biogears::BioGears Class Reference

Manages and controls execution of all data/systems in BioGears. More...

#include <BioGears.h>

Inheritance diagram for biogears::BioGears:

Public Member Functions
	BioGears (Logger *logger)
	BioGears (const std::string &logfileName)
	BioGears (Logger *logger, const std::string &working_dir)
	BioGears (const std::string &logfileName, const std::string &working_dir)
virtual	~BioGears ()
EngineState	GetState ()
const EngineState	GetState () const
DataTrack &	GetDataTrack ()
SaturationCalculator &	GetSaturationCalculator ()
const SaturationCalculator &	GetSaturationCalculator () const
DiffusionCalculator &	GetDiffusionCalculator ()
const DiffusionCalculator &	GetDiffusionCalculator () const
BioGearsSubstances &	GetSubstances ()
const BioGearsSubstances &	GetSubstances () const
SEPatient &	GetPatient ()
const SEPatient &	GetPatient () const
bool	GetPatientAssessment (SEPatientAssessment &assessment)
SEBloodChemistrySystem &	GetBloodChemistry ()
SECardiovascularSystem &	GetCardiovascular ()
SEDrugSystem &	GetDrugs ()
SEEndocrineSystem &	GetEndocrine ()
SEEnergySystem &	GetEnergy ()
SEGastrointestinalSystem &	GetGastrointestinal ()
SEHepaticSystem &	GetHepatic ()
SENervousSystem &	GetNervous ()
SERenalSystem &	GetRenal ()
SERespiratorySystem &	GetRespiratory ()
SETissueSystem &	GetTissue ()
SEEnvironment &	GetEnvironment ()
SEAnesthesiaMachine &	GetAnesthesiaMachine ()
SEElectroCardioGram &	GetECG ()
SEInhaler &	GetInhaler ()
SEActionManager &	GetActions ()
SEConditionManager &	GetConditions ()
BioGearsCircuits &	GetCircuits ()
BioGearsCompartments &	GetCompartments ()
const BioGearsConfiguration &	GetConfiguration ()
const SEScalarTime &	GetEngineTime ()
const SEScalarTime &	GetSimulationTime ()
const SEScalarTime &	GetTimeStep ()
CDM::enumBioGearsAirwayMode::value	GetAirwayMode ()
CDM::enumOnOff::value	GetIntubation ()
const SEBloodChemistrySystem &	GetBloodChemistry () const
const SECardiovascularSystem &	GetCardiovascular () const
const SEDrugSystem &	GetDrugs () const
const SEEndocrineSystem &	GetEndocrine () const
const SEEnergySystem &	GetEnergy () const
const SEGastrointestinalSystem &	GetGastrointestinal () const
const SEHepaticSystem &	GetHepatic () const
const SENervousSystem &	GetNervous () const
const SERenalSystem &	GetRenal () const
const SERespiratorySystem &	GetRespiratory () const
const SETissueSystem &	GetTissue () const
const SEEnvironment &	GetEnvironment () const
const SEAnesthesiaMachine &	GetAnesthesiaMachine () const
const SEElectroCardioGram &	GetECG () const
const SEInhaler &	GetInhaler () const
const SEActionManager &	GetActions () const
const SEConditionManager &	GetConditions () const
const BioGearsCircuits &	GetCircuits () const
const BioGearsCompartments &	GetCompartments () const
const BioGearsConfiguration &	GetConfiguration () const
const SEScalarTime &	GetEngineTime () const
const SEScalarTime &	GetSimulationTime () const
const SEScalarTime &	GetTimeStep () const
const CDM::enumBioGearsAirwayMode::value	GetAirwayMode () const
const CDM::enumOnOff::value	GetIntubation () const
bool	CreateCircuitsAndCompartments ()
void	SetIntubation (CDM::enumOnOff::value s)
void	SetAirwayMode (CDM::enumBioGearsAirwayMode::value mode)
Logger *	GetLogger () const

Protected Member Functions
void	SetupCardiovascular ()
void	SetupCerebral ()
void	SetupRenal ()
void	SetupTissue ()
void	SetupGastrointestinal ()
void	SetupRespiratory ()
void	SetupAnesthesiaMachine ()
void	SetupInhaler ()
void	SetupMechanicalVentilator ()
void	SetupExternalTemperature ()
void	SetupInternalTemperature ()
bool	Initialize (const PhysiologyEngineConfiguration *config)
bool	SetupPatient ()
void	SetUp ()
virtual void	AtSteadyState (EngineState state)
void	PreProcess ()
void	Process ()
void	PostProcess ()
void	ForwardFatal (const std::string &msg, const std::string &origin)

Protected Attributes
EngineState	m_State
DataTrack *	m_DataTrack
std::unique_ptr< SEScalarTime >	m_CurrentTime
std::unique_ptr< SEScalarTime >	m_SimulationTime
CDM::enumBioGearsAirwayMode::value	m_AirwayMode
CDM::enumOnOff::value	m_Intubation
std::unique_ptr< BioGearsConfiguration >	m_Config
std::unique_ptr< SaturationCalculator >	m_SaturationCalculator
std::unique_ptr< DiffusionCalculator >	m_DiffusionCalculator
std::unique_ptr< BioGearsSubstances >	m_Substances
std::unique_ptr< SEActionManager >	m_Actions
std::unique_ptr< SEConditionManager >	m_Conditions
std::unique_ptr< BioGearsCircuits >	m_Circuits
std::unique_ptr< BioGearsCompartments >	m_Compartments
std::unique_ptr< Environment >	m_Environment
std::unique_ptr< BloodChemistry >	m_BloodChemistrySystem
std::unique_ptr< Cardiovascular >	m_CardiovascularSystem
std::unique_ptr< Endocrine >	m_EndocrineSystem
std::unique_ptr< Energy >	m_EnergySystem
std::unique_ptr< Gastrointestinal >	m_GastrointestinalSystem
std::unique_ptr< Hepatic >	m_HepaticSystem
std::unique_ptr< Nervous >	m_NervousSystem
std::unique_ptr< Renal >	m_RenalSystem
std::unique_ptr< Respiratory >	m_RespiratorySystem
std::unique_ptr< Drugs >	m_DrugSystem
std::unique_ptr< Tissue >	m_TissueSystem
std::unique_ptr< ECG >	m_ECG
std::unique_ptr< AnesthesiaMachine >	m_AnesthesiaMachine
std::unique_ptr< Inhaler >	m_Inhaler
std::unique_ptr< SEPatient >	m_Patient
bool	m_logger_self_managed
Logger *	m_Logger

Friends
class	BioGearsEngineTest
class	BioGearsScenarioExec

Detailed Description

Manages and controls execution of all data/systems in BioGears.

Constructor & Destructor Documentation

biogears::BioGears::BioGears

(

Logger *

logger

)

biogears::BioGears::BioGears

(

const std::string &

logfileName

)

biogears::BioGears::BioGears	(	Logger *	logger,
		const std::string &	working_dir
	)

biogears::BioGears::BioGears	(	const std::string &	logfileName,
		const std::string &	working_dir
	)

biogears::BioGears::~BioGears ( )

virtual

Member Function Documentation

void biogears::BioGears::AtSteadyState ( EngineState  state )

protectedvirtual

bool biogears::BioGears::CreateCircuitsAndCompartments

(

)

void biogears::BioGears::ForwardFatal ( const std::string &  msg, const std::string &  origin  )

protected

SEActionManager & biogears::BioGears::GetActions

(

)

const SEActionManager & biogears::BioGears::GetActions

(

)

const

CDM::enumBioGearsAirwayMode::value biogears::BioGears::GetAirwayMode

(

)

const CDM::enumBioGearsAirwayMode::value biogears::BioGears::GetAirwayMode

(

)

const

SEAnesthesiaMachine & biogears::BioGears::GetAnesthesiaMachine

(

)

const SEAnesthesiaMachine & biogears::BioGears::GetAnesthesiaMachine

(

)

const

SEBloodChemistrySystem & biogears::BioGears::GetBloodChemistry

(

)

const SEBloodChemistrySystem & biogears::BioGears::GetBloodChemistry

(

)

const

SECardiovascularSystem & biogears::BioGears::GetCardiovascular

(

)

const SECardiovascularSystem & biogears::BioGears::GetCardiovascular

(

)

const

BioGearsCircuits & biogears::BioGears::GetCircuits

(

)

const BioGearsCircuits & biogears::BioGears::GetCircuits

(

)

const

BioGearsCompartments & biogears::BioGears::GetCompartments

(

)

const BioGearsCompartments & biogears::BioGears::GetCompartments

(

)

const

SEConditionManager & biogears::BioGears::GetConditions

(

)

const SEConditionManager & biogears::BioGears::GetConditions

(

)

const

const BioGearsConfiguration & biogears::BioGears::GetConfiguration

(

)

const BioGearsConfiguration & biogears::BioGears::GetConfiguration

(

)

const

DataTrack & biogears::BioGears::GetDataTrack

(

)

DiffusionCalculator & biogears::BioGears::GetDiffusionCalculator

(

)

const DiffusionCalculator & biogears::BioGears::GetDiffusionCalculator

(

)

const

SEDrugSystem & biogears::BioGears::GetDrugs

(

)

const SEDrugSystem & biogears::BioGears::GetDrugs

(

)

const

SEElectroCardioGram & biogears::BioGears::GetECG

(

)

const SEElectroCardioGram & biogears::BioGears::GetECG

(

)

const

SEEndocrineSystem & biogears::BioGears::GetEndocrine

(

)

const SEEndocrineSystem & biogears::BioGears::GetEndocrine

(

)

const

SEEnergySystem & biogears::BioGears::GetEnergy

(

)

const SEEnergySystem & biogears::BioGears::GetEnergy

(

)

const

const SEScalarTime & biogears::BioGears::GetEngineTime

(

)

const SEScalarTime & biogears::BioGears::GetEngineTime

(

)

const

SEEnvironment & biogears::BioGears::GetEnvironment

(

)

const SEEnvironment & biogears::BioGears::GetEnvironment

(

)

const

SEGastrointestinalSystem & biogears::BioGears::GetGastrointestinal

(

)

const SEGastrointestinalSystem & biogears::BioGears::GetGastrointestinal

(

)

const

SEHepaticSystem & biogears::BioGears::GetHepatic

(

)

const SEHepaticSystem & biogears::BioGears::GetHepatic

(

)

const

SEInhaler & biogears::BioGears::GetInhaler

(

)

const SEInhaler & biogears::BioGears::GetInhaler

(

)

const

CDM::enumOnOff::value biogears::BioGears::GetIntubation

(

)

const CDM::enumOnOff::value biogears::BioGears::GetIntubation

(

)

const

Logger * biogears::BioGears::GetLogger

(

)

const

SENervousSystem & biogears::BioGears::GetNervous

(

)

const SENervousSystem & biogears::BioGears::GetNervous

(

)

const

SEPatient & biogears::BioGears::GetPatient

(

)

const SEPatient & biogears::BioGears::GetPatient

(

)

const

bool biogears::BioGears::GetPatientAssessment

(

SEPatientAssessment &

assessment

)

SERenalSystem & biogears::BioGears::GetRenal

(

)

const SERenalSystem & biogears::BioGears::GetRenal

(

)

const

SERespiratorySystem & biogears::BioGears::GetRespiratory

(

)

const SERespiratorySystem & biogears::BioGears::GetRespiratory

(

)

const

SaturationCalculator & biogears::BioGears::GetSaturationCalculator

(

)

const SaturationCalculator & biogears::BioGears::GetSaturationCalculator

(

)

const

const SEScalarTime & biogears::BioGears::GetSimulationTime

(

)

const SEScalarTime & biogears::BioGears::GetSimulationTime

(

)

const

EngineState biogears::BioGears::GetState

(

)

const EngineState biogears::BioGears::GetState

(

)

const

BioGearsSubstances & biogears::BioGears::GetSubstances

(

)

const BioGearsSubstances & biogears::BioGears::GetSubstances

(

)

const

const SEScalarTime & biogears::BioGears::GetTimeStep

(

)

const SEScalarTime & biogears::BioGears::GetTimeStep

(

)

const

SETissueSystem & biogears::BioGears::GetTissue

(

)

const SETissueSystem & biogears::BioGears::GetTissue

(

)

const

bool biogears::BioGears::Initialize ( const PhysiologyEngineConfiguration *  config )

protected

void biogears::BioGears::PostProcess ( )

protected

void biogears::BioGears::PreProcess ( )

protected

void biogears::BioGears::Process ( )

protected

void biogears::BioGears::SetAirwayMode

(

CDM::enumBioGearsAirwayMode::value

mode

)

void biogears::BioGears::SetIntubation

(

CDM::enumOnOff::value

s

)

void biogears::BioGears::SetUp ( )

protected

void biogears::BioGears::SetupAnesthesiaMachine ( )

protected

void biogears::BioGears::SetupCardiovascular ( )

protected

Todo:

Make these a function of the systolic and diastolic pressure by fitting a curve to the data from the variations test

void biogears::BioGears::SetupCerebral ( )

protected

void biogears::BioGears::SetupExternalTemperature ( )

protected

void biogears::BioGears::SetupGastrointestinal ( )

protected

void biogears::BioGears::SetupInhaler ( )

protected

void biogears::BioGears::SetupInternalTemperature ( )

protected

void biogears::BioGears::SetupMechanicalVentilator ( )

protected

bool biogears::BioGears::SetupPatient ( )

protected

[108]

[249]

[231]

[326] [38]

[113]

[115]

[284]

cite ganong1995review

[78]

[300]

[plowman2013exercise]

void biogears::BioGears::SetupRenal ( )

protected

Todo:

The bladder is currently not being modeled as a compliance

Todo:

Use a compliance here - make sure you remove the current handling of bladder volume in the renal system as a pressure source

void biogears::BioGears::SetupRespiratory ( )

protected

void biogears::BioGears::SetupTissue ( )

protected

: Use P-V relationship in Himeno2015Mechanisms to get better initial compliance estimate

Todo:

Put Initial Circuit/Compartment data values into the configuration file.

[Mazonni1988Dynamic]

Friends And Related Function Documentation

friend class BioGearsEngineTest

friend

friend class BioGearsScenarioExec

friend

Member Data Documentation

std::unique_ptr<SEActionManager> biogears::BioGears::m_Actions

protected

CDM::enumBioGearsAirwayMode::value biogears::BioGears::m_AirwayMode

protected

std::unique_ptr<AnesthesiaMachine> biogears::BioGears::m_AnesthesiaMachine

protected

std::unique_ptr<BloodChemistry> biogears::BioGears::m_BloodChemistrySystem

protected

std::unique_ptr<Cardiovascular> biogears::BioGears::m_CardiovascularSystem

protected

std::unique_ptr<BioGearsCircuits> biogears::BioGears::m_Circuits

protected

std::unique_ptr<BioGearsCompartments> biogears::BioGears::m_Compartments

protected

std::unique_ptr<SEConditionManager> biogears::BioGears::m_Conditions

protected

std::unique_ptr<BioGearsConfiguration> biogears::BioGears::m_Config

protected

std::unique_ptr<SEScalarTime> biogears::BioGears::m_CurrentTime

protected

DataTrack* biogears::BioGears::m_DataTrack

protected

std::unique_ptr<DiffusionCalculator> biogears::BioGears::m_DiffusionCalculator

protected

std::unique_ptr<Drugs> biogears::BioGears::m_DrugSystem

protected

std::unique_ptr<ECG> biogears::BioGears::m_ECG

protected

std::unique_ptr<Endocrine> biogears::BioGears::m_EndocrineSystem

protected

std::unique_ptr<Energy> biogears::BioGears::m_EnergySystem

protected

std::unique_ptr<Environment> biogears::BioGears::m_Environment

protected

std::unique_ptr<Gastrointestinal> biogears::BioGears::m_GastrointestinalSystem

protected

std::unique_ptr<Hepatic> biogears::BioGears::m_HepaticSystem

protected

std::unique_ptr<Inhaler> biogears::BioGears::m_Inhaler

protected

CDM::enumOnOff::value biogears::BioGears::m_Intubation

protected

Logger* biogears::BioGears::m_Logger

protected

bool biogears::BioGears::m_logger_self_managed

protected

std::unique_ptr<Nervous> biogears::BioGears::m_NervousSystem

protected

std::unique_ptr<SEPatient> biogears::BioGears::m_Patient

protected

std::unique_ptr<Renal> biogears::BioGears::m_RenalSystem

protected

std::unique_ptr<Respiratory> biogears::BioGears::m_RespiratorySystem

protected

std::unique_ptr<SaturationCalculator> biogears::BioGears::m_SaturationCalculator

protected

std::unique_ptr<SEScalarTime> biogears::BioGears::m_SimulationTime

protected

EngineState biogears::BioGears::m_State

protected

std::unique_ptr<BioGearsSubstances> biogears::BioGears::m_Substances

protected

std::unique_ptr<Tissue> biogears::BioGears::m_TissueSystem

protected