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AVICA: Automated VLBI pipeline in CASA

Accepted for publication in Astronomy & Astrophysics journal.

asciicast

Full documentation: https://avica.readthedocs.io/en/latest/

Contents

Installation

Requirements:

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

The avica package is publicly available on PyPI. Use uv or pipx for an isolated command-line installation.

Recommended installation

Using uv:

uv tool install avica --python 3.10

Using pipx:

pipx install avica

Using pip:

pip install avica

If you install with pip, use a virtual environment unless you already manage Python packages another way.

Manual installation

Clone the repository and install it locally:

git clone https://github.com/avikhagol/avica.git
cd avica/
pip install .

Usage

The pipeline calibration steps rely on rPicard. Follow the rPicard setup instructions first. After rPicard is configured, AVICA only needs a minimal configuration file to get started; see Configuration.

Pipeline

Run the default pipeline:

avica pipe run --fitsfilenames <file1.uvfits,file2.uvfits> --target <source-name>

The default pipeline executes these steps:

  • preprocess_fitsidi
  • fits_to_ms
  • phaseshift
  • avica_avg
  • avicameta_ms
  • avica_snr
  • avica_fill_input
  • avica_split_ms
  • rpicard

You can pass one or more step names to run only part of the pipeline:

avica pipe run preprocess_fitsidi fits_to_ms --fitsfilenames <file.uvfits>

Common options:

Option Description
--f, --fitsfilenames Comma-separated FITS-IDI file names.
--t, --target Selected field or source name.
--configfile Configuration file containing key=value entries. Defaults to avica.inp.
--help Show the full command help.

Manipulating FITS-IDI

Check FITS-IDI files for known issues:

avica fitsidi_check <file.uvfits>

Useful options:

Option Description
--fix, --no-fix Apply available fixes. Defaults to --no-fix.
--desc, --no-desc Show issue descriptions. Defaults to --no-desc.
--help Show the full command help.

Example output:

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     | []             | []       |
+--------------------+---------+-------+-------+----------------+----------+

List observation information:

avica listobs <file.uvfits>

Configuration

asciicast

The pipeline configuration is a key=value file. By default, AVICA looks for avica.inp in the current directory. See the example configuration for a minimal setup.

Pass a custom configuration file with --configfile:

avica pipe run --configfile <path/to/config/file>

If --configfile is not provided, AVICA uses avica.inp by default.

To store defaults persistently, create ~/.avica/avica.inp from an existing file:

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

You can also set default values directly:

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

To set global defaults in AVICA's installed directory, use --global in the same way:

avica pipe config --global --inpfile <path/to/avica.inp>
avica pipe config --global key=value key2=value2 key3=value3

To supersede the rPicard input_template files (array.inp, observation.inp, array_finetune.inp, flagging.inp, constants.inp) used by the rpicard step, point picard_input_template_update at a folder containing the parameters you want to fix:

picard_input_template_update   =   "path/to/folder/with/fixed/inp/files"

Parameter summary

Use --summary to print a report of every pipeline parameter, its resolved value, and where that value came from (inpfile, default, context, or a per-step override):

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

If --inpfile is omitted and avica.inp exists in the current directory, it's read automatically. Combine --summary with key=value overrides on the command line to preview how they would change the resolved configuration before writing it out.

Cleaning up intermediate data

Each pipeline step can remove its own intermediate files (temporary files, superseded Measurement Sets, etc.) once it finishes. This is controlled by:

Option Description
delete_removables Master switch; must be True for any cleanup to happen. Defaults to False.
removables List of glob patterns (relative to the step's working directory) to delete. Can be set globally or per step as <step_name>.removables.
rm_pre / <step_name>.rm_pre If True, delete the matching files before the step runs instead of after.
rm_only Only perform the deletion and skip running the step itself.

Several steps ship with sensible defaults, e.g.:

delete_removables            =   True
preprocess_fitsidi.removables    =   ["raw/*.tmp"]
rpicard.removables               =   ["wd_[SLKQXPD]/VLBI_*.ms"]
fits_to_ms.removables            =   ["*.old"]

Deletion is always confined to the step's working directory; patterns that resolve outside it are ignored.

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).

Project links

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Credits

Author: Avinash Kumar

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License

MIT License (MIT)

Requires

Python >=3.9

Provides Extra

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BLAKE2b-256 e472013da28d9efeb98f247e26304485cce94e250d64ea376e6ac677dd9ee93f

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Provenance

The following attestation bundles were made for avica-0.3.1.10-cp39-cp39-macosx_11_0_arm64.whl:

Publisher: build_wheels.yml on avikhagol/avica

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

This release

0.3.1.10 This release

16 files

0.3.1.9

16 files

0.3.1.8

16 files

0.3.1.7

16 files

0.3.1.6

16 files

0.3.1.5

16 files

0.3.1.4

16 files

0.3.1.3

16 files

0.3.1.2

16 files

0.3.1.1

16 files

0.3.1.0

16 files

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