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

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

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

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

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

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

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>>

vtkITK: Example Case: Perform a edge-preserving filtering as a preprocessing before segmentation. Algorithm: Anisotropic diffusion process. Code: itk::GradientAnisotropicDiffusionImageFilter. http://www.itk.org/Doxygen16/html/classitk_1_1GradientAnisotropicDiffusionImageFilter.html

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

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

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);

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

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

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"

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 } …..

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 }

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) }

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]

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

Demo

Enjoy!

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