Slicer3:Batchmake Integration

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Introduction

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.

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).

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.

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
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
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
Registration BatchMake module
- Distributed via Slicer3's getbuildtest2.tcl script
  - Slicer3 GUI Access: Filters/BatchProcessing/Registration BatchMake Module
  - Supports parameters space exploration to optimize registration
  - Supports batch registration of multiple files (e.g., registration of multiple patients with an atlas).

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.