Reader for amiraMesh (.am) files. More...

#include <WMReadAmiraMesh.h>

Inheritance diagram for WMReadAmiraMesh:

Collaboration diagram for WMReadAmiraMesh:

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

virtual	~WMReadAmiraMesh ()
	Destructor for cleaning up resources. 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...

virtual void	requirements ()
	Initialize requirements 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 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 Member Functions
bool	readAmiraMesh (std::string fileName)
	Very prelimiary and specialized way of reading a spatial graph from an amira mesh. More...

void	findAndReadVertices (std::string startLabel, size_t numVertices, std::string fileName)
	Function for reading coordinates of vertices. More...

void	findAndReadEdgeConnectivity (std::string startLabel, size_t numConnections, std::string fileName)
	Function for reading connectivity of edges. More...

void	findAndReadNumEdgePoints (std::string startLabel, size_t numEdges, std::string fileName)
	Function for reading number of edgepoints per edge. More...

void	findAndReadEdgePoints (std::string startLabel, size_t numPoints, std::string fileName)
	Function for reading edgepoints. More...

void	prepareResult ()
	This function prepares the resulting dataset for being provided at the connector by construting it from the basic data that has been read. More...

Private Attributes
WPropFilename	m_dataFile
	The data will be read from this file. More...

std::shared_ptr< WCondition >	m_propCondition
	A condition used to notify about changes in several properties. More...

std::vector< WPosition >	m_vertices
	vertices of the spatial graph More...

std::vector< std::pair< size_t, size_t > >	m_edges
	Edge connectivity of the spatial graph. More...

std::vector< size_t >	m_numEdgePoints
	Number "points" per edge. More...

std::vector< WPosition >	m_edgePoints
	The positions of the points building the edges between the vertices. More...

std::shared_ptr< WModuleOutputData< WDataSetFibers > >	m_output
	The only output of this data module. More...

std::shared_ptr< WDataSetFibers >	m_graph
	The resulting fiber dataset respresenting the spatial graph. More...

Friends
class	WMReadAmiraMeshTest
	Only UnitTests may be friends. 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

Reader for amiraMesh (.am) files.

Definition at line 45 of file WMReadAmiraMesh.h.

Constructor & Destructor Documentation

◆ WMReadAmiraMesh()

WMReadAmiraMesh::WMReadAmiraMesh ( )

Standard constructor.

Definition at line 42 of file WMReadAmiraMesh.cpp.

Referenced by factory().

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◆ ~WMReadAmiraMesh()

WMReadAmiraMesh::~WMReadAmiraMesh ( )

virtual

Destructor for cleaning up resources.

Definition at line 47 of file WMReadAmiraMesh.cpp.

Member Function Documentation

◆ connectors()

void WMReadAmiraMesh::connectors ( )

protectedvirtual

Initialize the connectors this module is using.

Reimplemented from WModule.

Definition at line 71 of file WMReadAmiraMesh.cpp.

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

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◆ factory()

std::shared_ptr< WModule > WMReadAmiraMesh::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 52 of file WMReadAmiraMesh.cpp.

References WMReadAmiraMesh().

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◆ findAndReadEdgeConnectivity()

void WMReadAmiraMesh::findAndReadEdgeConnectivity	(	std::string	startLabel,
		size_t	numConnections,
		std::string	fileName
	)

private

Function for reading connectivity of edges.

It searches for the startLabel and starts reading from there

Parameters

startLabel	This label marks the location in the file where the data starts.
numConnections	The number of connections that are being read.
fileName	File containing the data to be read.

Definition at line 205 of file WMReadAmiraMesh.cpp.

References m_edges.

Referenced by readAmiraMesh().

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◆ findAndReadEdgePoints()

void WMReadAmiraMesh::findAndReadEdgePoints	(	std::string	startLabel,
		size_t	numPoints,
		std::string	fileName
	)

private

Function for reading edgepoints.

It searches for the startLabel and starts reading from there

Parameters

startLabel	This label marks the location in the file where the data starts.
numPoints	The number of points for which coordinates are being read.
fileName	File containing the data to be read.

Definition at line 180 of file WMReadAmiraMesh.cpp.

References m_edgePoints.

Referenced by readAmiraMesh().

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◆ findAndReadNumEdgePoints()

void WMReadAmiraMesh::findAndReadNumEdgePoints	(	std::string	startLabel,
		size_t	numEdges,
		std::string	fileName
	)

private

Function for reading number of edgepoints per edge.

It searches for the startLabel and starts reading from there

Parameters

startLabel	This label marks the location in the file where the data starts.
numEdges	The number of edges for which number of points are being read.
fileName	File containing the data to be read.

Definition at line 192 of file WMReadAmiraMesh.cpp.

References m_numEdgePoints.

Referenced by readAmiraMesh().

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◆ findAndReadVertices()

void WMReadAmiraMesh::findAndReadVertices	(	std::string	startLabel,
		size_t	numVertices,
		std::string	fileName
	)

private

Function for reading coordinates of vertices.

It searches for the startLabel and starts reading from there

Parameters

startLabel	This label marks the location in the file where the data starts.
numVertices	The number of vertices that are being read.
fileName	File containing the data to be read.

Definition at line 219 of file WMReadAmiraMesh.cpp.

References m_vertices.

Referenced by readAmiraMesh().

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◆ getDescription()

const std::string WMReadAmiraMesh::getDescription ( ) const

virtual

Gives back a description of this module.

Returns: description to module.

Implements WPrototyped.

Definition at line 66 of file WMReadAmiraMesh.cpp.

◆ getName()

const std::string WMReadAmiraMesh::getName ( ) const

virtual

Gives back the name of this module.

Returns: the module's name.

Implements WPrototyped.

Definition at line 61 of file WMReadAmiraMesh.cpp.

◆ getXPMIcon()

const char ** WMReadAmiraMesh::getXPMIcon ( ) const

virtual

Get the icon for this module in XPM format.

Returns: The icon.

Reimplemented from WModule.

Definition at line 57 of file WMReadAmiraMesh.cpp.

◆ moduleMain()

void WMReadAmiraMesh::moduleMain ( )

protectedvirtual

Entry point after loading the module.

Runs in separate thread.

Implements WModule.

Definition at line 94 of file WMReadAmiraMesh.cpp.

References WConditionSet::add(), m_dataFile, WModule::m_moduleState, m_propCondition, WThreadedRunner::m_shutdownFlag, prepareResult(), readAmiraMesh(), WModule::ready(), and WConditionSet::wait().

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◆ prepareResult()

void WMReadAmiraMesh::prepareResult ( )

private

This function prepares the resulting dataset for being provided at the connector by construting it from the basic data that has been read.

Definition at line 115 of file WMReadAmiraMesh.cpp.

References m_edgePoints, m_edges, m_graph, m_numEdgePoints, m_output, and WDataSetFiberVector::toWDataSetFibers().

Referenced by moduleMain().

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◆ properties()

void WMReadAmiraMesh::properties ( )

protectedvirtual

Initialize the properties for this module.

Reimplemented from WModule.

Definition at line 81 of file WMReadAmiraMesh.cpp.

References WPathHelper::getAppPath(), m_dataFile, m_propCondition, WModule::m_properties, and WModule::properties().

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◆ readAmiraMesh()

bool WMReadAmiraMesh::readAmiraMesh ( std::string fileName )

private

Very prelimiary and specialized way of reading a spatial graph from an amira mesh.

Parameters

fileName The name of the file containing the data that wil be read.

Returns: Indicates whether reading has been successful.

Definition at line 234 of file WMReadAmiraMesh.cpp.

References WLogger::addLogMessage(), findAndReadEdgeConnectivity(), findAndReadEdgePoints(), findAndReadNumEdgePoints(), findAndReadVertices(), and WLogger::getLogger().

Referenced by moduleMain().

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◆ requirements()

void WMReadAmiraMesh::requirements ( )

protectedvirtual

Initialize requirements for this module.

Reimplemented from WModule.

Definition at line 89 of file WMReadAmiraMesh.cpp.

Friends And Related Function Documentation

◆ WMReadAmiraMeshTest

friend class WMReadAmiraMeshTest

friend

Only UnitTests may be friends.

Definition at line 50 of file WMReadAmiraMesh.h.

Member Data Documentation

◆ m_dataFile

WPropFilename WMReadAmiraMesh::m_dataFile

private

The data will be read from this file.

Definition at line 166 of file WMReadAmiraMesh.h.

Referenced by moduleMain(), and properties().

◆ m_edgePoints

std::vector< WPosition > WMReadAmiraMesh::m_edgePoints

private

The positions of the points building the edges between the vertices.

Definition at line 172 of file WMReadAmiraMesh.h.

Referenced by findAndReadEdgePoints(), and prepareResult().

◆ m_edges

std::vector< std::pair< size_t, size_t > > WMReadAmiraMesh::m_edges

private

Edge connectivity of the spatial graph.

Definition at line 170 of file WMReadAmiraMesh.h.

Referenced by findAndReadEdgeConnectivity(), and prepareResult().

◆ m_graph

std::shared_ptr< WDataSetFibers > WMReadAmiraMesh::m_graph

private

The resulting fiber dataset respresenting the spatial graph.

Definition at line 175 of file WMReadAmiraMesh.h.

Referenced by prepareResult().

◆ m_numEdgePoints

std::vector< size_t > WMReadAmiraMesh::m_numEdgePoints

private

Number "points" per edge.

Definition at line 171 of file WMReadAmiraMesh.h.

Referenced by findAndReadNumEdgePoints(), and prepareResult().

◆ m_output

std::shared_ptr< WModuleOutputData< WDataSetFibers > > WMReadAmiraMesh::m_output

private

The only output of this data module.

Definition at line 174 of file WMReadAmiraMesh.h.

Referenced by connectors(), and prepareResult().

◆ m_propCondition

std::shared_ptr< WCondition > WMReadAmiraMesh::m_propCondition

private

A condition used to notify about changes in several properties.

Definition at line 167 of file WMReadAmiraMesh.h.

Referenced by moduleMain(), and properties().

◆ m_vertices

std::vector< WPosition > WMReadAmiraMesh::m_vertices

private

vertices of the spatial graph

Definition at line 169 of file WMReadAmiraMesh.h.

Referenced by findAndReadVertices().

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

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ WMReadAmiraMesh()

◆ ~WMReadAmiraMesh()

Member Function Documentation

◆ connectors()

◆ factory()

◆ findAndReadEdgeConnectivity()

◆ findAndReadEdgePoints()

◆ findAndReadNumEdgePoints()

◆ findAndReadVertices()

◆ getDescription()

◆ getName()

◆ getXPMIcon()

◆ moduleMain()

◆ prepareResult()

◆ properties()

◆ readAmiraMesh()

◆ requirements()

Friends And Related Function Documentation

◆ WMReadAmiraMeshTest

Member Data Documentation

◆ m_dataFile

◆ m_edgePoints

◆ m_edges

◆ m_graph

◆ m_numEdgePoints

◆ m_output

◆ m_propCondition

◆ m_vertices