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Text replacement - "slicerWiki/index.php" to "wiki"

UpdateBot: Nightly -> 4.4

2014-12-25T06:54:54Z

Nightly -> 4.4

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<noinclude>{{documentation/versioncheck}}</noinclude>

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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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: '''Contact:''' Julien Finet, <email>julien.finet@kitware.com</email> 
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{{documentation/{{documentation/version}}/module-section|Module Description}}
{{documentation/{{documentation/version}}/module-description}}
Only UNSIGNED CHAR images are supported for now. You can convert your images into UCHAR by using the [[Documentation/{{documentation/version}}/Modules/CastScalarVolume|Cast Scalar Volume]] module.


{{documentation/{{documentation/version}}/module-section|Use Cases}}
<gallery widths="200px" perrow="4">
Image:Tumor-Volume-Rendering-PostGad-2011.png|Tumor post pad (preset: MR-Default)
Image:Modules-VolumeRendering-LabelMap.png|Segmented (labelmap) knee (interpolation: nearest neighbor, shading: off)
Image:QSlicerVolumeRendering-default.png|Default view of the module. Inputs and Advanced... are hidden by default
Image:VolumeRenderingSettings.png|Volume Rendering settings ''Edit -> Application Settings -> Volume Rendering settings''
</gallery>


{{documentation/{{documentation/version}}/module-section|Tutorials}}

Tutorial about [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials using the volume rendering module].

===Labelmap rendering===
[[File:Modules-VolumeRendering-LabelMap.png|right|500px]]
A labelmap is a volume, and as such it can be visualized using the Volume Rendering method. It can be an alternative from [[Documentation/{{documentation/version}}/Modules/ModelMaker|creating surface models]] from labelmap.
# First you need to load your labelmap.
## Make sure you check the "Labelmap" check box at load time.
## Make sure the labelmap is a Unsigned Char image, not Unsigned/Signed Short, Int or Long. If needed, you can [[Documentation/{{documentation/version}}/Modules/CastScalarVolume| cast]] the labelmap to UCHAR.
# Open the Volume Rendering module
## As usual, click on the eye to start the Volume Rendering.
# To turn off shading:
## go to Advanced../Volume Properties/Advanced group box and uncheck the "Shade" checkbox
# To turn on/off a specific label:
## Go to the Advanced.../Volume Properties/Scalar Opacity Mapping group box
## Toggle down the '>>' button to show the Opacity controls.
## Browse each label with the "Point:" spinbox. When the spinbox shows the current label value,
## Set the Opacity spinbox value to 0.0/1.0 to hide/show the label.

===Render 2 volumes in 2 views===
[[File:DualVR.png|right|500px]]
# [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Layouts|Change layout]] into "Dual 3D"
# [[Documentation/{{documentation/version}}/SlicerApplication/LoadingData|Load]] your 2 volumes
# [[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI#Module_Selection_.26_Navigation|Open]] Volume Rendering module
# For the first volume:
## Open the "Inputs" section
## Uncheck "View2" -> only "View1" is checked
## Don't click the "eye" icon yet.
# Select the 2nd volume
## Check "View2"
## Uncheck "View1" -> only "View2" is checked
## Click the eye icon for the VR to show up in View2
# Select the 1st volume
## Click the eye icon for the VR to show up in View1


{{documentation/{{documentation/version}}/module-section|Panels and their use}}
[[File:VolumeRenderingPanel.png|right|]]
{{documentation/{{documentation/version}}/module-parametersdescription}}


{{documentation/{{documentation/version}}/module-section|Similar Modules}}
[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]]


{{documentation/{{documentation/version}}/module-section|References}}
Publications related to this module go here. Links to pdfs would be useful.
For extensions: link to the source code repository and additional documentation


{{documentation/{{documentation/version}}/module-section|Information for Developers}}
===Limitations===
*To date, only 1 volume can be visible at a time. This happens because the current volume rendering displayable node is hidden when changing to a different volume node.
*Only UNSIGNED CHAR images are supported for now. You can convert your images into UCHAR by using the [[Documentation/{{documentation/version}}/Modules/CastScalarVolume|Cast Scalar Volume]] module.

===Key [[Documentation/{{documentation/version}}/Developers/MRML|nodes]] and classes===
* [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayNode.html vtkMRMLVolumeRenderingDisplayNode] controls the volume rendering properties. Each volume rendering technique has its own subclass.
* [http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html vtkSlicerVolumeRenderingLogic] contains utility functions
* [http://slicer.org/doc/html/classvtkMRMLScalarVolumeNode.html vtkMRMLScalarVolumeNode] contains the volume itself
* [http://slicer.org/doc/html/classvtkMRMLVolumePropertyNode.html vtkMRMLVolumePropertyNode] points to the transfer functions
* [http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode] controls the clipping planes
* [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayableManager.html vtkMRMLVolumeRenderingDisplayableManager] adds the volume renderings into the views

===How Tos===
*How to programmatically volume render your volume node?
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
qSlicerAbstractCoreModule* volumeRenderingModule =
qSlicerCoreApplication::application()->moduleManager()->module("VolumeRendering");
vtkSlicerVolumeRenderingLogic* volumeRenderingLogic =
volumeRenderingModule ? vtkSlicerVolumeRenderingLogic::SafeDownCast(volumeRenderingModule->logic()) : 0;
vtkMRMLVolumeNode* volumeNode = mrmlScene->GetNodeByID('vtkMRMLScalarVolumeNode1');
if (volumeRenderingLogic)
{
vtkMRMLVolumeRenderingDisplayNode* displayNode =
volumeRenderingLogic->CreateVolumeRenderingDisplayNode();
mrmlScene->AddNode(displayNode);
displayNode->Delete();
volumeRenderingLogic->UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode);
volumeNode->AddAndObserveDisplayNodeID(displayNode->GetID());
}
See [[Documentation/{{documentation/version}}/Developers/Tutorials/CreateLoadableModule#Dependency_between_modules|here]] for more about volume dependency.
| valign="top" |
>>> logic = slicer.modules.volumerendering.logic()
>>> volumeNode = slicer.mrmlScene.GetNodeByID('vtkMRMLScalarVolumeNode1')
>>> displayNode = logic.CreateVolumeRenderingDisplayNode()
>>> slicer.mrmlScene.AddNode(displayNode)
>>> displayNode.UnRegister(logic)
>>> logic.UpdateDisplayNodeFromVolumeNode(displayNode, volumeNode)
>>> volumeNode.AddAndObserveDisplayNodeID(displayNode.GetID())
|}

*How to programmatically apply a custom color/opacity transfer function?
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
vtkColorTransferFunction* colors = ...
vtkPiecewiseFunction* opacities = ...
vtkMRMLVolumeRenderingDisplayNode* displayNode = ...
vtkMRMLVolumePropertyNode* propertyNode = displayNode->GetVolumePropertyNode();
propertyNode->SetColor(colorTransferFunction);
propertyNode->SetScalarOpacity(opacities);
// optionally set the gradients opacities with SetGradientOpacity
The logic has utility functions to help you create those transfer functions:
volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#ab8dbda38ad81b39b445b01e1bf8c7a86 SetWindowLevelToVolumeProp](...)
volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a1dcbe614493f3cbb9aa50c68a64764ca SetThresholdToVolumeProp](...)
volumeRenderingLogic->[http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html#a359314889c2b386fd4c3ffe5414522da SetLabelMapToVolumeProp](...)
| valign="top" |
>>> propertyNode = displayNode.GetVolumePropertyNode()
>>> ...
|}

*How to programmatically limit volume rendering to a subset of the volume?
{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |
[http://slicer.org/doc/html/classvtkMRMLAnnotationROINode.html vtkMRMLAnnotationROINode]* roiNode =...
vtkMRMLVolumeRenderingDisplayNode* displayNode = ...
displayNode->SetAndObserveROINodeID(roiNode->GetID());
displayNode->SetCroppingEnabled(1);
| valign="top" |
>>> displayNode.SetAndObserveROINodeID(roiNode.GetID())
>>> displayNode.CroppingEnabled = 1
|}

*How to register a new Volume Rendering mapper?
You need to derive from [http://slicer.org/doc/html/classvtkMRMLVolumeRenderingDisplayNode.html vtkMRMLVolumeRenderingDisplayNode] and register your class within [http://slicer.org/doc/html/classvtkSlicerVolumeRenderingLogic.html vtkSlicerVolumeRenderingLogic].

{|width = "100%"
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|C++
! style="border-bottom: 1px solid darkgrey;font-size: 75%;"|Python
|-
| valign="top" |

void qSlicerMyABCVolumeRenderingModule::setup()
{
vtkMRMLThreeDViewDisplayableManagerFactory::GetInstance()->
RegisterDisplayableManager("vtkMRMLMyABCVolumeRenderingDisplayableManager");

this->Superclass::setup();

qSlicerAbstractCoreModule* volumeRenderingModule =
qSlicerCoreApplication::application()->moduleManager()->module("VolumeRendering");
if (volumeRenderingModule)
{
vtkNew<vtkMRMLMyABCVolumeRenderingDisplayNode> displayNode;
vtkSlicerVolumeRenderingLogic* volumeRenderingLogic =
vtkSlicerVolumeRenderingLogic::SafeDownCast(volumeRenderingModule->logic());
volumeRenderingLogic->RegisterRenderingMethod(
"My ABC Volume Rendering", displayNode->GetClassName());
}
else
{
qWarning() << "Volume Rendering module is not found";
}
}
If you want to expose control widgets for your volume rendering method, then register your widget with [http://slicer.org/doc/html/classqSlicerVolumeRenderingModuleWidget.html#acd9cdb60f1fd260f3ebf74428bb7c45b addRenderingMethodWidget()]
|}


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@@ Line 36: / Line 36: @@
 {{documentation/{{documentation/version}}/module-section|Tutorials}}
-Tutorial about [http://www.slicer.org/slicerWiki/index.php/Slicer3:Volume_Rendering_Tutorials using the volume rendering module].
+Tutorial about [http://www.slicer.org/wiki/Slicer3:Volume_Rendering_Tutorials using the volume rendering module].
 ===Labelmap rendering===

Documentation/4.4/Modules/VolumeRendering - Revision history

Unknown user: Text replacement - "slicerWiki/index.php" to "wiki"

UpdateBot: Nightly -> 4.4