Difference between revisions of "Slicer3:Batchmake Integration"
From Slicer Wiki
(→To do) |
m (Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2") |
||
| (3 intermediate revisions by one other user not shown) | |||
| Line 37: | Line 37: | ||
#** Slicer3 GUI Access: Filters/BatchProcessing/GaussianBlur BatchMake Module | #** Slicer3 GUI Access: Filters/BatchProcessing/GaussianBlur BatchMake Module | ||
#* Provides a simple example of how to batchmake-ify your Slicer3 modules | #* 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). | ||
=== To do === | === To do === | ||
| Line 48: | Line 53: | ||
=== Related links === | === Related links === | ||
| + | * [[Slicer3:Python | Python in Slicer]] | ||
| + | * [[Slicer3:Python:ipython | iPython in Slicer]] | ||
| + | * [[Modules:PythonNumpyScript-Documentation-3.4|Numpy in Slicer]] | ||
* [[Slicer3:Large_scale_experiment_control_brainstorming| Large scale experiment control brainstorming]] | * [[Slicer3:Large_scale_experiment_control_brainstorming| Large scale experiment control brainstorming]] | ||
Latest revision as of 02:34, 27 November 2019
Home < Slicer3:Batchmake IntegrationContents
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
- 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).
- 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.
