CIBC:Documentation:SCIRun:Installation

From SCIRun Documentation Wiki

1 Getting Started Guide
2 SCIRun Data
3 Installation Instructions
4 Module Renaming
5 Known Bugs / Ongoing Tasks / Upcoming Projects

Getting Started Guide

The SCIRun build process has recently changed to use CMake. The build tree has been split up into three main pieces: SCIRun 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 our SCIRun Thirdparty packages.

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.

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SCIRun Data

The SCIRun Datasets can be downloaded through the normal SCIRun download process found here. The compressed datasets are 360 MB in size. Note, the set of data files is almost the same as the 1.24.1 release, with the addition of one heart geometry for higher order finite elements. If you already have the old set and do not wish to use the heart geomery, you can either rename the directory to 3.0.2, set the SCIRun datasets variable to the old directory, or navigate to the old directory in the file browser as necessary.

For users local to the SCI network, the data is mounted on most machines in /usr/sci/data/SCIRunData/3.0.2 or can be found as a tarball in /usr/sci/data/SCIRunData/tarballs.

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Installation Instructions

FYI: If you have problems with installing SCIRun, please read the appropriate section: Unix or Windows.

We have separate installation instructions for the Unix (Linux, and OSX) and Windows platforms. For each of these, we provide two links below -- the first is to instructions on how to install the 3.0.0 release version of our software, the second is how to install the 3.0.x development version. Most users are encouraged to use the release version, as it is the most stable. Over the coming weeks, we will complete development on the 3.0.x branch, and will then turn that into a stable 3.0.2 release.

Note: In order to use the build script to install ITK, users must follow Unix Environment instructions for the 3.0.2 Version.

Development version (Version 3.1)
- Unix (Linux/Mac OSX)
  - 3.1 (Source) On going development
- Windows (XP)
  - 3.1 (Source) On going development
Current Release (Version 3.0.2)
- Unix (Linux/Mac OSX)
  - 3.0.2 (Source) Release
- Windows (XP)
  - 3.0.2 (Source) Release
  - 3.0.2 Binary Release

Past Releases
- Unix (Linux/Mac OSX)
  - 3.0.0 (Source) Release
- Windows (XP)
  - 3.0.0 (Source) Release

Link title

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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.

Copy your old .net file to .net.old so you have the original. The conversion script will overwrite your input file.
Convert the .net module names with the provided script.
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 :

cp myoldnetwork.net myoldnetork.net.old
python SCIRun/src/scripts/remap_modules_in_net.py myoldnetwork.net SCIRun/src/scripts/module-remapping.txt
./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.

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

example: to convert myoldnetwork.srn :

cp myoldnetwork.srn myoldnetork.srn.old
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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