#include <Process.hpp>

Inheritance diagram for mgx::Process:

Classes
class	CheckState

Public Types
enum	ProcessAction { PROCESS_RUN, PROCESS_STEP, PROCESS_REWIND }
	Enumeration for process flow control. More...

enum	StackCheckType { STACK_ANY, STACK_NON_EMPTY, STACK_VISIBLE, STACK_EMPTY, STACK_SCALED, STACK_TRANSFORMED, STACK_NON_SCALED, STACK_NON_TRANSFORMED }
	Enumeration for the bitfield that identifies stack properties. More...

enum	StoreCheckType { STORE_ANY, STORE_NON_EMPTY, STORE_VISIBLE, STORE_EMPTY, STORE_LABEL, STORE_NON_LABEL, STORE_SCALED, STORE_TRANSFORMED, STORE_NON_SCALED, STORE_NON_TRANSFORMED, STORE_WORK, STORE_MAIN }
	Enumeration for the bitfield that identifies store properties. More...

enum	MeshCheckType { MESH_ANY, MESH_NON_EMPTY, MESH_VISIBLE, MESH_HEAT, MESH_LABEL, MESH_NORMAL, MESH_SIGNAL, MESH_TEXTURE, MESH_IMAGE, MESH_SHOW_MESH, MESH_SHOW_SURF, MESH_ALL, MESH_BORDER, MESH_CELLMAP, MESH_CELLS, MESH_IMG_TEX, MESH_SCALED, MESH_TRANSFORMED, MESH_EMPTY, MESH_NON_CELLS, MESH_NON_IMG_TEX, MESH_NON_SCALED, MESH_NON_TRANSFORMED, MESH_USE_PARENTS }
	Enumeration for the bitfield that identifies mesh properties. More...

enum	CheckType { CHECK_STACK, CHECK_STORE, CHECK_MESH }
	Enumeration of the type of checks that can be performed. More...

enum	CheckWhich { CHECK_CURRENT }

typedef std::vector< Stack * >::iterator	stack_iterator

typedef std::vector< Stack * >::const_iterator	const_stack_iterator

typedef std::vector< Mesh * >::iterator	mesh_iterator

typedef std::vector< Mesh * >::const_iterator	const_mesh_iterator

Public Member Functions
	Process (const Process &p)
	Copy constructor. More...

virtual	~Process ()
	Virtual destructor. More...

void	actingFile (const QString &filename, bool project_file=false)
	Method to be called anytime a file is acted on (i.e. More...

QString	actingFile () const
	Get the file currently defining the path of the system. More...

QString	pythonCall (const QStringList &parms) const
	Return the python call describing the current process. More...

int	stackCount () const
	Number of stacks available to the process. More...

Stack *	stack (int i)
	Returns the ith stack, or 0 if there is no such stack. More...

Stack *	currentStack ()
	Returns the current stack (i.e. More...

Stack *	otherStack ()
	Returns the other stack (i.e. More...

int	currentStackId () const
	Return the id (i.e. More...

int	otherStackId () const
	Return the id (i.e. More...

void	setCurrentStackId (int i)
	Change which stack is current. More...

bool	setCurrentStack (int id, const QString &store)

bool	takeSnapshot (QString filename, float overSampling=1.0f, int width=0, int height=0, int quality=95, bool expand_frustum=false)
	Save screen shot to a file. More...

bool	setStatus (const QString &msg, bool alsoPrint=true)
	Display a message in the status bar More...

bool	systemCommand (int command, const QStringList &parms)
	Run a system command. More...

MGXCamera *	camera ()
	Get the camera. More...

std::pair< stack_iterator, stack_iterator >	stacks ()
	Iterate over all the stacks. More...

std::pair< const_stack_iterator, const_stack_iterator >	stacks () const
	Iterate over all the stacks. More...

Stack *	addStack ()
	Add a new stack to the process. More...

bool	deleteStack (int i)
	Delete the stack of given id. More...

int	meshCount () const
	Returns the number of mesh available to the process. More...

Mesh *	mesh (int i)
	Returns the ith mesh. More...

Mesh *	currentMesh ()
	Returns the current mesh (i.e. More...

Mesh *	otherMesh ()
	Returns the other mesh (i.e. More...

int	currentMeshId () const
	Returns the id (i.e. More...

int	otherMeshId () const
	Returns the id (i.e. More...

void	setCurrentMeshId (int i)
	Change which mesh is current. More...

std::pair< mesh_iterator, mesh_iterator >	meshes ()
	Iterate over all the meshs. More...

std::pair< const_mesh_iterator, const_mesh_iterator >	meshes () const
	Iterate over all the meshs. More...

Mesh *	addMesh (const Stack *stack)
	Add a mesh to the process for the given stack. More...

bool	deleteMesh (int i)
	Remove a mesh from the process. More...

int	selectedLabel () const
	Get the current selected label. More...

void	setSelectedLabel (int label)
	Change the current selected label. More...

float	globalBrightness ()
	Return the current setting for the global brightness level. More...

float	globalContrast ()
	Return the current setting for the global contrast level. More...

void	setGlobalBrightness (float value)
	Change the current setting for the global brightness level. More...

void	setGlobalContrast (float value)
	Change the current setting for the global contrast level. More...

bool	meshSelection () const
	Returns if the user has mesh selection active. More...

bool	lineBorderSelection () const
	Returns is the user has line border selection active. More...

bool	updateState ()
	Update the Gui of MorphoGraphX. More...

bool	updateViewer ()
	Tell the viewer to redraw. More...

bool	loadView (const QString &fileName)
	Load viewfile. More...

bool	saveView (const QString &fileName)
	Save viewfile. More...

bool	setErrorMessage (const QString &str)
	Set an error message that will be displayed if the process returns false. More...

QString	errorMessage () const
	Get the current error message. More...

void	setWarningMessage (const QString &str)
	Set a warning message that will be displayed if the process returns true. More...

QString	warningMessage () const
	Get the current warning message. More...

void	userCancel () const
	Throw an exception informing the system that the user canceled the current process. More...

const QString &	file () const
	Get the name of the file that was used to load the current process (i.e. More...

Clip *	clip1 ()
	Return the object defining the first clipping region. More...

Clip *	clip2 ()
	Return the object defining the second clipping region. More...

Clip *	clip3 ()
	Return the object defining the third clipping region. More...

const Clip *	clip1 () const
	Return the object defining the first clipping region. More...

const Clip *	clip2 () const
	Return the object defining the second clipping region. More...

const Clip *	clip3 () const
	Return the object defining the third clipping region. More...

CuttingSurface *	cuttingSurface ()
	Return the cutting surface. More...

const CuttingSurface *	cuttingSurface () const
	Return the cutting surface. More...

Process *	makeProcess (const QString &processName)
	Creates a process object by name. More...

template<typename ProcessT >
bool	getProcess (const QString &processName, ProcessT *&p)
	Gets process. More...

bool	setCurrentParms ()
	Set the parms from the GUI. More...

bool	runProcess (Process &proc, QStringList &parms) throw ()
	Launch a process with generic arguments. More...

bool	runProcess (const QString &processName, QStringList &parms) throw ()
	Launch a process by name. More...

virtual bool	initialize (QWidget *)
	Initialize the process. More...

virtual bool	run ()
	Runs the process. More...

virtual bool	finalize (QWidget *)
	This is an optional method that is called from the main thread before the process is run. More...

CheckState	checkState ()
	Call this function and convert the result to a boolean. More...

Public Member Functions inherited from mgx::ProcessParms
	ProcessParms ()

virtual	~ProcessParms ()

QString	name () const
	Process name that is using the parameters. More...

QString	description () const
	Process description. More...

QStringList	parmNames () const
	List of named parameters. More...

QStringList	parmDescs () const
	List of parameters descriptions. More...

QStringList	parmDefaults () const
	List of default parms. More...

ParmChoiceList	parmChoice () const
	Allows the parameter to have a pick list in the GUI. More...

QIcon	icon () const
	Icon to use to represent the process in the GUI. More...

QString	parm (const QString &name) const
	Get a single parameter value by name. More...

const QStringList &	getParms ()
	Get the list of parameter values. More...

bool	setName (const QString &name)
	Set the name. More...

bool	setDesc (const QString &description)
	Set the description. More...

bool	addParm (const QString &parmName, const QString &desc, const QString &def, const QStringList &choices=QStringList())
	Add a parameter to the list. More...

bool	insertParm (const QString &parmName, const QString &desc, const QString &def, int pos, const QStringList &choices=QStringList())
	Insert a parameter to the list. More...

bool	setParm (const QString &parmName, const QString &parm)
	Set the parameter's value. More...

bool	setParms (const QStringList &parms)
	Set all the parameter values. More...

bool	setParmDesc (const QString &parmName, const QString &desc)
	Set the parameter's description. More...

bool	setParmDefault (const QString &parmName, const QString &def)
	Set the parameter's default value. More...

bool	setParmChoices (const QString &parmName, const QStringList &choices)
	Set the parameter's choices. More...

bool	setIcon (const QIcon &icon)
	Set the icon. More...

QStringList	parmList (const QString &key=QString()) const
	Return a list of parameter names. More...

Public Attributes
PrivateProcess *	p

Static Public Attributes
static unsigned int	processVersion

static std::vector< Colorf > &	LabelColors

Friends
class	SetupProcess

class	Process::CheckState

Internal methods
bool	stackCheck (int checks, int which)
	Check stack properties. More...

bool	storeCheck (int checks, int which)
	Check store properties. More...

bool	meshCheck (int checks, int which)
	Check mesh properties. More...

QString	stackError (int checks, int which)
	Generate a standardised string describing how the stack should be to not generate an error. More...

QString	storeError (int checks, int which)
	Generate a standardised string describing how the store should be to not generate an error. More...

QString	meshError (int checks, int which)
	Generate a standardised string describing how the mesh should be to not generate an error. More...

void	systemCommandGui (mgx::Process *, int, QStringList)

void	systemCommandProcess (mgx::Process *, int, QStringList)

Additional Inherited Members
Static Public Member Functions inherited from mgx::ProcessParms
static QStringList	booleanChoice ()
	Helper function that provides a list of choices for a boolean argument. More...

static QStringList	storeChoice ()
	Helper function that provides a list of choices for choosing from the main or work stack. More...

static QStringList	stackChoice ()
	Helper function that provides a list of choices for choosing between stack 1 and 2. More...

static QStringList	meshChoice ()
	Helper function that provides a list of choices for choosing between stack 1 and 2. More...

static QStringList	dimensionChoice ()
	Helper function that provides a list of choices for choosing the dimension. More...

static QStringList	dimChoice ()
	Helper function that provides a list of choices for choosing the dimension. More...

Detailed Description

This is the main process class, the one all process inherit from.

Definition at line 219 of file Process.hpp.

Member Typedef Documentation

◆ const_mesh_iterator

typedef std::vector<Mesh*>::const_iterator mgx::Process::const_mesh_iterator

Definition at line 230 of file Process.hpp.

◆ const_stack_iterator

typedef std::vector<Stack*>::const_iterator mgx::Process::const_stack_iterator

Definition at line 227 of file Process.hpp.

◆ mesh_iterator

typedef std::vector<Mesh*>::iterator mgx::Process::mesh_iterator

Definition at line 229 of file Process.hpp.

◆ stack_iterator

typedef std::vector<Stack*>::iterator mgx::Process::stack_iterator

Definition at line 226 of file Process.hpp.

Member Enumeration Documentation

◆ CheckType

enum mgx::Process::CheckType

Enumeration of the type of checks that can be performed.

Enumerator
CHECK_STACK	Check stack properties.
CHECK_STORE	Check store properties.
CHECK_MESH	Check mesh properties.

Definition at line 673 of file Process.hpp.

◆ CheckWhich

enum mgx::Process::CheckWhich

Enumerator
CHECK_CURRENT	Constant marking the element to check is the current one.

Definition at line 679 of file Process.hpp.

◆ MeshCheckType

enum mgx::Process::MeshCheckType

Enumeration for the bitfield that identifies mesh properties.

Enumerator
MESH_ANY	Any mesh.
MESH_NON_EMPTY	Non-empty mesh.
MESH_VISIBLE	Either mesh or surface are visible.
MESH_HEAT	Show the heat map.
MESH_LABEL	Show the label.
MESH_NORMAL	Show the normal.
MESH_SIGNAL	Show the signal.
MESH_TEXTURE	Show the texture.
MESH_IMAGE	Show the image.
MESH_SHOW_MESH	Show the mesh.
MESH_SHOW_SURF	Show the surface.
MESH_ALL	Show the all mesh.
MESH_BORDER	Show border only.
MESH_CELLMAP	Show the cell map.
MESH_CELLS	This mesh is a cell mesh.
MESH_IMG_TEX	This mesh has a texture.
MESH_SCALED	This mesh is scaled.
MESH_TRANSFORMED	This mesh is transformed.
MESH_EMPTY	Empty mesh.
MESH_NON_CELLS	This mesh is not a cell mesh.
MESH_NON_IMG_TEX	This mesh doesn't have an image texture.
MESH_NON_SCALED	This mesh is non-scaled.
MESH_NON_TRANSFORMED	This mesh is non-transformed.
MESH_USE_PARENTS	Show the parent label.

Definition at line 636 of file Process.hpp.

◆ ProcessAction

enum mgx::Process::ProcessAction

Enumeration for process flow control.

Enumerator
PROCESS_RUN
PROCESS_STEP
PROCESS_REWIND

Definition at line 540 of file Process.hpp.

◆ StackCheckType

enum mgx::Process::StackCheckType

Enumeration for the bitfield that identifies stack properties.

Enumerator
STACK_ANY	Any stack.
STACK_NON_EMPTY	Non-empty stack.
STACK_VISIBLE	Visible stack.
STACK_EMPTY	Empty stack.
STACK_SCALED	Scaled stack.
STACK_TRANSFORMED	Transformed stack.
STACK_NON_SCALED	Non-Scaled stack.
STACK_NON_TRANSFORMED	Non-Transformed stack.

Definition at line 600 of file Process.hpp.

◆ StoreCheckType

enum mgx::Process::StoreCheckType

Enumeration for the bitfield that identifies store properties.

Enumerator
STORE_ANY	Any store.
STORE_NON_EMPTY	Non-Empty store.
STORE_VISIBLE	Visible store.
STORE_EMPTY	Empty store.
STORE_LABEL	Label store.
STORE_NON_LABEL	Non-Label store.
STORE_SCALED	Scaled store.
STORE_TRANSFORMED	Transformed store.
STORE_NON_SCALED	Non-Scaled store.
STORE_NON_TRANSFORMED	Non-Transformed store.
STORE_WORK	Work store.
STORE_MAIN	Main store.

Definition at line 615 of file Process.hpp.

Constructor & Destructor Documentation

◆ Process()

mgx::Process::Process ( const Process & p )

Copy constructor.

Use when inheriting from Process. Normally makeProcess is used to create new processes.

◆ ~Process()

virtual mgx::Process::~Process ( )

inlinevirtual

Virtual destructor.

Definition at line 249 of file Process.hpp.

Member Function Documentation

◆ actingFile() [1/2]

QString mgx::Process::actingFile ( ) const

Get the file currently defining the path of the system.

◆ actingFile() [2/2]

void mgx::Process::actingFile	(	const QString &	filename,
		bool	project_file = `false`
	)

Method to be called anytime a file is acted on (i.e.

saved/loaded).

If needed, it will set the current folder to the one containing the file and start a session

If it is a project file (i.e. ending in mgxv), then project_file should be set to true to force the change in folder.

◆ addMesh()

Mesh* mgx::Process::addMesh ( const Stack * stack )

Add a mesh to the process for the given stack.

◆ addStack()

Stack* mgx::Process::addStack ( )

Add a new stack to the process.

◆ camera()

MGXCamera* mgx::Process::camera ( )

Get the camera.

◆ checkState()

CheckState mgx::Process::checkState ( )

Call this function and convert the result to a boolean.

If the checks hold, it will return true. If not, it will return false and set the error message to a standard, fully descriptive description of what conditions should be met to use this process.

Syntax:

checkState().TYPE(CONSTRAINTS).TYPE(CONSTRAINTS)...;

Example:

if(!checkState().store(STORE_MAIN | STORE_NON_EMPTY) .store(STORE_WORK | STORE_LABEL)) return false;

FIXME: what does the state apply to? FIXME: why is it necessary to check it? FIXME: how is the state changed?

◆ clip1() [1/2]

Clip* mgx::Process::clip1 ( )

Return the object defining the first clipping region.

◆ clip1() [2/2]

const Clip* mgx::Process::clip1 ( ) const

Return the object defining the first clipping region.

◆ clip2() [1/2]

Clip* mgx::Process::clip2 ( )

Return the object defining the second clipping region.

◆ clip2() [2/2]

const Clip* mgx::Process::clip2 ( ) const

Return the object defining the second clipping region.

◆ clip3() [1/2]

Clip* mgx::Process::clip3 ( )

Return the object defining the third clipping region.

◆ clip3() [2/2]

const Clip* mgx::Process::clip3 ( ) const

Return the object defining the third clipping region.

◆ currentMesh()

Mesh* mgx::Process::currentMesh ( )

Returns the current mesh (i.e.

the mesh currently selected by the user)

◆ currentMeshId()

int mgx::Process::currentMeshId ( ) const

Returns the id (i.e.

number) of the current mesh

◆ currentStack()

Stack* mgx::Process::currentStack ( )

Returns the current stack (i.e.

the stack currently selected by the user).

◆ currentStackId()

int mgx::Process::currentStackId ( ) const

Return the id (i.e.

number) of the current stack.

◆ cuttingSurface() [1/2]

CuttingSurface* mgx::Process::cuttingSurface ( )

Return the cutting surface.

◆ cuttingSurface() [2/2]

const CuttingSurface* mgx::Process::cuttingSurface ( ) const

Return the cutting surface.

◆ deleteMesh()

bool mgx::Process::deleteMesh ( int i )

Remove a mesh from the process.

◆ deleteStack()

bool mgx::Process::deleteStack ( int i )

Delete the stack of given id.

Note: The current implementation assumes there are at least two stacks always available

◆ errorMessage()

QString mgx::Process::errorMessage ( ) const

Get the current error message.

◆ file()

const QString& mgx::Process::file ( ) const

Get the name of the file that was used to load the current process (i.e.

the mgxv file), if any.

◆ finalize()

virtual bool mgx::Process::finalize ( QWidget * )

inlinevirtual

This is an optional method that is called from the main thread before the process is run.

If there is an active GUI, then parent will be set.

Parameters

parent Pointer to the parent widget if there is an active GUI.

Definition at line 587 of file Process.hpp.

◆ getProcess()

template<typename ProcessT >

bool mgx::Process::getProcess	(	const QString &	processName,
		ProcessT *&	p
	)

inline

Gets process.

Definition at line 523 of file Process.hpp.

◆ globalBrightness()

float mgx::Process::globalBrightness ( )

Return the current setting for the global brightness level.

◆ globalContrast()

float mgx::Process::globalContrast ( )

Return the current setting for the global contrast level.

◆ initialize()

virtual bool mgx::Process::initialize ( QWidget * )

inlinevirtual

Initialize the process.

Called from the main (GUI) thread before the process is run. If there is an active GUI, then parent will be set.

The process can use the method to update the argument list with a dialog. If the arguments are updates, the process should return true

Parameters

parent Pointer to the parent widget if there is an active GUI.

Returns: false if the process is not to run afterwards

Reimplemented in mgx::ExportPlaneData, mgx::CreateJunctionGraphStack, mgx::CreateJunctionGraph, mgx::LoadTransform, mgx::MeshCircularHistogram, mgx::SaveTransform, mgx::HeatAndChangeMap, mgx::StackOpenSaveFolder, mgx::LabelledStackComparison, mgx::WriteGrowthMapData, mgx::CombineAttrMaps, mgx::QuickSaveFile, mgx::SaveViewFile, mgx::DataAnalysisGUS, mgx::MeshExport, mgx::DataAnalysis, mgx::LoadParents, mgx::ImportParentAttrNew, mgx::SaveParents, mgx::LoadViewFile, mgx::CellAtlas, mgx::LoadHeatMap, mgx::MergeParentFiles, mgx::MeshImport, mgx::SaveHeatMap, mgx::MeshSave, mgx::LoadCellData, mgx::DisplayPDGsVertex, mgx::MeshLoad, mgx::ExportJunctionAnglesNew, mgx::FlipBezierLine, mgx::DisplayPCAOld, mgx::NewBezierRingFromSelected, mgx::ExportJunctionAngles, mgx::SaveNeighborhoodData2D, mgx::StackOpen, mgx::NewBezierRing, mgx::ExportInternalAngles, mgx::SaveNeighborhoodData, mgx::DisplayPDGs, mgx::SaveCellData, mgx::StackExport, mgx::MeasureBezierExport, mgx::ComputeHeatMap, mgx::SaveCellContourFile, mgx::StackHistogramBezier, mgx::SaveAttributesCSVExtended, mgx::LoadPlyFileCellGraph, mgx::StackSave, mgx::StackCircularHistogram, mgx::NewBezier, mgx::StackImport, mgx::SaveAttributesCSV, mgx::SaveGlobalTransform, mgx::PythonProcess, mgx::SavePlyFile, mgx::LoadCellAxis, mgx::SaveBezier, mgx::ManageAttributes, mgx::SaveCellAxis, and mgx::LoadBezier.

Definition at line 572 of file Process.hpp.

◆ lineBorderSelection()

bool mgx::Process::lineBorderSelection ( ) const

Returns is the user has line border selection active.

◆ loadView()

bool mgx::Process::loadView ( const QString & fileName )

Load viewfile.

◆ makeProcess()

Process* mgx::Process::makeProcess ( const QString & processName )

Creates a process object by name.

◆ mesh()

Mesh* mgx::Process::mesh ( int i )

Returns the ith mesh.

◆ meshCheck()

bool mgx::Process::meshCheck	(	int	checks,
		int	which
	)

protected

Check mesh properties.

◆ meshCount()

int mgx::Process::meshCount ( ) const

Returns the number of mesh available to the process.

◆ meshError()

QString mgx::Process::meshError	(	int	checks,
		int	which
	)

protected

Generate a standardised string describing how the mesh should be to not generate an error.

◆ meshes() [1/2]

std::pair<mesh_iterator, mesh_iterator> mgx::Process::meshes ( )

Iterate over all the meshs.

◆ meshes() [2/2]

std::pair<const_mesh_iterator, const_mesh_iterator> mgx::Process::meshes ( ) const

Iterate over all the meshs.

◆ meshSelection()

bool mgx::Process::meshSelection ( ) const

Returns if the user has mesh selection active.

◆ otherMesh()

Mesh* mgx::Process::otherMesh ( )

Returns the other mesh (i.e.

the mesh not currently selected by the user)

◆ otherMeshId()

int mgx::Process::otherMeshId ( ) const

Returns the id (i.e.

number) of the other mesh

◆ otherStack()

Stack* mgx::Process::otherStack ( )

Returns the other stack (i.e.

the stack not currently selected by the user).

◆ otherStackId()

int mgx::Process::otherStackId ( ) const

Return the id (i.e.

number) of the other stack.

◆ pythonCall()

QString mgx::Process::pythonCall ( const QStringList & parms ) const

Return the python call describing the current process.

◆ run()

virtual bool mgx::Process::run ( )

inlinevirtual

Runs the process.

Returns: false if process failed, true otherwise (FIXME: what kind of fail do we care about?)

Reimplemented in mgx::DivisionAnalysisMulti3D, mgx::TestDivisionPlanes3D, mgx::FlatDivisionPlane3D, mgx::ExportPlaneData, mgx::AngleTwoPlanes, mgx::CreatePlaneFromSelectedVtxs, mgx::MeasureBetweenessCurrentFlow3D, mgx::MeasureBetweenessCurrentFlow, mgx::MeasureBetweenessCentrality3D, mgx::MeasureBetweenessCentrality, mgx::DivisionPlaneHeat, mgx::OrganDivisionSimulation, mgx::CreateJunctionGraphStack, mgx::CreateJunctionGraph, mgx::CellTypeRecognitionAllMeasures, mgx::OutsideCellWall, mgx::CellAxisAngles3D, mgx::DistanceStackToMesh, mgx::CellAxisAngles, mgx::MergeCellsMGXM3D, mgx::LoadTransform, mgx::MeshCircularHistogram, mgx::SaveTransform, mgx::JoinCellsMGX3D, mgx::CellAxisAttrMapImport, mgx::JunctionDistance, mgx::DeleteOutsideMesh, mgx::CellAxisAttrMapExport, mgx::MeasureCellCoord, mgx::HeatMapSmooth, mgx::AnalysisDivPlanes, mgx::MeasureCellDistance, mgx::StackRelabelFromMesh, mgx::DisplayCustomOrientations3D, mgx::HeatMapAllMeasures2D, mgx::SurfaceAnalyzeBezierLine, mgx::DisplayAllPlanes, mgx::MeasureNeighborhoodVariabilityRadius, mgx::HeatMapCellType, mgx::AddNoiseStack, mgx::StackRelabel, mgx::DisplayCellAxisFromTensor, mgx::BezierFromCellFile, mgx::MeasureNeighborhoodNeighbors, mgx::RunAllParentHeat, mgx::DisplayOptimalPlanesSimple, mgx::MeasureDistanceToBezierPlane3D, mgx::SetSignalProcess, mgx::MeasureNeighborhoodAspectRatio, mgx::ShiftStack, mgx::TopHatStack, mgx::HeatAndChangeMap, mgx::MeasureBezierLineCoord3D, mgx::MeasureNeighborhoodPerimeter, mgx::DisplayOptimalPlanes, mgx::GrowthAnalysis3D, mgx::RescaleSignal, mgx::ScaleStack, mgx::CellGraph3D, mgx::DisplayCustomOrientations, mgx::MeasureNeighborhoodArea, mgx::CImgLaplaceStack, mgx::MeasureDistanceToBezier3D, mgx::CellAnalysis3D, mgx::SwitchHeatParent, mgx::SetDivisionPoint, mgx::StackOpenSaveFolder, mgx::MeshOpening, mgx::MeasureStomataArea, mgx::ResizeCanvas, mgx::CustomDirectionsAngle3D, mgx::CImgMedianBlurStack, mgx::Measure3DDistanceToMesh, mgx::LabelledStackComparison, mgx::SelectByHeat, mgx::MeasureCommonNhbrs, mgx::MeshClosing, mgx::DistanceCells, mgx::TakeSnapshot, mgx::ChangeVoxelSize, mgx::Measure3DCellCoord, mgx::CustomDirectionsAngle, mgx::WriteGrowthMapData, mgx::CImgGaussianBlurStack, mgx::CombineAttrMaps, mgx::MeasureVariabilityRadius, mgx::SelectShortWalls, mgx::MeshLabelErosion, mgx::DisplayShortestPath, mgx::Measure3DCellDistanceBezierRing, mgx::CreateCustomDirectionsBezier3D, mgx::QuickSaveFile, mgx::AnalyzeSurface, mgx::ReverseStack, mgx::MeasurePolarCoord, mgx::SelectSpecial, mgx::NormalizeStack, mgx::MeshErosion, mgx::ExamineBadVasculature, mgx::CleanHeatMap, mgx::CreateCustomDirectionsBezierLine3D, mgx::MeshKeepVertices, mgx::MeasureBezierLineCoord, mgx::Measure3DCellDistance, mgx::SwapStacks, mgx::ActualPlaneStack, mgx::ExtendSelectionByNeighbors, mgx::SaveViewFile, mgx::MeshLabelDilation, mgx::DataAnalysisGUS, mgx::HeatMapGrowth, mgx::MeasureBezierCoord, mgx::MeshDeleteSelection, mgx::TrimStackToBezier, mgx::CreateCustomDirectionsBezierLine, mgx::Measure3DOutsideWallAreaPercent, mgx::ResetParents, mgx::SelectParentLabelsT1, mgx::CountSelectedCells, mgx::FillStack3D, mgx::MeshDilation, mgx::FlatDivisionPlane, mgx::MeasureDistanceToBezier, mgx::CreateAttrMap, mgx::DeleteEdge, mgx::SelectParentLabel, mgx::DataAnalysis, mgx::DisplayPCA3D, mgx::TrimStackProcess, mgx::LoadParents, mgx::Measure3DOutsideWallArea, mgx::MeshExport, mgx::ProjectCustomDirections, mgx::AreaSelectedTris, mgx::ApplyMaskLabels, mgx::MeshNormalize, mgx::MeasureMajorAxisTheta, mgx::FillStackToMesh, mgx::NormalizeHeatMap, mgx::SharpenStack, mgx::SplitEdges, mgx::Measure3DVolumeSurfaceRatio, mgx::ImportParentAttrNew, mgx::CreateCustomDirectionsBezier, mgx::AssignCorticalCells, mgx::SelectSharedTriangles, mgx::SaveParents, mgx::MeshLocalMinima, mgx::ScaleHeatMap, mgx::MeasureDistanceToMesh, mgx::MergeVertices, mgx::ApplyMaskToStack, mgx::AssignColumella, mgx::DivisionAnalysisMulti3DOld, mgx::ResetMeshProcess, mgx::SelectByNormal, mgx::ImportParentAttr, mgx::Measure3DSizeCustom, mgx::DiffGaussians, mgx::MeasureAvgRadius, mgx::CustomDirectionsClear, mgx::MeshDiffGaussians, mgx::MeshDeleteValence, mgx::LoadViewFile, mgx::UniqueParentsFromAttr, mgx::MeasureMaxRadius, mgx::ExtendByConnectivity, mgx::CopySwapStacks, mgx::RootDivisionAnalysis, mgx::PCAnalysis3D, mgx::CloseStackLabel, mgx::MeshGaussianBlur, mgx::CustomDirectionsEnforceOrthogonality, mgx::Measure3DSizeZ, mgx::ScaleMesh, mgx::GaussianBlurStack, mgx::LoadAllData, mgx::CellAtlas, mgx::MeasureMinRadius, mgx::CreateParentAttr, mgx::MeshSelectDuplicateCells, mgx::CopyWorkToMain, mgx::MeshSignalGrad, mgx::Measure3DSizeY, mgx::TestDivisionPlanesCellAtlas, mgx::CreateCustomDirectionsSurface, mgx::MeasureNeighbors, mgx::SubdivideBisectMesh3D, mgx::LoadHeatMap, mgx::MergeParentFiles, mgx::MeshSelectWholeLabelExtend, mgx::OpenStackLabel, mgx::FilterStack, mgx::TopologicalCheck, mgx::StackExportByLabel, mgx::SelectDuplicatedNuclei, mgx::Measure3DSizeX, mgx::CopyMainToWork, mgx::MeasureMinorAxis, mgx::AveragePDGs, mgx::DisplayPCA, mgx::ImportCustomDirectionsVector, mgx::SubdivideBisectMesh, mgx::MeshImport, mgx::MeshSelectClip, mgx::ExtendCells, mgx::SetParent, mgx::ProjectCurvature, mgx::DistanceNuclei, mgx::SaveHeatMap, mgx::MeshAutoSegment, mgx::MeasureMajorAxis, mgx::Measure3DSizeRad, mgx::InvertStack, mgx::ImportCustomDirections, mgx::ClipStack, mgx::FillHolesProcess, mgx::LoadCellData, mgx::AdaptiveSubdivideSignalMesh, mgx::EraseAtBorderStack, mgx::MeshUnselectLabel, mgx::RelabelFragments, mgx::LabelNuclei, mgx::CorrectLabelingStack, mgx::MeshSave, mgx::TestDivisionPlanes, mgx::ClearMeshSignal, mgx::DisplayPDGsVertex, mgx::MeasureAspectRatio, mgx::CopyCustomDirections, mgx::Measure3DSizeCirc, mgx::ClearMainStack, mgx::MeshCombineRegions, mgx::DisplayCellData, mgx::ColorGradient, mgx::FlipBezierLine, mgx::MeshSelectValence, mgx::RotateCamera, mgx::AdaptiveSubdivideBorderMesh, mgx::DisplayPCAOld, mgx::ExportJunctionAnglesNew, mgx::RescaleHeatMap, mgx::OpeningStack, mgx::MeshLoad, mgx::FillLabelStack, mgx::CorrectLabeling, mgx::SmoothCustomDirections, mgx::MeshBrightness, mgx::SurfaceFromMGX3D, mgx::MeasureStomatalBending, mgx::Measure3DSizeLong, mgx::ClearWorkStack, mgx::NewBezierRingFromSelected, mgx::DivideCell3DMGX3D, mgx::SaveNeighborhoodData2D, mgx::RelabelCells3D, mgx::SubdivideMesh, mgx::SelectVerticesOfCell, mgx::BinarizeStack, mgx::FindCellWallCenters, mgx::ExportJunctionAngles, mgx::CreateCustomDirectionsHeat, mgx::MeshSelectLabels, mgx::MarkPrim, mgx::MeasureBending, mgx::CopyLabelsToParents, mgx::SmoothMeshSignal, mgx::ConvertToMgx3d, mgx::DeleteHeatRangeLabels, mgx::MeshFromLocalMaxima, mgx::LocalMaximaStack, mgx::ClosingStack, mgx::StackOpen, mgx::Measure3DCoordRad, mgx::NewBezierRing, mgx::BlobDetect, mgx::LabelSelected, mgx::LoopSubdivisionMesh, mgx::PCAnalysis2D, mgx::CreateIntrinsicHeat, mgx::SaveNeighborhoodData, mgx::RestoreCellLabels, mgx::DisplayPDGs, mgx::ClearAttrMap, mgx::MeasurePerimeter, mgx::ExportInternalAngles, mgx::CopyParentsToLabels, mgx::StackBorderFromSegmented, mgx::MeshSelectLabeled, mgx::DisplayCellGraph3D, mgx::DisplayFibrilOrientationsVertex, mgx::LabelMeristem, mgx::ConvertToMgx2d, mgx::VoxelFaceMesh, mgx::ProjectLabelsOnMesh, mgx::BrightenStack, mgx::CollapseBezier, mgx::Measure3DCoordCirc, mgx::ShrinkMesh, mgx::SaveCellData, mgx::LabelCellWalls, mgx::StackExport, mgx::MeasureArea, mgx::MeasureBezierExport, mgx::MeshSelectUnlabeled, mgx::ErodeStack, mgx::ThresholdLabelDelete, mgx::ConvertToMgxc, mgx::CuttingSurfMesh, mgx::SaveCellContourFile, mgx::StackHistogramBezier, mgx::MakeMeshTetraDA, mgx::SaveAttributesCSVExtended, mgx::HeatMapAreaAsymmetry, mgx::GrabLabelsSegment, mgx::MarkMeristem, mgx::DisplayCellGraph2D, mgx::DisplaySignalOrientation3D, mgx::ProjectLabel, mgx::ApplyTransferFunction, mgx::MergeStacks, mgx::Measure3DCoordLong, mgx::CellAtlasFindCells, mgx::FibrilOrientationsVertex, mgx::SmoothMesh, mgx::ComputeDivPlaneAngles, mgx::MeasureSignalTotal, mgx::AnimationLoad, mgx::MeasureBezier, mgx::MedianOfMediansStack, mgx::SetParentExploded, mgx::MeshSelectNewWalls, mgx::MeshInvertSelection, mgx::GrowthDirections, mgx::LoadPlyFileCellGraph, mgx::StackSave, mgx::DetectCellLayers2, mgx::DivisionAnalysisMulti2D, mgx::JoinRegionsSegment, mgx::CellAtlasStack, mgx::ConvertToMgxm, mgx::MeshRelabel, mgx::ConsolidateRegionsNormalized, mgx::StackCircularHistogram, mgx::DisplayCellGraph, mgx::ClearCellAxis, mgx::AnimationSave, mgx::NewBezier, mgx::Measure3DWallArea, mgx::MakeMeshCircleDA, mgx::SignalOrientation3D, mgx::StackImport, mgx::MeasureSignalInterior, mgx::ProjectSignal, mgx::RestoreOriginalMesh, mgx::MarchingCube3D, mgx::ReverseMesh, mgx::DilateStack, mgx::SaveAttributesCSV, mgx::ComputeHeatMap, mgx::SelectBadCells, mgx::CombineStacks, mgx::AutoScaleStack, mgx::MeshUnselect, mgx::DisplayTissueCurvature, mgx::DisplayFibrilOrientations, mgx::DetectCellLayers, mgx::FixBorderTriangles, mgx::SaveGlobalTransform, mgx::HeatMapProliferation, mgx::MedianStack, mgx::ResetDivPlaneData, mgx::AnimationClear, mgx::PythonProcess, mgx::SavePlyFile, mgx::TestDivisionPlanes2D, mgx::LoadCellAxis, mgx::ConsolidateRegions, mgx::MeasureSignalBorder, mgx::SegmentClear, mgx::ViewMeshProcess, mgx::DisplaySignalOrientation, mgx::StackVoxelCount, mgx::ProjectLeafPrimStack, mgx::TranslateByParent, mgx::Measure3DNeighbors, mgx::MeshAddOtherMesh, mgx::SaveBezier, mgx::MeshSelectBadNormals, mgx::AnimationPlay, mgx::AnalyzeCells, mgx::DetectLayers, mgx::PCAnalysis, mgx::ManageAttributes, mgx::AlignCanvas, mgx::StackSwapBytes, mgx::FixMeshCorners, mgx::TransformMesh, mgx::Annihilate, mgx::MeasureSignal, mgx::CorrespondenceJunctions, mgx::SaveCellAxis, mgx::FibrilOrientations, mgx::AverageStack, mgx::MarchingCubeSurface, mgx::SegmentMesh, mgx::EdgeDetectProcess, mgx::TissueCurvature, mgx::StatsTriangleValues, mgx::ComputeVolume, mgx::FilterPlanes, mgx::LoadBezier, mgx::CorrectParents, mgx::AnimationAddKeyFrame, mgx::AutoTrim, mgx::SetCurrentStack, mgx::ExplodeMesh, mgx::Load3DFrom2View, mgx::CopySwapMeshes, mgx::WatershedStack, mgx::Measure3DVolume, mgx::MeshSelectAll, mgx::AnalyzeLeafPrimSurf, mgx::FlatDivisionPlane2D, mgx::SignalOrientation, and mgx::AnalyzeMeristem.

Definition at line 579 of file Process.hpp.

◆ runProcess() [1/2]

bool mgx::Process::runProcess	(	const QString &	processName,
		QStringList &	parms
	)
throw	(
	)

Launch a process by name.

Note that exceptions are filtered and converted into an error message and the process returning false.

◆ runProcess() [2/2]

bool mgx::Process::runProcess	(	Process &	proc,
		QStringList &	parms
	)
throw	(
	)

Launch a process with generic arguments.

Note that exceptions are filtered and converted into an error message and the process returning false.

◆ saveView()

bool mgx::Process::saveView ( const QString & fileName )

Save viewfile.

◆ selectedLabel()

int mgx::Process::selectedLabel ( ) const

Get the current selected label.

◆ setCurrentMeshId()

void mgx::Process::setCurrentMeshId ( int i )

Change which mesh is current.

◆ setCurrentParms()

bool mgx::Process::setCurrentParms ( )

Set the parms from the GUI.

◆ setCurrentStack()

bool mgx::Process::setCurrentStack	(	int	id,
		const QString &	store
	)

◆ setCurrentStackId()

void mgx::Process::setCurrentStackId ( int i )

Change which stack is current.

◆ setErrorMessage()

bool mgx::Process::setErrorMessage ( const QString & str )

Set an error message that will be displayed if the process returns false.

◆ setGlobalBrightness()

void mgx::Process::setGlobalBrightness ( float value )

Change the current setting for the global brightness level.

The brightness is clamped to the range [-1;1]

◆ setGlobalContrast()

void mgx::Process::setGlobalContrast ( float value )

Change the current setting for the global contrast level.

The contrast is clamped to the range [0;2]

◆ setSelectedLabel()

void mgx::Process::setSelectedLabel ( int label )

Change the current selected label.

◆ setStatus()

bool mgx::Process::setStatus	(	const QString &	msg,
		bool	alsoPrint = `true`
	)

Display a message in the status bar

◆ setWarningMessage()

void mgx::Process::setWarningMessage ( const QString & str )

Set a warning message that will be displayed if the process returns true.

◆ stack()

Stack* mgx::Process::stack ( int i )

Returns the ith stack, or 0 if there is no such stack.

◆ stackCheck()

bool mgx::Process::stackCheck	(	int	checks,
		int	which
	)

protected

Check stack properties.

◆ stackCount()

int mgx::Process::stackCount ( ) const

Number of stacks available to the process.

◆ stackError()

QString mgx::Process::stackError	(	int	checks,
		int	which
	)

protected

Generate a standardised string describing how the stack should be to not generate an error.

◆ stacks() [1/2]

std::pair<stack_iterator, stack_iterator> mgx::Process::stacks ( )

Iterate over all the stacks.

◆ stacks() [2/2]

std::pair<const_stack_iterator, const_stack_iterator> mgx::Process::stacks ( ) const

Iterate over all the stacks.

◆ storeCheck()

bool mgx::Process::storeCheck	(	int	checks,
		int	which
	)

protected

Check store properties.

◆ storeError()

QString mgx::Process::storeError	(	int	checks,
		int	which
	)

protected

Generate a standardised string describing how the store should be to not generate an error.

◆ systemCommand()

bool mgx::Process::systemCommand	(	int	command,
		const QStringList &	parms
	)

Run a system command.

◆ systemCommandGui

void mgx::Process::systemCommandGui	(	mgx::Process *	,
		int	,
		QStringList
	)

signal

◆ systemCommandProcess

void mgx::Process::systemCommandProcess	(	mgx::Process *	,
		int	,
		QStringList
	)

signal

◆ takeSnapshot()

bool mgx::Process::takeSnapshot	(	QString	filename,
		float	overSampling = `1.0f`,
		int	width = `0`,
		int	height = `0`,
		int	quality = `95`,
		bool	expand_frustum = `false`
	)

Save screen shot to a file.

◆ updateState()

bool mgx::Process::updateState ( )

Update the Gui of MorphoGraphX.

◆ updateViewer()

bool mgx::Process::updateViewer ( )

Tell the viewer to redraw.

◆ userCancel()

void mgx::Process::userCancel ( ) const

inline

Throw an exception informing the system that the user canceled the current process.

Definition at line 467 of file Process.hpp.

◆ warningMessage()

QString mgx::Process::warningMessage ( ) const

Get the current warning message.

Friends And Related Function Documentation

◆ Process::CheckState

friend class Process::CheckState

friend

Definition at line 724 of file Process.hpp.

◆ SetupProcess

friend class SetupProcess

friend

Definition at line 222 of file Process.hpp.

Member Data Documentation

◆ LabelColors

std::vector<Colorf>& mgx::Process::LabelColors

static

Definition at line 591 of file Process.hpp.

◆ p

PrivateProcess* mgx::Process::p

Definition at line 748 of file Process.hpp.

◆ processVersion

unsigned int mgx::Process::processVersion

static

Definition at line 224 of file Process.hpp.

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

src/Process.hpp

Classes

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Friends

Internal methods

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ const_mesh_iterator

◆ const_stack_iterator

◆ mesh_iterator

◆ stack_iterator

Member Enumeration Documentation

◆ CheckType

◆ CheckWhich

◆ MeshCheckType

◆ ProcessAction

◆ StackCheckType

◆ StoreCheckType

Constructor & Destructor Documentation

◆ Process()

◆ ~Process()

Member Function Documentation

◆ actingFile() [1/2]

◆ actingFile() [2/2]

◆ addMesh()

◆ addStack()

◆ camera()

◆ checkState()

◆ clip1() [1/2]

◆ clip1() [2/2]

◆ clip2() [1/2]

◆ clip2() [2/2]

◆ clip3() [1/2]

◆ clip3() [2/2]

◆ currentMesh()

◆ currentMeshId()

◆ currentStack()

◆ currentStackId()

◆ cuttingSurface() [1/2]

◆ cuttingSurface() [2/2]

◆ deleteMesh()

◆ deleteStack()

◆ errorMessage()

◆ file()

◆ finalize()

◆ getProcess()

◆ globalBrightness()

◆ globalContrast()

◆ initialize()

◆ lineBorderSelection()

◆ loadView()

◆ makeProcess()

◆ mesh()

◆ meshCheck()

◆ meshCount()

◆ meshError()

◆ meshes() [1/2]

◆ meshes() [2/2]

◆ meshSelection()

◆ otherMesh()

◆ otherMeshId()

◆ otherStack()

◆ otherStackId()

◆ pythonCall()

◆ run()

◆ runProcess() [1/2]

◆ runProcess() [2/2]

◆ saveView()

◆ selectedLabel()

◆ setCurrentMeshId()

◆ setCurrentParms()

◆ setCurrentStack()

◆ setCurrentStackId()

◆ setErrorMessage()

◆ setGlobalBrightness()

◆ setGlobalContrast()

◆ setSelectedLabel()