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The ITK Software Guide

The ITK Software GuideThe Insight Toolkit (ITK) is an open-source, cross-platform system for medical image processing. It provides medical imaging researchers with an extensive suite of leading-edge algorithms for registering, segmenting, analyzing, and quantifying medical data. It is used in thousands of research and commercial applications, from major labs to individual ITK Software Guide is the handbook for developing Software with ITK. It is divided into two companion first book covers building and installation, general architecture and design, as well as the process of contributing in the ITK second book covers detailed design and functionality for reading and writing images, filtering, registration, segmentation, and performing statistical : This PDF is a concatenation of both Book 1 and Book 2 of the ITK Software Guide into a single ITK Software GuideBook 1: Introduction and Development Guidelines ..Pages 2 - 409 Book 2: Design and Functionality.

images, filtering, registration, segmentation, and performing statistical analysis. NOTICE: This PDF is a concatenation of both Book 1 and Book 2 of …

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Transcription of The ITK Software Guide

1 The ITK Software GuideThe Insight Toolkit (ITK) is an open-source, cross-platform system for medical image processing. It provides medical imaging researchers with an extensive suite of leading-edge algorithms for registering, segmenting, analyzing, and quantifying medical data. It is used in thousands of research and commercial applications, from major labs to individual ITK Software Guide is the handbook for developing Software with ITK. It is divided into two companion first book covers building and installation, general architecture and design, as well as the process of contributing in the ITK second book covers detailed design and functionality for reading and writing images, filtering, registration, segmentation, and performing statistical : This PDF is a concatenation of both Book 1 and Book 2 of the ITK Software Guide into a single ITK Software GuideBook 1: Introduction and Development Guidelines ..Pages 2 - 409 Book 2: Design and Functionality.

2 Pages 410 - 983 The ITK Software GuideBook 1: Introduction and DevelopmentGuidelinesFourth EditionUpdated for ITK version J. Johnson, Matthew M. McCormick, Luis Ib a nez,and theInsight Software ConsortiumApril 16, 2021 purpose of computing is Insight, not HammingABSTRACTThe National Library of Medicine Insight Segmentation and Registration Toolkit, shortened as theInsight Toolkit(ITK), is an open-source Software toolkit for performing registration and the process of identifying and classifying data found in adigitally sampledrepresentation. Typically the sampled representation is an image acquired from such medical instru-mentation as CT or MRI the task of aligning or developing correspondencesbetween data. For example, in the medical environment, a CT scan may be aligned with a MRI scanin order to combine the information contained in is a cross-platform Software . It uses a build environment known asCMaketo manage platform-specific project generation and compilation process in a platform-independent way.

3 ITK is imple-mented in C++. ITK s implementation style employs generic programming, which involves theuse of templates to generate, at compile-time, code that canbe appliedgenericallyto any class ordata-type that supports the operations used by the template. The use of C++ templating means thatthe code is highly efficient and many issues are discovered atcompile-time, rather than at run-timeduring program execution. It also means that many of ITK s algorithms can be applied to arbitraryspatial dimensions and pixel automated wrapping system integrated with ITK generatesan interface between C++ and a high-level programming languagePython. This enables rapid prototyping and faster exploration of ideasby shortening the edit-compile-execute cycle. In additionto automated wrapping, theSimpleITKproject provides a streamlined interface to ITK that is available for C++, Python, Java, CSharp, R,Tcl and from around the world can use, debug, maintain, and extend the Software because ITKis an open-source project.

4 ITK uses a model of Software development known as Extreme Program-ming. Extreme Programming collapses the usual Software development methodology into a simulta-neous iterative process of design-implement-test-release. The key features of Extreme Programmingare communication and testing. Communication among the members of the ITK community is whathelps manage the rapid evolution of the Software . Testing iswhat keeps the Software stable. Anextensive testing process supported by the system known asCDashmeasures the quality of ITKcode on a daily basis. The ITK Testing Dashboard is updated continuously, reflecting the quality ofthe code at any most recent version of this document is available This book is a Guide for developing softwarewith ITK; it is the first of two companion books. This book covers building and installation, generalarchitecture and design, as well as the process of contributing in the ITK community. The secondbook covers detailed design and functionality for reading and writing images, filtering, registration,segmentation, and performing statistical Insight Toolkit(ITK)has been created by the efforts of many talented individualsand presti-gious organizations.

5 It is also due in great part to the vision of the program established by Dr. TerryYoo and Dr. Michael Ackerman at the National Library of book lists a few of these contributors in the following paragraphs. Not all developers of ITK arecredited here, so please visit the Web pages the names ofadditional contributors, as well as checking the GIT sourcelogs for code following is a brief description of the contributors to this Software Guide and their Ib a nezis principal author of this text. He assisted in the design and layout of the text, im-plemented the bulk of the LATEX and CMake build process, and was responsible for the bulk ofthecontent. He also developed most of the example code found in Schroederhelped design and establish the organization of this text and theInsight/Examplesdirectory. He is principal content editor, and has authoredseveral Ngauthored the description for the registration framework and its components, the sectionon the multiresolution framework, and the section on deformable registration methods.

6 She alsoedited the section on the resampling image filter and the sections on various level set Catesauthored the iterators chapter and the text and examples describing watershed seg-mentation. He also co-authored the level-set Kimauthored the chapter on the statistics Jomiercontributed the chapter on spatial objects and examples on model-based registrationusing spatial Krishnanreconfigured the process for automatically generating images from all the exam-ples. Added a large number of new examples and updated the Filtering and Segmentation chaptersvifor the second Aylwardcontributed material describing spatial objects and Sundaramcontributed the section on deformable registration using the finite element Foskeycontributed the examples on Malaterrecontributed the entire section on the description and use ofDICOM readers andwriters based on the GDCM library. He also contributed an example on the use of the Bakercontributed the section on how to write composite filters.

7 Also known as the Software Guide is generated in part from the ITK source code itself, many ITK developershave been involved in updating and extending the ITK documentation. These includeDavid Doria,Bradley Lowekamp,Mark Foskey,Ga etan Lehmann,Andreas Schuh,Tom Vercauteren,CoryQuammen,Daniel Blezek,Paul Hughett,Matthew McCormick,Josh Cates,Arnaud Gelas,Jim Miller,Brad King,Gabe Hart,Hans Johnson,Kent Williams,Constantine Zakkaroff,Xiaoxiao Liu,Ali Ghayoor, andMatthew McCormickupdated the documentation for the initial ITK Version 4 Ib a nezandS ebastien Barr edesigned the original Book 1 McCormickandBrad Kingupdated the code to produce the Book 1 cover for ITK 4 and VTK Liu,BillLorensen,Luis Ib a nez, andMatthew McCormickcreated the 3D printed anatomical objects thatwere photographed byS ebastien Barr efor the Book 2 Jordandesigned the layout ofthe Avila,Hans Johnson,Matthew McCormick,Sandy McKenzie,Christopher Mullins,Katie Osterdahl, andMichka Popoffprepared the book for the print Introduction11 Organization.

8 How to Learn ITK.. Software Organization.. The Insight Community and Support.. A Brief History of ITK.. 82 Configuring and Building Obtaining the Software .. Downloading Packaged Releases.. Downloading From Git.. Data.. Using CMake for Configuring and Building ITK.. Preparing CMake.. Configuring ITK.. Advanced Module Configuration.. Static and Shared Libraries.. Compiling ITK.. Installing ITK on Your System.. Cross compiling ITK.. Getting Started With ITK.. Using ITK as an External Library.. Hello World!.. 21II Architecture233 System System Organization.. Essential System Concepts.. Generic Programming.. Include Files and Class Definitions.. Object Factories.. Smart Pointers and Memory Management.. Error Handling and Exceptions.. Event Handling.. Multi-Threading.. Numerics.

9 Data Representation.. Data Processing Pipeline.. Spatial Objects.. Wrapping.. Python Setup.. 39 Install Stable Python Packages.. 39 Install Latest Python Packages.. 39 Build Python Packages from Source.. 394 Data Image.. Creating an Image.. Reading an Image from a File.. Accessing Pixel Data.. Defining Origin and Spacing.. RGB Images.. Vector Images.. Importing Image Data from a Buffer.. PointSet.. Creating a PointSet.. Getting Access to Points.. Getting Access to Data in Points.. RGB as Pixel Type.. Vectors as Pixel Type.. Normals as Pixel Type.. Mesh.. Creating a Mesh.. Inserting Cells.. Managing Data in Cells.. Customizing the Mesh.. Topology and the K-Complex.. Representing a PolyLine.. Simplifying Mesh Creation.. Iterating Through Cells.. Visiting Cells.. More on Visiting Cells.

10 Path.. Creating a PolyLineParametricPath.. 1035 Spatial Introduction.. Hierarchy.. Transformations.. Types of Spatial Objects.. ArrowSpatialObject.. BlobSpatialObject.. EllipseSpatialObject.. GaussianSpatialObject.. GroupSpatialObject.. ImageSpatialObject.. ImageMaskSpatialObject.. LandmarkSpatialObject.. LineSpatialObject.. MeshSpatialObject.. SurfaceSpatialObject.. TubeSpatialObject.. DTITubeSpatialObject.. Read/Write SpatialObjects.. Statistics Computation via SpatialObjects.. 1396 Introduction.. Programming Interface.. Creating Iterators.. Moving Iterators.. Accessing Data.. Iteration Loops.. Image Iterators.. ImageRegionIterator.. ImageRegionIteratorWithIndex.. ImageLinearIteratorWithIndex.. ImageSliceIteratorWithIndex.. ImageRandomConstIteratorWithIndex.. Neighborhood Iterators.


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