Getting Started#
AVICA: Automated VLBI pipeline in CASA.
Demo of the AVICA pipeline running end-to-end.
About#
AVICA is a Python package for the automated calibration of Very Long Baseline Interferometry (VLBI) data. It provides modules to ingest, manipulate, and calibrate FITS-IDI and Measurement Set files containing raw visibilities.
Installation#
> Needs Ubuntu 18.04+, Debian 10+, RHEL/CentOS 8+ > Python >=3.9
The avica package is publicly available on [PyPI](https://pypi.org/project/avica/). Installation is recommended using [uv](https://docs.astral.sh/uv/getting-started/installation/#standalone-installer) or [pipx](https://pipx.pypa.io/stable/how-to/install-pipx/) within a isolated environment:
using uv
uv tool install avica --python 3.11
or using pipx
pipx install avica
or using pip
pip install avica
Note
It is recommended to use venv for installation, if you are not using pipx or uv.
Setup#
Since the pipeline’s calibration features rely on rPicard please follow the linked setup instructions first. Once rPicard is properly configured, you only need a minimal avica configuration file to get started.
Configuration#
The pipeline is configured via a plain-text file in the current working directory, defaulting to avica.inp.
# required
# assumes `folder_for_fits` is a folder containing all the raw visibility fits files.
# `casadir` is the path to the monolithic CASA installation used for running CASA tasks.
folder_for_fits = /path/to/source/folder/with/raw/visibility/fitsfiles
casadir = "path/to/monolithic-casa/casa-6.x.x-xx-py3.xx.xxx/"
# optional-1
# `picard_input_template` is a template for the picard input file, see https://bitbucket.org/M_Janssen/picard/src/master/input_template/.
# assumes `target_dir` is a folder where the pipeline output will be saved.
# `accor_solint` is the number of solint partitions to use.
target_dir = "reductions"
picard_input_template = "path/to/rpicard"
accor_solint = 4
mpi_cores_rpicard = 10
mpi_cores_snrating = 5
mpi_cores_importfitsidi = 5
hi_freq_ref = 11
snr_threshold_phref = 7
flux_threshold_phref = 0.15
min_channel_flagging = 32
n_calib = 5
n_refant = 4
minsnr = 3.2
sci_solints = auto
solint_max_scan_partitions= 8
apply_flag_from_idi = True
size_limit = 2000.0
# configure google sheet
sheet_url = None
worksheet = None
# configure below if using CSV or google sheet to save all the result in a common sheet.
primary_colname = TARGET_NAME
primary_value = None
filename_col = FILENAMES
targetname_col = TARGET_NAME
# optional-2 sheet configurations
working_col = None
working_col_only = False
do_pcol_validation = False
# experimental
use_casadir_pythonpath = False
separation_thres = 850.0
source_extract_multi_fitsfiles = False
Usage#
The pipeline steps can be invoked from the terminal as follows:
avica pipe run --t TARGET_NAME --f FITSFILE_NAME [STEPS]
The output folder structure follows the following convention:
CWD (with avica.inp)
└── reductions/
└── PROJECT_CODE/
└── wd/
└── wd_{BAND}/
└── wd_{BAND}_{TARGET_NAME}/
using --help will print the pipeline steps and usage instructions as follows:
Usage: avica pipe run [OPTIONS] [STPS]...
_______________________
pipeline steps:
- preprocess_fitsidi
- fits_to_ms
- avica_avg
- avicameta_ms
- avica_snr
- avica_fill_input
- avica_split_ms
- rpicard
________________________
╭─ Arguments ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ stps [STPS]... steps for execution [default: preprocess_fitsidi, fits_to_ms, avica_avg, avicameta_ms, avica_snr, avica_fill_input, avica_split_ms, rpicard] │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --f,--fitsfilenames TEXT fitsfile names comma separated │
│ --t,--target TEXT Selected field / sourc name │
│ --configfile TEXT config file containing key=value [default: avica.inp] │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯