#include <SystemProcessSave.hpp>

Inheritance diagram for mgx::StackSave:

Public Member Functions
	StackSave (const Process &proc)

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

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

bool	run (Stack stack, Store store, const QString &filename, int compressionLevel=0)
	Save the stack. More...

QIcon	icon () const

Public Member Functions inherited from mgx::Process
	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	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...

Additional Inherited Members
Public Types inherited from mgx::Process
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

Signals inherited from mgx::Process
void	systemCommandGui (mgx::Process *, int, QStringList)

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

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...

Public Attributes inherited from mgx::Process
PrivateProcess *	p

Static Public Attributes inherited from mgx::Process
static unsigned int	processVersion

static std::vector< Colorf > &	LabelColors

Protected Member Functions inherited from mgx::Process
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...

Detailed Description

Save the data into a MGXS or INRIA format.

Description of the MGXS file format

MGXS is a binary file format to store 3D images with all the metadata needed for proper rendering in MorphoGraphX.

There are many versions, from 1.0 to 1.3. This version of MorphoGraphX will always generate MGXS files version 1.3.

Each MGXS file starts with the ASCII string MGXS followed by a space, the version number in ASCII and another space. For instance, for the current version, the file starts with the ASCII string "MGXS 1.3 ".

A binary header follows the version number. New versions simply added fields to the header. The header is made of:

Field	Size (bytes)	type	Version	Description
isLabel	1	bool	1.1	True if the stack's values are labels and not intensities
sxum	4	float	1.3	Position of the stack's origin on the X axis, in micrometers
syum	4	float	1.3	Position of the stack's origin on the Y axis, in micrometers
szum	4	float	1.3	Position of the stack's origin on the Z axis, in micrometers
xsz	4	uint	1.0	Number of voxels along the X axis
ysz	4	uint	1.0	Number of voxels along the Y axis
zsz	4	uint	1.0	Number of voxels along the Z axis
xum	4	float	1.0	Resolution along the X axis, in micrometers
yum	4	float	1.0	Resolution along the Y axis, in micrometers
zum	4	float	1.0	Resolution along the Z axis, in micrometers
datasz	8	uint	1.0	Size in bytes of the data. It should be `2xszysz*zsz`
cl	1	uint	1.0	Compression level

If the compression level is 0, the header is then followed by the raw, uncompressed, data. Voxels are ordered C-style (e.g. vertices consecutives along the X axis are consecutive in the file, vertices consecutives along the Y axis are separated by xsz voxels in the file, and vertices consecutive in the Z axis are separated by xsz*ysz voxels in the files).

If the compression level is greater than 0, the stack is cut into slice. Each slice is compressed using the gzip algorithm (using the qCompress Qt function). In the file, the size of the compressed slice is written as a 4 bytes unsigned integer, followed by the compressed data. A pseudo code to read the compressed data is:

current_size = 0
while current_size < datasz
    slice_size = read 4 bytes
    compressed_data = read slice_size bytes
    data = uncompress compressed_data
    store data
    current_size += size of data

Note before version 1.3, if the stack was labeled, the label numbers were store as big endian. Starting 1.3, they are stores as little endian. Stack intensities are always stored as little endian.

Definition at line 89 of file SystemProcessSave.hpp.

Constructor & Destructor Documentation

◆ StackSave()

mgx::StackSave::StackSave ( const Process & proc )

inline

Definition at line 91 of file SystemProcessSave.hpp.

Member Function Documentation

◆ icon()

QIcon mgx::StackSave::icon ( ) const

inline

Definition at line 114 of file SystemProcessSave.hpp.

◆ initialize()

bool mgx::StackSave::initialize ( QWidget * )

virtual

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 from mgx::Process.

◆ run() [1/2]

bool mgx::StackSave::run ( )

virtual

Runs the process.

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

Reimplemented from mgx::Process.

◆ run() [2/2]

bool mgx::StackSave::run	(	Stack *	stack,
		Store *	store,
		const QString &	filename,
		int	compressionLevel = `0`
	)

Save the stack.