#include <PhysiologyEngine.h>

Inherits Loggable.

Public Member Functions
	PhysiologyEngine (Logger *logger=nullptr)

virtual	~PhysiologyEngine ()

virtual std::string	GetTypeName () const =0
	Returns the engine type, such as "Human Adult Whole Body". More...

virtual bool	SerializeFromFile (const std::string &file)=0
	Reset engine and set it to the state in the provided file. The file may contain json or binary. Anything but an extension of .json will be interpreted as binary. 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	SerializeToFile (const std::string &filename) const =0
	Save the current state of the engine to provided filename. Using a .json extension will save a json/ascii file. Anything else will save as binary. More...

virtual bool	SerializeFromString (const std::string &state, eSerializationFormat m)=0
	Reset engine and set it to the state in the provided string. The string can contain JSON or binary. Note that a string of bytes are binary, not text; we only use the string class as a convenient container. 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	SerializeToString (std::string &state, eSerializationFormat m) const =0
	Save the current state of the engine. The state can be saved as JSON or bytes in the given string. Note that the bytes are binary, not text; we only use the string class as a convenient container. More...

virtual bool	InitializeEngine (const std::string &patient_configuration, eSerializationFormat m)=0
	Initialize an engine based on the engines initialization structure. More...

virtual bool	InitializeEngine (const SEPatientConfiguration &patient_configuration)=0
	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 void	Clear ()=0
	Closes out any files and resets state. More...

virtual const SEConditionManager &	GetConditionManager () const =0
	Get the Condition Manager. Allows a user to check the state of active conditions. More...

virtual bool	SetConfigurationOverride (const SEEngineConfiguration *config)=0
	Engines can have a configuration for allowing a user to set certain internal parameters Engines with configurations will have all configuration parameters defaulted, This allows you to change one or more or those parameters. The parameters provided will be applied during SerializeFrom* and InitializeEngine methods. Use with caution! (Use nullptr to revert back to using all engine defaults) More...

virtual const SEEngineConfiguration *	GetConfiguration () const =0
	returns the engine configuration. More...

virtual SEEngineTracker *	GetEngineTracker () const =0
	Retrieve the SEEngineTracker associated with tracking data from this engine to a file The SEEngineTracker is a class set up to pull data requested from the engine (via SEDataRequest's) and provide access to the data easily (ex. to easily write data to csv files) More...

virtual double	GetTimeStep (const TimeUnit &unit) const =0
	returns the engine time step that is used when advancing time. More...

virtual double	GetSimulationTime (const TimeUnit &unit) const =0
	returns the current time of the simulation. More...

virtual void	SetSimulationTime (const SEScalarTime &time)=0
	Set the current time of the simulation. Engine Simulation time will be advanced from this time point. More...

virtual bool	AdvanceModelTime ()=0
	executes one pass through the time loop of the engine at the fixed timestep More...

virtual bool	AdvanceModelTime (double time, const TimeUnit &unit)=0
	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 void	SetAdvanceHandler (SEAdvanceHandler *handler)=0
	Add a callback object that will be called after each timestep. More...

virtual bool	ProcessAction (const SEAction &action)=0
	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 const SEActionManager &	GetActionManager () const =0
	Get the Action Manager. Allows a user to check the state of active actions. More...

virtual const SESubstanceManager &	GetSubstanceManager () const =0
	Retrieves the associated substance manager. More...

virtual const SEEventManager &	GetEventManager () const =0
	Retrieves the associated event manager. More...

virtual const SEPatient &	GetPatient () const =0
	Returns the patient object used by the engine. More...

virtual const SEPatient &	GetInitialPatient () const =0
	Returns the initial simulation patient object used by the engine. More...

virtual bool	GetPatientAssessment (SEPatientAssessment &assessment) const =0
	Determines the assessment type and fills the data object with current data. More...

virtual const SEEnvironment *	GetEnvironment () const =0
	Returns the environment object used by the engine. More...

virtual const SEBloodChemistrySystem *	GetBloodChemistrySystem () const =0
	Returns the current state of the Blood Chemistry System. More...

virtual const SECardiovascularSystem *	GetCardiovascularSystem () const =0
	Returns the current state of the Cardiovascular System. More...

virtual const SEDrugSystem *	GetDrugSystem () const =0
	Returns the current state of the drug system More...

virtual const SEEndocrineSystem *	GetEndocrineSystem () const =0
	Returns the current state of the Endocrine System. More...

virtual const SEEnergySystem *	GetEnergySystem () const =0
	Returns the current state of the Energy System. More...

virtual const SEGastrointestinalSystem *	GetGastrointestinalSystem () const =0
	Returns the current state of the Gastrointestinal System. More...

virtual const SEHepaticSystem *	GetHepaticSystem () const =0
	Returns the current state of the Hepatic System. More...

virtual const SENervousSystem *	GetNervousSystem () const =0
	Returns the current state of the Nervous System. More...

virtual const SERenalSystem *	GetRenalSystem () const =0
	Returns the current state of the Renal System. More...

virtual const SERespiratorySystem *	GetRespiratorySystem () const =0
	Returns the current state of the Respiratory System. More...

virtual const SETissueSystem *	GetTissueSystem () const =0
	Returns the current state of the tissue system More...

virtual const SEAnesthesiaMachine *	GetAnesthesiaMachine () const =0
	Returns the current state of the Anesthesia machine. More...

virtual const SEBagValveMask *	GetBagValveMask () const =0
	Returns the current state of the Bag Valve Mask. More...

virtual const SEECMO *	GetECMO () const =0
	Returns the current state of the ECMO machine. More...

virtual const SEElectroCardioGram *	GetElectroCardioGram () const =0
	Returns the current state of the Electrocardiogram machine. More...

virtual const SEInhaler *	GetInhaler () const =0
	Returns the current state of the Inhaler. More...

virtual const SEMechanicalVentilator *	GetMechanicalVentilator () const =0
	Returns the current state of the Mechanical ventilator. More...

virtual const SECompartmentManager &	GetCompartments () const =0
	Retrieves the engine compartments, providing such data as: flows, pressure, volume as well as substance volumes and volume fractions. More...

virtual SEBlackBoxManager &	GetBlackBoxes () const =0
	Retrieves the engine black box manager Black boxes allow users to inject or retrieve flows, pressure, volume as well as substance volumes and volume fractions into the engine, use with caution. These are intended to allow integration between Pulse and other systems at a low level. More...

Public Member Functions inherited from Loggable
	Loggable (Logger *logger=nullptr)

	Loggable (std::string const &logfile)

virtual	~Loggable ()

virtual Logger *	GetLogger () const

virtual void	SetLogger (Logger &logger)

virtual void	Debug (std::string const &msg) const

virtual void	Debug (std::stringstream &msg) const

virtual void	Debug (std::ostream &msg) const

virtual void	Info (std::string const &msg) const

virtual void	Info (std::stringstream &msg) const

virtual void	Info (const std::stringstream &msg) const

virtual void	Info (std::ostream &msg) const

virtual void	Warning (std::string const &msg) const

virtual void	Warning (std::stringstream &msg) const

virtual void	Warning (std::ostream &msg) const

virtual void	Error (std::string const &msg) const

virtual void	Error (std::stringstream &msg) const

virtual void	Error (std::ostream &msg) const

virtual void	Fatal (std::string const &msg) const

virtual void	Fatal (std::stringstream &msg) const

virtual void	Fatal (std::ostream &msg) const

Additional Inherited Members
Protected Attributes inherited from Loggable
bool	myLogger

Logger *	m_Logger

Constructor & Destructor Documentation

◆ PhysiologyEngine()

PhysiologyEngine::PhysiologyEngine ( Logger * logger = nullptr )

inline

◆ ~PhysiologyEngine()

virtual PhysiologyEngine::~PhysiologyEngine ( )

inlinevirtual

Member Function Documentation

◆ AdvanceModelTime() [1/2]

virtual bool PhysiologyEngine::AdvanceModelTime ( )

pure virtual

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.

◆ AdvanceModelTime() [2/2]

virtual bool PhysiologyEngine::AdvanceModelTime	(	double	time,
		const TimeUnit &	unit
	)

pure virtual

executes time loop of the engine beginning at the current time and running for the duration specified in the call at the fixed timestep

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

◆ Clear()

virtual void PhysiologyEngine::Clear ( )

pure virtual

Closes out any files and resets state.

◆ GetActionManager()

virtual const SEActionManager & PhysiologyEngine::GetActionManager ( ) const

pure virtual

Get the Action Manager. Allows a user to check the state of active actions.

◆ GetAnesthesiaMachine()

virtual const SEAnesthesiaMachine * PhysiologyEngine::GetAnesthesiaMachine ( ) const

pure virtual

Returns the current state of the Anesthesia machine.

◆ GetBagValveMask()

virtual const SEBagValveMask * PhysiologyEngine::GetBagValveMask ( ) const

pure virtual

Returns the current state of the Bag Valve Mask.

◆ GetBlackBoxes()

virtual SEBlackBoxManager & PhysiologyEngine::GetBlackBoxes ( ) const

pure virtual

Retrieves the engine black box manager Black boxes allow users to inject or retrieve flows, pressure, volume as well as substance volumes and volume fractions into the engine, use with caution. These are intended to allow integration between Pulse and other systems at a low level.

◆ GetBloodChemistrySystem()

virtual const SEBloodChemistrySystem * PhysiologyEngine::GetBloodChemistrySystem ( ) const

pure virtual

Returns the current state of the Blood Chemistry System.

◆ GetCardiovascularSystem()

virtual const SECardiovascularSystem * PhysiologyEngine::GetCardiovascularSystem ( ) const

pure virtual

Returns the current state of the Cardiovascular System.

◆ GetCompartments()

virtual const SECompartmentManager & PhysiologyEngine::GetCompartments ( ) const

pure virtual

Retrieves the engine compartments, providing such data as: flows, pressure, volume as well as substance volumes and volume fractions.

◆ GetConditionManager()

virtual const SEConditionManager & PhysiologyEngine::GetConditionManager ( ) const

pure virtual

Get the Condition Manager. Allows a user to check the state of active conditions.

◆ GetConfiguration()

virtual const SEEngineConfiguration * PhysiologyEngine::GetConfiguration ( ) const

pure virtual

returns the engine configuration.

◆ GetDrugSystem()

virtual const SEDrugSystem * PhysiologyEngine::GetDrugSystem ( ) const

pure virtual

Returns the current state of the drug system

◆ GetECMO()

virtual const SEECMO * PhysiologyEngine::GetECMO ( ) const

pure virtual

Returns the current state of the ECMO machine.

◆ GetElectroCardioGram()

virtual const SEElectroCardioGram * PhysiologyEngine::GetElectroCardioGram ( ) const

pure virtual

Returns the current state of the Electrocardiogram machine.

◆ GetEndocrineSystem()

virtual const SEEndocrineSystem * PhysiologyEngine::GetEndocrineSystem ( ) const

pure virtual

Returns the current state of the Endocrine System.

◆ GetEnergySystem()

virtual const SEEnergySystem * PhysiologyEngine::GetEnergySystem ( ) const

pure virtual

Returns the current state of the Energy System.

◆ GetEngineTracker()

virtual SEEngineTracker * PhysiologyEngine::GetEngineTracker ( ) const

pure virtual

Retrieve the SEEngineTracker associated with tracking data from this engine to a file The SEEngineTracker is a class set up to pull data requested from the engine (via SEDataRequest's) and provide access to the data easily (ex. to easily write data to csv files)

◆ GetEnvironment()

virtual const SEEnvironment * PhysiologyEngine::GetEnvironment ( ) const

pure virtual

Returns the environment object used by the engine.

◆ GetEventManager()

virtual const SEEventManager & PhysiologyEngine::GetEventManager ( ) const

pure virtual

Retrieves the associated event manager.

◆ GetGastrointestinalSystem()

virtual const SEGastrointestinalSystem * PhysiologyEngine::GetGastrointestinalSystem ( ) const

pure virtual

Returns the current state of the Gastrointestinal System.

◆ GetHepaticSystem()

virtual const SEHepaticSystem * PhysiologyEngine::GetHepaticSystem ( ) const

pure virtual

Returns the current state of the Hepatic System.

◆ GetInhaler()

virtual const SEInhaler * PhysiologyEngine::GetInhaler ( ) const

pure virtual

Returns the current state of the Inhaler.

◆ GetInitialPatient()

virtual const SEPatient & PhysiologyEngine::GetInitialPatient ( ) const

pure virtual

Returns the initial simulation patient object used by the engine.

◆ GetMechanicalVentilator()

virtual const SEMechanicalVentilator * PhysiologyEngine::GetMechanicalVentilator ( ) const

pure virtual

Returns the current state of the Mechanical ventilator.

◆ GetNervousSystem()

virtual const SENervousSystem * PhysiologyEngine::GetNervousSystem ( ) const

pure virtual

Returns the current state of the Nervous System.

◆ GetPatient()

virtual const SEPatient & PhysiologyEngine::GetPatient ( ) const

pure virtual

Returns the patient object used by the engine.

◆ GetPatientAssessment()

virtual bool PhysiologyEngine::GetPatientAssessment ( SEPatientAssessment & assessment ) const

pure virtual

Determines the assessment type and fills the data object with current data.

Assessments can be queried at any point in the calculation and as many times are desired.

◆ GetRenalSystem()

virtual const SERenalSystem * PhysiologyEngine::GetRenalSystem ( ) const

pure virtual

Returns the current state of the Renal System.

◆ GetRespiratorySystem()

virtual const SERespiratorySystem * PhysiologyEngine::GetRespiratorySystem ( ) const

pure virtual

Returns the current state of the Respiratory System.

◆ GetSimulationTime()

virtual double PhysiologyEngine::GetSimulationTime ( const TimeUnit & unit ) const

pure virtual

returns the current time of the simulation.

◆ GetSubstanceManager()

virtual const SESubstanceManager & PhysiologyEngine::GetSubstanceManager ( ) const

pure virtual

Retrieves the associated substance manager.

◆ GetTimeStep()

virtual double PhysiologyEngine::GetTimeStep ( const TimeUnit & unit ) const

pure virtual

returns the engine time step that is used when advancing time.

◆ GetTissueSystem()

virtual const SETissueSystem * PhysiologyEngine::GetTissueSystem ( ) const

pure virtual

Returns the current state of the tissue system

◆ GetTypeName()

virtual std::string PhysiologyEngine::GetTypeName ( ) const

pure virtual

Returns the engine type, such as "Human Adult Whole Body".

◆ InitializeEngine() [1/2]

virtual bool PhysiologyEngine::InitializeEngine ( const SEPatientConfiguration & patient_configuration )

pure virtual

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.

◆ InitializeEngine() [2/2]

virtual bool PhysiologyEngine::InitializeEngine	(	const std::string &	patient_configuration,
		eSerializationFormat	m
	)

pure virtual

Initialize an engine based on the engines initialization structure.

An initialization structure is up to every engine. It should have a SEPatientConfiguration (or derivative) But it may also have more stuctures associated with it, it's up to the engine.

◆ ProcessAction()

virtual bool PhysiologyEngine::ProcessAction ( const SEAction & action )

pure virtual

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.

◆ SerializeFromFile()

virtual bool PhysiologyEngine::SerializeFromFile ( const std::string & file )

pure virtual

Reset engine and set it to the state in the provided file. The file may contain json or binary. Anything but an extension of .json will be interpreted as binary. Return value indicates engine was able to load provided state file. Engine will be in a cleared state if this method fails.

◆ SerializeFromString()

virtual bool PhysiologyEngine::SerializeFromString	(	const std::string &	state,
		eSerializationFormat	m
	)

pure virtual

Reset engine and set it to the state in the provided string. The string can contain JSON or binary. Note that a string of bytes are binary, not text; we only use the string class as a convenient container. Return value indicates engine was able to load provided state file. Engine will be in a cleared state if this method fails.

◆ SerializeToFile()

virtual bool PhysiologyEngine::SerializeToFile ( const std::string & filename ) const

pure virtual

Save the current state of the engine to provided filename. Using a .json extension will save a json/ascii file. Anything else will save as binary.

◆ SerializeToString()

virtual bool PhysiologyEngine::SerializeToString	(	std::string &	state,
		eSerializationFormat	m
	)		const

pure virtual

Save the current state of the engine. The state can be saved as JSON or bytes in the given string. Note that the bytes are binary, not text; we only use the string class as a convenient container.

◆ SetAdvanceHandler()

virtual void PhysiologyEngine::SetAdvanceHandler ( SEAdvanceHandler * handler )

pure virtual

Add a callback object that will be called after each timestep.

◆ SetConfigurationOverride()

virtual bool PhysiologyEngine::SetConfigurationOverride ( const SEEngineConfiguration * config )

pure virtual

Engines can have a configuration for allowing a user to set certain internal parameters Engines with configurations will have all configuration parameters defaulted, This allows you to change one or more or those parameters. The parameters provided will be applied during SerializeFrom* and InitializeEngine methods. Use with caution! (Use nullptr to revert back to using all engine defaults)

◆ SetSimulationTime()

virtual void PhysiologyEngine::SetSimulationTime ( const SEScalarTime & time )

pure virtual

Set the current time of the simulation. Engine Simulation time will be advanced from this time point.

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ PhysiologyEngine()

◆ ~PhysiologyEngine()

Member Function Documentation

◆ AdvanceModelTime() [1/2]

◆ AdvanceModelTime() [2/2]

◆ Clear()

◆ GetActionManager()

◆ GetAnesthesiaMachine()

◆ GetBagValveMask()

◆ GetBlackBoxes()

◆ GetBloodChemistrySystem()

◆ GetCardiovascularSystem()

◆ GetCompartments()

◆ GetConditionManager()

◆ GetConfiguration()

◆ GetDrugSystem()

◆ GetECMO()

◆ GetElectroCardioGram()

◆ GetEndocrineSystem()

◆ GetEnergySystem()

◆ GetEngineTracker()

◆ GetEnvironment()

◆ GetEventManager()

◆ GetGastrointestinalSystem()

◆ GetHepaticSystem()

◆ GetInhaler()

◆ GetInitialPatient()

◆ GetMechanicalVentilator()

◆ GetNervousSystem()

◆ GetPatient()

◆ GetPatientAssessment()

◆ GetRenalSystem()

◆ GetRespiratorySystem()

◆ GetSimulationTime()

◆ GetSubstanceManager()

◆ GetTimeStep()

◆ GetTissueSystem()

◆ GetTypeName()

◆ InitializeEngine() [1/2]

◆ InitializeEngine() [2/2]

◆ ProcessAction()

◆ SerializeFromFile()

◆ SerializeFromString()

◆ SerializeToFile()

◆ SerializeToString()

◆ SetAdvanceHandler()

◆ SetConfigurationOverride()

◆ SetSimulationTime()