integration of itk into scirun

Integration of ITK IntoSCIRun

Yarden LivnatDarby Van Uitert

Joshua Cates

Aims

Integrate ITK into SCIRun No changes to ITK Minimal changes to SCIRun Easy to apply to all old and new ITK

filters

The Players

SCIRun

The Players

Anisotropic DiffusionFilter Parameters

SCIRun ITK

Filter

Filter

Watershed Filter

Proposed Solution

ITK Filter

Automated as much as possible

GUI

XML

itk_filter.xml XSL sci_filter.h sci_filter.cc

sci_filter.tcl sci_filter.xml

XML

itk_filter.xml XSL sci_filter.h sci_filter.cc

sci_filter_gui.xml XSL sci_filter.tcl

sci_filter.tcl sci_filter.xml

XML

itk_filter.xml XSL sci_filter.h sci_filter.cc

sci_filter_gui.xml XSL sci_filter.tcl

sci_filter.tcl sci_filter.xml

sci_filter_gui.xmlsci_filter_gui.xml

sci_filter_gui.xmlsci_filter_gui.xml

GUIGUI

GUIGUI

XML

itk_filter.xml XSL sci_filter.h sci_filter.cc

sci_filter_gui.xml XSL sci_filter.tcl

sci_filter.tcl sci_filter.xml

sci_filter.xml XSL: include files, more instantiation information

Templated Filters

1) One module per instantiation Trivial

2) Switch statement

Instantiation information in an XML file to be used during code generation

3) Dynamic Compilation Non-templated base classes

Summary

XML Files – 3 per filteritk_filter.xml created by ITK developerssci_filter.xml created by developer/ITK usersci_filter_gui.xml created by developer/ITK user

Validated with DTD !

Summary

XML Files – 3 per filteritk_filter.xml created by ITK developerssci_filter.xml created by developer/ITK usersci_filter_gui.xml created by developer/ITK user

Validated with DTD !

Summary

XML Files – 3 per filteritk_filter.xml created by ITK developerssci_filter.xml created by developer/ITK usersci_filter_gui.xml created by developer/ITK user

XSL Files – 3 per systemGenerateCC.xsl created by us forGenerateTCL.xsl generating our GenerateXML.xsl specific code

Validated with DTD !

Adding a New Filter

ReflectImageFilter

Steps: Write itk_ReflectImageFilter.xml Write basic sci_ReflectImageFilter.xml Generate module Write gui_ReflectImageFilter.xml

Example – itk_filter.xml<filter-itk name=“itk::ReflectImageFilter”>

<description> Reflects an image along a selected direction. </description>

<templated> … </templated>

<inputs> … </inputs>

<outputs> … </outputs> <parameters> … </parameters>

<includes> … </includes></filter-itk>

Example – itk_filter.xml<filter-itk name=“itk::ReflectImageFilter”>

<description> Reflects an image along a selected direction. </description>

<templated> … </templated>

<inputs> … </inputs>

<outputs> … </outputs> <parameters> … </parameters>

<includes> … </includes></filter-itk>

<templated> <template>InputImageType</template> <template>OutputImageType</template> <defaults> <default> itk::Image< float, 2> </default> <default> itk::Image< float, 2> </default> </defaults></templated>

Example – itk_filter.xml<filter-itk name=“itk::ReflectImageFilter”>

<description> Reflects an image along a selected direction. </description>

<templated> … </templated>

<inputs> … </inputs>

<outputs> … </outputs> <parameters> … </parameters>

<includes> … </includes></filter-itk>

<inputs> <input name=“SourceImage” > <type> InputImageType </type> <call> SetInput </call> </input></inputs>

Example – itk_filter.xml<filter-itk name=“itk::ReflectImageFilter”>

<description> Reflects an image along a selected direction. </description>

<templated> … </templated>

<inputs> … </inputs>

<outputs> … </outputs> <parameters> … </parameters>

<includes> … </includes></filter-itk>

<parameters> <param> <name> direction </name> <type> int </type> <call> SetDirection </call> </param></parameters>

Example – itk_filter.xml<filter-itk name=“itk::ReflectImageFilter”>

<description> Reflects an image along a selected direction. </description>

<templated> … </templated>

<inputs> … </inputs>

<outputs> … </outputs> <parameters> … </parameters>

<includes> … </includes></filter-itk>

<includes> <file> itkReflectImageFilter.h </file></includes>

Example – sci_filter.xml

<filter name=“ReflectImageFilter”>

<include href=“” />

<filter-sci> … </filter-sci>

</filter>

Example – sci_filter.xml

<filter name=“ReflectImageFilter”>

<include href=“” />

<filter-sci> … </filter-sci>

</filter>

<include href=“ITK/itk_ReflectImageFilter.xml”/>

Example – sci_filter.xml

<filter name=“ReflectImageFilter”>

<include href=“” />

<filter-sci> … </filter-sci>

</filter>

<filter-sci name=“ReflectImageFilter”> <package> Insight </package>

<category> Filters </category> <instantiations use-defaults=“yes”/> <includes> <file>Packages/Insight/Dataflow/ Ports/ITKDatatypePort.h </file> </includes> </filter-sci>

Generate Process

Steps for module generation Add to Dataflow/Modules/Filters/sub.mk Add to Dataflow/GUI/sub.mk

Module sub.mk

XMLS := \

sci_DiscreteGaussianImageFilter.xml \

sci_ReflectImageFilter.xml \

GUI sub.mk

$(SRCDIR)/tclIndex: \

$(SRCDIR)/Switch.tcl \

$(SRCDIR)/ReflectImageFilter.tcl \

Sample Network

Sample Network

Default GUI

gui_ReflectImageFilter.xml

<filter-gui name=“ReflectImageFilterGUI”>

<parameters>

<param> … </param> <param> … </param>

</parameters>

</filter-gui>

gui_ReflectImageFilter.xml

<filter-gui name=“ReflectImageFilterGUI”>

<parameters>

<param> … </param>

<param> … </param>

</parameters>

</filter-gui>

<param name= “direction” > <gui> radiobutton </gui> <values> <val> 0 </val> <val> 1 </val> </values> <default> 1 </default></param>

Add GUI to sci_filter.xml

<filter name=“ReflectImageFilter”>

<include href=“” />

<filter-sci> … </filter-sci>

</filter>

<include href=“ITK/itk_ReflectImageFilter.xml”/>

sci_filter.xml

itk_filter.xml

Add GUI to sci_filter.xml

<filter name=“ReflectImageFilter”>

<include href=“” />

<filter-sci> … </filter-sci>

</filter>

<include href=“ITK/itk_ReflectImageFilter.xml”/>

<include href=“Dataflow/Modules/Filters/XML/

gui_ReflectImageFilter.xml”/>

sci_filter.xml

itk_filter.xml

gui_filter.xml

Sample Network

Defined GUI

ITKDatatypeclass ITKDatatype : public Datatype {public:

string fname; itk::Object::Pointer data_;

ITKDatatype():ITKDatatype(const ITKDatatype);~ITKDatatype();

virtual void io(Piostream&);static PersistentTypeID type_id;

};

Field and Image Conversion

SCIRun ITK

ITKField wrap Image

ITKField unwrap Image

Field copy data Image

ITKField wrap Image

ITKLatVolField.htemplate<class Data>class ITKLatVolField : public GenericField< LatVolMesh, ITKFData3d< Data > >{public:

ITKLatVolField();ITKLatVolField(Field::data_location data_at);ITKLatVolField(LatVolMeshHandle mesh, Field::data_location data_at);ITKLatVolField(LatVolMeshHandle mesh, Field::data_location data_at, itk::Object* image);

void SetImage(itk::Object* image);...

private:static Persistent* maker();

};

ITKLatVolField.htemplate <class Data>class ITKFData3d {public:

typedef Data value_type;typedef itk::Image< Data, 3 > image_type;typedef ITKIterator< Data > iterator;typedef ITKConstIterator< Data > const_iterator;

iterator *begin_, *end_;const_iterator *const_begin_, *const_end_;

const iterator & begin() { return *begin_; }const iterator & end() { return *end_; }…const value_type &operator[]( LatVolMesh::Node::index_type idx) const;…void set_image(itk::Image< Data, 3 >* img);

private:typename image_type::Pointer image_;

};

ITKLatVolField.htemplate <class Data>class ITKFData3d {public:

typedef Data value_type;typedef itk::Image< Data, 3 > image_type;typedef ITKIterator< Data > iterator;typedef ITKConstIterator< Data > const_iterator;

iterator *begin_, *end_;const_iterator *const_begin_, *const_end_;

const iterator & begin() { return *begin_; }const iterator & end() { return *end_; }…const value_type &operator[]( LatVolMesh::Node::index_type idx) const;…void set_image(itk::Image< Data, 3 >* img);

private:typename image_type::Pointer image_;

};

void set_image(itk::Image< Data, 3 >* img) {

image_ = img;

begin_ = new iterator(image_,

image_->GetRequestedRegion());

begin_->GoToBegin();

…

}

Current ITK Filters

DiscreteGaussianImageFilterGradientAnisotropicDiffusionImageFilterCannySegmentationLevelSetImageFilterGradientMagnitudeImageFilterReflectImageFilterWatershedRelabelerWatershedSegmenterWatershedSegmentTreeGenerator

There are almost 200 filters

Example Network

Example Network

Example Network

Example Network

Example Images

Source Image

Diffused Image

Segmented Image

What’s Left to Do Finish recursive filters for ITK mini

pipeline

Enable complex GUI’s Have: Slider, Check and Radio ButtonNeed: Layout Manager

Port Issue – all are of type ITKDatatypeSame base class issue

Write DocumentationWrite more ITK filters

Filter

Filter

Watershed Filter

Issues

• Object base class (e.g. ImageReader )• SCIRun2

– Common Component Architecture (CCA)– Separable GUIs

• GTK• XML description

• Dynamic Compilation– TypeDescription– Compile_info

• Const pipes