Configuration and Setup

TOIREx is controlled through an INI-style configuration file. The configuration file is divided into several sections, each controlling a different stage of the reduction pipeline.

Setting Up

Download the default configuration file from

https://github.com/varghesereji/TOIREx/blob/main/src/toirex/config/TOIREX_config.config

or copy it from your TOIREx installation.

/path/to/env/TOIREx/src/toirex/config/TOIREX_config.config

Place the configuration file in the same directory as your observational data. Modify the required parameters before running the pipeline.

Configuration Sections

The configuration file contains the following sections:

• [inits] – General pipeline settings.

• [outputs] – Output directory and filenames.

• [visual] – Display options.

• [logging] – Logging configuration.

• [inputs] – Input image processing.

• [dither] – Dither alignment.

• [spectral_extraction] – Spectroscopic extraction.

• [wcs] – World Coordinate System parameters.

• [photometry] – Photometric reduction.

[inits]

General pipeline settings.

Parameter	Description	Allowed values
INSTRUMENT	Name of the instrument.	TIRSPEC, TANSPEC
TODO	Type of reduction to perform.	P (Photometry), S (Spectroscopy)
DATA	Name of the directory containing the raw observations.	Any valid directory
EDITOR	Text editor used during manual operations.	e.g. gedit, nano
TIMESERIES	Enable time-series extraction.	Y or N
MODE	Pipeline execution mode.	AUTO or MANUAL

[outputs]

Output directory and filenames.

Parameter	Description
OP_DIR	Output directory where reduced products are stored.
EXCLUDE_REG	Comma-separated wildcard patterns of files to ignore.
CATALOGUE_NAME	Name of the generated observation catalogue.

[visual]

Image display options.

Parameter	Description
SCIENCE	Display science frames.
FLAT	Display flat-field frames.
LAMP	Display lamp frames.

All options accept Y or N.

[logging]

Logging configuration.

Parameter	Description
LEVEL	Logging level. Possible values are DEBUG, INFO, WARNING and ERROR.

[inputs]

Input image processing.

Parameter	Description
FLUXEXT	FITS extension containing the science image.
VAREXT	FITS extension containing the variance image.
SKY	Perform sky subtraction.
REMOVECR	Remove cosmic rays before reduction.
BADPIXMASK	Use the default bad-pixel mask (Y), disable masking (N), or specify the path to a custom bad-pixel mask.
FRAMECOMBINE	Method used to combine multiple images.

FRAMECOMBINE can be

• mean

• median

• biweight

[dither]

Image alignment parameters.

Parameter	Description
DITHERING	Enable dither reduction.
CROP	Region used for determining image shifts.
UPSAMPLE	Upsampling factor used for image registration.
AUTODITHER	Automatically determine dither shifts.
REF_FRAME	Reference frame used for image alignment.

[spectral_extraction]

Spectroscopic extraction parameters.

Parameter	Description	Allowed values
EXTRACTORCONFIG	Configuration file for SpectrumExtractor.	Keep blank to use default
SELECT_APERTURE	Aperture selection mode.	AUTO or MANUAL
APERTUREWINDOW	Extraction aperture window.	e.g. -10 10
BKGWINDOWS	Background windows.	e.g. -20 -15 15 20
SUBTRACT_BKG	Perform background subtraction.	Y or N
SCOMBINE	Combine dithered spectra.	Y or N
REFITAPERTUREINXD	Refit the aperture in the cross-dispersion direction.	e.g. p2, p3 etc.
REFITAPERTUREINXD_DWINDOW	Dispersion window used for aperture refitting.	e.g. (500, 1200)
REFITAPERTUREINXD_BKGMEDIANFILT	Median filter size before aperture refitting.	e.g. 51
DCOEFFMODELFORAPERREFIT	Polynomial model used for aperture refitting.	e.g. p0
FLUX_CALIB	Apply flux calibration.	Y or N

REFITAPERTUREINXD supports

• False – Disable refitting.

• p0 – Constant shift.

• p1 – Linear shift.

• p2 – Quadratic shift.

• [(coefficients), (xmin, xmax)] – Apply a precomputed shift.

[wcs]

World Coordinate System parameters.

Parameter	Description
REF_EPOCH	Reference epoch.
OBS_EPOCH	Observation epoch.

[photometry]

Photometric reduction parameters.

Source Detection

Parameter	Description
FINDSOURCE	Source detection mode.
THRESHOLD	Detection threshold.
SOURCELIST	File containing manually selected sources.
FWHM	Estimated seeing FWHM in pixels.

FINDSOURCE may be

• AUTO

• MANUAL

Photometry

Parameter	Description
METHOD	Photometric extraction method.
MODEL	PSF model.
PSF_FWHM	Initial PSF FWHM estimate.
PSF_ANGLE	PSF rotation angle.
APERTURE	Aperture type.
ANNULUS	Background annulus type.
RADIUS	Aperture radius.
BKGWINDOWS	Background annulus dimensions.

Available PSF models

• EPSF

• GaussianPSF

• CircularGaussianPSF

Available aperture types

• CircularAperture

• EllipticalAperture

Available annulus types

• CircularAnnulus

• EllipticalAnnulus

Notes

• Configuration files follow the standard INI format.

• Boolean options use Y and N.

• Relative paths are interpreted relative to the working directory.

• Values enclosed in parentheses represent Python tuples.