\thesischapter{Instrumentation}
\label{instru}

The chromosphere has long been studied from ground-based telescopes in optical wavelengths, especially the strong Fraunhofer lines. This has the benefits of being relatively cheap and simple to implement, with {\em in situ} corrections easy to perform. Advances in both telescope technology and post-processing has also improved the quality of data from ground-based telescopes. However space-based telescopes will always have the advantages of being able to provide long-duration observations, free of any atmospheric distortion, in all wavelengths. The work in this thesis utilises both ground- and space- based observations, with the aim of maximising the respective advantages of each.

\section{Richard B. Dunn Solar Telescope}
\begin{figure}
\begin{center}
\epsfig{figure=vttblue4.eps,width=4in}
\caption[The Richard B. Dunn Solar Telescope]{The Richard B. Dunn solar telescope. The large tower houses the optic benches, and half of the telescope is underground}
\label{DST}
\end{center}
\end{figure}
\subsection{General Description}

At an altitude of 2804~m, the National Solar Observatory{\footnotemark[1]} at Sacramento Peak is in a prime location for high-resolution imaging of the Sun. The Dunn Solar Telescope (Figure~\ref{DST}) at Sacramento Peak was originally dedicated the Vacuum Tower Telescope in 1969 and rededicated in 1998 after Richard Dunn who was the main driving force behind it. Its basic design consists of a large 41~m tower with a 0.76~m window at the top. Sunlight is reflected by a pair of movable 1.1~m mirrors down a 1.2~m diameter, 100~m long evacuated tube. Light reflects off a concave 1.6~m main mirror at the bottom of the telescope, 57~m below ground, and then back up to the observing room. The two mirrors at the top act as a heliostat, therefore compensating for proper motion. The entire set-up hangs from a low-friction tank that contains about 10 tons of mercury and hence it is easy to rotate the 200 tons of tube and instruments to compensate for apparent image rotation. 
\footnotetext[1]{The National Solar Observatory is operated by the Association of Universities for Research in Astronomy under a cooperative agreement with the National Science Foundation}

\subsection{Optical Lines}

\begin{figure}
\begin{center}
\epsfig{figure=vtt_setup.eps,angle=90,width=5in}
\caption[Optical set-up for {\dst}]{{\dst} optical bench set-up}
\label{VTT_setup}
\end{center}
\end{figure}

The observations were taken on 1998 September 22 as part of an eleven day long joint campaign with {\trace}. The aim of the campaign was to examine the relationship between quiet-Sun events in the photosphere, chromosphere, and transition region. The set-up for the observing run is displayed in Figure~\ref{VTT_setup} and the data is described in Table~\ref{dstdata}. The Universal Birefringent Filter ({\ubf}; Bonnacini {\etal} 1989) was tuned successively through eight wavelengths, with a cycle time of 45~s. At each {\ubf} image acquisition step, images through the Halle filter ({\cak}) and Thompson filter (G-band) were also acquired onto separate CCDs. Each cycle was saved in {\sc fits} format, such that each {\ubf} file contained one image at each wavelength, and each Halle (and Thompson) file contained 8 images. Flatfields were acquired by rapidly slewing the telescope. Darks were acquired by blocking all light to the CCD. Co-alignment of the field-of-view (FOV) with {\trace} data led to a calculated spatial pixel size of 0.33~{\arcsec} per pixel for the \cak\ images and 0.18~{\arcsec} per pixel for the {\ubf} images.

\begin{table}
\begin{center}
\caption[{\dst} data summary]{Summary of {\dst} data}
\label{dstdata}
\begin{tabular}{lcll} 
\hline
\hline
Line		& Wavelength (\AA)	& Instrument	& CCD size \\
\hline
\cak		& 3933.7		& Halle		& 512 $\times$ 512	\\ \\
G-band		& 4305.0		& Thompson	& 1024 $\times$ 1024	\\ \\
\ha		& 6562.8		& {\ubf}	& 934 $\times$ 968	\\
\ha+0.7\AA 	& 6563.5		& {\ubf}	& 934 $\times$ 968	\\
\ha+1.0\AA 	& 6563.8		& {\ubf}	& 934 $\times$ 968	\\
\mgb 		& 5172.7		& {\ubf}	& 934 $\times$ 968	\\
\mgbw		& 5183.2		& {\ubf}	& 934 $\times$ 968	\\
Fe{\sc i} 	& 6302.5		& {\ubf}	& 934 $\times$ 968	\\
Fe{\sc i} 	& 6032.5		& {\ubf}	& 934 $\times$ 968	\\
continuum 	& 5256.4		& {\ubf}	& 934 $\times$ 968	\\
\hline
\end{tabular}
\end{center}   
\end{table}

\subsection{Magnetograms}
The Zeeman effect states that the emission from an atom in an external magnetic field will be split into several components. The shift of these components from the normal wavelength of emission is directly proportional to the field strength. Viewed along the magnetic field, these shifted components are left- (L) and right- (R) circularly polarised. Hence, by imaging the L and R circularly polarised components, both the Stokes I (=R+L) and Stokes V =(R-L) signal can be easily calculated for each pixel. The degree of polarisation, P (=V/I), is directly proportional to the magnetic field.   

For this dataset, both circularly polarised components of an Fe~{\sc i} line ($\lambda = 6302.5$~{\AA}) were imaged in the {\ubf} cycle. This was achieved by initially passing the light through a $\lambda/4$ plate in order to change the polarisation from circular to linear. Then a linear polariser only accepts light polarised parallel to its optical axis. Reversing the $\lambda/4$ retardation will change the direction of the two polarised components. Unfortunately the time delay (a few secs) between the acquisition of L and R images means that large scale seeing effects dominate the data. These can be reduced by firstly destretching the data, aligning to sub-pixel accuracy, then combining the R and L images, integrating over several of these combinations and applying a spatial smoothing. This meant that it took $\sim$30 minutes of data to create one magnetogram, and hence time series analysis of magnetic field information was not possible. However it was possible to identify photospheric magnetic features with increased intensity in the chromosphere (Chapter~4).     

\begin{figure}
\begin{center}
\epsfig{figure=trace_sat_hi.eps,width=5in}
\caption[{\trace} spacecraft]{{\trace} spacecraft. The three triangular windows are the EUV filters. The fourth circular window is the UV entrance filter.}
\label{trace_spacecraft}
\end{center}
\end{figure}

\section{Transition Region and Coronal Explorer}

\begin{table}
\begin{center}
\caption[{\trace} passbands]{Summary of {\trace} filter passbands (Handy {\etal} 1999a)}
\label{tracedata}
\begin{tabular}{lcll} 
\hline
\hline
Central		& Emission 	& Bandwidth	& Temperature \\
Wavelength (\AA)&		& (\AA)		& log$_{10}$ (K) \\
\hline
171		& Fe~{\sc ix/x}	& 6.4		& 5.2--6.3 \\
195		& Fe~{\sc xii/xxiv}	& 6.5	& 5.7--6.4, 7.0--7.4 \\
284		& Fe~{\sc xv}	& 10.7		& 6.1--6.6 \\ \\
1216		& {\lya}	& 84		& 4.0--4.5 \\
1550		& C~{\sc iv}	& 30		& 4.8--5.4 \\
1600		& UV cont.	& 275		& 3.6--4.0 \\
1700		& UV cont.	& 200		& 3.6--4.0 \\
5000		& White light	& broad 	& 3.6--3.8 \\
\hline
\end{tabular}
\end{center}   
\end{table}

\subsection{Characteristics}
The Transition Region and Coronal Explorer ({\trace}; Handy {\etal} 1999a) is a single-instrument 0.3~m Cassegrain telescope capable of imaging the solar atmosphere in a temperature range of $6\times10^3$--$1\times10^6$~K at a spatial resolution of 1{\arcsec} (pixel size 0.5{\arcsec}), equivalent to $\sim$~770~km on the sun, with typical temporal cadence of 20--40~s. It was launched on a Small Explorer spacecraft from a Pegasus XL vehicle on 1998~April~2 into a geo-polar orbit. As such it provides uninterrupted observations for a 9-month period, followed by a 3-month partial eclipse. The {\trace} orbit passes through the South Atlantic Anomaly (Sherrill 1991) and auroral radiation belts, which limit the duration of continuous observation sequences. 

\subsection{Imaging in the Ultraviolet}

The $1024\times1024$ pixel$^2$ CCD is sensitive in both the ultraviolet (UV) and extreme ultraviolet (EUV). The telescope is divided into four quadrants, three of which are designed for EUV imaging (Figure~\ref{trace_spacecraft}). In this thesis I work on data from the fourth quadrant, designed to image in UV wavelengths.

\begin{figure}
\begin{center}
\epsfig{figure=truv.eps}
\caption[{\trace} ultraviolet filter passbands]{The four {\trace} UV filter passbands are displayed. From top to bottom these are {\lya}, C~{\sc iv}, 1600~{\AA} continuum and fused silica. The fused silica and 1600~{\AA} continuum  filters are combined to form a further filter passband centred on 1700~{\AA} (Handy {\etal} 1999a)}
\label{trace_filters}
\end{center}
\end{figure}

\begin{figure}
\begin{center}
\epsfig{figure=tr3002.eps}
\caption[{\trace} ultraviolet response functions]{Combined response function of {\trace} UV optics and quantum efficiency of the CCDs. (Handy {\etal} 1999a)}
\label{trace_filters_uv}
\end{center}
\end{figure}

The UV filter entrance has a multi-layer dielectric coating on a MgF$_2$ substrate, which acts to block long-wavelengths ($>2000$~{\AA}), whilst optimising transmission at both C~{\sc iv} (1550~{\AA}) and {\lya} (1216~{\AA}). Various combinations of filters are used to image a number of wavelengths, namely 1216~{\AA}, 1550~{\AA}, 1600~{\AA}, 1700~{\AA} and white light. Details of the passbands and filters used are provided in Table~\ref{tracedata} and Figure~\ref{trace_filters}. Essentially the C~{\sc iv}, {\lya} and UV continuum (centred on 1600~{\AA}) provide three individual passbands. The 1600~{\AA} and fused silica filters are used in tandem to create a fourth filter, centred on 1700~{\AA}, whilst the fused silica filter also provides white light images. The response function of each passband (including quantum efficiency of the CCDs) are displayed in Figure~\ref{trace_filters_uv}. Linear combinations of images in these passbands can then be used to isolate both the C~{\sc iv} and {\lya} emission from the continuum (Handy {\etal} 1998, Handy {\etal} 1999b). Depending on the aims of the observing program, images may be taken in all eight passbands, obviously at the expense of a lower cadence for the dataset.

\subsection{Data Reduction}
The extensive {\trace} branch of the SolarSoftWare ({\ssw}; Freeland \& Handy 1998) tree of {\sc idl} provides a comprehensive suite of data reduction and analysis tools. Data are provided from several data centres worldwide and commonly downloaded as hour-long multi-fits (.mxf) files. The {\em structure} format of {\trace} data is vital as the shear size of these files can be overwhelming. The structure format provides a means of perusing the data without loading the image files, and extracting the relevant data by keyword (e.g., only certain passbands or specific times).   
