MorphoGraphX
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Save the data into a MGXS or INRIA format. More...
#include <SystemProcessSave.hpp>
Public Member Functions | |
StackSave (const StackProcess &proc) | |
bool | initialize (QStringList &parms, QWidget *parent) |
This is an optional method that is called only when a process is launched from the GUI. More... | |
bool | operator() (const QStringList &parms) |
Implementation of the process with generic arguments. More... | |
bool | operator() (Stack *stack, Store *store, const QString &filename, int compressionLevel=0) |
Save the stack. More... | |
QString | folder () const |
Folder in which to place the process. More... | |
QString | name () const |
Returns the name of the process. More... | |
QString | description () const |
Returns a description of the process for the GUI. | |
QStringList | parmNames () const |
List of named parameters. More... | |
QStringList | parmDescs () const |
List of parameters descriptions. More... | |
QStringList | parmDefaults () const |
List of default parms. | |
ParmChoiceMap | parmChoice () const |
Purely for GUI purposes, provides for some of the parms parameter a choice. More... | |
QIcon | icon () const |
Icon to use to represent the process in the GUI. More... | |
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StackProcess (const StackProcess ©) | |
Copy constructor. More... | |
virtual QString | type () const |
Returns a string identifying the process type. | |
const Mesh * | mesh (int i) |
const Mesh * | currentMesh () |
std::pair< const_mesh_iterator, const_mesh_iterator > | meshes () const |
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Process () | |
Default constructor. | |
Process (const Process &p) | |
Copy constructor. More... | |
virtual | ~Process () |
Virtual destructor. | |
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. | |
QString | pythonCall (const QStringList &parms) const |
Return the python call describing the current process. | |
int | stackCount () const |
Number of stacks available to the process. | |
Stack * | stack (int i) |
Returns the ith stack, or 0 if there is no such stack. | |
Stack * | currentStack () |
Returns the current stack (i.e. More... | |
int | currentStackId () const |
Return the id (i.e. More... | |
void | setCurrentStackId (int i) |
Change which stack is current. | |
std::pair< stack_iterator, stack_iterator > | stacks () |
Iterate over all the stacks. | |
std::pair < const_stack_iterator, const_stack_iterator > | stacks () const |
Iterate over all the stacks. | |
Stack * | addStack () |
Add a new stack to the process. | |
bool | deleteStack (int i) |
Delete the stack of given id. More... | |
int | meshCount () const |
Returns the number of mesh available to the process. | |
Mesh * | mesh (int i) |
Returns the ith mesh. | |
Mesh * | currentMesh () |
Returns the current mesh (i.e. More... | |
int | currentMeshId () const |
Returns the id (i.e. More... | |
void | setCurrentMeshId (int i) |
Change which mesh is current. | |
std::pair< mesh_iterator, mesh_iterator > | meshes () |
Iterate over all the meshs. | |
std::pair< const_mesh_iterator, const_mesh_iterator > | meshes () const |
Iterate over all the meshs. | |
Mesh * | addMesh (const Stack *stack) |
Add a mesh to the process for the given stack. | |
bool | deleteMesh (int i) |
Remove a mesh from the process. | |
int | selectedLabel () const |
Get the current selected label. | |
void | setSelectedLabel (int label) |
Change the current selected label. | |
float | globalBrightness () |
Return the current setting for the global brightness level. | |
float | globalContrast () |
Return the current setting for the global contrast level. | |
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. | |
bool | lineBorderSelection () const |
Returns is the user has line border selection active. | |
void | updateState () |
Update the state of the application from the current data. More... | |
void | updateViewer () |
Force the viewer to refresh, without pausing the process. | |
bool | setErrorMessage (const QString &str) |
Set an error message that will be displayed if the process returns false. | |
QString | errorMessage () const |
Get the current error message. | |
void | setWarningMessage (const QString &str) |
Set a warning message that will be displayed if the process returns true. | |
QString | warningMessage () const |
Get the current warning message. | |
void | userCancel () const |
Throw an exception informing the system that the user canceled the current process. | |
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. | |
Clip * | clip2 () |
Return the object defining the second clipping region. | |
Clip * | clip3 () |
Return the object defining the third clipping region. | |
const Clip * | clip1 () const |
Return the object defining the first clipping region. | |
const Clip * | clip2 () const |
Return the object defining the second clipping region. | |
const Clip * | clip3 () const |
Return the object defining the third clipping region. | |
CuttingSurface * | cuttingSurface () |
Return the cutting surface. | |
const CuttingSurface * | cuttingSurface () const |
Return the cutting surface. | |
QStringList | booleanChoice () const |
Helper function that provides a list of choices for a boolean argument. | |
QStringList | storeChoice () const |
Helper function that provides a list of choices for choosing from the main or work stack. | |
virtual uint | numParms () const |
Returns the number of named string for this process. | |
Process * | makeProcess (const QString &processType, const QString &processName) |
Creates a process object by name. | |
bool | RunProcess (Process &proc, const QStringList &parms) throw () |
Launch a process with generic arguments. More... | |
bool | RunProcess (const QString &processType, const QString &processName, const QStringList &parms) throw () |
Launch a process by name. More... | |
CheckState | checkState () |
Call this function and convert the result to a boolean. More... | |
Additional Inherited Members | |
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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 |
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_PARENT, MESH_LABEL_PARENT } |
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 } |
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PrivateProcess * | p |
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static unsigned int | processVersion |
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bool | systemCommand (SystemCommand cmd, const QStringList &parms) |
Method that can be used to launch a system command. More... | |
bool | stackCheck (int checks, int which) |
Check stack properties. | |
bool | storeCheck (int checks, int which) |
Check store properties. | |
bool | meshCheck (int checks, int which) |
Check mesh properties. | |
QString | stackError (int checks, int which) |
Generate a standardised string describing how the stack should be to not generate an error. | |
QString | storeError (int checks, int which) |
Generate a standardised string describing how the store should be to not generate an error. | |
QString | meshError (int checks, int which) |
Generate a standardised string describing how the mesh should be to not generate an error. | |
Save the data into a MGXS or INRIA 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 2*xsz*ysz*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.
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inlinevirtual |
Folder in which to place the process.
Subfolders can be specified by placing '/' in the path
Reimplemented from mgx::process::Process.
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inlinevirtual |
Icon to use to represent the process in the GUI.
Note that to use an icon present in the resources, you must precede the path with a colon (i.e. ":/images/myicon.png".
Reimplemented from mgx::process::Process.
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virtual |
This is an optional method that is called only when a process is launched from the GUI.
If reimplemented, it receives a potential argument list, and should provide a GUI for editing it. Once the user finishing the edition, this method should modify the provided arguments and return true. If the user aborts, the method should return false. Note that returning false does not produce an error.
parms | List of arguments |
parent | Pointer to the parent widget. If the configure method creates a GUI, it should be a child of this widget. |
Reimplemented from mgx::process::Process.
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inlinevirtual |
Returns the name of the process.
Note that the name must be a valid identifier in Python once the spaces are replaced by underscores. Also, all underscore in the name will be replaced by spaces for user presentation.
Implements mgx::process::Process.
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virtual |
Implementation of the process with generic arguments.
The number of arguments is guaranteed to be at least as many as the ones named in the process.
Implements mgx::process::Process.
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inlinevirtual |
Purely for GUI purposes, provides for some of the parms parameter a choice.
In this case, the user will be presented with a combo box presenting the provided list. Note that no mechanism forces the user to choose one of this choice.
Reimplemented from mgx::process::Process.
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inlinevirtual |
List of parameters descriptions.
There must be as many parameters than defaults.
Reimplemented from mgx::process::Process.
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inlinevirtual |
List of named parameters.
There must be as many parameters than defaults.
Implements mgx::process::Process.