%APN3_PROCEEDINGS_FORM%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% TEMPLATE.TEX -- APN3 (2003) ASP Conference Proceedings template.
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\documentclass[11pt,twoside]{article}  % Leave intact
\usepackage{adassconf}

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\begin{document}   % Leave intact

%-----------------------------------------------------------------------
%                           Paper ID Code
%-----------------------------------------------------------------------
% Enter the proper paper identification code.  The ID code for your
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% EXAMPLE: \paperID{P7-7}
%

\paperID{P10-3}
%%%% ID=P10-3

%-----------------------------------------------------------------------
%                           Paper Title 
%-----------------------------------------------------------------------
% Enter the title of the paper.
%
% EXAMPLE: \title{A Breakthrough in Astronomical Software Development}
% 
% If your title is so long as to fill the page header when you print it,
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%  \titlemark{Rapid Development for Distributed Computing}
%

\title{Model Based Corrections to Data from Radiation Damaged Detectors.}
\titlemark{Modelling Damaged Detectors}

%-----------------------------------------------------------------------
%                         Authors of Paper
%-----------------------------------------------------------------------
% Enter the authors followed by their affiliations.  The \author and
% \affil commands may appear multiple times as necessary (see example
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% followed by the last name.  Authors with the same affiliations
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%
% EXAMPLE: \author{Raymond Plante, Doug Roberts, 
%                  R.\ M.\ Crutcher\altaffilmark{1}}
%          \affil{National Center for Supercomputing Applications, 
%                 University of Illinois Urbana-Champaign, Urbana, IL
%                 61801}
%          \author{Tom Troland}
%          \affil{University of Kentucky}
%
%          \altaffiltext{1}{Astronomy Department, UIUC}
%
% In this example, the first three authors, "Plante", "Roberts", and
% "Crutcher" are affiliated with "NCSA".  "Crutcher" has an alternate 
% affiliation with the "Astronomy Department".  The fourth author,
% "Troland", is affiliated with "University of Kentucky"

\author{Paul Bristow}
\affil{ST-ECF, ESO, Karl-Schwarzschild-Str. 2, D-85748, Garching bei M$\ddot{\rm u}$nchen, Germany}

%-----------------------------------------------------------------------
%                        Contact Information
%-----------------------------------------------------------------------
% This information will not appear in the paper but will be used by
% the editors in case you need to be contacted concerning your
% submission.  Enter your name as the contact along with your email
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% EXAMPLE:  \contact{Dennis Crabtree}
%           \email{crabtree@cfht.hawaii.edu}
%

\contact{Paul Bristow}
\email{bristowp@eso.org}

%-----------------------------------------------------------------------
%                     Author Index Specification
%-----------------------------------------------------------------------
% Specify how each author name should appear in the author index.  The 
% \paindex{ } should be used to indicate the primary author, and the
% \aindex for all other co-authors.  You MUST use the following
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% SYNTAX:  \aindex{Lastname, F. M.}
% 
% where F is the first initial and M is the second initial (if
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% EXAMPLE: \paindex{Crabtree, D.}
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\paindex{Bristow, P.}
%\aindex{ }     % Remove this line if there is only one author

%-----------------------------------------------------------------------
%                     Author list for page header       
%-----------------------------------------------------------------------
% Please supply a list of author last names for the page header. in
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% EXAMPLES:
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%
% Use the "et al." form in the case of seven or more authors, or if
% the preferred form is too long to fit in the header.

\authormark{Bristow}

%-----------------------------------------------------------------------
%                       Subject Index keywords
%-----------------------------------------------------------------------
% Enter a comma separated list of up to 6 keywords describing your
% paper.  These will NOT be printed as part of your paper; however,
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% There is no standard list; however, you can consult the indices
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% EXAMPLE:  \keywords{visualization, astronomy: radio, parallel
%                     computing, AIPS++, Galactic Center}
%
% In this example, the author noticed that "radio astronomy" appeared
% in the ADASS VII Index as "astronomy" being the major keyword and
% "radio" as the minor keyword.  The colon is used to introduce another
% level into the index.

\keywords{instrument modelling, CCD, detector read out, radiation damage, pipelines}

%-----------------------------------------------------------------------
%                              Abstract
%-----------------------------------------------------------------------
% Type abstract in the space below.  Consult the User Guide and Latex
% Information file for a list of supported macros (e.g. for typesetting 
% special symbols). Do not leave a blank line between \begin{abstract} 
% and the start of your text.

\begin{abstract}          % Leave intact
Space based CCDs suffer continual bombardment from the hostile
radiation environment which gradually degrades their performance and
potentially limits their operational lifetime. As part of our effort
to enhance the calibration of STIS (a spectrograph on-board the Hubble
Space Telescope), we have developed a model of the readout process for
CCD detectors suffering from degraded charge transfer efficiency. The
model enables us to make predictive corrections to data obtained with
such detectors. We present examples of the corrections possible using
this technique and compare them to what can be achieved using a more
conventional empirical approach. In addition we discuss some of the
difficulties of providing users with automated implementations of this
this kind of data analysis software.% Place the text of your abstract here - NO BLANK LINES

\end{abstract}

%-----------------------------------------------------------------------
%                             Main Body
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%           ...
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% It is recommended that you look at the sample papers, sample1.tex
% and sample2.tex, for examples for formatting references, footnotes,
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\section{Introduction}

Charge Coupled Devices (CCDs) operating in hostile radiation
environments suffer a gradual decline in their Charge Transfer
Efficiency (CTE, or equivalently, an increase in charge transfer
inefficiency, CTI). STIS and WFPC2 have both had their CTE monitored
during their operation in orbit and both indeed show a measurable
decline in CTE which has reached a level which can significantly
effect scientific results (eg. Cawley et al 2001, Heyer 2001, Kimble,
Goudfrooij and Gililand 2000).

As part of the Instrument Physical Modelling Group's effort
to enhance the calibration of STIS we have developed a model of the
readout process for CCD detectors suffering from degraded charge
transfer efficiency. The model enables us to make predictive
corrections to data obtained with such detectors.

\section{The Model}

Detailed discussion of the model development and the physics involved
can be found in Bristow \& Alexov et al. 2002 and Bristow 2003a. Our
approach is to simulate the readout process at the level of individual 
charge transfers. That is we take an image (a charge distribution on a 
two dimensional pixel array) and transfer the charges out as they
would be on a real chip. Throughout we keep track of the status of
bulk traps in the silicon pixels as they interact with the charge
distribution. The timescales and densities for
these known traps are appropriate to the operating temperature and
on-orbit radiation exposure respectively. The model has been optimised 
for the correction of STIS data, but could in principle be ported to
other detectors.

\section{Cleaning CTE Trails}

The clearest aesthetic diagnostic of data suffering from poor CTE is
the presence of trails under bright objects. This can be seen clearly
in the section of STIS data shown in figure 1 (left), the read out
direction is upwards. Figure 1 (right) shows the
success of the simulation derived correction in cleaning these trails.
\begin{figure}
\plottwo{P10-3_1a.eps}{P10-3_1b.eps}%{P10-3_1b.eps}  %%% P10-3_1b.eps INERROR
\caption{Left: A section of STIS image data suffering from significant 
  CTI. Right: The same section after correction with the physical
  model. Note that trails under bright sources have been removed}
\end{figure}

\section{Photometric Corrections}

Probably the most important effect of CTI is the loss of flux from the
central isophotes of sources. It is possible
to calibrate an empirical flux correction
as a function of signal strength, background, epoch and position on
the chip. Such a correction must be formulated and calibrated
differently for photometric and spectroscopic data because of the
differing nature of the spatial distributions of illumination and
resulting charge. Moreover, empirical corrections {\it only apply to
point sources}. On the other hand, modelling the readout process we
are able to correct for any charge distribution and can therefore
apply this method to all data whether photometric or spectroscopic and
obtain a correction for every pixel, not just extracted sources or
spectra.

Nevertheless the empirical corrections for STIS provide an ideal means 
of testing and calibrating the physical model, as the
empirical corrections are essentially a distillation of what is to be
learnt from the calibration data with respect to CTI. If the physical model
reproduces empirical results on average for point sources then it is
reasonable to conclude that it is correctly modifying the charge
distribution and will also therefore correctly predict the CTI in
extended sources and indeed the whole image array.
\begin{figure}
\plotfiddle{P10-3_2a.eps}{90.0mm}{-90.0}{40}{50}{-145.0}{275.0}
\caption{Comparison between empirical and model based corrections }
\end{figure}
A comparison between model based and empirical corrections, for sources 
to which the empirical corrections apply, is shown if figure
2. Beyond the general good agreement, there are many
sources for which the model based and empirical corrections differ
significantly.

The scatter is due to the fact that the non uniformity of the charge
distribution causes the CTI experienced by each source to vary in a
way which cannot be accounted for in the empirical
corrections. Indeed, if we examine sources corresponding to outlying
points in figure 2 in the raw image array, we find that the anomalous
correction factor assigned by the physical model is easily understood
by considering charge distribution in the surrounding
pixels. For example, nearby sources, falling between the
source in question and the read out register, will trail charge into
the aperture, 
leading to a smaller CTI effect than the empirical calibration would
suggest. (See Bristow 2003a\&b).

\begin{figure}
\plotone{P10-3_4.eps}
\caption{Schematic showing the preparation of CTI corrected data for the CALSTIS pipeline}
\end{figure}

\section{Pipeline Integration}

A complex and comprehensive data pipeline already exists for STIS. It
relies upon a database of empirically derived and continually updated
reference files selected by header keywords in each
dataset. Introducing a model based component of the calibration leads
to some conflicts. Some aspects of the calibration which fit neatly
into one reference file have more than one physical source and vice
versa. Specifically:

\begin{itemize}
\item Reference files (bias and dark) must themselves be corrected for
  CTI effects
\item The readout simulation generates hot columns from the hot pixels
  and thereby includes a correction for these features as well as
  CTI. However, the bias files provided for use in the pipeline,
  include these hot columns and other features not dealt with by the
  readout simulation.
\end{itemize}
However, a complete model based calibration of STIS is not yet
possible. In addition, the simulation is CPU intensive and adds
considerably to the total processing time, therefore the possibility to
execute this as a stand alone process is also desirable. Figure 3
illustrates the incorporation of the model in a way which takes the
above into account.





%-----------------------------------------------------------------------
%                             References
%-----------------------------------------------------------------------
% List your references below within the reference environment
% (i.e. between the \begin{references} and \end{references} tags).
% Each new reference should begin with a \reference command which sets
% up the proper indentation.  Observe the following order when listing
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% publication year, journal name, volume, and page number for
% articles.  Note that many journal names are available as macros; see
% the User Guide listing "macro-ized" journals.   
%
% EXAMPLE:  \reference Hagiwara, K., \& Zeppenfeld, D.\  1986, 
%                Nucl.Phys., 274, 1
%           \reference H\'enon, M.\  1961, Ann.d'Ap., 24, 369
%           \reference King, I.\ R.\  1966, \aj, 71, 276
%           \reference King, I.\ R.\  1975, in Dynamics of Stellar 
%                Systems, ed.\ A.\ Hayli (Dordrecht: Reidel), 99
%           \reference Tody, D.\  1998, \adassvii, 146
%           \reference Zacharias, N.\ \& Zacharias, M.\ 2003,
%                \adassxii, \paperref{P7.6}
% 
% Note the following tricks used in the example above:
%
%   o  \& is used to format an ampersand symbol (&).
%   o  \'e puts an accent agu over the letter e.  See the User Guide
%      and the sample files for details on formatting special
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%   o  "\ " after a period prevents LaTeX from interpreting the period 
%      as an end of a sentence.
%   o  \aj is a macro that expands to "Astron. J."  See the User Guide
%      for a full list of journal macros
%   o  \adassvii is a macro that expands to the full title, editor,
%      and publishing information for the ADASS VII conference
%      proceedings.  Such macros are defined for ADASS conferences I
%      through XI.
%   o  When referencing a paper in the current volume, use the
%      \adassxii and \paperref macros.  The argument to \paperref is
%      the paper ID code for the paper you are referencing.  See the 
%      note in the "Paper ID Code" section above for details on how to 
%      determine the paper ID code for the paper you reference.  
%
\begin{references}

\reference Bohlin, R.\ \& Goudfrooij, P.\ 2003, STIS Instrument
Science Report 2003-03
\reference Bristow, P.\ \& Alexov, A.\ 2002, CE-STIS-Instrument
Science Report 2002-001
\reference Bristow, P.\ 2003a CE-STIS-Instrument Science Report 2003-003, in preparation
\reference Bristow, P.\ 2003b CE-STIS-Instrument Science Report 2003-001
\reference Bristow, P.\ 2003c CE-STIS-Instrument Science Report 2003-002
\reference Cawley, L., Goudfrooij, P.\ \& Whitmore, B.\ 2001,
Instrument Science Report WFC3 2001-05
\reference Goudfrooij, P.\ \& Kimble, R. A.\ 2002 in Proceedings of the 2002 HST Calibration Workshop, Eds Arribas, S., Koekemoer, A and Whitmore, B. (Space Telescope Science Institute)
\reference Heyer, I.,\ 2001, WFPC2 Instrument Science Report 2001-009
\reference Kimble, R. A., Goudfrooij, P.\ \& Gililand, R.L.\ 2000, Proc. SPIE  Vol. 4013, p. 532-544, in UV, Optical, and IR Space Telescopes and Instruments, Ed. J. B. Breckinridge; P. Jakobsen



\end{references}

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\end{document}  % Leave intact
