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt )
{
// BioFVM Indices
static int oxygen_substrate_index = microenvironment.find_density_index( "oxygen" );
static int glucose_substrate_index = microenvironment.find_density_index( "glucose" );
static int lactate_substrate_index = microenvironment.find_density_index( "lactate");

// Cell Volume
double cell_volume = pCell->phenotype.volume.total;

// Phenotype Simulation
pCell->phenotype.intracellular->update_phenotype_parameters(pCell->phenotype);

// Internalized Chemical Update After SBML Simulation
pCell->phenotype.molecular.internalized_total_substrates[oxygen_substrate_index] = pCell->phenotype.intracellular->get_parameter_value("Oxygen") * cell_volume;
pCell->phenotype.molecular.internalized_total_substrates[glucose_substrate_index] = pCell->phenotype.intracellular->get_parameter_value("Glucose") * cell_volume;
pCell->phenotype.molecular.internalized_total_substrates[lactate_substrate_index] = pCell->phenotype.intracellular->get_parameter_value("Lactate") * cell_volume;


//Save custom data
set_single_behavior( pCell , "custom:intra_oxy" , pCell->phenotype.intracellular->get_parameter_value("Oxygen") );
set_single_behavior( pCell , "custom:intra_glu" , pCell->phenotype.intracellular->get_parameter_value("Glucose") );
set_single_behavior( pCell , "custom:intra_lac" , pCell->phenotype.intracellular->get_parameter_value("Lactate") );
set_single_behavior( pCell , "custom:intra_energy" , pCell->phenotype.intracellular->get_parameter_value("Energy") );
}

std::vector<std::string> my_coloring_function( Cell* pCell )
{
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8 changes: 2 additions & 6 deletions sample_projects_intracellular/ode/ode_energy/custom_modules/custom.h
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Expand Up @@ -82,12 +82,8 @@ void setup_microenvironment( void );
// custom pathology coloring function

std::vector<std::string> my_coloring_function( Cell* );
void update_intracellular();
void pre_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt );
void post_update_intracellular( Cell* pCell, Phenotype& phenotype, double dt );

// custom functions can go here

void predator_hunting_function( Cell* pCell, Phenotype& phenotype, double dt );
void predator_cycling_function( Cell* pCell, Phenotype& phenotype, double dt );

void prey_cycling_function( Cell* pCell , Phenotype& phenotype, double dt );
std::vector<std::vector<double>> create_cell_circle_positions(double cell_radius, double sphere_radius);
27 changes: 0 additions & 27 deletions sample_projects_intracellular/ode/ode_energy/main.cpp
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Expand Up @@ -161,14 +161,6 @@ int main( int argc, char* argv[] )
report_file<<"simulated time\tnum cells\tnum division\tnum death\twall time"<<std::endl;
}

//
double intracellular_dt = 0.01;
double last_intracellular_time = 0.0;
double intracellular_dt_tolerance = 0.001 * intracellular_dt;
double next_intracellular_update = intracellular_dt;



// main loop

try
Expand Down Expand Up @@ -211,32 +203,13 @@ int main( int argc, char* argv[] )
// update the microenvironment
microenvironment.simulate_diffusion_decay( diffusion_dt );


/* double dt_intracellular = 1.0;
//std::cout << "Current_Time : " << PhysiCell_globals.current_time << " - FMOD : " << fmod(PhysiCell_globals.current_time,1.0) << std::endl;
if ( fabs((fmod (PhysiCell_globals.current_time, dt_intracellular) - 1 )) < 0.001 || (fmod (PhysiCell_globals.current_time, dt_intracellular) < 0.00001) )
{
std::cout << "DIVIDED" <<std::endl;
} */

// run PhysiCell
((Cell_Container *)microenvironment.agent_container)->update_all_cells( PhysiCell_globals.current_time );

/*
Custom add-ons could potentially go here.
*/

double time_since_last_intracellular = PhysiCell_globals.current_time - last_intracellular_time;

//update_intracellular();

if( PhysiCell_globals.current_time >= next_intracellular_update )
{
update_intracellular();

next_intracellular_update += intracellular_dt;
}

PhysiCell_globals.current_time += diffusion_dt;
}

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