VirusP Pipeline

Overview

VirusP (VIRUS-P) is a fiber-fed IFU spectrograph on the 2.7 m Harlan J. Smith Telescope at McDonald Observatory (HET heritage instrument). It features 246 fibers with 4.16” diameter, covering a 1.7’ x 1.7’ field of view, operating in the optical range (3400–6800 A typical).

CLI Entry Point

The VirusP pipeline is accessed via the vpcubetools command:

vpcubetools vpcube [options]

The vpcube command generates a reconstructed data cube from one or more VirusP observation pointings.

Basic Usage

# With a config file:
vpcubetools vpcube -c config_vpcube.yml

# With CLI options:
vpcubetools vpcube --name_list Name1 Name2 --redux_dir /path/to/rss \
    --out_path out_cubes/ --namef OutputName

CLI Options

Option	Default	Description
`-c, --config_file`	`''`	YAML configuration file (overrides CLI options)
`-i, --name_list`	–	List of input observation pointing names
`-o, --out_path`	`out_cubes/`	Output directory for the cube
`-r, --redux_dir`	`''`	Path to the directory containing reduced RSS files
`-s, --sigm_s`	`32.2`	Smoothing kernel size (arcsec)
`-p, --pix_s`	`0.0`	Spaxel size (0 = `0.75 * sigm_s`)
`-a, --alph_s`	`2.0`	Kernel shape factor
`-f, --flu16`	`True`	Use 10^-16 erg/s/cm²/A units
`-n, --namef`	–	Output root name for the data cube
`-m, --fib`	`4.16`	Fiber diameter (arcsec)
`-t, --base_namewcs`	`NAME_wcs.txt`	WCS text file basename template
`-y, --basename`	`NAME_abscal_HST.fits`	Input RSS file basename template
`-h, --basenamec`	`vpCube-NAME.fits`	Output cube basename template
`-e, --errors`	`True`	Enable error propagation
`-u, --fac_sizey`	`1.1`	FoV extent factor in Y
`-x, --fac_sizex`	`1.1`	FoV extent factor in X
`-k, --radvel`	`True`	Apply heliocentric velocity correction
`-z, --adrcor`	`True`	Apply Atmospheric Differential Refraction correction
`-g, --spec_range`	`(None, None)`	Spectral range `(lambda_min, lambda_max)` in Angstroms
`-b, --pbars`	`True`	Show progress bars

Configuration File

The VirusP pipeline accepts a YAML configuration file. A template is provided at CubeGen/virustools/configfiles/config_vpcube.yml:

---
vpcube:
  - survey_type: virusP
    name_list: [Name1, Name2]
    out_path: out_cubes/
    redux_dir: ''
    fib: 4.16
    sigm_s: 4.16
    pix_s: 0.0
    alph_s: 2.0
    flu16: True
    nameF: NameF
    spec_range: [0, 0]
    pbars: True
    base_nameWCS: NAME_wcs.txt
    basename: NAME_abscal_HST.fits
    basenameC: vpCube-NAME.fits
    errors: True
    fac_sizeY: 1.1
    fac_sizeX: 1.1
    radvel: True
    adrcor: True

VirusP-Specific Features

Separate WCS files

Unlike LVM (which reads astrometry from the SLITMAP extension of each RSS file), VirusP uses external WCS text files. The base_nameWCS parameter specifies the basename template; for each pointing in name_list, the code reads <redux_dir>/<name>_wcs.txt to obtain the fiber positions on sky.

Heliocentric velocity correction

When radvel: True, the pipeline applies a heliocentric velocity correction to shift the wavelength solution from the topocentric to the heliocentric frame.

ADR correction

When adrcor: True, fiber positions are adjusted per wavelength channel to correct for Atmospheric Differential Refraction. This activates the ADR-aware interpolation mode described in Reconstruction Algorithm, where the kernel weights become wavelength-dependent.

Configurable fiber diameter

The fib parameter sets the fiber diameter (default 4.16”), which affects both the radius cutoff and the flux area scaling factor. This differs from LVM (fixed at 35.3”) and MEGARA (derived from the bundle geometry).

Differences from LVM

Aspect	VirusP	LVM
Fiber count	246	~1800 science fibers
Fiber diameter	4.16” (configurable)	35.3” (fixed)
Default `sigm_s`	4.16” (fiber-matched)	32.2”
Astrometry source	External WCS text files	SLITMAP extension in RSS FITS
Directory structure	Flat (`redux_dir/`)	SAS tree (version/tilegroup/tile/mjd)
Heliocentric correction	Built-in (`radvel`)	Applied during RSS reduction
ADR correction	Built-in (`adrcor`)	Not available