Slicer3:Batchmake Integration - Revision history

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New page

== 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 ==

* [http://www.batchmake.org BatchMake] provides an open-source toolkit for launching a controlled sequence of applications on the local computer or a GRID.
* [http://www.cs.wisc.edu/condor 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
# 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

=== To do ===
* Provide documentation
* Provide tutorial at AHM in January 2008
* Determine how to deliver BatchMake's GRID monitoring tool with Slicer3
** Requires FLTK - will not be re-written into KWWidgets
* Consider general (no programming required) solution to using BatchMake with other Slicer modules
** User browses to execution modules and specifies where wildcards should be substituted into command line
* Provide batch registration module
** Requires completion of Registration Modules (non-batch versions)
*** See: http://www.na-mic.org/Wiki/index.php/NAC_Grid_Enabled_ITK
*** See: http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization

=== Related links ===

* http://wiki.na-mic.org/Wiki/index.php/Slicer3:Large_scale_experiment_control_brainstorming

@@ Line 55: / Line 55: @@
 * [[Slicer3:Python | Python in Slicer]]
 * [[Slicer3:Python:ipython | iPython in Slicer]]
-* [http://www.slicer.org/slicerWiki/index.php/Modules:PythonNumpyScript-Documentation-3.4 Numpy in Slicer]
+* [[Modules:PythonNumpyScript-Documentation-3.4|Numpy in Slicer]]
 * [[Slicer3:Large_scale_experiment_control_brainstorming| Large scale experiment control brainstorming]]

@@ Line 48: / Line 48: @@
 === Related links ===
-* [[Slicer3:Python:ipython | iPython]]
+* [[Slicer3:Python | Python in Slicer]]
 * [[Slicer3:Large_scale_experiment_control_brainstorming| Large scale experiment control brainstorming]]

← Older revision		Revision as of 20:00, 25 January 2010
Line 48:		Line 48:
	=== Related links ===		=== Related links ===

		+	* [[Slicer3:Python:ipython \| iPython]]
	* [[Slicer3:Large_scale_experiment_control_brainstorming\| Large scale experiment control brainstorming]]		* [[Slicer3:Large_scale_experiment_control_brainstorming\| Large scale experiment control brainstorming]]

← Older revision		Revision as of 17:03, 19 May 2008
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	=== Related links ===		=== Related links ===

−	* ~~http://wiki.na-mic.org/Wiki/index.php/~~Slicer3:Large_scale_experiment_control_brainstorming	+	* [[Slicer3:Large_scale_experiment_control_brainstorming\| Large scale experiment control brainstorming]]

@@ Line 37: / Line 37: @@
 #** Slicer3 GUI Access: Filters/BatchProcessing/GaussianBlur BatchMake Module
 #* Provides a simple example of how to batchmake-ify your Slicer3 modules
 === To do ===

@@ Line 40: / Line 40: @@
 === To do ===
 * Provide documentation
-* Provide tutorial at AHM in January 2008
+* Determine how to integrate BatchMake with Slicer's new focus on iPython for distributed computing
-* Determine how to deliver BatchMake's GRID monitoring tool with Slicer3
+* 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
-* Provide batch registration module
+* Port lesson's learned to the iPython development effort
-** Requires completion of Registration Modules (non-batch versions)
+** e.g., leave-one-out looping mechanism, taguchi factor analysis, etc.
 === Related links ===
 * [[Slicer3:Large_scale_experiment_control_brainstorming| Large scale experiment control brainstorming]]

@@ Line 47: / Line 47: @@
 * Provide batch registration module
 ** Requires completion of Registration Modules (non-batch versions)
-*** See: http://www.na-mic.org/Wiki/index.php/NAC_Grid_Enabled_ITK
+*** See [http://www.na-mic.org/Wiki/index.php/NAC_Grid_Enabled_ITK NAC Grid Enabled ITK]
-*** See: http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization
+*** See [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization ITK Registration Optimization]
 === Related links ===
 * [[Slicer3:Large_scale_experiment_control_brainstorming| Large scale experiment control brainstorming]]

← Older revision	Revision as of 17:57, 15 May 2008
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