OpenWalnut  1.5.0dev
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
WMPartition2Mesh Class Reference

This module projects a clustering partition result onto a (freesurfer) mesh Meant to work with hierchClustDisplay. More...

#include <WMPartition2Mesh.h>

+ Inheritance diagram for WMPartition2Mesh:
+ Collaboration diagram for WMPartition2Mesh:

Public Member Functions

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< WModulefactory () const
 Due to the prototype design pattern used to build modules, this method returns a new instance of this method. More...
 
- Public Member Functions inherited from WModule
 WModule ()
 Constructs a new WModule instance. More...
 
virtual ~WModule ()
 Destructor. More...
 
const InputConnectorListgetInputConnectors () const
 Gives back input connectors. More...
 
std::shared_ptr< WModuleInputConnectorgetInputConnector (std::string name)
 Finds the named connector for the module. More...
 
std::shared_ptr< WModuleInputConnectorfindInputConnector (std::string name)
 Finds the named connector for the module. More...
 
const OutputConnectorListgetOutputConnectors () const
 Gives back output connectors. More...
 
std::shared_ptr< WModuleOutputConnectorgetOutputConnector (std::string name)
 Finds the named connector for the module. More...
 
std::shared_ptr< WModuleOutputConnectorfindOutputConnector (std::string name)
 Finds the named connector for the module. More...
 
std::shared_ptr< WModuleConnectorgetConnector (std::string name)
 Finds the named connector for the module. More...
 
std::shared_ptr< WModuleConnectorfindConnector (std::string name)
 Finds the named connector for the module. More...
 
std::shared_ptr< WPropertiesgetProperties () const
 Return a pointer to the properties object of the module. More...
 
std::shared_ptr< WPropertiesgetInformationProperties () const
 Return a pointer to the information properties object of the module. More...
 
const WBoolFlagisInitialized () const
 Determines whether the module instance is properly initialized. More...
 
const WBoolFlagisUseable () const
 Checks whether the module instance is ready to be used. More...
 
const WBoolFlagisAssociated () const
 Checks whether this module is associated with an container. More...
 
const WBoolFlagisReady () const
 Checks whether this module is ready. More...
 
const WBoolFlagisReadyOrCrashed () const
 This is the logical or of isReady and isCrashed. More...
 
const WBoolFlagisRunning () 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< WModuleContainergetAssociatedContainer () 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< WProgressCombinergetRootProgressCombiner ()
 Gets the modules base progress. More...
 
virtual const char ** getXPMIcon () const
 Get the icon for this module in XPM format. 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 WRequirementcheckRequirements () 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 WBoolFlagisCrashed () 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

void writeLabels ()
 writes a freesurfer set of labels and tcl loading file More...
 

Private Attributes

std::shared_ptr< WModuleInputData< WDataSetScalar > > m_coordInput
 An input connector that accepts order 1 datasets. More...
 
std::shared_ptr< WModuleInputData< WTriangleMesh > > m_meshInput1
 An input connector for the reference mesh. More...
 
std::shared_ptr< WModuleInputData< WTriangleMesh > > m_meshInput2
 An input connector for the mesh. More...
 
std::shared_ptr< WModuleInputData< WDataSetVector > > m_colorInput
 This is a pointer to the color input dataset. More...
 
std::shared_ptr< WDataSetScalarm_coordinateVector
 This is a pointer to the coord vector. More...
 
std::shared_ptr< WDataSetVectorm_colorVector
 This is a pointer to the color vector. More...
 
std::shared_ptr< WModuleOutputData< WTriangleMesh > > m_meshOutput
 Output connector provided by this module. More...
 
std::shared_ptr< WTriangleMeshm_referenceMesh
 A pointer to the currently processed tri mesh. More...
 
std::shared_ptr< WTriangleMeshm_outMesh
 A pointer to the currently processed tri mesh. More...
 
std::vector< size_t > m_refs
 a vector holding the cluster id corresponding to each vertex More...
 
unsigned int m_datasetSizeX
 Size of the dataset (X) More...
 
unsigned int m_datasetSizeY
 Size of the dataset (Y) More...
 
unsigned int m_datasetSizeZ
 Size of the dataset (Z) More...
 
bool m_blankOutMesh
 if set mesh colors must be initialized More...
 
std::shared_ptr< WConditionm_propCondition
 A condition used to notify about changes in several properties. More...
 
WPropColor m_propNonActiveColor
 color for the non labeled texture voxels More...
 
WPropColor m_propHoleColor
 color for the non labeled texture voxels More...
 
WPropBool m_monochrome
 if used all labels will have m_propNonActiveColor More...
 
WPropDouble m_propProjectDistance
 maximum distance to project the voxels More...
 
WPropFilename m_propLabelFolder
 folder where the labels will be written More...
 
WPropFilename m_propAnnotationFile
 filename for the annotation file More...
 
WPropTrigger m_propWriteTrigger
 trigger the writing of the labels More...
 
WPropInt m_infoTotalVertices
 Info property: number of vertices. More...
 
WPropInt m_infoUnassignedVertices
 Info property: number of vertices without match. 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< WModuleSPtr
 Shared pointer to a WModule. More...
 
typedef std::shared_ptr< const WModuleConstSPtr
 Shared pointer to a const WModule. More...
 
- Public Types inherited from WThreadedRunner
typedef std::shared_ptr< WThreadedRunnerSPtr
 Abbreviation to a shared_ptr to this type. More...
 
typedef std::shared_ptr< const WThreadedRunnerConstSPtr
 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< WPropertiesm_properties
 The property object for the module. More...
 
std::shared_ptr< WPropertiesm_infoProperties
 The property object for the module containing only module whose purpose is "PV_PURPOSE_INFORMNATION". More...
 
std::shared_ptr< WProgressCombinerm_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< WProgressm_readyProgress
 Progress indicator for the "ready" state. More...
 
WConditionSet m_moduleState
 The internal state of the module. More...
 
std::shared_ptr< WModuleContainerm_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

This module projects a clustering partition result onto a (freesurfer) mesh Meant to work with hierchClustDisplay.

It accepts 4 different inputs:

Definition at line 64 of file WMPartition2Mesh.h.

Member Function Documentation

◆ connectors()

void WMPartition2Mesh::connectors ( )
protectedvirtual

Initialize the connectors this module is using.

Reimplemented from WModule.

Definition at line 80 of file WMPartition2Mesh.cpp.

References WModule::connectors(), WModuleInputData< T >::createAndAdd(), WModuleOutputData< T >::createAndAdd(), m_colorInput, m_coordInput, m_meshInput1, m_meshInput2, and m_meshOutput.

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◆ factory()

std::shared_ptr< WModule > WMPartition2Mesh::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 61 of file WMPartition2Mesh.cpp.

◆ getDescription()

const std::string WMPartition2Mesh::getDescription ( ) const
virtual

Gives back a description of this module.

Returns
description to module.

Implements WPrototyped.

Definition at line 73 of file WMPartition2Mesh.cpp.

◆ getName()

const std::string WMPartition2Mesh::getName ( ) const
virtual

Gives back the name of this module.

Returns
the module's name.

Implements WPrototyped.

Definition at line 67 of file WMPartition2Mesh.cpp.

◆ moduleMain()

void WMPartition2Mesh::moduleMain ( )
protectedvirtual

◆ properties()

void WMPartition2Mesh::properties ( )
protectedvirtual

◆ requirements()

void WMPartition2Mesh::requirements ( )
protectedvirtual

Initialize requirements for this module.

Reimplemented from WModule.

Definition at line 119 of file WMPartition2Mesh.cpp.

◆ writeLabels()

void WMPartition2Mesh::writeLabels ( )
private

writes a freesurfer set of labels and tcl loading file

Definition at line 474 of file WMPartition2Mesh.cpp.

References WModule::infoLog(), m_datasetSizeX, m_datasetSizeY, m_datasetSizeZ, m_monochrome, m_outMesh, m_propLabelFolder, m_propNonActiveColor, and string_utils::toString().

Referenced by moduleMain().

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Member Data Documentation

◆ m_blankOutMesh

bool WMPartition2Mesh::m_blankOutMesh
private

if set mesh colors must be initialized

Definition at line 142 of file WMPartition2Mesh.h.

Referenced by moduleMain().

◆ m_colorInput

std::shared_ptr< WModuleInputData< WDataSetVector > > WMPartition2Mesh::m_colorInput
private

This is a pointer to the color input dataset.

Definition at line 129 of file WMPartition2Mesh.h.

Referenced by connectors(), and moduleMain().

◆ m_colorVector

std::shared_ptr< WDataSetVector > WMPartition2Mesh::m_colorVector
private

This is a pointer to the color vector.

Definition at line 132 of file WMPartition2Mesh.h.

Referenced by moduleMain().

◆ m_coordinateVector

std::shared_ptr< WDataSetScalar > WMPartition2Mesh::m_coordinateVector
private

This is a pointer to the coord vector.

Definition at line 131 of file WMPartition2Mesh.h.

Referenced by moduleMain().

◆ m_coordInput

std::shared_ptr< WModuleInputData< WDataSetScalar > > WMPartition2Mesh::m_coordInput
private

An input connector that accepts order 1 datasets.

Definition at line 126 of file WMPartition2Mesh.h.

Referenced by connectors(), and moduleMain().

◆ m_datasetSizeX

unsigned int WMPartition2Mesh::m_datasetSizeX
private

Size of the dataset (X)

Definition at line 139 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and writeLabels().

◆ m_datasetSizeY

unsigned int WMPartition2Mesh::m_datasetSizeY
private

Size of the dataset (Y)

Definition at line 140 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and writeLabels().

◆ m_datasetSizeZ

unsigned int WMPartition2Mesh::m_datasetSizeZ
private

Size of the dataset (Z)

Definition at line 141 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and writeLabels().

◆ m_infoTotalVertices

WPropInt WMPartition2Mesh::m_infoTotalVertices
private

Info property: number of vertices.

Definition at line 152 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and properties().

◆ m_infoUnassignedVertices

WPropInt WMPartition2Mesh::m_infoUnassignedVertices
private

Info property: number of vertices without match.

Definition at line 153 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and properties().

◆ m_meshInput1

std::shared_ptr< WModuleInputData< WTriangleMesh > > WMPartition2Mesh::m_meshInput1
private

An input connector for the reference mesh.

Definition at line 127 of file WMPartition2Mesh.h.

Referenced by connectors(), and moduleMain().

◆ m_meshInput2

std::shared_ptr< WModuleInputData< WTriangleMesh > > WMPartition2Mesh::m_meshInput2
private

An input connector for the mesh.

Definition at line 128 of file WMPartition2Mesh.h.

Referenced by connectors(), and moduleMain().

◆ m_meshOutput

std::shared_ptr< WModuleOutputData< WTriangleMesh > > WMPartition2Mesh::m_meshOutput
private

Output connector provided by this module.

Definition at line 133 of file WMPartition2Mesh.h.

Referenced by connectors(), and moduleMain().

◆ m_monochrome

WPropBool WMPartition2Mesh::m_monochrome
private

if used all labels will have m_propNonActiveColor

Definition at line 147 of file WMPartition2Mesh.h.

Referenced by properties(), and writeLabels().

◆ m_outMesh

std::shared_ptr< WTriangleMesh > WMPartition2Mesh::m_outMesh
private

A pointer to the currently processed tri mesh.

Definition at line 136 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and writeLabels().

◆ m_propAnnotationFile

WPropFilename WMPartition2Mesh::m_propAnnotationFile
private

filename for the annotation file

Definition at line 150 of file WMPartition2Mesh.h.

Referenced by properties().

◆ m_propCondition

std::shared_ptr< WCondition > WMPartition2Mesh::m_propCondition
private

A condition used to notify about changes in several properties.

Definition at line 144 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and properties().

◆ m_propHoleColor

WPropColor WMPartition2Mesh::m_propHoleColor
private

color for the non labeled texture voxels

Definition at line 146 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and properties().

◆ m_propLabelFolder

WPropFilename WMPartition2Mesh::m_propLabelFolder
private

folder where the labels will be written

Definition at line 149 of file WMPartition2Mesh.h.

Referenced by properties(), and writeLabels().

◆ m_propNonActiveColor

WPropColor WMPartition2Mesh::m_propNonActiveColor
private

color for the non labeled texture voxels

Definition at line 145 of file WMPartition2Mesh.h.

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

◆ m_propProjectDistance

WPropDouble WMPartition2Mesh::m_propProjectDistance
private

maximum distance to project the voxels

Definition at line 148 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and properties().

◆ m_propWriteTrigger

WPropTrigger WMPartition2Mesh::m_propWriteTrigger
private

trigger the writing of the labels

Definition at line 151 of file WMPartition2Mesh.h.

Referenced by moduleMain(), and properties().

◆ m_referenceMesh

std::shared_ptr< WTriangleMesh > WMPartition2Mesh::m_referenceMesh
private

A pointer to the currently processed tri mesh.

Definition at line 135 of file WMPartition2Mesh.h.

Referenced by moduleMain().

◆ m_refs

std::vector<size_t> WMPartition2Mesh::m_refs
private

a vector holding the cluster id corresponding to each vertex

Definition at line 137 of file WMPartition2Mesh.h.

Referenced by moduleMain().


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