avica 0.3.1.5

AVICA: Automated VLBI pipeline in CASA

AVICA: Automated VLBI pipeline in CASA

Submitted to A&A

Demo of the AVICA pipeline running end-to-end. Documentation : https://avica.readthedocs.io/en/latest/

Installation

Requires Ubuntu 18.04+, Debian 10+, RHEL/CentOS 8+
Python >=3.9

The avica package is publicly available on PyPI. Installation is recommended using uv or pipx within a isolated environment:

using uv

uv tool install avica --python 3.10

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.

Manual

1. Clone the repository to the desired destination.

git clone https://github.com/avikhagol/avica.git

2. Install using pip

cd avica/

pip install .

Usage

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. (see Configuration)

Pipeline

Usage: avica pipe run [OPTIONS] [STPS]...                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                              
 _______________________                                                                                                                                                                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                              
 pipeline steps:
 
 -  preprocess_fitsidi
 -  fits_to_ms
 -  phaseshift
 -  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.                                                                                                                                                                                                                                                               │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Manipulating FITS-IDI

To check known FITS-IDI issues run the following:

 Usage: avica fitsidi_check [OPTIONS] [FITSFILENAMES]... COMMAND [ARGS]...                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                              
 validate and fix, known FITS-IDI problems                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                                              
╭─ Arguments ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│   fitsfilenames      [FITSFILENAMES]...                                                                                                                                                                                                                                                                                    │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --fix     --no-fix       [default: no-fix]                                                                                                                                                                                                                                                                                 │
│ --desc    --no-desc      [default: no-desc]                                                                                                                                                                                                                                                                                │
│ --help                   Show this message and exit.                                                                                                                                                                                                                                                                       │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Example

avica fitsidi_check VLBA_VSN005412_file3.uvfits
+--------------------+---------+-------+-------+----------------+----------+
| hdu                | fixable | total | fixed | problem_code   | affected |
+==========================================================================+
| ARRAY_GEOMETRY     | 0       | 8     | 0     | []             | []       |
| ANTENNA            | 0       | 16    | 0     | []             | []       |
| FREQUENCY          | 0       | 8     | 0     | []             | []       |
| PHASE-CAL          | 0       | 12    | 0     | []             | []       |
| PRIMARY            | 1       | 10    | 0     | ["extra_byte"] | [""]     |
| SOURCE             | 0       | 8     | 0     | []             | []       |
| FLAG               | 0       | 12    | 0     | []             | []       |
| UV_DATA            | 0       | 8     | 0     | []             | []       |
| GAIN_CURVE         | 0       | 8     | 0     | []             | []       |
| SYSTEM_TEMPERATURE | 0       | 8     | 0     | []             | []       |
+--------------------+---------+-------+-------+----------------+----------+

To get the information on the observation run the following:

avica listobs [FITSFILENAMES]... 

Configuration

The pipeline configuration is defined in a custom file with key=value defaults to avica.inp in the current directory. See the example for a minimal configuration. To store default values persistently, create a avica.inp file in your home directory (~/.avica/avica.inp) using the following command, the default value is used if no avica.inp file is found:

avica pipe config --default --inpfile <path/to/avica.inp>

or

avica pipe config --default key=value key2=value2 key3=value3

Attribution

When using AVICA, please add a link to this repository in a footnote.

Acknowledgement

"AVICA was developed within the "Search for Milli-Lenses" (SMILE) project. SMILE has received funding from the European Research Council (ERC) under the HORIZON ERC Grants 2021 programme (grant agreement No. 101040021).