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docs: SC/21---Reorder more graphics so that they appear in the correc…
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…t locations in the hypertext.

(cherry picked from commit 441ac6e)
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MalcolmCurrie committed Sep 17, 2012
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56 changes: 28 additions & 28 deletions docs/sc/021/sc21.tex
Expand Up @@ -1037,20 +1037,6 @@ \subsubsection{\xlabel{scan_pat}Displaying scan patterns}
\subsubsection{\xlabel{display_cube}Displaying time-series data}
\label{sec:gaiacube}

\myfig{sc21_gaia1}{[h!]}{width=\linewidth}{fig:gaia_main}{
Initial \gaia\ windows displayed upon loading a data cube.
The main window in the left shows a map of bolometer values at a fixed
sample in time. You may have to zoom in multiple times by clicking the
`Z' icon. On the right-hand side, the `Display image sections of a cube'
dialogue enables the user to navigate the time axis.}

\myfig{sc21_gaia2}{[h!]}{width=0.8\linewidth}{fig:gaia_spec}{
The \emph{Spectral Plot} window displaying its time-varying
signal, appears automatically once a bolometer is clicked in the main window.
The vertical red line indicates the time slice that is currently selected
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 \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.
Expand All @@ -1069,11 +1055,25 @@ \subsubsection{\xlabel{display_cube}Displaying time-series data}
plane' slider towards the top of this window may be moved to display
different time slices in the main window.

\myfig{sc21_gaia1}{[h!]}{width=\linewidth}{fig:gaia_main}{
Initial \gaia\ windows displayed upon loading a data cube.
The main window in the left shows a map of bolometer values at a fixed
sample in time. You may have to zoom in multiple times by clicking the
`Z' icon. On the right-hand side, the `Display image sections of a cube'
dialogue enables you to navigate the time axis.}

A third window will appear when you click on a bolometer -- the
`Spectral plot'. This shows an automatically scaled plot of the raw
time stream of data for that given bolometer. It will be overridden
when you click on a different bolometer.

\myfig{sc21_gaia2}{[h!]}{width=0.8\linewidth}{fig:gaia_spec}{
The \emph{Spectral Plot} window displaying its time-varying
signal, appears automatically once a bolometer is clicked in the main window.
The vertical red line indicates the time slice that is currently selected
in the `Display image sections of a cube' dialogue -- this can be dragged
across the spectrum to scroll through the time-slices.}

A second way to scroll through the time axis is to click and drag the
vertical red bar on the `Spectral plot' window. As you do so array
shown in the main window will automatically update.
Expand Down Expand Up @@ -3006,7 +3006,12 @@ \subsection{\xlabel{Galactic}Extended galactic sources}
The final mask is shown in the right-panel of \cref{Figure}{fig:mask}{this figure},
note how is encompasses more emission and has softer edges than the
first threshold map.
\\ \\
\\
\myfigduo{sc21_gal_mask1}{sc21_gal_mask2}{t!}{width=0.475\linewidth}{fig:mask}{2mm}{
\textbf{(left)} The initial mask created by thresholding 850map\_snr
to 3$\sigma$. \textbf{(right)} Second mask made by thresholding the
smoothed map to 0.02.}

\textbf{(3) Rerunning the map-maker with an external mask supplied}\\
As a last step the map is re-made with this mask supplied as an external
file. For this run we apply the additional parameters in a
Expand Down Expand Up @@ -3034,15 +3039,18 @@ \subsection{\xlabel{Galactic}Extended galactic sources}
\end{verbatim}
\end{myquote}

\myfigduo{sc21_gal_mask1}{sc21_gal_mask2}{t!}{width=0.475\linewidth}{fig:mask}{2mm}{
\textbf{(left)} The initial mask created by thresholding 850map\_snr
to 3$\sigma$. \textbf{(right)} Second mask made by thresholding the
smoothed map to 0.02.}

\textbf{(4) Cropping the map}\\
We can now crop the map to remove the noisy edges using the \picard\ recipe
\drrecipe{CROP\_JCMT\_IMAGES}. To determine what to trim we can look
at the exposure-time image with \gaia.

\myfig{sc21_gal_exptime}{[th!]}{width=0.7\linewidth}{fig:exptime}{
The exposure-time image of the science map from
Figure~\ref{fig:galmakemap}. You can right-click and drag the mouse
between two points to measure the distance. Here we see the exposure
time dropping off sharply at a radius of 30~arcmin. A non-default
colour scale has been chosen to illustrate the morphology.}

\cref{Figure}{fig:exptime}{The exposure-time image} shows a sharp drop
off at a radius of 30~arcmin. We can thus specify a parameter file like so:

Expand All @@ -3063,14 +3071,6 @@ \subsection{\xlabel{Galactic}Extended galactic sources}
(\cref{Figure}{fig:galmakemap}{first map}),
slightly more of the faint extended emission is apparent.

\myfig{sc21_gal_exptime}{[th!]}{width=0.7\linewidth}{fig:exptime}{
The exposure-time image of the science map from
Figure~\ref{fig:galmakemap}. You can right-click and drag the mouse
between two points to measure the distance. Here we see the exposure
time dropping off sharply at a radius of 30~arcmin. A non-default
colour scale has been chosen to illustrate the morphology.}


One of the challenges facing this type of reduction is the need to
account for both faint extended structure and very bright sources in
the same map. You may find some degree of bowling remains around the
Expand Down

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