NA-MIC National Alliance for Medical Image Computing IGT Software Design and Process Bill Lorensen GE Research.

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

IGTSoftware Design and Process

Bill Lorensen

GE Research

National Alliance for Medical Image Computing http://na-mic.org

Outline

• Background• Design Principles• Software Process• Challenges

National Alliance for Medical Image Computing http://na-mic.org

Open Source Menu for Success

• A Community with a common vision• A pool of talented and motivated

developers/scientists• A mix of academic and commercial• An organized, light weight approach to

software development• A leadership structure• Communication• A business model

National Alliance for Medical Image Computing http://na-mic.org

Guiding Principles

• Open is good

• Proprietary is bad

• Reuse is good

• NIH* is bad

• Modularity is good

• Monolithic is bad

*Not invented here

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Design Principles

National Alliance for Medical Image Computing http://na-mic.org

Toolkits and Libraries

• Visualization - VTK

• Segmentation/Registration - ITK

• State machines – IGSTK

• UI – KWWidgets, ??

• Tracking – OpenTracker, ??

• DICOM – dcmtk, gdcm

• File I/O – nrrd, meta, pnglib, …

National Alliance for Medical Image Computing http://na-mic.org

Object-Oriented Design

• Dominated software systems throughout the 1990’s

• Continues to be the accepted software design technique

• Particularly useful for dealing with complexity• Provides programmatic abstractions to deal

with generalization and encapsulation• C++ and Java have mechanisms to support

OOD

National Alliance for Medical Image Computing http://na-mic.org

Generic Programming

• Organize libraries consisting of generic—or reusable—software components.

• The essential ideas of generic programming are containers to hold data, iterators to access the data, and generic algorithms that use containers and iterators to create efficient, fundamental algorithms.

• ITK uses generic programming to process n-dimensional “images”.

National Alliance for Medical Image Computing http://na-mic.org

Design Patterns

• Good object-oriented software systems have recurring designs (patterns) that occur frequently

• ITK employs a number of powerful design patterns– object factories– command/observer– smart pointer memory management

National Alliance for Medical Image Computing http://na-mic.org

Frameworks

• Define how a group of participants can be put together to solve a particular task.

• Particularly suitable for describing complex flows or algorithms that have a number of steps that can be varied

• ITK Frameworks– A demand-driven data processing pipeline

that connects algorithms to process n-dimensional image data

– Registration framework– Level-set framework

National Alliance for Medical Image Computing http://na-mic.org

Separation of Algorithms from Interfaces

• Implement the algorithms with a clear separation from the applications and especially the user interfaces.

• Uses the Command/Observer design pattern that permits applications to watch for significant events during the execution of an algorithm

• ITK has no built-in visualization, but has been interfaced to several systems including 3D Slicer, Analyze, SciRun and Volview.

National Alliance for Medical Image Computing http://na-mic.org

Slicer 3 Execution Model: Goals

• Provide interface to batch programs– Simplify and unify command line

processing• Auto generate C++ command line

processing

– Simplify and unify GUI• Auto generate GUI

National Alliance for Medical Image Computing http://na-mic.org

UserDesktop

Slicer 3.0

Algorithms ITK VTK SlicerModules

VTK AppsUsing ITK

Scripts ofSlicer Mods

BatchPrograms

Non-NAMICCmd tools

LONIPipeline

Birn GridData/Compute

Slicer 3.0

National Alliance for Medical Image Computing http://na-mic.org

Execution Model: Plugins

• XML Interface Description– Describes command line options– Describes suggestions for GUI

• GenerateCLP– Generates C++ command line

processing code from XML– Reports XML description

National Alliance for Medical Image Computing http://na-mic.org

Program Flow

UserDesktopprog.xml GenerateCLP progCLP.h

SlicerModules

prog.cxx

Non-NAMICCmd tools

LONIPipeline

Birn GridData/Compute

Slicer 3.0

National Alliance for Medical Image Computing http://na-mic.org

Resample --xml<?xml version="1.0" encoding="utf-8"?><executable> <category>filtering</category> <title>Resample Volume</title> <description>Resamples a volume</description> <version>1.0</version> <documentationurl></documentationurl> <license></license> <contributor>Bill Lorensen</contributor> <parameters> <label>Resampling Parameters</label> <description>Parameters used for resampling</description> <float-vector> <name>outputPixelSpacing</name> <flag>-s</flag> <longflag>--spacing</longflag> <description>Spacing along each dimension (0 means use

input spacing)</description> <label>Spacing</label> <default>0,0,0</default> </float-vector> </parameters>

<label>IO</label> <description>Input/output parameters</description> <image> <name>InputVolume</name> <label>input Volume</label> <channel>input</channel> <index>0</index> <description>Input volume to be

resampled</description> </image> <image> <name>OutputVolume</name> <label>Output Volume</label> <channel>output</channel> <index>1</index> <description>Resampled Volume</description> </image> </parameters></executable>

National Alliance for Medical Image Computing http://na-mic.org

Resample.cxx

.

.

.#include “ResampleCLP.h”

Main (int argc, char *argv[]){ PARSE_ARGS; algorithm code}

National Alliance for Medical Image Computing http://na-mic.org

Resample --helpUSAGE: ResampleVolume [--xml] [--echo] [-s <std::vector<float>>]

[--] [--version] [-h] <std::string> <std::string>Where: --xml Produce xml description of command line arguments (default: 0) --echo Echo the command line arguments (default: 0) -s <std::vector<float>>, --spacing <std::vector<float>> Spacing along each dimension (0 means use input spacing) (default: 0,0,0) --, --ignore_rest Ignores the rest of the labeled arguments following this flag. --version Displays version information and exits. -h, --help Displays usage information and exits. <std::string> (required) Input volume to be resampled (default: None) <std::string> (required) Resampled Volume (default: None)

Resamples a volume

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Software Process

National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Rhythms

• Yearly All-Hands Meeting

• Bi-annual Programmers’ Week

• Weekly Engineering T-Cons

• Nightly Build/Test– ITK– VTK– Slicer

National Alliance for Medical Image Computing http://na-mic.org

NA-MIC Tools

• CMake– Cross-platform build

• Dart 2– Build/Test server

• CTest– Build/Test client

• Cpack– Packaging and Distribution

• Media Wiki– Reporting/discussion forum

• POTS– T-cons

National Alliance for Medical Image Computing http://na-mic.org

How DART Enables Collaboration

CVSSVN

Results posted on web(the dashboard)

CVS/SVN maintainssource code

revisions DART compilessource code, runs tests

Developers review results

Developers check-in code

National Alliance for Medical Image Computing http://na-mic.org

Dart

Dart

National Alliance for Medical Image Computing http://na-mic.org

National Alliance for Medical Image Computing http://na-mic.org

Multi-Platform Builds

National Alliance for Medical Image Computing http://na-mic.org

IGT Challenges

• Define an architecture tailored to IGT requirements

• Leverage existing toolkits

• Fill in toolkit gaps

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

IGTSoftware Design and Process

Bill Lorensen

GE Research