[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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[1049] | 15 | \title{ATNF Spectral Analysis Package\\User Guide v2.0 } |
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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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[794] | 26 | \makeindex |
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| 27 | |
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| 28 | |
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[534] | 29 | \begin{document} |
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| 30 | |
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| 31 | \maketitle |
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| 32 | |
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| 33 | \section{Introduction} |
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| 34 | |
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[544] | 35 | ASAP is a single dish spectral line processing package currently being |
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| 36 | developed by the ATNF. It is intended to process data from all ATNF |
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[770] | 37 | antennas, and can probably be used for other antennas if they can |
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[544] | 38 | produce ``Single Dish FITS'' format. It is based on the AIPS++ |
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| 39 | package. |
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| 40 | |
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[1011] | 41 | This userguide is currently being updated for the ASAP 2.0 release |
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[953] | 42 | which has a number of significant changes which affect the user |
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| 43 | interface. Please report any mistakes you find in this userguide. |
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[534] | 44 | |
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[544] | 45 | \section{Installation and Running} |
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[534] | 46 | |
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[738] | 47 | Currently there are installations running on Linux machines at |
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[534] | 48 | |
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| 49 | \begin{itemize} |
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| 50 | \item Epping - use hosts {\tt draco} or {\tt hydra} |
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| 51 | \item Narrabri - use host {\tt kaputar} |
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[537] | 52 | \item Parkes - use host {\tt bourbon} |
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[534] | 53 | \item Mopra - use host {\tt minos} |
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| 54 | \end{itemize} |
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| 55 | |
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[794] | 56 | \index{Running}To start asap log onto one of these Linux hosts and enter |
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[534] | 57 | |
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| 58 | \begin{verbatim} |
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| 59 | > cd /my/data/directory |
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[966] | 60 | > asap |
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[534] | 61 | \end{verbatim} |
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| 62 | |
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[544] | 63 | This starts the ASAP. To quit, you need to type \verb+^+-d |
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[971] | 64 | (control-d) or type \cmd{\%Exit}. |
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[534] | 65 | |
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| 66 | \section{Interface} |
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| 67 | |
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[794] | 68 | \index{Interface}ASAP is written in C++ and python. The user interface uses the |
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[534] | 69 | ``ipython'' interactive shell, which is a simple interactive interface |
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| 70 | to python. The user does not need to understand python to use this, |
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| 71 | but certain aspects python affect what the user can do. The current |
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| 72 | interface is object oriented. In the future, we will build a |
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| 73 | functional (non object oriented) shell on top of this to ease |
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| 74 | interactive use. |
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| 75 | |
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| 76 | \subsection {Integer Indices are 0-relative} |
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| 77 | |
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| 78 | Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. |
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| 79 | |
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| 80 | \subsection{Objects} |
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[794] | 81 | \index{objects} |
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[534] | 82 | The ASAP interface is based around a number of ``objects'' which the |
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| 83 | user deals with. Objects range from the data which have been read from |
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| 84 | disk, to tools used for fitting functions to the data. The following |
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| 85 | main objects are used : |
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| 86 | |
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| 87 | \begin{itemize} |
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[544] | 88 | \item[\cmd{scantable}] The data container (actual spectra and header |
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| 89 | information) |
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[953] | 90 | \item[\cmd{selector}] Allows the user to select a subsection of the |
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| 91 | data, such as a specified or ramge of beam numbers, IFs, etc. |
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| 92 | \item[\cmd{plotter}] A tool used to plot the spectral line data |
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[544] | 93 | \item[\cmd{fitter}] A tool used to fit functions to the spectral data |
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| 94 | \item[\cmd{reader}] A tool which can be used to read data from disks |
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[971] | 95 | into a scantable object (advanced use). |
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[534] | 96 | \end{itemize} |
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| 97 | |
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[738] | 98 | There can be many objects of the same type. Each object is referred to |
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[534] | 99 | by a variable name made by the user. The name of this variable is not |
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[770] | 100 | important and can be set to whatever the user prefers (i.e. ``s'' and |
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[534] | 101 | ``ParkesHOH-20052002'' are equivalent). However, having a simple and |
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| 102 | consistent naming convention will help you a lot. |
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| 103 | |
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[544] | 104 | \subsection{Member Functions (functions)} |
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[534] | 105 | |
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[794] | 106 | \index{Functions!member}Following the object oriented approach, |
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| 107 | objects have associated ``member functions'' which can either be used |
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| 108 | to modify the data in some way or change global properties of the |
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| 109 | object. In this document member functions will be referred to simply |
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| 110 | as functions. From the command line, the user can execute these |
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| 111 | functions using the syntax: |
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[534] | 112 | \begin{verbatim} |
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| 113 | ASAP> out = object.function(arguments) |
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| 114 | \end{verbatim} |
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| 115 | |
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| 116 | Where \cmd{out} is the name of the returned variable (could be a new |
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[544] | 117 | scantable object, or a vector of data, or a status return), |
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| 118 | \cmd{object} is the object variable name (set by the user), |
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| 119 | \cmd{function} is the name of the member function and \cmd{arguments} |
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| 120 | is a list of arguments to the function. The arguments can be provided |
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| 121 | either though position or \cmd{name=}. A mix of the two can be used. |
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| 122 | E.g. |
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[534] | 123 | |
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| 124 | \begin{verbatim} |
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[953] | 125 | ASAP> av = scans.average_time(msk,weight='tsys') |
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| 126 | ASAP> av = scans.average_time(mask=msk,weight='tsys') |
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| 127 | ASAP> av = scans.average_time(msk,tsys) |
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[971] | 128 | ASAP> scans.poly_baseline(mask=msk, order=0, insitu=True) |
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| 129 | ASAP> scans.poly_baseline(msk,0,True) |
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| 130 | ASAP> scans.poly_baseline(mask, insitu=True) |
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[534] | 131 | \end{verbatim} |
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| 132 | |
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| 133 | \subsection{Global Functions} |
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| 134 | |
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[794] | 135 | \index{Functions!global}It does not make sense to implement some functions as member |
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[544] | 136 | functions, typically functions which operate on more than one |
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| 137 | scantable (e.g. time averaging of many scans). These functions will |
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| 138 | always be referred to as global functions. |
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[534] | 139 | |
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[538] | 140 | \subsection{Interactive environment} |
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[534] | 141 | |
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[794] | 142 | \index{ipython!environment}ipython has a number of useful interactive |
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| 143 | features and a few things to be aware of for the new user. |
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[534] | 144 | |
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| 145 | \subsubsection{String completion} |
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| 146 | |
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[794] | 147 | \index{ipython!string completion}Tab completion is enabled for all |
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| 148 | function names. If you type the first few letters of a function name, |
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| 149 | then type {\tt <TAB>} the function name will be auto completed if it |
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| 150 | is un-ambiguous, or a list of possibilities will be |
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| 151 | given. Auto-completion works for the user object names as well as |
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| 152 | function names. It does not work for filenames, nor for function |
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| 153 | arguments. |
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[534] | 154 | |
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| 155 | Example |
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| 156 | \begin{verbatim} |
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| 157 | ASAP> scans = scantable('MyData.rpf') |
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| 158 | ASAP> scans.se<TAB> |
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| 159 | ASAP> scans.set_in<TAB> |
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[971] | 160 | scans.set_cursor scans.set_freqframe scans.set_selection |
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| 161 | scans.set_doppler scans.set_instrument scans.set_unit |
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| 162 | scans.set_fluxunit scans.set_restfreqs |
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| 163 | |
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[794] | 164 | ASAP> scans.set_instrument() |
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[534] | 165 | \end{verbatim} |
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| 166 | |
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[544] | 167 | \subsubsection{Leading Spaces} |
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| 168 | |
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[794] | 169 | \index{ipython!leading space}Python uses leading space to mark blocks |
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| 170 | of code. This means that it you start a command line with a space, the |
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| 171 | command generally will fail with an syntax error. |
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[544] | 172 | |
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[770] | 173 | \subsubsection{Variable Names} |
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| 174 | |
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[794] | 175 | \index{ipython!variable names}During normal data processing, the user |
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| 176 | will have to create named variables to hold spectra etc. These must |
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| 177 | conform to the normal python syntax, specifically they cannot contain |
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| 178 | ``special'' characters such as \@ \$ etc and cannot start with a |
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| 179 | number (but can contain numbers). Variable (and function) names are |
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| 180 | case sensitive. |
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[770] | 181 | |
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[534] | 182 | \subsubsection{Unix Interaction} |
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| 183 | |
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[794] | 184 | \index{ipython!unix interaction}Basic unix shell commands (\cmd{pwd}, |
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| 185 | \cmd{ls}, \cmd{cd} etc) can be issued from within ASAP. This allows |
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| 186 | the user to do things like look at files in the current directory. The |
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| 187 | shell command ``\cmd{cd}'' works within ASAP, allowing the user to |
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| 188 | change between data directories. Unix programs cannot be run this way, |
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| 189 | but the shell escape ``$!$'' can be used to run arbitrary |
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| 190 | programs. E.g. |
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[534] | 191 | |
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| 192 | \begin{verbatim} |
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| 193 | ASAP> pwd |
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| 194 | ASAP> ls |
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[953] | 195 | ASAP> cd /my/data/directory |
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[534] | 196 | ASAP> ! mozilla& |
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| 197 | \end{verbatim} |
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| 198 | |
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| 199 | \subsection{Help} |
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| 200 | |
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[794] | 201 | \index{Help}ASAP has built in help for all functions. To get a list of |
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| 202 | functions type: |
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[534] | 203 | |
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[538] | 204 | \begin{verbatim} |
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[794] | 205 | ASAP> commands() |
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[538] | 206 | \end{verbatim} |
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| 207 | |
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| 208 | To get help on specific functions, the built in help needs to be given |
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| 209 | the object and function name. E.g. |
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| 210 | |
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| 211 | \begin{verbatim} |
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[971] | 212 | ASAP> help scantable.get_scan # or help(scantable.get_scan) |
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[538] | 213 | ASAP> help scantable.stats |
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| 214 | ASAP> help plotter.plot |
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| 215 | ASAP> help fitter.plot |
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| 216 | |
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| 217 | ASAP> scans = scantable('mydata.asap') |
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| 218 | ASAP> help scans.get_scan # Same as above |
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[544] | 219 | \end{verbatim} |
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[538] | 220 | |
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[544] | 221 | Global functions just need their name |
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[538] | 222 | |
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[544] | 223 | \begin{verbatim} |
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[738] | 224 | ASAP> help average_time |
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[538] | 225 | \end{verbatim} |
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| 226 | |
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| 227 | Note that if you just type \cmd{help} the internal ipython help is |
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| 228 | invoked, which is probably {\em not} what you want. Type \verb+^+-d |
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| 229 | (control-d) to escape from this. |
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| 230 | |
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[738] | 231 | \subsection{Customisation - .asaprc} |
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[534] | 232 | |
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[794] | 233 | \index{.asaprc}ASAP use an \cmd{.asaprc} file to control the user's |
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| 234 | preference of default values for various functions arguments. This |
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| 235 | includes the defaults for arguments such as \cmd{insitu}, scantable |
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| 236 | \cmd{freqframe} and the plotters \cmd{set\_mode} values. The help on |
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| 237 | individual functions says which arguments can be set default values |
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| 238 | from the \cmd{.asaprc} file. To get a sample contents for the |
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| 239 | \cmd{.asaprc} file use then command \cmd{list\_rcparameters}. |
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[534] | 240 | |
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[538] | 241 | Common values include: |
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| 242 | \begin{verbatim} |
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| 243 | # apply operations on the input scantable or return new one |
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| 244 | insitu : False |
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| 245 | |
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[738] | 246 | # default output format when saving scantable |
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[953] | 247 | scantable.save : ASAP |
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[538] | 248 | |
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| 249 | # default frequency frame to set when function |
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| 250 | # scantable.set_freqframe is called |
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[953] | 251 | scantable.freqframe : LSRK |
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[538] | 252 | |
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| 253 | # auto averaging on read |
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| 254 | scantable.autoaverage : True |
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| 255 | \end{verbatim} |
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| 256 | |
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[953] | 257 | For a complete list of \cmd{.asaprc} values, see the Appendix. |
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[770] | 258 | |
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[534] | 259 | \section{Scantables} |
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[794] | 260 | \index{Scantables} |
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[534] | 261 | \subsection {Description} |
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| 262 | |
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| 263 | \subsubsection {Basic Structure} |
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| 264 | |
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[794] | 265 | \index{Scantable!structure}ASAP data handling works on objects called |
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| 266 | scantables. A scantable holds your data, and also provides functions |
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| 267 | to operate upon it. |
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[534] | 268 | |
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| 269 | The building block of a scantable is an integration, which is a single |
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[971] | 270 | row of a scantable. Each row contains just one spectrum for each beam, IF and |
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[534] | 271 | polarisation. For example Parkes multibeam data would contain many |
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| 272 | beams, one IF and 2-4 polarisations, while the new Mopra 8-GHz |
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| 273 | filterbank will eventually produce one beam, many IFs, and 2-4 |
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[971] | 274 | polarisations. All of the combinations of Beams/IFs an Polarisations are |
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[1011] | 275 | contained in seperate rows. These rows are grouped in cycles (same time stamp). |
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[534] | 276 | |
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[1011] | 277 | A collection of cycles for one source is termed |
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| 278 | a scan (and each scan has a unique numeric identifier, the SCANNO). A |
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[534] | 279 | scantable is then a collection of one or more scans. If you have |
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[971] | 280 | scan-averaged your data in time, i.e. you have averegaed all cycles within |
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| 281 | a scan, then each scan would hold just one (averaged) integration. |
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[534] | 282 | |
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| 283 | Many of the functions which work on scantables can either return a |
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| 284 | new scantable with modified data or change the scantable insitu. Which |
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| 285 | method is used depends on the users preference. The default can be |
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| 286 | changed via the {\tt .asaprc} resource file. |
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| 287 | |
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[1011] | 288 | For example a Mopra scan with a 4s intergration time, two IFs and |
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| 289 | dual polarisations has two (2s) cycles. |
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| 290 | |
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| 291 | \begin{verbatim} |
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| 292 | SCANNO CYCLENO BEAMNO IFNO POLNO |
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| 293 | 0 0 0 0 0 |
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| 294 | 0 0 0 0 1 |
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| 295 | 0 0 0 1 0 |
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| 296 | 0 0 0 1 1 |
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| 297 | 0 1 0 0 0 |
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| 298 | 0 1 0 0 1 |
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| 299 | 0 1 0 1 0 |
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| 300 | 0 1 0 1 1 |
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| 301 | |
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| 302 | \end{verbatim} |
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| 303 | |
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| 304 | |
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[534] | 305 | \subsubsection {Contents} |
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| 306 | |
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[794] | 307 | \index{Scantable!contents}A scantable has header information and data |
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[953] | 308 | (a scantable is actually an AIPS++ Table and it is generally stored in |
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| 309 | memory when you are manipulating it with ASAP. You can save it to |
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| 310 | disk and then browse it with the AIPS++ Table browser if you know how |
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| 311 | to do that !). |
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[534] | 312 | |
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| 313 | The data are stored in columns (the length of a column is the number of |
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[1011] | 314 | rows/spectra of course). |
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[534] | 315 | |
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[953] | 316 | |
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[534] | 317 | Two important columns are those that describe the frequency setup. We mention |
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[538] | 318 | them explicitly here because you need to be able to understand the presentation |
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[534] | 319 | of the frequency information and possibly how to manipulate it. |
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| 320 | |
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[1011] | 321 | These columns are called FREQ\_ID and MOLECULE\_ID. They contain indices, for |
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[971] | 322 | each IF, pointing into tables with all of the frequency and rest-frequency |
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[1049] | 323 | information for that integration. |
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[534] | 324 | |
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| 325 | There are of course many other columns which contain the actual spectra, |
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[971] | 326 | the flags, the Tsys, the source names and so on. |
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[534] | 327 | |
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| 328 | There is also a function \cmd{summary} to list a summary of the scantable. |
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| 329 | You will find this very useful. |
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| 330 | |
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| 331 | Example: |
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| 332 | |
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| 333 | \begin{verbatim} |
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| 334 | ASAP> scans = scantable('MyData.rpf') |
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| 335 | ASAP> scans.summary() # Brief listing |
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[544] | 336 | |
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| 337 | # Equivalent to brief summary function call |
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[738] | 338 | ASAP> print scan |
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[534] | 339 | \end{verbatim} |
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| 340 | |
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[971] | 341 | The summary function gives you a scan-based summary, presenting the |
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[1049] | 342 | scantable as a cascading view of Beams and IFs. Note that the output |
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| 343 | of summary is redirected into your current pager specified by the |
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| 344 | \$PAGER environment variable. If you find the screen is reset to the |
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| 345 | original state when summary is finished (ie the output from summary |
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| 346 | disappears), you may need to set the \$LESS environment variable to |
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| 347 | include the \cmd{-X} option. |
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[534] | 348 | |
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[953] | 349 | \subsection{Data Selection} |
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| 350 | \label{sec:selection} |
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| 351 | |
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[966] | 352 | ASAP contains flexible data selection. Data can be selected based on |
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| 353 | IF, beam, polarisation, scan number as well as values such as |
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| 354 | Tsys. Advanced users can also make use of the AIPS++ TAQL language to |
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[971] | 355 | create selections based on almost any of the values recorded. |
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[953] | 356 | |
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[966] | 357 | Selection is based on a \cmd{selector} object. This object is created |
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| 358 | and various selection functions applied to it (\cmd{set\_ifs}, |
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| 359 | \cmd{set\_beams} etc). The selection object then must be applied to a |
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| 360 | scantable using the \cmd{set\_selection} function. A single selection |
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| 361 | object can be created and setup then applied to multiple scantables. |
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[534] | 362 | |
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[966] | 363 | Once a selection has been applied, all following functions will only |
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| 364 | ``see'' the selected spectra (including functions such as |
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| 365 | \cmd{summary}). The selection can then be reset and all spectra are |
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| 366 | visible. Note that if functions such as \cmd{copy} are run on a |
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| 367 | scantable with active selection, only the selected spectra are copied. |
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[534] | 368 | |
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[966] | 369 | The common selection functions are: |
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[534] | 370 | |
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[966] | 371 | \begin{itemize} |
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| 372 | |
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| 373 | \item[\cmd{set\_beams}] Select beams by index number |
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| 374 | \item[\cmd{set\_ifs}] Select ifs by index number |
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| 375 | \item[\cmd{set\_name}] Select by source name. Can contain ``*'' as a |
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| 376 | wildcard, e.g. ``Orion*\_R''. |
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| 377 | \item[\cmd{set\_ifs}] Select ifs by index number |
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| 378 | \item[\cmd{set\_polarisation}] Select but polarisation index or |
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| 379 | name. If polarisation names are given, the data will be on-the-fly |
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[971] | 380 | converted (for example from linears to Stokes). |
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[966] | 381 | \item[\cmd{set\_query}] Set query directly. For power users only! |
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| 382 | \item[\cmd{set\_tsys}] Select data based on Tsys. Also example of user |
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| 383 | definable query. |
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| 384 | \item[\cmd{reset}] Reset the selection to include all spectra. |
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| 385 | |
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| 386 | |
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| 387 | Note that all indices are zero based. |
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| 388 | |
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| 389 | Examples: |
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| 390 | |
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| 391 | \begin{verbatim} |
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| 392 | ASAP> selection = selector() # Create selection object |
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| 393 | ASAP> selection.set_ifs(0) # Just select the first IF |
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| 394 | ASAP> scans.set_selection(selection) # Apply the selection |
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| 395 | ASAP> print scans # Will just show the first IF |
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| 396 | |
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| 397 | ASAP> selection.set_ifs([0,1]) # Select the first two IFs |
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| 398 | ASAP> selection.set_beams([1,3,5]) # Also select three of the beams |
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| 399 | ASAP> scans.set_selection(selection) # Apply the selection |
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| 400 | |
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| 401 | ASAP> selection.set_name('G308*') # Select by source name |
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| 402 | |
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| 403 | ASAP> selection.reset() # Turn off selection |
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| 404 | ASAP> scans.set_selection(selection) # Apply the reset selection |
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| 405 | |
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[970] | 406 | \end{verbatim} |
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| 407 | |
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[966] | 408 | \end{itemize} |
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| 409 | |
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[534] | 410 | \subsection{State} |
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| 411 | |
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[794] | 412 | \index{Scantable!state}Each scantable contains "state"; these are |
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| 413 | properties applying to all of the data in the scantable. |
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[534] | 414 | |
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| 415 | Examples are the selection of beam, IF and polarisation, spectral unit |
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[770] | 416 | (e.g. km/s), frequency reference frame (e.g. BARY) and velocity Doppler |
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[534] | 417 | type (e.g. RADIO). |
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| 418 | |
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| 419 | \subsubsection{Units, Doppler and Frequency Reference Frame} |
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| 420 | |
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| 421 | The information describing the frequency setup for each integration |
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| 422 | is stored fundamentally in frequency in the reference frame |
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[738] | 423 | of observation (E.g. TOPO). |
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[534] | 424 | |
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[544] | 425 | When required, this is converted to the desired reference frame |
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| 426 | (e.g. LSRK), Doppler (e.g. OPTICAL) and unit (e.g. km/s) on-the-fly. |
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| 427 | This is important, for example, when you are displaying the data or |
---|
[971] | 428 | fitting to it. The reference frame is set on file read to the value |
---|
| 429 | set in the user \cmd{.asaprc} file. |
---|
[534] | 430 | |
---|
| 431 | For units, the user has the choice of frequency, velocity or channel. |
---|
| 432 | The \cmd{set\_unit} function is used to set the current unit for a |
---|
| 433 | scantable. All functions will (where relevant) work with the selected |
---|
| 434 | unit until this changes. This is mainly important for fitting (the fits |
---|
[738] | 435 | can be computed in any of these units), plotting and mask creation. |
---|
[534] | 436 | |
---|
[544] | 437 | The velocity definition can be changed with the \cmd{set\_doppler} |
---|
| 438 | function, and the frequency reference frame can be changed with the |
---|
[534] | 439 | \cmd{set\_freqframe} function. |
---|
| 440 | |
---|
| 441 | Example usage: |
---|
| 442 | |
---|
| 443 | \begin{verbatim} |
---|
| 444 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data |
---|
| 445 | ASAP> scans.set_freqframe('LSRK') # Use the LSR velocity frame |
---|
| 446 | ASAP> scans.set_unit('km/s') # Use velocity for plots etc from now on |
---|
| 447 | ASAP> scans.set_doppler('OPTICAL') # Use the optical velocity convention |
---|
| 448 | ASAP> scans.set_unit('MHz') # Use frequency in MHz from now on |
---|
| 449 | \end{verbatim} |
---|
| 450 | |
---|
| 451 | |
---|
| 452 | \subsubsection{Rest Frequency} |
---|
| 453 | |
---|
[794] | 454 | \index{Scantable!rest frequency}ASAP reads the line rest frequency |
---|
| 455 | from the RPFITS file when reading the data. The values stored in the |
---|
| 456 | RPFITS file are not always correct and so there is a function |
---|
[953] | 457 | \cmd{set\_restfreq} to set the rest frequencies for the currently |
---|
| 458 | selected data. |
---|
[534] | 459 | |
---|
| 460 | For each integration, there is a rest-frequency per IF (the rest |
---|
| 461 | frequencies are just stored as a list with an index into them). |
---|
| 462 | There are a few ways to set the rest frequencies with this function. |
---|
| 463 | |
---|
[953] | 464 | If you specify just one rest frequency, then it is set for all IF. |
---|
[534] | 465 | |
---|
| 466 | \begin{verbatim} |
---|
[953] | 467 | # Set all IFs |
---|
[738] | 468 | ASAP> scans.set_restfreqs(freqs=1.667359e9) |
---|
[534] | 469 | \end{verbatim} |
---|
| 470 | |
---|
[953] | 471 | If set a rest frequency for each IF, specify a list of frequencies (of |
---|
| 472 | length the number of IFs). Regardless of the source, the rest |
---|
| 473 | frequency will be set for each IF to the corresponding value in the |
---|
[970] | 474 | provided list. |
---|
[534] | 475 | |
---|
| 476 | \begin{verbatim} |
---|
[770] | 477 | # Set rest frequency for all IFs |
---|
| 478 | ASAP> scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,]) |
---|
[538] | 479 | |
---|
[534] | 480 | \end{verbatim} |
---|
| 481 | |
---|
[953] | 482 | {\em Currently this is not implemented} |
---|
| 483 | |
---|
[534] | 484 | In both of the above modes, you can also specify the rest frequencies via |
---|
| 485 | names in a known list rather than by their values. |
---|
| 486 | |
---|
| 487 | Examples: |
---|
| 488 | |
---|
| 489 | \begin{verbatim} |
---|
[953] | 490 | ASAP> scans.set_restfreqs(freqs=['OH1665','OH1667']) |
---|
[534] | 491 | \end{verbatim} |
---|
| 492 | |
---|
| 493 | |
---|
| 494 | \subsubsection{Masks} |
---|
| 495 | |
---|
[970] | 496 | \index{Masks}\index{Scantable!masks} |
---|
[534] | 497 | |
---|
[966] | 498 | Many tasks (fitting, baseline subtraction, statistics etc) should only |
---|
| 499 | be run on range of channels. Depending on the current ``unit'' setting |
---|
| 500 | this range is set directly as channels, velocity or frequency |
---|
| 501 | ranges. Internally these are converted into a simple boolean mask for |
---|
| 502 | each channel of the abscissa. This means that if the unit setting is |
---|
| 503 | later changed, previously created mask are still valid. (This is not |
---|
| 504 | true for functions which change the shape or shift the frequency |
---|
| 505 | axis). You create masks with the function \cmd{create\_mask} and this |
---|
| 506 | specified the channels to be included in the selection. When setting |
---|
| 507 | the mask in velocity, the conversion from velocity to channels is |
---|
| 508 | based on the current cursor setting, selected row and selected |
---|
| 509 | frequency reference frame. |
---|
[534] | 510 | |
---|
[966] | 511 | |
---|
| 512 | Note that for multi IF data with different number of channels per IF a |
---|
| 513 | single mask cannot be applied to different IFs. To use a mask on such |
---|
| 514 | data the selector should be applied to select all IFs with the same |
---|
| 515 | number of channels. |
---|
| 516 | |
---|
[534] | 517 | Example : |
---|
| 518 | \begin{verbatim} |
---|
| 519 | |
---|
| 520 | # Select channel range for baselining |
---|
| 521 | ASAP> scans.set_unit('channels') |
---|
[544] | 522 | ASAP> msk = scans.create_mask([100,400],[600,800]) |
---|
[738] | 523 | |
---|
[534] | 524 | # Select velocity range for fitting |
---|
| 525 | ASAP> scans.set_unit('km/s') |
---|
[544] | 526 | ASAP> msk = scans.create_mask([-30,-10]) |
---|
[534] | 527 | \end{verbatim} |
---|
| 528 | |
---|
[544] | 529 | Sometimes it is more convenient to specify the channels to be |
---|
| 530 | excluded, rather included. You can do this with the ``invert'' |
---|
| 531 | argument. |
---|
[534] | 532 | |
---|
| 533 | Example : |
---|
| 534 | \begin{verbatim} |
---|
| 535 | ASAP> scans.set_unit('channels') |
---|
[738] | 536 | ASAP> msk = scans.create_mask([0,100],[900-1023], invert=True) |
---|
[534] | 537 | \end{verbatim} |
---|
| 538 | |
---|
[544] | 539 | By default \cmd{create\_mask} uses the frequency setup of the first row |
---|
| 540 | to convert velocities into a channel mask. If the rows in the data |
---|
| 541 | cover different velocity ranges, the scantable row to use should be |
---|
| 542 | specified: |
---|
| 543 | |
---|
| 544 | \begin{verbatim} |
---|
| 545 | ASAP> scans.set_unit('km/s') |
---|
| 546 | ASAP> msk = q.create_mask([-30,-10], row=5) |
---|
| 547 | \end{verbatim} |
---|
| 548 | |
---|
[534] | 549 | Because the mask is stored in a simple python variable, the users is |
---|
| 550 | able to combine masks using simple arithmetic. To create a mask |
---|
| 551 | excluding the edge channels, a strong maser feature and a birdie in |
---|
| 552 | the middle of the band: |
---|
| 553 | |
---|
| 554 | \begin{verbatim} |
---|
| 555 | ASAP> scans.set_unit('channels') |
---|
| 556 | ASAP> msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True) |
---|
| 557 | ASAP> scans.set_unit('km/s') |
---|
| 558 | ASAP> msk2 = q.create_mask([-20,-10],invert=True) |
---|
| 559 | |
---|
| 560 | ASAP> mask = msk1 and msk2 |
---|
| 561 | \end{verbatim} |
---|
| 562 | |
---|
| 563 | |
---|
[953] | 564 | \subsection{Management} |
---|
| 565 | |
---|
| 566 | \index{Scantable!management}During processing it is possible to create |
---|
| 567 | a large number of scan tables. These all consume memory, so it is best |
---|
| 568 | to periodically remove unneeded scan tables. Use \cmd{list\_scans} to |
---|
| 569 | print a list of all scantables and \cmd{del} to remove unneeded ones. |
---|
| 570 | |
---|
| 571 | Example: |
---|
| 572 | |
---|
| 573 | \begin{verbatim} |
---|
| 574 | ASAP> list_scans() |
---|
| 575 | The user created scantables are: |
---|
| 576 | ['s', 'scans', 'av', 's2', 'ss'] |
---|
| 577 | |
---|
| 578 | ASAP> del s2 |
---|
| 579 | ASAP> del ss |
---|
| 580 | \end{verbatim} |
---|
| 581 | |
---|
[534] | 582 | \section{Data Input} |
---|
| 583 | |
---|
[971] | 584 | \index{Reading data}Data can be loaded in one of two ways; using the |
---|
| 585 | reader object or via the scantable constructor. The scantable method |
---|
| 586 | is simpler but the reader allows the user more control on what is read. |
---|
[534] | 587 | |
---|
| 588 | \subsection{Scantable constructor} |
---|
| 589 | |
---|
[794] | 590 | \index{Scantable constructor}\index{Scantable!constructor}This loads |
---|
| 591 | all of the data from filename into the scantable object scans and |
---|
| 592 | averages all the data within a scan (i.e. the resulting scantable |
---|
[534] | 593 | will have one row per scan). The recognised input file formats are |
---|
| 594 | RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ |
---|
[738] | 595 | MeasurementSet2 format. |
---|
[534] | 596 | |
---|
| 597 | Example usage: |
---|
| 598 | |
---|
| 599 | \begin{verbatim} |
---|
| 600 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf') |
---|
[544] | 601 | |
---|
| 602 | # Don't scan average the data |
---|
| 603 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf', average=False) |
---|
[534] | 604 | \end{verbatim} |
---|
| 605 | |
---|
| 606 | |
---|
| 607 | \subsection{Reader object} |
---|
| 608 | |
---|
[794] | 609 | \index{Reader object}\index{Scantable!reader object}For more control |
---|
| 610 | when reading data into ASAP, the reader object should be used. This |
---|
[953] | 611 | has the option of only reading in a range of integrations, only a |
---|
| 612 | specified beam or IF and does not perform any scan averaging of the |
---|
| 613 | data, allowing analysis of the individual integrations. Note that due |
---|
| 614 | to limitation of the RPFITS library, only one reader object can be |
---|
| 615 | open at one time reading RPFITS files. To read multiple RPFITS files, |
---|
| 616 | the old reader must be destroyed before the new file is opened. |
---|
| 617 | However, multiple readers can be created and attached to SDFITS files. |
---|
[534] | 618 | |
---|
| 619 | |
---|
| 620 | Example usage: |
---|
| 621 | |
---|
| 622 | \begin{verbatim} |
---|
| 623 | ASAP> r = reader('2003-03-16_082048_t0002.rpf') |
---|
[794] | 624 | ASAP> r.summary() |
---|
[534] | 625 | ASAP> scan = r.read() |
---|
| 626 | ASAP> del r |
---|
| 627 | \end{verbatim} |
---|
| 628 | |
---|
| 629 | \section{Basic Processing} |
---|
| 630 | |
---|
| 631 | In the following section, a simple data reduction to form a quotient |
---|
[544] | 632 | spectrum of a single source is followed. It has been assume that the |
---|
| 633 | \cmd{.asaprc} file has {\em not} been used to change the \cmd{insitu} |
---|
| 634 | default value from \cmd{True}. |
---|
[534] | 635 | |
---|
[738] | 636 | \subsection{Auto quotient} |
---|
[794] | 637 | \index{Auto quotient}Quotients can be computed ``automatically''. This |
---|
| 638 | requires the data to have matching source/reference pairs or one |
---|
| 639 | reference for multiple sources. Auto quotient assumes reference scans |
---|
| 640 | have a trailing ``\_R'' in the source name for data from Parkes and |
---|
| 641 | Mopra, and a trailing ``e'' or ``w'' for data fro, Tidbinbilla. |
---|
[534] | 642 | |
---|
[738] | 643 | \begin{verbatim} |
---|
| 644 | ASAP> q = s.auto_quotient() |
---|
| 645 | \end{verbatim} |
---|
| 646 | |
---|
[971] | 647 | By default the quotient spectra is calculated |
---|
| 648 | to preserve continuum emission. If you wish to remove the continuum |
---|
| 649 | contribution, use the \cmd{preserve} argument: |
---|
| 650 | |
---|
| 651 | \begin{verbatim} |
---|
| 652 | ASAP> q = s.auto_quotient(preserve=True) |
---|
| 653 | \end{verbatim} |
---|
| 654 | |
---|
[953] | 655 | %If this is not sufficient the following alternative method can be used. |
---|
| 656 | % |
---|
| 657 | %\subsection{Separate reference and source observations} |
---|
| 658 | % |
---|
| 659 | %\index{Quotient spectra}Most data from ATNF observatories |
---|
| 660 | %distinguishes on and off source data using the file name. This makes |
---|
| 661 | %it easy to create two scantables with the source and reference |
---|
| 662 | %data. As long as there was exactly one reference observation for each |
---|
| 663 | %on source observation for following method will work. |
---|
| 664 | % |
---|
| 665 | %For Mopra and Parkes data: |
---|
| 666 | %\begin{verbatim} |
---|
| 667 | % ASAP> r = scans.get_scan('*_R') |
---|
| 668 | % ASAP> s = scans.get_scan('*_S') |
---|
| 669 | %\end{verbatim} |
---|
| 670 | % |
---|
| 671 | %For Tidbinbilla data |
---|
| 672 | %\begin{verbatim} |
---|
| 673 | % ASAP> r = scans.get_scan('*_[ew]') |
---|
| 674 | % ASAP> s = scans.get_scan('*_[^ew]') |
---|
| 675 | %\end{verbatim} |
---|
| 676 | % |
---|
| 677 | %\subsection{Make the quotient spectra} |
---|
| 678 | % |
---|
| 679 | %Use the quotient function |
---|
| 680 | % |
---|
| 681 | %\begin{verbatim} |
---|
| 682 | % ASAP> q = s.quotient(r) |
---|
| 683 | %\end{verbatim} |
---|
| 684 | % |
---|
| 685 | %This uses the rows in scantable \cmd{r} as reference spectra for the |
---|
| 686 | %rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row |
---|
| 687 | %(which is applied to all rows in \cmd{s}) or both scantables must have |
---|
[971] | 688 | %the same number of rows. |
---|
[738] | 689 | |
---|
[534] | 690 | \subsection{Time average separate scans} |
---|
| 691 | |
---|
[794] | 692 | \index{Time average}If you have observed the source with multiple |
---|
| 693 | source/reference cycles you will want to scan-average the quotient |
---|
| 694 | spectra together. |
---|
[534] | 695 | |
---|
| 696 | \begin{verbatim} |
---|
[953] | 697 | ASAP> av = q.average_time() |
---|
[534] | 698 | \end{verbatim} |
---|
| 699 | |
---|
[544] | 700 | If for some you want to average multiple sets of scantables together |
---|
| 701 | you can: |
---|
[534] | 702 | |
---|
| 703 | \begin{verbatim} |
---|
| 704 | ASAP> av = average_time(q1, q2, q3) |
---|
| 705 | \end{verbatim} |
---|
| 706 | |
---|
[544] | 707 | The default is to use integration time weighting. The alternative is |
---|
[770] | 708 | to use none, variance, Tsys weighting or Tsys \& integration time. |
---|
[534] | 709 | |
---|
[544] | 710 | \begin{verbatim} |
---|
| 711 | ASAP> av = average_time(q, weight='tintsys') |
---|
| 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} |
---|
[544] | 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 |
---|
| 723 | \cmd{freq\_align} explicitally) you should align the data in frequency |
---|
| 724 | before averaging. |
---|
[794] | 725 | |
---|
[953] | 726 | \begin{verbatim} |
---|
| 727 | ASAP> av = scans.average_time(align=True) |
---|
| 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} |
---|
| 740 | ASAP> msk = scans.create_mask([100,400],[600,900]) |
---|
[971] | 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} |
---|
| 759 | ASAP> scans.auto_poly_baseline(order=2,threshold=5) |
---|
| 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 |
---|
| 774 | ASAP> scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3) |
---|
| 775 | |
---|
| 776 | # Only fit a given region around the line |
---|
| 777 | ASAP> scans.set_unit('km/s') |
---|
[971] | 778 | ASAP> msk = scans.create_mask([-60,-20]) |
---|
[534] | 779 | ASAP> scans.auto_poly_baseline(mask=msk,order=3,threshold=3) |
---|
| 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} |
---|
| 789 | ASAP> scans.average_pol() |
---|
| 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} |
---|
[971] | 811 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf', unit='Jy') |
---|
[534] | 812 | # Or in two steps |
---|
[971] | 813 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf') |
---|
[534] | 814 | ASAP> scans.set_fluxunit('Jy) |
---|
| 815 | \end{verbatim} |
---|
| 816 | |
---|
| 817 | \subsubsection{Tsys scaling} |
---|
| 818 | |
---|
[794] | 819 | \index{Tsys scaling}Sometime the nominal Tsys measurement at the |
---|
| 820 | telescope is wrong due to an incorrect noise diode calibration. This |
---|
| 821 | can easily be corrected for with the scale function. By default, |
---|
| 822 | \cmd{scale} only scans the spectra and not the corresponding Tsys. |
---|
[534] | 823 | |
---|
| 824 | \begin{verbatim} |
---|
[738] | 825 | ASAP> scans.scale(1.05, tsys=True) |
---|
[534] | 826 | \end{verbatim} |
---|
| 827 | |
---|
| 828 | \subsubsection{Unit Conversion} |
---|
| 829 | |
---|
[794] | 830 | \index{Unit conversion}To convert measurements in Kelvin to Jy (and |
---|
| 831 | vice versa) the global function \cmd{convert\_flux} is needed. This |
---|
| 832 | converts and scales the data from K to Jy or vice-versa depending on |
---|
| 833 | what the current brightness unit is set to. The function knows the |
---|
| 834 | basic parameters for some frequencies and telescopes, but the user may |
---|
| 835 | need to supply the aperture efficiency, telescope diameter or the Jy/K |
---|
| 836 | factor. |
---|
[534] | 837 | |
---|
| 838 | \begin{verbatim} |
---|
[794] | 839 | ASAP> scans.convert_flux() # If efficency known |
---|
[534] | 840 | ASAP> scans.convert_flux(eta=0.48) # If telescope diameter known |
---|
| 841 | ASAP> scans.convert_flux(eta=0.48,d=35) # Unknown telescope |
---|
| 842 | ASAP> scans.convert_flux(jypk=15) # Alternative |
---|
| 843 | \end{verbatim} |
---|
| 844 | |
---|
| 845 | \subsubsection{Gain-Elevation and Opacity Corrections} |
---|
[794] | 846 | \label{sec:gainel} |
---|
[534] | 847 | |
---|
[794] | 848 | \index{Gain-elevation}As higher frequencies (particularly $>$20~GHz) |
---|
| 849 | it is important to make corrections for atmospheric opacity and |
---|
| 850 | gain-elevation effects. |
---|
[534] | 851 | |
---|
[794] | 852 | Note that currently the elevation is not written correctly into |
---|
[770] | 853 | Tidbinbilla rpfits files. This means that gain-elevation and opacity |
---|
[794] | 854 | corrections will not work unless these get recalculated. |
---|
[770] | 855 | |
---|
[794] | 856 | \begin{verbatim} |
---|
| 857 | ASAP> scans.recalc_azel() # recalculate az/el based on pointing |
---|
| 858 | \end{verbatim} |
---|
| 859 | |
---|
[544] | 860 | Gain-elevation curves for some telescopes and frequencies are known to |
---|
[794] | 861 | ASAP (currently only for Tidbinbilla at 20~GHz). In these cases |
---|
| 862 | making gain-corrections is simple. If the gain curve for your data is |
---|
| 863 | not known, the user can supply either a gain polynomial or text file |
---|
[534] | 864 | tabulating gain factors at a range of elevations (see \cmd{help |
---|
[544] | 865 | scantable.gain\_el}). |
---|
[534] | 866 | |
---|
| 867 | Examples: |
---|
| 868 | |
---|
| 869 | \begin{verbatim} |
---|
| 870 | ASAP> scans.gain_el() # If gain table known |
---|
| 871 | ASAP> scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) |
---|
| 872 | \end{verbatim} |
---|
| 873 | |
---|
[794] | 874 | \index{Opacity}Opacity corrections can be made with the global |
---|
| 875 | function \cmd{opacity}. This should work on all telescopes as long as |
---|
| 876 | a measurement of the opacity factor was made during the observation. |
---|
[534] | 877 | |
---|
| 878 | \begin{verbatim} |
---|
| 879 | ASAP> scans.opacity(0.083) |
---|
| 880 | \end{verbatim} |
---|
| 881 | |
---|
| 882 | Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, |
---|
| 883 | which takes opacity effects into account (to first order). ASAP |
---|
[544] | 884 | opacity corrections should not be used for Mopra 3-mm data. |
---|
[534] | 885 | |
---|
| 886 | \subsection{Frequency Frame Alignment} |
---|
[794] | 887 | \label{sec:freqalign} |
---|
[534] | 888 | |
---|
[794] | 889 | \index{Frequency alignment}\index{Velicity alignment}When time |
---|
| 890 | averaging a series of scans together, it is possible that the velocity |
---|
| 891 | scales are not exactly aligned. This may be for many reasons such as |
---|
| 892 | not Doppler tracking the observations, errors in the Doppler tracking |
---|
| 893 | etc. This mostly affects very long integrations or integrations |
---|
| 894 | averaged together from different days. Before averaging such data |
---|
| 895 | together, they should be frequency aligned using \cmd{freq\_align}. |
---|
[534] | 896 | |
---|
| 897 | E.g.: |
---|
| 898 | |
---|
| 899 | \begin{verbatim} |
---|
| 900 | ASAP> scans.freq_align() |
---|
| 901 | ASAP> av = average_time(scans) |
---|
| 902 | \end{verbatim} |
---|
| 903 | |
---|
[953] | 904 | {\em A Global freq\_align command will be made eventually} |
---|
[534] | 905 | |
---|
| 906 | To average together data taken on different days, which are in |
---|
| 907 | different scantables, each scantable must aligned to a common |
---|
| 908 | reference time then the scantables averaged. The simplest way of |
---|
| 909 | doing this is to allow ASAP to choose the reference time for the first |
---|
[738] | 910 | scantable then using this time for the subsequent scantables. |
---|
[534] | 911 | |
---|
| 912 | \begin{verbatim} |
---|
| 913 | ASAP> scans1.freq_align() # Copy the refeference Epoch from the output |
---|
| 914 | ASAP> scans2.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 915 | ASAP> scans3.freq_align(reftime='2004/11/23/18:43:35') |
---|
| 916 | ASAP> av = average_time(scans1, scans2, scans3) |
---|
| 917 | \end{verbatim} |
---|
| 918 | |
---|
| 919 | \section{Scantable manipulation} |
---|
| 920 | |
---|
[794] | 921 | \index{Scantable!manipulation}While it is very useful to have many |
---|
| 922 | independent sources within one scantable, it is often inconvenient for |
---|
| 923 | data processing. The \cmd{get\_scan} function can be used to create a |
---|
| 924 | new scantable with a selection of scans from a scantable. The |
---|
| 925 | selection can either be on the source name, with simple wildcard |
---|
[953] | 926 | matching or set of scan ids. Internally this uses the selector object, |
---|
| 927 | so for more complicated selection the selector should be used directly |
---|
| 928 | instead. |
---|
[534] | 929 | |
---|
| 930 | For example: |
---|
| 931 | |
---|
| 932 | \begin{verbatim} |
---|
| 933 | ASAP> ss = scans.get_scan(10) # Get the 11th scan (zero based) |
---|
| 934 | ASAP> ss = scans.get_scan(range(10)) # Get the first 10 scans |
---|
[538] | 935 | ASAP> ss = scans.get_scan(range(10,20)) # Get the next 10 scans |
---|
[534] | 936 | ASAP> ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans |
---|
| 937 | |
---|
| 938 | ASAP> ss = scans.get_scan('345p407') # Get a specific source |
---|
| 939 | ASAP> ss = scans.get_scan('345*') # Get a few sources |
---|
| 940 | |
---|
| 941 | ASAP> r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra) |
---|
| 942 | ASAP> s = scans.get_scan('*_S') # Get all program sources (Parkes/Mopra) |
---|
[953] | 943 | ASAP> r = scans.get_scan('*[ew]') # Get all reference sources (Tid) |
---|
| 944 | ASAP> s = scans.get_scan('*[^ew]') # Get all program sources (Tid) |
---|
[534] | 945 | |
---|
| 946 | \end{verbatim} |
---|
| 947 | |
---|
| 948 | To copy a scantable the following does not work: |
---|
| 949 | |
---|
| 950 | \begin{verbatim} |
---|
| 951 | ASAP> ss = scans |
---|
| 952 | \end{verbatim} |
---|
| 953 | |
---|
[544] | 954 | as this just creates a reference to the original scantable. Any |
---|
| 955 | changes made to \cmd{ss} are also seen in \cmd{scans}. To duplicate a |
---|
[534] | 956 | scantable, use the copy function. |
---|
| 957 | |
---|
| 958 | \begin{verbatim} |
---|
[794] | 959 | ASAP> ss = scans.copy() |
---|
[534] | 960 | \end{verbatim} |
---|
| 961 | |
---|
| 962 | \section{Data Output} |
---|
| 963 | |
---|
[794] | 964 | \index{Scantable!save}\index{Saving data}ASAP can save scantables in a |
---|
| 965 | variety of formats, suitable for reading into other packages. The |
---|
| 966 | formats are: |
---|
[534] | 967 | |
---|
| 968 | \begin{itemize} |
---|
| 969 | \item[ASAP] This is the internal format used for ASAP. It is the only |
---|
[544] | 970 | format that allows the user to restore the data, fits etc. without |
---|
| 971 | loosing any information. As mentioned before, the ASAP scantable is |
---|
| 972 | an AIPS++ Table (a memory-based table). This function just converts |
---|
| 973 | it to a disk-based Table. You can the access that Table with the |
---|
| 974 | AIPS++ Table browser or any other AIPS++ tool. |
---|
[534] | 975 | |
---|
[544] | 976 | \item[SDFITS] The Single Dish FITS format. This format was designed to |
---|
| 977 | for interchange between packages, but few packages actually can read |
---|
| 978 | it. |
---|
[534] | 979 | |
---|
| 980 | \item[FITS] This uses simple ``image'' fits to save the data, each row |
---|
[544] | 981 | being written to a separate fits file. This format is suitable for |
---|
| 982 | importing the data into CLASS. |
---|
[534] | 983 | |
---|
| 984 | \item[ASCII] A simple text based format suitable for the user to |
---|
| 985 | processing using Perl or, Python, gnuplot etc. |
---|
| 986 | |
---|
| 987 | \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. |
---|
| 988 | You can also access this with the Table browser and other AIPS++ |
---|
| 989 | tools. |
---|
| 990 | |
---|
| 991 | \end{itemize} |
---|
| 992 | |
---|
[738] | 993 | The default output format can be set in the users {\tt .asaprc} file. |
---|
[534] | 994 | Typical usages are: |
---|
| 995 | |
---|
| 996 | \begin{verbatim} |
---|
| 997 | ASAP> scans.save('myscans') # Save in default format |
---|
| 998 | ASAP> scans.save('myscans', 'FITS') # Save as FITS for exporting into CLASS |
---|
| 999 | ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file |
---|
| 1000 | \end{verbatim} |
---|
| 1001 | |
---|
| 1002 | |
---|
| 1003 | \section{Plotter} |
---|
| 1004 | |
---|
[794] | 1005 | \index{Plotter}Scantable spectra can be plotted at any time. An asapplotter object is |
---|
[534] | 1006 | used for plotting, meaning multiple plot windows can be active at the |
---|
| 1007 | same time. On start up a default asapplotter object is created called |
---|
| 1008 | ``plotter''. This would normally be used for standard plotting. |
---|
| 1009 | |
---|
[538] | 1010 | The plotter, optionally, will run in a multipanel mode and contain |
---|
[534] | 1011 | multiple plots per panel. The user must tell the plotter how they want |
---|
| 1012 | the data distributed. This is done using the set\_mode function. The |
---|
| 1013 | default can be set in the users {\tt .asaprc} file. The units (and frame |
---|
[538] | 1014 | etc) of the abscissa will be whatever has previously been set by |
---|
| 1015 | \cmd{set\_unit}, \cmd{set\_freqframe} etc. |
---|
[534] | 1016 | |
---|
| 1017 | Typical plotter usage would be: |
---|
| 1018 | |
---|
| 1019 | \begin{verbatim} |
---|
| 1020 | ASAP> scans.set_unit('km/s') |
---|
| 1021 | ASAP> plotter.set_mode(stacking='p',panelling='t') |
---|
| 1022 | ASAP> plotter.plot(scans) |
---|
| 1023 | \end{verbatim} |
---|
| 1024 | |
---|
| 1025 | This will plot multiple polarisation within each plot panel and each |
---|
[544] | 1026 | scan row in a separate panel. |
---|
[534] | 1027 | |
---|
[538] | 1028 | Other possibilities include: |
---|
[534] | 1029 | |
---|
| 1030 | \begin{verbatim} |
---|
| 1031 | # Plot multiple IFs per panel |
---|
| 1032 | ASAP> plotter.set_mode(stacking='i',panelling='t') |
---|
[538] | 1033 | |
---|
| 1034 | # Plot multiple beams per panel |
---|
| 1035 | ASAP> plotter.set_mode(stacking='b',panelling='t') |
---|
| 1036 | |
---|
| 1037 | # Plot one IF per panel, time stacked |
---|
| 1038 | ASAP> plotter.set_mode('t', 'i') |
---|
| 1039 | |
---|
| 1040 | # Plot each scan in a seperate panel |
---|
| 1041 | ASAP> plotter.set_mode('t', 's') |
---|
| 1042 | |
---|
[534] | 1043 | \end{verbatim} |
---|
| 1044 | |
---|
[538] | 1045 | \subsection{Plot Selection} |
---|
| 1046 | \label{sec:plotter_cursor} |
---|
| 1047 | |
---|
[794] | 1048 | \index{Plotter!selection}The plotter can plot up to 25 panels and |
---|
| 1049 | stacked spectra per panel. If you have data larger than this (or for |
---|
| 1050 | your own sanity) you need to select a subset of this data. This is |
---|
[953] | 1051 | particularly true for multibeam or multi IF data. The selector object |
---|
[971] | 1052 | should be used for this purpose. Selection can either be applied to |
---|
[953] | 1053 | the scantable or directly to the plotter, the end result is the same. |
---|
[971] | 1054 | You don't have to reset the scantable slection though, if you set |
---|
| 1055 | the selection on the plotter. |
---|
[538] | 1056 | |
---|
| 1057 | Examples: |
---|
| 1058 | |
---|
| 1059 | \begin{verbatim} |
---|
[953] | 1060 | ASAP> selection = selector() |
---|
[538] | 1061 | # Select second IF |
---|
[966] | 1062 | ASAP> selection.set_ifs(1) |
---|
[953] | 1063 | ASAP> plotter.set_selection(selection) |
---|
[538] | 1064 | |
---|
| 1065 | # Select first 4 beams |
---|
[966] | 1066 | ASAP> selection.set_beams([0,1,2,3]) |
---|
[953] | 1067 | ASAP> plotter.set_selection(selection) |
---|
[538] | 1068 | |
---|
[953] | 1069 | # Select a few scans |
---|
| 1070 | ASAP> selection.set_scans([2,4,6,10]) |
---|
| 1071 | ASAP> plotter.set_selection(selection) |
---|
[538] | 1072 | |
---|
| 1073 | # Multiple selection |
---|
[966] | 1074 | ASAP> selection.set_ifs(1) |
---|
[953] | 1075 | ASAP> selection.set_scans([2,4,6,10]) |
---|
| 1076 | ASAP> plotter.set_selection(selection) |
---|
| 1077 | |
---|
[538] | 1078 | \end{verbatim} |
---|
| 1079 | |
---|
[544] | 1080 | \subsection{Plot Control} |
---|
| 1081 | |
---|
[794] | 1082 | \index{Plotter!control}The plotter window has a row of buttons on the |
---|
| 1083 | lower left. These can be used to control the plotter (mostly for |
---|
| 1084 | zooming the individual plots). From left to right: |
---|
[534] | 1085 | |
---|
| 1086 | \begin{itemize} |
---|
| 1087 | |
---|
| 1088 | \item[Home] This will unzoom the plots to the original zoom factor |
---|
| 1089 | |
---|
| 1090 | \item[Plot history] (left and right arrow). The plotter keeps a |
---|
| 1091 | history of zoom settings. The left arrow sets the plot zoom to the |
---|
| 1092 | previous value. The right arrow returns back again. This allows you, |
---|
| 1093 | for example, to zoom in on one feature then return the plot to how it |
---|
| 1094 | was previously. |
---|
| 1095 | |
---|
| 1096 | \item[Pan] (The Cross) This sets the cursor to pan, or scroll mode |
---|
[953] | 1097 | allowing you to shift the plot within the window. Useful when |
---|
| 1098 | zoomed in on a feature. |
---|
[534] | 1099 | |
---|
| 1100 | \item[Zoom] (the letter with the magnifying glass) lets you draw a |
---|
[953] | 1101 | rectangle around a region of interest then zooms in on that |
---|
| 1102 | region. Use the plot history to unzoom again. |
---|
[534] | 1103 | |
---|
[953] | 1104 | \item[Adjust] (rectangle with 4 arrows) adjust subplot paramaters |
---|
| 1105 | (space at edge of plots) |
---|
| 1106 | |
---|
[534] | 1107 | \item[Save] (floppy disk). Save the plot as a postscript or .png file |
---|
| 1108 | |
---|
[794] | 1109 | You can also type ``g'' in the plot window to toggle on and off grid |
---|
| 1110 | lines. Typing 'l' turns on and off logarithmic Y-axis. |
---|
| 1111 | |
---|
[534] | 1112 | \end{itemize} |
---|
| 1113 | |
---|
| 1114 | \subsection{Other control} |
---|
| 1115 | |
---|
| 1116 | The plotter has a number of functions to describe the layout of the |
---|
| 1117 | plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. |
---|
| 1118 | |
---|
| 1119 | To set the exact velocity or channel range to be plotted use the |
---|
| 1120 | \cmd{set\_range} function. To reset to the default value, call |
---|
| 1121 | \cmd{set\_range} with no arguments. E.g. |
---|
| 1122 | |
---|
| 1123 | \begin{verbatim} |
---|
| 1124 | ASAP> scans.set_unit('km/s') |
---|
| 1125 | ASAP> plotter.plot(scans) |
---|
| 1126 | ASAP> plotter.set_range(-150,-50) |
---|
[544] | 1127 | ASAP> plotter.set_range() # To reset |
---|
[534] | 1128 | \end{verbatim} |
---|
| 1129 | |
---|
[544] | 1130 | Both the range of the ``x'' and ``y'' axis can be set at once, if desired: |
---|
| 1131 | |
---|
| 1132 | \begin{verbatim} |
---|
| 1133 | ASAP> plotter.set_range(-10,30,-1,6.6) |
---|
| 1134 | \end{verbatim} |
---|
| 1135 | |
---|
[738] | 1136 | To save a hardcopy of the current plot, use the save function, e.g. |
---|
[534] | 1137 | |
---|
| 1138 | \begin{verbatim} |
---|
| 1139 | ASAP> plotter.save('myplot.ps') |
---|
[971] | 1140 | ASAP> plotter.save('myplot.png', dpi=80) |
---|
[534] | 1141 | \end{verbatim} |
---|
| 1142 | |
---|
| 1143 | \section{Fitting} |
---|
| 1144 | |
---|
[794] | 1145 | \index{Fitting}Currently multicomponent Gaussian function is |
---|
| 1146 | available. This is done by creating a fitting object, setting up the |
---|
| 1147 | fit and actually fitting the data. Fitting can either be done on a |
---|
[966] | 1148 | single scantable selection or on an entire scantable using the |
---|
| 1149 | \cmd{auto\_fit} function. If single value fitting is used, and the |
---|
| 1150 | current selection includes multiple spectra (beams, IFs, scans etc) |
---|
[971] | 1151 | then the first spectrum in the scantable will be used for fitting. |
---|
[534] | 1152 | |
---|
| 1153 | \begin{verbatim} |
---|
| 1154 | ASAP> f = fitter() |
---|
| 1155 | ASAP> f.set_function(gauss=2) # Fit two Gaussians |
---|
| 1156 | ASAP> f.set_scan(scans) |
---|
[966] | 1157 | ASAP> selection = selector() |
---|
[971] | 1158 | ASAP> selection.set_polarisations(1) # Fit the second polarisation |
---|
[966] | 1159 | ASAP> scans.set_selection(selection) |
---|
[534] | 1160 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
---|
| 1161 | ASAP> f.fit(1) # Run the fit on the second row in the table |
---|
| 1162 | ASAP> f.plot() # Show fit in a plot window |
---|
| 1163 | ASAP> f.get_parameters() # Return the fit paramaters |
---|
| 1164 | \end{verbatim} |
---|
| 1165 | |
---|
| 1166 | This auto-guesses the initial values of the fit and works well for data |
---|
| 1167 | without extra confusing features. Note that the fit is performed in |
---|
| 1168 | whatever unit the abscissa is set to. |
---|
| 1169 | |
---|
| 1170 | If you want to confine the fitting to a smaller range (e.g. to avoid |
---|
| 1171 | band edge effects or RFI you must set a mask. |
---|
| 1172 | |
---|
| 1173 | \begin{verbatim} |
---|
| 1174 | ASAP> f = fitter() |
---|
| 1175 | ASAP> f.set_function(gauss=2) |
---|
| 1176 | ASAP> scans.set_unit('km/s') # Set the mask in channel units |
---|
| 1177 | ASAP> msk = s.create_mask([1800,2200]) |
---|
| 1178 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
---|
| 1179 | ASAP> f.set_scan(s,msk) |
---|
| 1180 | ASAP> f.fit() |
---|
| 1181 | ASAP> f.plot() |
---|
| 1182 | ASAP> f.get_parameters() |
---|
| 1183 | \end{verbatim} |
---|
| 1184 | |
---|
[544] | 1185 | If you wish, the initial parameter guesses can be specified and |
---|
| 1186 | specific parameters can be fixed: |
---|
[534] | 1187 | |
---|
| 1188 | \begin{verbatim} |
---|
| 1189 | ASAP> f = fitter() |
---|
| 1190 | ASAP> f.set_function(gauss=2) |
---|
| 1191 | ASAP> f.set_scan(s,msk) |
---|
| 1192 | ASAP> f.fit() # Fit using auto-estimates |
---|
[738] | 1193 | # Set Peak, centre and fwhm for the second gaussian. |
---|
[534] | 1194 | # Force the centre to be fixed |
---|
| 1195 | ASAP> f.set_gauss_parameters(0.4,450,150,0,1,0,component=1) |
---|
| 1196 | ASAP> f.fit() # Re-run the fit |
---|
| 1197 | \end{verbatim} |
---|
| 1198 | |
---|
| 1199 | The fitter \cmd{plot} function has a number of options to either view |
---|
| 1200 | the fit residuals or the individual components (by default it plots |
---|
| 1201 | the sum of the model components). |
---|
| 1202 | |
---|
| 1203 | Examples: |
---|
| 1204 | |
---|
| 1205 | \begin{verbatim} |
---|
| 1206 | # Plot the residual |
---|
[738] | 1207 | ASAP> f.plot(residual=True) |
---|
[534] | 1208 | |
---|
| 1209 | # Plot the first 2 componentsa |
---|
[738] | 1210 | ASAP> f.plot(components=[0,1]) |
---|
[534] | 1211 | |
---|
| 1212 | # Plot the first and third component plus the model sum |
---|
| 1213 | ASAP> f.plot(components=[-1,0,2]) # -1 means the compoment sum |
---|
| 1214 | \end{verbatim} |
---|
| 1215 | |
---|
[544] | 1216 | \subsection{Fit saving} |
---|
| 1217 | |
---|
[794] | 1218 | \index{Fitter!Fit saving}One you are happy with your fit, it is |
---|
| 1219 | possible to store it as part of the scantable. |
---|
[544] | 1220 | |
---|
| 1221 | \begin{verbatim} |
---|
| 1222 | ASAP> f.storefit() |
---|
| 1223 | \end{verbatim} |
---|
| 1224 | |
---|
| 1225 | This will be saved to disk with the data, if the ``ASAP'' file format |
---|
| 1226 | is selected. Multiple fits to the same data can be stored in the |
---|
[738] | 1227 | scantable. |
---|
[544] | 1228 | |
---|
| 1229 | The scantable function \cmd{get\_fit} can be used to retrieve the |
---|
| 1230 | stored fits. Currently the fit parameters are just printed to the |
---|
| 1231 | screen. |
---|
| 1232 | |
---|
| 1233 | \begin{verbatim} |
---|
| 1234 | ASAP> scans.get_fit(4) # Print fits for row 4 |
---|
| 1235 | \end{verbatim} |
---|
| 1236 | |
---|
[534] | 1237 | \section{Polarisation} |
---|
| 1238 | |
---|
[794] | 1239 | \index{Polarisation}Currently ASAP only supports polarmetric analysis |
---|
| 1240 | on linearly polarised feeds and the cross polarisation products |
---|
[971] | 1241 | measured. Other cases will be added on an as needed basis. |
---|
[534] | 1242 | |
---|
[538] | 1243 | Conversions of linears to Stokes or Circular polarisations are done |
---|
[966] | 1244 | ``on-the-fly''. Leakage cannot be corrected for nor are there routines |
---|
| 1245 | to calibrate position angle offsets. |
---|
[534] | 1246 | |
---|
[538] | 1247 | \subsection{Simple Calibration} |
---|
| 1248 | |
---|
[794] | 1249 | \index{Polarisation!calibration}It is possible that there is a phase |
---|
| 1250 | offset between polarisation which will effect the phase of the cross |
---|
| 1251 | polarisation correlation, and so give rise to spurious |
---|
| 1252 | polarisation. \cmd{rotate\_xyphase} can be used to correct for this |
---|
| 1253 | error. At this point, the user must know how to determine the size of |
---|
| 1254 | the phase offset themselves. |
---|
[538] | 1255 | |
---|
| 1256 | \begin{verbatim} |
---|
[546] | 1257 | ASAP> scans.rotate_xyphase(10.5) # Degrees |
---|
[538] | 1258 | \end{verbatim} |
---|
| 1259 | |
---|
| 1260 | Note that if this function is run twice, the sum of the two values is |
---|
[546] | 1261 | applied because it is done in-situ. |
---|
[538] | 1262 | |
---|
[546] | 1263 | A correction for the receiver parallactic angle may need to be made, |
---|
[953] | 1264 | generally because of how it is mounted. Use \cmd{rotate\_linpolphase} |
---|
| 1265 | to correct the position angle. Running this function twice results in |
---|
| 1266 | the sum of the corrections being applied because it is applied |
---|
| 1267 | in-situ. |
---|
[538] | 1268 | |
---|
| 1269 | \begin{verbatim} |
---|
[953] | 1270 | ASAP> scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting |
---|
| 1271 | \end{verbatim} |
---|
[538] | 1272 | |
---|
[953] | 1273 | If the sign of the complex correlation is wrong (this can happen |
---|
| 1274 | depending on the correlator configuration), use \cmd{invert\_phase} to |
---|
| 1275 | change take the complex conjugate of the complex correlation |
---|
| 1276 | term. This is always performed in-situ. |
---|
| 1277 | |
---|
| 1278 | \begin{verbatim} |
---|
| 1279 | ASAP> scans.invert_phase() |
---|
[538] | 1280 | \end{verbatim} |
---|
| 1281 | |
---|
[953] | 1282 | Depending on how the correlator is configured, ``BA'' may be |
---|
| 1283 | correlated insead of ``AB''. Use \cmd{swap\_linears} to correct for |
---|
| 1284 | this problem: |
---|
| 1285 | |
---|
| 1286 | \begin{verbatim} |
---|
[970] | 1287 | ASAP> scans.swap_linears() |
---|
[953] | 1288 | \end{verbatim} |
---|
| 1289 | |
---|
[1011] | 1290 | \subsection{Conversion} |
---|
| 1291 | \label{sec:polconv} |
---|
| 1292 | Data can be converted between linear and circular polarisations and stokes. |
---|
| 1293 | |
---|
| 1294 | \begin{verbatim} |
---|
| 1295 | ASAP> stokescans = linearscans.convert_pol("stokes") |
---|
| 1296 | \end{verbatim} |
---|
| 1297 | |
---|
| 1298 | |
---|
[538] | 1299 | \subsection{Plotting} |
---|
| 1300 | \label{sec:polplot} |
---|
| 1301 | |
---|
[953] | 1302 | \index{Polarisation!plotting}To plot Stokes values, a selector object |
---|
| 1303 | must be created and the set\_polarisation function used to select the |
---|
| 1304 | desired polarisation products. |
---|
| 1305 | |
---|
| 1306 | The values which can be plotted include a selection of [I,Q,U,V], [I, |
---|
| 1307 | Plinear, Pangle, V], [RR, LL] or [XX, YY, Real(XY), |
---|
[794] | 1308 | Imaginary(XY)]. (Plinear and Pangle are the percentage and position |
---|
[1011] | 1309 | angle of linear polarisation). |
---|
[538] | 1310 | |
---|
| 1311 | Example: |
---|
| 1312 | |
---|
| 1313 | \begin{verbatim} |
---|
[953] | 1314 | ASAP> selection = selector() |
---|
[970] | 1315 | |
---|
[971] | 1316 | ASAP> selection.set_polarisations(``I Q U V'') |
---|
[953] | 1317 | ASAP plotter.set_selection(selection); # Select I, Q, U \& V |
---|
| 1318 | |
---|
[971] | 1319 | ASAP> selection.set_polarisations(``I Q'') |
---|
[953] | 1320 | ASAP plotter.set_selection(selection); # Select just I \& Q |
---|
| 1321 | |
---|
[971] | 1322 | ASAP> selection.set_polarisations(``RR LL'') |
---|
[953] | 1323 | ASAP plotter.set_selection(selection); # Select just RR \& LL |
---|
| 1324 | |
---|
[971] | 1325 | ASAP> selection.set_polarisations(``XX YY'') |
---|
[953] | 1326 | ASAP plotter.set_selection(selection); # Select linears |
---|
| 1327 | |
---|
[971] | 1328 | ASAP> selection.set_polarisations(``I Plinear'') |
---|
[966] | 1329 | ASAP plotter.set_selection(selection); # Fractional linear |
---|
[953] | 1330 | |
---|
[971] | 1331 | ASAP> selection.set_polarisations(``Pangle'') |
---|
[966] | 1332 | ASAP plotter.set_selection(selection); # Position angle |
---|
| 1333 | |
---|
[538] | 1334 | \end{verbatim} |
---|
| 1335 | |
---|
[970] | 1336 | Scan, beam and IF selection are also available in the selector object as |
---|
[953] | 1337 | describe in section~\ref{sec:selection}. |
---|
[538] | 1338 | |
---|
| 1339 | \subsection{Saving} |
---|
| 1340 | |
---|
[794] | 1341 | \index{Polarisation!saving}When saving data using the \cmd{save} |
---|
| 1342 | function, the \cmd{stokes} argument can be used to save the data as |
---|
| 1343 | Stoke values when saving in FITS format. |
---|
[538] | 1344 | |
---|
| 1345 | Example: |
---|
| 1346 | |
---|
| 1347 | \begin{verbatim} |
---|
| 1348 | ASAP> scans.save('myscan.sdfits', 'SDFITS', stokes=True) |
---|
| 1349 | \end{verbatim} |
---|
| 1350 | |
---|
[770] | 1351 | \section{Scantable Mathematics} |
---|
| 1352 | |
---|
[794] | 1353 | \index{Scantable!maths}It is possible to to simple mathematics |
---|
| 1354 | directly on scantables from the command line using the \cmd{+, -, *, |
---|
| 1355 | /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works |
---|
[971] | 1356 | between a scantable and a float. (Note that it does |
---|
[794] | 1357 | not work for integers). |
---|
[770] | 1358 | |
---|
[971] | 1359 | {\em Currently mathematics between two scantables is not available } |
---|
[966] | 1360 | |
---|
[971] | 1361 | % ASAP> sum = scan1+scan2 |
---|
[534] | 1362 | \begin{verbatim} |
---|
[770] | 1363 | ASAP> scan2 = scan1+2.0 |
---|
| 1364 | ASAP> scan *= 1.05 |
---|
| 1365 | \end{verbatim} |
---|
| 1366 | |
---|
| 1367 | \section{Scripting} |
---|
| 1368 | |
---|
[794] | 1369 | \index{Scripting}Because asap is based on python, it easy for the user |
---|
| 1370 | write their own scripts and functions to process data. This is highly |
---|
| 1371 | recommended as most processing of user data could then be done in a |
---|
| 1372 | couple of steps using a few simple user defined functions. A Python |
---|
| 1373 | primer is beyond the scope of this userguide. See the asap home pages |
---|
| 1374 | for a scripting tutorial or the main python website for comprehensive |
---|
| 1375 | documentation. |
---|
[770] | 1376 | |
---|
| 1377 | \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials |
---|
[953] | 1378 | |
---|
[770] | 1379 | \hspace{1cm} http://www.python.org/doc/Introduction.html |
---|
| 1380 | |
---|
| 1381 | \subsection{Running scripts} |
---|
| 1382 | |
---|
| 1383 | The asap global function \cmd{execfile} reads the named text file and |
---|
| 1384 | executes the contained python code. This file can either contain |
---|
| 1385 | function definitions which will be used in subsequent processing or |
---|
| 1386 | just a set of commands to process a specific dataset. |
---|
| 1387 | |
---|
| 1388 | \subsection{asapuserfuncs.py} |
---|
| 1389 | |
---|
| 1390 | The file $\sim$/.asap/asapuserfuncs.py is automatically read in when |
---|
| 1391 | asap is started. The user can use this to define a set of user |
---|
| 1392 | functions which are automatically available each time asap is |
---|
| 1393 | used. The \cmd{execfile} function can be called from within this file. |
---|
| 1394 | |
---|
| 1395 | \section{Worked examples} |
---|
| 1396 | |
---|
| 1397 | In the following section a few examples of end-to-end processing of |
---|
[794] | 1398 | some data in asap are given. |
---|
[770] | 1399 | |
---|
| 1400 | \subsection{Mopra} |
---|
[794] | 1401 | \index{Mopra} |
---|
[770] | 1402 | |
---|
[794] | 1403 | The following example is of some dual polarisation, position switched |
---|
| 1404 | data from Mopra. The source has been observed mulitple times split |
---|
| 1405 | into a number of seperate rpfits files. To make the processing easier, |
---|
| 1406 | the first step is to \cmd{cat} the seeprate rpfits files together and |
---|
| 1407 | load as a whole (future versions of asap will make this unnecessary). |
---|
| 1408 | |
---|
| 1409 | |
---|
| 1410 | \begin{verbatim} |
---|
[1011] | 1411 | # get a list of the individual rpfits files in the current directory |
---|
| 1412 | myfiles = list_files() |
---|
[794] | 1413 | |
---|
| 1414 | # Load the data into a scantable |
---|
[1011] | 1415 | data = scantable(myfiles) |
---|
[794] | 1416 | print data |
---|
| 1417 | |
---|
| 1418 | # Form the quotient spectra |
---|
| 1419 | q = data.auto_quotient() |
---|
| 1420 | print q |
---|
| 1421 | |
---|
| 1422 | # Look at the spectra |
---|
| 1423 | plotter.plot(q) |
---|
| 1424 | |
---|
[1011] | 1425 | # Set unit and reference frame |
---|
[794] | 1426 | q.set_unit('km/s') |
---|
| 1427 | q.set_freqframe('LSRK') |
---|
| 1428 | |
---|
[966] | 1429 | # Average all scans in time, aligning in velocity |
---|
| 1430 | av = q.average_time(align=True) |
---|
[794] | 1431 | plotter.plot(av) |
---|
| 1432 | |
---|
| 1433 | # Remove the baseline |
---|
| 1434 | msk = av.create_mask([100,130],[160,200]) |
---|
| 1435 | av.poly_baseline(msk,2) |
---|
| 1436 | |
---|
| 1437 | # Average the two polarisations together |
---|
| 1438 | iav = av.average_pol() |
---|
| 1439 | print iav |
---|
| 1440 | plotter.plot(iav) |
---|
| 1441 | |
---|
| 1442 | # Set a sensible velocity range on the plot |
---|
| 1443 | plotter.set_range(85,200) |
---|
| 1444 | |
---|
| 1445 | # Smooth the data a little |
---|
| 1446 | av.smooth('gauss',4) |
---|
| 1447 | plotter.plot() |
---|
| 1448 | |
---|
| 1449 | # Fit a guassian to the emission |
---|
| 1450 | f = fitter() |
---|
| 1451 | f.set_function(gauss=1) |
---|
| 1452 | f.set_scan(av) |
---|
| 1453 | f.fit() |
---|
| 1454 | |
---|
| 1455 | # View the fit |
---|
| 1456 | f.plot() |
---|
| 1457 | |
---|
| 1458 | # Get the fit parameters |
---|
| 1459 | f.get_parameters() |
---|
| 1460 | |
---|
| 1461 | \end{verbatim} |
---|
| 1462 | |
---|
| 1463 | |
---|
[770] | 1464 | \subsection{Parkes Polarimetry} |
---|
| 1465 | |
---|
[794] | 1466 | \index{Parkes}\index{Polarisation}The following example is processing |
---|
| 1467 | of some Parkes polarmetric observations of OH masers at |
---|
| 1468 | 1.6~GHz. Because digital filters where used in the backend, the |
---|
| 1469 | baselines are stable enough not to require a quotient spectra. The |
---|
| 1470 | 4~MHz bandwidth is wide enough to observe both the 1665 and 1667~MHz |
---|
| 1471 | OH maser transitions. Each source was observed once for about 10 |
---|
| 1472 | minutes. Tsys information was not written to the rpfits file (a |
---|
| 1473 | nominal 25K values was used), so the amplitudes need to be adjusted |
---|
| 1474 | based on a separate log file. A simple user function is used to |
---|
| 1475 | simplify this, contained in a file called mypol.py: |
---|
[770] | 1476 | |
---|
| 1477 | \begin{verbatim} |
---|
| 1478 | def xyscale(data,xtsys=1.0,ytsys=1.0,nomtsys=25.0) : |
---|
| 1479 | |
---|
[966] | 1480 | selection = selector() |
---|
[971] | 1481 | selection.set_polarisations(0) |
---|
[966] | 1482 | data.set_selection(selection) |
---|
| 1483 | data.scale(xtsys/nomtsys) |
---|
[770] | 1484 | |
---|
[971] | 1485 | selection.set_polarisations(1) |
---|
[966] | 1486 | data.set_selection(selection) |
---|
| 1487 | data.scale(ytsys/nomtsys) |
---|
[770] | 1488 | |
---|
[971] | 1489 | selection.set_polarisations(0) |
---|
[966] | 1490 | data.set_selection(selection) |
---|
| 1491 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
[770] | 1492 | |
---|
[971] | 1493 | selection.set_polarisations(0) |
---|
[966] | 1494 | data.set_selection(selection) |
---|
| 1495 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
[770] | 1496 | \end{verbatim} |
---|
| 1497 | |
---|
| 1498 | The typical asap session would be |
---|
| 1499 | |
---|
| 1500 | \begin{verbatim} |
---|
[794] | 1501 | |
---|
[770] | 1502 | # Remind ourself the name of the rpfits files |
---|
[794] | 1503 | ls |
---|
[770] | 1504 | |
---|
| 1505 | # Load data from an rpfits file |
---|
| 1506 | d1665 = scantable('2005-10-27_0154-P484.rpf') |
---|
| 1507 | |
---|
| 1508 | # Check what we have just loaded |
---|
[1011] | 1509 | d1665.summary() |
---|
[770] | 1510 | |
---|
| 1511 | # View the data in velocity |
---|
| 1512 | d1665.set_unit('km/s') |
---|
| 1513 | d1665.set_freqframe('LSRK') |
---|
| 1514 | |
---|
| 1515 | # Correct for the known phase offset in the crosspol data |
---|
| 1516 | d1665.rotate_xyphase(-4) |
---|
| 1517 | |
---|
[794] | 1518 | # Create a copy of the data and set the rest frequency to the 1667 MHz |
---|
[770] | 1519 | # transition |
---|
| 1520 | d1667 = d1665.copy() |
---|
[966] | 1521 | d1667.set_restfreqs([1667.3590], 'MHz') |
---|
| 1522 | d1667.summary() |
---|
[770] | 1523 | |
---|
| 1524 | # Copy out the scan we wish to process |
---|
| 1525 | g351_5 = d1665.get_scan('351p160') |
---|
| 1526 | g351_7 = d1667.get_scan('351p160') |
---|
| 1527 | |
---|
[966] | 1528 | # Baseline both |
---|
| 1529 | msk = g351_5.create_mask([-30,-25],[-5,0]) |
---|
| 1530 | g351_5.poly_baseline(msk,order=1) |
---|
| 1531 | msk = g351_7.create_mask([-30,-25],[-5,0]) |
---|
| 1532 | g351_7.poly_baseline(msk,order=1) |
---|
[770] | 1533 | |
---|
[966] | 1534 | |
---|
| 1535 | # Plot the data. The plotter can only plot a single scantable |
---|
| 1536 | # So we must merge the two tables first |
---|
| 1537 | |
---|
| 1538 | plotscans = merge(g351_5, g351_7) |
---|
| 1539 | |
---|
| 1540 | plotter.plot(plotscans) # Only shows one panel |
---|
| 1541 | |
---|
[770] | 1542 | # Tell the plotter to stack polarisation and panel scans |
---|
| 1543 | plotter.set_mode('p','s') |
---|
| 1544 | |
---|
| 1545 | # Correct for the Tsys using our predefined function |
---|
[971] | 1546 | execfile('mypol.py') # Read in the function xyscale |
---|
[770] | 1547 | xyscale(g351_5,23.2,22.7) # Execute it on the data |
---|
| 1548 | xyscale(g351_7,23.2,22.7) |
---|
| 1549 | |
---|
| 1550 | # Only plot the velocity range of interest |
---|
| 1551 | plotter.set_range(-30,10) |
---|
| 1552 | |
---|
| 1553 | # Update the plot with the baselined data |
---|
| 1554 | plotter.plot() |
---|
| 1555 | |
---|
| 1556 | # Look at the various polarisation products |
---|
[966] | 1557 | selection = selector() |
---|
| 1558 | selection.set_polarisations(``RR LL'') |
---|
| 1559 | plotter.set_selection(selection) |
---|
| 1560 | selection.set_polarisations(``I Plinear'') |
---|
| 1561 | plotter.set_selection(selection) |
---|
| 1562 | selection.set_polarisations(``I Q U V'') |
---|
| 1563 | plotter.set_selection(selection) |
---|
[770] | 1564 | |
---|
| 1565 | # Save the plot as postscript |
---|
[966] | 1566 | plotter.save('g351_stokes.ps') |
---|
[770] | 1567 | |
---|
| 1568 | # Save the process spectra |
---|
[966] | 1569 | plotscans.save('g351.asap') |
---|
[770] | 1570 | |
---|
| 1571 | \end{verbatim} |
---|
| 1572 | |
---|
| 1573 | \subsection{Tidbinbilla} |
---|
| 1574 | |
---|
[794] | 1575 | \index{Tidbinbilla}The following example is processing of some |
---|
| 1576 | Tidbinbilla observations of NH$_3$ at 12~mm. Tidbinbilla has (at the |
---|
| 1577 | time of observations) a single polarisation, but can process two IFs |
---|
| 1578 | simultaneously. In the example, the first half of the observation was |
---|
| 1579 | observing the (1,1) and (2,2) transitions simultaneously). The second |
---|
| 1580 | half observed only the (4,4) transition due to bandwidth |
---|
| 1581 | limitations. The data is position switched, observing first an |
---|
| 1582 | reference to the west, then the source twice and finally reference to |
---|
| 1583 | the east. |
---|
[770] | 1584 | |
---|
| 1585 | \begin{verbatim} |
---|
| 1586 | |
---|
| 1587 | # Load the rpfits file and inspect |
---|
| 1588 | d = scantable('2003-03-16_082048_t0002.rpf') |
---|
| 1589 | print d |
---|
| 1590 | |
---|
| 1591 | # Make the quotient spectra |
---|
| 1592 | q = d.auto_quotient() |
---|
| 1593 | print q |
---|
| 1594 | |
---|
[966] | 1595 | del d |
---|
| 1596 | |
---|
[770] | 1597 | # Plot/select in velocity |
---|
| 1598 | q.set_freqframe('LSRK') |
---|
| 1599 | q.set_unit('km/s') |
---|
| 1600 | |
---|
[966] | 1601 | # Correct for gain/el effects |
---|
| 1602 | |
---|
| 1603 | q.recalc_azel() # Tid does not write the elevation |
---|
| 1604 | q.gain_el() |
---|
| 1605 | q.opacity(0.05) |
---|
| 1606 | |
---|
[770] | 1607 | # Seperate data from the (1,1)&(2,2) and (4,4) transitions |
---|
[971] | 1608 | g1 = q.get_scan(range(6)) # scans 0..5 |
---|
| 1609 | g2 = q.get_scan(range(6,12)) # scans 6..11 |
---|
[770] | 1610 | |
---|
[794] | 1611 | # Align data in velocity |
---|
[966] | 1612 | g1.freq_align() |
---|
| 1613 | g2.freq_align() |
---|
[770] | 1614 | |
---|
| 1615 | # Average individual scans |
---|
| 1616 | a1 = g1.average_time() |
---|
| 1617 | a2 = g2.average_time() |
---|
| 1618 | |
---|
[1011] | 1619 | # Rpfits file only contains a single rest frequency. Set both |
---|
[966] | 1620 | a1.set_restfreqs([23694.4700e6,23722.6336e6]) |
---|
[770] | 1621 | |
---|
[966] | 1622 | plotter.plot(a1) |
---|
[1011] | 1623 | plotter.set_mode('i','t') |
---|
[770] | 1624 | |
---|
| 1625 | a1.auto_poly_baseline() |
---|
| 1626 | |
---|
| 1627 | plotter.plot() |
---|
| 1628 | |
---|
| 1629 | a1.smooth('gauss',5) |
---|
| 1630 | plotter.plot() |
---|
| 1631 | |
---|
[966] | 1632 | |
---|
[770] | 1633 | \end{verbatim} |
---|
| 1634 | |
---|
| 1635 | \newpage |
---|
| 1636 | |
---|
| 1637 | \section{Appendix} |
---|
| 1638 | |
---|
| 1639 | \subsection{Function Summary} |
---|
| 1640 | |
---|
[794] | 1641 | \index{Functions!summary}% |
---|
[770] | 1642 | \begin{verbatim} |
---|
[1011] | 1643 | ASAP> commands() |
---|
[738] | 1644 | [The scan container] |
---|
[534] | 1645 | scantable - a container for integrations/scans |
---|
| 1646 | (can open asap/rpfits/sdfits and ms files) |
---|
| 1647 | copy - returns a copy of a scan |
---|
| 1648 | get_scan - gets a specific scan out of a scantable |
---|
[1011] | 1649 | (by name or number) |
---|
| 1650 | set_selection - set a new subselection of the data |
---|
| 1651 | get_selection - get the current selection object |
---|
[534] | 1652 | summary - print info about the scantable contents |
---|
| 1653 | stats - get specified statistic of the spectra in |
---|
| 1654 | the scantable |
---|
| 1655 | stddev - get the standard deviation of the spectra |
---|
| 1656 | in the scantable |
---|
| 1657 | get_tsys - get the TSys |
---|
| 1658 | get_time - get the timestamps of the integrations |
---|
[1011] | 1659 | get_sourcename - get the source names of the scans |
---|
[794] | 1660 | get_azimuth - get the azimuth of the scans |
---|
| 1661 | get_elevation - get the elevation of the scans |
---|
| 1662 | get_parangle - get the parallactic angle of the scans |
---|
[1011] | 1663 | get_unit - get the current unit |
---|
[534] | 1664 | set_unit - set the abcissa unit to be used from this |
---|
| 1665 | point on |
---|
| 1666 | get_abcissa - get the abcissa values and name for a given |
---|
| 1667 | row (time) |
---|
| 1668 | set_freqframe - set the frame info for the Spectral Axis |
---|
| 1669 | (e.g. 'LSRK') |
---|
| 1670 | set_doppler - set the doppler to be used from this point on |
---|
[1011] | 1671 | set_dirframe - set the frame for the direction on the sky |
---|
[534] | 1672 | set_instrument - set the instrument name |
---|
| 1673 | get_fluxunit - get the brightness flux unit |
---|
| 1674 | set_fluxunit - set the brightness flux unit |
---|
| 1675 | create_mask - return an mask in the current unit |
---|
| 1676 | for the given region. The specified regions |
---|
| 1677 | are NOT masked |
---|
| 1678 | get_restfreqs - get the current list of rest frequencies |
---|
| 1679 | set_restfreqs - set a list of rest frequencies |
---|
[1011] | 1680 | flag_spectrum - flag data |
---|
[534] | 1681 | save - save the scantable to disk as either 'ASAP' |
---|
| 1682 | or 'SDFITS' |
---|
| 1683 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
[1011] | 1684 | nscan - the number of scans in the scantable |
---|
| 1685 | nrow - te number of spectra in the scantable |
---|
[534] | 1686 | history - print the history of the scantable |
---|
[544] | 1687 | get_fit - get a fit which has been stored witnh the data |
---|
[738] | 1688 | average_time - return the (weighted) time average of a scan |
---|
[534] | 1689 | or a list of scans |
---|
| 1690 | average_pol - average the polarisations together. |
---|
| 1691 | The dimension won't be reduced and |
---|
| 1692 | all polarisations will contain the |
---|
| 1693 | averaged spectrum. |
---|
[1011] | 1694 | convert_pol - convert to a different polarisation type |
---|
[738] | 1695 | auto_quotient - return the on/off quotient with |
---|
| 1696 | automatic detection of the on/off scans |
---|
[1011] | 1697 | (matched pairs and 1 off - n on) |
---|
[534] | 1698 | scale - return a scan scaled by a given factor |
---|
[738] | 1699 | add - return a scan with given value added |
---|
[534] | 1700 | bin - return a scan with binned channels |
---|
| 1701 | resample - return a scan with resampled channels |
---|
| 1702 | smooth - return the spectrally smoothed scan |
---|
| 1703 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
[738] | 1704 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
[794] | 1705 | recalc_azel - recalculate azimuth and elevation based on |
---|
| 1706 | the pointing |
---|
[534] | 1707 | gain_el - apply gain-elevation correction |
---|
| 1708 | opacity - apply opacity correction |
---|
| 1709 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
| 1710 | units |
---|
| 1711 | freq_align - align spectra in frequency frame |
---|
| 1712 | rotate_xyphase - rotate XY phase of cross correlation |
---|
| 1713 | rotate_linpolphase - rotate the phase of the complex |
---|
| 1714 | polarization O=Q+iU correlation |
---|
[1011] | 1715 | freq_switch - perform frequency switching on the data |
---|
| 1716 | stats - Determine the specified statistic, e.g. 'min' |
---|
| 1717 | 'max', 'rms' etc. |
---|
| 1718 | stddev - Determine the standard deviation of the current |
---|
| 1719 | beam/if/pol |
---|
| 1720 | |
---|
[534] | 1721 | [Math] Mainly functions which operate on more than one scantable |
---|
| 1722 | |
---|
[738] | 1723 | average_time - return the (weighted) time average |
---|
[534] | 1724 | of a list of scans |
---|
| 1725 | quotient - return the on/off quotient |
---|
[544] | 1726 | simple_math - simple mathematical operations on two scantables, |
---|
| 1727 | 'add', 'sub', 'mul', 'div' |
---|
[534] | 1728 | [Fitting] |
---|
| 1729 | fitter |
---|
| 1730 | auto_fit - return a scan where the function is |
---|
| 1731 | applied to all Beams/IFs/Pols. |
---|
| 1732 | commit - return a new scan where the fits have been |
---|
| 1733 | commited. |
---|
| 1734 | fit - execute the actual fitting process |
---|
[1011] | 1735 | store_fit - store the fit parameters in the data (scantable) |
---|
[534] | 1736 | get_chi2 - get the Chi^2 |
---|
| 1737 | set_scan - set the scantable to be fit |
---|
| 1738 | set_function - set the fitting function |
---|
| 1739 | set_parameters - set the parameters for the function(s), and |
---|
| 1740 | set if they should be held fixed during fitting |
---|
[544] | 1741 | set_gauss_parameters - same as above but specialised for individual |
---|
| 1742 | gaussian components |
---|
[534] | 1743 | get_parameters - get the fitted parameters |
---|
| 1744 | plot - plot the resulting fit and/or components and |
---|
| 1745 | residual |
---|
| 1746 | [Plotter] |
---|
| 1747 | asapplotter - a plotter for asap, default plotter is |
---|
| 1748 | called 'plotter' |
---|
[1011] | 1749 | plot - plot a scantable |
---|
[534] | 1750 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
| 1751 | set_mode - set the state of the plotter, i.e. |
---|
| 1752 | what is to be plotted 'colour stacked' |
---|
| 1753 | and what 'panelled' |
---|
[1011] | 1754 | set_selection - only plot a selected part of the data |
---|
| 1755 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
---|
[534] | 1756 | set_legend - specify user labels for the legend indeces |
---|
| 1757 | set_title - specify user labels for the panel indeces |
---|
[1011] | 1758 | set_abcissa - specify a user label for the abcissa |
---|
[534] | 1759 | set_ordinate - specify a user label for the ordinate |
---|
| 1760 | set_layout - specify the multi-panel layout (rows,cols) |
---|
[1011] | 1761 | set_colors - specify a set of colours to use |
---|
| 1762 | set_linestyles - specify a set of linestyles to use if only |
---|
| 1763 | using one color |
---|
| 1764 | set_mask - set a plotting mask for a specific polarization |
---|
[738] | 1765 | |
---|
[534] | 1766 | [Reading files] |
---|
| 1767 | reader - access rpfits/sdfits files |
---|
[1011] | 1768 | open - attach reader to a file |
---|
| 1769 | close - detach reader from file |
---|
[534] | 1770 | read - read in integrations |
---|
| 1771 | summary - list info about all integrations |
---|
| 1772 | |
---|
| 1773 | [General] |
---|
| 1774 | commands - this command |
---|
| 1775 | print - print details about a variable |
---|
| 1776 | list_scans - list all scantables created bt the user |
---|
[1011] | 1777 | list_files - list all files readable by asap (default rpf) |
---|
[534] | 1778 | del - delete the given variable from memory |
---|
| 1779 | range - create a list of values, e.g. |
---|
| 1780 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
| 1781 | help - print help for one of the listed functions |
---|
[538] | 1782 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
[544] | 1783 | list_rcparameters - print out a list of possible values to be |
---|
[1011] | 1784 | put into $HOME/.asaprc |
---|
[534] | 1785 | mask_and,mask_or, |
---|
| 1786 | mask_not - boolean operations on masks created with |
---|
| 1787 | scantable.create_mask |
---|
[738] | 1788 | |
---|
[534] | 1789 | Note: |
---|
| 1790 | How to use this with help: |
---|
| 1791 | # function 'summary' |
---|
| 1792 | [xxx] is just a category |
---|
[544] | 1793 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
[738] | 1794 | using help |
---|
[534] | 1795 | Example: |
---|
| 1796 | ASAP> help scantable # to get info on ths scantable |
---|
| 1797 | ASAP> help scantable.summary # to get help on the scantable's |
---|
| 1798 | ASAP> help average_time |
---|
[544] | 1799 | |
---|
[1011] | 1800 | |
---|
[534] | 1801 | \end{verbatim} |
---|
| 1802 | |
---|
| 1803 | \subsection{ASCII output format} |
---|
| 1804 | |
---|
| 1805 | \subsection{.asaprc settings} |
---|
[794] | 1806 | \index{.asaprc} |
---|
[971] | 1807 | \asaprc{verbose}{{\bf True}/False}{Print verbose output, good to disable in scripts} |
---|
[770] | 1808 | |
---|
| 1809 | \asaprc{insitu}{{\bf True}/False}{Apply operations on the input |
---|
| 1810 | scantable or return new one} |
---|
| 1811 | |
---|
| 1812 | % plotting |
---|
| 1813 | |
---|
| 1814 | \asaprc{useplotter}{{\bf True}/False}{Preload a default plotter} |
---|
| 1815 | |
---|
| 1816 | \asaprc{plotter.gui}{{\bf True}/False}{Do we want a GUI or plot to a |
---|
| 1817 | file} |
---|
| 1818 | |
---|
| 1819 | \asaprc{plotter.stacking}{{\bf Pol} Beam IF Scan Time}{Default mode for |
---|
| 1820 | colour stacking} |
---|
| 1821 | |
---|
| 1822 | \asaprc{plotter.panelling}{Pol Beam IF {\bf Scan} Time}{Default mode |
---|
| 1823 | for panelling} |
---|
| 1824 | |
---|
| 1825 | \asaprc{plotter.ganged}{{\bf True}/False}{Push panels together, to |
---|
| 1826 | share axislabels} |
---|
| 1827 | |
---|
| 1828 | \asaprc{plotter.decimate}{True/{\bf False}}{Decimate the number of |
---|
| 1829 | points plotted by a factor of nchan/1024} |
---|
| 1830 | |
---|
| 1831 | % default colours/linestyles |
---|
| 1832 | %\asaprc{plotter.colours}{.}{.} |
---|
| 1833 | %\asaprc{plotter.linestyles{.}{.} |
---|
| 1834 | |
---|
| 1835 | % scantable |
---|
| 1836 | \asaprc{scantable.save}{{\bf ASAP} SDFITS FITS ASCII MS2}{Default output |
---|
[794] | 1837 | format when saving} |
---|
[770] | 1838 | |
---|
| 1839 | \asaprc{scantable.autoaverage}{{\bf True}/False}{Auto averaging on |
---|
| 1840 | read} |
---|
| 1841 | |
---|
| 1842 | \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default |
---|
| 1843 | frequency frame to set when function scantable.set\_freqframe is |
---|
[971] | 1844 | called or the data is imported} |
---|
[770] | 1845 | |
---|
[953] | 1846 | \subsection{Installation} |
---|
| 1847 | |
---|
| 1848 | \index{Installation}ASAP depends on a number of third-party libraries which you must |
---|
| 1849 | have installed before attempting to build ASAP. These are: |
---|
| 1850 | |
---|
| 1851 | \begin{itemize} |
---|
| 1852 | \item AIPS++ |
---|
| 1853 | \item Boost |
---|
| 1854 | \item Matplotlib |
---|
| 1855 | \item python/ipython |
---|
| 1856 | \end{itemize} |
---|
| 1857 | |
---|
| 1858 | Debian Linux is currently supported and we intend also |
---|
| 1859 | to support other popular Linux flavours, Solaris and Mac. |
---|
| 1860 | |
---|
| 1861 | Of the dependencies, AIPS++ is the most complex to install. |
---|
| 1862 | |
---|
[794] | 1863 | \printindex |
---|
| 1864 | |
---|
[534] | 1865 | \end{document} |
---|
[770] | 1866 | |
---|