OpenWalnut
1.5.0dev
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This module projects a clustering partition result onto a (freesurfer) mesh Meant to work with hierchClustDisplay. More...
#include <WMPartition2Mesh.h>
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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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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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.
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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protectedvirtual |
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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protectedvirtual |
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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protectedvirtual |
Initialize requirements for this module.
Reimplemented from WModule.
Definition at line 119 of file WMPartition2Mesh.cpp.
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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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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().