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Non-Interactive Tools. Stephen Aylward, Kitware 2010.01.07. Non-interactive tools. Software Process. Schizophrenia Neurodevelopment Austism MRI, PET, MR Perf Shape Analysis TBI, HD RadOnc, Neurosurgery. 3,224 commits 914,446 lines of code 68 developers GPU, GRID Modularity

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Non interactive tools

Non-Interactive Tools

Stephen Aylward, Kitware 2010.01.07


Non interactive tools1
Non-interactive tools

Software Process

  • Schizophrenia

  • Neurodevelopment

  • Austism

  • MRI, PET, MR Perf

  • Shape Analysis

  • TBI, HD

  • RadOnc, Neurosurgery

  • 3,224 commits

  • 914,446 lines of code

  • 68 developers

  • GPU, GRID

  • Modularity

  • Qt, KWWidgets

  • C++, Python, TCL

  • Mac, Windows, Linux


Na mic kit infrastructure
NA-MIC Kit Infrastructure

  • Software process

    • CMake and CPack

    • CDash and CTest

    • Data management

    • High-performance computing

  • Future work (NA-MIC Renewal)


Software process
Software process

Challenges:

  • Provide effective resources for developers…and users

  • Uphold community standards (quality, style, doc.)

  • Minimize burden on developers…and users


Cmake and cpack
CMake and CPack

  • Summary

    • Cross-platform build control from a single configuration file

    • Release Candidate 2.9

    • 1200 downloads per day

    • Users: KDE, Blizzard (WoW), Nvidia

  • Features added

    • Library support: Qt, R

    • Superbuild: single run to download and configure multiple libraries and executables

  • Use cases

    • 3DSlicer, Teem, CLI Modules, MRML, 3DSlicer Qt


Cdash and ctest
CDash and CTest

  • Summary

    • Regression testing on multiple platforms (OS, CPU, Compilers)

    • Popular: 100 projects freely hosted on cdash.org

    • Robust: Over 1,000 submissions to ITK’s dashboard fest

  • Features added

    • CDash: new statistics, compression of historical data

    • CTest: parallel tests (ctest –j 8)

  • Use cases

    • Over 100 tests added to Slicer in the past few weeks

    • Coverage, Win7, Snow Leopard, …


Data management
Data management

  • PubDB (MIDAS / Insight Journal)

  • The Extensible Neuroimaging Archive Toolkit (XNAT)

    • Management and exploration of neuroimaging and related data.

    • Secure database backend

    • Rich web-based user interface

    • XNAT 1.4 RC3

    • XNAT Desktop (XND)


XNAT

  • Features Added

    • More robust QC modeling

    • REST and LDAP support.

    • Improved memory footprint and efficiency.

    • Refactored Search UI in the listing engine.

    • Prebuilt XNAT images using VMWare and Virtualbox

    • xnatfs provides WebDav access to XNAT instances

  • Use cases

    • FetchMI, XNAT Desktop


High performance computing
High-performance computing

  • GPU volume rendering

  • BatchMake

    • Scripting multiple Slicer modules for grid computing

  • Grid Wizard Enterprise (GWE)

    • Application scheduler that can run multiple (thousands) modules simultaneously on clusters / grids.


GWE

Features added

  • Interactive experiments' results browser.

    • Next generation: Record set explorer

  • CSV and generated commands dumps and preview.

  • Support for LSF and Lava cluster DRMs.

  • Ability to override auto-discovered DRMs with configured ones.

  • Ability to override default database installation location.

  • Function to extract experiments' parameters from text files.

  • Operations to delete, pause and resume experiments.

    Use Cases

  • Parameter space explorations, GWE MiniRetreats, Project Week


Future work
Future work

MUCH, including:

1. Integrated project tracking

  • Goal: generate a comprehensive timeline of a project.

  • Integrate SVN, CMake, CTest, CDash, Wiki, and BugTracker

    • E.g., Commit a code change:

      • wiki page is created for developer to describe the change,

      • related bug report is annotated,

      • subsequent dashboard changes are recorded,

      • all are linked from a central timeline


Future work cont
Future work (cont.)

2. Centralized Test Management via CDash / MIDAS integration

  • CDash operates as a master for Dashboard slaves

    • Dashboard slaves set their availability and resources

    • CDash server allocates tests and testing data to the slaves

  • Ensures testing of important configurations

  • More efficient use of available resources

  • Allocations can change nightly to cover complex combinations

CDash


Future work cont1
Future work (cont.)

3. IPython for interactive distributed computing

  • Python chosen as a favored scripting language for Slicer

    • VTK and Qt are well supported by python

    • ITK v4 will have python as a target language

    • Considered perl (biologists), tcl (comp sci), BatchMake, JavaScript, ...

  • IPython = extensions to python for interactive distributed computing

    • Threaded, grid, and distributed computing

    • Reduced setup and learning curve

    • Broad support


Software process1
Software process

Challenges:

  • Provide effective resources for developers…and users

  • Uphold community standards (quality, style, doc.)

  • Minimize burden on developers…and users


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