MATLAB scripts and functions
Installation:
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Log-in to a GPU node on the Maxwell cluster
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Download latest MATLAB files from Github:
git clone https://github.com/moosmann/matlab.git
OR
Update to latest version: Fetch latest version of the 'master' branch from the remote repository 'origin' and reset/overwrite all local changes. New files that were created locally and which do not exist in the latest branch are not deleted.
git fetch origin master & git reset --hard origin/master
Before updating you can back-up local files by branching if necessary:
git add --all git commit -m "COMMIT MESSAGE" git branch NAME_OF_BRANCH
To check which files were modified and which new (untracked files):
git status
How to start a reconstruction:
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Change directory to downloaded 'matlab' folder:
cd matlab
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Start MATLAB with predefined settings from within the 'matlab' folder:
./startmatlab.sh
This sets environment variables in order to use a local installation of the ASTRA toolbox, starts MATLAB, and sets the search path (this overwrites local user settings, for details see 'startup.m'_)
If 'startmatlab.sh' is not executable: chmod +x startmatlab.sh
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Open 'p05_reco' in MATLAB located at './matlab/experiments/p05/' if not already opened, eg type 'edit p05_reco' in MATLAB's command line
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Check and modify reconstruction parameters, at least 'scan_path'
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Start reconstruction by one of the following:
- Type 'p05_reco' in MATLAB's command line
- Click 'RUN' button in editor tab
- Type 'F5' key when focus is in the 'p05_reco' file -
How to set up automatized reconstruction loop:
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Make a copy of 'p05_reco_template.m' and follow the instructions of the help within.
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Adjust default parameter section: modify, delete, or copy parameter from 'p05_reco'
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Add data or parameter sets and run file.