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    OpenWalnut
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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< WModule > | factory () 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 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 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 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 | |
| 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< WDataSetScalar > | m_coordinateVector | 
| This is a pointer to the coord vector.  More... | |
| std::shared_ptr< WDataSetVector > | m_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< WTriangleMesh > | m_referenceMesh | 
| A pointer to the currently processed tri mesh.  More... | |
| std::shared_ptr< WTriangleMesh > | m_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< WCondition > | m_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< 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... | |
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.
      
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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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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.
Implements WModule.
Definition at line 61 of file WMPartition2Mesh.cpp.
      
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Gives back a description of this module.
Implements WPrototyped.
Definition at line 73 of file WMPartition2Mesh.cpp.
      
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Gives back the name of this module.
Implements WPrototyped.
Definition at line 67 of file WMPartition2Mesh.cpp.
      
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Entry point after loading the module.
Runs in separate thread.
Implements WModule.
Definition at line 124 of file WMPartition2Mesh.cpp.
References WConditionSet::add(), WModule::infoLog(), WModule::m_active, m_blankOutMesh, m_colorInput, m_colorVector, m_coordinateVector, m_coordInput, m_datasetSizeX, m_datasetSizeY, m_datasetSizeZ, m_infoTotalVertices, m_infoUnassignedVertices, m_meshInput1, m_meshInput2, m_meshOutput, WModule::m_moduleState, m_outMesh, m_propCondition, m_propHoleColor, m_propNonActiveColor, m_propProjectDistance, m_propWriteTrigger, m_referenceMesh, m_refs, WThreadedRunner::m_shutdownFlag, WPVBaseTypes::PV_TRIGGER_READY, WPVBaseTypes::PV_TRIGGER_TRIGGERED, WModule::ready(), WConditionSet::setResetable(), WConditionSet::wait(), and writeLabels().
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Initialize the properties for this module.
Reimplemented from WModule.
Definition at line 92 of file WMPartition2Mesh.cpp.
References WPropertyHelper::PC_PATHEXISTS::addTo(), WPropertyHelper::PC_ISDIRECTORY::addTo(), WModule::m_infoProperties, m_infoTotalVertices, m_infoUnassignedVertices, m_monochrome, m_propAnnotationFile, m_propCondition, WModule::m_properties, m_propHoleColor, m_propLabelFolder, m_propNonActiveColor, m_propProjectDistance, m_propWriteTrigger, WModule::properties(), and WPVBaseTypes::PV_TRIGGER_READY.
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Initialize requirements for this module.
Reimplemented from WModule.
Definition at line 119 of file WMPartition2Mesh.cpp.
      
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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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if set mesh colors must be initialized
Definition at line 142 of file WMPartition2Mesh.h.
Referenced by moduleMain().
      
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This is a pointer to the color input dataset.
Definition at line 129 of file WMPartition2Mesh.h.
Referenced by connectors(), and moduleMain().
      
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This is a pointer to the color vector.
Definition at line 132 of file WMPartition2Mesh.h.
Referenced by moduleMain().
      
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This is a pointer to the coord vector.
Definition at line 131 of file WMPartition2Mesh.h.
Referenced by moduleMain().
      
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An input connector that accepts order 1 datasets.
Definition at line 126 of file WMPartition2Mesh.h.
Referenced by connectors(), and moduleMain().
      
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Size of the dataset (X)
Definition at line 139 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and writeLabels().
      
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Size of the dataset (Y)
Definition at line 140 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and writeLabels().
      
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Size of the dataset (Z)
Definition at line 141 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and writeLabels().
      
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Info property: number of vertices.
Definition at line 152 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and properties().
      
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Info property: number of vertices without match.
Definition at line 153 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and properties().
      
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An input connector for the reference mesh.
Definition at line 127 of file WMPartition2Mesh.h.
Referenced by connectors(), and moduleMain().
      
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An input connector for the mesh.
Definition at line 128 of file WMPartition2Mesh.h.
Referenced by connectors(), and moduleMain().
      
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Output connector provided by this module.
Definition at line 133 of file WMPartition2Mesh.h.
Referenced by connectors(), and moduleMain().
      
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if used all labels will have m_propNonActiveColor
Definition at line 147 of file WMPartition2Mesh.h.
Referenced by properties(), and writeLabels().
      
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A pointer to the currently processed tri mesh.
Definition at line 136 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and writeLabels().
      
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filename for the annotation file
Definition at line 150 of file WMPartition2Mesh.h.
Referenced by properties().
      
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A condition used to notify about changes in several properties.
Definition at line 144 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and properties().
      
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color for the non labeled texture voxels
Definition at line 146 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and properties().
      
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folder where the labels will be written
Definition at line 149 of file WMPartition2Mesh.h.
Referenced by properties(), and writeLabels().
      
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color for the non labeled texture voxels
Definition at line 145 of file WMPartition2Mesh.h.
Referenced by moduleMain(), properties(), and writeLabels().
      
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maximum distance to project the voxels
Definition at line 148 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and properties().
      
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trigger the writing of the labels
Definition at line 151 of file WMPartition2Mesh.h.
Referenced by moduleMain(), and properties().
      
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A pointer to the currently processed tri mesh.
Definition at line 135 of file WMPartition2Mesh.h.
Referenced by moduleMain().
      
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a vector holding the cluster id corresponding to each vertex
Definition at line 137 of file WMPartition2Mesh.h.
Referenced by moduleMain().