Physics Computer Science
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Computer Science
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An Automatic Image Reduction Pipeline for the Advanced Camera for Surveys

We have written an automatic image processing pipeline for the Advanced Camera for Surveys (ACS) Guaranteed Time Observation (GTO) program. The pipeline, known as Apsis, supports the different cameras available on the ACS instrument and is written in Python with a flexible object-oriented design that simplifies the incorporation of new pipeline modules. The processing steps include empirical determination of image offsets and rotation, cosmic ray rejection, image combination using the drizzle routine called via the STScI Pyraf package, object detection and photometry using SExtractor, and photometric redshift estimation in the event of multiple bandpasses. The products are encapsulated in XML markup for automated ingestion into the ACS Team archive.


Introduction and Basic Operation
The ACS science team was apportioned about 550 orbits of GTO time in exchange for its instrument development and calibration work. A robust and flexible astronomical data reduction and analysis pipeline was required for processing these data and other observations for which the science team is responsible. To fill this need, we developed a package called "Apsis" (ACS pipeline science investigation software), written in the Python programming language using a flexible, modular design. Apsis was used for processing the ACS early release observation (ERO) images of the Tadpole and Mice galaxies, the Cone Nebula, and M17 soon after ACS was installed on the Hubble Space Telescope. Since then, it has developed and been used extensively on Linux and Solaris platforms for processing WFC and HRC data from both science and calibration programs.
A given processing run starts with flat-fielded multi-extension FITS images that have been processed through the CALACS software at STScI (Hack 1999). The basic Apsis "observation object" consists of all the images of a given program field (or mosaic of adjacent fields). These are grouped into separate "associations" according to the different imaging/grism filters used or (sometimes) different epochs, and FITS tables are constructed similar to those used in STScI OPUS pipeline. Reading and manipulation of FITS images and tables are done with the aid of the PyFits and Numarray Python modules, and any IRAF/STSDAS routines are called through Pyraf (see Greenfield et al. 2002). Other external programs are accessed via system calls.
The observation object is then passed to the various python modules in succession, which have "methods" (python functions) for performing the following general tasks: image offset measurement corrected for distortion, sky estimation and subtraction, cosmic ray (CR) rejection and "drizzling," construction of error arrays and a multi-band "detection image," object detection and measurement, photometric calibration, and photo-z estimation. A running log keeps track of progress and records diagnostics. After completion, each module object is written to disk as a byte stream using the Python "pickling" utility; this allows for recovery of information in the event of failure and simplifies debugging. The modules also contain detailed methods for producing XML messages and markup of the data products (images and catalogs) for archiving purposes.
Although Apsis was designed primarily as an automated pipeline, it can be run by users as a standalone program, and provides a suite of commandline options for this purpose. These include switches for turning off various parts of the processing (e.g., sky subtraction, cataloging), specifying a particular input image as reference for the shifts, supplying an alternate distortion model, externally measured shifts, or sky values, lowering the CR rejection thresholds, changing the output image pixels scale, and several other options. The following sections provide a few details on the major processing steps.

Image Registration and Sky Subtraction
The align module determines the relative x, y shifts and rotations, as well as the sky levels, of the input images. SExtractor (Bertin & Arnout 1996) is run with a signal-to-noise threshold of 10 on each science extension of each image (there are two science extensions for WFC; one for HRC and SBC). The resultant catalogs are culled on the basis of object size and shape parameters, thereby rejecting the vast majority of cosmic rays and CCD artifacts as well as overly diffuse objects. If fewer than ten "good" sources remain, then SExtractor is rerun at lower thresholds. The x, y coordinates of each "good" source are corrected using the distortion model read from the IDCTAB FITS table specified in the image headers or on the command line. Sources from different extensions (different CCD chips) of the same image are placed on a common rectified frame using the IDCTAB parameters V2REF and V3REF.
We use the "Match" program (Richmond 2002) to derive shifts and rotations with respect to a reference image, by default the one having the most "good" sources. We modified Match to accept an input guessed transformation (derived from the headers) and to report more diagnostics for evaluating the success of the matching. In the event of failure, Match is rerun without an input guess, using the full triangle-matching search algorithm on the N brightest sources; this is repeated with larger N , and an N 6 hit in processor time, if necessary. All sources are used for tuning up the final transformation once it is found. We also evaluate the median x, y shifts for all matched sources, and we revert to these if the derived rotation is negligible.
This automatic, adaptive matching procedure works quite well in practice. Images taken at large offsets and in different visits can have header shift errors of ∼ 1 ′′ (∼ 20 WFC pixels), but this is irrelevant for the triangle matching algorithm. Typical WFC GTO fields produce one-to-several hundred matched sources per exposure, and the resulting shift uncertainty is typically ∼ 0.02 pix.
Problems have only occurred for some images of blank fields taken with the HRC, which has an area 1/64 of the WFC. In this case Apsis defaults to the header shifts, although it is also possible to supply external shifts. Grism (G800L) images are by default aligned with direct images according to the headers.
The sky values and sigmas returned by SExtractor for each image extension are used as inputs to the STSDAS dither.sky task, which in turn uses the STS-DAS gstatistics routine. However, experimentation indicated that the mean sky levels reported by SExtractor were more robust, although tended to be biased high in more crowded fields. For this reason, we adopt the SExtractor sky value when it is the lower estimate, and the mean of the two otherwise. The sky is then subtracted, with the option of averaging the values for different extensions of the same image. This step removes sky level differences for the image combination and CR rejection routines described in the following section.

Image Combination
The modules combDither and pyblot combine all exposures within each filter into a single geometrically corrected image while rejecting cosmic rays. This is done through the STSDAS Dither package drizzle-blot-drizzle cycle outlined by Gonzaga et al. (1998), although here coded in Python. First the images are "drizzled" to separate output images using the shifts and rotations supplied by the Apsis align module. These individually drizzled images are then median stacked using exposure time weighting and a 'minmax' clipping algorithm. The median image is then "blotted" back to each of the input image positions, rescaled in exposure time, and used as a template for CR rejection with the driz cr task. The driz cr parameters were optimized to achieve good CR rejection without harming the centers of any stars. In particular, this meant setting the derivative scale parameter to a value near unity.
A cosmic ray mask is produced for each science extension and is multiplied by the bad pixel mask that we produce from the data quality arrays using a call to Pydrizzle with the 'bits' parameter set to 8578 to include 'good', 'replaced', 'saturated,' and 'repaired' pixels (see Hack 1999). These combined CR/badpix masks are then used for the final drizzling of the input images in each filter to a single output image. We again use the shifts and rotations found by align and produce drizzled images in units of electrons. In so doing, it is necessary to divide the output pixel values by the number of science extensions, since the drizzle task does not recognize the different extensions as being part of the same image. The default drizzle pixfrac and scale parameters are unity but can be reset with flags on the Apsis command line.
After the final images are produced, the image headers are thoroughly updated and corrected. This includes calculating new CD matrices from scratch based on the output pixel scale and image orientation, which is derived through spherical geometry from the PA V3 header keyword of the reference image, the declination, and the detector orientation and location in the V2,V3 plane. The code also ensures that all of the output images have identical WCS information, as they should all be well aligned at this stage. At this writing, the WCS zero points are off by roughly 2 ′′ due to systematic pointing errors, but this is expected to improve with a recent FGS realignment.
We produce an "RMS image" for each output science image. The RMS images have pixel values equal to the estimated error per pixel, based on the total read noise, signal level, Apsis cosmic ray rejection, and the effects of the multiple bias and dark frame subtractions. The actual root-mean-square pixel variation in the science image is of course lower due to the noise correlation induced by non-integer shifts and geometric correction. However, we verified that the RMS images reflect the pixel variation when images are stacked without shifting or correction. The RMS images are used in estimating photometric errors.

Object Detection, Photometry, and Redshift Estimation
A series of modules do the object photometry. The combFilter module produces a multi-band "detection image," which is the variance-weighted average of the science images in the different bandpasses. Images in specific filters (e.g., grism, polarizers) can be omitted from this average. This module also produces a detection weight image, which is a similarly weighted sum of the exposure maps from the drizzling process. The detectionCatalog and filterCatalog modules create parameter files and run SExtractor, first on the detection image alone, and then multiple times in "dual image mode." In dual mode, the detection image defines the object position and apertures, but the photometric measurements are done on the filter image with its associated RMS image.
The colorCatalog module derives the photometric zero points from the image header catalogs, sorts through the different SExtractor catalogs, and produces a single, calibrated multicolor catalog. It also uses simple logic for flagging apparently bad or anomalous magnitudes. Finally, the photoz module feeds the multicolor catalog to the Bayesian Photometric Redshift package (Benítez 2000), which is itself coded in Python. A final XML "run message" is written in the same format as the individual module messages. The images and XML catalogs can then be ingested into the ACS team data archive.