Source code version of CERR - cerr/CERR GitHub Wiki

Getting the latest source code

The source code of CERR is distributed on gitHub. Hence, the first step is to download the "master" branch of CERR. This can be done using the git bash. After going to the directory where you want to download the files, use the following command to download the "master" branch of CERR:

git clone https://github.com/cerr/CERR.git

After downloading the "master" branch to (say) /home/.../.../cerr_from_gitHub/, follow the steps listed below to use CERR.

  1. Fire up Matlab. Go to Home --> Set Path. Set the path to "Default". Add /home/.../.../cerr_from_gitHub/ with sub-directories to the Matlab path.

  2. To use CERR Graphical User Interface, type CERR in Matlab command window.

Getting a specific commit version(SHA) of source code from GitHub

  1. First follow the steps indicated above to get the latest version of the source code.

  2. To see what's in a specific commit version from the repository and make it the working tree, but not do a merge with the master branch, use the following commands:

'git fetch origin' 'git checkout YOUR_SHA_HERE'

To get the specific version, and make it the new "master" (or another branch), use the following commands:

'git fetch origin' 'git reset --hard YOUR_SHA_HERE'

FAQs

Q. How do I read in and convert an AAPM/RTOG or DICOM archive formatted directory into CERR format?
Varios optins for importing data can be set in CERROptions.json. In the section labeled 'importing' are several self-explanatory options concerning what will be read in, etc. Importing DICOM and Importing mha further describe the workflow to import datasets into CERR.

Q. How do I view stored CERR archives?
A. Type 'CERR', select Viewer, and select the .mat or .bz2 archive.

Q. How do I close CERR?
A. Close the "viewer" window in the usual way for that operating system. All the other CERR windows should close automatically, except for the CERR main menu.

Q. How do I overwrite default settings?
A. Many of the program options are described and set in the file CERROptions.json. The options and their selectable values are documented there. This file is automatically loaded when CERR is invoked. You can change any options and reload them by issuing the 'reload options' command at the viewer command line, and then selecting the (possibly different) options file desired.

Q. Development philosophy?
A. The stable version of CERR is released under the master branch. The feature branches are based on the testing branch, which gets tested every night. The contributors generate an ssh key using git-bash:
ssh-keygen -t rsa -b 4096 -C your_github_account_email
Copy the public key using:
clip < /g/.ssh/id_rsa.pub for Windows
pbcopy < ~/.ssh/id_rsa.pub for Mac OS X