1. Steve Pieper, PhD Raul San Jose, PhD Alex Yarmarkovich, PhD
Slicer and ITK
Steve Pieper, PhD
Raul San Jose, PhD
Alex Yarmarkovich, PhD

2. Overview Embedding ITK Filtering Example Generic Reader Example
vtkITK framework
Filtering Example
Generic Reader Example

3. How to use ITK? “Conventional Way”: Develop your own application
My application
Rendering Library
GUI
My Algorithm
My classes
ITK pipeline

4. How to use ITK? “Embedding”: Develop inside your platform (Slicer way)
My platform
GUI Module
Rendering Module
(vtk)
ITK Pipeline
Core Library
(vtk)
Library wrappers
ITK

5. Slicer and ITK Data Flow: VTK – ITK – VTK VTK ITK VTK
vtkImageExport
itk::VTKImageImport
itk::VTKImageExport
vtkImageImport

6. vtkITK: Overview vtkITKMyFilter itk::MyFilter VTK ITK
vtkImageExport
itk::VTKImageImport
itk::VTKImageExport
vtkImageImport
itk::MyFilter
vtkITKMyFilter

7. vtkITK: Base classes vtkImageExport vtkImageImport
vtkITKImageToImageFilter2DFF
vtkImageToImageFilter
vtkITKImageToImageFilterUSUS
vtkITKImageToImageFilterF2F2
vtkITKImageToImageFilter
vtkITKMyFilter
vtkITKImageToImageFilterF3F3
vtkImageExport
vtkImageImport
vtkITKImageToImageFilterFF
itk::VTKImageExport<itk::Image<float>,3>>
itk::VTKImageImport<itk::Image<float>,3>>

8. vtkITK: Example
Case: Perform a edge-preserving filtering as a preprocessing before segmentation.
Algorithm: Anisotropic diffusion process.
Code: itk::GradientAnisotropicDiffusionImageFilter.

9. vtkITK: Wrapping
#include "vtkITKImageToImageFilterFF.h"
#include "itkGradientAnisotropicDiffusionImageFilter.h"
#include "vtkObjectFactory.h"
class VTK_EXPORT vtkITKGradientAnisotropicDiffusionImageFilter : public vtkITKImageToImageFilterFF {
public:
static vtkITKGradientAnisotropicDiffusionImageFilter *New();
vtkTypeRevisionMacro(vtkITKGradientAnisotropicDiffusionImageFilter, vtkITKImageToImageFilterFF);

10. vtkITK: Wrapping
void SetConductanceParameter ( double value ) {
DelegateITKInputMacro ( SetConductanceParameter, value ); };
double GetConductanceParameter ()
DelegateITKOutputMacro(GetConductanceParameter) ;
double GetTimeStep ()
DelegateITKOutputMacro(GetTimeStep) ;
m_Filter.GetPointer()->SetConductanceParameter(value)

11. vtkITK: Wrapping protected: //BTX
typedef itk::GradientAnisotropicDiffusionImageFilter<Superclass::InputImageType,
Superclass::InputImageType> ImageFilterType;
vtkITKGradientAnisotropicDiffusionImageFilter() : Superclass ( ImageFilterType::New() ){};
~vtkITKGradientAnisotropicDiffusionImageFilter() {};
ImageFilterType* GetImageFilterPointer() { return dynamic_cast<ImageFilterType*> ( m_Filter.->GetPointer() );
//ETX
private:
vtkITKGradientAnisotropicDiffusionImageFilter(const vtkITKGradientAnisotropicDiffusionImageFilter&); // Not implemented.
void operator=(const vtkITKGradientAnisotropicDiffusionImageFilter&); // Not implemented. };
vtkStandardNewMacro(vtkITKGradientAnisotropicDiffusionImageFilter);

12. Slicer Module ITKFilters.tcl Modules methods: core methods
proc ITKFiltersInit
proc ITKFiltersBuildGUI
proc ITKFiltersBuildVTK
proc ITKFiltersEnter
proc ITKFiltersExit
Other methods: callback methods
proc ITKFiltersApply
…..

13. Slicer Module proc ITKFiltersInit set m ITKFilters
set Module($m,author) “NAMIC people"
set Module($m,row1List) "Help Main"
set Module($m,row1Name) "{Help} {Main}"
set Module($m,row1,tab) Main
set Module($m,procGUI) ITKFiltersBuildGUI
set Module($m,procVTK) ITKFiltersBuildVTK
set Module($m,procMRML) ITKFiltersUpdateGUI
set Module($m,procEnter) ITKFiltersEnter
set Module($m,procExit) ITKFiltersExit

14. Slicer Module proc ITKFiltersInit
set ITKFilters(filters) " GradientAnisotropicDiffusionImageFilter “
set ITKFilters($filter,params) "SetConductanceParameter SetNumberOfIterations \ SetTimeStep"
set param SetConductanceParameter
set ITKFilters($filter,$param) 1
set ITKFilters($filter,$param,text) "Conductance"
set ITKFilters($filter,$param,maxmin) "1 10“
set ITKFilters($filter,$param,res) 0.1
set ITKFilters($filter,$param,widget) "scale"

15. proc ITKFiltersBuildGUI
Slicer Module
proc ITKFiltersBuildGUI
set fMain $Module(ITKFilters,fMain)
set f $fMain
foreach frame "Top Middle Floating Bottom" {
frame $f.f$frame -bg $Gui(activeWorkspace)
pack $f.f$frame -side top -padx 0 -pady $Gui(pad) -fill x }
…..

16. proc ITKFiltersBuildGUI
Slicer Module
proc ITKFiltersBuildGUI
"scale" {
eval {label $fwidget.l$param -text $ITKFilters($filter,$param,text) \
-width 12 -justify right } $Gui(WLA)
eval {entry $fwidget.e$param -justify right -width 4 \
-textvariable ITKFilters($filter,$param) } $Gui(WEA)
eval {scale $fwidget.s$param \
-from [lindex $ITKFilters($filter,$param,maxmin) 0] \
-to [lindex $ITKFilters($filter,$param,maxmin) 1] \
-variable ITKFilters($filter,$param)\
-orient vertical \
-resolution $ITKFilters($filter,$param,res) } $Gui(WSA)
pack $fwidget.l$param $fwidget.e$param $fwidget.s$param \
-side left -padx $Gui(pad) -pady 0 }

17. Slicer Module proc ITKFiltersApply #Preparing INPUT and OUTPUT volume
If {$v2 == -5} {
set name [Volume($v1,node) GetName]
set v2 [DevCreateNewCopiedVolume $v1 "" ${name}_filter ]
set node [Volume($v2,vol) GetMrmlNode]
Mrml(dataTree) RemoveItem $node
set nodeBefore [Volume($v1,vol) GetMrmlNode]
Mrml(dataTree) InsertAfterItem $nodeBefore $node MainUpdateMRML
} else {
set v2name [Volume($v2,node) GetName]
set continue [DevOKCancel "Overwrite $v2name?"]
if {$continue == "cancel"} { return 1 }
# They say it is OK, so overwrite!
Volume($v2,node) Copy Volume($v1,node) }

18. Slicer Module proc ITKFiltersApply #Caster vtkImageCast _cast
_cast SetOutputScalarTypeToFloat
_cast SetInput [Volume($v1,vol) GetOutput]
_cast Update
#Create Object
vtkITK$filter _filter
foreach param $ITKFilters($filter,params) {
_filter $param $ITKFilters($filter,$param) }
_filter SetInput [_cast GetOutput]

19. Slicer Module proc ITKFiltersApply
_filter AddObserver StartEvent MainStartProgress
_filter AddObserver EndEvent MainEndProgress
_filter AddObserver ProgressEvent "MainShowProgress _filter"
_filter Update
#Assign output
[Volume($v2,vol) GetOutput] DeepCopy [_filter GetOutput]
#Destroy pipeline
_cast Delete
_filter SetOutput ""
_filter Delete

20. Demo

21. Enjoy!

22. vtkConnectVTKITK ITK itkMyFilterFF Slicer Module VTK ITK VTK CableSwig
vtkImageExport
itk::VTKImageImport
itk::VTKImageExport
vtkImageImport