Script feeding into the LOFAR long-baseline pipeline

How to use loop 2

• Log in to CEP3.
• Make a clean directory (mkdir loop-2-tests then cd loop-2-tests).
• Move the HDF5 files here (mv [file.h5] .).
• Clone the repository (git clone https://github.com/mooneyse/lb-loop-2.git).
• Load the LOFAR software and LoSoTo (module load lofar losoto).
• Loop 2 is the hdf5_fuctions.py script. It runs with Python 2.
• View the arguments with lb-loop-2/hdf5_functions.py --help.
• Do something like this:

$ lb-loop-2/hdf5_functions.py

• This will make the master text file if it does not exist, evaluate the solutions in the HDF5 files, make a new HDF5 file in the direction supplied, and apply this HDF5 file to the MS, outputting a new MS.
• Then run loop 3 on this new MS (python2 lb-loop-2/loop3B_v1.py [file.ms]).
• When loop 3 is done, edit main() in hdf5_fuctions.py to run the update_list function, passing it the HDF5 file originally applied to the MS, the HDF5 file outputted by loop 3, and the master text file. This function combines these incremental solutions, evaluates them, and writes the output to the master text file.
• For a list of issues with loop 2, see the Issues on GitHub.
• The plot_h5.py script is something I was using to compare HDF5 solutions after running loop 2. It is not part of the loop 2 code.