A module that calculates the generalized fractional anisotropy for every voxel of the input dataset. More...

#include <WMCalculateGFA.h>

Inheritance diagram for WMCalculateGFA:

Collaboration diagram for WMCalculateGFA:

Public Member Functions
	WMCalculateGFA ()
	Standard constructor. More...

virtual	~WMCalculateGFA ()
	Destructor. More...

virtual const std::string	getName () const
	Gives back the name of this module. More...

virtual const std::string	getDescription () const
	Gives back a description of this module. More...

virtual std::shared_ptr< WModule >	factory () const
	Due to the prototype design pattern used to build modules, this method returns a new instance of this method. More...

virtual const char **	getXPMIcon () const
	Get the icon for this module in XPM format. More...

Public Member Functions inherited from WModule
	WModule ()
	Constructs a new WModule instance. More...

virtual	~WModule ()
	Destructor. More...

const InputConnectorList &	getInputConnectors () const
	Gives back input connectors. More...

std::shared_ptr< WModuleInputConnector >	getInputConnector (std::string name)
	Finds the named connector for the module. More...

std::shared_ptr< WModuleInputConnector >	findInputConnector (std::string name)
	Finds the named connector for the module. More...

const OutputConnectorList &	getOutputConnectors () const
	Gives back output connectors. More...

std::shared_ptr< WModuleOutputConnector >	getOutputConnector (std::string name)
	Finds the named connector for the module. More...

std::shared_ptr< WModuleOutputConnector >	findOutputConnector (std::string name)
	Finds the named connector for the module. More...

std::shared_ptr< WModuleConnector >	getConnector (std::string name)
	Finds the named connector for the module. More...

std::shared_ptr< WModuleConnector >	findConnector (std::string name)
	Finds the named connector for the module. More...

std::shared_ptr< WProperties >	getProperties () const
	Return a pointer to the properties object of the module. More...

std::shared_ptr< WProperties >	getInformationProperties () const
	Return a pointer to the information properties object of the module. More...

const WBoolFlag &	isInitialized () const
	Determines whether the module instance is properly initialized. More...

const WBoolFlag &	isUseable () const
	Checks whether the module instance is ready to be used. More...

const WBoolFlag &	isAssociated () const
	Checks whether this module is associated with an container. More...

const WBoolFlag &	isReady () const
	Checks whether this module is ready. More...

const WBoolFlag &	isReadyOrCrashed () const
	This is the logical or of isReady and isCrashed. More...

const WBoolFlag &	isRunning () const
	Returns a flag denoting whether the thread currently is running or nor. More...

void	waitRestored ()
	This method waits for the module to be restored completely. More...

bool	isRestoreNeeded () const
	Check whether this module is in restore mode. More...

void	setRestoreNeeded (bool restore=true)
	Change the restore mode. More...

void	reportRestoreComplete ()
	Called by loaders to tell the module that loading has been completed. More...

std::shared_ptr< WModuleContainer >	getAssociatedContainer () const
	The container this module is associated with. More...

virtual boost::signals2::connection	subscribeSignal (MODULE_SIGNAL signal, t_ModuleGenericSignalHandlerType notifier)
	Connects a specified notify function with a signal this module instance is offering. More...

virtual boost::signals2::connection	subscribeSignal (MODULE_SIGNAL signal, t_ModuleErrorSignalHandlerType notifier)
	Connects a specified notify function with a signal this module instance is offering. More...

virtual std::shared_ptr< WProgressCombiner >	getRootProgressCombiner ()
	Gets the modules base progress. More...

virtual MODULE_TYPE	getType () const
	Gets the type of the module. More...

void	disconnect ()
	Completely disconnects all connected connectors of this module. More...

WCombinerTypes::WDisconnectList	getPossibleDisconnections ()
	Gives a list of all WDisconnectCombiners possible. More...

boost::filesystem::path	getLocalPath () const
	Returns the local path of the module. More...

boost::filesystem::path	getLibPath () const
	Returns the absolute path to the library containing this module. More...

std::string	getPackageName () const
	Returns the name of the package the module belongs to, The package name basically is the name of the library containing this and maybe other modules. More...

bool	isDeprecated () const
	Checks whether the module was marked as deprecated. More...

std::string	getDeprecationMessage () const
	Queries the deprecation message of a module if specified. More...

virtual WModuleMetaInformation::ConstSPtr	getMetaInformation () const
	The meta information of this module. More...

const std::string &	getUUID () const
	Get the UUID of the module instance. More...

WPropString	getRuntimeName () const
	Returns the name the user has given this module. More...

const WRequirement *	checkRequirements () const
	This method checks whether all the requirements of the module are complied. More...

virtual boost::signals2::connection	subscribeSignal (THREAD_SIGNAL signal, t_ThreadErrorSignalHandlerType notifier)
	Connects a specified notify function with a signal this thread instance is offering. More...

Public Member Functions inherited from WThreadedRunner
	WThreadedRunner ()
	Default constructor. More...

virtual	~WThreadedRunner ()
	Destructor. More...

virtual void	run ()
	Run thread. More...

void	run (THREADFUNCTION f)
	Run thread. More...

void	wait (bool requestFinish=false)
	Wait for the thread to be finished. More...

virtual void	requestStop ()
	This method's purpose is to request a stop without waiting for it. More...

virtual boost::signals2::connection	subscribeSignal (THREAD_SIGNAL signal, t_ThreadErrorSignalHandlerType notifier)
	Connects a specified notify function with a signal this thread instance is offering. More...

const WBoolFlag &	isCrashed () const
	Checks whether this thread has been crashed. More...

const std::string &	getCrashMessage () const
	Get the message of the exception finally causing the crash. More...

void	setThreadName (std::string name)
	Set the name of the thread. More...

std::string	getThreadName () const
	Returns the current thread name. More...

Public Member Functions inherited from WPrototyped
	WPrototyped ()
	Default constructor. More...

virtual	~WPrototyped ()
	Destructor. More...

template<typename T >
bool	isA ()
	Checks whether the actual prototype has the specified runtime type. More...

Protected Member Functions
virtual void	moduleMain ()
	Entry point after loading the module. More...

virtual void	connectors ()
	Initialize the connectors this module is using. More...

virtual void	properties ()
	Initialize the properties for this module. More...

Protected Member Functions inherited from WModule
void	threadMain ()
	Thread entry point. More...

virtual void	onThreadException (const WException &e)
	This method is called if an exception was caught, which came from the custom thread code. More...

void	setAssociatedContainer (std::shared_ptr< WModuleContainer > container)
	Sets the container this module is associated with. More...

virtual void	requirements ()
	Initialize requirements in this function. More...

virtual std::string	deprecated () const
	This function allows module programmers to mark their modules deprecated in a user-friendly way. More...

void	initialize ()
	Manages initialization. More...

virtual void	cleanup ()
	Called whenever the module should shutdown. More...

void	addConnector (std::shared_ptr< WModuleInputConnector > con)
	Adds the specified connector to the list of inputs. More...

void	addConnector (std::shared_ptr< WModuleOutputConnector > con)
	Adds the specified connector to the list of outputs. More...

void	removeConnectors ()
	Removes all connectors properly. More...

virtual void	activate ()
	Callback for m_active. More...

virtual const t_GenericSignalHandlerType	getSignalHandler (MODULE_CONNECTOR_SIGNAL signal)
	Gives the signal handler function responsible for a given signal. More...

virtual void	notifyConnectionEstablished (std::shared_ptr< WModuleConnector > here, std::shared_ptr< WModuleConnector > there)
	Gets called whenever a connector gets connected to the specified input. More...

virtual void	notifyConnectionClosed (std::shared_ptr< WModuleConnector > here, std::shared_ptr< WModuleConnector > there)
	Gets called whenever a connection between a remote and local connector gets closed. More...

virtual void	notifyDataChange (std::shared_ptr< WModuleConnector > input, std::shared_ptr< WModuleConnector > output)
	Gets called when the data on one input connector changed. More...

void	ready ()
	Call this whenever your module is ready and can react on property changes. More...

wlog::WStreamedLogger	infoLog () const
	Logger instance for comfortable info logging. More...

wlog::WStreamedLogger	debugLog () const
	Logger instance for comfortable debug logging. More...

wlog::WStreamedLogger	warnLog () const
	Logger instance for comfortable warning- logs. More...

wlog::WStreamedLogger	errorLog () const
	Logger instance for comfortable error logging. More...

void	setLocalPath (boost::filesystem::path path)
	Sets the local module path. More...

void	setLibPath (boost::filesystem::path path)
	Set the path to the library which contains this module. More...

void	setPackageName (std::string name)
	Set the package name. More...

Protected Member Functions inherited from WThreadedRunner
virtual void	notifyStop ()
	Gets called when the thread should be stopped. More...

void	yield () const
	Give remaining execution timeslice to another thread. More...

void	sleep (const int32_t t) const
	Sets thread asleep. More...

void	msleep (const int32_t t) const
	Sets thread asleep. More...

void	waitForStop ()
	Let the thread sleep until a stop request was given. More...

void	handleDeadlyException (const WException &e, std::string sender="WThreadedRunner")
	Handle the specified exception which was not caught in the thread, which basically means the thread has crashed. More...

Private Types
typedef WMCalculateGFA	This
	a conveniance typedef More...

typedef WThreadedPerVoxelOperation< double, 15, double, 1 >	GFAFuncType
	the threaded function type for gfa computation More...

typedef WThreadedFunction< GFAFuncType >	GFAPoolType
	the threadpool More...

Private Member Functions
boost::array< double, 1 >	perVoxelGFAFunc (WValueSet< double >::SubArray const &s)
	A function that gets called for every voxel in the input SH-dataset. More...

void	resetGFAPool ()
	Reset the threaded functions. More...

void	handleException (WException const &e)
	Handle an exception thrown by a worker thread. More...

void	resetProgress (std::size_t todo)
	Reset the progress indicator in the ui. More...

Private Attributes
std::shared_ptr< WDataSetSphericalHarmonics >	m_dataSet
	A pointer to the input dataset. More...

std::shared_ptr< WDataSetScalar >	m_result
	The output dataset. More...

std::shared_ptr< WModuleOutputData< WDataSetScalar > >	m_output
	The output Connector. More...

std::shared_ptr< WModuleInputData< WDataSetSphericalHarmonics > >	m_input
	The input Connector for the SH data. More...

std::shared_ptr< WProgress >	m_currentProgress
	The object that keeps track of the current progress. More...

std::shared_ptr< WException >	m_lastException
	The last exception thrown by any worker thread. More...

std::shared_ptr< WCondition >	m_exceptionCondition
	Condition indicating if any exception was thrown. More...

std::shared_ptr< GFAFuncType >	m_gfaFunc
	The threaded function object. More...

std::shared_ptr< GFAPoolType >	m_gfaPool
	The threadpool. More...

WMatrix< double >	m_BMat
	A matrix of SH base function values for various gradients. More...

Additional Inherited Members
Public Types inherited from WModule
typedef std::vector< std::shared_ptr< WModuleInputConnector > >	InputConnectorList
	The type for the list of input connectors. More...

typedef std::vector< std::shared_ptr< WModuleOutputConnector > >	OutputConnectorList
	The type for the list of output connectors. More...

typedef std::shared_ptr< WModule >	SPtr
	Shared pointer to a WModule. More...

typedef std::shared_ptr< const WModule >	ConstSPtr
	Shared pointer to a const WModule. More...

Public Types inherited from WThreadedRunner
typedef std::shared_ptr< WThreadedRunner >	SPtr
	Abbreviation to a shared_ptr to this type. More...

typedef std::shared_ptr< const WThreadedRunner >	ConstSPtr
	Abbreviation to a const shared_ptr to this type. More...

typedef boost::function< void(void) >	THREADFUNCTION
	Type used for simple thread functions. More...

Static Public Member Functions inherited from WModule
static SPtr	findByUUID (std::string uuid)
	Find a module instance by UUID. More...

Static Public Member Functions inherited from WThreadedRunner
static void	setThisThreadName (std::string name)
	Static function to set the name of the calling thread. More...

Protected Types inherited from WModule
typedef std::vector< WRequirement * >	Requirements
	The type of the requirement list. More...

Protected Attributes inherited from WModule
std::shared_ptr< WProperties >	m_properties
	The property object for the module. More...

std::shared_ptr< WProperties >	m_infoProperties
	The property object for the module containing only module whose purpose is "PV_PURPOSE_INFORMNATION". More...

std::shared_ptr< WProgressCombiner >	m_progress
	Progress indicator used as parent for all progress' of this module. More...

WBoolFlag	m_initialized
	True if everything is initialized and ready to be used. More...

WBoolFlag	m_isAssociated
	True if container got associated with this flag. More...

WBoolFlag	m_isUsable
	True if associated && initialized. More...

WBoolFlag	m_isReady
	True if ready() was called. More...

WBoolFlag	m_isReadyOrCrashed
	It is true whenever m_isReady or WThreadedRunner::m_isCrashed is true. More...

WBoolFlag	m_isRunning
	True if the module currently is running. More...

WBoolFlag	m_isLoadFinished
	Flag to denote whether the module container and the project loader have finished their work. More...

bool	m_restoreMode
	Flag denoting the current restore mode. More...

std::shared_ptr< WProgress >	m_readyProgress
	Progress indicator for the "ready" state. More...

WConditionSet	m_moduleState
	The internal state of the module. More...

std::shared_ptr< WModuleContainer >	m_container
	The container this module belongs to. More...

InputConnectorList	m_inputConnectors
	Set of input connectors associated with this module. More...

OutputConnectorList	m_outputConnectors
	Set of output connectors associated with this module. More...

WPropBool	m_active
	True whenever the module should be active. More...

WPropString	m_runtimeName
	This property holds a user specified name for the current module instance. More...

boost::filesystem::path	m_localPath
	The path where the module binary resides in. More...

boost::filesystem::path	m_libPath
	The absolute path to the library containing this module. More...

std::string	m_packageName
	The name of the lib/the package containing this module. More...

Requirements	m_requirements
	The list of requirements. More...

Protected Attributes inherited from WThreadedRunner
boost::thread	m_thread
	Thread instance. More...

WBoolFlag	m_shutdownFlag
	Condition getting fired whenever the thread should quit. More...

WBoolFlag	m_isCrashed
	True whenever an exception is thrown during threadMain. More...

std::string	m_crashMessage
	The crash message. More...

Detailed Description

A module that calculates the generalized fractional anisotropy for every voxel of the input dataset.

Definition at line 48 of file WMCalculateGFA.h.

Member Typedef Documentation

◆ GFAFuncType

typedef WThreadedPerVoxelOperation< double, 15, double, 1 > WMCalculateGFA::GFAFuncType

private

the threaded function type for gfa computation

Definition at line 108 of file WMCalculateGFA.h.

◆ GFAPoolType

typedef WThreadedFunction< GFAFuncType > WMCalculateGFA::GFAPoolType

private

the threadpool

Definition at line 111 of file WMCalculateGFA.h.

◆ This

typedef WMCalculateGFA WMCalculateGFA::This

private

a conveniance typedef

Definition at line 51 of file WMCalculateGFA.h.

Constructor & Destructor Documentation

◆ WMCalculateGFA()

WMCalculateGFA::WMCalculateGFA ( )

Standard constructor.

Definition at line 40 of file WMCalculateGFA.cpp.

Referenced by factory().

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◆ ~WMCalculateGFA()

WMCalculateGFA::~WMCalculateGFA ( )

virtual

Destructor.

Definition at line 46 of file WMCalculateGFA.cpp.

Member Function Documentation

◆ connectors()

void WMCalculateGFA::connectors ( )

protectedvirtual

Initialize the connectors this module is using.

Reimplemented from WModule.

Definition at line 69 of file WMCalculateGFA.cpp.

References WModule::addConnector(), WModule::connectors(), m_input, and m_output.

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◆ factory()

std::shared_ptr< WModule > WMCalculateGFA::factory ( ) const

virtual

Due to the prototype design pattern used to build modules, this method returns a new instance of this method.

NOTE: it should never be initialized or modified in some other way. A simple new instance is required.

Returns: the prototype used to create every module in OpenWalnut.

Implements WModule.

Definition at line 50 of file WMCalculateGFA.cpp.

References WMCalculateGFA().

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◆ getDescription()

const std::string WMCalculateGFA::getDescription ( ) const

virtual

Gives back a description of this module.

Returns: description to module.

Implements WPrototyped.

Definition at line 64 of file WMCalculateGFA.cpp.

◆ getName()

const std::string WMCalculateGFA::getName ( ) const

virtual

Gives back the name of this module.

Returns: the module's name.

Implements WPrototyped.

Definition at line 59 of file WMCalculateGFA.cpp.

◆ getXPMIcon()

const char ** WMCalculateGFA::getXPMIcon ( ) const

virtual

Get the icon for this module in XPM format.

Returns: The icon.

Reimplemented from WModule.

Definition at line 55 of file WMCalculateGFA.cpp.

◆ handleException()

void WMCalculateGFA::handleException ( WException const & e )

private

Handle an exception thrown by a worker thread.

Parameters

e	The exception that was thrown during multithreaded computation.

Definition at line 197 of file WMCalculateGFA.cpp.

References m_exceptionCondition, and m_lastException.

Referenced by resetGFAPool().

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◆ moduleMain()

void WMCalculateGFA::moduleMain ( )

protectedvirtual

Entry point after loading the module.

Runs in separate thread.

Implements WModule.

Definition at line 94 of file WMCalculateGFA.cpp.

References WConditionSet::add(), WSymmetricSphericalHarmonic< T >::calcBaseMatrix(), WModule::debugLog(), m_BMat, m_currentProgress, m_dataSet, m_exceptionCondition, m_gfaFunc, m_gfaPool, m_input, m_lastException, WModule::m_moduleState, m_output, m_result, WThreadedRunner::m_shutdownFlag, WModule::ready(), resetGFAPool(), WConditionSet::setResetable(), and WConditionSet::wait().

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◆ perVoxelGFAFunc()

boost::array< double, 1 > WMCalculateGFA::perVoxelGFAFunc ( WValueSet< double >::SubArray const & s )

private

A function that gets called for every voxel in the input SH-dataset.

Calculates a fractional anisotropy measure.

Parameters

s	An array of SH-coefficients.

Returns: A boost::array of size 1 that contains the result for the given voxel.

Definition at line 213 of file WMCalculateGFA.cpp.

References WSymmetricSphericalHarmonic< T >::calcGFA(), m_BMat, and m_currentProgress.

Referenced by resetGFAPool().

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◆ properties()

void WMCalculateGFA::properties ( )

protectedvirtual

Initialize the properties for this module.

Reimplemented from WModule.

Definition at line 87 of file WMCalculateGFA.cpp.

References m_exceptionCondition, and WModule::properties().

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◆ resetGFAPool()

void WMCalculateGFA::resetGFAPool ( )

private

Reset the threaded functions.

Definition at line 168 of file WMCalculateGFA.cpp.

References WConditionSet::add(), handleException(), m_dataSet, m_gfaFunc, m_gfaPool, WModule::m_moduleState, perVoxelGFAFunc(), WConditionSet::remove(), and resetProgress().

Referenced by moduleMain().

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◆ resetProgress()

void WMCalculateGFA::resetProgress ( std::size_t todo )

private

Reset the progress indicator in the ui.

Parameters

todo	The number of steps needed to complete the job.

Definition at line 203 of file WMCalculateGFA.cpp.

References m_currentProgress, and WModule::m_progress.

Referenced by resetGFAPool().

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Member Data Documentation

◆ m_BMat

WMatrix<double> WMCalculateGFA::m_BMat

private

A matrix of SH base function values for various gradients.

Definition at line 169 of file WMCalculateGFA.h.

Referenced by moduleMain(), and perVoxelGFAFunc().

◆ m_currentProgress

std::shared_ptr< WProgress > WMCalculateGFA::m_currentProgress

private

The object that keeps track of the current progress.

Definition at line 154 of file WMCalculateGFA.h.

Referenced by moduleMain(), perVoxelGFAFunc(), and resetProgress().

◆ m_dataSet

std::shared_ptr< WDataSetSphericalHarmonics > WMCalculateGFA::m_dataSet

private

A pointer to the input dataset.

Definition at line 142 of file WMCalculateGFA.h.

Referenced by moduleMain(), and resetGFAPool().

◆ m_exceptionCondition

std::shared_ptr< WCondition > WMCalculateGFA::m_exceptionCondition

private

Condition indicating if any exception was thrown.

Definition at line 160 of file WMCalculateGFA.h.

Referenced by handleException(), moduleMain(), and properties().

◆ m_gfaFunc

std::shared_ptr< GFAFuncType > WMCalculateGFA::m_gfaFunc

private

The threaded function object.

Definition at line 163 of file WMCalculateGFA.h.

Referenced by moduleMain(), and resetGFAPool().

◆ m_gfaPool

std::shared_ptr< GFAPoolType > WMCalculateGFA::m_gfaPool

private

The threadpool.

Definition at line 166 of file WMCalculateGFA.h.

Referenced by moduleMain(), and resetGFAPool().

◆ m_input

std::shared_ptr< WModuleInputData< WDataSetSphericalHarmonics > > WMCalculateGFA::m_input

private

The input Connector for the SH data.

Definition at line 151 of file WMCalculateGFA.h.

Referenced by connectors(), and moduleMain().

◆ m_lastException

std::shared_ptr< WException > WMCalculateGFA::m_lastException

private

The last exception thrown by any worker thread.

Definition at line 157 of file WMCalculateGFA.h.

Referenced by handleException(), and moduleMain().

◆ m_output

std::shared_ptr< WModuleOutputData< WDataSetScalar > > WMCalculateGFA::m_output

private

The output Connector.

Definition at line 148 of file WMCalculateGFA.h.

Referenced by connectors(), and moduleMain().

◆ m_result

std::shared_ptr< WDataSetScalar > WMCalculateGFA::m_result

private

The output dataset.

Definition at line 145 of file WMCalculateGFA.h.

Referenced by moduleMain().

The documentation for this class was generated from the following files:

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ GFAFuncType

◆ GFAPoolType

◆ This

Constructor & Destructor Documentation

◆ WMCalculateGFA()

◆ ~WMCalculateGFA()

Member Function Documentation

◆ connectors()

◆ factory()

◆ getDescription()

◆ getName()

◆ getXPMIcon()

◆ handleException()

◆ moduleMain()

◆ perVoxelGFAFunc()

◆ properties()

◆ resetGFAPool()

◆ resetProgress()

Member Data Documentation

◆ m_BMat

◆ m_currentProgress

◆ m_dataSet

◆ m_exceptionCondition

◆ m_gfaFunc

◆ m_gfaPool

◆ m_input

◆ m_lastException

◆ m_output

◆ m_result