This is the implementation of the PhysiologyEngine interface for the biogears engines. More...

#include <BioGearsEngine.h>

Inheritance diagram for biogears::BioGearsEngine:

Public Member Functions
	BioGearsEngine (Logger *logger)

	BioGearsEngine (const std::string &logFileName)

	BioGearsEngine (const char *logFileName)

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

	BioGearsEngine (Logger logger, const char working_dir)

	BioGearsEngine (const std::string &, const std::string &working_dir)

	BioGearsEngine (const char , const char )

virtual	~BioGearsEngine () override

virtual bool	LoadState (const char file, const SEScalarTime simTime=nullptr) override
	Reset engine and set it to the state in the provided file. You may provided a Simulation Time to be used if desired. It will be reflected in the GetSimulationTime method. Return value indicates engine was able to load provided state file. Engine will be in a cleared state if this method fails. More...

virtual bool	LoadState (const std::string &file, const SEScalarTime *simTime=nullptr) override

virtual bool	LoadState (const CDM::PhysiologyEngineStateData &state, const SEScalarTime *simTime=nullptr) override
	Reset engine and set it to the state in the provided file. You may provided a Simulation Time to be used if desired. It will be reflected in the GetSimulationTime method. Return value indicates engine was able to load provided state file. Engine will be in a cleared state if this method fails. More...

virtual std::unique_ptr< CDM::PhysiologyEngineStateData >	SaveState (const char *file) override
	Save the current state of the engine. State will be written to a file if provided. State object will be returned. Engine will be in a cleared state if this method fails. More...

virtual std::unique_ptr< CDM::PhysiologyEngineStateData >	SaveState (const std::string &file="") override

virtual Logger *	GetLogger () override
	Retrieve the Logger associated with this engine More...

virtual PhysiologyEngineTrack *	GetEngineTrack () override
	Retrieve the PhysiologyEngineTrack associated with tracking data from this engine to a file More...

virtual bool	InitializeEngine (const char patientFile, const std::vector< const SECondition > conditions=nullptr, const PhysiologyEngineConfiguration config=nullptr) override
	locates the xml patient file and reads in the values. More...

virtual bool	InitializeEngine (const std::string &patientFile, const std::vector< const SECondition * > conditions=nullptr, const PhysiologyEngineConfiguration config=nullptr) override

virtual bool	InitializeEngine (const SEPatient &patient, const std::vector< const SECondition * > conditions=nullptr, const PhysiologyEngineConfiguration config=nullptr) override
	This will create an engine that you can send instructions (patient,actions,conditions) to dynamically. The return value will indicate success failure of the creation of the engine. Some combinations of patients and conditions may prevent the engine from stabilizing. More...

virtual const PhysiologyEngineConfiguration *	GetConfiguration () override
	returns the engine configuration. More...

virtual double	GetTimeStep (const TimeUnit &unit) override
	returns the engine time step that is used when advancing time. More...

virtual double	GetSimulationTime (const TimeUnit &unit) override
	returns the current time of the simulation. More...

virtual void	AdvanceModelTime (bool appendDataTrack=false) override
	executes one pass through the time loop of the engine at the fixed timestep More...

virtual void	AdvanceModelTime (double time, const TimeUnit &unit=TimeUnit::s, bool appendDataTrack=false) override
	executes time loop of the engine beginning at the current time and running for the duration specified in the call at the fixed timestep More...

virtual bool	ProcessAction (const SEAction &action) override
	Execute the provided action. true will be returned if the engine supports the action false will be returned if the engine does not support the action. More...

virtual SESubstanceManager &	GetSubstanceManager () override
	Retrieves the associated substance manager. More...

virtual void	SetEventHandler (SEEventHandler *handler) override
	Add a callback object that will be called whenever a pateint or anesthesia machine event changes state More...

virtual const SEPatient &	GetPatient () override
	Returns the patient object used by the engine. More...

virtual bool	GetPatientAssessment (SEPatientAssessment &assessment) override
	Determines the assessment type and fills the data object with current data. More...

virtual const SEEnvironment *	GetEnvironment () override
	Returns the environment object used by the engine. More...

virtual const SEBloodChemistrySystem *	GetBloodChemistrySystem () override
	Returns the current state of the Blood Chemistry System. More...

virtual const SECardiovascularSystem *	GetCardiovascularSystem () override
	Returns the current state of the Cardiovascular System. More...

virtual const SEDrugSystem *	GetDrugSystem () override
	Returns the current state of the drug system. More...

virtual const SEEndocrineSystem *	GetEndocrineSystem () override
	Returns the current state of the Endocrine System. More...

virtual const SEEnergySystem *	GetEnergySystem () override
	Returns the current state of the Energy System. More...

virtual const SEGastrointestinalSystem *	GetGastrointestinalSystem () override
	Returns the current state of the Gastrointestinal System. More...

virtual const SEHepaticSystem *	GetHepaticSystem () override
	Returns the current state of the Hepatic System. More...

virtual const SENervousSystem *	GetNervousSystem () override
	Returns the current state of the Nervous System. More...

virtual const SERenalSystem *	GetRenalSystem () override
	Returns the current state of the Renal System. More...

virtual const SERespiratorySystem *	GetRespiratorySystem () override
	Returns the current state of the Respiratory System. More...

virtual const SETissueSystem *	GetTissueSystem () override
	Returns the current state of the tissue system. More...

virtual const SEAnesthesiaMachine *	GetAnesthesiaMachine () override
	Returns the current state of the Anesthesia machine. More...

virtual const SEElectroCardioGram *	GetElectroCardioGram () override
	Returns the current state of the Electrocardiogram machine. More...

virtual const SEInhaler *	GetInhaler () override
	Returns the current state of the Inhaler. More...

virtual const SECompartmentManager &	GetCompartments () override
	Retrieves the engine compartments, providing such data as: flows, pressure, volume as well as substance volumes and volume fractions. More...

virtual Tree< const char * >	GetDataRequestGraph () const override
	Return a Graph of DataRequest that the current PhysiologyEngine Supports. More...

virtual bool	IsAutoTracking () const override
	Returns the current state of the AutoTracking Property. True implies for each time advance All DataRequest will be tracked if the current simulation time is a multiple of GetDataRequestManager().GetSamplesPerSecond(); More...

virtual void	SetAutoTrackFlag (bool flag) override
	Return Allows the toggling of the SetAutoTrackFlag to On/Off More...

virtual bool	IsTrackingStabilization () const override
	Returns the current state of the Track Stabilization Property. When true the user expects the Results file to include engine values during stabilization routines When false the user expects the 0 time index to be the first engine readout post stabilization. More...

virtual void	SetTrackStabilizationFlag (bool flag) override
	This value will be overridden if TrackingStabilizationCriteria is loaded by any means After it is set. But can be used as a shortcut to modify m_Config->GetStabilizationCriteria()->TrackStabilization() After stabiliztion criteira has been loaded. More...

Public Member Functions inherited from biogears::PhysiologyEngine
virtual	~PhysiologyEngine ()

Public Member Functions inherited from biogears::BioGears
	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
virtual bool	IsReady ()

virtual bool	InitializeEngine (const std::vector< const SECondition * > conditions=nullptr, const PhysiologyEngineConfiguration config=nullptr)

Protected Member Functions inherited from biogears::BioGears
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
double	m_timeStep_remainder = 0.0

double	m_timeSinceLastDataTrack = 0.0

SEEventHandler *	m_EventHandler

PhysiologyEngineTrack	m_EngineTrack

std::stringstream	m_ss

bool	m_isAutoTracking = true

bool	m_areTrackingStabilization = false

Protected Attributes inherited from biogears::BioGears
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

Detailed Description

This is the implementation of the PhysiologyEngine interface for the biogears engines.

It contains the necessary execution calls, patient customization calls, insult and intervention calls as well as assessment calls for obtaining the results. During engine execution a log files is generated containing information, warning and error data.

Constructor & Destructor Documentation

biogears::BioGearsEngine::BioGearsEngine ( Logger * logger )

biogears::BioGearsEngine::BioGearsEngine ( const std::string & logFileName )

biogears::BioGearsEngine::BioGearsEngine ( const char * logFileName )

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

biogears::BioGearsEngine::BioGearsEngine	(	Logger *	logger,
		const char *	working_dir
	)

biogears::BioGearsEngine::BioGearsEngine	(	const std::string &	logFileName,
		const std::string &	working_dir
	)

biogears::BioGearsEngine::BioGearsEngine	(	const char *	logFileName,
		const char *	working_dir
	)

biogears::BioGearsEngine::~BioGearsEngine ( )

overridevirtual

Member Function Documentation

void biogears::BioGearsEngine::AdvanceModelTime ( bool appendDataTrack = false )

overridevirtual

executes one pass through the time loop of the engine at the fixed timestep

Events, errors, and warning as are logged to file not errors are returned through the API at this time.

Public Member Functions

Engine will be in a cleared state if this method fails.

Engine will be in a cleared state if this method fails.

Engine will be in a cleared state if this method fails.

Retrieve the Logger associated with this engine

Retrieve the PhysiologyEngineTrack associated with tracking data from this engine to a file

returns the engine configuration.

returns the current time of the simulation.

Add a callback object that will be called whenever a pateint or anesthesia machine event changes state

Return a Graph of DataRequest that the current PhysiologyEngine Supports.

GetDataRequestManager().GetSamplesPerSecond();

Return Allows the toggling of the SetAutoTrackFlag to On/Off

When false the user expects the 0 time index to be the first engine readout post stabilization.

After stabiliztion criteira has been loaded.

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

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returns the engine configuration.

Return a Graph of DataRequest that the current PhysiologyEngine Supports.

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Retrieve the PhysiologyEngineTrack associated with tracking data from this engine to a file

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Retrieve the Logger associated with this engine

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returns the current time of the simulation.

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GetDataRequestManager().GetSamplesPerSecond();

When false the user expects the 0 time index to be the first engine readout post stabilization.

Engine will be in a cleared state if this method fails.

Engine will be in a cleared state if this method fails.

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Engine will be in a cleared state if this method fails.

Return Allows the toggling of the SetAutoTrackFlag to On/Off

Add a callback object that will be called whenever a pateint or anesthesia machine event changes state

After stabiliztion criteira has been loaded.

Member Data Documentation