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Introduction
Description
COSMOS is a set of programs for the reduction of multislit spectra obtained
with the IMACS and LDSS3 spectrographs on the Magellan Telescopes. It can be
used for the quick-look analysis of data at the telescope as well as for
pipeline reduction of large data sets. COSMOS is based on a precise optical
model of the spectrographs, which allows (after alignment and calibration) an
accurate prediction of the location of spectra features. This eliminates the
line search procedure which is fundamental to many spectral reduction programs
and allows a robust data pipeline to be run in an almost fully automatic mode,
so that large amounts of data can be reduced with minimal intervention. The
COSMOS reduction process consists of three steps:
- Alignment of the slitmask relative to the CCD focal plane.
After proper alignment, the COSMOS optical model can predict the location
of slit position/wavelength points on the CCD images to an accuracy of 1
to 2 pixels. If the optical models were perfect, the accuracy of these
predictions would be even better. Since they are not, they must be
improved by the following step. This alignment need only be done once for
each mask in each observing run,
- Production of an accurate spectral map, during which the
optical model predictions are corrected using one or more comparison arcs.
This step reduces the errors in predicted positions to a small fraction of
a pixel. The map created in this step forms the basis of all following
data reduction steps. This step is normally performed for each science
exposure, using adjacent comparison arc exposures.
- Spectral reduction.
Each of these steps consists of several procedures, which are summarized
below.
Input Data
The COSMOS reduction process requires the following input data:
- A mask definition file which describes the slitmask used.
This file was produced by the program maskgen which was used to produce
the mask, and will have the name
maskname.SMF
- A dewar offset file, which describes the positional
zero-point of a particular slitmask + instrumental configuration. Default
dewar offset files exist for each of the principal configurations and can
be used as starting points for the alignment process
- An observation definition file which defines the
observational setup, including instrument, slitmask (i.e. SMF file),
camera, disperser element (and tilt, if a grating), and dewar offset file.
These files are created by the program defineobs.
- Input data frames, including bias, flat field, comparison
arc, and object spectra.
Stitching
LDSS3 data needs to be stitched together before the alignment. The program stitch
will combine the LDSS3 CCD files into one FITS file and makes bias and gain
corrections for all the chips.
Alignment
Although the spectral mapping routines described below are able to correct
errors in the COSMOS optical model, they need a reasonably accurate starting
point. Variations in the way that masks are mounted in their frames, and
season-to-season variations in the ambient temperature inevitably produce some
errors in the predicted positions of slit images. The program align-mask
uses either a direct or dispersed mask image to correct for errors in x and y
position, position angle, and scale of the mask image, by adjusting the values
of these parameters in the dewar offset file. Corrections to the dewar offset
file can also be made manually using the program adjust-mask.
Spectral mapping
The process of generating and calibrating a spectral map serves two
purposes:
- It creates a polynomial representation of the mapping from
the science coordinate system of slit position and wavelength to the
observing coordinate system of CCD coordinates, using the program map-spectra.
This polynomial representation allows the data analysis to proceed without
the computational machinery involved in the optical model.
- It uses one or more comparison arcs to calibrate the
spectral map to high precision, using the program adjust-map.
Spectral reduction
Once an accurate spectral map has been produced, reduction of science
exposures proceeds in the following steps:
- Subtraction of bias, and division by flats, using the
programs Sflats and biasflat.
- Optional masking of bad pixels and different order
spectral features using badorders.
- Subtraction of sky, using the program subsky.
- Extraction of individual 1 or 2 dimensional spectral
exposures using extract-spec or 1dspec. Multiple sets of
extracted spectra can be combined, with optional cosmic ray removal, using
sumspec
Reduction Pipeline
Execution of the spectral mapping and spectral reduction steps described
above can be pipelined together for a set of spectral exposures from a single
night using the script-generator process-spec.
Display and visualization
A number of programs help to display the data and compare them with the
predictions of the optical model and spectral map, including display, mark-slits,
and whatsthat, which allow one to compare spectral and direct images
with the predictions of the model, and viewspectra, which provides some
spectral visualization and analysis features.
- Bugs persist. Please report problems to
cosmos[at]ociw.edu. We will respond to all emails, but please first ensure
that you have read the documentation carefully and are using the software
correctly.
Next: Data Files
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