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sc21.tex
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sc21.tex
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\documentclass[twoside,11pt]{article}
% ? Specify used packages
\usepackage{graphicx} % Use this one for final production.
% \usepackage[draft]{graphicx} % Use this one for drafting.
\usepackage{array}
\usepackage{fancyhdr}
\usepackage{multirow}
% ? End of specify used packages
\pagestyle{myheadings}
% -----------------------------------------------------------------------------
% ? Document identification
\newcommand{\stardoccategory} {Starlink Cookbook}
\newcommand{\stardocinitials} {SC}
\newcommand{\stardocsource} {sc\stardocnumber}
\newcommand{\stardoccopyright} {Copyright \copyright\ 2012 Science and Technology Facilities Council}
\newcommand{\stardocnumber} {21.0}
\newcommand{\stardocauthors} {H. S. Thomas}
\newcommand{\stardocdate} {12 September 2012}
\newcommand{\stardoctitle} {The SCUBA-2 Data Reduction Cookbook}
\newcommand{\stardocversion} {1.1}
\newcommand{\stardocmanual} {\ }
\newcommand{\stardocabstract} {
This cookbook provides a short introduction to Starlink facilities,
especially \textsc{Smurf}, the Sub-Millimetre User Reduction
Facility, for reducing, displaying, and calibrating SCUBA-2 data.
It describes some of the data artefacts present in SCUBA-2
time-series and methods to mitigate them. In particular, this
cookbook illustrates the various steps required to reduce the data;
and gives an overview of the Dynamic Iterative Map-Maker, which
carries out all of these steps using a single command controlled by
a configuration file. Specialised configuration files are
presented.}
% ? End of document identification
% -----------------------------------------------------------------------------
% +
% Name:
% sc.tex
%
% Purpose:
% Template for Starlink Cookbook (SC) documents.
% Refer to SUN/199
%
% Authors:
% AJC: A.J.Chipperfield (Starlink, RAL)
% BLY: M.J.Bly (Starlink, RAL)
% PWD: Peter W. Draper (Starlink, Durham University)
%
% History:
% 16-JUN-1997 (BLY):
% Original, based on SUN/SG templates.
% 13-AUG-1998 (PWD):
% Converted for use with LaTeX2HTML version 98.2 and
% Star2HTML version 1.3.
% 1-FEB-2000 (AJC):
% Add Copyright statement in LaTeX
% {Add further history here}
%
% -
\newcommand{\stardocname}{\stardocinitials /\stardocnumber}
\markboth{\stardocname}{\stardocname}
\setlength{\textwidth}{160mm}
\setlength{\textheight}{230mm}
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\setlength{\oddsidemargin}{0mm}
\setlength{\evensidemargin}{0mm}
\setlength{\parindent}{0mm}
\setlength{\parskip}{\medskipamount}
\setlength{\unitlength}{1mm}
% -----------------------------------------------------------------------------
% Hypertext definitions.
% ======================
% These are used by the LaTeX2HTML translator in conjunction with star2html.
% Comment.sty: version 2.0, 19 June 1992
% Selectively in/exclude pieces of text.
%
% Author
% Victor Eijkhout <eijkhout@cs.utk.edu>
% Department of Computer Science
% University Tennessee at Knoxville
% 104 Ayres Hall
% Knoxville, TN 37996
% USA
% Do not remove the %begin{latexonly} and %end{latexonly} lines (used by
% LaTeX2HTML to signify text it shouldn't process).
%begin{latexonly}
\makeatletter
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\def\ThrowAwayComment#1{\begingroup
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\def\includecomment
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% Define environments that ignore their contents.
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\excludecomment{rawhtml}
\excludecomment{htmlonly}
% Hypertext commands etc. This is a condensed version of the html.sty
% file supplied with LaTeX2HTML by: Nikos Drakos <nikos@cbl.leeds.ac.uk> &
% Jelle van Zeijl <jvzeijl@isou17.estec.esa.nl>. The LaTeX2HTML documentation
% should be consulted about all commands (and the environments defined above)
% except \xref and \xlabel which are Starlink specific.
\newcommand{\htmladdnormallinkfoot}[2]{#1\footnote{#2}}
\newcommand{\htmladdnormallink}[2]{#1}
\newcommand{\htmladdimg}[1]{}
\newcommand{\hyperref}[4]{#2\ref{#4}#3}
\newcommand{\htmlref}[2]{#1}
\newcommand{\htmlimage}[1]{}
\newcommand{\htmladdtonavigation}[1]{}
\newenvironment{latexonly}{}{}
\newcommand{\latex}[1]{#1}
\newcommand{\html}[1]{}
\newcommand{\latexhtml}[2]{#1}
\newcommand{\HTMLcode}[2][]{}
% Starlink cross-references and labels.
\newcommand{\xref}[3]{#1}
\newcommand{\xlabel}[1]{}
% LaTeX2HTML symbol.
\newcommand{\latextohtml}{\LaTeX2\texttt{HTML}}
% Define command to re-centre underscore for Latex and leave as normal
% for HTML (severe problems with \_ in tabbing environments and \_\_
% generally otherwise).
\renewcommand{\_}{\texttt{\symbol{95}}}
% -----------------------------------------------------------------------------
% Debugging.
% =========
% Remove % on the following to debug links in the HTML version using Latex.
% \newcommand{\hotlink}[2]{\fbox{\begin{tabular}[t]{@{}c@{}}#1\\\hline{\footnotesize #2}\end{tabular}}}
% \renewcommand{\htmladdnormallinkfoot}[2]{\hotlink{#1}{#2}}
% \renewcommand{\htmladdnormallink}[2]{\hotlink{#1}{#2}}
% \renewcommand{\hyperref}[4]{\hotlink{#1}{\S\ref{#4}}}
% \renewcommand{\htmlref}[2]{\hotlink{#1}{\S\ref{#2}}}
% \renewcommand{\xref}[3]{\hotlink{#1}{#2 -- #3}}
%end{latexonly}
% -----------------------------------------------------------------------------
% ? Document specific \newcommand or \newenvironment commands.
% Include special HTML versions of commands.
\newcommand{\eg}{{\it e.g.}}
\newcommand{\ie}{{\it i.e.}}
\newsavebox{\fmbox}
\newenvironment{fmpage}[1]{\begin{lrbox}{\fmbox}\begin{minipage}{#1}}{\end{minipage}\end{lrbox}\fbox{\usebox{\fmbox}}}
% A new environment for quoting verbatim
% Environment for indenting and using a small font.
\newenvironment{myquote}{\begin{quote}\begin{small}}{\end{small}\end{quote}}
% Shortcuts
% ---------
% Typographical shortcuts
\newcommand{\fcfbe}{$\mathrm{FCF_{beamequiv}}$}
\newcommand{\fcfb}{$\mathrm{FCF_{beam}}$}
\newcommand{\fcfa}{$\mathrm{FCF_{arcsec}}$}
\newcommand{\fcfm}{$\mathrm{FCF_{match}}$}
% SCUBA reference
%\newcommand{\scuba}{\htmladdnormallink{SCUBA}{http://www.jach.hawaii.edu/JCMT/}}
% Starlink Package names
\newcommand{\starlink}{\htmladdnormallink{Starlink}{http://starlink.jach.hawaii.edu}}
% Set up some common package names
\newcommand{\ccdpack}{\xref{\textsc{Ccdpack}}{sun139}{}}
\newcommand{\convert}{\xref{\textsc{Convert}}{sun55}{}}
\newcommand{\cupid}{\xref{\textsc{Cupid}}{sun255}{}}
\newcommand{\Figaro}{\xref{\textsc{Figaro}}{sun86}{}}
\newcommand{\fluxes}{\xref{\textsc{Fluxes}}{sun213}{}}
\newcommand{\gaia}{\xref{\textsc{Gaia}}{sun214}{}}
\newcommand{\Kappa}{\xref{\textsc{Kappa}}{sun95}{}}
\newcommand{\agi}{\xref{AGI}{sun48}{}}
\newcommand{\ndf}{\xref{NDF}{sun33}{}}
\newcommand{\surf}{\xref{\textsc{Surf}}{sun216}{}}
\newcommand{\jcmtdr}{\xref{\textsc{JCMTdr}}{sun132}{}}
\newcommand{\oracdr}{\htmladdnormallink{\textsc{Orac-dr}}{http://www.oracdr.org/oracdr}}
\newcommand{\photom}{\xref{\textsc{Photom}}{sun45}{}}
\newcommand{\picard}{\xref{\textsc{Picard}}{sun265}{}}
\newcommand{\smurf}{\xref{\textsc{Smurf}}{sun258}{}}
\newcommand{\ssds}{\xref{\textsc{Starlink Standard Data Structures}}{sgp38}{}}
\newcommand{\topcat}{\htmladdnormallink{\textsc{Topcat}}{http://www.starlink.ac.uk/topcat}}
% DR recipe names
\newcommand{\drrecipe}[1]{\texttt{#1}}
% Application tasks
\newcommand{\task}[1]{\textsf{#1}}
% ADAM parameters
\newcommand{\param}[1]{\texttt{#1}}
% SMURF tasks
\newcommand{\calcnoise}{\xref{\task{calcnoise}}{sun258}{CALCNOISE}}
\newcommand{\clean}{\xref{\task{sc2clean}}{sun258}{SC2CLEAN}}
\newcommand{\concat}{\xref{\task{sc2concat}}{sun258}{SC2CONCAT}}
\newcommand{\flatfield}{\xref{\task{flatfield}}{sun258}{FLATFIELD}}
\newcommand{\jcmtstate}{\xref{\task{jcmtstate2cat}}{sun258}{JCMTSTATE2CAT}}
\newcommand{\makemap}{\xref{\task{makemap}}{sun258}{MAKEMAP}}
% KAPPA
\newcommand{\beamfit}{\xref{\task{beamfit}}{sun95}{BEAMFIT}}
\newcommand{\cmult}{\xref{\task{cmult}}{sun95}{CMULT}}
\newcommand{\fitslist}{\xref{\task{fitslist}}{sun95}{FITSLIST}}
\newcommand{\fitsval}{\xref{\task{fitsval}}{sun95}{FITSVAL}}
\newcommand{\hislist}{\xref{\task{hislist}}{sun95}{HISLIST}}
\newcommand{\histogram}{\xref{\task{histogram}}{sun95}{HISTOGRAM}}
\newcommand{\makesnr}{\xref{\task{makesnr}}{sun95}{MAKESNR}}
\newcommand{\ndfcopy}{\xref{\task{ndfcopy}}{sun95}{NDFCOPY}}
\newcommand{\ndftrace}{\xref{\task{ndftrace}}{sun95}{NDFTRACE}}
\newcommand{\stats}{\xref{\task{stats}}{sun95}{STATS}}
\newcommand{\sub}{\xref{\task{sub}}{sun95}{SUB}}
\newcommand{\wcsmosaic}{\xref{\task{wcsmosaic}}{sun95}{WCSMOSAIC}}
% CCDPACK
\newcommand{\makemos}{\xref{\task{makemos}}{sun139}{MAKEMOS}}
% CUPID
\newcommand{\findback}{\xref{\task{findback}}{sun255}{FINDBACK}}
% Misc
\newcommand{\autophotom}{\xref{\task{autophotom}}{sun45}{AUTOPHOTOM}}
% Documents
\newcommand{\gaiasun}{\xref{\textbf{SUN/214}}{sun214}{}}
\newcommand{\kappasun}{\xref{\textbf{SUN/95}}{sun95}{}}
\newcommand{\picardsun}{\xref{\textbf{SUN/265}}{sun265}{}}
\newcommand{\pipelinesun}{\xref{\textbf{SUN/264}}{sun264}{}}
\newcommand{\smurfsun}{\xref{\textbf{SUN/258}}{sun258}{}}
% JAC
\newcommand{\Coulson}{\htmladdnormallink{Coulson}{http://www.jach.hawaii.edu/JACdocs/JCMT/SCD/SN/003/ }}
%FONT
%\renewcommand\familydefault{\sfdefault}
%\titleformat*{\section}{\LARGE\bfseries}
%\titleformat*{\subsection}{\large\bfseries}
% Chapter title in the header. This is using package fancyhdr.
\pagestyle{fancy}
\renewcommand{\sectionmark}[1]{\markboth{\stardocname---#1}{\stardocname---#1}}
\renewcommand{\subsectionmark}[1]{}
\renewcommand{\headrulewidth}{0pt}
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\fancyfoot[c]{}
\fancyfoot[r]{}
% Figure environment. Defined for latex2html to produce good quality
% graphics in the hypertext. It assumes that the files are
% encapsulated PostScript with extension .eps, and PNG with extension
% .png. The arguments are: #1 graphics filename without an extension;
% #2 figure environment location including brackets, or leave empty for
% none; #3 the includegraphics % qualifiers; #4 the label; and #5 the
% caption.
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\begin{figure}#2
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% Address twin (side-by-side) graphics in a similar fashion where the
% second argument is the second graphic, and the remaining arguments
% incremented by one slot save an extra argument #6 for the size of
% the gap between the two graphics, thus #7 is the caption.
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\newcommand{\myfigduo}[7]{
\label{#5} \htmladdimg{#1.png}\htmladdimg{#2.png}\\
\\
Figure: #7\\
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\end{htmlonly}
% ? End of document specific commands
% -----------------------------------------------------------------------------
% Title Page.
% ===========
\renewcommand{\thepage}{\roman{page}}
\begin{document}
\thispagestyle{empty}
% Latex document header.
% ======================
\begin{latexonly}
\textsc{Joint Astronomy Centre} \hfill \textbf{\stardocname}\\
{\large Science \& Technology Facilities Council}\\
{\large Starlink Project\\}
{\large \stardoccategory\ \stardocnumber}
\begin{flushright}
\stardocauthors\\
\stardocdate
\end{flushright}
\vspace{-4mm}
\rule{\textwidth}{0.5mm}
\vspace{5mm}
\begin{center}
{\Huge\textbf{\stardoctitle \\ [2.5ex]}}
{\LARGE\textbf{\stardocversion \\ [4ex]}}
{\Huge\textbf{\stardocmanual}}
\end{center}
\vspace{5mm}
% ? Add picture here if required for the LaTeX version.
% e.g. \includegraphics[scale=0.3]{filename.ps}
% ? End of picture
\begin{center}
\includegraphics[scale=0.4]{sc21_s2logo.eps}
\end{center}
\vspace{5mm}
\rule{\textwidth}{0.5mm}\\
\vspace{15mm}
% ? Heading for abstract if used.
\vspace{10mm}
\begin{center}
{\Large\textbf{Abstract}}
\end{center}
% ? End of heading for abstract.
\end{latexonly}
% HTML documentation header.
% ==========================
\begin{htmlonly}
\xlabel{}
\begin{rawhtml} <H1> \end{rawhtml}
\stardoctitle\\
\stardocversion\\
\stardocmanual
\begin{rawhtml} </H1> <HR> \end{rawhtml}
% ? Add picture here if required for the hypertext version.
% e.g. \includegraphics[scale=0.5]{filename.ps}
\includegraphics[width=90mm]{sc21_s2logo.eps}
% ? End of picture
\begin{rawhtml} <P> <I> \end{rawhtml}
\stardoccategory\ \stardocnumber \\
\stardocauthors \\
\stardocdate
\begin{rawhtml} </I> </P> <H3> \end{rawhtml}
\htmladdnormallink{Joint Astronomy Centre}
{http://www.jach.hawaii.edu}\\
\htmladdnormallink{Science \& Technology Facilities Council}
{http://www.scitech.ac.uk} \\
\begin{rawhtml} </H3> <H2> \end{rawhtml}
\htmladdnormallink{Starlink Project}{http://www.starlink.ac.uk/}
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\htmladdnormallink{\htmladdimg{source.gif} Retrieve hardcopy}
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\section{\xlabel{introduction}Introduction}
\label{sec:intro}
\subsection{\xlabel{using_guide}This Cookbook}
The Submillimetre Common User Bolometer Array-2 (SCUBA-2) is a
10,000-pixel bolometer camera for the 15-m James Clerk Maxwell
Telescope (JCMT). It has two arrays operating simultaneously to map
the sky in the atmospheric windows of 450 and 850$\mu$m.
This guide is designed to instruct SCUBA-2 users on the best ways to
reduce and visualise their data using \starlink\ packages,
\smurf \cite{smurf}, \Kappa \cite{kappa}, \gaia \cite{gaia} and \picard
\cite{picard}. This guide is {\em not} aimed at users of the
polarimeter (POL-2) or Fourier transform spectrometer (FTS-2). If you
have shared risk data (SRO) you should refer to the
\xref{SMURF SRO
Cookbook.}{sc19}{}\latex{\footnote{\texttt{http://www.starlink.ac.uk/docs/sc19.htx/sc19.html}}}
A brief description of the instrument and the observing modes is given
in Section~\ref{sec:s2}. Details on data acquisition and instructions
for examining raw data are given in Section~\ref{sec:raw}.
Section~\ref{sec:dimm} introduces the Dynamic Iterative Map-Maker
(DIMM). This section offers an in-depth description of the map-making
process and introduces the configuration files necessary to run the
reduction. The most important section will be Section~\ref{sec:maps};
this outlines all the steps that may be taken to produce your final
science map, including running the DIMM, applying the flux conversion
factor (FCF), co-adding multiple maps and estimating the noise.
Section~\ref{sec:tweak} discusses your options for tweaking the configuration
parameters when running the map-maker; this gives you added control
and flexibility over the map-making routine. Two worked examples
covering different science case are shown in Section~\ref{sec:eg} -- a
blank cosmology field (\S\ref{sec:cosmology}) and a galactic field
(\S\ref{sec:bright_ex}) with bright, extended emission. Section
\ref{sec:pipe} introduces the science pipeline and data retrieval from
the JCMT Science Archive. Data calibration is discussed in Section
\ref{sec:cal}, along with instructions for calculating your own FCF.
\subsection{\xlabel{computing}Before you start: Computing resources}
Before reducing SCUBA-2 data using the Dynamic Iterative Map-Maker, we
recommend you confirm your resources are sufficient for your type of
map.
For large-area maps it is important to process a full observation in a
single chunk -- see the text box on Page~\pageref{page:text} for a
discussion of the effects of chunking. For normal map-maker parameters
this implies that a machine of 96GB should be acceptable. It is
important that the memory is as fast as can be afforded as RAM speed
has a direct linear effect on processing time given that the
time-series data are continually being funneled through the CPU. For
blank field surveys, data that only use 850 microns, or smaller
regions of the sky you can usefully run the map-maker with less memory
and 32 to 64GB is reasonable depending on the specifics of your data
set. SMURF is multi-threaded so multiple cores do help although above
8 cores the price/performance gains tend to drop off.
If you have a very large machine (128GB and 24 cores) you can to run
two instances of the map-maker in parallel. Use the SMURF\_THREADS
environment variable to restrict each map-maker to half the available
cores.
An alternative option is to download your reduced data from the
\htmladdnormallink{JCMT Science Archive at
CADC.}{http://www3.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/jcmt/}
\latex{\footnote{\texttt{http://www3.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/jcmt/}}}
See Section~\ref{sec:pipe} for details on the science pipeline and
retrieving your data from CADC.
\subsection{\xlabel{software}Before you start: Software}
This manual only uses software from the \starlink\ package;
\smurf\ \cite{smurf}, \Kappa\ \cite{kappa}, \gaia\ \cite{gaia} and
\picard\ \cite{picard}.
Starlink software must be installed on your system, and Starlink aliases
and environment variables must be defined before attempting any
reduction of SCUBA-2 data detailed here. We also discuss the ORAC-DR
Data Reduction Pipeline\cite{oracdr} (hereafter just \oracdr) which is
an automated reduction pipeline, and \textsc{Picard} which is a similar
pipeline system for processing reduced data.
The Sub-Millimetre User Reduction Facility, or \textsc{Smurf}, contains the
Dynamic Iterative Map-Maker (DIMM) that will process raw SCUBA-2 data
into images (see \smurfsun). \textsc{Kappa} meanwhile is an application
package comprising general purpose commands for manipulating and
visualising NDF data (see \kappasun). Before starting any data
reduction you will want to initiate both \textsc{Smurf} and \textsc{Kappa}.
\begin{myquote}
\begin{verbatim}
% smurf
SMURF commands are now available -- (Version 1.4.0)
Type smurfhelp for help on SMURF commands.
Type 'showme sun258' to browse the hypertext documentation.
Type 'showme sc21' to view the SCUBA-2 map-making cookbook.
% kappa
KAPPA commands are now available -- (Version 1.13-9)
Type kaphelp for help on KAPPA commands.
Type 'showme sun95' to browse the hypertext documentation.
See the 'Release Notes' section of SUN/95 for details of the
changes made for this release.
\end{verbatim}
\end{myquote}
%\textbf{\textsc{Gaia}}\\
Image visualisation can be done with \gaia\ (see \gaiasun). \gaia\ is an
image and data-cube display and analysis tool which incorporates tools such
as source detection, 3\textsc{d} visualisation, photometry and the ability
to query and overlay on-line or local catalogues.
\begin{myquote}
\begin{verbatim}
% gaia 850_map.sdf
\end{verbatim}
\end{myquote}
Post-processing analysis is performed using \textsc{Picard}. \textsc{Picard} documentation can be
found at \htmladdnormallinkfoot{the ORAC-DR web page}{http://www.oracdr.org/oracdr/PICARD},
or at \picardsun. All \textsc{Picard} recipes follow the same structure and are run like so:
\begin{myquote}
\begin{verbatim}
% picard -recpars <recipe_params_file> RECIPE <input_files>
\end{verbatim}
\end{myquote}
where \param{<recipe\_param\_file>} is a text file containing the
relevant recipe parameters, \param{RECIPE} is the name of the recipe
to be run (note the caps) and \param{<input\_files>} is a list of
files to be run, which must be int the current directory, or a
directory defined by \param{ORAC\_DATA\_OUT}. A number of \textsc{Picard}
recipes will be demonstrated in Section~\ref{sec:maps}.
\textbf{Note:} The \textsc{Picard} recipes require all input files to have
the \texttt{.sdf} extension included; this is not the case for the
Starlink packages \textsc{Kappa} and textsc{Smurf}.
\clearpage
\section{\xlabel{scuba2_overview}SCUBA-2 Overview}
\subsection{\xlabel{scuba2}The instrument}
\label{sec:s2}
The SCUBA-2 bolometers are integrated arrays of superconducting
transition edge sensors (TESs) with a characteristic transition
temperature, $T_c$. In addition, each TES is ringed with a resistive
heater which can compensate for changes in sky power. The SCUBA-2
focal plane is kept at a base temperature slightly below $T_c$,
however a voltage is applied across each TES resistance to position
the bolometer at the transition temperature. From this point, any
increase of temperature on the bolometers (e.g. from an astronomical
signal) will increase the TES resistance and heat it up. This causes a
drop in current and therefore a drop in temperature making the system
self-regulating.
For properly performing bolometers, the change in current through the
TES is proportional to the change in resistance, with the response
calibrated using flat-field observations (described below). This
changing current generates a magnetic field which is amplified by a
chain of superconducting quantum interference devices (SQUIDs). This
induces a feedback current which is proportional to the current
flowing through the TES, and it is this feedback current that is
recorded during data acquisition.
Before science data can be taken the system must be optimised. These
`setups' are performed after slewing to the azimuth of the source,
where the SQUID, TES and heater biases are set to pre-determined
nominal values, in order to position the bolometers in the middle of
the transition range.
This is followed by a 10-second noise observation carried out while
the shutter is still closed. The shutter then opens onto the sky, and
as it does so the gradual increase in sky power hitting the array is
compensated for by a decrease in the resistive heater power via a
servo loop designed to keep the TES output constant. This acts to keep
the bolometers positioned at the centre of the transition range and is
known as \textbf{heater tracking}.
The responsivity of the bolometers will change slightly between the
dark and the sky; therefore, once the shutter is fully open a fast
\textbf{flat-field} observation is carried out to recalibrate them.
\textbf{A flat-field measures the responsivity of each bolometer to
changing sky power}. It does this by utilising the resistance heaters
which are ramped up and down around the nominal value. The change in
current through the TES is then recorded for each bolometer giving a
measure of its responsivity. The flat field solution is then the
inverse linear gradient of the current as a function of heater power.
At this point bolometers with responsivities above or below a
threshold limit are rejected, along with bolometers which display a
non-linear response or have a poor S/N. A second flat-field is
performed at the end of an observation so bolometers whose
responsivity has changed over the course of the observation can be
flagged.
For full details of the array setup and operation see Holland et al.
(2012) \cite{s2main}.
\begin{figure}[t!]
\begin{center}
\includegraphics[width=0.4\linewidth]{sc21_450array.eps}
\hspace{1cm}
\includegraphics[width=0.4\linewidth]{sc21_850array.eps}
\label{fig:arrays}
\caption{\small The layout of the arrays at 450$\mu$m (left) and
850$\mu$m (right). The labels denote the name assigned to each
sub-array. Raw data files are generated separately for each sub-array
and must be co-added. This figure was made my running \wcsmosaic\ on
raw files from each sub-array.}
\end{center}
\end{figure}
\subsection{\xlabel{obs_modes}Observing modes}
\label{sec:mmodes}
Two observing modes are offered for SCUBA-2 -- \textsc{daisy} and
\textsc{pong}. As much of the work SCUBA-2 will be doing involves
large area mapping, both observing modes are scan patterns. Your
choice depends on the size of the area you wish to map, where you
would like your integration time concentrated and the degree of
extended emission you wish to recover
In contrast to SCUBA which observed an area of sky while
simultaneously chopping, SCUBA-2 removes atmospheric noise in the data
processing stage (Holland et al. 2012) \cite{s2main}. The power spectrum
of data taken by SCUBA-2 has a $1/f$ noise curve at lower frequencies. To
ensure astronomical signals are far away from this $1/f$ noise, fast
scanning speeds are required.
In order to disentangle source structure from other
slowly varying signals (e.g. extinction, sky noise, $1/f$ noise), the
scan pattern must pass across each region of the map from different
directions and at different times. The scan patterns themselves, along
with the associated parameters (velocity and scan-spacing), have been
designed and optimised to meet both these criteria.
\\ \\
\begin{minipage}[t]{0.12\linewidth}
\textbf{PONG}
\end{minipage}
\begin{minipage}[t]{0.85\linewidth}\textsc{pong} maps are the scan
strategy for covering large areas. The default options allow for 3
sizes -- 900~arcsec, 1800~arcsec and 3600~arcsec. A single \textsc{pong} map is
a square of these dimensions and the telescope fills in the square by
bouncing off the edge of the area. To ensure an even sky background it
is recommended a minimum of 3, but preferably more than 5,
\textsc{pong} maps are included in a single observation with a
rotation introduced between each one. In this way a circular pattern
is built up, (see the right hand panel of Figure~\ref{fig:scan}), with
a diameter equal to your requested map size.
\vspace{0.2cm}\\
To recover large scale extended structure you are advised to use
larger \textsc{pong} maps which scan at a higher rate. This option is
in preference to tiling multiple smaller maps. Ultimately it is the
size of the SCUBA-2 field-of-view that determines the sensitivity to
large scale structure.
\end{minipage}
\\ \\ \\
\begin{minipage}[t]{0.12\linewidth}
\textbf{DAISY}
\end{minipage}
\begin{minipage}[t]{0.85\linewidth}
\textsc{daisy} maps are the option for point-like or compact sources
($<$3\,arcmin) by maximising the exposure time on the centre of the
image. The telescope moves at a constant velocity in a `spirograph'
pattern that has the advantage of keeping the source on the array
throughout the observation. This is shown in the top panel of Figure
\ref{fig:scan}.
\end{minipage}
\myfig{sc21_wayne_scan}{[b!]}{width=0.9\linewidth}{fig:scan}{
Telescope track in offsets of azimuth and elevation for the SCUBA-2
observing patterns. \textbf{Top Left}: A single rotation of the
\textsc{daisy} pattern; \textbf{Top Right}: Multiple rotations of
the \textsc{daisy} pattern for a typical map based on a 180-arcsec
demanded diameter; \textbf{Bottom Left}: A single \textsc{pong}
pattern; \textbf{Bottom Right}: Multiple rotations of the
\textsc{pong} pattern for a typical map based on an 1800-arcsec
demanded map size. The scan pattern for your observation can be
visualised like this with \topcat\ using the output from \jcmtstate.
See Section~\ref{sec:exam} for more details. Figure taken from
Holland et al. (2012).}
\clearpage
\section{\xlabel{data_files}Raw SCUBA-2 Data}
\label{sec:raw}
A normal science observation will follow the following sequence.
\vspace{-2mm}
\begin{itemize}\itemsep-0.5em
\item Noise
\item Flat-field
\item Multiple Science scans
\item Flat-field
\end{itemize}
\vspace{-2mm}
The \param{SEQ\_TYPE} parameter in the FITS header may be used to
identify the nature of each scan (see Section~\ref{sec:fitsheader}).
When you access you data either at the JCMT or by downloading from the
\htmladdnormallink{Science Archive}{http://www3.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/jcmt/}
\begin{latexonly}
\footnote{http://www3.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/jcmt/}
\end{latexonly}
you will get \emph{all} of the files listed above. Later when you
reduce your data using the map-maker you will include \emph{all} of
the files (noise + flat-fields + science).
Shown below is a list of the raw files for a single sub-array (in this
case s8a) for a short calibration observation. The first file is the
short, dark noise; the second and last scans are the fast flat-field
observations which occur after the shutter open to the sky at the
start of the observation and closes at the end (note the identical
file size); all of the scans in between are science. The SCUBA-2 data
acquisition (DA) system writes out a data file every 30 seconds; each
of which contains 23MB of data. The only exception is the final science
scan which will usually be smaller (7.3MB in the example below), typically
requiring less than 30 seconds of data to complete the observation.
\begin{myquote}
\begin{verbatim}
-rw-r--r-- 1 jcmtarch jcmt 6.2M Jul 19 21:33 s8a20120720_00030_0001.sdf
-rw-r--r-- 1 jcmtarch jcmt 9.6M Jul 19 21:34 s8a20120720_00030_0002.sdf
-rw-r--r-- 1 jcmtarch jcmt 23M Jul 19 21:34 s8a20120720_00030_0003.sdf
-rw-r--r-- 1 jcmtarch jcmt 23M Jul 19 21:35 s8a20120720_00030_0004.sdf
-rw-r--r-- 1 jcmtarch jcmt 23M Jul 19 21:36 s8a20120720_00030_0005.sdf
-rw-r--r-- 1 jcmtarch jcmt 23M Jul 19 21:36 s8a20120720_00030_0006.sdf
-rw-r--r-- 1 jcmtarch jcmt 7.3M Jul 19 21:36 s8a20120720_00030_0007.sdf
-rw-r--r-- 1 jcmtarch jcmt 9.6M Jul 19 21:37 s8a20120720_00030_0008.sdf
\end{verbatim}
\end{myquote}
\textbf{Note:} All of these files are written out 8 times for each of the
8 sub-arrays.
The main data arrays of each file are cubes, with the first two
dimensions enumerating columns and rows, and the third time slices
(sampled at 200\,Hz).
Raw SCUBA-2 data comes in uncalibrated units. The first calibration
step is to scale the raw data to units proportional to picowatts (pW)
by applying the flat-field solution. From there the data must be
scaled by the flux conversion factor (FCF) to give units of janskys
(Jy).
The first step is applied internally by the map-maker but can be done
manually when examining the raw data -- see Section~\ref{sec:concat}.
The second step must be done manually with the instructions given in
Section~\ref{sec:cmult}.
\subsection{\xlabel{examine}Examining raw data}
\label{sec:exam}
In this section a number of procedures are described for visualising
and assessing raw data files. These steps are not a necessary part of
the data reduction process and do not concern the iterative map-maker.
However, there are reason you may wish to examine your raw data in
greater depth. The most likely motivation is unusual result from the
map-maker. These might be higher noise than anticipated, patterns in
the data or inconsistent noise across multiple tiles. This section
will help you get to the bottom of any issues concerning raw data.
\subsubsection{\xlabel{concat}Concatenate \& apply a flat-field}
\label{sec:concat}
Since SCUBA-2 data for a given sub-array are broken into multiple
30-second scans by the data acquisition (DA) system, it is useful to
concatenate the data into a single file. The \smurf\ task \concat\ can
be used for this operation. The example below combines all of the
files associated with observation 8 for the s8a array into a single
file called \texttt{s8a20120725\_00058\_con}.
\begin{myquote}
\begin{verbatim}
% sc2concat 's8a20120725_0008*.sdf' s8a20120725_0008_con
\end{verbatim}
\end{myquote}
\task{sc2concat} will automatically filter out any dark or flat-field
observations, so that the concatenated file contains only the science
data. Be careful when concatenating a very long observation since the
output file may be too large to reasonably handle. Fifteen minute
chunks (30 files) should be sufficient.
\task{sc2concat} applies the flat-field by default (although it can be
disabled using the `noflat' option on the command-line).
The flat-field can also be applied manually using the \flatfield\ command.
\begin{myquote}
\begin{verbatim}
% flatfield 's8a20120701_0008*.sdf' '*_flat'
\end{verbatim}
\end{myquote}
Here, the output will be a flat-fielded version of each science scan
in observation number 8; the file names will be the original input
names with \_flat appended to them.
As a rule of thumb, you should apply the flat-field to your data
before examining it. \textbf{You do not need to apply the flat-field
prior to reducing your data with the map-maker as it will be applied
internally.}
\subsubsection{\xlabel{header}Headers and file structure}
\label{sec:fitsheader}
There are two \Kappa\ tasks which are extremely useful for examining
your data: \fitslist\ and \ndftrace, which can be used to view the
FITS headers and dimensions of the data.
\\ \\
\begin{minipage}[t]{0.12\linewidth}
\textbf{fitslist}
\end{minipage}
\begin{minipage}[t]{0.85\linewidth}This lists the FITS header information
for any file (raw or reduced). This extensive list includes dates \& times,
source name, scan type, pattern and velocity, size of the map, exposure
time, start and end elevation, opacity and the temperature of the
instrument. An example is given below:
\begin{myquote}
\begin{verbatim}
% fitslist s8a20120720_00030_000\*.sdf | grep SEQ_TYPE
\end{verbatim}
\end{myquote}
If you already know the name of the parameter you want to view you can
use the \fitsval\ command instead, e.g.
\texttt{\% fitsval file.sdf TAU225ST}.\\
\end{minipage}
\begin{minipage}[t]{0.12\linewidth}
\textbf{ndftrace}
\end{minipage}
\begin{minipage}[t]{0.85\linewidth}
\task{ndftrace} displays the attributes of the data structure. This will tell
you the units of the data, pixel bounds, dimensions and axis assignations.\\
\end{minipage}
\\ \\
Full details of these commands can be found in the \xref{\textsc{Kappa} manual}{sun95}{}.
\begin{latexonly}
\begin{figure}[ht!]
\begin{center}
\begin{fmpage}{0.95\linewidth}
\vspace{0.2cm}
\textbf{ Topcat Example}
\vspace{0.5cm}
\begin{minipage}[c]{0.6\linewidth}
\begin{myquote}
\begin{verbatim}
% topcat -f tst 20120720_30.tst
\end{verbatim}
\end{myquote}
\end{minipage}
\hspace{0.3cm}
\begin{minipage}[c]{0.32\linewidth}
Load the file into \topcat\ with this command.
\end{minipage}
\vspace{0.5cm}
\begin{minipage}[c]{0.6\linewidth}
\centering
\includegraphics[width=0.95\textwidth]{sc21_topcat1.eps}
\end{minipage}
\hspace{0.3cm}
\begin{minipage}[c]{0.32\linewidth}
Once the file has loaded into \topcat, select the scatter plot option
from the menu bar across the top of the window.
\end{minipage}
\vspace{0.5cm}
\begin{minipage}[c]{0.6\linewidth}
\centering
\includegraphics[width=0.75\textwidth]{sc21_topcat2.eps}
\vspace{0.2cm}
\end{minipage}
\hspace{0.3cm}
\begin{minipage}[c]{0.32\linewidth}
When the scatter plot has loaded, you should adjust the $X$-axis and
$Y$-axis values to DRA and DDEC respectively to display the scan pattern.
If you are interested in seeing how any of the variables change over time,
select the the $X$ Axis to be either Id or RTS\_NUM.
\end{minipage}
\end{fmpage}
\end{center}
\caption{\small \topcat\ example demonstrating how to display the scan pattern
for an observation.}
\label{fig:topcat}
\end{figure}
\end{latexonly}
\subsubsection{\xlabel{scan_pat}Displaying scan patterns}
\label{sec:scan}
The movement of the telescope throughout a scan (as well as other
state information) is stored in the \texttt{MORE.SMURF.JCMTSTATE}
extension of a data file. The \smurf\ task \jcmtstate\ converts this
information into a simple ASCII tab-separated table.
\begin{myquote}
\begin{verbatim}
% jcmtstate2cat s8a20120701_00008_*.sdf > state.tst
\end{verbatim}
\end{myquote}
The \texttt{-h} option to \task{jcmtstate} can be used to find more
information on the command. In particular, multiple files can be supplied
to the command using standard shell wild cards. If you have already
concatenated your data you can simply input the single concatenated
file. \textbf{It may be useful to view the scan pattern for your
observation, particularly for maps taken at high elevations, to ensure
the pattern completed successfully.}
This catalogue can be loaded into \topcat\ for plotting, making sure
to specify the TST format during loading.
\begin{myquote}
\begin{verbatim}
% topcat -f tst state.tst
\end{verbatim}
\end{myquote}
Example of scan patterns displayed with \topcat\ can be seen in
Figure~\ref{fig:scan}. Detailed instruction on how to display the scan
pattern for your observation are given in Figure~\ref{fig:topcat}. All
of the time-varying header values are available for plotting. Other
values include the azimuth and elevation offsets (DAZ \& DEL), the WVM
and 225\,GHz opacity values, and the instrument temperatures (e.g.
SC2\_FPUTEMP gives the temperature of the focal plane).
% The minipages used for the dvi version give latex2html problems.
\begin{htmlonly}
\label{fig:topcat} \htmladdimg{sc21_topcat_example.png}
\\
Figure: \topcat\ example demonstrating how to display the scan