Slicer3:Batchmake Integration
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Contents
Introduction
Goals
- Enable Slicer3 execution modules to process multiple datasets with minimal user interactions ("batch processing")
- Enable the exploration of the parameter spaces of Slicer3 execution modules ("parameter space evaluations")
- Support using local computer resources or local GRID resources for batch process and parameter space evaluations.
Summary
- BatchMake integration with Slicer3 is complete.
- Real-world applications (EMSegmenter) are using BatchMake from within Slicer.
- Examples are given on how to use BatchMake with your Slicer3 Execution Modules (GaussianBlur example).
Background
- BatchMake provides an open-source toolkit for launching a controlled sequence of applications on the local computer or a GRID.
- Condor is used as the open-source toolkit that provides access to GRID resource. It also provides an easy-to-install and easy-to-configure GRID implementation/network. We highly recommend it for your GRID needs.
- BatchMake and Condor work together to sequence tasks and to allocate and monitor resources and job progress.
Status
Completed
- BatchMake Library
- Distributed via Slicer3's getbuildtest2.tcl script
- Slicer3 code location: Slicer3-lib/BatchMake
- Default distribution does not include Condor
- Can be installed by users
- Changing two BatchMake variables will configure BatchMake to use Condor
- Distributed via Slicer3's getbuildtest2.tcl script
- EMSegmenter BatchMake module
- Distributed via Slicer3's getbuildtest2.tcl script
- Slicer3 GUI Access: Filters/BatchProcessing/EMSegmenter BatchMake Module
- Slicer3 code location: Slicer3/Applications/CLI/BatchMake
- Applies EMSegmenter algorithm to a collection of data using local computer or GRID
- Distributed via Slicer3's getbuildtest2.tcl script
- GaussianBlur BatchMake module
- Distributed via Slicer3's getbuildtest2.tcl script
- Slicer3 GUI Access: Filters/BatchProcessing/GaussianBlur BatchMake Module
- Provides a simple example of how to batchmake-ify your Slicer3 modules
- Distributed via Slicer3's getbuildtest2.tcl script
To do
- Provide documentation
- Determine how to integrate BatchMake with Slicer's new focus on iPython for distributed computing
- Consider general (no programming required) solution to using BatchMake/iPython with other Slicer modules
- User browses to execution modules and specifies where wildcards should be substituted into command line
- Port lesson's learned to the iPython development effort
- e.g., leave-one-out looping mechanism, taguchi factor analysis, etc.