Getting Started with ITK in Python Language I. Introduction to ITK, Python Wrapping and VTK-ITK Connection

Outline ITK Overview (most slides are adopted from Documents in Insight Toolkit 1.2 CD) Python Wrapping Installations Examples Filter Registration ITK-VTK connection Where to get help?

Open Source C++ Toolkit What is ITK Open Source C++ Toolkit Medical Image Processing Registration Segmentation

ITK Overview Core design concepts Generic programming (e.g. temper late, containers, iterators.) Smart pointers for memory management Object factories for adaptable object instantiation Command/observer design paradigm for event management Multithreading support Cross-platform (CMake) Efficient n-dimensional implementation

The Big Picture Common Basic Filters ITK Numerics Algorithms

Common Common System Data Pipeline Basic MultiThreader Mutex Exceptions Data Basic PointSet Pipeline Image VectorContainer MapContainer ListFeatures Histogram Mesh Point Matrix Vector ProcessObject DataObject Events Observer Size Transforms Index

Numerics Numerics Optimizers VNL Statistics FEM Eigen SVD Matrix Membership Functions Classifiers Vector Linear Algebra Evolutionary Algorithms Gradient Descent Histogram methods Optimizers List methods Optimizers VNL Element Statistics Node Numerics Solver FEM Load Material

Basic Filters Basic Filters PixelWise Neighborhood IO Global Arithmetic Basic Filters PixelWise Trigonometric Intensity Transf MorphoMath Neighborhood IO Median Global Derivative Laplacian EdgeDetection PNG VTK DICOM Meta DistanceMap HaussdorfDistance Anisotropic Diffusion Connected Components

Algorithms Algorithms Markov RF Level Sets Registration PDE Interpolators Narrow Band Shape Detection Fast Marching Transforms Optimizers Geodesic Contours Metrics Multi Resolution Watershed Markov RF Level Sets Registration Demons CurvatureFlow PDE Algorithms Fuzzy Connectedness Hard SimpleFuzzy Deformable Models Balloon Force

Pipeline Architecture Data Flow Data Objects Image Mesh Process Objects (Algorithms) Segmentation Registration Image Processing Streaming capable

Pipeline Architecture Image Filter

Streaming – Processing Large Images Architecture Streaming – Processing Large Images Input Image Output Image Filter

Registration Framework Multi Resolution Registration Framework Image Registration Framework Components PDE Based Registration FEM Based Registration

Registration Components Registration Method Fixed Image Metric Optimizer Transform Interpolator Moving Image Metric: Mutual Information, Mean Squares, Normalized Correlation and Pattern Intensity Optimizer: Gradient Descent, Regular Step Gradient Descent, Conjugate Gradient, Levenberg-Marquardt Transform: Translation, Scale, Rotation, Rigid3D, Rigid2D, Affine and Splines (TPS, EBS, VS) Interpolator: Nearest neighbor, Linear, BSpline

Other Frameworks Level Set Framework for segmentation FEM Framework A subsystem for solving general FEM problems, in particular non-rigid registration IO Framework Use a flexible object factory mechanism to support a variety of file formats

Why Python Wrapping ? Interpreted Language Interactive Simplifies teaching and learning Facilitates rapid prototyping Large python-vtk user base in our Labs

How Does It Work? ITK Core is implemented in C++ Tcl and Python bindings are generated automatically using a combination of gccxml -- a modified version of gcc Cable -- processes XML info from gccxml and generates input for CSWIG CSWIG -- modified version of SWIG that produces Python (or Tcl ) binding Under active development, no binary installation package yet.

Python wrapping requires fully specified C++ types How does it work ? Python wrapping requires fully specified C++ types C++ Python Image<T,N> Image<ushort,2> ImageUS2 Image<ushort,3> ImageUS3 Image<float,2> ImageF2 Image<float,3> ImageF3

How does it work ? ITK Filters are Templated over Image Type GaussianImageFilter< InputImage, OutputImage > GaussianImageFilter< ImageU2 , ImageU2 > GaussianImageFilter< ImageF2 , ImageF2 > GaussianImageFilter< ImageU2 , ImageF2 > GaussianImageFilter< ImageF2 , ImageU2 > GaussianImageFilter< ImageF3 , ImageU3 >

How does it work? C++ Python Python wrapper for filters should define type combinations C++ Python GaussianImageFilter<ImageUS2,ImageUS2> GaussianFilterUS2US2 GaussianImageFilter<ImageF2,ImageF2> GaussianFilterF2F2 GaussianImageFilter<ImageUS2,ImageF2> GaussianFilterUS2F2 GaussianImageFilter<ImageF2,ImageUS2> GaussianFilterF2US2 GaussianImageFilter<ImageF3,ImageUS3> GaussianFilterF3US3

VTK-ITK Connection in Python Implemented as an module ConnectVTKITK in InsightApplication repository Connect the pipeline with Import and Export classed in VTK and ITK VTK exporter  ITK importer ITK exporter  VTK importer Use ITK for image processing, registration, segmentation and VTK for visualization Status: Under active development

Installation What do I need? C++ Compiler -- gcc 2.95 to 3.3, Visual C++ 6 -7.1 ) CMake (1.67 or cvs checkout) Python (2.1, 2.2, or 2.3) VTK (4.2.2 or cvs checkout) Insight (cvs checkout) InsightApplications Installation for Python-VTK-ITK is not straight forward right now, no binary distribution. A step by step instruction will be posted on Image Lab coders’ web page.

Step 1 Python and modules Linux comes with python and tcl/tk Windows: python 2.2, tcl/tk 8.3 Numpy (Numeric Python) Scientific Python (Install NetCDF library first for NetCDF and MINC support)

Step 2 CMake Download the latest (1.67) binary for your platform from www.cmake.org

Step 3 Install VTK Install VTK 4.2.2 from source distribution . Turn on the following flags VTK_USE_HYBRID VTK_USE_PATENTED VTK_WRAP_PYTHON VTK_USE_ANSI_STDLIB

Step 4 Install Insight Get the source cvs Build with CMake CSWIG_WRAP_PYTHON USE_VTK

Step 5 Install InsightApplications CVS checkout CMake CONNECT_VTK_ITK

Step 6 Environment Variables Linux/Unix PYTHONPATH LD_LIBRARY_PATY Windows PATH

Examples CurvatureAnisotropicDiffusionImageFilter.py

Examples ImageRegistration3.py

Examples : VTK-ITK Connection CannyEdgeDetectionImageFilterConnectVTKITK.py

Where to get help? www.itk.org Image Labs coders mailing lists: ITK Software Guild : PDF document (Over 500 pages) Doxygen generated manual pages Insight-users Mailing Lists Image Labs coders mailing lists: http://www.imaging.robarts.ca/coders