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Astronomical Data Analysis Software and Systems VII
ASP Conference Series, Vol. 145, 1998
R. Albrecht, R. N. Hook and H. A. Bushouse, e
Ö Copyright 1998 Astronomical Society of the Pacific. All rights reserved.
ds.
The IRAF Mosaic Data Reduction Package
Francisco G. Valdes
IRAF Group, NOAO 1 , PO Box 26732, Tucson, AZ 85726
Abstract. The IRAF Mosaic Data Reduction Package, mscred, pro­
cesses data from mosaics of CCDs such as the NOAO CCD Mosaic Camera 2 .
A brief design of the package was presented earlier by Valdes (1997a).
Since then a first implementation of the software has been completed.
This paper summarizes the current status of the software and our plans
for future developments.
1. Current Status
Most of the components of the original design (Valdes 1997a) for an IRAF Mo­
saic Data Reduction Package have been implemented in the first version of the
mscred package. This has allowed complete, end­to­end reductions of data
from the NOAO CCD Mosaic Camera. The package operates on multiexten­
sion FITS format (MEF) files consisting of a global header and individual image
extensions for each amplifier (Valdes 1997b). The raw data files are processed
so that each image extension is flux and coordinate system calibrated. Mosaic
cameras have gaps and misalignments between the CCD elements so, when a
complete image of the sky is desired, multiple ``dithered'' exposures are taken.
The mscred package provides tasks to resample the data into a final image with
the geometric e#ects (gaps, alignments, and optical distortions) removed. This
process can also improve the signal­to­noise and eliminate cosmic rays and cos­
metic defects. Observations have been obtained with the NOAO CCD Mosaic
Camera and processed with the mscred package which produce images of high
scientific and aesthetic quality despite the engineering grade CCDs used in the
current instrument.
The functionality of the mscred package can be broken down into the
following categories: (1) display, (2) basic CCD calibrations, (3) coordinate
registration, (4) mosaicing, (5) taping, and (6) miscellaneous. The package is
used both at the telescope and after the observing run for quick­look or full
reductions and for data analysis. Some of the categories apply to both uses as,
for example, the display of mosaic data. In this paper the package tasks are
identified with their names in bold font.
1 National Optical Astronomy Observatories, operated by the Association of Universities for
Research in Astronomy, Inc. (AURA) under cooperative agreement with the National Science
Foundation.
2 http://www.noao.edu/kpno/mosaic/
53

54 Valdes
Being able to display an exposure as an approximation of a complete (mo­
saiced) image of the sky is a prime requirement both at the telescope and during
data reduction. We are developing a new display capability for this purpose as
part of the NOAO Mosaic Data Handling System (Tody 1997). The mscred
package provides an interim task (mscdisplay) to display multiextension data
as an image in a standard display server such as Ximtool. Mscdisplay in­
cludes real­time capabilities to display the data while a readout is in progress.
Related tools allow users to interact with the displayed mosaic exposure (even
during readout) to evaluate focus (mscfocus) and to do quick­look analysis
(mscexamine) including PSF fitting, statistics, graphics, and celestial coordi­
nate measurements.
Basic CCD calibration provides for combining sequences of calibration expo­
sures (zerocombine, darkcombine, and flatcombine) and the standard CCD
calibration operations of overscan subtraction, trimming, bad pixel replacement,
zero level subtraction, dark count subtraction, and flat­fielding (ccdproc). The
input and output of these operations are MEF files.
The mscred package places emphasis on having an accurate celestial co­
ordinate system (called the world coordinate system or WCS). Using prototype
astrometry tools in the mscred package (msctpeak) an accurate WCS con­
sisting of independent solutions for each CCD relative to a common reference
pointing including all optical distortion and alignment terms has been derived
for the NOAO Mosaic at the Kitt Peak National Observatory Mayall 4­meter
and 0.9­meter telescopes (Davis, 1998). This was done using exposures of as­
trometric fields. This WCS is part of the raw data produced by the Mosaic
Data Capture Agent (DCA) (Tody & Valdes 1998) with the coordinate system
reference point set to the telescope pointing coordinates.
The zero point of the WCS, which is initially set by the telescope pointing,
can be adjusted to a precise absolute coordinate or to common coordinates in
a dithered set of exposures by displaying the exposures and identifying one or
more reference stars (msczero). Given that the raw data already have relatively
good coordinates there is a task (still evolving) that takes a set of overlapping
exposures and either a set of coordinates or random regions and registers their
WCS using cross­correlation (mscregister).
Using the WCS, the multiple images from each amplifier in a mosaic can
be resampled to make a single image on a uniform pixel grid having a standard
WCS, such as a tangent plane projection (mscimage). By using one exposure
as a reference, multiple dithered exposures can all be resampled to the same
pixel grid system (the same tangent point and pixel scale) so that the images
may be stacked (mscstack) to make a final image without further resampling.
The stacking process excludes the gaps and may include use of bad pixel masks
and various scaling and pixel rejection algorithms found in the standard IRAF
imcombine routine. Since combining dithered exposures is a common opera­
tion a higher level task (mscdither) combines mscregister, mscimage, and
mscstack to directly produce a final image.
Tasks for taping of data are only included as an interim measure until
generic IRAF tasks include direct support for disk FITS files in MEF format.
For MEF data the duties of the taping tasks (mscwfits and mscrfits) are simply
to transfer the FITS file to and from tape with the appropriate FITS blocking,

The IRAF Mosaic Data Reduction Package 55
e#cient listing of the contents of tapes with multiextension files, and recording
the disk filenames and restoring the files to disk with their original filenames.
The tape is a valid FITS tape.
The mscred software is packaged as a standard IRAF external package for
IRAF version 2.11 and later. Although this is an early version of the software
it has been made available to users of the NOAO Mosaic Camera and other
interested parties developing mosaic cameras. Releases of the software will be
made periodically as new features are added.
2. Future Work
There are many things which still need to be added. These range from minor
improvements to a few major research and development items. The major items
are discussed in the following sections. The minor items consist of an improved
syntax to interface MEF data to existing IRAF tasks that operate on lists of
images, expanding the CCD processing task ccdproc to provide for incremen­
tal reductions, using a better WCS representation, and a task to restore flux
conservation in flat­fielded data.
A wildcard syntax is needed to easily select a set of image extensions from
an MEF file rather than the current requirement that each extension be listed
explicitly. It takes special care to produce a good flat­field for a wide­field mosaic
so for quick­look and initial reductions it is desired to apply archival calibration
data, such as a high quality master sky flat, and then continue with incremental
calibration using data acquired during the course of observing. Ccdproc needs
to be modified to easily support incremental calibration.
The WCS representation for a wide­field optical image is better given as a
radial projection (as proposed for a FITS world coordinate system standard) al­
though a general polynomial distortion residual will still be required. Currently
a tangent plane projection is used in combination with a separate text file defin­
ing a polynomial distortion function. Another property of wide­field images,
such as with the NOAO Mosaic at the 4­meter telescope, which is not obvious
at first is that the pixel area (square arc seconds per pixel) may vary signifi­
cantly. This means the sky and object counts vary with position. Flat­fielding
attempts to make the sky counts constant which leads to flux errors. A task
based on the WCS is required to restore the correct flux per pixel to flat­fielded
data prior to doing any photometry. This only a#ects the MEF files because
the resampling operation (mscimage) naturally accounts for the varying pixel
areas.
2.1. Pixel Masks
Pixel masks assign integer codes to each pixel. IRAF provides a pixel mask
format which is very compact for masks containing regions of constant value.
In mscred pixel masks are used to identify bad pixels with codes values for
cosmetic defects, saturated pixels, and cosmic rays. The masks are assigned to
data exposures and the software uses these assignments to determine bad pixel
information for the data pixels. The current software supports the first category
of predetermined cosmetic defects for replacement by interpolation, avoiding bad
data in automatic display scaling, excluding bad data from statistical sampling

56 Valdes
of scaling factors for combining, and exclusion during the stacking of dithered
exposures.
The issues that still have to be addressed are updating other pieces of the the
software to add to the mask, such as the flagging of saturated pixels, additional
uses of the bad pixel information, such as during resampling, and storage of
the bad pixel information in multiextension FITS files. The last topic requires
mapping the compact IRAF pixel mask format to a FITS format; most likely as
a binary table extension.
2.2. Pixel Uncertainty Information
The propagation of pixel value uncertainty information naturally starts with
the raw data. The mscred tasks need to be expanded to propagate the pixel
uncertainties from the raw data during each step that modifies or transforms
the pixel values. There are two development stages that need to be completed.
The first is to define the data format representing the pixel uncertainties and
the second is to understand how the uncertainties propagate in operations such
as flat­fielding, resampling, and combining with pixel rejection.
Research in representing the pixel uncertainties is needed to, hopefully, find
a compact description requiring much less than one uncertainty value for each
data pixel. Preliminary research suggests a combination of a scaling relative to
the pixel data, header keywords, and mapping to a finite set of discrete values
that give uncertainties to a useful precision. A key feature of this is the use of
pixel masks which can be stored in a compact format as described previously.
2.3. Astrometry
The mscred package supports a coordinate system that is quite accurate. The
software maintains and propagates this coordinate system. Much of the coor­
dinate system description is fairly static and only terms relating to zero points
and rotations need to be calibrated on an individual exposure or run basis. Cur­
rently the instrument support personnel provide the static part of the coordinate
system description and the mscred package provides tools to modify the zero
point to yield absolute coordinates and to register overlapping exposures. The
problem is that if users want to modify anything but the zero point they have to
do a complete astrometric solution which requires a good astrometric field with
many stars.
The desired enhancements are to let users to have more control of the coor­
dinate system calibration and to integrate catalog servers to ease the determi­
nation of a zero point for absolute coordinates. The first part relates to allowing
adjustments of the coordinate system representation short of requiring a com­
pete new astrometric solution. For instance with just a few good astrometric
objects users should be able to adjust the scale and rotation in addition to the
zero point.
2.4. Data Reduction Agent
The Data Reduction Agent (DRA) is an ambitious part of the NOAO Data Han­
dling System which was described in the original design. It is not directly a part
of the mscred package. However, this pipeline tool is intended to be portable
with the mscred package and be closely tied to the mscred functionality. As

The IRAF Mosaic Data Reduction Package 57
work progresses on the DRA there may be enhancements of the mscred package
to support the automatic reduction of mosaic data in a data handling system
environment.
References
Davis, L. 1998, this volume
Tody, D. 1997, in ASP Conf. Ser., Vol. 125, Astronomical Data Analysis Software
and Systems VI, ed. Gareth Hunt & H. E. Payne (San Francisco: ASP),
451
Tody, D. and Valdes, F. 1998, this volume
Valdes, F. 1997a, in ASP Conf. Ser., Vol. 125, Astronomical Data Analysis
Software and Systems VI, ed. Gareth Hunt & H. E. Payne (San Francisco:
ASP), 455
Valdes, F. 1997b, in ASP Conf. Ser., Vol. 125, Astronomical Data Analysis
Software and Systems VI, ed. Gareth Hunt & H. E. Payne (San Francisco:
ASP), 459