[534] | 1 | %% TODO |
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| 2 | %% Help doco |
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| 3 | %% .asaprc |
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| 4 | %% Intro |
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| 5 | %% Plotter options - pol etc |
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| 6 | %% Fit saving |
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| 7 | |
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| 8 | \documentclass[11pt]{article} |
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| 9 | \usepackage{a4} |
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| 10 | \usepackage[dvips]{graphicx} |
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| 11 | |
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| 12 | % Adjust the page size |
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| 13 | \addtolength{\oddsidemargin}{-0.4in} |
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| 14 | \addtolength{\evensidemargin}{+0.4in} |
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| 15 | \addtolength{\textwidth}{+0.8in} |
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| 16 | |
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| 17 | \setlength{\parindent}{0mm} |
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| 18 | \setlength{\parskip}{1ex} |
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| 19 | |
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| 20 | |
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| 21 | \title{ATNF Spectral Analysis Package\\Cookbook } |
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| 22 | \author{Chris Phillips} |
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| 23 | |
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| 24 | |
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| 25 | \newcommand{\cmd}[1]{{\tt #1}} |
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| 26 | |
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| 27 | \begin{document} |
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| 28 | |
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| 29 | \maketitle |
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| 30 | |
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| 31 | \section{Introduction} |
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| 32 | |
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| 33 | %\section{Documentation Standards} |
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| 34 | |
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| 35 | %In most of the examples in this document, it has been assumed that the |
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| 36 | |
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| 37 | \section{Installation and running} |
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| 38 | |
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| 39 | Currently there are installations running on Linux machines at |
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| 40 | |
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| 41 | \begin{itemize} |
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| 42 | \item Epping - use hosts {\tt draco} or {\tt hydra} |
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| 43 | \item Narrabri - use host {\tt kaputar} |
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[537] | 44 | \item Parkes - use host {\tt bourbon} |
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[534] | 45 | \item Mopra - use host {\tt minos} |
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| 46 | \end{itemize} |
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| 47 | |
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| 48 | To start asap log onto one of these Linux hosts and enter |
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| 49 | |
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| 50 | \begin{verbatim} |
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| 51 | > cd /my/data/directory |
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| 52 | > source /nfs/aips++/daily/aipsinit.csh # Temporary measure |
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| 53 | > asap |
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| 54 | \end{verbatim} |
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| 55 | |
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| 56 | This starts the asap. To quit, you need to type \verb+^+-d (control-d). |
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| 57 | |
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| 58 | \section{Interface} |
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| 59 | |
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| 60 | ASAP is written in C++ and python. The user interface uses the |
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| 61 | ``ipython'' interactive shell, which is a simple interactive interface |
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| 62 | to python. The user does not need to understand python to use this, |
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| 63 | but certain aspects python affect what the user can do. The current |
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| 64 | interface is object oriented. In the future, we will build a |
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| 65 | functional (non object oriented) shell on top of this to ease |
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| 66 | interactive use. |
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| 67 | |
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| 68 | \subsection {Integer Indices are 0-relative} |
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| 69 | |
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| 70 | Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. |
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| 71 | |
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| 72 | \subsection{Objects} |
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| 73 | |
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| 74 | The ASAP interface is based around a number of ``objects'' which the |
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| 75 | user deals with. Objects range from the data which have been read from |
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| 76 | disk, to tools used for fitting functions to the data. The following |
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| 77 | main objects are used : |
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| 78 | |
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| 79 | \begin{itemize} |
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| 80 | \item[scantable] The data container (actual spectra and header information) |
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| 81 | \item[fitter] A tool used to fit functions to the spectral data |
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| 82 | \item[plotter] A tool used to plot the spectral line data |
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| 83 | \item[reader] A tool which can be used to read data from disks |
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| 84 | into a scantable object. |
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| 85 | \end{itemize} |
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| 86 | |
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| 87 | These are all described below. |
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| 88 | |
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| 89 | There can be many objects of the same type. Each object is referred to |
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| 90 | by a variable name made by the user. The name of this variable is not |
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| 91 | important and can be set to whatever the user prefers (ie ``s'' and |
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| 92 | ``ParkesHOH-20052002'' are equivalent). However, having a simple and |
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| 93 | consistent naming convention will help you a lot. |
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| 94 | |
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| 95 | \subsection{Member functions(functions)} |
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| 96 | |
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| 97 | Following the object oriented approach, objects have associated |
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| 98 | ``member functions'' which can either be used to modify the data in |
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| 99 | some way or change global properties of the object. In this document |
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| 100 | member functions will be referred to simply as functions. From the |
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| 101 | command line, the user can excute these functions using the syntax: |
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| 102 | \begin{verbatim} |
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| 103 | ASAP> out = object.function(arguments) |
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| 104 | \end{verbatim} |
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| 105 | |
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| 106 | Where \cmd{out} is the name of the returned variable (could be a new |
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| 107 | scantable object, or a vector of data, or a status retrn), \cmd{object} is the |
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| 108 | object variable name (set by the user), \cmd{function} is the name of |
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| 109 | the member function and \cmd{arguments} is a list of arguments to the |
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| 110 | function. The arguments can be provided either though position or names. |
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| 111 | A mix of the two can be used. E.g. |
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| 112 | |
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| 113 | \begin{verbatim} |
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| 114 | ASAP> av = scans(msk,weight='tsys') |
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| 115 | ASAP> av = scans(mask=msk,weight='tsys') |
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| 116 | ASAP> av = scans(msk,True) |
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| 117 | ASAP> scans.polybaseline(mask=msk, order=0, insitue=True) |
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| 118 | ASAP> scans.polybaseline(msk,0,True) |
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| 119 | ASAP> scans.polybaseline(mask, insitu=True) |
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| 120 | \end{verbatim} |
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| 121 | |
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| 122 | \subsection{Global Functions} |
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| 123 | |
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| 124 | Some functions do not make sense to be implemented as member |
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| 125 | functions, typically fuctions which operate on more than one scantable |
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| 126 | (e.g. time averaging of many scans). These functions will always be |
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| 127 | refered to as global functions. |
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| 128 | |
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| 129 | \subsection{Interactive enviroment} |
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| 130 | |
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| 131 | ipython has a number of useful interactive features and a few things to be aware |
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| 132 | of for the new user. |
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| 133 | |
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| 134 | \subsubsection{String completion} |
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| 135 | |
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| 136 | Tab completion is enabled for all function names. If you type the |
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| 137 | first few letters of a function name, then type <TAB> the function |
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| 138 | name will be auto completed if it is un-ambigious, or a list of |
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| 139 | possibilities will be given. Auto-completion works for the user |
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| 140 | object names as well as function names. It does not work for filenames, |
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| 141 | nor for function arguments. |
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| 142 | |
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| 143 | Example |
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| 144 | \begin{verbatim} |
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| 145 | ASAP> scans = scantable('MyData.rpf') |
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| 146 | ASAP> scans.se<TAB> |
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| 147 | scans.set_cursor scans.set_freqframe scans.set_unit scans.setpol |
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| 148 | scans.set_doppler scans.set_instrument scans.setbeam |
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| 149 | scans.set_fluxunit scans.set_restfreqs scans.setif |
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| 150 | ASAP> scans.set_in<TAB> |
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| 151 | ASAP> scans.set_instrument |
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| 152 | \end{verbatim} |
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| 153 | |
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| 154 | \subsubsection{Unix Interaction} |
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| 155 | |
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| 156 | Basic unix shell commands (pwd, ls, cd etc) can be issued from within |
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| 157 | ASAP. This allows the user to do things list look at files in the |
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| 158 | current directory. The shell command ``cd'' does work within ASAP |
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| 159 | allowing the user to change between data directories. Unix programs |
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| 160 | cannot be run this way, but the shell escape ``$!$'' can be used to run |
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| 161 | arbitrary programs. E.g. |
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| 162 | |
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| 163 | \begin{verbatim} |
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| 164 | ASAP> pwd |
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| 165 | ASAP> ls |
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| 166 | ASAP> ! mozilla& |
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| 167 | \end{verbatim} |
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| 168 | |
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| 169 | \subsection{Help} |
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| 170 | |
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| 171 | Help me... |
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| 172 | |
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| 173 | \subsection{.asaprc} |
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| 174 | |
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| 175 | |
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| 176 | \section{Scantables} |
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| 177 | |
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| 178 | \subsection {Description} |
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| 179 | |
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| 180 | \subsubsection {Basic Structure} |
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| 181 | |
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| 182 | ASAP data handling works on objects called scantables. A scantable |
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| 183 | holds your data, and also provides functions to operate |
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| 184 | upon it. |
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| 185 | |
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| 186 | The building block of a scantable is an integration, which is a single |
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| 187 | row of a scantable. Each row contains spectra for each beam, IF and |
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| 188 | polarisation. For example Parkes multibeam data would contain many |
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| 189 | beams, one IF and 2-4 polarisations, while the new Mopra 8-GHz |
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| 190 | filterbank will eventually produce one beam, many IFs, and 2-4 |
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| 191 | polarisations. |
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| 192 | |
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| 193 | A collection of sequential integrations (rows) for one source is termed |
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| 194 | a scan (and each scan has a unique numeric identifier, the ScanID). A |
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| 195 | scantable is then a collection of one or more scans. If you have |
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| 196 | scan-averaged your data in time, then each scan would hold just one |
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| 197 | (averaged) integration. |
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| 198 | |
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| 199 | Many of the functions which work on scantables can either return a |
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| 200 | new scantable with modified data or change the scantable insitu. Which |
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| 201 | method is used depends on the users preference. The default can be |
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| 202 | changed via the {\tt .asaprc} resource file. |
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| 203 | |
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| 204 | \subsubsection {Contents} |
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| 205 | |
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[537] | 206 | A scantable has header information and data (a scantable is actually an AIPS++ |
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| 207 | Table and it is stored in Memory when you are manipulating it with ASAP. |
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[534] | 208 | You can store it to disk and then browse it with the AIPS++ |
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[537] | 209 | Table browser if you know how to do that !). |
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[534] | 210 | |
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| 211 | The data are stored in columns (the length of a column is the number of |
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| 212 | rows/integrations of course). |
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| 213 | |
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| 214 | Two important columns are those that describe the frequency setup. We mention |
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| 215 | them explicitly here because you need to be able to undertand the presentation |
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| 216 | of the frequency information and possibly how to manipulate it. |
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| 217 | |
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| 218 | These columns are called FreqID and RestFreqID. They contain indices, for |
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| 219 | each IF, pointing into tables with all of the frequency information for that |
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| 220 | integration. More on these below when we discuss the \cmd{summary} function |
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| 221 | in the next subsection. |
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| 222 | |
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| 223 | There are of course many other columns which contain the actual spectra, |
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| 224 | the flags, the Tsys, the source names and so on, but those are a little |
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| 225 | more transparently handled. |
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| 226 | |
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| 227 | \subsection{Management} |
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| 228 | |
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| 229 | During processing it is possible to create a large number of scan |
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| 230 | tables. These all consume memory, so it is best to periodically remove |
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| 231 | unneeded scan tables. Use \cmd{list\_scans} to print a list of all |
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| 232 | scantables and \cmd{del} to remove unneeded ones. |
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| 233 | |
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| 234 | Example: |
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| 235 | |
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| 236 | \begin{verbatim} |
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| 237 | ASAP> list_scans |
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| 238 | The user created scantables are: |
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| 239 | ['s', 'scans', 'av', 's2', 'ss'] |
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| 240 | |
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| 241 | ASAP> del s2 |
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| 242 | ASAP> del ss |
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| 243 | \end{verbatim} |
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| 244 | |
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| 245 | There is also a function \cmd{summary} to list a summary of the scantable. |
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| 246 | You will find this very useful. |
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| 247 | |
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| 248 | Example: |
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| 249 | |
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| 250 | \begin{verbatim} |
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| 251 | ASAP> scans = scantable('MyData.rpf') |
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| 252 | ASAP> scans.summary() # Brief listing |
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| 253 | ASAP> scans.summary(verbose=True) # Include frequency information |
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[537] | 254 | ASAP> print scan # Equivalent to brief summary function call |
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[534] | 255 | \end{verbatim} |
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| 256 | |
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| 257 | Most of what the \cmd{summary} function prints out is obvious. However, |
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| 258 | it also prints out the FreqIDs and RestFreqIDs to which we alluded above. |
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| 259 | These are the last column of the listing. |
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| 260 | |
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| 261 | The summary function gives you a scan-based summary. So it lists all of |
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| 262 | the FreqIDs and RestFreqIDs that it encountered for each scan. If you'd |
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| 263 | like to see what each FreqID actually means, then set the verbose |
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| 264 | argument to True and the frequency table will be listed at the end. |
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| 265 | FreqID of 3 say, refers to the fourth row of the frequency table (ASAP |
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| 266 | is 0-relative). The list of rest frequencies, to which the RestFreqIDs |
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| 267 | refer, is always listed. |
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| 268 | |
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| 269 | You can copy one scantable to another with the \cmd{copy} function. |
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| 270 | |
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| 271 | Example: |
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| 272 | |
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| 273 | \begin{verbatim} |
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| 274 | ASAP> scans = scantable('MyData.rpf') |
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| 275 | ASAP> scan2 = scans.copy() |
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| 276 | \end{verbatim} |
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| 277 | |
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| 278 | |
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| 279 | |
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| 280 | \subsection{State} |
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| 281 | |
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| 282 | |
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| 283 | Each scantable contains "state"; these are properties applying to all |
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| 284 | of the data in the scantable. |
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| 285 | |
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| 286 | Examples are the selection of beam, IF and polarisation, spectral unit |
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| 287 | (e.g. $km/s$) frequency reference frame (e.g. BARY) and velocity doppler |
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| 288 | type (e.g. RADIO). |
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| 289 | |
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| 290 | |
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| 291 | |
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| 292 | \subsubsection{Units, Doppler and Frequency Reference Frame} |
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| 293 | |
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| 294 | The information describing the frequency setup for each integration |
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| 295 | is stored fundamentally in frequency in the reference frame |
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| 296 | of observation (E.g. TOPO). |
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| 297 | |
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| 298 | When required, this is converted to the desired reference frame (e.g. LSRK), |
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| 299 | Doppler (e.g. OPTICAL) and unit (e.g. $km/s$) on-the-fly. For example, |
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| 300 | this is important when you are displaying the data or fitting to it. |
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| 301 | |
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| 302 | For units, the user has the choice of frequency, velocity or channel. |
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| 303 | The \cmd{set\_unit} function is used to set the current unit for a |
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| 304 | scantable. All functions will (where relevant) work with the selected |
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| 305 | unit until this changes. This is mainly important for fitting (the fits |
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| 306 | can be computed in any of these units), plotting and mask creation. |
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| 307 | |
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| 308 | The velocity doppler can be changed with the \cmd{set\_doppler} |
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| 309 | function, and the frequency reference frame can be changed with the |
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| 310 | \cmd{set\_freqframe} function. |
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| 311 | |
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| 312 | Example usage: |
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| 313 | |
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| 314 | \begin{verbatim} |
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| 315 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data |
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| 316 | ASAP> scans.set_freqframe('LSRK') # Use the LSR velocity frame |
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| 317 | ASAP> scans.set_unit('km/s') # Use velocity for plots etc from now on |
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| 318 | ASAP> scans.set_doppler('OPTICAL') # Use the optical velocity convention |
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| 319 | ASAP> scans.set_unit('MHz') # Use frequency in MHz from now on |
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| 320 | \end{verbatim} |
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| 321 | |
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| 322 | |
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| 323 | \subsubsection{Rest Frequency} |
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| 324 | |
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| 325 | ASAP reads the line rest frequency from the RPFITS file when reading |
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| 326 | the data. The values stored in the RPFITS file are not always correct |
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| 327 | and so there is a function \cmd{set\_restfreq} to set the rest frequencies. |
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| 328 | |
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| 329 | For each integration, there is a rest-frequency per IF (the rest |
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| 330 | frequencies are just stored as a list with an index into them). |
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| 331 | There are a few ways to set the rest frequencies with this function. |
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| 332 | |
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| 333 | If you specify just one rest frequency, then it is selected for the |
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| 334 | specified source and IF and added to the list of rest frequencies. |
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| 335 | |
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| 336 | \begin{verbatim} |
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| 337 | ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0) # Selected for specified source/IF |
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| 338 | ASAP> scans.set_restfreqs(freqs=1.667359e9) # Selected for all sources and IFs |
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| 339 | \end{verbatim} |
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| 340 | |
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| 341 | |
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| 342 | If you specify a list of frequencies, then it must be of length the |
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| 343 | number of IFs. Regardless of the source, the rest frequency will be set |
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| 344 | for each IF to the corresponding value in the provided list. The |
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| 345 | internally stored list of rest frequencies will be replaced by this |
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| 346 | list. |
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| 347 | |
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| 348 | |
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| 349 | \begin{verbatim} |
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| 350 | ASAP> scans.set_restfreqs(freqs=1.667359e9, source='NGC253', theif=0) # Selected for specified source/IF |
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| 351 | ASAP> scans.set_restfreqs(freqs=1.667359e9) # Selected for all sources and IFs |
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| 352 | \end{verbatim} |
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| 353 | |
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| 354 | |
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| 355 | In both of the above modes, you can also specify the rest frequencies via |
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| 356 | names in a known list rather than by their values. |
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| 357 | |
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| 358 | Examples: |
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| 359 | |
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| 360 | \begin{verbatim} |
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| 361 | ASAP> scans.lines() # Print list of known lines |
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| 362 | ASAP> scans.set_restfreqs(lines=['OH1665','OH1667']) |
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| 363 | \end{verbatim} |
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| 364 | |
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| 365 | |
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| 366 | |
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| 367 | \subsection{Data Selection} |
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| 368 | |
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| 369 | Data selection is currently fairly limited. This will be improved in |
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| 370 | the future. |
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| 371 | |
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| 372 | |
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| 373 | \subsubsection{Cursor} |
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| 374 | |
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| 375 | Generally the user will want to run functions on all rows in a |
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| 376 | scantable. This allows very fast reduction of data. There are situations |
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| 377 | when functions should only operate on specific elements of the spectra. This |
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| 378 | is handled by the scantable cursor, which allows the user to select a |
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| 379 | single beam, IF and polarisation combination. |
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| 380 | |
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| 381 | Example : |
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| 382 | |
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| 383 | \begin{verbatim} |
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| 384 | ASAP> scans.set_cursor(0,2,1) # beam, IF, pol |
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| 385 | ASAP> scans.smooth(allaxes=F) # in situ by default or .aipsrc |
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| 386 | \end{verbatim} |
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| 387 | |
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| 388 | \subsubsection{Row number} |
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| 389 | |
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| 390 | Most functions work on all rows of a scan table. Exceptions are the |
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| 391 | fitter and plotter. If you wish to only operate on a selected set of |
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| 392 | scantable rows, usw the \cmd{get_scan} function to copy the rows into |
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| 393 | a new scantable. |
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| 394 | |
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| 395 | \subsubsection{Allaxes} |
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| 396 | |
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| 397 | Many functions have an \cmd{allaxes} option which controls whether the |
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| 398 | function will operate on all elements within a scantable row, or just |
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| 399 | those selected with the current cursor. The default is taken from the |
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| 400 | users {\tt .asaprc} file. |
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| 401 | |
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| 402 | \subsubsection{Masks} |
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| 403 | |
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| 404 | Many tasks (fitting, baseline subtraction, statistics etc) should only |
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| 405 | be run on range of channels. Depending on the current ``unit'' setting |
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| 406 | this range is set directly as channels, velocity or frequency |
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| 407 | ranges. Internally these are converted into a simple boolean mask for |
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| 408 | each channel of the abscissa. This means that if the unit setting is |
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| 409 | later changed, previously created mask are still valid. (This is not |
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| 410 | true for functions which change the shape or shift the frequency axis). |
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| 411 | You create masks with the function \cmd{create\_mask} and this specified |
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| 412 | the channels to be included in the selection. |
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| 413 | |
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| 414 | When setting the mask in velocity, the conversion from velocity |
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| 415 | to channels is based on the current cursor setting, selected row and |
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| 416 | selected frequency reference frame (**Currently first row only**) |
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| 417 | |
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| 418 | |
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| 419 | Example : |
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| 420 | \begin{verbatim} |
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| 421 | |
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| 422 | # Select channel range for baselining |
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| 423 | ASAP> scans.set_unit('channels') |
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| 424 | ASAP> msk = q.create_mask([100,400],[600,800]) |
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| 425 | |
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| 426 | # Select velocity range for fitting |
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| 427 | ASAP> scans.set_unit('km/s') |
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| 428 | ASAP> msk = q.create_mask([-30,-10]) |
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| 429 | \end{verbatim} |
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| 430 | |
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| 431 | |
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| 432 | Sometimes it is more convenient to specify the channels to be |
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| 433 | excluded, rather included. You can do this with the ``invert'' argument. |
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| 434 | |
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| 435 | Example : |
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| 436 | \begin{verbatim} |
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| 437 | ASAP> scans.set_unit('channels') |
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| 438 | ASAP> msk = q.create_mask([0,100],[900-1023], invert=True) # Excludes specified channels |
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| 439 | \end{verbatim} |
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| 440 | |
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| 441 | Because the mask is stored in a simple python variable, the users is |
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| 442 | able to combine masks using simple arithmetic. To create a mask |
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| 443 | excluding the edge channels, a strong maser feature and a birdie in |
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| 444 | the middle of the band: |
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| 445 | |
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| 446 | \begin{verbatim} |
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| 447 | ASAP> scans.set_unit('channels') |
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| 448 | ASAP> msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True) |
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| 449 | ASAP> scans.set_unit('km/s') |
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| 450 | ASAP> msk2 = q.create_mask([-20,-10],invert=True) |
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| 451 | |
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| 452 | ASAP> mask = msk1 and msk2 |
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| 453 | \end{verbatim} |
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| 454 | |
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| 455 | |
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| 456 | \section{Data Input} |
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| 457 | |
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| 458 | Data can be loaded in one of two ways; using the reader object or via |
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| 459 | the scantable constructor. The scantable method is simpler but the |
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| 460 | reader allow the user more control on what is read. |
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| 461 | |
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| 462 | \subsection{Scantable constructor} |
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| 463 | |
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| 464 | This loads all of the data from filename into the scantable object scans |
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| 465 | and averages all the data within a scan (i.e. the resulting scantable |
---|
| 466 | will have one row per scan). The recognised input file formats are |
---|
| 467 | RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ |
---|
| 468 | MeasurementSet2 format. |
---|
| 469 | |
---|
| 470 | |
---|
| 471 | Example usage: |
---|
| 472 | |
---|
| 473 | \begin{verbatim} |
---|
| 474 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf') |
---|
| 475 | \end{verbatim} |
---|
| 476 | |
---|
| 477 | |
---|
| 478 | \subsection{Reader object} |
---|
| 479 | |
---|
| 480 | For more control when reading data into ASAP, the reader object should |
---|
| 481 | be used. This has the option of only reading in a range of integrations |
---|
| 482 | and does not perform any scan averaging of the data, allowing analysis |
---|
| 483 | of the individual integrations. Note that due to limitation of the |
---|
| 484 | RPFITS library, only one reader object can be open at one time reading |
---|
| 485 | RPFITS files. To read multiple RPFITS files, the old reader must be |
---|
| 486 | destroyed before the new file is opened. However, multiple readers can |
---|
| 487 | be created and attached to SDFITS files. |
---|
| 488 | |
---|
| 489 | |
---|
| 490 | Example usage: |
---|
| 491 | |
---|
| 492 | \begin{verbatim} |
---|
| 493 | ASAP> r = reader('2003-03-16_082048_t0002.rpf') |
---|
| 494 | ASAP> r.summary |
---|
| 495 | ASAP> scan = r.read() |
---|
| 496 | ASAP> s = r.read(range(100)) # To read in the first 100 integrations |
---|
| 497 | ASAP> del r |
---|
| 498 | \end{verbatim} |
---|
| 499 | |
---|
| 500 | \section{Basic Processing} |
---|
| 501 | |
---|
| 502 | In the following section, a simple data reduction to form a quotient |
---|
| 503 | spectrum of a single source is followed. Variations of this approach |
---|
| 504 | are given later. |
---|
| 505 | |
---|
| 506 | %\subsection{Editing} |
---|
| 507 | |
---|
| 508 | %How and when? |
---|
| 509 | |
---|
| 510 | \subsection{Separate reference and source observations} |
---|
| 511 | |
---|
| 512 | Most data from ATNF observatories distinguishes on and off source data |
---|
| 513 | using the file name. This makes it easy to create two scantables with |
---|
| 514 | the source and reference data. As long as there was exactly one |
---|
| 515 | reference observation for each on source observation for following |
---|
| 516 | method will work. |
---|
| 517 | |
---|
| 518 | For Mopra and Parkes data: |
---|
| 519 | \begin{verbatim} |
---|
| 520 | ASAP> r = scans.get_scan('*_R') |
---|
| 521 | ASAP> s = scans.get_scan('*_S') |
---|
| 522 | \end{verbatim} |
---|
| 523 | |
---|
| 524 | For Tidbinbilla data |
---|
| 525 | \begin{verbatim} |
---|
| 526 | ASAP> r = scans.get_scan('*_[ew]') |
---|
| 527 | ASAP> s = scans.get_scan('*_[^ew]') |
---|
| 528 | \end{verbatim} |
---|
| 529 | |
---|
| 530 | \subsection{Make the quotient spectra} |
---|
| 531 | |
---|
| 532 | Use the quotient function |
---|
| 533 | |
---|
| 534 | \begin{verbatim} |
---|
| 535 | ASAP> q = s.quotient(r) |
---|
| 536 | \end{verbatim} |
---|
| 537 | |
---|
| 538 | This uses the rows in scantable \cmd{r} as reference spectra for the |
---|
| 539 | rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row |
---|
| 540 | (which is applied to all rows in \cmd{s}) or both scantables must have |
---|
| 541 | the same number of rows. By default the quotient spectra is calculated |
---|
| 542 | to preserve continuum emission. If you wish to remove continuum |
---|
| 543 | contribution, use the \cmd{preserve} argument: |
---|
| 544 | |
---|
| 545 | \begin{verbatim} |
---|
| 546 | ASAP> q = s.quotient(r, preserve=True) |
---|
| 547 | \end{verbatim} |
---|
| 548 | |
---|
| 549 | \subsection{Time average separate scans} |
---|
| 550 | |
---|
| 551 | If you have observed the source with multiple source/reference cycles you |
---|
| 552 | will want to scan-average the quotient spectra together. |
---|
| 553 | |
---|
| 554 | \begin{verbatim} |
---|
| 555 | ASAP> av = average_time(q) |
---|
| 556 | \end{verbatim} |
---|
| 557 | |
---|
| 558 | If for some you want to average multiple sets of scan tables together you can: |
---|
| 559 | |
---|
| 560 | \begin{verbatim} |
---|
| 561 | ASAP> av = average_time(q1, q2, q3) |
---|
| 562 | \end{verbatim} |
---|
| 563 | |
---|
| 564 | The default is not to use any weighting, which probably is not what |
---|
| 565 | you want. The alternative is to use variance or Tsys weighting. |
---|
| 566 | |
---|
| 567 | To use variance based weighting, you need to supply a mask saying which |
---|
| 568 | channel range you want it to calculate the variance from. |
---|
| 569 | |
---|
| 570 | \begin{verbatim} |
---|
| 571 | ASAP> av = average_time(q, weight='tsys') |
---|
| 572 | |
---|
| 573 | ASAP> msk = q.create_mask([200,400],[600,800]) |
---|
| 574 | ASAP> av = average_time(q, mask=msk, weight='var') |
---|
| 575 | \end{verbatim} |
---|
| 576 | |
---|
| 577 | \subsection{Baseline fitting} |
---|
| 578 | |
---|
| 579 | To make a baseline fit, you must first create a mask of channels to |
---|
| 580 | use in the baseline fit. |
---|
| 581 | |
---|
| 582 | \begin{verbatim} |
---|
| 583 | ASAP> msk = scans.create_mask([100,400],[600,900]) |
---|
| 584 | ASAP> scans.poly_baseline(msk, 1) |
---|
| 585 | \end{verbatim} |
---|
| 586 | |
---|
| 587 | This will fit a first order polynomial to the selected channels and subtract |
---|
| 588 | this polynomial from the full spectra. |
---|
| 589 | |
---|
| 590 | \subsubsection{Auto-baselining} |
---|
| 591 | |
---|
| 592 | The function \cmd{auto\_poly\_baseline} can be used to automatically |
---|
| 593 | baseline your data with out having to specify channel ranges for |
---|
| 594 | the line free data. It automatically figures out the line-free |
---|
| 595 | emission and fits a polynomial baseline to that data. The user can use |
---|
| 596 | masks to fix the range of channels or velocity range for the fit as |
---|
| 597 | well as mark the band edge as invalid. |
---|
| 598 | |
---|
| 599 | Simple example |
---|
| 600 | |
---|
| 601 | \begin{verbatim} |
---|
| 602 | ASAP> scans.auto_poly_baseline(order=2,threshold=5) |
---|
| 603 | \end{verbatim} |
---|
| 604 | |
---|
| 605 | \cmd{order} is the polynomial order for the fit. \cmd{threshold} is |
---|
| 606 | the SNR threshold to use to deliminate line emission from |
---|
| 607 | signal. Making this too small or too large will result in a poor fit, |
---|
| 608 | but generally the value is not critical. |
---|
| 609 | |
---|
| 610 | Other examples: |
---|
| 611 | |
---|
| 612 | \begin{verbatim} |
---|
| 613 | # Don't try and fit the edge of the bandpass which is noisier |
---|
| 614 | ASAP> scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3) |
---|
| 615 | |
---|
| 616 | # Only fit a given region around the line |
---|
| 617 | ASAP> scans.set_unit('km/s') |
---|
| 618 | ASAP> msk = scans.create_mask((-60,-20)) |
---|
| 619 | ASAP> scans.auto_poly_baseline(mask=msk,order=3,threshold=3) |
---|
| 620 | |
---|
| 621 | \end{verbatim} |
---|
| 622 | |
---|
| 623 | \subsection{Average the polarisations} |
---|
| 624 | |
---|
| 625 | If you are just interested in the highest SNR for total intensity you |
---|
| 626 | will want to average the parallel polarisations together. |
---|
| 627 | |
---|
| 628 | \begin{verbatim} |
---|
| 629 | ASAP> scans.average_pol() |
---|
| 630 | \end{verbatim} |
---|
| 631 | |
---|
| 632 | \subsection{Calibration} |
---|
| 633 | |
---|
| 634 | For most uses, calibration happens transparently as the input data |
---|
| 635 | contains the Tsys measurements taken during observations. The nominal |
---|
| 636 | ``Tsys'' values may be in Kelvin or Jansky. The user may wish to |
---|
| 637 | supply a Tsys correction or apply gain-elevation and opacity |
---|
| 638 | corrections. |
---|
| 639 | |
---|
| 640 | \subsubsection{Brightness Units} |
---|
| 641 | |
---|
| 642 | RPFITS files to not contain any information as to whether the telescope |
---|
| 643 | calibration was in units of Kelvin or Janskys. On reading the data a |
---|
| 644 | default value is set depending on the telescope and frequency of |
---|
| 645 | observation. If this default is incorrect (you can see it in the |
---|
| 646 | listing from the \cmd{summary} function) the user can either override |
---|
| 647 | this value on reading the data or later. E.g: |
---|
| 648 | |
---|
| 649 | \begin{verbatim} |
---|
| 650 | ASAP> scans = scantable(('2004-11-23_1841-P484.rpf', unit='Jy') |
---|
| 651 | # Or in two steps |
---|
| 652 | ASAP> scans = scantable(('2004-11-23_1841-P484.rpf') |
---|
| 653 | ASAP> scans.set_fluxunit('Jy) |
---|
| 654 | \end{verbatim} |
---|
| 655 | |
---|
| 656 | \subsubsection{Tsys scaling} |
---|
| 657 | |
---|
| 658 | Sometime the nominal Tsys measurement at the telescope is wrong due to |
---|
| 659 | an incorrect noise diode calibration. This can easily be corrected for |
---|
| 660 | with the scale function. By default, \cmd{scale} only scans the |
---|
| 661 | spectra and not the corresponding Tsys. |
---|
| 662 | |
---|
| 663 | \begin{verbatim} |
---|
| 664 | ASAP> scans.scale(1.05, tsys=True) |
---|
| 665 | \end{verbatim} |
---|
| 666 | |
---|
| 667 | \subsubsection{Unit Conversion} |
---|
| 668 | |
---|
| 669 | To convert measurements in Kelvin to Jy (and vice versa) the global |
---|
| 670 | function \cmd{convert\_flux} is needed. This converts and scales the data |
---|
| 671 | from K to Jy or vice-versa depending on what the current brightness unit is |
---|
| 672 | set to. The function knows the basic parameters for some frequencies |
---|
| 673 | and telescopes, but the user may need to supply the aperture |
---|
| 674 | efficiency, telescope diameter or the Jy/K factor. |
---|
| 675 | |
---|
| 676 | \begin{verbatim} |
---|
| 677 | ASAP> scans.convert_flux # If efficency known |
---|
| 678 | ASAP> scans.convert_flux(eta=0.48) # If telescope diameter known |
---|
| 679 | ASAP> scans.convert_flux(eta=0.48,d=35) # Unknown telescope |
---|
| 680 | ASAP> scans.convert_flux(jypk=15) # Alternative |
---|
| 681 | \end{verbatim} |
---|
| 682 | |
---|
| 683 | \subsubsection{Gain-Elevation and Opacity Corrections} |
---|
| 684 | |
---|
| 685 | As higher frequencies (particularly $>$20~GHz) it is important to make |
---|
| 686 | corrections for atmospheric opacity and gain-elevation effects. |
---|
| 687 | |
---|
| 688 | Gain-elevation curves for some telescopes and frequencies and known to |
---|
| 689 | ASAP (currently only for Tid at 20~GHz). In these cases making |
---|
| 690 | gain-corrections is simple. If the gain curve for your data is not |
---|
| 691 | known the user can supply either a gain polynomial or text file |
---|
| 692 | tabulating gain factors at a range of elevations (see \cmd{help |
---|
| 693 | gain\_el}). |
---|
| 694 | |
---|
| 695 | Examples: |
---|
| 696 | |
---|
| 697 | \begin{verbatim} |
---|
| 698 | ASAP> scans.gain_el() # If gain table known |
---|
| 699 | ASAP> scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) |
---|
| 700 | \end{verbatim} |
---|
| 701 | |
---|
| 702 | Opacity corrections can be made with the global function |
---|
| 703 | \cmd{opacity}. This should work on all telescopes as long as a |
---|
| 704 | measurement of the opacity factor, was made during the |
---|
| 705 | observation. |
---|
| 706 | |
---|
| 707 | \begin{verbatim} |
---|
| 708 | ASAP> scans.opacity(0.083) |
---|
| 709 | \end{verbatim} |
---|
| 710 | |
---|
| 711 | Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, |
---|
| 712 | which takes opacity effects into account (to first order). ASAP |
---|
| 713 | opacity corrections should not then be used for Mopra 3-mm data. |
---|
| 714 | |
---|
| 715 | \subsection{Frequency Frame Alignment} |
---|
| 716 | |
---|
| 717 | When time averaging a series of scans together, it is possible that the |
---|
| 718 | velocity scales are not exactly aligned. This may be for many reasons |
---|
| 719 | such as not Doppler tracking the observations, errors in the Doppler |
---|
| 720 | tracking etc. This mostly affects very long integrations or |
---|
| 721 | integrations averaged together from different days data. Before |
---|
| 722 | averaging such data together, they should be frequency aligned using |
---|
| 723 | \cmd{freq\_align}. |
---|
| 724 | |
---|
| 725 | E.g.: |
---|
| 726 | |
---|
| 727 | \begin{verbatim} |
---|
| 728 | ASAP> scans.freq_align() |
---|
| 729 | ASAP> av = average_time(scans) |
---|
| 730 | \end{verbatim} |
---|
| 731 | |
---|
| 732 | \cmd{freq\_align} has two modes of operations controlled by the |
---|
| 733 | \cmd{perif} argument. By default it will align each source and freqid |
---|
| 734 | separately. This is needed for scan tables containing multiple |
---|
| 735 | sources. However if scan-based Doppler tracking has been made at the observatory, |
---|
| 736 | each row will have a different freqid. In these cases run with |
---|
| 737 | \cmd{perif=True} and all rows of a source will be aligned to the same |
---|
| 738 | frame. In general \cmd{perif=True} will be needed for most |
---|
| 739 | observations as Doppler tracking of some form is made at Parkes, Tid |
---|
| 740 | and Mopra. |
---|
| 741 | |
---|
| 742 | \begin{verbatim} |
---|
| 743 | ASAP> scans.freq_align(perif=True) |
---|
| 744 | \end{verbatim} |
---|
| 745 | |
---|
| 746 | To average together data taken on different days, which are in |
---|
| 747 | different scantables, each scantable must aligned to a common |
---|
| 748 | reference time then the scantables averaged. The simplest way of |
---|
| 749 | doing this is to allow ASAP to choose the reference time for the first |
---|
| 750 | scantable then using this time for the subsequent scantables. |
---|
| 751 | |
---|
| 752 | \begin{verbatim} |
---|
| 753 | ASAP> scans1.freq_align() # Copy the refeference Epoch from the output |
---|
| 754 | ASAP> scans2.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 755 | ASAP> scans3.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 756 | ASAP> av = average_time(scans1, scans2, scans3) |
---|
| 757 | \end{verbatim} |
---|
| 758 | |
---|
| 759 | \section{Scantable manipulation} |
---|
| 760 | |
---|
| 761 | While it is very useful to have many independent sources within one |
---|
| 762 | scantable, it is often inconvenient for data processing. The |
---|
| 763 | \cmd{get\_scan} function can be used to create a new scantable with a |
---|
| 764 | selection of scans from a scantable. The selection can either be on |
---|
| 765 | the source name, with simple wildcard matching or set of scan ids. |
---|
| 766 | |
---|
| 767 | For example: |
---|
| 768 | |
---|
| 769 | \begin{verbatim} |
---|
| 770 | ASAP> ss = scans.get_scan(10) # Get the 11th scan (zero based) |
---|
| 771 | ASAP> ss = scans.get_scan(range(10)) # Get the first 10 scans |
---|
| 772 | ASAP> ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans |
---|
| 773 | |
---|
| 774 | ASAP> ss = scans.get_scan('345p407') # Get a specific source |
---|
| 775 | ASAP> ss = scans.get_scan('345*') # Get a few sources |
---|
| 776 | |
---|
| 777 | ASAP> r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra) |
---|
| 778 | ASAP> s = scans.get_scan('*_S') # Get all program sources (Parkes/Mopra) |
---|
| 779 | ASAP> r = scans.get_scan('*_[ew]') # Get all reference sources (Tid) |
---|
| 780 | ASAP> s = scans.get_scan('*_[^ew]') # Get all program sources (Tid) |
---|
| 781 | |
---|
| 782 | \end{verbatim} |
---|
| 783 | |
---|
| 784 | To copy a scantable the following does not work: |
---|
| 785 | |
---|
| 786 | \begin{verbatim} |
---|
| 787 | ASAP> ss = scans |
---|
| 788 | \end{verbatim} |
---|
| 789 | |
---|
| 790 | as this just creates a reference to the original scantable. Any changes |
---|
| 791 | made to \cmd{ss} and also seen in \cmd{scans}. To duplicate a |
---|
| 792 | scantable, use the copy function. |
---|
| 793 | |
---|
| 794 | \begin{verbatim} |
---|
| 795 | ASAP> ss = scans.copy |
---|
| 796 | \end{verbatim} |
---|
| 797 | |
---|
| 798 | \section{Data Output} |
---|
| 799 | |
---|
| 800 | ASAP can save scantables in a variety of formats, suitable for reading |
---|
| 801 | into other packages. The formats are: |
---|
| 802 | |
---|
| 803 | \begin{itemize} |
---|
| 804 | \item[ASAP] This is the internal format used for ASAP. It is the only |
---|
[537] | 805 | format that allows the user to restore the data, fits etc. without |
---|
[534] | 806 | loosing any information. As mentioned before, the ASAP scantable |
---|
| 807 | is just an AIPS++ Table (a memory-based table). |
---|
| 808 | This function just converts it to a disk-based |
---|
| 809 | Table. You can the access that Table with the AIPS++ Table browser |
---|
| 810 | or any other AIPS++ tool. |
---|
| 811 | |
---|
[537] | 812 | \item[SDFITS] The Single Dish FITS format. This format was |
---|
[534] | 813 | designed to for interchange between packages, but few packages |
---|
| 814 | actually can read it. |
---|
| 815 | |
---|
| 816 | \item[FITS] This uses simple ``image'' fits to save the data, each row |
---|
| 817 | being written to a separate fits file. This format is suitable for |
---|
| 818 | importing the data into CLASS. |
---|
| 819 | |
---|
| 820 | \item[ASCII] A simple text based format suitable for the user to |
---|
| 821 | processing using Perl or, Python, gnuplot etc. |
---|
| 822 | |
---|
| 823 | \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. |
---|
| 824 | You can also access this with the Table browser and other AIPS++ |
---|
| 825 | tools. |
---|
| 826 | |
---|
| 827 | \end{itemize} |
---|
| 828 | |
---|
| 829 | The default output format can be set in the users {\tt .asaprc} file. |
---|
| 830 | Typical usages are: |
---|
| 831 | |
---|
| 832 | \begin{verbatim} |
---|
| 833 | ASAP> scans.save('myscans') # Save in default format |
---|
| 834 | ASAP> scans.save('myscans', 'FITS') # Save as FITS for exporting into CLASS |
---|
| 835 | |
---|
| 836 | ASAP> scans.save('myscans', stokes=True) # Convert raw polarisations into Stokes |
---|
| 837 | ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file |
---|
| 838 | \end{verbatim} |
---|
| 839 | |
---|
| 840 | |
---|
| 841 | |
---|
| 842 | \section{Plotter} |
---|
| 843 | |
---|
| 844 | Scantable spectra can be plotter at any time. An asapplotter object is |
---|
| 845 | used for plotting, meaning multiple plot windows can be active at the |
---|
| 846 | same time. On start up a default asapplotter object is created called |
---|
| 847 | ``plotter''. This would normally be used for standard plotting. |
---|
| 848 | |
---|
| 849 | The plotter, optionally, will run in a mulipanel mode and contain |
---|
| 850 | multiple plots per panel. The user must tell the plotter how they want |
---|
| 851 | the data distributed. This is done using the set\_mode function. The |
---|
| 852 | default can be set in the users {\tt .asaprc} file. The units (and frame |
---|
| 853 | etc) of the abcissa will be whatever has previously been set by |
---|
| 854 | set\_unit, set\_freqframe etc. |
---|
| 855 | |
---|
| 856 | Typical plotter usage would be: |
---|
| 857 | |
---|
| 858 | \begin{verbatim} |
---|
| 859 | ASAP> scans.set_unit('km/s') |
---|
| 860 | ASAP> plotter.set_mode(stacking='p',panelling='t') |
---|
| 861 | ASAP> plotter.plot(scans) |
---|
| 862 | \end{verbatim} |
---|
| 863 | |
---|
| 864 | This will plot multiple polarisation within each plot panel and each |
---|
| 865 | scanrow in a separate panel. |
---|
| 866 | |
---|
| 867 | Other possbilities include: |
---|
| 868 | |
---|
| 869 | \begin{verbatim} |
---|
| 870 | # Plot multiple IFs per panel |
---|
| 871 | ASAP> plotter.set_mode(stacking='i',panelling='t') |
---|
| 872 | more???? |
---|
| 873 | \end{verbatim} |
---|
| 874 | |
---|
| 875 | \subsection{Plot control} |
---|
| 876 | |
---|
| 877 | The plotter window has a row of buttons on the lower left. These can |
---|
| 878 | be used to control the plotter (mostly for zooming the individual |
---|
| 879 | plots). From left to right: |
---|
| 880 | |
---|
| 881 | \begin{itemize} |
---|
| 882 | |
---|
| 883 | \item[Home] This will unzoom the plots to the original zoom factor |
---|
| 884 | |
---|
| 885 | \item[Plot history] (left and right arrow). The plotter keeps a |
---|
| 886 | history of zoom settings. The left arrow sets the plot zoom to the |
---|
| 887 | previous value. The right arrow returns back again. This allows you, |
---|
| 888 | for example, to zoom in on one feature then return the plot to how it |
---|
| 889 | was previously. |
---|
| 890 | |
---|
| 891 | \item[Pan] (The Cross) This sets the cursor to pan, or scroll mode |
---|
| 892 | allowing you to shift the plot within the window. Useful when |
---|
| 893 | zoomed in on a feature. |
---|
| 894 | |
---|
| 895 | \item[Zoom] (the letter with the magnifying glass) lets you draw a |
---|
| 896 | rectangle around a region of interest then zooms in on that |
---|
| 897 | region. Use the plot history to unzoom again. |
---|
| 898 | |
---|
| 899 | \item[Save] (floppy disk). Save the plot as a postscript or .png file |
---|
| 900 | |
---|
| 901 | \end{itemize} |
---|
| 902 | |
---|
| 903 | \subsection{Other control} |
---|
| 904 | |
---|
| 905 | The plotter has a number of functions to describe the layout of the |
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| 906 | plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. |
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| 907 | |
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| 908 | To set the exact velocity or channel range to be plotted use the |
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| 909 | \cmd{set\_range} function. To reset to the default value, call |
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| 910 | \cmd{set\_range} with no arguments. E.g. |
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| 911 | |
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| 912 | \begin{verbatim} |
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| 913 | ASAP> scans.set_unit('km/s') |
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| 914 | ASAP> plotter.plot(scans) |
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| 915 | ASAP> plotter.set_range(-150,-50) |
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| 916 | ASAP> plotter.set_range() |
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| 917 | \end{verbatim} |
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| 918 | |
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| 919 | To save a hardcopy of the current plot, use the save function, e.g. |
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| 920 | |
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| 921 | \begin{verbatim} |
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| 922 | ASAP> plotter.save('myplot.ps') |
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| 923 | \end{verbatim} |
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| 924 | |
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| 925 | \section{Fitting} |
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| 926 | |
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| 927 | Currently multicomponent Gaussian function is available. This is done |
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| 928 | by creating a fitting object, setting up the fit and actually fitting |
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| 929 | the data. Fitting can either be done on a single scantable row/cursor |
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| 930 | selection or on an entire scantable using the \cmd{auto\_fit} function. |
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| 931 | |
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| 932 | \begin{verbatim} |
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| 933 | ASAP> f = fitter() |
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| 934 | ASAP> f.set_function(gauss=2) # Fit two Gaussians |
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| 935 | ASAP> f.set_scan(scans) |
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| 936 | ASAP> scans.set_cursor(0,0,1) # Fit the second polarisation |
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| 937 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
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| 938 | ASAP> f.fit(1) # Run the fit on the second row in the table |
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| 939 | ASAP> f.plot() # Show fit in a plot window |
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| 940 | ASAP> f.get_parameters() # Return the fit paramaters |
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| 941 | \end{verbatim} |
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| 942 | |
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| 943 | This auto-guesses the initial values of the fit and works well for data |
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| 944 | without extra confusing features. Note that the fit is performed in |
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| 945 | whatever unit the abscissa is set to. |
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| 946 | |
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| 947 | If you want to confine the fitting to a smaller range (e.g. to avoid |
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| 948 | band edge effects or RFI you must set a mask. |
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| 949 | |
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| 950 | \begin{verbatim} |
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| 951 | ASAP> f = fitter() |
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| 952 | ASAP> f.set_function(gauss=2) |
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| 953 | ASAP> scans.set_unit('km/s') # Set the mask in channel units |
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| 954 | ASAP> msk = s.create_mask([1800,2200]) |
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| 955 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
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| 956 | ASAP> f.set_scan(s,msk) |
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| 957 | ASAP> f.fit() |
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| 958 | ASAP> f.plot() |
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| 959 | ASAP> f.get_parameters() |
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| 960 | \end{verbatim} |
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| 961 | |
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| 962 | If you wish, the initial parameter guesses can be specified specific |
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| 963 | parameters can be fixed: |
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| 964 | |
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| 965 | \begin{verbatim} |
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| 966 | ASAP> f = fitter() |
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| 967 | ASAP> f.set_function(gauss=2) |
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| 968 | ASAP> f.set_scan(s,msk) |
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| 969 | ASAP> f.fit() # Fit using auto-estimates |
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| 970 | # Set Peak, centre and fwhm for the second gaussian. |
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| 971 | # Force the centre to be fixed |
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| 972 | ASAP> f.set_gauss_parameters(0.4,450,150,0,1,0,component=1) |
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| 973 | ASAP> f.fit() # Re-run the fit |
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| 974 | \end{verbatim} |
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| 975 | |
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| 976 | The fitter \cmd{plot} function has a number of options to either view |
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| 977 | the fit residuals or the individual components (by default it plots |
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| 978 | the sum of the model components). |
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| 979 | |
---|
| 980 | Examples: |
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| 981 | |
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| 982 | \begin{verbatim} |
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| 983 | # Plot the residual |
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| 984 | ASAP> f.plot(residual=True) |
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| 985 | |
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| 986 | # Plot the first 2 componentsa |
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| 987 | ASAP> f.plot(components=[0,1]) |
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| 988 | |
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| 989 | # Plot the first and third component plus the model sum |
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| 990 | ASAP> f.plot(components=[-1,0,2]) # -1 means the compoment sum |
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| 991 | |
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| 992 | \end{verbatim} |
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| 993 | |
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| 994 | \section{Polarisation} |
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| 995 | |
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| 996 | Currently ASAP only supports polarmetric analysis on linearly |
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| 997 | polarised feeds and the cross polarisation products measured. Other |
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| 998 | cases will be added on an as needed basic. |
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| 999 | |
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| 1000 | But how do you actually do it... |
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| 1001 | |
---|
| 1002 | \section{Function Summary} |
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| 1003 | |
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| 1004 | \begin{verbatim} |
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| 1005 | |
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| 1006 | [The scan container] |
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| 1007 | scantable - a container for integrations/scans |
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| 1008 | (can open asap/rpfits/sdfits and ms files) |
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| 1009 | copy - returns a copy of a scan |
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| 1010 | get_scan - gets a specific scan out of a scantable |
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| 1011 | summary - print info about the scantable contents |
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| 1012 | set_cursor - set a specific Beam/IF/Pol 'cursor' for |
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| 1013 | further use |
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| 1014 | get_cursor - print out the current cursor position |
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| 1015 | stats - get specified statistic of the spectra in |
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| 1016 | the scantable |
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| 1017 | stddev - get the standard deviation of the spectra |
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| 1018 | in the scantable |
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| 1019 | get_tsys - get the TSys |
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| 1020 | get_time - get the timestamps of the integrations |
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| 1021 | get_unit - get the currnt unit |
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| 1022 | set_unit - set the abcissa unit to be used from this |
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| 1023 | point on |
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| 1024 | get_abcissa - get the abcissa values and name for a given |
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| 1025 | row (time) |
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| 1026 | set_freqframe - set the frame info for the Spectral Axis |
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| 1027 | (e.g. 'LSRK') |
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| 1028 | set_doppler - set the doppler to be used from this point on |
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| 1029 | set_instrument - set the instrument name |
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| 1030 | get_fluxunit - get the brightness flux unit |
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| 1031 | set_fluxunit - set the brightness flux unit |
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| 1032 | create_mask - return an mask in the current unit |
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| 1033 | for the given region. The specified regions |
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| 1034 | are NOT masked |
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| 1035 | get_restfreqs - get the current list of rest frequencies |
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| 1036 | set_restfreqs - set a list of rest frequencies |
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| 1037 | lines - print list of known spectral lines |
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| 1038 | flag_spectrum - flag a whole Beam/IF/Pol |
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| 1039 | save - save the scantable to disk as either 'ASAP' |
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| 1040 | or 'SDFITS' |
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| 1041 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
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| 1042 | history - print the history of the scantable |
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| 1043 | |
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| 1044 | average_time - return the (weighted) time average of a scan |
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| 1045 | or a list of scans |
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| 1046 | average_pol - average the polarisations together. |
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| 1047 | The dimension won't be reduced and |
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| 1048 | all polarisations will contain the |
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| 1049 | averaged spectrum. |
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| 1050 | quotient - return the on/off quotient |
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| 1051 | scale - return a scan scaled by a given factor |
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| 1052 | add - return a scan with given value added |
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| 1053 | bin - return a scan with binned channels |
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| 1054 | resample - return a scan with resampled channels |
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| 1055 | smooth - return the spectrally smoothed scan |
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| 1056 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
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| 1057 | gain_el - apply gain-elevation correction |
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| 1058 | opacity - apply opacity correction |
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| 1059 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
| 1060 | units |
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| 1061 | freq_align - align spectra in frequency frame |
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| 1062 | rotate_xyphase - rotate XY phase of cross correlation |
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| 1063 | rotate_linpolphase - rotate the phase of the complex |
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| 1064 | polarization O=Q+iU correlation |
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| 1065 | [Math] Mainly functions which operate on more than one scantable |
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| 1066 | |
---|
| 1067 | average_time - return the (weighted) time average |
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| 1068 | of a list of scans |
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| 1069 | quotient - return the on/off quotient |
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| 1070 | simple_math - simple mathematical operations on two scantables, 'add', 'sub', 'mul', 'div' |
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| 1071 | [Fitting] |
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| 1072 | fitter |
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| 1073 | auto_fit - return a scan where the function is |
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| 1074 | applied to all Beams/IFs/Pols. |
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| 1075 | commit - return a new scan where the fits have been |
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| 1076 | commited. |
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| 1077 | fit - execute the actual fitting process |
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| 1078 | get_chi2 - get the Chi^2 |
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| 1079 | set_scan - set the scantable to be fit |
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| 1080 | set_function - set the fitting function |
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| 1081 | set_parameters - set the parameters for the function(s), and |
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| 1082 | set if they should be held fixed during fitting |
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| 1083 | set_gauss_parameters - same as above but specialised for individual gaussian components |
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| 1084 | get_parameters - get the fitted parameters |
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| 1085 | plot - plot the resulting fit and/or components and |
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| 1086 | residual |
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| 1087 | [Plotter] |
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| 1088 | asapplotter - a plotter for asap, default plotter is |
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| 1089 | called 'plotter' |
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| 1090 | plot - plot a (list of) scantable |
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| 1091 | save - save the plot to a file ('png' ,'ps' or 'eps') |
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| 1092 | set_mode - set the state of the plotter, i.e. |
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| 1093 | what is to be plotted 'colour stacked' |
---|
| 1094 | and what 'panelled' |
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| 1095 | set_range - set the abcissa 'zoom' range |
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| 1096 | set_legend - specify user labels for the legend indeces |
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| 1097 | set_title - specify user labels for the panel indeces |
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| 1098 | set_ordinate - specify a user label for the ordinate |
---|
| 1099 | set_abcissa - specify a user label for the abcissa |
---|
| 1100 | set_layout - specify the multi-panel layout (rows,cols) |
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| 1101 | |
---|
| 1102 | [Reading files] |
---|
| 1103 | reader - access rpfits/sdfits files |
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| 1104 | read - read in integrations |
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| 1105 | summary - list info about all integrations |
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| 1106 | |
---|
| 1107 | [General] |
---|
| 1108 | commands - this command |
---|
| 1109 | print - print details about a variable |
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| 1110 | list_scans - list all scantables created bt the user |
---|
| 1111 | del - delete the given variable from memory |
---|
| 1112 | range - create a list of values, e.g. |
---|
| 1113 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 1114 | help - print help for one of the listed functions |
---|
| 1115 | execfile - execute an asap script, e.g. execfile('myscript') list_rcparameters - print out a list of possible values to be |
---|
| 1116 | put into $HOME/.asaprc |
---|
| 1117 | mask_and,mask_or, |
---|
| 1118 | mask_not - boolean operations on masks created with |
---|
| 1119 | scantable.create_mask |
---|
| 1120 | |
---|
| 1121 | Note: |
---|
| 1122 | How to use this with help: |
---|
| 1123 | # function 'summary' |
---|
| 1124 | [xxx] is just a category |
---|
| 1125 | Every 'sub-level' in this list should be replaces by a '.' Period when using help |
---|
| 1126 | Example: |
---|
| 1127 | ASAP> help scantable # to get info on ths scantable |
---|
| 1128 | ASAP> help scantable.summary # to get help on the scantable's |
---|
| 1129 | ASAP> help average_time |
---|
| 1130 | |
---|
| 1131 | |
---|
| 1132 | \end{verbatim} |
---|
| 1133 | |
---|
| 1134 | \section{Scripting} |
---|
| 1135 | |
---|
| 1136 | Malte to add something |
---|
| 1137 | |
---|
| 1138 | \section{Appendix} |
---|
| 1139 | |
---|
| 1140 | \subsection{Installation} |
---|
| 1141 | |
---|
| 1142 | |
---|
| 1143 | ASAP depends on a number of third-party libraries which you must |
---|
| 1144 | have installed before attempting to build ASAP. These are: |
---|
| 1145 | |
---|
| 1146 | \begin{itemize} |
---|
| 1147 | \item AIPS++ |
---|
| 1148 | \item Boost |
---|
| 1149 | \item Matplotlib |
---|
| 1150 | \item ipython/python |
---|
| 1151 | \end{itemize} |
---|
| 1152 | |
---|
| 1153 | Debian Linux is currently supported and we intend also |
---|
| 1154 | to support other popular Linux flavours, Solaris and Mac. |
---|
| 1155 | |
---|
| 1156 | Of the dependencies, AIPS++ is the most complex to install. |
---|
| 1157 | |
---|
| 1158 | \subsection{ASCII output format} |
---|
| 1159 | |
---|
| 1160 | \subsection{.asaprc settings} |
---|
| 1161 | |
---|
| 1162 | \end{document} |
---|
| 1163 | |
---|
| 1164 | |
---|