Source code version of CERR

Getting the source code

Initial download

This github repository is used to distribute CERR's source code. Cloning the "master" branch using Git bash will give you a copy of the current code-base.

From the directory to which you want to download CERR, run the following git command to download the "master" branch of CERR, run:

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

Getting the latest updates

As CERR continues to evolve, with several changes introduced weekly, you will need to run git pull to obtain these modifications.

From your CERR directory:

git pull origin master

Getting a specific version from a previous commit (SHA)

1. First download the source code as described above (Initial download).

2. To see what's in a specific commit version from the repository, use the following commands.

• To make the specified version the new working tree without merging it with the master branch:

  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
  

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Using CERR

After downloading the "master" branch to, say, /home/.../.../cerr_from_gitHub/, follow these steps to get started.

1. Fire up Matlab, and add CERR to your Matlab path.
   Go to Home --> Set Path --> Set to "Default" -> Then point to the CERR directory (/home/.../.../cerr_from_gitHub/) using the "add with sub-directories" option.

2. To use the CERR Graphical User Interface, type CERR into the Matlab Command Window.

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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