From 9fe1c1d07c403cc34c4e5b197d6e0212afd64cfe Mon Sep 17 00:00:00 2001 From: "Malcolm J. Currie" Date: Sat, 15 Sep 2012 22:17:02 -1000 Subject: [PATCH] docs: SC/21---remove duplicate links from a screen's worth of hypertext. (cherry picked from commit 8ab2e2021dfd471486ec565cc48649c19ef8e32c) --- docs/sc/021/sc21.tex | 92 ++++++++++++++++++++++---------------------- 1 file changed, 46 insertions(+), 46 deletions(-) diff --git a/docs/sc/021/sc21.tex b/docs/sc/021/sc21.tex index e2fac04d77d..7d51a70959e 100644 --- a/docs/sc/021/sc21.tex +++ b/docs/sc/021/sc21.tex @@ -533,19 +533,19 @@ \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\ must be installed on your system, and \starlink\ aliases +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 \picard\ which is a similar +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). \Kappa\ meanwhile is an application +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 \smurf\ and \Kappa. +reduction you will want to initiate both \textsc{Smurf} and \textsc{Kappa}. \begin{myquote} \begin{verbatim} % smurf @@ -578,10 +578,9 @@ \subsection{\xlabel{software}Before you start: Software} \end{verbatim} \end{myquote} -%\textbf{\textsc{Picard}}\\ -Post-processing analysis is performed using \picard. \picard\ documentation can be +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 \picard\ recipes follow the same structure and are run like so: +or at \picardsun. All \textsc{Picard} recipes follow the same structure and are run like so: \begin{myquote} \begin{verbatim} % picard -recpars RECIPE @@ -591,12 +590,12 @@ \subsection{\xlabel{software}Before you start: Software} relevant recipe parameters, \param{RECIPE} is the name of the recipe to be run (note the caps) and \param{} 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 \picard\ +directory defined by \param{ORAC\_DATA\_OUT}. A number of \textsc{Picard} recipes will be demonstrated in Section~\ref{sec:maps}. -\textbf{Note:} The \picard\ recipes require all input files to have +\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 \Kappa\ and \smurf. +Starlink packages \textsc{Kappa} and textsc{Smurf}. \clearpage \section{\xlabel{scuba2_overview}SCUBA-2 Overview} @@ -831,13 +830,13 @@ \subsubsection{\xlabel{concat}Concatenate \& apply a flat-field} % sc2concat 's8a20120725_0008*.sdf' s8a20120725_0008_con \end{verbatim} \end{myquote} -\concat\ will automatically filter out any dark or flat-field +\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. -\concat\ applies the flat-field by default (although it can be +\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. @@ -886,11 +885,11 @@ \subsubsection{\xlabel{header}Headers and file structure} \textbf{ndftrace} \end{minipage} \begin{minipage}[t]{0.85\linewidth} -\ndftrace\ displays the attributes of the data structure. This will tell +\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{\Kappa\ manual}{sun95}{}. +Full details of these commands can be found in the \xref{\textsc{Kappa} manual}{sun95}{}. \begin{latexonly} \begin{figure}[ht!] @@ -965,9 +964,9 @@ \subsubsection{\xlabel{scan_pat}Displaying scan patterns} \end{verbatim} \end{myquote} -The \texttt{-h} option to \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 +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 @@ -1027,7 +1026,7 @@ \subsubsection{\xlabel{display_cube}Displaying time-series data} in the `Display image sections of a cube' dialogue -- this can be dragged across the spectrum to scroll through the time-slices.} -Use the \starlink\ application \gaia\ to visualise the bolometer time +Use the \starlink\ application \textsc{Gaia} to visualise the bolometer time series data (or indeed \emph{any} SCUBA-2 data file). This is initiated simply typing \texttt{gaia} into a terminal. @@ -1037,7 +1036,7 @@ \subsubsection{\xlabel{display_cube}Displaying time-series data} \end{verbatim} \end{myquote} -Loading a file in \gaia\ produces two windows (see +Loading a file in \textsc{Gaia} produces two windows (see Figure~\ref{fig:gaia_main}). The main window shows a map of bolometer values at a given point in time. The time slice displayed may be changed by scrolling through the time axis. This is done in the second @@ -1058,8 +1057,8 @@ \subsubsection{\xlabel{display_cube}Displaying time-series data} need to change the auto cut and (depending on your preference) the colour scheme -- both are controlled by buttons on the sidebar. -See the \xref{\gaia\ manual}{sun214}{} for full -details.\footnote{http://docs.jach.hawaii.edu/star/sun214.htx/sun214.html} +See the \xref{\textsc{Gaia} manual}{sun214}{} for full +details.\latex{\footnote{http://docs.jach.hawaii.edu/star/sun214.htx/sun214.html}} \clearpage \subsection{\xlabel{regrid_map}Regridding data into a map} @@ -1069,7 +1068,7 @@ \subsection{\xlabel{regrid_map}Regridding data into a map} coordinates using the \smurf\ \makemap\ task in regrid mode. This involves no processing of the data. The following command produces a map from the raw concatenated data; unlike the iterative mode of -\makemap\ described in the next chapter, no configuration file is +\task{makemap} described in the next chapter, no configuration file is required. \begin{myquote} \begin{verbatim} @@ -1961,7 +1960,7 @@ \subsection{\xlabel{running_dimm}Running the map-maker} Section~\ref{sec:config}. As an input to the map-maker, any of the standard \smurf\ -configuration files can be called directly from the \starlink\ path +configuration files can be called directly from the Starlink path with \texttt{\^\,\$STARLINK\_DIR/share/smurf/dimmconfig*.lis}. Alternatively, a local copy can be made and called with \texttt{\^\,dimmconfig*.lis}. Details of how to edit any of the @@ -2305,13 +2304,13 @@ \subsection{\xlabel{coadd}Co-adding multiple maps} in the list, and with a suffix \texttt{\_mos}. There are a number of options associated with -\param{MOSAIC\_JCMT\_IMAGES} (see the \picard\ manual for a full +\param{MOSAIC\_JCMT\_IMAGES} (see the \textsc{Picard} manual for a full description). However, the main one is choosing between \wcsmosaic\ (default) and the \ccdpack\ option \makemos\ for the combination -method. For more information on \makemos\ and advice on choosing the +method. For more information on \task{makemos} and advice on choosing the best method see SUN/139. -An example parameter file like the one below chooses \makemos\ using a +An example parameter file like the one below chooses \task{makemos} using a 3-$\sigma$ clipping threshold. \begin{myquote} \begin{verbatim} @@ -2374,8 +2373,9 @@ \subsection{\xlabel{crop}Cropping your map} data will be lost of you chose a square or rectangular map. The output from \param{CROP\_JCMT\_IMAGES} is a file with the suffix -\texttt{\_crop}. Full details of this recipe can be found in the \picard\ -manual\footnote{http://www.oracdr.org/oracdr/PICARD}. +\texttt{\_crop}. Full details of this recipe can be found in the +\htmladdnormallink{\textsc{Picard} website}{http://www.oracdr.org/oracdr/PICARD} +\latex{\footnote{http://www.oracdr.org/oracdr/PICARD}}. \subsection{\xlabel{noise}Calculating the noise} @@ -2408,7 +2408,7 @@ \subsection{\xlabel{noise}Calculating the noise} \\ \\ \textbf{Visualising the error map}\\ You can plot the noise or error component of your map using the -\Kappa\ command \histogram. This allows you to visualise the +\textsc{Kappa} command \histogram. This allows you to visualise the distribution with more ease. Again the \param{comp=err} option is used. \begin{myquote} @@ -2421,11 +2421,11 @@ \subsection{\xlabel{noise}Calculating the noise} \myfigduo{sc21_noihist}{sc21_crl2688_err}{}{width=0.47\linewidth}{fig:bfnoi}{3mm}{ The error map of the cropped make-map output viewed in two different ways. \textbf{(left)} Histogram of the noise component created using - the \Kappa\ command \histogram. \textbf{(right)} Opened with \gaia.} + the \textsc{Kappa} command \task{histogram}. \textbf{(right)} Opened with \gaia.} It is also useful to view the error map itself to check its uniformity. To do this you will need to copy out the error component -of your map into a new file; this can be done with the \Kappa\ command +of your map into a new file; this can be done with the \textsc{Kappa} command \ndfcopy. \begin{myquote} \begin{verbatim} @@ -2472,8 +2472,8 @@ \subsection{\xlabel{match_filter}Point source extraction -- Applying a matched This is a fairly common technique used throughout the extra-galactic sub-millimetre community to identify potential sources. A full description of the matched filter principle is given in -Appendix~\ref{app:mf}, while the \picard\ manual gives full details of -all the available parameters. +Appendix~\ref{app:mf}, while the \textsc{Picard} manual gives full details +of all the available parameters. \clearpage \section{\xlabel{tweak}Tweaking the Configuration File} @@ -2598,7 +2598,7 @@ \section{\xlabel{tweak}Tweaking the Configuration File} \begin{htmlonly} \label{fig:stack} \htmladdimg{sc21_view_itermaps.png} \\ \\ - Figure: Example using the \smurf\ command \texttt{stackframes} and + Figure: Example using the \textsc{Smurf} command \texttt{stackframes} and \gaia\ to view the `itermaps' map for each iteration. \end{htmlonly} @@ -2784,7 +2784,7 @@ \subsection{\xlabel{Cosmology}Deep point-source maps} \end{myquote} \textbf{(2) Combining the maps}\\ -These three maps are then combined using the \picard\ recipe +These three maps are then combined using the \textsc{Picard} recipe \texttt{MOSAIC\_JCMT\_IMAGES}. In this case we accept the default of \wcsmosaic\ mosaicking and nearest-neighbour pixel spreading and so do not supply a parameter file. @@ -2795,7 +2795,7 @@ \subsection{\xlabel{Cosmology}Deep point-source maps} \end{myquote} The output map, \texttt{cosmo2\_mos.sdf}, is shown in the left-hand panel of Figure~\ref{fig:cosmomap}. The advantage of using the -\picard\ recipe over standalone \Kappa\ commands is that the exposure +\textsc{Picard} recipe over standalone \Kappa\ commands is that the exposure time is also propagated correctly to the output mosaic (it is stored in the \texttt{MORE.SMURF.EXP\_TIME} extension). \\ @@ -2851,7 +2851,7 @@ \subsection{\xlabel{Cosmology}Deep point-source maps} \textbf{(5) Making a SNR map}\\ Finally, we need to find sources. The filtered map contains a VARIANCE component, so it is easy to produce a S/N map using the -\Kappa\ task \makesnr: +\textsc{Kappa} task \makesnr: \begin{myquote} \begin{verbatim} % makesnr cosmo2_mos_mf_crop cosmo2_mos_mf_crop_snr @@ -3216,15 +3216,15 @@ \subsection{\xlabel{fcf}Flux conversion factors (FCF)} relative performance of the instrument from night to night. The noise equivalent flux density (NEFD) is a measure of the instrument sensitivity, and while not discussed here, is also produced by the -\picard\ recipe shown here. For calibration of primary and secondary +\textsc{Picard} recipe shown here. For calibration of primary and secondary calibrators, the FCFs and NEFDs have been calculated as follows: \begin{enumerate} -\item{The \picard\ recipe \drrecipe{SCUBA2\_FCFNEFD} takes the reduced +\item{The \textsc{Picard} recipe \drrecipe{SCUBA2\_FCFNEFD} takes the reduced map, crops it, and runs background removal. Surface-fitting - parameters are changeable in the \picard\ parameter file.} + parameters are changeable in the \textsc{Picard} parameter file.} \item{It then runs the \Kappa\ \beamfit\ task on the specified point - source. The \beamfit\ task will estimate the peak (uncalibrated) + source. The \task{beamfit} task will estimate the peak (uncalibrated) flux density and the FWHM. The integrated flux density within a given aperture (30-arcsec radius default) is calculated using \photom\ \autophotom. Flux densities for calibrators such as Uranus, @@ -3235,7 +3235,7 @@ \subsection{\xlabel{fcf}Flux conversion factors (FCF)} and \texttt{FLUX\_850.MYSRC = 0.005} (where the values are in Jy), for example. } - An example of a \picard\ parameter file (used for reduction of the + An example of a \textsc{Picard} parameter file (used for reduction of the 850$\mu$m calibrators) is shown here: \begin{myquote} @@ -3320,7 +3320,7 @@ \subsection{\xlabel{ownfcf}Calculating your own FCF} This recipe will produce a log file log.fcfnefd which records the FCFs mentioned above along with a third (\fcfm\ which is not currently recommended). These can then be applied to your data using -\texttt{cmult} (see Section~\ref{sec:cmult}). +\cmult\ (see Section~\ref{sec:cmult}). \end{enumerate} \subsection{\xlabel{extinction}Extinction correction} @@ -3439,7 +3439,7 @@ \section{\xlabel{app_clean}Cleaning the Raw Data} \label{app:clean} You can use the \smurf\ task \clean\ to help inspect time-series. -\clean\ can be used to do two basic tasks in one go: concatenate data +\task{sc2clean} can be used to do two basic tasks in one go: concatenate data (with or without applying a flatfield); and cleaning (fix up steps and spikes, remove the means, filter, remove common-mode etc.). It uses the same configuration files as the iterative map-maker (though @@ -3486,7 +3486,7 @@ \section{\xlabel{app_clean}Cleaning the Raw Data} Part of the reason the signals look the same is because they have been flatfielded. You can turn off flatfielding using the \texttt{noflat} -option to \clean, and you should then see that all of the detector +option to \task{sc2clean}, and you should then see that all of the detector amplitudes vary. Another very useful option is to remove the common signal observed by @@ -3575,7 +3575,7 @@ \section{\xlabel{matchedfilter}SCUBA-2 Matched Filter} image. The same operation is also applied to the PSF to estimate the effective shape of a point-source in this background-subtracted map. -Before running \picard\, a simple parameters file called \texttt{smooth.ini} +Before running \textsc{Picard}, a simple parameters file called \texttt{smooth.ini} may be created. \begin{myquote} \begin{verbatim}