shuck

shuck is a scriptable, non-interactive Python reduction pipeline for NASA IRTF/iSHELL spectra. Its current focus is reproducing the scientifically relevant behavior of Spextool 5.0.3 for a narrow workflow with inspectable intermediate products.

Shuck is an independent project. It is not an official NASA IRTF or Spextool product.

Installation

shuck is not yet available on PyPI. For now, install it directly from GitHub.

Because the bundled Spextool calibration/reference assets are managed with Git LFS, install and initialize Git LFS first:

git lfs install
pip install "git+https://github.com/brackham/shuck.git"

For development from a source checkout:

git clone https://github.com/brackham/shuck.git
cd shuck
git lfs pull

python -m venv .venv
.venv/bin/pip install -e '.[dev]'

Quick start

The standard night layout has an existing raw/ directory. Setup creates sibling cal/, proc/, and qa/ directories as needed.

shuck setup /path/to/night --write-log
# Review/edit /path/to/night/night.overrides.toml.
shuck setup /path/to/night
shuckit /path/to/night/night.shuck

Passing /path/to/night/raw to shuck setup is equivalent. Use -o FILE.shuck to override the default control-file path. Developer/power-user stage commands are also available:

shuck calibrate night.shuck
shuck extract night.shuck
shuck combine night.shuck
shuck telluric night.shuck
shuck merge night.shuck

See the control-file specification for the complete format and association rules.

Current scope

Version 0.1 supports iSHELL J3 and Kgas point-source observations reduced as A-Sky/Dark, with one positive aperture, optimal extraction, ThAr wavelength calibration and rectification, spectral combination, A0V/Vega telluric correction using the iSHELL instrument profile, and order merging.

Deliberate exclusions include other iSHELL modes, A-B and extended-source extraction, multiple apertures, spectral shifting/pruning/shape correction, residual telluric shift fitting, xcleanspec, and GUI interaction. The pipeline has unit and synthetic numerical coverage and has run end to end on the private 260406 night; direct Spextool regression work remains part of science validation.

Relationship to Spextool

Shuck's algorithms and bundled calibration/reference assets derive from, and are intended to reproduce the relevant behavior of, Spextool 5.0.3. Selected upstream assets are bundled with permission so installed copies of shuck are self-contained for the supported workflow. Original filenames and layout are retained where practical, and a checksum manifest makes the import auditable.

Citation

Users of shuck should cite:

Cushing, M. C., Vacca, W. D., & Rayner, J. T. 2004, "Spextool: A Spectral Extraction Package for SpeX, a 0.8–5.5 Micron Cross-Dispersed Spectrograph," PASP, 116, 362. https://doi.org/10.1086/382907

Because shuck implements the Spextool telluric-correction procedure, users of that procedure should also cite:

Vacca, W. D., Cushing, M. C., & Rayner, J. T. 2003, "A Method of Correcting Near-Infrared Spectra for Telluric Absorption," PASP, 115, 389. https://doi.org/10.1086/346193

The Spextool documentation requests citation of both papers when its telluric algorithms are used.

License and bundled material

Shuck's original code is available under the MIT License. Bundled Spextool-derived material is not represented as MIT-licensed; see THIRD_PARTY_NOTICES.md and the provenance README under src/shuck/data/spextool/ for its attribution and terms.