pypeit-wrapit

Lightweight wrappers to run PypeIt reductions in a single step.

Supports the Liverpool Telescope (LT) SPRAT spectrograph for now.

pypeit-wrapit implements a small CLI (pypeit-wrapit lt-sprat) that prepares raw inputs, runs the relevant PypeIt pipelines, performs flux calibration, optionally stacks spectra, and writes final ASCII spectral products.

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Installation

Install the repository via pip:

pip install git+https://github.com/Lyalpha/pypeit-wrapit.git

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Command Line Interface (CLI)

Important: pypeit-wrapit currently supports processing only one instrumental setup at a time. All input files in a single run must correspond to the same observational setup (e.g. same disperser/grism). Multiple targets in this single observational set-up can be processed in the same run, and any targets with multiple input spectra, will have their spectra stacked.

Usage

The main CLI entry point is:

pypeit-wrapit

You can append -v or -vv flags after this entrypoint (and before any of the below commands) for increased verbosity.

All available commands can be listed with:

pypeit-wrapit --help

LT SPRAT Command

pypeit-wrapit lt-sprat INPUT_FILES OUTPUT_DIR [OPTIONS]

Arguments

• INPUT_FILES One or more input spectra FITS files to process. You may pass:

  • One or more file paths or
  • A glob pattern (shell-expanded) This should include the science frames and any necessary calibration frames (e.g. arcs) for a observational setup.

• OUTPUT_DIR Output directory for intermediate and final reduced products.

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Options

• --sensitivity-file Path to sensitivity file. Default: packaged sensitivity files precomputed with PypeIt for SPRAT .

• --stacked-bin-size Bin size in angstroms for the stacked spectrum. Default: 5.0

• --lam-lim-low, --lam-lim-upp Wavelength limits in angstroms for output spectra. Defaults: 4000.0, 9000.0

• --overwrite Removes contents of OUTPUT_DIR if it is not empty (interactive confirmation).

• --cleanup Removes intermediate raw and pypeit_products directories within OUTPUT_DIR after completion.

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Examples

Run with a shell-expanded glob at INFO verbosity

pypeit-wrapit -v lt-sprat path/to/*.fits /tmp/outdir

Pass a list of specific file paths and run with DEBUG verbosity

pypeit-wrapit -vv lt-sprat obj_spec1.fits obj_spec2.fits obj_arc.fits /tmp/outdir

Specify a sensitivity file and request cleanup with WARNING verbosity

pypeit-wrapit lt-sprat data/*.fits /tmp/outdir \
  --sensitivity-file calibs/lt_sprat/sensfunc_red.fits \
  --cleanup

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Behavior Notes

Flux Scaling

• Fluxes in ASCII outputs are return in units of erg / s / cm^2 / Å

Stacking

• If there are multiple spectra of the target provided, they are:
  • Normalized by their mean flux within a broad normalization window
  • Resampled onto a regular wavelength grid
  • Stacked using inverse-variance weighting

The stacked spectrum has its observation time updated and output as a single stacked spectrum file (see below).

Output Files

Final ASCII spectra are written under:

OUTPUT_DIR/final/

Naming Convention

If a single spectrum of the target is passed:

{TARGET}_LTSPRAT_{dispname}_{YYYY-MM-DDTHH:MM}.dat

If multiple spectra of the target are passed, individual spectra are written as: individual_{TARGET}_LTSPRAT_{dispname}_{YYYY-MM-DDTHH:MM}.dat

with their stacked spectrum written following the same convention as the single spectrum case.

• {TARGET} is the target name extracted from the FITS headers
• {dispname} is the spectrograph disperser name
• {YYYY-MM-DDTHH:MM} is the DATE-OBS timestamp of the observation

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Dependencies

• Python 3.12+
• pypeit (mpursiai's fork with LT SPRAT support)
• astropy
• numpy
• loguru
• rich-click

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Code Structure

Key files in the repository:

• CLI entry point src/pypeit_wrapit/cli.py

• LT SPRAT workflow src/pypeit_wrapit/lt_sprat.py

• Common utilities (flux writing, FITS unpacking, stacking) src/pypeit_wrapit/common.py