skarabina-cargo 0.6.18

Stimela cab definitions for skarabina

skarabina-cargo

Stimela cab definitions for skarabina, the 1GC radio astronomy RFI flagger.

Provides two cabs:

Cab	Command	Purpose
skarabina	skarabina	Flag, average, and clean measurement sets
skarabina-analyze	skarabina-analyze	Recommend image size for synthesis imaging

Install

pip install skarabina-cargo

Requires stimela ≥ 2.1.2 and the skarabina container image (pulled automatically by stimela on first use, or build from the Dockerfile).

Usage

skarabina cab

_include:
  - (cargo):
      - skarabina.yml

my-recipe:
  info: "Flag, average, and optimize a measurement set"
  inputs:
    ms: MS

  steps:
    flag-n-clean:
      cab: skarabina
      params:
        ms: =recipe.ms
        flag-nan: true
        flag-uv-above: 4000
        time-average-factor: 3
        optimize: true
        msout: cleaned.ms
        clobber: true
        summary: true

Run it:

stimela run recipe.yml ms=~/data/observation.ms

Spectral window flagging

steps:
  spw-flag:
    cab: skarabina
    params:
      ms: =recipe.ms
      flag-spectral-window: spectral-flags.yml
      msout: spw-flagged.ms

Where spectral-flags.yml defines frequency ranges to flag:

# Flag all baselines
- spw:
    - [850, 900]
    - [1419.8, 1421.3]

# Flag short baselines only (uv < 600 m)
- spw:
    - [1166, 1186]
    - [1217, 1237]
  uv_below: 600

skarabina-analyze cab

steps:
  analyze:
    cab: skarabina-analyze
    params:
      ms: =recipe.ms
      image-fov: 2.5
      oversampling-factor: 5.0
      output-json: analysis.json

Run it:

stimela run recipe.yml ms=~/data/observation.ms

The output-json option writes machine-readable analysis results for scripting or downstream processing:

{
  "image_size": 8192,
  "pixel_size_arcsec": 1.1,
  "field_of_view_deg": 2.5,
  "max_uv": 34427.18,
  "synthesized_beam_arcsec": 5.5,
  "observation_frequency_hz": 2052500000.0
}

To run directly without stimela:

skarabina-analyze --ms observation.ms --image-fov 2.5 --output-json analysis.json

Printing outputs from a previous step

Both cabs expose outputs that can be consumed by downstream steps:

steps:
  flag-summary:
    cab: skarabina
    params:
      ms: =recipe.ms
      summary: true

  print-max-uv:
    cab: echo
    params:
      args:
        - "Max UV:"
        - =previous.max-uv

  print-ref-ant:
    cab: echo
    params:
      args:
        - "Reference antenna:"
        - =previous.reference-antenna