This repository provides a processing script used to calibrate data from the ATCA QUOCKA survey of polarized radio galaxies.

This is a Python 3 package.

Clone this repository and install using pip:

git clone https://github.com/AlecThomson/quocka
cd quocka
pip install .

The quocka pipeline primary provides a calibration strategy for ATCA CABB data in the L and C/X bands. You'll need to obtain data in the CABB format (usually from the ATOA, with the name *.C1234).

To initial the directory structure, run quocka init (pointing to your raw data):

❯ quocka_init -h
usage: quocka_init [-h] [-o OUT_DIR] raw_vis_list [raw_vis_list ...]

Set up the QUOCKA directory structure and copy the default config files.

positional arguments:
  raw_vis_list          List of raw visibility files to copy to the raw directory

optional arguments:
  -h, --help            show this help message and exit
  -o OUT_DIR, --out-dir OUT_DIR
                        Output directory

This will create a directory structure like:

.
├── cal
│   ├── badchans_2100.txt
│   ├── badchans_5500.txt
│   ├── badchans_7500.txt
│   ├── setup.txt
│   └── template.cfg
└── raw
    └── raw_data.C1234

Your raw data will be symlinked into the raw directory. In the cal directory you'll find the default calibration setup files. You'll need to edit these to suit your data.

• badchans_*.txt: A list of bad channels to flag. These are in the format start-end where start and end are the first and last channels to flag. The files are named according to the frequency of the bandpass calibration. The default files are for the L band (2100 MHz), C band (5500 MHz) and X band (7500 MHz).
• setup.txt: A list of setup correlator files that should be ignored by the pipeline.
• template.cfg: A template calibration configuration file. Here you can set the input and output data, calibration steps to run, and which sources to use for calibration. You'll need to ensure observations of the calibration sources are in the raw directory.

To run the primary calibration stages, run quocka_cal:

❯ quocka_cal -h
usage: quocka_cal [-h] [-s SETUP_FILE] [-l LOG_FILE] config_file

positional arguments:
  config_file           Input configuration file

optional arguments:
  -h, --help            show this help message and exit
  -s SETUP_FILE, --setup_file SETUP_FILE
                        Name of text file with setup correlator file names included so that they can be ignored during
                        the processing [default setup.txt]
  -l LOG_FILE, --log_file LOG_FILE
                        Name of output log file [default log.txt]

This will split the raw visibilities and perform flagging, gain calibration, bandpass calibration, and cross calibration using the primary and secondary calibrator sources. The output data will be written to the directory specified in the configuration file.

To run the self-calibration stages, run quocka_selfcal:

❯ quocka_selfcal -h
usage: quocka_selfcal [-h] [--ncores NCORES] [-l LOG_FILE] config_file vislist [vislist ...]

positional arguments:
  config_file           Input configuration file
  vislist

optional arguments:
  -h, --help            show this help message and exit
  --ncores NCORES
  -l LOG_FILE, --log_file LOG_FILE
                        Name of output log file [default log.txt]

This will run self-calibration in parallel on the specified visibilities. The output data will be written to the directory specified in the configuration file.

TODO

The quocka package also provides a number of auxiliary scripts for working with the data.

• cutout_400
• cutout_source_finding
• get_spec_coor
• makebigcube
• qu_fdf
• quocka_bin_cx
• quocka_simulate
• run_chanimage
• selfcal_quality
• source_finding_quality
• uptimes

TODO: Write usage instructions.

TODO: Add these as scripts in pyproject.toml.

MIT. See LICENSE for details.

The QUOCKA pipeline is mostly based on the recommened strategy outlined in the ATCA User Guide and uses the MIRIAD software package.

TODO: Add more details.

TODO

TODO