Documentation/Nightly/Developers/Slice Orientation Presets
Contents
- 1 Overview
- 2 API
- 3 FAQ
- 3.1 Where are slice orientation presets stored ?
- 3.2 Where are default presets defined ?
- 3.3 Why default presets are not added in the vtkMRMLSliceNode contructor ?
- 3.4 How to ensure slice orientation presets are defined in unit tests ?
- 3.5 How to instantiate a new vtkMRMLSliceNode ?
- 3.6 What is "Reformat" orientation ?
- 3.7 How to modify and set the orientation presets in Extensions ?
Overview
Slicer provides an API to manage slice orientation presets.
By default, three slice orientation presets representing the anatomical coordinate system are available in Slicer: Axial
, Coronal
and Sagittal
.
Feature originally integrated to Slicer core in r25171
Contributors: Davide Punzo (Kapteyn astronomical institute), Jean-Christophe Fillion-Robin (Kitware) and Andras Lasso (PerkLab, Queen's University).
API
The vtkMRMLSliceNode class provides the following API for managing slice orientation presets:
bool SetOrientationToAxial() bool SetOrientationToSagittal() bool SetOrientationToCoronal() std::string GetOrientation() bool SetOrientation(const char* orientation) std::string GetOrientation(vtkMatrix4x4* sliceToRAS) vtkMatrix4x4 *GetSliceToRAS() void SetSliceToRAS(vtkMatrix4x4* sliceToRAS) bool AddSliceOrientationPreset(const std::string &name, vtkMatrix3x3 *orientationMatrix) bool RemoveSliceOrientationPreset(const std::string& name) bool RenameSliceOrientationPreset(const std::string& name, const std::string& updatedName) bool HasSliceOrientationPreset(const std::string& name) vtkMatrix3x3 *GetSliceOrientationPreset(const std::string& name) std::string GetSliceOrientationPresetName(vtkMatrix3x3* orientationMatrix) void GetSliceOrientationPresetNames(vtkStringArray* presetOrientationNames) int GetNumberOfSliceOrientationPresets() const # Convenience static methods static void InitializeAxialMatrix(vtkMatrix3x3* orientationMatrix) static void InitializeSagittalMatrix(vtkMatrix3x3* orientationMatrix) static void InitializeCoronalMatrix(vtkMatrix3x3* orientationMatrix) static void AddDefaultSliceOrientationPresets(vtkMRMLScene* scene)
FAQ
Where are slice orientation presets stored ?
Every vtkMRMLSliceNode
contains an ordered list of (orientationPresetName, orientationMatrix)
tuples.
The list is automatically initialized with the list of default presets each time a node is created using vtkMRMLScene::CreateNodeByClass(const char* className)
.
Where are default presets defined ?
Each time vtkMRMLApplicationLogic::SetMRMLScene
is invoked, method vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(vtkMRMLScene *scene)
is called.
Then, method vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(vtkMRMLScene *scene)
ends up adding a default vtkMRMLSliceNode that will be used a template each time vtkMRMLScene::CreateNodeByClass(const char* className)
.
Why default presets are not added in the vtkMRMLSliceNode contructor ?
Associating the list of default presets to the default vtkMRMLSliceNode
allows to customize the template once and ensure any new node created using vtkMRMLScene::CreateNodeByClass(const char* className)
will have the expected list of presets.
How to ensure slice orientation presets are defined in unit tests ?
When writing tests that depend on MRMLLogic
, instantiating vtkMRMLApplicationLogic is sufficient:
vtkNew<vtkMRMLScene> scene; vtkNew<vtkMRMLApplicationLogic> appLogic; appLogic->SetMRMLScene(scene.GetPointer());
When writing test within that only depend on MRMLCore
, the static method vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(vtkMRMLScene *scene)
is available:
vtkNew<vtkMRMLScene> scene; vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(scene.GetPointer());
How to instantiate a new vtkMRMLSliceNode ?
vtkMRMLSliceNode* sliceNode = scene->CreateNodeByClass("vtkMRMLSliceNode");
What is "Reformat" orientation ?
"Reformat" is a reserved orientation name describing an arbitrary orientation matrix that do not correspond to an existing orientation preset.
This means that a preset can NOT be named "Reformat".
How to modify and set the orientation presets in Extensions ?
Given an extension XXX, it is possible to set, globally, the orientation presets for the SliceNode using:
vtkSmartPointer<vtkMRMLNode> defaultNode = vtkMRMLSliceNode::SafeDownCast (this->mrmlScene()->GetDefaultNodeByClass("vtkMRMLSliceNode")); if (!defaultNode) { vtkMRMLNode * foo = this->mrmlScene()->CreateNodeByClass("vtkMRMLSliceNode"); defaultNode.TakeReference(foo); this->mrmlScene()->AddDefaultNode(defaultNode); } vtkMRMLSliceNode * defaultSliceNode = vtkMRMLSliceNode::SafeDownCast(defaultNode); defaultSliceNode->RenameSliceOrientationPreset("Axial", "XZ"); defaultSliceNode->RemoveSliceOrientationPreset("Sagittal"); etc..
To be noted is that SliceNodes already instantiated must be updated as follow:
vtkSmartPointer<vtkCollection> sliceNodes = vtkSmartPointer<vtkCollection>::Take (this->mrmlScene()->GetNodesByClass("vtkMRMLSliceNode")); for(int i = 0; i < sliceNodes->GetNumberOfItems(); i++) { vtkMRMLSliceNode* sliceNode = vtkMRMLSliceNode::SafeDownCast(sliceNodes->GetItemAsObject(i)); if (sliceNode) { sliceNode->DisableModifiedEventOn(); sliceNode->RenameSliceOrientationPreset("Axial", "XZ"); sliceNode->RemoveSliceOrientationPreset("Sagittal"); etc... sliceNode->DisableModifiedEventOff(); } }