View source for Documentation/4.10/Developers/Slice Orientation Presets


== Overview ==

Slicer provides an API to manage slice orientation presets.

By default, three slice orientation presets representing the [[Coordinate_systems#Anatomical_coordinate_system|anatomical coordinate system]] are available in Slicer: <code>Axial</code>, <code>Coronal</code> and <code>Sagittal</code>.

Feature originally integrated to Slicer core in [http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=25171 r25171] and contributed by:
* Davide Punzo (Kapteyn astronomical institute)
* Jean-Christophe Fillion-Robin (Kitware)
* Andras Lasso (PerkLab, Queen's University). 

== API ==

The [{{doxygen-class-url|vtkMRMLSliceNode}} vtkMRMLSliceNode] class provides the following API for managing slice orientation presets:

<pre>
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)
</pre>

== FAQ ==

=== Where are slice orientation presets stored ? ===

Every <code>vtkMRMLSliceNode</code> contains an ordered list of <code>(orientationPresetName, orientationMatrix)</code> tuples.

The list is automatically initialized with the list of default presets each time a node is created using <code>vtkMRMLScene::CreateNodeByClass(const char* className)</code>.


=== Where are default presets defined ? ===

Each time <code>vtkMRMLApplicationLogic::SetMRMLScene</code> is invoked, method <code>vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(vtkMRMLScene *scene)</code>  is called.

Then, method <code>vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(vtkMRMLScene *scene)</code> ends up adding a default [{{doxygen-class-url|vtkMRMLSliceNode}} vtkMRMLSliceNode] that will be used a template each time <code>vtkMRMLScene::CreateNodeByClass(const char* className)</code>.

=== Why default presets are not added in the vtkMRMLSliceNode contructor ? ===

Associating the list of default presets to the default <code>vtkMRMLSliceNode</code> allows to customize the template once and ensure any new node created using <code>vtkMRMLScene::CreateNodeByClass(const char* className)</code> will have the expected list of presets.

=== How to ensure slice orientation presets are defined in unit tests ? ===

When writing tests that depend on <code>MRMLLogic</code>, instantiating [{{doxygen-class-url|vtkMRMLApplicationLogic}} vtkMRMLApplicationLogic] is sufficient:

<pre>
vtkNew<vtkMRMLScene> scene;
vtkNew<vtkMRMLApplicationLogic> appLogic;
appLogic->SetMRMLScene(scene.GetPointer());
</pre>

When writing test within that only depend on <code>MRMLCore</code>, the static method <code>vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(vtkMRMLScene *scene)</code> is available:

<pre>
vtkNew<vtkMRMLScene> scene;
vtkMRMLSliceNode::AddDefaultSliceOrientationPresets(scene.GetPointer());
</pre>

=== How to instantiate a new vtkMRMLSliceNode ? ===

<pre>
vtkMRMLSliceNode* sliceNode = scene->CreateNodeByClass("vtkMRMLSliceNode");
</pre>

=== 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: 

<pre>
  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..
</pre>

To be noted is that SliceNodes already instantiated must be updated as follow: 

<pre>
  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();
      }
    }
</pre>