[534] | 1 | \documentclass[11pt]{article} |
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| 2 | \usepackage{a4} |
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[770] | 3 | \usepackage{calc} |
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[534] | 4 | \usepackage[dvips]{graphicx} |
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[794] | 5 | \usepackage{makeidx} |
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[534] | 6 | |
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| 7 | % Adjust the page size |
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| 8 | \addtolength{\oddsidemargin}{-0.4in} |
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| 9 | \addtolength{\evensidemargin}{+0.4in} |
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| 10 | \addtolength{\textwidth}{+0.8in} |
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| 11 | |
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| 12 | \setlength{\parindent}{0mm} |
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| 13 | \setlength{\parskip}{1ex} |
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| 14 | |
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[1757] | 15 | \title{ATNF Spectral Analysis Package\\User Guide v2.3 } |
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[534] | 16 | \author{Chris Phillips} |
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| 17 | |
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| 18 | \newcommand{\cmd}[1]{{\tt #1}} |
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| 19 | |
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[770] | 20 | \newcommand{\asaprc}[3]{ |
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| 21 | \begin{minipage}[t]{45mm}#1\end{minipage} |
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| 22 | \begin{minipage}[t]{30mm}\raggedright #2\end{minipage}\hspace{3mm} |
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| 23 | \begin{minipage}[t]{\textwidth-75mm}#3\end{minipage} |
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| 24 | } |
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| 25 | |
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[1217] | 26 | \newcommand{\commanddef}[3]{ |
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| 27 | \begin{minipage}[t]{27mm}\tt #1\end{minipage}\hspace{3mm} |
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| 28 | \begin{minipage}[t]{\textwidth-30mm}#2 \\ \tt #3\end{minipage} |
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| 29 | } |
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| 30 | |
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| 31 | \newcommand{\bigcommanddef}[3]{ |
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| 32 | \begin{minipage}[t]{45mm}\tt #1\end{minipage}\hspace{3mm} |
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| 33 | \begin{minipage}[t]{\textwidth-47mm}#2 \\ \tt #3\end{minipage} |
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| 34 | } |
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| 35 | |
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[794] | 36 | \makeindex |
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| 37 | |
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[534] | 38 | \begin{document} |
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| 39 | |
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| 40 | \maketitle |
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| 41 | |
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| 42 | \section{Introduction} |
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| 43 | |
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[544] | 44 | ASAP is a single dish spectral line processing package currently being |
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| 45 | developed by the ATNF. It is intended to process data from all ATNF |
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[770] | 46 | antennas, and can probably be used for other antennas if they can |
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[544] | 47 | produce ``Single Dish FITS'' format. It is based on the AIPS++ |
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| 48 | package. |
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| 49 | |
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[1757] | 50 | This userguide has been updated for the ASAP 2.3. Please report any |
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[1217] | 51 | mistakes you find. |
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[534] | 52 | |
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[544] | 53 | \section{Installation and Running} |
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[534] | 54 | |
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[738] | 55 | Currently there are installations running on Linux machines at |
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[534] | 56 | |
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| 57 | \begin{itemize} |
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| 58 | \item Epping - use hosts {\tt draco} or {\tt hydra} |
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| 59 | \item Narrabri - use host {\tt kaputar} |
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[1757] | 60 | \item Parkes - use host {\tt ?} |
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| 61 | \item Mopra - use host {\tt minos} or {\tt kaputar} if at Narrabri |
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[534] | 62 | \end{itemize} |
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| 63 | |
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[1217] | 64 | Or use your own Linux desktop. |
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| 65 | |
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[1757] | 66 | {\em Note. ASAP2.2 only runs on ATNF Linux machines which have been |
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[1267] | 67 | updated to Debian Sarge and are using the ``DEBIANSarge'' |
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[1217] | 68 | /usr/local. If your favourite machine has not been upgraded, send a |
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[1757] | 69 | request to your friendly IT support.} |
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[1217] | 70 | |
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[794] | 71 | \index{Running}To start asap log onto one of these Linux hosts and enter |
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[534] | 72 | |
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| 73 | \begin{verbatim} |
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| 74 | > cd /my/data/directory |
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[966] | 75 | > asap |
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[534] | 76 | \end{verbatim} |
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| 77 | |
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[1267] | 78 | This starts ASAP. To quit, you need to type \verb+^+-d (control-d) or |
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| 79 | type \cmd{\%Exit}. |
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[534] | 80 | |
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| 81 | \section{Interface} |
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| 82 | |
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[1064] | 83 | \index{Interface}ASAP is written in C++ and python. The user interface |
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| 84 | uses the ``ipython'' interactive shell, which is a simple interactive |
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| 85 | interface to python. The user does not need to understand python to |
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| 86 | use this, but certain aspects python affect what the user can do. The |
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| 87 | current interface is object oriented. |
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[534] | 88 | |
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| 89 | \subsection {Integer Indices are 0-relative} |
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| 90 | |
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| 91 | Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. |
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| 92 | |
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| 93 | \subsection{Objects} |
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[794] | 94 | \index{objects} |
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[534] | 95 | The ASAP interface is based around a number of ``objects'' which the |
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| 96 | user deals with. Objects range from the data which have been read from |
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| 97 | disk, to tools used for fitting functions to the data. The following |
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| 98 | main objects are used : |
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| 99 | |
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[1267] | 100 | \begin{tabular}{ll} |
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[534] | 101 | |
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[1267] | 102 | \cmd{scantable} & \parbox[t]{0.7\textwidth}{The data container (actual |
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| 103 | spectra and header information)} \\ |
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| 104 | \cmd{selector} & \parbox[t]{0.80\textwidth}{Allows the user to select |
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| 105 | a subsection of the data, such as a specified or range of beam |
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| 106 | numbers, IFs, etc.} \\ |
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| 107 | \cmd{plotter} & A tool used to plot the spectral line data \\ |
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| 108 | \cmd{fitter} & A tool used to fit functions to the spectral data \\ |
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| 109 | \cmd{reader} & \parbox[t]{0.8\textwidth}{A tool which can be used to |
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| 110 | read data from disks into a scantable object (advanced use).}\\ |
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| 111 | \end{tabular} |
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| 112 | |
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[738] | 113 | There can be many objects of the same type. Each object is referred to |
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[534] | 114 | by a variable name made by the user. The name of this variable is not |
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[770] | 115 | important and can be set to whatever the user prefers (i.e. ``s'' and |
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[534] | 116 | ``ParkesHOH-20052002'' are equivalent). However, having a simple and |
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| 117 | consistent naming convention will help you a lot. |
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| 118 | |
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[544] | 119 | \subsection{Member Functions (functions)} |
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[534] | 120 | |
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[794] | 121 | \index{Functions!member}Following the object oriented approach, |
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| 122 | objects have associated ``member functions'' which can either be used |
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| 123 | to modify the data in some way or change global properties of the |
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| 124 | object. In this document member functions will be referred to simply |
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| 125 | as functions. From the command line, the user can execute these |
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| 126 | functions using the syntax: |
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[534] | 127 | \begin{verbatim} |
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[1259] | 128 | ASAP>out = object.function(arguments) |
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[534] | 129 | \end{verbatim} |
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| 130 | |
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| 131 | Where \cmd{out} is the name of the returned variable (could be a new |
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[544] | 132 | scantable object, or a vector of data, or a status return), |
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| 133 | \cmd{object} is the object variable name (set by the user), |
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| 134 | \cmd{function} is the name of the member function and \cmd{arguments} |
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| 135 | is a list of arguments to the function. The arguments can be provided |
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| 136 | either though position or \cmd{name=}. A mix of the two can be used. |
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| 137 | E.g. |
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[534] | 138 | |
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| 139 | \begin{verbatim} |
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[1259] | 140 | ASAP>av = scans.average_time(msk,weight='tsys') |
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| 141 | ASAP>av = scans.average_time(mask=msk,weight='tsys') |
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| 142 | ASAP>av = scans.average_time(msk,tsys) |
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| 143 | ASAP>scans.poly_baseline(mask=msk, order=0, insitu=True) |
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| 144 | ASAP>scans.poly_baseline(msk,0,True) |
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| 145 | ASAP>scans.poly_baseline(mask, insitu=True) |
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[534] | 146 | \end{verbatim} |
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| 147 | |
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| 148 | \subsection{Global Functions} |
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| 149 | |
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[794] | 150 | \index{Functions!global}It does not make sense to implement some functions as member |
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[544] | 151 | functions, typically functions which operate on more than one |
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| 152 | scantable (e.g. time averaging of many scans). These functions will |
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| 153 | always be referred to as global functions. |
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[534] | 154 | |
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[538] | 155 | \subsection{Interactive environment} |
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[534] | 156 | |
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[794] | 157 | \index{ipython!environment}ipython has a number of useful interactive |
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| 158 | features and a few things to be aware of for the new user. |
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[534] | 159 | |
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| 160 | \subsubsection{String completion} |
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| 161 | |
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[794] | 162 | \index{ipython!string completion}Tab completion is enabled for all |
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| 163 | function names. If you type the first few letters of a function name, |
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| 164 | then type {\tt <TAB>} the function name will be auto completed if it |
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| 165 | is un-ambiguous, or a list of possibilities will be |
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| 166 | given. Auto-completion works for the user object names as well as |
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[1757] | 167 | function names and even file names It does not work for for function |
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[794] | 168 | arguments. |
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[534] | 169 | |
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| 170 | Example |
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| 171 | \begin{verbatim} |
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[1259] | 172 | ASAP>scans = scantable('MyData.rpf') |
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| 173 | ASAP>scans.se<TAB> |
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| 174 | ASAP>scans.set_in<TAB> |
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[971] | 175 | scans.set_cursor scans.set_freqframe scans.set_selection |
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| 176 | scans.set_doppler scans.set_instrument scans.set_unit |
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| 177 | scans.set_fluxunit scans.set_restfreqs |
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| 178 | |
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[1259] | 179 | ASAP>scans.set_instrument() |
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[534] | 180 | \end{verbatim} |
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| 181 | |
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[544] | 182 | \subsubsection{Leading Spaces} |
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| 183 | |
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[794] | 184 | \index{ipython!leading space}Python uses leading space to mark blocks |
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| 185 | of code. This means that it you start a command line with a space, the |
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| 186 | command generally will fail with an syntax error. |
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[544] | 187 | |
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[770] | 188 | \subsubsection{Variable Names} |
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| 189 | |
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[794] | 190 | \index{ipython!variable names}During normal data processing, the user |
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| 191 | will have to create named variables to hold spectra etc. These must |
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| 192 | conform to the normal python syntax, specifically they cannot contain |
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| 193 | ``special'' characters such as \@ \$ etc and cannot start with a |
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| 194 | number (but can contain numbers). Variable (and function) names are |
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| 195 | case sensitive. |
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[770] | 196 | |
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[534] | 197 | \subsubsection{Unix Interaction} |
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| 198 | |
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[794] | 199 | \index{ipython!unix interaction}Basic unix shell commands (\cmd{pwd}, |
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| 200 | \cmd{ls}, \cmd{cd} etc) can be issued from within ASAP. This allows |
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| 201 | the user to do things like look at files in the current directory. The |
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| 202 | shell command ``\cmd{cd}'' works within ASAP, allowing the user to |
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| 203 | change between data directories. Unix programs cannot be run this way, |
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| 204 | but the shell escape ``$!$'' can be used to run arbitrary |
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| 205 | programs. E.g. |
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[534] | 206 | |
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| 207 | \begin{verbatim} |
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[1259] | 208 | ASAP>pwd |
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| 209 | ASAP>ls |
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| 210 | ASAP>cd /my/data/directory |
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[1757] | 211 | ASAP>! firefox& |
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[534] | 212 | \end{verbatim} |
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| 213 | |
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| 214 | \subsection{Help} |
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| 215 | |
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[794] | 216 | \index{Help}ASAP has built in help for all functions. To get a list of |
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| 217 | functions type: |
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[534] | 218 | |
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[538] | 219 | \begin{verbatim} |
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[1259] | 220 | ASAP>commands() |
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[538] | 221 | \end{verbatim} |
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| 222 | |
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| 223 | To get help on specific functions, the built in help needs to be given |
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| 224 | the object and function name. E.g. |
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| 225 | |
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| 226 | \begin{verbatim} |
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[1259] | 227 | ASAP>help scantable.get_scan # or help(scantable.get_scan) |
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| 228 | ASAP>help scantable.stats |
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| 229 | ASAP>help plotter.plot |
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| 230 | ASAP>help fitter.plot |
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[538] | 231 | |
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[1259] | 232 | ASAP>scans = scantable('mydata.asap') |
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| 233 | ASAP>help scans.get_scan # Same as above |
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[544] | 234 | \end{verbatim} |
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[538] | 235 | |
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[544] | 236 | Global functions just need their name |
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[538] | 237 | |
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[544] | 238 | \begin{verbatim} |
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[1259] | 239 | ASAP>help average_time |
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[538] | 240 | \end{verbatim} |
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| 241 | |
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| 242 | Note that if you just type \cmd{help} the internal ipython help is |
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| 243 | invoked, which is probably {\em not} what you want. Type \verb+^+-d |
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| 244 | (control-d) to escape from this. |
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| 245 | |
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[738] | 246 | \subsection{Customisation - .asaprc} |
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[534] | 247 | |
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[794] | 248 | \index{.asaprc}ASAP use an \cmd{.asaprc} file to control the user's |
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| 249 | preference of default values for various functions arguments. This |
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| 250 | includes the defaults for arguments such as \cmd{insitu}, scantable |
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| 251 | \cmd{freqframe} and the plotters \cmd{set\_mode} values. The help on |
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| 252 | individual functions says which arguments can be set default values |
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| 253 | from the \cmd{.asaprc} file. To get a sample contents for the |
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[1064] | 254 | \cmd{.asaprc} file use the command \cmd{list\_rcparameters}. |
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[534] | 255 | |
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[538] | 256 | Common values include: |
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| 257 | \begin{verbatim} |
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| 258 | # apply operations on the input scantable or return new one |
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| 259 | insitu : False |
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| 260 | |
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[738] | 261 | # default output format when saving scantable |
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[953] | 262 | scantable.save : ASAP |
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[538] | 263 | |
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| 264 | # default frequency frame to set when function |
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| 265 | # scantable.set_freqframe is called |
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[953] | 266 | scantable.freqframe : LSRK |
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[538] | 267 | |
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| 268 | # auto averaging on read |
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| 269 | scantable.autoaverage : True |
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| 270 | \end{verbatim} |
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| 271 | |
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[953] | 272 | For a complete list of \cmd{.asaprc} values, see the Appendix. |
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[770] | 273 | |
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[534] | 274 | \section{Scantables} |
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[794] | 275 | \index{Scantables} |
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[534] | 276 | \subsection {Description} |
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| 277 | |
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| 278 | \subsubsection {Basic Structure} |
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| 279 | |
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[794] | 280 | \index{Scantable!structure}ASAP data handling works on objects called |
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| 281 | scantables. A scantable holds your data, and also provides functions |
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| 282 | to operate upon it. |
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[534] | 283 | |
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| 284 | The building block of a scantable is an integration, which is a single |
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[1217] | 285 | row of a scantable. Each row contains just one spectrum for each beam, |
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| 286 | IF and polarisation. For example Parkes OH-multibeam data would |
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| 287 | normally contain 13 beams, 1 IF and 2 polarisations, Parkes |
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| 288 | methanol-multibeam data would contain 7 beams, 2 IFs and 2 |
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[1259] | 289 | polarisations while the Mopra 8-GHz MOPS filterbank will produce one |
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[1217] | 290 | beam, many IFs, and 2-4 polarisations. |
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| 291 | |
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| 292 | All of the combinations of Beams/IFs an Polarisations are |
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[1259] | 293 | contained in separate rows. These rows are grouped in cycles (same time stamp). |
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[534] | 294 | |
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[1217] | 295 | A collection of cycles for one source is termed a scan (and each scan |
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| 296 | has a unique numeric identifier, the SCANNO). A scantable is then a |
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| 297 | collection of one or more scans. If you have scan-averaged your data |
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[1259] | 298 | in time, i.e. you have averaged all cycles within a scan, then each |
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[1217] | 299 | scan would hold just one (averaged) integration. |
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[534] | 300 | |
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[1217] | 301 | Many of the functions which work on scantables can either return a new |
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| 302 | scantable with modified data or change the scantable insitu. Which |
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[534] | 303 | method is used depends on the users preference. The default can be |
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| 304 | changed via the {\tt .asaprc} resource file. |
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| 305 | |
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[1259] | 306 | For example a Mopra scan with a 4s integration time, two IFs and |
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[1011] | 307 | dual polarisations has two (2s) cycles. |
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| 308 | \begin{verbatim} |
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[1064] | 309 | SCANNO CYCLENO BEAMNO IFNO POLNO |
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| 310 | 0 0 0 0 0 |
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| 311 | 0 0 0 0 1 |
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| 312 | 0 0 0 1 0 |
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| 313 | 0 0 0 1 1 |
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| 314 | 0 1 0 0 0 |
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| 315 | 0 1 0 0 1 |
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| 316 | 0 1 0 1 0 |
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| 317 | 0 1 0 1 1 |
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[1011] | 318 | \end{verbatim} |
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| 319 | |
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| 320 | |
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[534] | 321 | \subsubsection {Contents} |
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| 322 | |
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[794] | 323 | \index{Scantable!contents}A scantable has header information and data |
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[953] | 324 | (a scantable is actually an AIPS++ Table and it is generally stored in |
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| 325 | memory when you are manipulating it with ASAP. You can save it to |
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| 326 | disk and then browse it with the AIPS++ Table browser if you know how |
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| 327 | to do that !). |
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[534] | 328 | |
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| 329 | The data are stored in columns (the length of a column is the number of |
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[1011] | 330 | rows/spectra of course). |
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[534] | 331 | |
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| 332 | Two important columns are those that describe the frequency setup. We mention |
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[538] | 333 | them explicitly here because you need to be able to understand the presentation |
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[534] | 334 | of the frequency information and possibly how to manipulate it. |
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| 335 | |
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[1011] | 336 | These columns are called FREQ\_ID and MOLECULE\_ID. They contain indices, for |
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[971] | 337 | each IF, pointing into tables with all of the frequency and rest-frequency |
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[1054] | 338 | information for that integration. |
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[534] | 339 | |
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| 340 | There are of course many other columns which contain the actual spectra, |
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[971] | 341 | the flags, the Tsys, the source names and so on. |
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[534] | 342 | |
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| 343 | There is also a function \cmd{summary} to list a summary of the scantable. |
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| 344 | You will find this very useful. |
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| 345 | |
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| 346 | Example: |
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| 347 | |
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| 348 | \begin{verbatim} |
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[1259] | 349 | ASAP>scans = scantable('MyData.rpf') |
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| 350 | ASAP>scans.summary() # Brief listing |
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[544] | 351 | |
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| 352 | # Equivalent to brief summary function call |
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[1757] | 353 | ASAP>print scans |
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[534] | 354 | \end{verbatim} |
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| 355 | |
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[971] | 356 | The summary function gives you a scan-based summary, presenting the |
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[1054] | 357 | scantable as a cascading view of Beams and IFs. Note that the output |
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| 358 | of summary is redirected into your current pager specified by the |
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| 359 | \$PAGER environment variable. If you find the screen is reset to the |
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[1259] | 360 | original state when summary is finished (i.e. the output from summary |
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[1054] | 361 | disappears), you may need to set the \$LESS environment variable to |
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| 362 | include the \cmd{-X} option. |
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[534] | 363 | |
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[953] | 364 | \subsection{Data Selection} |
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| 365 | \label{sec:selection} |
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| 366 | |
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[966] | 367 | ASAP contains flexible data selection. Data can be selected based on |
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| 368 | IF, beam, polarisation, scan number as well as values such as |
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| 369 | Tsys. Advanced users can also make use of the AIPS++ TAQL language to |
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[971] | 370 | create selections based on almost any of the values recorded. |
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[953] | 371 | |
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[966] | 372 | Selection is based on a \cmd{selector} object. This object is created |
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| 373 | and various selection functions applied to it (\cmd{set\_ifs}, |
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| 374 | \cmd{set\_beams} etc). The selection object then must be applied to a |
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| 375 | scantable using the \cmd{set\_selection} function. A single selection |
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| 376 | object can be created and setup then applied to multiple scantables. |
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[534] | 377 | |
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[966] | 378 | Once a selection has been applied, all following functions will only |
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| 379 | ``see'' the selected spectra (including functions such as |
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| 380 | \cmd{summary}). The selection can then be reset and all spectra are |
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| 381 | visible. Note that if functions such as \cmd{copy} are run on a |
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| 382 | scantable with active selection, only the selected spectra are copied. |
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[534] | 383 | |
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[966] | 384 | The common selection functions are: |
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[534] | 385 | |
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[1267] | 386 | \begin{tabular}{ll} |
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[966] | 387 | |
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[1267] | 388 | \cmd{set\_beams} & Select beams by index number \\ |
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| 389 | \cmd{set\_ifs} & Select ifs by index number \\ |
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| 390 | \cmd{set\_name} & Select by source name. Can contain ``*'' as a |
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| 391 | wildcard, e.g. ``Orion*\_R''. \\ |
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| 392 | \cmd{set\_ifs} & Select IFs by index number \\ |
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[966] | 393 | |
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[1267] | 394 | \cmd{set\_polarisation} & \parbox[t]{0.73\textwidth}{Select by |
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| 395 | polarisation index or name. If polarisation names are given, the data |
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| 396 | will be on-the-fly onverted (for example from linears to Stokes). }\\ |
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[966] | 397 | |
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[1267] | 398 | \cmd{set\_query} & Set query directly. For power users only! \\ |
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| 399 | \cmd{set\_tsys} & Select data based on Tsys. Also example of user |
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| 400 | definable query. \\ |
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| 401 | \cmd{reset} & Reset the selection to include all spectra. \\ |
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| 402 | |
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| 403 | \end{tabular} |
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| 404 | |
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[966] | 405 | Note that all indices are zero based. |
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| 406 | |
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| 407 | Examples: |
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| 408 | |
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| 409 | \begin{verbatim} |
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[1259] | 410 | ASAP>selection = selector() # Create selection object |
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| 411 | ASAP>selection.set_ifs(0) # Just select the first IF |
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| 412 | ASAP>scans.set_selection(selection) # Apply the selection |
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| 413 | ASAP>print scans # Will just show the first IF |
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[966] | 414 | |
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[1259] | 415 | ASAP>selection.set_ifs([0,1]) # Select the first two IFs |
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| 416 | ASAP>selection.set_beams([1,3,5]) # Also select three of the beams |
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| 417 | ASAP>scans.set_selection(selection) # Apply the selection |
---|
[966] | 418 | |
---|
[1259] | 419 | ASAP>selection.set_name('G308*') # Select by source name |
---|
[966] | 420 | |
---|
[1259] | 421 | ASAP>selection.reset() # Turn off selection |
---|
| 422 | ASAP>scans.set_selection(selection) # Apply the reset selection |
---|
[1757] | 423 | ASAP>scans.set_selection() # alternative to reset selection |
---|
[966] | 424 | |
---|
[970] | 425 | \end{verbatim} |
---|
| 426 | |
---|
[534] | 427 | \subsection{State} |
---|
| 428 | |
---|
[794] | 429 | \index{Scantable!state}Each scantable contains "state"; these are |
---|
| 430 | properties applying to all of the data in the scantable. |
---|
[534] | 431 | |
---|
| 432 | Examples are the selection of beam, IF and polarisation, spectral unit |
---|
[770] | 433 | (e.g. km/s), frequency reference frame (e.g. BARY) and velocity Doppler |
---|
[534] | 434 | type (e.g. RADIO). |
---|
| 435 | |
---|
| 436 | \subsubsection{Units, Doppler and Frequency Reference Frame} |
---|
| 437 | |
---|
| 438 | The information describing the frequency setup for each integration |
---|
| 439 | is stored fundamentally in frequency in the reference frame |
---|
[738] | 440 | of observation (E.g. TOPO). |
---|
[534] | 441 | |
---|
[544] | 442 | When required, this is converted to the desired reference frame |
---|
| 443 | (e.g. LSRK), Doppler (e.g. OPTICAL) and unit (e.g. km/s) on-the-fly. |
---|
| 444 | This is important, for example, when you are displaying the data or |
---|
[971] | 445 | fitting to it. The reference frame is set on file read to the value |
---|
| 446 | set in the user \cmd{.asaprc} file. |
---|
[534] | 447 | |
---|
| 448 | For units, the user has the choice of frequency, velocity or channel. |
---|
| 449 | The \cmd{set\_unit} function is used to set the current unit for a |
---|
| 450 | scantable. All functions will (where relevant) work with the selected |
---|
| 451 | unit until this changes. This is mainly important for fitting (the fits |
---|
[738] | 452 | can be computed in any of these units), plotting and mask creation. |
---|
[534] | 453 | |
---|
[544] | 454 | The velocity definition can be changed with the \cmd{set\_doppler} |
---|
| 455 | function, and the frequency reference frame can be changed with the |
---|
[534] | 456 | \cmd{set\_freqframe} function. |
---|
| 457 | |
---|
| 458 | Example usage: |
---|
| 459 | |
---|
| 460 | \begin{verbatim} |
---|
[1259] | 461 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data |
---|
[1757] | 462 | ASAP>scans.set_freqframe('LSRK') # Use the LSR velocity frame |
---|
[1259] | 463 | ASAP>scans.set_unit('km/s') # Use velocity for plots etc from now on |
---|
| 464 | ASAP>scans.set_doppler('OPTICAL') # Use the optical velocity convention |
---|
| 465 | ASAP>scans.set_unit('MHz') # Use frequency in MHz from now on |
---|
[534] | 466 | \end{verbatim} |
---|
| 467 | |
---|
| 468 | |
---|
| 469 | \subsubsection{Rest Frequency} |
---|
| 470 | |
---|
[794] | 471 | \index{Scantable!rest frequency}ASAP reads the line rest frequency |
---|
| 472 | from the RPFITS file when reading the data. The values stored in the |
---|
| 473 | RPFITS file are not always correct and so there is a function |
---|
[953] | 474 | \cmd{set\_restfreq} to set the rest frequencies for the currently |
---|
| 475 | selected data. |
---|
[534] | 476 | |
---|
| 477 | For each integration, there is a rest-frequency per IF (the rest |
---|
| 478 | frequencies are just stored as a list with an index into them). |
---|
| 479 | There are a few ways to set the rest frequencies with this function. |
---|
| 480 | |
---|
[953] | 481 | If you specify just one rest frequency, then it is set for all IF. |
---|
[534] | 482 | |
---|
| 483 | \begin{verbatim} |
---|
[953] | 484 | # Set all IFs |
---|
[1259] | 485 | ASAP>scans.set_restfreqs(freqs=1.667359e9) |
---|
[534] | 486 | \end{verbatim} |
---|
| 487 | |
---|
[953] | 488 | If set a rest frequency for each IF, specify a list of frequencies (of |
---|
| 489 | length the number of IFs). Regardless of the source, the rest |
---|
| 490 | frequency will be set for each IF to the corresponding value in the |
---|
[970] | 491 | provided list. |
---|
[534] | 492 | |
---|
| 493 | \begin{verbatim} |
---|
[770] | 494 | # Set rest frequency for all IFs |
---|
[1259] | 495 | ASAP>scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,]) |
---|
[538] | 496 | |
---|
[534] | 497 | \end{verbatim} |
---|
| 498 | |
---|
[1267] | 499 | A predetermined ``line catalog'' can be used to set the rest |
---|
| 500 | frequency. See section \S \ref{sec:linecat}. |
---|
[953] | 501 | |
---|
[534] | 502 | |
---|
| 503 | \subsubsection{Masks} |
---|
| 504 | |
---|
[970] | 505 | \index{Masks}\index{Scantable!masks} |
---|
[534] | 506 | |
---|
[966] | 507 | Many tasks (fitting, baseline subtraction, statistics etc) should only |
---|
| 508 | be run on range of channels. Depending on the current ``unit'' setting |
---|
| 509 | this range is set directly as channels, velocity or frequency |
---|
| 510 | ranges. Internally these are converted into a simple boolean mask for |
---|
| 511 | each channel of the abscissa. This means that if the unit setting is |
---|
| 512 | later changed, previously created mask are still valid. (This is not |
---|
| 513 | true for functions which change the shape or shift the frequency |
---|
| 514 | axis). You create masks with the function \cmd{create\_mask} and this |
---|
| 515 | specified the channels to be included in the selection. When setting |
---|
| 516 | the mask in velocity, the conversion from velocity to channels is |
---|
[1064] | 517 | based on the current selection, specified row and selected frequency |
---|
| 518 | reference frame. |
---|
[534] | 519 | |
---|
[966] | 520 | |
---|
| 521 | Note that for multi IF data with different number of channels per IF a |
---|
| 522 | single mask cannot be applied to different IFs. To use a mask on such |
---|
| 523 | data the selector should be applied to select all IFs with the same |
---|
| 524 | number of channels. |
---|
| 525 | |
---|
[534] | 526 | Example : |
---|
| 527 | \begin{verbatim} |
---|
| 528 | |
---|
| 529 | # Select channel range for baselining |
---|
[1757] | 530 | ASAP>scans.set_unit('channel') |
---|
[1259] | 531 | ASAP>msk = scans.create_mask([100,400],[600,800]) |
---|
[738] | 532 | |
---|
[534] | 533 | # Select velocity range for fitting |
---|
[1259] | 534 | ASAP>scans.set_unit('km/s') |
---|
| 535 | ASAP>msk = scans.create_mask([-30,-10]) |
---|
[534] | 536 | \end{verbatim} |
---|
| 537 | |
---|
[544] | 538 | Sometimes it is more convenient to specify the channels to be |
---|
| 539 | excluded, rather included. You can do this with the ``invert'' |
---|
| 540 | argument. |
---|
[534] | 541 | |
---|
| 542 | Example : |
---|
| 543 | \begin{verbatim} |
---|
[1757] | 544 | ASAP>scans.set_unit('channel') |
---|
[1259] | 545 | ASAP>msk = scans.create_mask([0,100],[900-1023], invert=True) |
---|
[534] | 546 | \end{verbatim} |
---|
| 547 | |
---|
[544] | 548 | By default \cmd{create\_mask} uses the frequency setup of the first row |
---|
| 549 | to convert velocities into a channel mask. If the rows in the data |
---|
| 550 | cover different velocity ranges, the scantable row to use should be |
---|
| 551 | specified: |
---|
| 552 | |
---|
| 553 | \begin{verbatim} |
---|
[1259] | 554 | ASAP>scans.set_unit('km/s') |
---|
| 555 | ASAP>msk = q.create_mask([-30,-10], row=5) |
---|
[544] | 556 | \end{verbatim} |
---|
| 557 | |
---|
[534] | 558 | Because the mask is stored in a simple python variable, the users is |
---|
| 559 | able to combine masks using simple arithmetic. To create a mask |
---|
| 560 | excluding the edge channels, a strong maser feature and a birdie in |
---|
| 561 | the middle of the band: |
---|
| 562 | |
---|
| 563 | \begin{verbatim} |
---|
[1757] | 564 | ASAP>scans.set_unit('channel') |
---|
[1259] | 565 | ASAP>msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True) |
---|
| 566 | ASAP>scans.set_unit('km/s') |
---|
| 567 | ASAP>msk2 = q.create_mask([-20,-10],invert=True) |
---|
[534] | 568 | |
---|
[1259] | 569 | ASAP>mask = msk1 and msk2 |
---|
[534] | 570 | \end{verbatim} |
---|
| 571 | |
---|
| 572 | |
---|
[953] | 573 | \subsection{Management} |
---|
| 574 | |
---|
| 575 | \index{Scantable!management}During processing it is possible to create |
---|
| 576 | a large number of scan tables. These all consume memory, so it is best |
---|
| 577 | to periodically remove unneeded scan tables. Use \cmd{list\_scans} to |
---|
| 578 | print a list of all scantables and \cmd{del} to remove unneeded ones. |
---|
| 579 | |
---|
| 580 | Example: |
---|
| 581 | |
---|
| 582 | \begin{verbatim} |
---|
[1259] | 583 | ASAP>list_scans() |
---|
[953] | 584 | The user created scantables are: |
---|
| 585 | ['s', 'scans', 'av', 's2', 'ss'] |
---|
| 586 | |
---|
[1259] | 587 | ASAP>del s2 |
---|
| 588 | ASAP>del ss |
---|
[953] | 589 | \end{verbatim} |
---|
| 590 | |
---|
[534] | 591 | \section{Data Input} |
---|
| 592 | |
---|
[971] | 593 | \index{Reading data}Data can be loaded in one of two ways; using the |
---|
| 594 | reader object or via the scantable constructor. The scantable method |
---|
| 595 | is simpler but the reader allows the user more control on what is read. |
---|
[534] | 596 | |
---|
| 597 | \subsection{Scantable constructor} |
---|
| 598 | |
---|
[794] | 599 | \index{Scantable constructor}\index{Scantable!constructor}This loads |
---|
| 600 | all of the data from filename into the scantable object scans and |
---|
| 601 | averages all the data within a scan (i.e. the resulting scantable |
---|
[534] | 602 | will have one row per scan). The recognised input file formats are |
---|
| 603 | RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ |
---|
[738] | 604 | MeasurementSet2 format. |
---|
[534] | 605 | |
---|
| 606 | Example usage: |
---|
| 607 | |
---|
| 608 | \begin{verbatim} |
---|
[1259] | 609 | ASAP>scan = scantable('2004-11-23_1841-P484.rpf') |
---|
[544] | 610 | |
---|
| 611 | # Don't scan average the data |
---|
[1259] | 612 | ASAP>scan = scantable('2004-11-23_1841-P484.rpf', average=False) |
---|
[534] | 613 | \end{verbatim} |
---|
| 614 | |
---|
| 615 | |
---|
[1757] | 616 | %\subsection{Reader object} |
---|
[534] | 617 | |
---|
[1757] | 618 | %\index{Reader object}\index{Scantable!reader object}For more control |
---|
| 619 | %when reading data into ASAP, the reader object should be used. This |
---|
| 620 | %has the option of only reading in a range of integrations, only a |
---|
| 621 | %specified beam or IF and does not perform any scan averaging of the |
---|
| 622 | %data, allowing analysis of the individual integrations. Note that due |
---|
| 623 | %to limitation of the RPFITS library, only one reader object can be |
---|
| 624 | %open at one time reading RPFITS files. To read multiple RPFITS files, |
---|
| 625 | %the old reader must be destroyed before the new file is opened. |
---|
| 626 | %However, multiple readers can be created and attached to SDFITS files. |
---|
| 627 | % |
---|
| 628 | % |
---|
| 629 | %Example usage: |
---|
| 630 | % |
---|
| 631 | %\begin{verbatim} |
---|
| 632 | % ASAP>r = reader('2003-03-16_082048_t0002.rpf') |
---|
| 633 | % ASAP>r.summary() |
---|
| 634 | % ASAP>scan = r.read() |
---|
| 635 | % ASAP>del r |
---|
| 636 | %\end{verbatim} |
---|
[534] | 637 | |
---|
| 638 | \section{Basic Processing} |
---|
| 639 | |
---|
| 640 | In the following section, a simple data reduction to form a quotient |
---|
[544] | 641 | spectrum of a single source is followed. It has been assume that the |
---|
| 642 | \cmd{.asaprc} file has {\em not} been used to change the \cmd{insitu} |
---|
| 643 | default value from \cmd{True}. |
---|
[534] | 644 | |
---|
[738] | 645 | \subsection{Auto quotient} |
---|
[794] | 646 | \index{Auto quotient}Quotients can be computed ``automatically''. This |
---|
| 647 | requires the data to have matching source/reference pairs or one |
---|
| 648 | reference for multiple sources. Auto quotient assumes reference scans |
---|
| 649 | have a trailing ``\_R'' in the source name for data from Parkes and |
---|
[1344] | 650 | Mopra, and a trailing ``e'' or ``w'' for data from Tidbinbilla. |
---|
[1757] | 651 | This functions has two \cmd{mode}s. \cmd{paired} (the default), which assumes |
---|
[1347] | 652 | matching adjacent pairs of source/reference scans and \cmd{time}, which finds |
---|
| 653 | the closest reference scan in time. |
---|
[534] | 654 | |
---|
[738] | 655 | \begin{verbatim} |
---|
[1259] | 656 | ASAP>q = s.auto_quotient() |
---|
[738] | 657 | \end{verbatim} |
---|
| 658 | |
---|
[971] | 659 | By default the quotient spectra is calculated |
---|
| 660 | to preserve continuum emission. If you wish to remove the continuum |
---|
| 661 | contribution, use the \cmd{preserve} argument: |
---|
| 662 | |
---|
| 663 | \begin{verbatim} |
---|
[1259] | 664 | ASAP>q = s.auto_quotient(preserve=True) |
---|
[971] | 665 | \end{verbatim} |
---|
| 666 | |
---|
[1217] | 667 | If this is not sufficient the following alternative method can be used. |
---|
[738] | 668 | |
---|
[1217] | 669 | \subsection{Separate reference and source observations} |
---|
| 670 | |
---|
| 671 | \index{Quotient spectra}Most data from ATNF observatories |
---|
| 672 | distinguishes on and off source data using the file name. This makes |
---|
| 673 | it easy to create two scantables with the source and reference |
---|
| 674 | data. As long as there was exactly one reference observation for each |
---|
| 675 | on source observation for following method will work. |
---|
| 676 | |
---|
| 677 | For Mopra and Parkes data: |
---|
| 678 | \begin{verbatim} |
---|
[1259] | 679 | ASAP>r = scans.get_scan('*_R') |
---|
[1344] | 680 | ASAP>s = scans.get_scan('*^_R') |
---|
[1217] | 681 | \end{verbatim} |
---|
| 682 | |
---|
| 683 | For Tidbinbilla data |
---|
| 684 | \begin{verbatim} |
---|
[1259] | 685 | ASAP>r = scans.get_scan('*_[ew]') |
---|
| 686 | ASAP>s = scans.get_scan('*_[^ew]') |
---|
[1217] | 687 | \end{verbatim} |
---|
| 688 | |
---|
[534] | 689 | \subsection{Time average separate scans} |
---|
| 690 | |
---|
[794] | 691 | \index{Time average}If you have observed the source with multiple |
---|
| 692 | source/reference cycles you will want to scan-average the quotient |
---|
| 693 | spectra together. |
---|
[534] | 694 | |
---|
| 695 | \begin{verbatim} |
---|
[1259] | 696 | ASAP>av = q.average_time() |
---|
[534] | 697 | \end{verbatim} |
---|
| 698 | |
---|
[544] | 699 | If for some you want to average multiple sets of scantables together |
---|
| 700 | you can: |
---|
[534] | 701 | |
---|
| 702 | \begin{verbatim} |
---|
[1259] | 703 | ASAP>av = average_time(q1, q2, q3) |
---|
[534] | 704 | \end{verbatim} |
---|
| 705 | |
---|
[544] | 706 | The default is to use integration time weighting. The alternative is |
---|
[1217] | 707 | to use none, variance, Tsys weighting, Tsys \& integration time or |
---|
| 708 | median averaging. |
---|
[534] | 709 | |
---|
[544] | 710 | \begin{verbatim} |
---|
[1259] | 711 | ASAP>av = average_time(q, weight='tintsys') |
---|
[544] | 712 | \end{verbatim} |
---|
| 713 | |
---|
[534] | 714 | To use variance based weighting, you need to supply a mask saying which |
---|
| 715 | channel range you want it to calculate the variance from. |
---|
| 716 | |
---|
| 717 | \begin{verbatim} |
---|
[1259] | 718 | ASAP>msk = scans.create_mask([200,400],[600,800]) |
---|
| 719 | ASAP>av = average_time(scans, mask=msk, weight='var') |
---|
[534] | 720 | \end{verbatim} |
---|
| 721 | |
---|
[953] | 722 | If you have not observed your data with Doppler tracking (or run |
---|
[1259] | 723 | \cmd{freq\_align} explicitly) you should align the data in frequency |
---|
[953] | 724 | before averaging. |
---|
[794] | 725 | |
---|
[953] | 726 | \begin{verbatim} |
---|
[1259] | 727 | ASAP>av = scans.average_time(align=True) |
---|
[953] | 728 | \end{verbatim} |
---|
| 729 | |
---|
| 730 | Note that, if needed, you should run \cmd{gain\_el} and \cmd{opacity} |
---|
| 731 | before you average the data in time (\S \ref{sec:gainel} \& |
---|
| 732 | \ref{sec:freqalign}). |
---|
| 733 | |
---|
[534] | 734 | \subsection{Baseline fitting} |
---|
| 735 | |
---|
[794] | 736 | \index{Baseline fitting}To make a baseline fit, you must first create |
---|
| 737 | a mask of channels to use in the baseline fit. |
---|
[534] | 738 | |
---|
| 739 | \begin{verbatim} |
---|
[1259] | 740 | ASAP>msk = scans.create_mask([100,400],[600,900]) |
---|
| 741 | ASAP>scans.poly_baseline(msk, order=1) |
---|
[534] | 742 | \end{verbatim} |
---|
| 743 | |
---|
| 744 | This will fit a first order polynomial to the selected channels and subtract |
---|
| 745 | this polynomial from the full spectra. |
---|
| 746 | |
---|
| 747 | \subsubsection{Auto-baselining} |
---|
| 748 | |
---|
[794] | 749 | \index{Auto-baseline}The function \cmd{auto\_poly\_baseline} can be used to automatically |
---|
[770] | 750 | baseline your data without having to specify channel ranges for the |
---|
| 751 | line free data. It automatically figures out the line-free emission |
---|
| 752 | and fits a polynomial baseline to that data. The user can use masks to |
---|
| 753 | fix the range of channels or velocity range for the fit as well as |
---|
| 754 | mark the band edge as invalid. |
---|
[534] | 755 | |
---|
| 756 | Simple example |
---|
| 757 | |
---|
| 758 | \begin{verbatim} |
---|
[1259] | 759 | ASAP>scans.auto_poly_baseline(order=2,threshold=5) |
---|
[534] | 760 | \end{verbatim} |
---|
| 761 | |
---|
| 762 | \cmd{order} is the polynomial order for the fit. \cmd{threshold} is |
---|
| 763 | the SNR threshold to use to deliminate line emission from |
---|
[548] | 764 | signal. Generally the value of threshold is not too critical, however |
---|
| 765 | making this too large will compromise the fit (as it will include |
---|
| 766 | strong line features) and making it too small will mean it cannot find |
---|
| 767 | enough line free channels. |
---|
[534] | 768 | |
---|
[548] | 769 | |
---|
[534] | 770 | Other examples: |
---|
| 771 | |
---|
| 772 | \begin{verbatim} |
---|
| 773 | # Don't try and fit the edge of the bandpass which is noisier |
---|
[1259] | 774 | ASAP>scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3) |
---|
[534] | 775 | |
---|
| 776 | # Only fit a given region around the line |
---|
[1259] | 777 | ASAP>scans.set_unit('km/s') |
---|
| 778 | ASAP>msk = scans.create_mask([-60,-20]) |
---|
| 779 | ASAP>scans.auto_poly_baseline(mask=msk,order=3,threshold=3) |
---|
[534] | 780 | |
---|
| 781 | \end{verbatim} |
---|
| 782 | |
---|
| 783 | \subsection{Average the polarisations} |
---|
| 784 | |
---|
[794] | 785 | \index{average\_pol}If you are just interested in the highest SNR for total intensity you |
---|
[534] | 786 | will want to average the parallel polarisations together. |
---|
| 787 | |
---|
| 788 | \begin{verbatim} |
---|
[1259] | 789 | ASAP>scans.average_pol() |
---|
[534] | 790 | \end{verbatim} |
---|
| 791 | |
---|
| 792 | \subsection{Calibration} |
---|
| 793 | |
---|
[794] | 794 | \index{Calibration}For most uses, calibration happens transparently as the input data |
---|
[534] | 795 | contains the Tsys measurements taken during observations. The nominal |
---|
| 796 | ``Tsys'' values may be in Kelvin or Jansky. The user may wish to |
---|
| 797 | supply a Tsys correction or apply gain-elevation and opacity |
---|
| 798 | corrections. |
---|
| 799 | |
---|
| 800 | \subsubsection{Brightness Units} |
---|
| 801 | |
---|
[794] | 802 | \index{Brightness Units}RPFITS files do not contain any information as |
---|
| 803 | to whether the telescope calibration was in units of Kelvin or |
---|
| 804 | Janskys. On reading the data a default value is set depending on the |
---|
| 805 | telescope and frequency of observation. If this default is incorrect |
---|
| 806 | (you can see it in the listing from the \cmd{summary} function) the |
---|
| 807 | user can either override this value on reading the data or later. |
---|
| 808 | E.g: |
---|
[534] | 809 | |
---|
| 810 | \begin{verbatim} |
---|
[1259] | 811 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf', unit='Jy') |
---|
[534] | 812 | # Or in two steps |
---|
[1259] | 813 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf') |
---|
| 814 | ASAP>scans.set_fluxunit('Jy') |
---|
[534] | 815 | \end{verbatim} |
---|
| 816 | |
---|
[1217] | 817 | \subsubsection{Feed Polarisation} |
---|
| 818 | |
---|
| 819 | \index{Brightness Units}The RPFITS files also do not contain any |
---|
| 820 | information as to the feed polarisation. ASAP will set a default based |
---|
| 821 | on the antenna, but this will often be wrong the data has been read, |
---|
| 822 | the default can be changed using the \cmd{set\_feedtype} function with |
---|
| 823 | an argument of \cmd{'linear'} or \cmd{'circular'}. |
---|
| 824 | |
---|
| 825 | E.g: |
---|
| 826 | |
---|
| 827 | \begin{verbatim} |
---|
[1259] | 828 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf') |
---|
| 829 | ASAP>scans.set_feedtype('circular') |
---|
[1217] | 830 | \end{verbatim} |
---|
| 831 | |
---|
[534] | 832 | \subsubsection{Tsys scaling} |
---|
| 833 | |
---|
[794] | 834 | \index{Tsys scaling}Sometime the nominal Tsys measurement at the |
---|
| 835 | telescope is wrong due to an incorrect noise diode calibration. This |
---|
| 836 | can easily be corrected for with the scale function. By default, |
---|
[1757] | 837 | \cmd{scale} only scaless the spectra and not the corresponding Tsys. |
---|
[534] | 838 | |
---|
| 839 | \begin{verbatim} |
---|
[1259] | 840 | ASAP>scans.scale(1.05, tsys=True) |
---|
[534] | 841 | \end{verbatim} |
---|
| 842 | |
---|
| 843 | \subsubsection{Unit Conversion} |
---|
| 844 | |
---|
[794] | 845 | \index{Unit conversion}To convert measurements in Kelvin to Jy (and |
---|
| 846 | vice versa) the global function \cmd{convert\_flux} is needed. This |
---|
| 847 | converts and scales the data from K to Jy or vice-versa depending on |
---|
| 848 | what the current brightness unit is set to. The function knows the |
---|
| 849 | basic parameters for some frequencies and telescopes, but the user may |
---|
| 850 | need to supply the aperture efficiency, telescope diameter or the Jy/K |
---|
| 851 | factor. |
---|
[534] | 852 | |
---|
| 853 | \begin{verbatim} |
---|
[1259] | 854 | ASAP>scans.convert_flux() # If efficency known |
---|
| 855 | ASAP>scans.convert_flux(eta=0.48) # If telescope diameter known |
---|
| 856 | ASAP>scans.convert_flux(eta=0.48,d=35) # Unknown telescope |
---|
| 857 | ASAP>scans.convert_flux(jypk=15) # Alternative |
---|
[534] | 858 | \end{verbatim} |
---|
| 859 | |
---|
| 860 | \subsubsection{Gain-Elevation and Opacity Corrections} |
---|
[794] | 861 | \label{sec:gainel} |
---|
[534] | 862 | |
---|
[794] | 863 | \index{Gain-elevation}As higher frequencies (particularly $>$20~GHz) |
---|
| 864 | it is important to make corrections for atmospheric opacity and |
---|
| 865 | gain-elevation effects. |
---|
[534] | 866 | |
---|
[794] | 867 | Note that currently the elevation is not written correctly into |
---|
[770] | 868 | Tidbinbilla rpfits files. This means that gain-elevation and opacity |
---|
[794] | 869 | corrections will not work unless these get recalculated. |
---|
[770] | 870 | |
---|
[794] | 871 | \begin{verbatim} |
---|
[1344] | 872 | ASAP>scans.recalc_azel() # recalculate az/el |
---|
[1757] | 873 | # based on pointing |
---|
[794] | 874 | \end{verbatim} |
---|
| 875 | |
---|
[544] | 876 | Gain-elevation curves for some telescopes and frequencies are known to |
---|
[1347] | 877 | ASAP (currently only for Tidbinbilla at 20~GHz and Parkes at K-band). |
---|
| 878 | In these cases making gain-corrections is simple. If the gain curve for your |
---|
| 879 | data is not known, the user can supply either a gain polynomial or text file |
---|
[534] | 880 | tabulating gain factors at a range of elevations (see \cmd{help |
---|
[544] | 881 | scantable.gain\_el}). |
---|
[534] | 882 | |
---|
| 883 | Examples: |
---|
| 884 | |
---|
| 885 | \begin{verbatim} |
---|
[1259] | 886 | ASAP>scans.gain_el() # If gain table known |
---|
| 887 | ASAP>scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) |
---|
[534] | 888 | \end{verbatim} |
---|
| 889 | |
---|
[794] | 890 | \index{Opacity}Opacity corrections can be made with the global |
---|
| 891 | function \cmd{opacity}. This should work on all telescopes as long as |
---|
| 892 | a measurement of the opacity factor was made during the observation. |
---|
[534] | 893 | |
---|
| 894 | \begin{verbatim} |
---|
[1259] | 895 | ASAP>scans.opacity(0.083) |
---|
[534] | 896 | \end{verbatim} |
---|
| 897 | |
---|
| 898 | Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, |
---|
| 899 | which takes opacity effects into account (to first order). ASAP |
---|
[544] | 900 | opacity corrections should not be used for Mopra 3-mm data. |
---|
[534] | 901 | |
---|
| 902 | \subsection{Frequency Frame Alignment} |
---|
[794] | 903 | \label{sec:freqalign} |
---|
[534] | 904 | |
---|
[1259] | 905 | \index{Frequency alignment}\index{Velocity alignment}When time |
---|
[794] | 906 | averaging a series of scans together, it is possible that the velocity |
---|
| 907 | scales are not exactly aligned. This may be for many reasons such as |
---|
| 908 | not Doppler tracking the observations, errors in the Doppler tracking |
---|
| 909 | etc. This mostly affects very long integrations or integrations |
---|
| 910 | averaged together from different days. Before averaging such data |
---|
| 911 | together, they should be frequency aligned using \cmd{freq\_align}. |
---|
[534] | 912 | |
---|
| 913 | E.g.: |
---|
| 914 | |
---|
| 915 | \begin{verbatim} |
---|
[1259] | 916 | ASAP>scans.freq_align() |
---|
| 917 | ASAP>av = average_time(scans) |
---|
[534] | 918 | \end{verbatim} |
---|
| 919 | |
---|
[953] | 920 | {\em A Global freq\_align command will be made eventually} |
---|
[534] | 921 | |
---|
| 922 | To average together data taken on different days, which are in |
---|
| 923 | different scantables, each scantable must aligned to a common |
---|
| 924 | reference time then the scantables averaged. The simplest way of |
---|
| 925 | doing this is to allow ASAP to choose the reference time for the first |
---|
[738] | 926 | scantable then using this time for the subsequent scantables. |
---|
[534] | 927 | |
---|
| 928 | \begin{verbatim} |
---|
[1259] | 929 | ASAP>scans1.freq_align() # Copy the refeference Epoch from the output |
---|
| 930 | ASAP>scans2.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 931 | ASAP>scans3.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 932 | ASAP>av = average_time(scans1, scans2, scans3) |
---|
[534] | 933 | \end{verbatim} |
---|
| 934 | |
---|
| 935 | \section{Scantable manipulation} |
---|
| 936 | |
---|
[794] | 937 | \index{Scantable!manipulation}While it is very useful to have many |
---|
| 938 | independent sources within one scantable, it is often inconvenient for |
---|
| 939 | data processing. The \cmd{get\_scan} function can be used to create a |
---|
| 940 | new scantable with a selection of scans from a scantable. The |
---|
| 941 | selection can either be on the source name, with simple wildcard |
---|
[953] | 942 | matching or set of scan ids. Internally this uses the selector object, |
---|
| 943 | so for more complicated selection the selector should be used directly |
---|
| 944 | instead. |
---|
[534] | 945 | |
---|
| 946 | For example: |
---|
| 947 | |
---|
| 948 | \begin{verbatim} |
---|
[1259] | 949 | ASAP>ss = scans.get_scan(10) # Get the 11th scan (zero based) |
---|
| 950 | ASAP>ss = scans.get_scan(range(10)) # Get the first 10 scans |
---|
| 951 | ASAP>ss = scans.get_scan(range(10,20)) # Get the next 10 scans |
---|
| 952 | ASAP>ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans |
---|
[534] | 953 | |
---|
[1259] | 954 | ASAP>ss = scans.get_scan('345p407') # Get a specific source |
---|
| 955 | ASAP>ss = scans.get_scan('345*') # Get a few sources |
---|
[534] | 956 | |
---|
[1259] | 957 | ASAP>r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra) |
---|
[1344] | 958 | ASAP>s = scans.get_scan('*^_R') # Get all program sources (Parkes/Mopra) |
---|
[1259] | 959 | ASAP>r = scans.get_scan('*[ew]') # Get all reference sources (Tid) |
---|
| 960 | ASAP>s = scans.get_scan('*[^ew]') # Get all program sources (Tid) |
---|
[534] | 961 | |
---|
| 962 | \end{verbatim} |
---|
| 963 | |
---|
[1757] | 964 | One can also apply the inverse of \cmd{get\_scan} \cmd{drop\_scan} |
---|
| 965 | |
---|
[534] | 966 | To copy a scantable the following does not work: |
---|
| 967 | |
---|
| 968 | \begin{verbatim} |
---|
[1259] | 969 | ASAP>ss = scans |
---|
[534] | 970 | \end{verbatim} |
---|
| 971 | |
---|
[544] | 972 | as this just creates a reference to the original scantable. Any |
---|
| 973 | changes made to \cmd{ss} are also seen in \cmd{scans}. To duplicate a |
---|
[534] | 974 | scantable, use the copy function. |
---|
| 975 | |
---|
| 976 | \begin{verbatim} |
---|
[1259] | 977 | ASAP>ss = scans.copy() |
---|
[534] | 978 | \end{verbatim} |
---|
| 979 | |
---|
| 980 | \section{Data Output} |
---|
| 981 | |
---|
[794] | 982 | \index{Scantable!save}\index{Saving data}ASAP can save scantables in a |
---|
| 983 | variety of formats, suitable for reading into other packages. The |
---|
| 984 | formats are: |
---|
[534] | 985 | |
---|
| 986 | \begin{itemize} |
---|
| 987 | \item[ASAP] This is the internal format used for ASAP. It is the only |
---|
[544] | 988 | format that allows the user to restore the data, fits etc. without |
---|
| 989 | loosing any information. As mentioned before, the ASAP scantable is |
---|
| 990 | an AIPS++ Table (a memory-based table). This function just converts |
---|
| 991 | it to a disk-based Table. You can the access that Table with the |
---|
| 992 | AIPS++ Table browser or any other AIPS++ tool. |
---|
[534] | 993 | |
---|
[544] | 994 | \item[SDFITS] The Single Dish FITS format. This format was designed to |
---|
| 995 | for interchange between packages, but few packages actually can read |
---|
| 996 | it. |
---|
[534] | 997 | |
---|
[1757] | 998 | \item[FITS] This uses simple ``image'' fits to save the data, each row |
---|
| 999 | being written to a separate fits file. |
---|
[534] | 1000 | |
---|
[1757] | 1001 | \item[CLASS] This uses simple ``image'' fits to save the data, each row |
---|
| 1002 | being written to a separate fits file. This format has modification so it |
---|
| 1003 | is suitable for importing the data into CLASS. |
---|
| 1004 | |
---|
[534] | 1005 | \item[ASCII] A simple text based format suitable for the user to |
---|
| 1006 | processing using Perl or, Python, gnuplot etc. |
---|
| 1007 | |
---|
| 1008 | \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. |
---|
| 1009 | You can also access this with the Table browser and other AIPS++ |
---|
| 1010 | tools. |
---|
| 1011 | |
---|
| 1012 | \end{itemize} |
---|
| 1013 | |
---|
[738] | 1014 | The default output format can be set in the users {\tt .asaprc} file. |
---|
[534] | 1015 | Typical usages are: |
---|
| 1016 | |
---|
| 1017 | \begin{verbatim} |
---|
[1259] | 1018 | ASAP>scans.save('myscans') # Save in default format |
---|
| 1019 | ASAP>scans.save('myscans', overwrite=True) # Overwrite an existing file |
---|
[534] | 1020 | \end{verbatim} |
---|
| 1021 | |
---|
| 1022 | \section{Plotter} |
---|
| 1023 | |
---|
[1259] | 1024 | \index{Plotter}Scantable spectra can be plotted at any time. An |
---|
| 1025 | asapplotter object is used for plotting, meaning multiple plot windows |
---|
| 1026 | can be active at the same time. On start up a default asapplotter |
---|
| 1027 | object is created called ``plotter''. This would normally be used for |
---|
| 1028 | standard plotting. |
---|
[534] | 1029 | |
---|
[1259] | 1030 | The plotter, optionally, will run in a multi-panel mode and contain |
---|
[534] | 1031 | multiple plots per panel. The user must tell the plotter how they want |
---|
| 1032 | the data distributed. This is done using the set\_mode function. The |
---|
| 1033 | default can be set in the users {\tt .asaprc} file. The units (and frame |
---|
[538] | 1034 | etc) of the abscissa will be whatever has previously been set by |
---|
| 1035 | \cmd{set\_unit}, \cmd{set\_freqframe} etc. |
---|
[534] | 1036 | |
---|
| 1037 | Typical plotter usage would be: |
---|
| 1038 | |
---|
| 1039 | \begin{verbatim} |
---|
[1259] | 1040 | ASAP>scans.set_unit('km/s') |
---|
[1344] | 1041 | ASAP>plotter.set_mode(stacking='p', panelling='t') |
---|
[1259] | 1042 | ASAP>plotter.plot(scans) |
---|
[534] | 1043 | \end{verbatim} |
---|
| 1044 | |
---|
| 1045 | This will plot multiple polarisation within each plot panel and each |
---|
[544] | 1046 | scan row in a separate panel. |
---|
[534] | 1047 | |
---|
[538] | 1048 | Other possibilities include: |
---|
[534] | 1049 | |
---|
| 1050 | \begin{verbatim} |
---|
| 1051 | # Plot multiple IFs per panel |
---|
[1344] | 1052 | ASAP>plotter.set_mode(stacking='i', panelling='t') |
---|
[538] | 1053 | |
---|
| 1054 | # Plot multiple beams per panel |
---|
[1344] | 1055 | ASAP>plotter.set_mode(stacking='b', panelling='t') |
---|
[538] | 1056 | |
---|
| 1057 | # Plot one IF per panel, time stacked |
---|
[1259] | 1058 | ASAP>plotter.set_mode('t', 'i') |
---|
[538] | 1059 | |
---|
| 1060 | # Plot each scan in a seperate panel |
---|
[1259] | 1061 | ASAP>plotter.set_mode('t', 's') |
---|
[538] | 1062 | |
---|
[534] | 1063 | \end{verbatim} |
---|
| 1064 | |
---|
[538] | 1065 | \subsection{Plot Selection} |
---|
| 1066 | \label{sec:plotter_cursor} |
---|
| 1067 | |
---|
[794] | 1068 | \index{Plotter!selection}The plotter can plot up to 25 panels and |
---|
| 1069 | stacked spectra per panel. If you have data larger than this (or for |
---|
| 1070 | your own sanity) you need to select a subset of this data. This is |
---|
[953] | 1071 | particularly true for multibeam or multi IF data. The selector object |
---|
[971] | 1072 | should be used for this purpose. Selection can either be applied to |
---|
[953] | 1073 | the scantable or directly to the plotter, the end result is the same. |
---|
[1259] | 1074 | You don't have to reset the scantable selection though, if you set |
---|
[971] | 1075 | the selection on the plotter. |
---|
[538] | 1076 | |
---|
| 1077 | Examples: |
---|
| 1078 | |
---|
| 1079 | \begin{verbatim} |
---|
[1259] | 1080 | ASAP>selection = selector() |
---|
[538] | 1081 | # Select second IF |
---|
[1259] | 1082 | ASAP>selection.set_ifs(1) |
---|
| 1083 | ASAP>plotter.set_selection(selection) |
---|
[538] | 1084 | |
---|
| 1085 | # Select first 4 beams |
---|
[1259] | 1086 | ASAP>selection.set_beams([0,1,2,3]) |
---|
| 1087 | ASAP>plotter.set_selection(selection) |
---|
[538] | 1088 | |
---|
[953] | 1089 | # Select a few scans |
---|
[1259] | 1090 | ASAP>selection.set_scans([2,4,6,10]) |
---|
| 1091 | ASAP>plotter.set_selection(selection) |
---|
[538] | 1092 | |
---|
| 1093 | # Multiple selection |
---|
[1259] | 1094 | ASAP>selection.set_ifs(1) |
---|
| 1095 | ASAP>selection.set_scans([2,4,6,10]) |
---|
| 1096 | ASAP>plotter.set_selection(selection) |
---|
[953] | 1097 | |
---|
[538] | 1098 | \end{verbatim} |
---|
| 1099 | |
---|
[544] | 1100 | \subsection{Plot Control} |
---|
| 1101 | |
---|
[794] | 1102 | \index{Plotter!control}The plotter window has a row of buttons on the |
---|
| 1103 | lower left. These can be used to control the plotter (mostly for |
---|
| 1104 | zooming the individual plots). From left to right: |
---|
[534] | 1105 | |
---|
[1267] | 1106 | \begin{tabular}{ll} |
---|
[534] | 1107 | |
---|
[1267] | 1108 | Home & This will unzoom the plots to the original zoom factor \\ |
---|
[534] | 1109 | |
---|
[1267] | 1110 | Plot history & \parbox[t]{0.8\textwidth}{(left and right arrow) The |
---|
| 1111 | plotter keeps a history of zoom settings. The left arrow sets the plot |
---|
| 1112 | zoom to the previous value. The right arrow returns back again. This |
---|
| 1113 | allows you, for example, to zoom in on one feature then return the |
---|
| 1114 | plot to how it was previously. }\\ |
---|
[534] | 1115 | |
---|
[1267] | 1116 | Pan & \parbox[t]{0.8\textwidth}{(The Cross) This sets the cursor to |
---|
| 1117 | pan, or scroll mode allowing you to shift the plot within the |
---|
| 1118 | window. Useful when zoomed in on a feature. }\\ |
---|
[534] | 1119 | |
---|
[1267] | 1120 | Zoom & \parbox[t]{0.8\textwidth}{(the letter with the magnifying |
---|
| 1121 | glass) lets you draw a rectangle around a region of interest then |
---|
| 1122 | zooms in on that region. Use the plot history to unzoom again.}\\ |
---|
[534] | 1123 | |
---|
[1267] | 1124 | Adjust & \parbox[t]{0.8\textwidth}{(rectangle with 4 arrows) adjust |
---|
| 1125 | subplot parameters (space at edge of plots)}\\ |
---|
[953] | 1126 | |
---|
[1267] | 1127 | Save & \parbox[t]{0.8\textwidth}{(floppy disk). Save the plot as a |
---|
| 1128 | postscript or .png file}\\ |
---|
[534] | 1129 | |
---|
[1267] | 1130 | \end{tabular} |
---|
| 1131 | |
---|
[794] | 1132 | You can also type ``g'' in the plot window to toggle on and off grid |
---|
| 1133 | lines. Typing 'l' turns on and off logarithmic Y-axis. |
---|
| 1134 | |
---|
[534] | 1135 | \subsection{Other control} |
---|
| 1136 | |
---|
| 1137 | The plotter has a number of functions to describe the layout of the |
---|
| 1138 | plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. |
---|
| 1139 | |
---|
| 1140 | To set the exact velocity or channel range to be plotted use the |
---|
| 1141 | \cmd{set\_range} function. To reset to the default value, call |
---|
| 1142 | \cmd{set\_range} with no arguments. E.g. |
---|
| 1143 | |
---|
| 1144 | \begin{verbatim} |
---|
[1259] | 1145 | ASAP>scans.set_unit('km/s') |
---|
| 1146 | ASAP>plotter.plot(scans) |
---|
| 1147 | ASAP>plotter.set_range(-150,-50) |
---|
| 1148 | ASAP>plotter.set_range() # To reset |
---|
[534] | 1149 | \end{verbatim} |
---|
| 1150 | |
---|
[544] | 1151 | Both the range of the ``x'' and ``y'' axis can be set at once, if desired: |
---|
| 1152 | |
---|
| 1153 | \begin{verbatim} |
---|
[1259] | 1154 | ASAP>plotter.set_range(-10,30,-1,6.6) |
---|
[544] | 1155 | \end{verbatim} |
---|
| 1156 | |
---|
[738] | 1157 | To save a hardcopy of the current plot, use the save function, e.g. |
---|
[534] | 1158 | |
---|
| 1159 | \begin{verbatim} |
---|
[1259] | 1160 | ASAP>plotter.save('myplot.ps') |
---|
| 1161 | ASAP>plotter.save('myplot.png', dpi=80) |
---|
[534] | 1162 | \end{verbatim} |
---|
| 1163 | |
---|
[1217] | 1164 | \subsection{Plotter Customisation} |
---|
| 1165 | |
---|
| 1166 | The plotter allows the user to change most properties such as text |
---|
[1259] | 1167 | size and colour. The \cmd{commands} function and {\cmd help\ |
---|
[1217] | 1168 | asapplotter} list all the possible commands that can be used with the |
---|
| 1169 | plotter. |
---|
| 1170 | |
---|
| 1171 | \commanddef{set\_colors}{Change the default colours used for line |
---|
| 1172 | plotting. Colours can be given either by name, using the html standard |
---|
| 1173 | (e.g. red, blue or hotpink), or hexadecimal code (e.g. for black |
---|
| 1174 | \#000000). If less colours are specified than lines plotted , the |
---|
| 1175 | plotter cycles through the colours. Example:} {ASAP> |
---|
| 1176 | plotter.set\_colors('red blue green')\\ ASAP> |
---|
| 1177 | plotter.set\_colors(`\#0000 blue \#FF00FF')\\ } |
---|
| 1178 | |
---|
| 1179 | \commanddef{set\_linestyles}{Change the line styles used for |
---|
| 1180 | plots. Allowable values are 'line', 'dashed', 'dotted', 'dashdot', |
---|
| 1181 | 'dashdotdot' and 'dashdashdot. Example: }{ |
---|
[1259] | 1182 | ASAP>plotter.set\_linestyles('line dash cotted datshot.)\\ |
---|
| 1183 | ASAP>plotter.set\_font(size=10)\\ |
---|
[1217] | 1184 | } |
---|
| 1185 | |
---|
| 1186 | \commanddef{set\_font}{Change the font style and size. Example}{ |
---|
[1259] | 1187 | ASAP>plotter.set\_font(weight='bold')\\ |
---|
| 1188 | ASAP>plotter.set\_font(size=10)\\ |
---|
| 1189 | ASAP>plotter.set\_font(style='italic')\\ |
---|
[1217] | 1190 | } |
---|
| 1191 | |
---|
[1259] | 1192 | \commanddef{set\_layout}{Change the multi-panel layout, i.e. now many |
---|
[1217] | 1193 | rows and columns}{ |
---|
[1259] | 1194 | ASAP>plotter.set\_layout(3,2) |
---|
[1217] | 1195 | } |
---|
| 1196 | |
---|
| 1197 | \commanddef{set\_legend}{Set the position, size and optional value of the legend}{ |
---|
[1259] | 1198 | ASAP>plotter.set\_legend(fontsize=16)\\ |
---|
| 1199 | ASAP>plotter.set\_legend(mode=0) \# ASAP chooses where to put the legend\\ |
---|
| 1200 | ASAP>plotter.set\_legend(mode=4) \# Put legend on lower right\\ |
---|
| 1201 | ASAP>plotter.set\_legend(mode=-1) \# No legend\\ |
---|
| 1202 | ASAP>plotter.set\_legend(mp=['RR','LL']) \# Specify legend labels\\ |
---|
| 1203 | ASAP>plotter.set\_legend(mp=[r'\$\^\{12\}CO\$',r'\$\^\{13\}CO\$']) \# Latex labels |
---|
[1217] | 1204 | } |
---|
| 1205 | |
---|
| 1206 | \commanddef{set\_title}{Set the plot title. If multiple panels are |
---|
| 1207 | plotted, multiple titles have to be specified}{ |
---|
[1259] | 1208 | ASAP>plotter.set\_title(`G323.12$-$1.79`)\\ |
---|
| 1209 | ASAP>plotter.set\_title([`SiO`, 'Methanol'], fontsize=18)\\ |
---|
[1217] | 1210 | } |
---|
| 1211 | |
---|
| 1212 | \subsection{Plotter Annotations} |
---|
| 1213 | |
---|
[1259] | 1214 | The plotter allows various annotations (lines, arrows, text and |
---|
[1217] | 1215 | ``spans'') to be added to the plot. These annotations are |
---|
| 1216 | ``temporary'', when the plotter is next refreshed |
---|
| 1217 | (e.g. \cmd{plotter.plot} or \cmd{plotter.set\_range}) the annotations |
---|
| 1218 | will be removed. |
---|
| 1219 | |
---|
[1259] | 1220 | \bigcommanddef{arrow(x,y,x+dx,y+dy)}{Draw an arrow from a specified |
---|
[1217] | 1221 | \cmd{(x,y)} position to \cmd{(x+dx, y+dy)}. The values are in world |
---|
[1267] | 1222 | coordinates. Addition arguments which must be passed are {\cmd head\_width} and \cmd{head\_length}}{ |
---|
| 1223 | ASAP>plotter.arrow(-40,7,35,0,head\_width=0.2, head\_length=10) |
---|
[1217] | 1224 | } |
---|
| 1225 | |
---|
| 1226 | \bigcommanddef{axhline(y, xmin, xmax)}{Draw a horizontal line at the |
---|
[1259] | 1227 | specified \cmd{y} position (in world coordinates) between xmin and xmax |
---|
| 1228 | (in relative coordinates, i.e. 0.0 is the left hand edge of the plot |
---|
[1267] | 1229 | while 1.0 is the right side of the plot).}{ |
---|
[1259] | 1230 | ASAP>plotter.axhline(6.0,0.2,0.8) |
---|
[1217] | 1231 | } |
---|
| 1232 | |
---|
| 1233 | \bigcommanddef{avhline(x, ymin, ymax)}{Draw a vertical line at the |
---|
[1259] | 1234 | specified \cmd{x} position (in world coordinates) between \cmd{ymin} |
---|
| 1235 | and \cmd{ymax} (in relative coordinates, i.e. 0.0 is the left hand edge |
---|
[1217] | 1236 | of the plot while 1.0 is the right side of the plot).}{ |
---|
[1259] | 1237 | ASAP>plotter.axvline(-50.0,0.1,1.0) |
---|
[1217] | 1238 | } |
---|
| 1239 | |
---|
| 1240 | \bigcommanddef{axhspan(ymin, ymax, \\ \hspace*{20mm}xmin, |
---|
| 1241 | xmax)}{Overlay a transparent colour rectangle. \cmd{ymin} and |
---|
[1259] | 1242 | \cmd{ymax} are given in world coordinates while \cmd{xmin} and |
---|
[1217] | 1243 | \cmd{xmax} are given in relative coordinates}{ |
---|
[1259] | 1244 | ASAP>plotter.axhspan(2,4,0.25,0.75) |
---|
[1217] | 1245 | } |
---|
| 1246 | |
---|
| 1247 | \bigcommanddef{axvspan(xmin, xmax, \\ \hspace*{20mm} ymin, |
---|
| 1248 | ymax)}{Overlay a transparent colour rectangle. \cmd{ymin} and |
---|
[1259] | 1249 | \cmd{ymax} are given in relative coordinates while \cmd{xmin} and |
---|
[1217] | 1250 | \cmd{xmax} are given in world coordinates}{ |
---|
[1259] | 1251 | ASAP>plotter.axvspan(-50,60,0.2,0.5) |
---|
[1217] | 1252 | } |
---|
| 1253 | |
---|
| 1254 | \bigcommanddef{text(x, y, str)}{Place the string \cmd{str} at the |
---|
| 1255 | given \cmd{(x,y)} position in world coordinates.}{ |
---|
| 1256 | ASAP>plotter.text(-10,7,"CO") |
---|
| 1257 | } |
---|
| 1258 | |
---|
| 1259 | These functions all take a set of \cmd{kwargs} commands. These can be |
---|
| 1260 | used to set colour, linewidth fontsize etc. These are standard |
---|
| 1261 | matplotlib settings. Common ones include: |
---|
| 1262 | |
---|
| 1263 | \begin{tabular}{ll} |
---|
[1267] | 1264 | \tt color, facecolor, edgecolor \\ |
---|
| 1265 | \tt width, linewidth \\ |
---|
[1217] | 1266 | \tt fontsize \\ |
---|
| 1267 | \tt fontname & Sans, Helvetica, Courier, Times etc\\ |
---|
| 1268 | \tt rotation & Text rotation (horizontal, vertical) \\ |
---|
| 1269 | \tt alpha & The alpha transparency on 0-1 scale\\ |
---|
| 1270 | \end{tabular} |
---|
| 1271 | |
---|
| 1272 | Examples: |
---|
| 1273 | \begin{verbatim} |
---|
[1259] | 1274 | ASAP>plotter.axhline(6.0,0.2,0.8, color='red', linewidth=3) |
---|
| 1275 | ASAP>plotter.text(-10,7,"CO", fontsize=20) |
---|
[1217] | 1276 | \end{verbatim} |
---|
| 1277 | |
---|
[1259] | 1278 | \section{Line Catalog} |
---|
[1267] | 1279 | \label{sec:linecat} |
---|
| 1280 | \index{Linecatalog}ASAP can load and manipulate line catlogs to |
---|
| 1281 | retrieve rest frequencies for \cmd{set\_restfreqs} and for line |
---|
| 1282 | identification in the plotter. All line catalogs are loaded into a ``linecatalog'' object. |
---|
[1259] | 1283 | |
---|
[1267] | 1284 | No line catalogs are built into ASAP, the user must load a ASCII based |
---|
| 1285 | table (which can optionally be saved in an internal format) either of |
---|
| 1286 | the users own creation or a standard line catalog such as the JPL line |
---|
| 1287 | catalog or Lovas. The ATNF asap ftp area as copies of the JPL and |
---|
| 1288 | Lovas catalog in the appropriate format: |
---|
[1259] | 1289 | |
---|
[1267] | 1290 | \hspace{1cm}\cmd{ftp://ftp.atnf.csiro.au/pub/software/asap/data} |
---|
| 1291 | |
---|
| 1292 | |
---|
[1259] | 1293 | \subsection{Loading a Line Catalog} |
---|
| 1294 | |
---|
[1267] | 1295 | \index{Linecatalog!loading}The ASCII text line catalog must have at |
---|
[1259] | 1296 | least 4 columns. The first four columns must contain (in order): |
---|
| 1297 | Molecule name, frequency in MHz, frequency error and ``intensity'' |
---|
| 1298 | (any units). If the molecule name contains any spaces, they must be |
---|
| 1299 | wrapped in quotes \verb+""+. |
---|
| 1300 | |
---|
| 1301 | A sample from the JPL line catalog: |
---|
| 1302 | |
---|
| 1303 | \begin{verbatim} |
---|
| 1304 | H2D+ 3955.2551 228.8818 -7.1941 |
---|
| 1305 | H2D+ 12104.7712 177.1558 -6.0769 |
---|
| 1306 | H2D+ 45809.2731 118.3223 -3.9494 |
---|
| 1307 | CH 701.6811 .0441 -7.1641 |
---|
| 1308 | CH 724.7709 .0456 -7.3912 |
---|
| 1309 | CH 3263.7940 .1000 -6.3501 |
---|
| 1310 | CH 3335.4810 .1000 -6.0304 |
---|
| 1311 | \end{verbatim} |
---|
| 1312 | |
---|
| 1313 | To load a line catalog then save it in the internal format: |
---|
| 1314 | |
---|
| 1315 | \begin{verbatim} |
---|
| 1316 | ASAP>jpl = linecatalog('jpl_pruned.txt') |
---|
| 1317 | ASAP>jpl.save('jpl.tbl') |
---|
| 1318 | \end{verbatim} |
---|
| 1319 | |
---|
| 1320 | Later the saved line catalog can reloaded: |
---|
| 1321 | |
---|
| 1322 | \begin{verbatim} |
---|
| 1323 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
| 1324 | \end{verbatim} |
---|
| 1325 | |
---|
[1267] | 1326 | {\em NOTE:} Due to a bug in ipython, if you do not \cmd{del} the |
---|
| 1327 | linecatalog table before quiting asap, you will be left with temporary |
---|
| 1328 | files. It is safe to delete these once asap has finished. |
---|
| 1329 | |
---|
[1259] | 1330 | \subsection{Line selection} |
---|
| 1331 | |
---|
[1267] | 1332 | \index{Linecatalog!line selection}The linecatalog has a number of |
---|
[1259] | 1333 | selection functions to select a range of lines from a larger catalog |
---|
| 1334 | (the JPL catalog has $>$180000 lines for |
---|
| 1335 | example). \cmd{set\_frequency\_limits} selects on frequency range, |
---|
| 1336 | \cmd{set\_strength\_limits} selects on intensity while \cmd{set\_name} |
---|
[1267] | 1337 | selects on molecule name (wild cards allowed). The \cmd{summary} |
---|
| 1338 | function lists the currently selected lines. |
---|
[1259] | 1339 | |
---|
| 1340 | \begin{verbatim} |
---|
| 1341 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
| 1342 | ASAP>jpl.set_frequency_limits(80,115,'GHz') # Lines for 3mm receiver |
---|
| 1343 | ASAP>jpl.set_name('*OH') # Select all alcohols |
---|
| 1344 | ASAP>jpl.set_name('OH') # Select only OH molecules |
---|
| 1345 | ASAP>jpl.summary() |
---|
| 1346 | |
---|
| 1347 | ASAP>jpl.reset() # Selections are accumulative |
---|
| 1348 | ASAP>jpl.set_frequency_limits(80,115,'GHz') |
---|
| 1349 | ASAP>jpl.set_strength_limits(-2,10) # Select brightest lines |
---|
| 1350 | ASAP>jpl.summary() |
---|
| 1351 | \end{verbatim} |
---|
| 1352 | |
---|
| 1353 | \subsection{Using Linecatalog} |
---|
| 1354 | |
---|
| 1355 | The line catalogs can be used for line overlays on the plotter or with |
---|
| 1356 | \cmd{set\_restfreq}. |
---|
| 1357 | |
---|
| 1358 | \subsubsection{Plotting linecatalog} |
---|
| 1359 | |
---|
[1267] | 1360 | \index{Linecatalog!plotting} |
---|
[1259] | 1361 | |
---|
| 1362 | The plotter \cmd{plot\_lines} function takes a line catalog as an |
---|
| 1363 | argument and overlays the lines on the spectrum. {\em Currently this |
---|
| 1364 | only works when plotting in units of frequency (Hz, GHz etc).} If a |
---|
| 1365 | large line catalog has been loaded (e.g. JPL) it is highly recommended |
---|
| 1366 | that you use the selection functions to narrow down the number of |
---|
| 1367 | lines. By default the line catalog overlay is plotted assuming a line |
---|
| 1368 | velocity of 0.0. This can be set using the \cmd{doppler} argument (in |
---|
| 1369 | km/s). Each time \cmd{plot\_lines} is called the new lines are added |
---|
| 1370 | to any existing line catalog annotations. These are all removed after |
---|
| 1371 | the next call to \cmd{plotter.plot()}. |
---|
| 1372 | |
---|
| 1373 | \begin{verbatim} |
---|
| 1374 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
| 1375 | ASAP>jpl.set_frequency_limits(23,24,'GHz') |
---|
| 1376 | ASAP>data.set_unit('GHz') # Only works with freq axis currently |
---|
| 1377 | ASAP>plotter.plot(data) |
---|
| 1378 | ASAP>plotter.plot_lines(jpl) |
---|
| 1379 | |
---|
| 1380 | ASAP>plotter.plot() # Reset plotter |
---|
[1267] | 1381 | ASAP>plotter.plot_lines(jpl,doppler=-10,location='Top') |
---|
| 1382 | # On top with -10 km/s velocity |
---|
[1259] | 1383 | \end{verbatim} |
---|
| 1384 | |
---|
| 1385 | \subsubsection{Setting Rest Frequencies} |
---|
| 1386 | |
---|
[1267] | 1387 | \index{Linecatalog!set\_restfreq}A linecatalog can be used as an |
---|
| 1388 | argument for \cmd{set\_restfreqs}. If a personal line catalog has been |
---|
| 1389 | used (which has the same size as the number of number of IFs) or |
---|
| 1390 | linecatalog selection has been used to reduce the number of entries, |
---|
| 1391 | the line catalog can be used directly as an argument to |
---|
| 1392 | \cmd{set\_restfreqs}, e.g.: |
---|
| 1393 | \begin{verbatim} |
---|
| 1394 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
| 1395 | ASAP>jpl.set_frequency_limits(23.66,23.75,'GHz') |
---|
| 1396 | ASAP>data = scantable('data.rpf') |
---|
| 1397 | ASAP>data.set_restfreqs(jpl) |
---|
| 1398 | \end{verbatim} |
---|
[1259] | 1399 | |
---|
[1267] | 1400 | If a larger linecatalog is used, individual elements can be used. Use |
---|
| 1401 | the \cmd{summary} to get the index number of the rest frequency you |
---|
| 1402 | wish to use. E.g.: |
---|
| 1403 | |
---|
| 1404 | \begin{verbatim} |
---|
| 1405 | ASAP>jpl.summary() |
---|
| 1406 | ASAP>data.set_restfreqs([jpl[11],[jpl[21]]) |
---|
| 1407 | \end{verbatim} |
---|
| 1408 | |
---|
[1757] | 1409 | For data with many IFs, such as from MOPS, it is recommended |
---|
| 1410 | that users creates their own line catalog table for the data and use this |
---|
[1267] | 1411 | to set the rest frequency for each IF. |
---|
| 1412 | |
---|
[534] | 1413 | \section{Fitting} |
---|
| 1414 | |
---|
[794] | 1415 | \index{Fitting}Currently multicomponent Gaussian function is |
---|
| 1416 | available. This is done by creating a fitting object, setting up the |
---|
| 1417 | fit and actually fitting the data. Fitting can either be done on a |
---|
[966] | 1418 | single scantable selection or on an entire scantable using the |
---|
| 1419 | \cmd{auto\_fit} function. If single value fitting is used, and the |
---|
| 1420 | current selection includes multiple spectra (beams, IFs, scans etc) |
---|
[971] | 1421 | then the first spectrum in the scantable will be used for fitting. |
---|
[534] | 1422 | |
---|
| 1423 | \begin{verbatim} |
---|
[1259] | 1424 | ASAP>f = fitter() |
---|
| 1425 | ASAP>f.set_function(gauss=2) # Fit two Gaussians |
---|
| 1426 | ASAP>f.set_scan(scans) |
---|
| 1427 | ASAP>selection = selector() |
---|
| 1428 | ASAP>selection.set_polarisations(1) # Fit the second polarisation |
---|
| 1429 | ASAP>scans.set_selection(selection) |
---|
| 1430 | ASAP>scans.set_unit('km/s') # Make fit in velocity units |
---|
| 1431 | ASAP>f.fit(1) # Run the fit on the second row in the table |
---|
| 1432 | ASAP>f.plot() # Show fit in a plot window |
---|
| 1433 | ASAP>f.get_parameters() # Return the fit paramaters |
---|
[534] | 1434 | \end{verbatim} |
---|
| 1435 | |
---|
| 1436 | This auto-guesses the initial values of the fit and works well for data |
---|
| 1437 | without extra confusing features. Note that the fit is performed in |
---|
| 1438 | whatever unit the abscissa is set to. |
---|
| 1439 | |
---|
| 1440 | If you want to confine the fitting to a smaller range (e.g. to avoid |
---|
| 1441 | band edge effects or RFI you must set a mask. |
---|
| 1442 | |
---|
| 1443 | \begin{verbatim} |
---|
[1259] | 1444 | ASAP>f = fitter() |
---|
| 1445 | ASAP>f.set_function(gauss=2) |
---|
| 1446 | ASAP>scans.set_unit('km/s') # Set the mask in channel units |
---|
| 1447 | ASAP>msk = s.create_mask([1800,2200]) |
---|
| 1448 | ASAP>scans.set_unit('km/s') # Make fit in velocity units |
---|
| 1449 | ASAP>f.set_scan(s,msk) |
---|
| 1450 | ASAP>f.fit() |
---|
| 1451 | ASAP>f.plot() |
---|
| 1452 | ASAP>f.get_parameters() |
---|
[534] | 1453 | \end{verbatim} |
---|
| 1454 | |
---|
[544] | 1455 | If you wish, the initial parameter guesses can be specified and |
---|
| 1456 | specific parameters can be fixed: |
---|
[534] | 1457 | |
---|
| 1458 | \begin{verbatim} |
---|
[1259] | 1459 | ASAP>f = fitter() |
---|
| 1460 | ASAP>f.set_function(gauss=2) |
---|
| 1461 | ASAP>f.set_scan(s,msk) |
---|
| 1462 | ASAP>f.fit() # Fit using auto-estimates |
---|
[738] | 1463 | # Set Peak, centre and fwhm for the second gaussian. |
---|
[534] | 1464 | # Force the centre to be fixed |
---|
[1259] | 1465 | ASAP>f.set_gauss_parameters(0.4,450,150,0,1,0,component=1) |
---|
| 1466 | ASAP>f.fit() # Re-run the fit |
---|
[534] | 1467 | \end{verbatim} |
---|
| 1468 | |
---|
| 1469 | The fitter \cmd{plot} function has a number of options to either view |
---|
| 1470 | the fit residuals or the individual components (by default it plots |
---|
| 1471 | the sum of the model components). |
---|
| 1472 | |
---|
| 1473 | Examples: |
---|
| 1474 | |
---|
| 1475 | \begin{verbatim} |
---|
| 1476 | # Plot the residual |
---|
[1259] | 1477 | ASAP>f.plot(residual=True) |
---|
[534] | 1478 | |
---|
| 1479 | # Plot the first 2 componentsa |
---|
[1259] | 1480 | ASAP>f.plot(components=[0,1]) |
---|
[534] | 1481 | |
---|
| 1482 | # Plot the first and third component plus the model sum |
---|
[1259] | 1483 | ASAP>f.plot(components=[-1,0,2]) # -1 means the compoment sum |
---|
[534] | 1484 | \end{verbatim} |
---|
| 1485 | |
---|
[544] | 1486 | \subsection{Fit saving} |
---|
| 1487 | |
---|
[794] | 1488 | \index{Fitter!Fit saving}One you are happy with your fit, it is |
---|
| 1489 | possible to store it as part of the scantable. |
---|
[544] | 1490 | |
---|
| 1491 | \begin{verbatim} |
---|
[1259] | 1492 | ASAP>f.store_fit() |
---|
[544] | 1493 | \end{verbatim} |
---|
| 1494 | |
---|
| 1495 | This will be saved to disk with the data, if the ``ASAP'' file format |
---|
| 1496 | is selected. Multiple fits to the same data can be stored in the |
---|
[738] | 1497 | scantable. |
---|
[544] | 1498 | |
---|
| 1499 | The scantable function \cmd{get\_fit} can be used to retrieve the |
---|
| 1500 | stored fits. Currently the fit parameters are just printed to the |
---|
| 1501 | screen. |
---|
| 1502 | |
---|
| 1503 | \begin{verbatim} |
---|
[1259] | 1504 | ASAP>scans.get_fit(4) # Print fits for row 4 |
---|
[544] | 1505 | \end{verbatim} |
---|
| 1506 | |
---|
[1259] | 1507 | A fit can also be exported to an ASCII file using the \cmd{store\_fit} |
---|
| 1508 | function. Simply give the name of the output file requires as an |
---|
| 1509 | argument. |
---|
| 1510 | |
---|
| 1511 | \begin{verbatim} |
---|
| 1512 | ASAP>f.store_fit('myfit.txt') |
---|
| 1513 | \end{verbatim} |
---|
| 1514 | |
---|
[534] | 1515 | \section{Polarisation} |
---|
| 1516 | |
---|
[794] | 1517 | \index{Polarisation}Currently ASAP only supports polarmetric analysis |
---|
| 1518 | on linearly polarised feeds and the cross polarisation products |
---|
[971] | 1519 | measured. Other cases will be added on an as needed basis. |
---|
[534] | 1520 | |
---|
[538] | 1521 | Conversions of linears to Stokes or Circular polarisations are done |
---|
[966] | 1522 | ``on-the-fly''. Leakage cannot be corrected for nor are there routines |
---|
| 1523 | to calibrate position angle offsets. |
---|
[534] | 1524 | |
---|
[538] | 1525 | \subsection{Simple Calibration} |
---|
| 1526 | |
---|
[794] | 1527 | \index{Polarisation!calibration}It is possible that there is a phase |
---|
| 1528 | offset between polarisation which will effect the phase of the cross |
---|
| 1529 | polarisation correlation, and so give rise to spurious |
---|
| 1530 | polarisation. \cmd{rotate\_xyphase} can be used to correct for this |
---|
| 1531 | error. At this point, the user must know how to determine the size of |
---|
| 1532 | the phase offset themselves. |
---|
[538] | 1533 | |
---|
| 1534 | \begin{verbatim} |
---|
[1259] | 1535 | ASAP>scans.rotate_xyphase(10.5) # Degrees |
---|
[538] | 1536 | \end{verbatim} |
---|
| 1537 | |
---|
| 1538 | Note that if this function is run twice, the sum of the two values is |
---|
[546] | 1539 | applied because it is done in-situ. |
---|
[538] | 1540 | |
---|
[546] | 1541 | A correction for the receiver parallactic angle may need to be made, |
---|
[953] | 1542 | generally because of how it is mounted. Use \cmd{rotate\_linpolphase} |
---|
| 1543 | to correct the position angle. Running this function twice results in |
---|
| 1544 | the sum of the corrections being applied because it is applied |
---|
| 1545 | in-situ. |
---|
[538] | 1546 | |
---|
| 1547 | \begin{verbatim} |
---|
[1259] | 1548 | ASAP>scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting |
---|
[953] | 1549 | \end{verbatim} |
---|
[538] | 1550 | |
---|
[953] | 1551 | If the sign of the complex correlation is wrong (this can happen |
---|
| 1552 | depending on the correlator configuration), use \cmd{invert\_phase} to |
---|
| 1553 | change take the complex conjugate of the complex correlation |
---|
| 1554 | term. This is always performed in-situ. |
---|
| 1555 | |
---|
| 1556 | \begin{verbatim} |
---|
[1259] | 1557 | ASAP>scans.invert_phase() |
---|
[538] | 1558 | \end{verbatim} |
---|
| 1559 | |
---|
[953] | 1560 | Depending on how the correlator is configured, ``BA'' may be |
---|
[1259] | 1561 | correlated instead of ``AB''. Use \cmd{swap\_linears} to correct for |
---|
[953] | 1562 | this problem: |
---|
| 1563 | |
---|
| 1564 | \begin{verbatim} |
---|
[1259] | 1565 | ASAP>scans.swap_linears() |
---|
[953] | 1566 | \end{verbatim} |
---|
| 1567 | |
---|
[1011] | 1568 | \subsection{Conversion} |
---|
| 1569 | \label{sec:polconv} |
---|
| 1570 | |
---|
[1064] | 1571 | Data can be permanently converted between linear and circular |
---|
| 1572 | polarisations and stokes. |
---|
| 1573 | |
---|
[1011] | 1574 | \begin{verbatim} |
---|
[1259] | 1575 | ASAP>stokescans = linearscans.convert_pol("stokes") |
---|
[1011] | 1576 | \end{verbatim} |
---|
| 1577 | |
---|
| 1578 | |
---|
[538] | 1579 | \subsection{Plotting} |
---|
| 1580 | \label{sec:polplot} |
---|
| 1581 | |
---|
[953] | 1582 | \index{Polarisation!plotting}To plot Stokes values, a selector object |
---|
| 1583 | must be created and the set\_polarisation function used to select the |
---|
| 1584 | desired polarisation products. |
---|
| 1585 | |
---|
| 1586 | The values which can be plotted include a selection of [I,Q,U,V], [I, |
---|
| 1587 | Plinear, Pangle, V], [RR, LL] or [XX, YY, Real(XY), |
---|
[794] | 1588 | Imaginary(XY)]. (Plinear and Pangle are the percentage and position |
---|
[1011] | 1589 | angle of linear polarisation). |
---|
[538] | 1590 | |
---|
| 1591 | Example: |
---|
| 1592 | |
---|
| 1593 | \begin{verbatim} |
---|
[1259] | 1594 | ASAP>selection = selector() |
---|
[970] | 1595 | |
---|
[1259] | 1596 | ASAP>selection.set_polarisations(``I Q U V'') |
---|
[953] | 1597 | ASAP plotter.set_selection(selection); # Select I, Q, U \& V |
---|
| 1598 | |
---|
[1259] | 1599 | ASAP>selection.set_polarisations(``I Q'') |
---|
[953] | 1600 | ASAP plotter.set_selection(selection); # Select just I \& Q |
---|
| 1601 | |
---|
[1259] | 1602 | ASAP>selection.set_polarisations(``RR LL'') |
---|
[953] | 1603 | ASAP plotter.set_selection(selection); # Select just RR \& LL |
---|
| 1604 | |
---|
[1259] | 1605 | ASAP>selection.set_polarisations(``XX YY'') |
---|
[953] | 1606 | ASAP plotter.set_selection(selection); # Select linears |
---|
| 1607 | |
---|
[1259] | 1608 | ASAP>selection.set_polarisations(``I Plinear'') |
---|
[966] | 1609 | ASAP plotter.set_selection(selection); # Fractional linear |
---|
[953] | 1610 | |
---|
[1259] | 1611 | ASAP>selection.set_polarisations(``Pangle'') |
---|
[966] | 1612 | ASAP plotter.set_selection(selection); # Position angle |
---|
| 1613 | |
---|
[538] | 1614 | \end{verbatim} |
---|
| 1615 | |
---|
[970] | 1616 | Scan, beam and IF selection are also available in the selector object as |
---|
[953] | 1617 | describe in section~\ref{sec:selection}. |
---|
[538] | 1618 | |
---|
[1217] | 1619 | \section{Specialised Processing} |
---|
| 1620 | |
---|
| 1621 | \subsection{Multibeam MX mode} |
---|
| 1622 | |
---|
| 1623 | MX mode is a specific observing approach with a multibeam where a |
---|
| 1624 | single source is observed cycling through each beam. The scans when |
---|
[1259] | 1625 | the beam is off source is used as a reference for the on-source |
---|
[1217] | 1626 | scan. The function \cmd{mx\_quotient} is used to make a quotient |
---|
| 1627 | spectrum from an MX cycle. This works averaging the ``off-source'' |
---|
| 1628 | scans for each beam (either a median average or mean) and using this |
---|
| 1629 | as a reference scan in a normal quotient (for each beam). The final |
---|
| 1630 | spectrum for each beam is returned on a new scantable containing |
---|
| 1631 | single scan (it the scan numbers are re-labelled to be the same). Note |
---|
| 1632 | that the current version of \cmd{mx\_quotient} only handles a single |
---|
[1259] | 1633 | MX cycle, i.e. if each beam has observed the source multiple times you |
---|
[1217] | 1634 | will need to use the selector object multiple times to select a single |
---|
| 1635 | MX cycle, run \cmd{mx\_quotient} for each cycle then merge the |
---|
| 1636 | resulting scan tables back together. |
---|
| 1637 | |
---|
| 1638 | Example: |
---|
| 1639 | |
---|
| 1640 | \begin{verbatim} |
---|
[1259] | 1641 | ASAP>scans = scantable('mydata.rpf') |
---|
| 1642 | ASAP>q = scans.mx_quotient() |
---|
| 1643 | ASAP>plotter.plot(q) |
---|
[1217] | 1644 | \end{verbatim} |
---|
| 1645 | |
---|
| 1646 | The function \cmd{average\_beam} averages multiple beam data |
---|
| 1647 | together. This is need if MX mode has been used to make a long |
---|
| 1648 | integration on a single source. E.g. |
---|
| 1649 | |
---|
| 1650 | \begin{verbatim} |
---|
[1259] | 1651 | ASAP>av = q.average_beam() |
---|
[1217] | 1652 | \end{verbatim} |
---|
| 1653 | |
---|
| 1654 | \subsection{Frequency Switching} |
---|
| 1655 | |
---|
| 1656 | {\em FILL ME IN} |
---|
| 1657 | |
---|
[1259] | 1658 | \subsection{Disk Based Processing} |
---|
[1267] | 1659 | \index{Scantable!disk based} |
---|
[1259] | 1660 | |
---|
[1267] | 1661 | Normally scantables exist entirely in memory during an ASAP |
---|
| 1662 | session. This has the advantage of speed, but causes limits on the |
---|
[1259] | 1663 | size of the dataset which can be loaded. ASAP can use ``disk based'' |
---|
[1267] | 1664 | scan tables which cache the bulk of the scantable on disk and require |
---|
[1757] | 1665 | significantly less memory usage. This should be used for all MOPS data! |
---|
[1259] | 1666 | |
---|
[1267] | 1667 | To use disk based tables you either need to change the default in your |
---|
[1344] | 1668 | \cmd{.asaprc} file, e.g. |
---|
[1267] | 1669 | \begin{verbatim} |
---|
| 1670 | scantable.storage : disk |
---|
| 1671 | \end{verbatim} |
---|
| 1672 | |
---|
| 1673 | or use set the ``\cmd{rc}'' value while running asap to change this |
---|
| 1674 | on-the-fly. E.g. |
---|
| 1675 | \begin{verbatim} |
---|
| 1676 | ASAP>rc('scantable',storage='disk') |
---|
| 1677 | ASAP>data = scantable('data.rpf') # Loaded using disk based table |
---|
| 1678 | ASAP>rc('scantable',storage='memory') # Memory tables will be used now |
---|
| 1679 | \end{verbatim} |
---|
| 1680 | |
---|
| 1681 | Changing the ``\cmd{rc}'' value affects the next time the |
---|
| 1682 | \cmd{scantable} constructor is called. |
---|
| 1683 | |
---|
[1259] | 1684 | {\bf NOTE: } Currently a bug in ipython means temporary files are not |
---|
| 1685 | cleaned up properly when you exit ASAP. If you use disk based scan |
---|
[1757] | 1686 | tables your directory will be left with 'tmpXXXXX\_X' directories. These can |
---|
[1259] | 1687 | be safely removed if ASAP is not running. |
---|
| 1688 | |
---|
[770] | 1689 | \section{Scantable Mathematics} |
---|
| 1690 | |
---|
[794] | 1691 | \index{Scantable!maths}It is possible to to simple mathematics |
---|
| 1692 | directly on scantables from the command line using the \cmd{+, -, *, |
---|
| 1693 | /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works |
---|
[971] | 1694 | between a scantable and a float. (Note that it does |
---|
[794] | 1695 | not work for integers). |
---|
[770] | 1696 | |
---|
[971] | 1697 | {\em Currently mathematics between two scantables is not available } |
---|
[966] | 1698 | |
---|
[534] | 1699 | \begin{verbatim} |
---|
[1259] | 1700 | ASAP>scan2 = scan1+2.0 |
---|
| 1701 | ASAP>scan *= 1.05 |
---|
[1757] | 1702 | ASAP>sum = scan1+scan2 |
---|
[770] | 1703 | \end{verbatim} |
---|
| 1704 | |
---|
| 1705 | \section{Scripting} |
---|
| 1706 | |
---|
[1259] | 1707 | \index{Scripting}Because ASAP is based on python, it easy for the user |
---|
[794] | 1708 | write their own scripts and functions to process data. This is highly |
---|
| 1709 | recommended as most processing of user data could then be done in a |
---|
| 1710 | couple of steps using a few simple user defined functions. A Python |
---|
[1259] | 1711 | primer is beyond the scope of this userguide. See the ASAP home pages |
---|
[794] | 1712 | for a scripting tutorial or the main python website for comprehensive |
---|
| 1713 | documentation. |
---|
[770] | 1714 | |
---|
| 1715 | \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials |
---|
[953] | 1716 | |
---|
[1344] | 1717 | \hspace{1cm} http://svn.atnf.csiro.au/trac/asap/wiki |
---|
| 1718 | |
---|
[770] | 1719 | \hspace{1cm} http://www.python.org/doc/Introduction.html |
---|
| 1720 | |
---|
[1757] | 1721 | \hspace{1cm} http:/ipython.scipy.org |
---|
| 1722 | |
---|
[770] | 1723 | \subsection{Running scripts} |
---|
| 1724 | |
---|
[1259] | 1725 | The ASAP global function \cmd{execfile} reads the named text file and |
---|
[770] | 1726 | executes the contained python code. This file can either contain |
---|
| 1727 | function definitions which will be used in subsequent processing or |
---|
| 1728 | just a set of commands to process a specific dataset. |
---|
| 1729 | |
---|
[1344] | 1730 | As an alternative to run scripts without entering ASAP, create a script which |
---|
| 1731 | starts with. |
---|
| 1732 | |
---|
| 1733 | \begin{verbatim} |
---|
| 1734 | from asap import * |
---|
| 1735 | |
---|
| 1736 | <your code> |
---|
| 1737 | \end{verbatim} |
---|
| 1738 | |
---|
| 1739 | And run it with \cmd{python scriptname}. |
---|
| 1740 | |
---|
[770] | 1741 | \subsection{asapuserfuncs.py} |
---|
| 1742 | |
---|
| 1743 | The file $\sim$/.asap/asapuserfuncs.py is automatically read in when |
---|
[1259] | 1744 | ASAP is started. The user can use this to define a set of user |
---|
| 1745 | functions which are automatically available each time ASAP is |
---|
[770] | 1746 | used. The \cmd{execfile} function can be called from within this file. |
---|
| 1747 | |
---|
| 1748 | \section{Worked examples} |
---|
| 1749 | |
---|
| 1750 | In the following section a few examples of end-to-end processing of |
---|
[1259] | 1751 | some data in ASAP are given. |
---|
[770] | 1752 | |
---|
| 1753 | \subsection{Mopra} |
---|
[794] | 1754 | \index{Mopra} |
---|
[770] | 1755 | |
---|
[794] | 1756 | The following example is of some dual polarisation, position switched |
---|
[1259] | 1757 | data from Mopra. The source has been observed multiple times split |
---|
| 1758 | into a number of separate RPFITS files. To make the processing easier, |
---|
| 1759 | the first step is to \cmd{cat} the separate RPFITS files together and |
---|
| 1760 | load as a whole (future versions of ASAP will make this unnecessary). |
---|
[794] | 1761 | |
---|
| 1762 | |
---|
| 1763 | \begin{verbatim} |
---|
[1011] | 1764 | # get a list of the individual rpfits files in the current directory |
---|
| 1765 | myfiles = list_files() |
---|
[794] | 1766 | |
---|
| 1767 | # Load the data into a scantable |
---|
[1011] | 1768 | data = scantable(myfiles) |
---|
[794] | 1769 | print data |
---|
| 1770 | |
---|
| 1771 | # Form the quotient spectra |
---|
| 1772 | q = data.auto_quotient() |
---|
| 1773 | print q |
---|
| 1774 | |
---|
| 1775 | # Look at the spectra |
---|
| 1776 | plotter.plot(q) |
---|
| 1777 | |
---|
[1011] | 1778 | # Set unit and reference frame |
---|
[794] | 1779 | q.set_unit('km/s') |
---|
| 1780 | q.set_freqframe('LSRK') |
---|
| 1781 | |
---|
[966] | 1782 | # Average all scans in time, aligning in velocity |
---|
| 1783 | av = q.average_time(align=True) |
---|
[794] | 1784 | plotter.plot(av) |
---|
| 1785 | |
---|
| 1786 | # Remove the baseline |
---|
| 1787 | msk = av.create_mask([100,130],[160,200]) |
---|
| 1788 | av.poly_baseline(msk,2) |
---|
| 1789 | |
---|
| 1790 | # Average the two polarisations together |
---|
| 1791 | iav = av.average_pol() |
---|
| 1792 | print iav |
---|
| 1793 | plotter.plot(iav) |
---|
| 1794 | |
---|
| 1795 | # Set a sensible velocity range on the plot |
---|
| 1796 | plotter.set_range(85,200) |
---|
| 1797 | |
---|
| 1798 | # Smooth the data a little |
---|
| 1799 | av.smooth('gauss',4) |
---|
| 1800 | plotter.plot() |
---|
| 1801 | |
---|
| 1802 | # Fit a guassian to the emission |
---|
| 1803 | f = fitter() |
---|
| 1804 | f.set_function(gauss=1) |
---|
| 1805 | f.set_scan(av) |
---|
| 1806 | f.fit() |
---|
| 1807 | |
---|
| 1808 | # View the fit |
---|
| 1809 | f.plot() |
---|
| 1810 | |
---|
| 1811 | # Get the fit parameters |
---|
| 1812 | f.get_parameters() |
---|
| 1813 | |
---|
| 1814 | \end{verbatim} |
---|
| 1815 | |
---|
| 1816 | |
---|
[770] | 1817 | \subsection{Parkes Polarimetry} |
---|
| 1818 | |
---|
[794] | 1819 | \index{Parkes}\index{Polarisation}The following example is processing |
---|
[1267] | 1820 | of some Parkes polarimetric observations of OH masers at |
---|
[794] | 1821 | 1.6~GHz. Because digital filters where used in the backend, the |
---|
| 1822 | baselines are stable enough not to require a quotient spectra. The |
---|
| 1823 | 4~MHz bandwidth is wide enough to observe both the 1665 and 1667~MHz |
---|
| 1824 | OH maser transitions. Each source was observed once for about 10 |
---|
[1259] | 1825 | minutes. Tsys information was not written to the RPFITS file (a |
---|
[794] | 1826 | nominal 25K values was used), so the amplitudes need to be adjusted |
---|
| 1827 | based on a separate log file. A simple user function is used to |
---|
| 1828 | simplify this, contained in a file called mypol.py: |
---|
[770] | 1829 | |
---|
| 1830 | \begin{verbatim} |
---|
| 1831 | def xyscale(data,xtsys=1.0,ytsys=1.0,nomtsys=25.0) : |
---|
| 1832 | |
---|
[966] | 1833 | selection = selector() |
---|
[971] | 1834 | selection.set_polarisations(0) |
---|
[966] | 1835 | data.set_selection(selection) |
---|
| 1836 | data.scale(xtsys/nomtsys) |
---|
[770] | 1837 | |
---|
[971] | 1838 | selection.set_polarisations(1) |
---|
[966] | 1839 | data.set_selection(selection) |
---|
| 1840 | data.scale(ytsys/nomtsys) |
---|
[770] | 1841 | |
---|
[971] | 1842 | selection.set_polarisations(0) |
---|
[966] | 1843 | data.set_selection(selection) |
---|
| 1844 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
[770] | 1845 | |
---|
[971] | 1846 | selection.set_polarisations(0) |
---|
[966] | 1847 | data.set_selection(selection) |
---|
| 1848 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
[770] | 1849 | \end{verbatim} |
---|
| 1850 | |
---|
[1259] | 1851 | The typical ASAP session would be |
---|
[770] | 1852 | |
---|
| 1853 | \begin{verbatim} |
---|
[794] | 1854 | |
---|
[770] | 1855 | # Remind ourself the name of the rpfits files |
---|
[794] | 1856 | ls |
---|
[770] | 1857 | |
---|
| 1858 | # Load data from an rpfits file |
---|
| 1859 | d1665 = scantable('2005-10-27_0154-P484.rpf') |
---|
| 1860 | |
---|
| 1861 | # Check what we have just loaded |
---|
[1011] | 1862 | d1665.summary() |
---|
[770] | 1863 | |
---|
| 1864 | # View the data in velocity |
---|
| 1865 | d1665.set_unit('km/s') |
---|
| 1866 | d1665.set_freqframe('LSRK') |
---|
| 1867 | |
---|
| 1868 | # Correct for the known phase offset in the crosspol data |
---|
| 1869 | d1665.rotate_xyphase(-4) |
---|
| 1870 | |
---|
[794] | 1871 | # Create a copy of the data and set the rest frequency to the 1667 MHz |
---|
[770] | 1872 | # transition |
---|
| 1873 | d1667 = d1665.copy() |
---|
[966] | 1874 | d1667.set_restfreqs([1667.3590], 'MHz') |
---|
| 1875 | d1667.summary() |
---|
[770] | 1876 | |
---|
| 1877 | # Copy out the scan we wish to process |
---|
| 1878 | g351_5 = d1665.get_scan('351p160') |
---|
| 1879 | g351_7 = d1667.get_scan('351p160') |
---|
| 1880 | |
---|
[966] | 1881 | # Baseline both |
---|
| 1882 | msk = g351_5.create_mask([-30,-25],[-5,0]) |
---|
| 1883 | g351_5.poly_baseline(msk,order=1) |
---|
| 1884 | msk = g351_7.create_mask([-30,-25],[-5,0]) |
---|
| 1885 | g351_7.poly_baseline(msk,order=1) |
---|
[770] | 1886 | |
---|
[966] | 1887 | |
---|
| 1888 | # Plot the data. The plotter can only plot a single scantable |
---|
| 1889 | # So we must merge the two tables first |
---|
| 1890 | |
---|
| 1891 | plotscans = merge(g351_5, g351_7) |
---|
| 1892 | |
---|
| 1893 | plotter.plot(plotscans) # Only shows one panel |
---|
| 1894 | |
---|
[770] | 1895 | # Tell the plotter to stack polarisation and panel scans |
---|
| 1896 | plotter.set_mode('p','s') |
---|
| 1897 | |
---|
| 1898 | # Correct for the Tsys using our predefined function |
---|
[971] | 1899 | execfile('mypol.py') # Read in the function xyscale |
---|
[770] | 1900 | xyscale(g351_5,23.2,22.7) # Execute it on the data |
---|
| 1901 | xyscale(g351_7,23.2,22.7) |
---|
| 1902 | |
---|
| 1903 | # Only plot the velocity range of interest |
---|
| 1904 | plotter.set_range(-30,10) |
---|
| 1905 | |
---|
| 1906 | # Update the plot with the baselined data |
---|
| 1907 | plotter.plot() |
---|
| 1908 | |
---|
| 1909 | # Look at the various polarisation products |
---|
[966] | 1910 | selection = selector() |
---|
| 1911 | selection.set_polarisations(``RR LL'') |
---|
| 1912 | plotter.set_selection(selection) |
---|
| 1913 | selection.set_polarisations(``I Plinear'') |
---|
| 1914 | plotter.set_selection(selection) |
---|
| 1915 | selection.set_polarisations(``I Q U V'') |
---|
| 1916 | plotter.set_selection(selection) |
---|
[770] | 1917 | |
---|
| 1918 | # Save the plot as postscript |
---|
[966] | 1919 | plotter.save('g351_stokes.ps') |
---|
[770] | 1920 | |
---|
| 1921 | # Save the process spectra |
---|
[966] | 1922 | plotscans.save('g351.asap') |
---|
[770] | 1923 | |
---|
| 1924 | \end{verbatim} |
---|
| 1925 | |
---|
| 1926 | \subsection{Tidbinbilla} |
---|
| 1927 | |
---|
[794] | 1928 | \index{Tidbinbilla}The following example is processing of some |
---|
| 1929 | Tidbinbilla observations of NH$_3$ at 12~mm. Tidbinbilla has (at the |
---|
| 1930 | time of observations) a single polarisation, but can process two IFs |
---|
| 1931 | simultaneously. In the example, the first half of the observation was |
---|
| 1932 | observing the (1,1) and (2,2) transitions simultaneously). The second |
---|
| 1933 | half observed only the (4,4) transition due to bandwidth |
---|
| 1934 | limitations. The data is position switched, observing first an |
---|
| 1935 | reference to the west, then the source twice and finally reference to |
---|
[1347] | 1936 | the east. Important to note, that \cmd{auto\_quotient} should be executed |
---|
| 1937 | using the \cmd{mode} `time'. |
---|
[770] | 1938 | |
---|
| 1939 | \begin{verbatim} |
---|
| 1940 | |
---|
| 1941 | # Load the rpfits file and inspect |
---|
| 1942 | d = scantable('2003-03-16_082048_t0002.rpf') |
---|
| 1943 | print d |
---|
| 1944 | |
---|
| 1945 | # Make the quotient spectra |
---|
[1347] | 1946 | q = d.auto_quotient(mode='time') |
---|
[770] | 1947 | print q |
---|
| 1948 | |
---|
[966] | 1949 | del d |
---|
| 1950 | |
---|
[770] | 1951 | # Plot/select in velocity |
---|
| 1952 | q.set_freqframe('LSRK') |
---|
| 1953 | q.set_unit('km/s') |
---|
| 1954 | |
---|
[966] | 1955 | # Correct for gain/el effects |
---|
| 1956 | |
---|
| 1957 | q.recalc_azel() # Tid does not write the elevation |
---|
| 1958 | q.gain_el() |
---|
| 1959 | q.opacity(0.05) |
---|
| 1960 | |
---|
[770] | 1961 | # Seperate data from the (1,1)&(2,2) and (4,4) transitions |
---|
[971] | 1962 | g1 = q.get_scan(range(6)) # scans 0..5 |
---|
| 1963 | g2 = q.get_scan(range(6,12)) # scans 6..11 |
---|
[770] | 1964 | |
---|
[794] | 1965 | # Align data in velocity |
---|
[966] | 1966 | g1.freq_align() |
---|
| 1967 | g2.freq_align() |
---|
[770] | 1968 | |
---|
| 1969 | # Average individual scans |
---|
| 1970 | a1 = g1.average_time() |
---|
| 1971 | a2 = g2.average_time() |
---|
| 1972 | |
---|
[1011] | 1973 | # Rpfits file only contains a single rest frequency. Set both |
---|
[966] | 1974 | a1.set_restfreqs([23694.4700e6,23722.6336e6]) |
---|
[770] | 1975 | |
---|
[966] | 1976 | plotter.plot(a1) |
---|
[1011] | 1977 | plotter.set_mode('i','t') |
---|
[770] | 1978 | |
---|
| 1979 | a1.auto_poly_baseline() |
---|
| 1980 | |
---|
| 1981 | plotter.plot() |
---|
| 1982 | |
---|
| 1983 | a1.smooth('gauss',5) |
---|
| 1984 | plotter.plot() |
---|
| 1985 | |
---|
[966] | 1986 | |
---|
[770] | 1987 | \end{verbatim} |
---|
| 1988 | |
---|
| 1989 | \newpage |
---|
| 1990 | |
---|
| 1991 | \section{Appendix} |
---|
| 1992 | |
---|
| 1993 | \subsection{Function Summary} |
---|
| 1994 | |
---|
[794] | 1995 | \index{Functions!summary}% |
---|
[770] | 1996 | \begin{verbatim} |
---|
[1267] | 1997 | [The scan container] |
---|
[534] | 1998 | scantable - a container for integrations/scans |
---|
| 1999 | (can open asap/rpfits/sdfits and ms files) |
---|
| 2000 | copy - returns a copy of a scan |
---|
| 2001 | get_scan - gets a specific scan out of a scantable |
---|
[1011] | 2002 | (by name or number) |
---|
[1217] | 2003 | drop_scan - drops a specific scan out of a scantable |
---|
| 2004 | (by number) |
---|
[1011] | 2005 | set_selection - set a new subselection of the data |
---|
| 2006 | get_selection - get the current selection object |
---|
[534] | 2007 | summary - print info about the scantable contents |
---|
| 2008 | stats - get specified statistic of the spectra in |
---|
| 2009 | the scantable |
---|
| 2010 | stddev - get the standard deviation of the spectra |
---|
| 2011 | in the scantable |
---|
| 2012 | get_tsys - get the TSys |
---|
| 2013 | get_time - get the timestamps of the integrations |
---|
[1011] | 2014 | get_sourcename - get the source names of the scans |
---|
[794] | 2015 | get_azimuth - get the azimuth of the scans |
---|
| 2016 | get_elevation - get the elevation of the scans |
---|
| 2017 | get_parangle - get the parallactic angle of the scans |
---|
[1011] | 2018 | get_unit - get the current unit |
---|
[534] | 2019 | set_unit - set the abcissa unit to be used from this |
---|
| 2020 | point on |
---|
| 2021 | get_abcissa - get the abcissa values and name for a given |
---|
| 2022 | row (time) |
---|
[1267] | 2023 | get_column_names - get the names of the columns in the scantable |
---|
| 2024 | for use with selector.set_query |
---|
[534] | 2025 | set_freqframe - set the frame info for the Spectral Axis |
---|
| 2026 | (e.g. 'LSRK') |
---|
| 2027 | set_doppler - set the doppler to be used from this point on |
---|
[1011] | 2028 | set_dirframe - set the frame for the direction on the sky |
---|
[534] | 2029 | set_instrument - set the instrument name |
---|
[1217] | 2030 | set_feedtype - set the feed type |
---|
[534] | 2031 | get_fluxunit - get the brightness flux unit |
---|
| 2032 | set_fluxunit - set the brightness flux unit |
---|
| 2033 | create_mask - return an mask in the current unit |
---|
| 2034 | for the given region. The specified regions |
---|
| 2035 | are NOT masked |
---|
| 2036 | get_restfreqs - get the current list of rest frequencies |
---|
| 2037 | set_restfreqs - set a list of rest frequencies |
---|
[1217] | 2038 | flag - flag selected channels in the data |
---|
| 2039 | save - save the scantable to disk as either 'ASAP', |
---|
| 2040 | 'SDFITS' or 'ASCII' |
---|
[534] | 2041 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
[1011] | 2042 | nscan - the number of scans in the scantable |
---|
| 2043 | nrow - te number of spectra in the scantable |
---|
[534] | 2044 | history - print the history of the scantable |
---|
[544] | 2045 | get_fit - get a fit which has been stored witnh the data |
---|
[738] | 2046 | average_time - return the (weighted) time average of a scan |
---|
[534] | 2047 | or a list of scans |
---|
| 2048 | average_pol - average the polarisations together. |
---|
[1217] | 2049 | average_beam - average the beams together. |
---|
[1011] | 2050 | convert_pol - convert to a different polarisation type |
---|
[738] | 2051 | auto_quotient - return the on/off quotient with |
---|
[1217] | 2052 | automatic detection of the on/off scans (closest |
---|
| 2053 | in time off is selected) |
---|
| 2054 | mx_quotient - Form a quotient using MX data (off beams) |
---|
| 2055 | scale, *, / - return a scan scaled by a given factor |
---|
| 2056 | add, +, - - return a scan with given value added |
---|
[534] | 2057 | bin - return a scan with binned channels |
---|
| 2058 | resample - return a scan with resampled channels |
---|
| 2059 | smooth - return the spectrally smoothed scan |
---|
| 2060 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
[738] | 2061 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
[794] | 2062 | recalc_azel - recalculate azimuth and elevation based on |
---|
| 2063 | the pointing |
---|
[534] | 2064 | gain_el - apply gain-elevation correction |
---|
| 2065 | opacity - apply opacity correction |
---|
| 2066 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
| 2067 | units |
---|
| 2068 | freq_align - align spectra in frequency frame |
---|
[1217] | 2069 | invert_phase - Invert the phase of the cross-correlation |
---|
| 2070 | swap_linears - Swap XX and YY |
---|
[534] | 2071 | rotate_xyphase - rotate XY phase of cross correlation |
---|
| 2072 | rotate_linpolphase - rotate the phase of the complex |
---|
| 2073 | polarization O=Q+iU correlation |
---|
[1011] | 2074 | freq_switch - perform frequency switching on the data |
---|
| 2075 | stats - Determine the specified statistic, e.g. 'min' |
---|
| 2076 | 'max', 'rms' etc. |
---|
| 2077 | stddev - Determine the standard deviation of the current |
---|
| 2078 | beam/if/pol |
---|
[1217] | 2079 | [Selection] |
---|
| 2080 | selector - a selection object to set a subset of a scantable |
---|
[1267] | 2081 | set_cycles - set (a list of) cycles by index |
---|
[1217] | 2082 | set_beams - set (a list of) beamss by index |
---|
| 2083 | set_ifs - set (a list of) ifs by index |
---|
| 2084 | set_polarisations - set (a list of) polarisations by name |
---|
| 2085 | or by index |
---|
| 2086 | set_names - set a selection by name (wildcards allowed) |
---|
| 2087 | set_tsys - set a selection by tsys thresholds |
---|
[1267] | 2088 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
---|
[1217] | 2089 | reset - unset all selections |
---|
| 2090 | + - merge to selections |
---|
[1011] | 2091 | |
---|
[534] | 2092 | [Math] Mainly functions which operate on more than one scantable |
---|
| 2093 | |
---|
[738] | 2094 | average_time - return the (weighted) time average |
---|
[534] | 2095 | of a list of scans |
---|
| 2096 | quotient - return the on/off quotient |
---|
[544] | 2097 | simple_math - simple mathematical operations on two scantables, |
---|
| 2098 | 'add', 'sub', 'mul', 'div' |
---|
[1217] | 2099 | quotient - build quotient of the given on and off scans |
---|
| 2100 | (matched pairs and 1 off/n on are valid) |
---|
| 2101 | merge - merge a list of scantables |
---|
| 2102 | |
---|
| 2103 | [Line Catalog] |
---|
| 2104 | linecatalog - a linecatalog wrapper, taking an ASCII or |
---|
| 2105 | internal format table |
---|
| 2106 | summary - print a summary of the current selection |
---|
| 2107 | set_name - select a subset by name pattern, e.g. '*OH*' |
---|
| 2108 | set_strength_limits - select a subset by line strength limits |
---|
| 2109 | set_frequency_limits - select a subset by frequency limits |
---|
| 2110 | reset - unset all selections |
---|
| 2111 | save - save the current subset to a table (internal |
---|
| 2112 | format) |
---|
| 2113 | get_row - get the name and frequency from a specific |
---|
| 2114 | row in the table |
---|
[534] | 2115 | [Fitting] |
---|
| 2116 | fitter |
---|
| 2117 | auto_fit - return a scan where the function is |
---|
| 2118 | applied to all Beams/IFs/Pols. |
---|
| 2119 | commit - return a new scan where the fits have been |
---|
| 2120 | commited. |
---|
| 2121 | fit - execute the actual fitting process |
---|
[1011] | 2122 | store_fit - store the fit parameters in the data (scantable) |
---|
[534] | 2123 | get_chi2 - get the Chi^2 |
---|
| 2124 | set_scan - set the scantable to be fit |
---|
| 2125 | set_function - set the fitting function |
---|
| 2126 | set_parameters - set the parameters for the function(s), and |
---|
| 2127 | set if they should be held fixed during fitting |
---|
[544] | 2128 | set_gauss_parameters - same as above but specialised for individual |
---|
| 2129 | gaussian components |
---|
[534] | 2130 | get_parameters - get the fitted parameters |
---|
| 2131 | plot - plot the resulting fit and/or components and |
---|
| 2132 | residual |
---|
| 2133 | [Plotter] |
---|
| 2134 | asapplotter - a plotter for asap, default plotter is |
---|
| 2135 | called 'plotter' |
---|
[1011] | 2136 | plot - plot a scantable |
---|
[1217] | 2137 | plot_lines - plot a linecatalog overlay |
---|
[534] | 2138 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
| 2139 | set_mode - set the state of the plotter, i.e. |
---|
| 2140 | what is to be plotted 'colour stacked' |
---|
| 2141 | and what 'panelled' |
---|
[1011] | 2142 | set_selection - only plot a selected part of the data |
---|
| 2143 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
---|
[534] | 2144 | set_legend - specify user labels for the legend indeces |
---|
| 2145 | set_title - specify user labels for the panel indeces |
---|
[1011] | 2146 | set_abcissa - specify a user label for the abcissa |
---|
[534] | 2147 | set_ordinate - specify a user label for the ordinate |
---|
| 2148 | set_layout - specify the multi-panel layout (rows,cols) |
---|
[1011] | 2149 | set_colors - specify a set of colours to use |
---|
| 2150 | set_linestyles - specify a set of linestyles to use if only |
---|
| 2151 | using one color |
---|
[1217] | 2152 | set_font - set general font properties, e.g. 'family' |
---|
| 2153 | set_histogram - plot in historam style |
---|
[1011] | 2154 | set_mask - set a plotting mask for a specific polarization |
---|
[1217] | 2155 | text - draw text annotations either in data or relative |
---|
| 2156 | coordinates |
---|
| 2157 | arrow - draw arrow annotations either in data or relative |
---|
| 2158 | coordinates |
---|
[1267] | 2159 | axhline,axvline - draw horizontal/vertical lines |
---|
| 2160 | axhspan,axvspan - draw horizontal/vertical regions |
---|
| 2161 | |
---|
| 2162 | xyplotter - matplotlib/pylab plotting functions |
---|
| 2163 | |
---|
| 2164 | [Reading files] |
---|
| 2165 | reader - access rpfits/sdfits files |
---|
[1217] | 2166 | arrow - draw arrow annotations either in data or relative |
---|
| 2167 | coordinates |
---|
| 2168 | axhline,axvline - draw horizontal/vertical lines |
---|
| 2169 | axhspan,axvspan - draw horizontal/vertical regions |
---|
[738] | 2170 | |
---|
[1217] | 2171 | xyplotter - matplotlib/pylab plotting functions |
---|
| 2172 | |
---|
[534] | 2173 | [Reading files] |
---|
| 2174 | reader - access rpfits/sdfits files |
---|
[1011] | 2175 | open - attach reader to a file |
---|
| 2176 | close - detach reader from file |
---|
[534] | 2177 | read - read in integrations |
---|
| 2178 | summary - list info about all integrations |
---|
| 2179 | |
---|
| 2180 | [General] |
---|
| 2181 | commands - this command |
---|
| 2182 | print - print details about a variable |
---|
| 2183 | list_scans - list all scantables created bt the user |
---|
[1011] | 2184 | list_files - list all files readable by asap (default rpf) |
---|
[534] | 2185 | del - delete the given variable from memory |
---|
| 2186 | range - create a list of values, e.g. |
---|
| 2187 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 2188 | help - print help for one of the listed functions |
---|
[538] | 2189 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
[544] | 2190 | list_rcparameters - print out a list of possible values to be |
---|
[1217] | 2191 | put into .asaprc |
---|
| 2192 | rc - set rc parameters from within asap |
---|
[534] | 2193 | mask_and,mask_or, |
---|
| 2194 | mask_not - boolean operations on masks created with |
---|
| 2195 | scantable.create_mask |
---|
| 2196 | \end{verbatim} |
---|
| 2197 | |
---|
| 2198 | \subsection{ASCII output format} |
---|
| 2199 | |
---|
| 2200 | \subsection{.asaprc settings} |
---|
[794] | 2201 | \index{.asaprc} |
---|
[971] | 2202 | \asaprc{verbose}{{\bf True}/False}{Print verbose output, good to disable in scripts} |
---|
[770] | 2203 | |
---|
| 2204 | \asaprc{insitu}{{\bf True}/False}{Apply operations on the input |
---|
| 2205 | scantable or return new one} |
---|
| 2206 | |
---|
| 2207 | \asaprc{useplotter}{{\bf True}/False}{Preload a default plotter} |
---|
| 2208 | |
---|
| 2209 | \asaprc{plotter.gui}{{\bf True}/False}{Do we want a GUI or plot to a |
---|
| 2210 | file} |
---|
| 2211 | |
---|
| 2212 | \asaprc{plotter.stacking}{{\bf Pol} Beam IF Scan Time}{Default mode for |
---|
| 2213 | colour stacking} |
---|
| 2214 | |
---|
| 2215 | \asaprc{plotter.panelling}{Pol Beam IF {\bf Scan} Time}{Default mode |
---|
| 2216 | for panelling} |
---|
| 2217 | |
---|
| 2218 | \asaprc{plotter.ganged}{{\bf True}/False}{Push panels together, to |
---|
| 2219 | share axislabels} |
---|
| 2220 | |
---|
| 2221 | \asaprc{plotter.decimate}{True/{\bf False}}{Decimate the number of |
---|
| 2222 | points plotted by a factor of nchan/1024} |
---|
| 2223 | |
---|
[1217] | 2224 | \asaprc{plotter.histogram}{True/{\bf False}}{Plot spectrum using |
---|
| 2225 | histogram rather than lines.} |
---|
[770] | 2226 | |
---|
[1217] | 2227 | \asaprc{plotter.colours}{}{Set default colours for plotting} |
---|
| 2228 | |
---|
| 2229 | \asaprc{plotter.colours}{}{Set default line styles} |
---|
| 2230 | |
---|
| 2231 | \asaprc{plotter.papersze}{{\bf A4}}{} |
---|
| 2232 | |
---|
[770] | 2233 | % scantable |
---|
[1280] | 2234 | \asaprc{scantable.save}{{\bf ASAP} SDFITS ASCII MS2}{Default output |
---|
[794] | 2235 | format when saving} |
---|
[770] | 2236 | |
---|
| 2237 | \asaprc{scantable.autoaverage}{{\bf True}/False}{Auto averaging on |
---|
| 2238 | read} |
---|
| 2239 | |
---|
| 2240 | \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default |
---|
| 2241 | frequency frame to set when function scantable.set\_freqframe is |
---|
[971] | 2242 | called or the data is imported} |
---|
[770] | 2243 | |
---|
[1217] | 2244 | \asaprc{scantable.verbosesummary}{True/{\bf False}}{Control the level |
---|
| 2245 | of information printed by summary} |
---|
| 2246 | |
---|
| 2247 | \asaprc{scantable.storage}{{\bf memory}/disk}{Storage of scantables in |
---|
| 2248 | memory of via based disk tables} |
---|
| 2249 | |
---|
[953] | 2250 | \subsection{Installation} |
---|
| 2251 | |
---|
[1267] | 2252 | \index{Installation} |
---|
[953] | 2253 | |
---|
[1267] | 2254 | Please refer to the asap wiki for instructions on downloading and/or |
---|
| 2255 | building asap from source. |
---|
[953] | 2256 | |
---|
[1267] | 2257 | \hspace{1cm}\cmd{http://www.atnf.csiro.au/computing/software/asap/} |
---|
[953] | 2258 | |
---|
[794] | 2259 | \printindex |
---|
| 2260 | |
---|
[534] | 2261 | \end{document} |
---|
[770] | 2262 | |
---|