CIBC:Documentation:SCIRun:Installation

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Contents 1 SCIRun Installation manual 1.1 Additional build notes 2 SCIRun Data 3 Module Renaming

SCIRun Installation manual

SCIRun installation manual.

Additional build notes

The SCIRun build process has recently changed to use CMake. The build tree has been split up into three main pieces: Core libraries, SCIRun Dataflow (which includes modules, packages, and the scirun executable), and stand alone applications (such as Seg3D). SCIRun also now requires users to use the external dependencies that are distributed with the SCIRun source code. Building with the build.sh script (see the Installation manual) will automatically configure and build these.

Note: Seg3D does not require all of SCIRun and (much smaller) binaries can be downloaded separately from the Seg3D page.

For clarity, the instructions have been broken up into those pertaining to a Unix environment (Linux and Mac OSX), and a Windows environment.

SCIRun Data

The SCIRun Datasets can be downloaded from the SCIRun download site. The compressed datasets are 390 MB in size. Individual datasets are also available from the NCRR Dataset Archive.

For users with access to SCI Subversion, the data can be checked out from https://code.sci.utah.edu/svn/CIBCData/SCIRunData.

Module Renaming

Two major changes to the SCIRun network files have occurred since 1.24. First, we switched our nets from tcl-based .net files to XML-based .srn (SCIRun Network) files. You can still load .net files, but can only save in the .srn xml format. We strongly suggest you convert your .net files to the new .srn format.

We also changed the names of all of the modules (and many of the categories) to use a more consistent / intuitive naming scheme. This change renders old .net files non functional. However you can convert the old .net files to the new .srn format in a few steps.

1. Copy your old .net file to .net.old so you have the original. The conversion script will overwrite your input file.
2. Convert the .net module names with the provided script.
3. Convert the .net to .srn with the scirun executable. The -c option loads an old tcl based .net file, writes the new xml based .srn file and exits.

example: to convert myoldnetwork.net :

1. cp myoldnetwork.net myoldnetork.net.old
2. python SCIRun/src/scripts/remap_modules_in_net.py myoldnetwork.net SCIRun/src/scripts/module-remapping.txt
3. ./scirun -c myoldnetwork.net

Then you can run your newly converted .srn file like so:

./scirun myoldnetwork.srn

Similarly for users who have been using SCIRun since the switch to .srn, there is a script for converting module names in any .srn files the new naming scheme.

1. Copy the old .srn file to .srn.old. The script will overwrite the input file.
2. Convert the .srn to the new module names with the provided script.

example: to convert myoldnetwork.srn :

1. cp myoldnetwork.srn myoldnetork.srn.old
2. python SCIRun/src/scripts/remap_modules_in_srn.py myoldnetwork.srn SCIRun/src/scripts/module-remapping.txt

This script can also run recursively on entire directory stuctures of .srn files by providing a path to the directory instead of to an individual file.

example: if you have all your nets in /user/joe/mynetworkfiles/ :

python SCIRun/src/scripts/remap_modules_in_srn.py /user/joe/mynetworkfiles SCIRun/src/scripts/module-remapping.txt

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This page was last updated on 11/13/2009

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