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Non-Interactive Tools

This document discusses the development of non-interactive tools for neuroimaging and related fields, focusing on software processes that support schizophrenia, autism, and neurodevelopmental research. It encompasses a comprehensive overview of the NA-MIC infrastructure, its software processes, and data management strategies, catering to high-performance computing across multiple platforms. The challenges and future work in delivering effective resources for developers and users, including the use of CMake, CDash, and XNAT, are emphasized, detailing the integration of functionalities beneficial for researchers in neuroimaging.

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Non-Interactive Tools

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  1. Non-Interactive Tools Stephen Aylward, Kitware 2010.01.07

  2. 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

  3. NA-MIC Kit Infrastructure • Software process • CMake and CPack • CDash and CTest • Data management • High-performance computing • Future work (NA-MIC Renewal)

  4. Software process Challenges: • Provide effective resources for developers…and users • Uphold community standards (quality, style, doc.) • Minimize burden on developers…and users

  5. 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

  6. 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, …

  7. 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)

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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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