1 | \documentclass[11pt]{article} |
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2 | \usepackage{a4} |
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3 | \usepackage{calc} |
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4 | \usepackage[dvips]{graphicx} |
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5 | \usepackage{makeidx} |
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14 | |
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15 | \title{ATNF Spectral Analysis Package\\User Guide v2.0 } |
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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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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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26 | \makeindex |
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27 | |
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28 | |
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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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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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37 | antennas, and can probably be used for other antennas if they can |
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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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41 | This userguide has been updated for the ASAP 2.0 release which has a |
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42 | number of significant changes which affect the user interface. Please |
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43 | report any mistakes you find. |
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44 | |
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45 | \section{Installation and Running} |
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46 | |
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47 | Currently there are installations running on Linux machines at |
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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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52 | \item Parkes - use host {\tt bourbon} |
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53 | \item Mopra - use host {\tt minos} |
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54 | \end{itemize} |
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55 | |
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56 | \index{Running}To start asap log onto one of these Linux hosts and enter |
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57 | |
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58 | \begin{verbatim} |
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59 | > cd /my/data/directory |
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60 | > asap |
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61 | \end{verbatim} |
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62 | |
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63 | This starts the ASAP. To quit, you need to type \verb+^+-d |
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64 | (control-d) or type \cmd{\%Exit}. |
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65 | |
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66 | \section{Interface} |
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67 | |
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68 | \index{Interface}ASAP is written in C++ and python. The user interface |
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69 | uses the ``ipython'' interactive shell, which is a simple interactive |
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70 | interface to python. The user does not need to understand python to |
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71 | use this, but certain aspects python affect what the user can do. The |
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72 | current interface is object oriented. |
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73 | |
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74 | \subsection {Integer Indices are 0-relative} |
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75 | |
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76 | Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. |
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77 | |
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78 | \subsection{Objects} |
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79 | \index{objects} |
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80 | The ASAP interface is based around a number of ``objects'' which the |
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81 | user deals with. Objects range from the data which have been read from |
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82 | disk, to tools used for fitting functions to the data. The following |
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83 | main objects are used : |
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84 | |
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85 | \begin{itemize} |
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86 | \item[\cmd{scantable}] The data container (actual spectra and header |
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87 | information) |
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88 | \item[\cmd{selector}] Allows the user to select a subsection of the |
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89 | data, such as a specified or range of beam numbers, IFs, etc. |
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90 | \item[\cmd{plotter}] A tool used to plot the spectral line data |
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91 | \item[\cmd{fitter}] A tool used to fit functions to the spectral data |
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92 | \item[\cmd{reader}] A tool which can be used to read data from disks |
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93 | into a scantable object (advanced use). |
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94 | \end{itemize} |
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95 | |
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96 | There can be many objects of the same type. Each object is referred to |
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97 | by a variable name made by the user. The name of this variable is not |
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98 | important and can be set to whatever the user prefers (i.e. ``s'' and |
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99 | ``ParkesHOH-20052002'' are equivalent). However, having a simple and |
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100 | consistent naming convention will help you a lot. |
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101 | |
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102 | \subsection{Member Functions (functions)} |
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103 | |
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104 | \index{Functions!member}Following the object oriented approach, |
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105 | objects have associated ``member functions'' which can either be used |
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106 | to modify the data in some way or change global properties of the |
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107 | object. In this document member functions will be referred to simply |
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108 | as functions. From the command line, the user can execute these |
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109 | functions using the syntax: |
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110 | \begin{verbatim} |
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111 | ASAP> out = object.function(arguments) |
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112 | \end{verbatim} |
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113 | |
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114 | Where \cmd{out} is the name of the returned variable (could be a new |
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115 | scantable object, or a vector of data, or a status return), |
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116 | \cmd{object} is the object variable name (set by the user), |
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117 | \cmd{function} is the name of the member function and \cmd{arguments} |
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118 | is a list of arguments to the function. The arguments can be provided |
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119 | either though position or \cmd{name=}. A mix of the two can be used. |
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120 | E.g. |
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121 | |
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122 | \begin{verbatim} |
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123 | ASAP> av = scans.average_time(msk,weight='tsys') |
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124 | ASAP> av = scans.average_time(mask=msk,weight='tsys') |
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125 | ASAP> av = scans.average_time(msk,tsys) |
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126 | ASAP> scans.poly_baseline(mask=msk, order=0, insitu=True) |
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127 | ASAP> scans.poly_baseline(msk,0,True) |
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128 | ASAP> scans.poly_baseline(mask, insitu=True) |
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129 | \end{verbatim} |
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130 | |
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131 | \subsection{Global Functions} |
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132 | |
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133 | \index{Functions!global}It does not make sense to implement some functions as member |
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134 | functions, typically functions which operate on more than one |
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135 | scantable (e.g. time averaging of many scans). These functions will |
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136 | always be referred to as global functions. |
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137 | |
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138 | \subsection{Interactive environment} |
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139 | |
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140 | \index{ipython!environment}ipython has a number of useful interactive |
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141 | features and a few things to be aware of for the new user. |
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142 | |
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143 | \subsubsection{String completion} |
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144 | |
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145 | \index{ipython!string completion}Tab completion is enabled for all |
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146 | function names. If you type the first few letters of a function name, |
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147 | then type {\tt <TAB>} the function name will be auto completed if it |
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148 | is un-ambiguous, or a list of possibilities will be |
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149 | given. Auto-completion works for the user object names as well as |
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150 | function names. It does not work for filenames, nor for function |
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151 | arguments. |
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152 | |
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153 | Example |
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154 | \begin{verbatim} |
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155 | ASAP> scans = scantable('MyData.rpf') |
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156 | ASAP> scans.se<TAB> |
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157 | ASAP> scans.set_in<TAB> |
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158 | scans.set_cursor scans.set_freqframe scans.set_selection |
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159 | scans.set_doppler scans.set_instrument scans.set_unit |
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160 | scans.set_fluxunit scans.set_restfreqs |
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161 | |
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162 | ASAP> scans.set_instrument() |
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163 | \end{verbatim} |
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164 | |
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165 | \subsubsection{Leading Spaces} |
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166 | |
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167 | \index{ipython!leading space}Python uses leading space to mark blocks |
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168 | of code. This means that it you start a command line with a space, the |
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169 | command generally will fail with an syntax error. |
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170 | |
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171 | \subsubsection{Variable Names} |
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172 | |
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173 | \index{ipython!variable names}During normal data processing, the user |
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174 | will have to create named variables to hold spectra etc. These must |
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175 | conform to the normal python syntax, specifically they cannot contain |
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176 | ``special'' characters such as \@ \$ etc and cannot start with a |
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177 | number (but can contain numbers). Variable (and function) names are |
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178 | case sensitive. |
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179 | |
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180 | \subsubsection{Unix Interaction} |
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181 | |
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182 | \index{ipython!unix interaction}Basic unix shell commands (\cmd{pwd}, |
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183 | \cmd{ls}, \cmd{cd} etc) can be issued from within ASAP. This allows |
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184 | the user to do things like look at files in the current directory. The |
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185 | shell command ``\cmd{cd}'' works within ASAP, allowing the user to |
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186 | change between data directories. Unix programs cannot be run this way, |
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187 | but the shell escape ``$!$'' can be used to run arbitrary |
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188 | programs. E.g. |
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189 | |
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190 | \begin{verbatim} |
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191 | ASAP> pwd |
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192 | ASAP> ls |
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193 | ASAP> cd /my/data/directory |
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194 | ASAP> ! mozilla& |
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195 | \end{verbatim} |
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196 | |
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197 | \subsection{Help} |
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198 | |
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199 | \index{Help}ASAP has built in help for all functions. To get a list of |
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200 | functions type: |
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201 | |
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202 | \begin{verbatim} |
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203 | ASAP> commands() |
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204 | \end{verbatim} |
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205 | |
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206 | To get help on specific functions, the built in help needs to be given |
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207 | the object and function name. E.g. |
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208 | |
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209 | \begin{verbatim} |
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210 | ASAP> help scantable.get_scan # or help(scantable.get_scan) |
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211 | ASAP> help scantable.stats |
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212 | ASAP> help plotter.plot |
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213 | ASAP> help fitter.plot |
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214 | |
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215 | ASAP> scans = scantable('mydata.asap') |
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216 | ASAP> help scans.get_scan # Same as above |
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217 | \end{verbatim} |
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218 | |
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219 | Global functions just need their name |
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220 | |
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221 | \begin{verbatim} |
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222 | ASAP> help average_time |
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223 | \end{verbatim} |
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224 | |
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225 | Note that if you just type \cmd{help} the internal ipython help is |
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226 | invoked, which is probably {\em not} what you want. Type \verb+^+-d |
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227 | (control-d) to escape from this. |
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228 | |
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229 | \subsection{Customisation - .asaprc} |
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230 | |
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231 | \index{.asaprc}ASAP use an \cmd{.asaprc} file to control the user's |
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232 | preference of default values for various functions arguments. This |
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233 | includes the defaults for arguments such as \cmd{insitu}, scantable |
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234 | \cmd{freqframe} and the plotters \cmd{set\_mode} values. The help on |
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235 | individual functions says which arguments can be set default values |
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236 | from the \cmd{.asaprc} file. To get a sample contents for the |
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237 | \cmd{.asaprc} file use the command \cmd{list\_rcparameters}. |
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238 | |
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239 | Common values include: |
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240 | \begin{verbatim} |
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241 | # apply operations on the input scantable or return new one |
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242 | insitu : False |
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243 | |
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244 | # default output format when saving scantable |
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245 | scantable.save : ASAP |
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246 | |
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247 | # default frequency frame to set when function |
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248 | # scantable.set_freqframe is called |
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249 | scantable.freqframe : LSRK |
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250 | |
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251 | # auto averaging on read |
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252 | scantable.autoaverage : True |
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253 | \end{verbatim} |
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254 | |
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255 | For a complete list of \cmd{.asaprc} values, see the Appendix. |
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256 | |
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257 | \section{Scantables} |
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258 | \index{Scantables} |
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259 | \subsection {Description} |
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260 | |
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261 | \subsubsection {Basic Structure} |
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262 | |
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263 | \index{Scantable!structure}ASAP data handling works on objects called |
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264 | scantables. A scantable holds your data, and also provides functions |
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265 | to operate upon it. |
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266 | |
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267 | The building block of a scantable is an integration, which is a single |
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268 | row of a scantable. Each row contains just one spectrum for each beam, IF and |
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269 | polarisation. For example Parkes multibeam data would contain many |
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270 | beams, one IF and 2-4 polarisations, while the new Mopra 8-GHz |
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271 | filterbank will eventually produce one beam, many IFs, and 2-4 |
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272 | polarisations. All of the combinations of Beams/IFs an Polarisations are |
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273 | contained in seperate rows. These rows are grouped in cycles (same time stamp). |
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274 | |
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275 | A collection of cycles for one source is termed |
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276 | a scan (and each scan has a unique numeric identifier, the SCANNO). A |
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277 | scantable is then a collection of one or more scans. If you have |
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278 | scan-averaged your data in time, i.e. you have averegaed all cycles within |
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279 | a scan, then each scan would hold just one (averaged) integration. |
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280 | |
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281 | Many of the functions which work on scantables can either return a |
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282 | new scantable with modified data or change the scantable insitu. Which |
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283 | method is used depends on the users preference. The default can be |
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284 | changed via the {\tt .asaprc} resource file. |
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285 | |
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286 | For example a Mopra scan with a 4s intergration time, two IFs and |
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287 | dual polarisations has two (2s) cycles. |
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288 | \begin{verbatim} |
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289 | SCANNO CYCLENO BEAMNO IFNO POLNO |
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290 | 0 0 0 0 0 |
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291 | 0 0 0 0 1 |
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292 | 0 0 0 1 0 |
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293 | 0 0 0 1 1 |
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294 | 0 1 0 0 0 |
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295 | 0 1 0 0 1 |
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296 | 0 1 0 1 0 |
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297 | 0 1 0 1 1 |
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298 | \end{verbatim} |
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299 | |
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300 | |
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301 | \subsubsection {Contents} |
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302 | |
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303 | \index{Scantable!contents}A scantable has header information and data |
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304 | (a scantable is actually an AIPS++ Table and it is generally stored in |
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305 | memory when you are manipulating it with ASAP. You can save it to |
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306 | disk and then browse it with the AIPS++ Table browser if you know how |
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307 | to do that !). |
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308 | |
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309 | The data are stored in columns (the length of a column is the number of |
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310 | rows/spectra of course). |
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311 | |
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312 | |
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313 | Two important columns are those that describe the frequency setup. We mention |
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314 | them explicitly here because you need to be able to understand the presentation |
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315 | of the frequency information and possibly how to manipulate it. |
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316 | |
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317 | These columns are called FREQ\_ID and MOLECULE\_ID. They contain indices, for |
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318 | each IF, pointing into tables with all of the frequency and rest-frequency |
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319 | information for that integration. |
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320 | |
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321 | There are of course many other columns which contain the actual spectra, |
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322 | the flags, the Tsys, the source names and so on. |
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323 | |
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324 | There is also a function \cmd{summary} to list a summary of the scantable. |
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325 | You will find this very useful. |
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326 | |
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327 | Example: |
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328 | |
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329 | \begin{verbatim} |
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330 | ASAP> scans = scantable('MyData.rpf') |
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331 | ASAP> scans.summary() # Brief listing |
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332 | |
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333 | # Equivalent to brief summary function call |
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334 | ASAP> print scan |
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335 | \end{verbatim} |
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336 | |
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337 | The summary function gives you a scan-based summary, presenting the |
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338 | scantable as a cascading view of Beams and IFs. Note that the output |
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339 | of summary is redirected into your current pager specified by the |
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340 | \$PAGER environment variable. If you find the screen is reset to the |
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341 | original state when summary is finished (ie the output from summary |
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342 | disappears), you may need to set the \$LESS environment variable to |
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343 | include the \cmd{-X} option. |
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344 | |
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345 | \subsection{Data Selection} |
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346 | \label{sec:selection} |
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347 | |
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348 | ASAP contains flexible data selection. Data can be selected based on |
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349 | IF, beam, polarisation, scan number as well as values such as |
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350 | Tsys. Advanced users can also make use of the AIPS++ TAQL language to |
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351 | create selections based on almost any of the values recorded. |
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352 | |
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353 | Selection is based on a \cmd{selector} object. This object is created |
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354 | and various selection functions applied to it (\cmd{set\_ifs}, |
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355 | \cmd{set\_beams} etc). The selection object then must be applied to a |
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356 | scantable using the \cmd{set\_selection} function. A single selection |
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357 | object can be created and setup then applied to multiple scantables. |
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358 | |
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359 | Once a selection has been applied, all following functions will only |
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360 | ``see'' the selected spectra (including functions such as |
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361 | \cmd{summary}). The selection can then be reset and all spectra are |
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362 | visible. Note that if functions such as \cmd{copy} are run on a |
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363 | scantable with active selection, only the selected spectra are copied. |
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364 | |
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365 | The common selection functions are: |
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366 | |
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367 | \begin{itemize} |
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368 | |
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369 | \item[\cmd{set\_beams}] Select beams by index number |
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370 | \item[\cmd{set\_ifs}] Select ifs by index number |
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371 | \item[\cmd{set\_name}] Select by source name. Can contain ``*'' as a |
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372 | wildcard, e.g. ``Orion*\_R''. |
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373 | \item[\cmd{set\_ifs}] Select IFs by index number |
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374 | \item[\cmd{set\_polarisation}] Select by polarisation index or |
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375 | name. If polarisation names are given, the data will be on-the-fly |
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376 | converted (for example from linears to Stokes). |
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377 | \item[\cmd{set\_query}] Set query directly. For power users only! |
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378 | \item[\cmd{set\_tsys}] Select data based on Tsys. Also example of user |
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379 | definable query. |
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380 | \item[\cmd{reset}] Reset the selection to include all spectra. |
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381 | |
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382 | |
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383 | Note that all indices are zero based. |
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384 | |
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385 | Examples: |
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386 | |
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387 | \begin{verbatim} |
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388 | ASAP> selection = selector() # Create selection object |
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389 | ASAP> selection.set_ifs(0) # Just select the first IF |
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390 | ASAP> scans.set_selection(selection) # Apply the selection |
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391 | ASAP> print scans # Will just show the first IF |
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392 | |
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393 | ASAP> selection.set_ifs([0,1]) # Select the first two IFs |
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394 | ASAP> selection.set_beams([1,3,5]) # Also select three of the beams |
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395 | ASAP> scans.set_selection(selection) # Apply the selection |
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396 | |
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397 | ASAP> selection.set_name('G308*') # Select by source name |
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398 | |
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399 | ASAP> selection.reset() # Turn off selection |
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400 | ASAP> scans.set_selection(selection) # Apply the reset selection |
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401 | |
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402 | \end{verbatim} |
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403 | |
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404 | \end{itemize} |
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405 | |
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406 | \subsection{State} |
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407 | |
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408 | \index{Scantable!state}Each scantable contains "state"; these are |
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409 | properties applying to all of the data in the scantable. |
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410 | |
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411 | Examples are the selection of beam, IF and polarisation, spectral unit |
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412 | (e.g. km/s), frequency reference frame (e.g. BARY) and velocity Doppler |
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413 | type (e.g. RADIO). |
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414 | |
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415 | \subsubsection{Units, Doppler and Frequency Reference Frame} |
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416 | |
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417 | The information describing the frequency setup for each integration |
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418 | is stored fundamentally in frequency in the reference frame |
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419 | of observation (E.g. TOPO). |
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420 | |
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421 | When required, this is converted to the desired reference frame |
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422 | (e.g. LSRK), Doppler (e.g. OPTICAL) and unit (e.g. km/s) on-the-fly. |
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423 | This is important, for example, when you are displaying the data or |
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424 | fitting to it. The reference frame is set on file read to the value |
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425 | set in the user \cmd{.asaprc} file. |
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426 | |
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427 | For units, the user has the choice of frequency, velocity or channel. |
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428 | The \cmd{set\_unit} function is used to set the current unit for a |
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429 | scantable. All functions will (where relevant) work with the selected |
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430 | unit until this changes. This is mainly important for fitting (the fits |
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431 | can be computed in any of these units), plotting and mask creation. |
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432 | |
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433 | The velocity definition can be changed with the \cmd{set\_doppler} |
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434 | function, and the frequency reference frame can be changed with the |
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435 | \cmd{set\_freqframe} function. |
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436 | |
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437 | Example usage: |
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438 | |
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439 | \begin{verbatim} |
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440 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data |
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441 | ASAP> scans.set_freqframe('LSRK') # Use the LSR velocity frame |
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442 | ASAP> scans.set_unit('km/s') # Use velocity for plots etc from now on |
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443 | ASAP> scans.set_doppler('OPTICAL') # Use the optical velocity convention |
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444 | ASAP> scans.set_unit('MHz') # Use frequency in MHz from now on |
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445 | \end{verbatim} |
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446 | |
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447 | |
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448 | \subsubsection{Rest Frequency} |
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449 | |
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450 | \index{Scantable!rest frequency}ASAP reads the line rest frequency |
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451 | from the RPFITS file when reading the data. The values stored in the |
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452 | RPFITS file are not always correct and so there is a function |
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453 | \cmd{set\_restfreq} to set the rest frequencies for the currently |
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454 | selected data. |
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455 | |
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456 | For each integration, there is a rest-frequency per IF (the rest |
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457 | frequencies are just stored as a list with an index into them). |
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458 | There are a few ways to set the rest frequencies with this function. |
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459 | |
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460 | If you specify just one rest frequency, then it is set for all IF. |
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461 | |
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462 | \begin{verbatim} |
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463 | # Set all IFs |
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464 | ASAP> scans.set_restfreqs(freqs=1.667359e9) |
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465 | \end{verbatim} |
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466 | |
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467 | If set a rest frequency for each IF, specify a list of frequencies (of |
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468 | length the number of IFs). Regardless of the source, the rest |
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469 | frequency will be set for each IF to the corresponding value in the |
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470 | provided list. |
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471 | |
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472 | \begin{verbatim} |
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473 | # Set rest frequency for all IFs |
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474 | ASAP> scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,]) |
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475 | |
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476 | \end{verbatim} |
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477 | |
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478 | {\em Currently the following is not implemented} |
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479 | |
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480 | In both of the above modes, you can also specify the rest frequencies via |
---|
481 | names in a known list rather than by their values. |
---|
482 | |
---|
483 | Examples: |
---|
484 | |
---|
485 | \begin{verbatim} |
---|
486 | ASAP> scans.set_restfreqs(freqs=['OH1665','OH1667']) |
---|
487 | \end{verbatim} |
---|
488 | |
---|
489 | |
---|
490 | \subsubsection{Masks} |
---|
491 | |
---|
492 | \index{Masks}\index{Scantable!masks} |
---|
493 | |
---|
494 | Many tasks (fitting, baseline subtraction, statistics etc) should only |
---|
495 | be run on range of channels. Depending on the current ``unit'' setting |
---|
496 | this range is set directly as channels, velocity or frequency |
---|
497 | ranges. Internally these are converted into a simple boolean mask for |
---|
498 | each channel of the abscissa. This means that if the unit setting is |
---|
499 | later changed, previously created mask are still valid. (This is not |
---|
500 | true for functions which change the shape or shift the frequency |
---|
501 | axis). You create masks with the function \cmd{create\_mask} and this |
---|
502 | specified the channels to be included in the selection. When setting |
---|
503 | the mask in velocity, the conversion from velocity to channels is |
---|
504 | based on the current selection, specified row and selected frequency |
---|
505 | reference frame. |
---|
506 | |
---|
507 | |
---|
508 | Note that for multi IF data with different number of channels per IF a |
---|
509 | single mask cannot be applied to different IFs. To use a mask on such |
---|
510 | data the selector should be applied to select all IFs with the same |
---|
511 | number of channels. |
---|
512 | |
---|
513 | Example : |
---|
514 | \begin{verbatim} |
---|
515 | |
---|
516 | # Select channel range for baselining |
---|
517 | ASAP> scans.set_unit('channels') |
---|
518 | ASAP> msk = scans.create_mask([100,400],[600,800]) |
---|
519 | |
---|
520 | # Select velocity range for fitting |
---|
521 | ASAP> scans.set_unit('km/s') |
---|
522 | ASAP> msk = scans.create_mask([-30,-10]) |
---|
523 | \end{verbatim} |
---|
524 | |
---|
525 | Sometimes it is more convenient to specify the channels to be |
---|
526 | excluded, rather included. You can do this with the ``invert'' |
---|
527 | argument. |
---|
528 | |
---|
529 | Example : |
---|
530 | \begin{verbatim} |
---|
531 | ASAP> scans.set_unit('channels') |
---|
532 | ASAP> msk = scans.create_mask([0,100],[900-1023], invert=True) |
---|
533 | \end{verbatim} |
---|
534 | |
---|
535 | By default \cmd{create\_mask} uses the frequency setup of the first row |
---|
536 | to convert velocities into a channel mask. If the rows in the data |
---|
537 | cover different velocity ranges, the scantable row to use should be |
---|
538 | specified: |
---|
539 | |
---|
540 | \begin{verbatim} |
---|
541 | ASAP> scans.set_unit('km/s') |
---|
542 | ASAP> msk = q.create_mask([-30,-10], row=5) |
---|
543 | \end{verbatim} |
---|
544 | |
---|
545 | Because the mask is stored in a simple python variable, the users is |
---|
546 | able to combine masks using simple arithmetic. To create a mask |
---|
547 | excluding the edge channels, a strong maser feature and a birdie in |
---|
548 | the middle of the band: |
---|
549 | |
---|
550 | \begin{verbatim} |
---|
551 | ASAP> scans.set_unit('channels') |
---|
552 | ASAP> msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True) |
---|
553 | ASAP> scans.set_unit('km/s') |
---|
554 | ASAP> msk2 = q.create_mask([-20,-10],invert=True) |
---|
555 | |
---|
556 | ASAP> mask = msk1 and msk2 |
---|
557 | \end{verbatim} |
---|
558 | |
---|
559 | |
---|
560 | \subsection{Management} |
---|
561 | |
---|
562 | \index{Scantable!management}During processing it is possible to create |
---|
563 | a large number of scan tables. These all consume memory, so it is best |
---|
564 | to periodically remove unneeded scan tables. Use \cmd{list\_scans} to |
---|
565 | print a list of all scantables and \cmd{del} to remove unneeded ones. |
---|
566 | |
---|
567 | Example: |
---|
568 | |
---|
569 | \begin{verbatim} |
---|
570 | ASAP> list_scans() |
---|
571 | The user created scantables are: |
---|
572 | ['s', 'scans', 'av', 's2', 'ss'] |
---|
573 | |
---|
574 | ASAP> del s2 |
---|
575 | ASAP> del ss |
---|
576 | \end{verbatim} |
---|
577 | |
---|
578 | \section{Data Input} |
---|
579 | |
---|
580 | \index{Reading data}Data can be loaded in one of two ways; using the |
---|
581 | reader object or via the scantable constructor. The scantable method |
---|
582 | is simpler but the reader allows the user more control on what is read. |
---|
583 | |
---|
584 | \subsection{Scantable constructor} |
---|
585 | |
---|
586 | \index{Scantable constructor}\index{Scantable!constructor}This loads |
---|
587 | all of the data from filename into the scantable object scans and |
---|
588 | averages all the data within a scan (i.e. the resulting scantable |
---|
589 | will have one row per scan). The recognised input file formats are |
---|
590 | RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ |
---|
591 | MeasurementSet2 format. |
---|
592 | |
---|
593 | Example usage: |
---|
594 | |
---|
595 | \begin{verbatim} |
---|
596 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf') |
---|
597 | |
---|
598 | # Don't scan average the data |
---|
599 | ASAP> scan = scantable('2004-11-23_1841-P484.rpf', average=False) |
---|
600 | \end{verbatim} |
---|
601 | |
---|
602 | |
---|
603 | \subsection{Reader object} |
---|
604 | |
---|
605 | \index{Reader object}\index{Scantable!reader object}For more control |
---|
606 | when reading data into ASAP, the reader object should be used. This |
---|
607 | has the option of only reading in a range of integrations, only a |
---|
608 | specified beam or IF and does not perform any scan averaging of the |
---|
609 | data, allowing analysis of the individual integrations. Note that due |
---|
610 | to limitation of the RPFITS library, only one reader object can be |
---|
611 | open at one time reading RPFITS files. To read multiple RPFITS files, |
---|
612 | the old reader must be destroyed before the new file is opened. |
---|
613 | However, multiple readers can be created and attached to SDFITS files. |
---|
614 | |
---|
615 | |
---|
616 | Example usage: |
---|
617 | |
---|
618 | \begin{verbatim} |
---|
619 | ASAP> r = reader('2003-03-16_082048_t0002.rpf') |
---|
620 | ASAP> r.summary() |
---|
621 | ASAP> scan = r.read() |
---|
622 | ASAP> del r |
---|
623 | \end{verbatim} |
---|
624 | |
---|
625 | \section{Basic Processing} |
---|
626 | |
---|
627 | In the following section, a simple data reduction to form a quotient |
---|
628 | spectrum of a single source is followed. It has been assume that the |
---|
629 | \cmd{.asaprc} file has {\em not} been used to change the \cmd{insitu} |
---|
630 | default value from \cmd{True}. |
---|
631 | |
---|
632 | \subsection{Auto quotient} |
---|
633 | \index{Auto quotient}Quotients can be computed ``automatically''. This |
---|
634 | requires the data to have matching source/reference pairs or one |
---|
635 | reference for multiple sources. Auto quotient assumes reference scans |
---|
636 | have a trailing ``\_R'' in the source name for data from Parkes and |
---|
637 | Mopra, and a trailing ``e'' or ``w'' for data fro, Tidbinbilla. |
---|
638 | |
---|
639 | \begin{verbatim} |
---|
640 | ASAP> q = s.auto_quotient() |
---|
641 | \end{verbatim} |
---|
642 | |
---|
643 | By default the quotient spectra is calculated |
---|
644 | to preserve continuum emission. If you wish to remove the continuum |
---|
645 | contribution, use the \cmd{preserve} argument: |
---|
646 | |
---|
647 | \begin{verbatim} |
---|
648 | ASAP> q = s.auto_quotient(preserve=True) |
---|
649 | \end{verbatim} |
---|
650 | |
---|
651 | %If this is not sufficient the following alternative method can be used. |
---|
652 | % |
---|
653 | %\subsection{Separate reference and source observations} |
---|
654 | % |
---|
655 | %\index{Quotient spectra}Most data from ATNF observatories |
---|
656 | %distinguishes on and off source data using the file name. This makes |
---|
657 | %it easy to create two scantables with the source and reference |
---|
658 | %data. As long as there was exactly one reference observation for each |
---|
659 | %on source observation for following method will work. |
---|
660 | % |
---|
661 | %For Mopra and Parkes data: |
---|
662 | %\begin{verbatim} |
---|
663 | % ASAP> r = scans.get_scan('*_R') |
---|
664 | % ASAP> s = scans.get_scan('*_S') |
---|
665 | %\end{verbatim} |
---|
666 | % |
---|
667 | %For Tidbinbilla data |
---|
668 | %\begin{verbatim} |
---|
669 | % ASAP> r = scans.get_scan('*_[ew]') |
---|
670 | % ASAP> s = scans.get_scan('*_[^ew]') |
---|
671 | %\end{verbatim} |
---|
672 | % |
---|
673 | %\subsection{Make the quotient spectra} |
---|
674 | % |
---|
675 | %Use the quotient function |
---|
676 | % |
---|
677 | %\begin{verbatim} |
---|
678 | % ASAP> q = s.quotient(r) |
---|
679 | %\end{verbatim} |
---|
680 | % |
---|
681 | %This uses the rows in scantable \cmd{r} as reference spectra for the |
---|
682 | %rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row |
---|
683 | %(which is applied to all rows in \cmd{s}) or both scantables must have |
---|
684 | %the same number of rows. |
---|
685 | |
---|
686 | \subsection{Time average separate scans} |
---|
687 | |
---|
688 | \index{Time average}If you have observed the source with multiple |
---|
689 | source/reference cycles you will want to scan-average the quotient |
---|
690 | spectra together. |
---|
691 | |
---|
692 | \begin{verbatim} |
---|
693 | ASAP> av = q.average_time() |
---|
694 | \end{verbatim} |
---|
695 | |
---|
696 | If for some you want to average multiple sets of scantables together |
---|
697 | you can: |
---|
698 | |
---|
699 | \begin{verbatim} |
---|
700 | ASAP> av = average_time(q1, q2, q3) |
---|
701 | \end{verbatim} |
---|
702 | |
---|
703 | The default is to use integration time weighting. The alternative is |
---|
704 | to use none, variance, Tsys weighting or Tsys \& integration time. |
---|
705 | |
---|
706 | \begin{verbatim} |
---|
707 | ASAP> av = average_time(q, weight='tintsys') |
---|
708 | \end{verbatim} |
---|
709 | |
---|
710 | To use variance based weighting, you need to supply a mask saying which |
---|
711 | channel range you want it to calculate the variance from. |
---|
712 | |
---|
713 | \begin{verbatim} |
---|
714 | ASAP> msk = scans.create_mask([200,400],[600,800]) |
---|
715 | ASAP> av = average_time(scans, mask=msk, weight='var') |
---|
716 | \end{verbatim} |
---|
717 | |
---|
718 | If you have not observed your data with Doppler tracking (or run |
---|
719 | \cmd{freq\_align} explicitally) you should align the data in frequency |
---|
720 | before averaging. |
---|
721 | |
---|
722 | \begin{verbatim} |
---|
723 | ASAP> av = scans.average_time(align=True) |
---|
724 | \end{verbatim} |
---|
725 | |
---|
726 | Note that, if needed, you should run \cmd{gain\_el} and \cmd{opacity} |
---|
727 | before you average the data in time (\S \ref{sec:gainel} \& |
---|
728 | \ref{sec:freqalign}). |
---|
729 | |
---|
730 | \subsection{Baseline fitting} |
---|
731 | |
---|
732 | \index{Baseline fitting}To make a baseline fit, you must first create |
---|
733 | a mask of channels to use in the baseline fit. |
---|
734 | |
---|
735 | \begin{verbatim} |
---|
736 | ASAP> msk = scans.create_mask([100,400],[600,900]) |
---|
737 | ASAP> scans.poly_baseline(msk, order=1) |
---|
738 | \end{verbatim} |
---|
739 | |
---|
740 | This will fit a first order polynomial to the selected channels and subtract |
---|
741 | this polynomial from the full spectra. |
---|
742 | |
---|
743 | \subsubsection{Auto-baselining} |
---|
744 | |
---|
745 | \index{Auto-baseline}The function \cmd{auto\_poly\_baseline} can be used to automatically |
---|
746 | baseline your data without having to specify channel ranges for the |
---|
747 | line free data. It automatically figures out the line-free emission |
---|
748 | and fits a polynomial baseline to that data. The user can use masks to |
---|
749 | fix the range of channels or velocity range for the fit as well as |
---|
750 | mark the band edge as invalid. |
---|
751 | |
---|
752 | Simple example |
---|
753 | |
---|
754 | \begin{verbatim} |
---|
755 | ASAP> scans.auto_poly_baseline(order=2,threshold=5) |
---|
756 | \end{verbatim} |
---|
757 | |
---|
758 | \cmd{order} is the polynomial order for the fit. \cmd{threshold} is |
---|
759 | the SNR threshold to use to deliminate line emission from |
---|
760 | signal. Generally the value of threshold is not too critical, however |
---|
761 | making this too large will compromise the fit (as it will include |
---|
762 | strong line features) and making it too small will mean it cannot find |
---|
763 | enough line free channels. |
---|
764 | |
---|
765 | |
---|
766 | Other examples: |
---|
767 | |
---|
768 | \begin{verbatim} |
---|
769 | # Don't try and fit the edge of the bandpass which is noisier |
---|
770 | ASAP> scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3) |
---|
771 | |
---|
772 | # Only fit a given region around the line |
---|
773 | ASAP> scans.set_unit('km/s') |
---|
774 | ASAP> msk = scans.create_mask([-60,-20]) |
---|
775 | ASAP> scans.auto_poly_baseline(mask=msk,order=3,threshold=3) |
---|
776 | |
---|
777 | \end{verbatim} |
---|
778 | |
---|
779 | \subsection{Average the polarisations} |
---|
780 | |
---|
781 | \index{average\_pol}If you are just interested in the highest SNR for total intensity you |
---|
782 | will want to average the parallel polarisations together. |
---|
783 | |
---|
784 | \begin{verbatim} |
---|
785 | ASAP> scans.average_pol() |
---|
786 | \end{verbatim} |
---|
787 | |
---|
788 | \subsection{Calibration} |
---|
789 | |
---|
790 | \index{Calibration}For most uses, calibration happens transparently as the input data |
---|
791 | contains the Tsys measurements taken during observations. The nominal |
---|
792 | ``Tsys'' values may be in Kelvin or Jansky. The user may wish to |
---|
793 | supply a Tsys correction or apply gain-elevation and opacity |
---|
794 | corrections. |
---|
795 | |
---|
796 | \subsubsection{Brightness Units} |
---|
797 | |
---|
798 | \index{Brightness Units}RPFITS files do not contain any information as |
---|
799 | to whether the telescope calibration was in units of Kelvin or |
---|
800 | Janskys. On reading the data a default value is set depending on the |
---|
801 | telescope and frequency of observation. If this default is incorrect |
---|
802 | (you can see it in the listing from the \cmd{summary} function) the |
---|
803 | user can either override this value on reading the data or later. |
---|
804 | E.g: |
---|
805 | |
---|
806 | \begin{verbatim} |
---|
807 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf', unit='Jy') |
---|
808 | # Or in two steps |
---|
809 | ASAP> scans = scantable('2004-11-23_1841-P484.rpf') |
---|
810 | ASAP> scans.set_fluxunit('Jy) |
---|
811 | \end{verbatim} |
---|
812 | |
---|
813 | \subsubsection{Tsys scaling} |
---|
814 | |
---|
815 | \index{Tsys scaling}Sometime the nominal Tsys measurement at the |
---|
816 | telescope is wrong due to an incorrect noise diode calibration. This |
---|
817 | can easily be corrected for with the scale function. By default, |
---|
818 | \cmd{scale} only scans the spectra and not the corresponding Tsys. |
---|
819 | |
---|
820 | \begin{verbatim} |
---|
821 | ASAP> scans.scale(1.05, tsys=True) |
---|
822 | \end{verbatim} |
---|
823 | |
---|
824 | \subsubsection{Unit Conversion} |
---|
825 | |
---|
826 | \index{Unit conversion}To convert measurements in Kelvin to Jy (and |
---|
827 | vice versa) the global function \cmd{convert\_flux} is needed. This |
---|
828 | converts and scales the data from K to Jy or vice-versa depending on |
---|
829 | what the current brightness unit is set to. The function knows the |
---|
830 | basic parameters for some frequencies and telescopes, but the user may |
---|
831 | need to supply the aperture efficiency, telescope diameter or the Jy/K |
---|
832 | factor. |
---|
833 | |
---|
834 | \begin{verbatim} |
---|
835 | ASAP> scans.convert_flux() # If efficency known |
---|
836 | ASAP> scans.convert_flux(eta=0.48) # If telescope diameter known |
---|
837 | ASAP> scans.convert_flux(eta=0.48,d=35) # Unknown telescope |
---|
838 | ASAP> scans.convert_flux(jypk=15) # Alternative |
---|
839 | \end{verbatim} |
---|
840 | |
---|
841 | \subsubsection{Gain-Elevation and Opacity Corrections} |
---|
842 | \label{sec:gainel} |
---|
843 | |
---|
844 | \index{Gain-elevation}As higher frequencies (particularly $>$20~GHz) |
---|
845 | it is important to make corrections for atmospheric opacity and |
---|
846 | gain-elevation effects. |
---|
847 | |
---|
848 | Note that currently the elevation is not written correctly into |
---|
849 | Tidbinbilla rpfits files. This means that gain-elevation and opacity |
---|
850 | corrections will not work unless these get recalculated. |
---|
851 | |
---|
852 | \begin{verbatim} |
---|
853 | ASAP> scans.recalc_azel() # recalculate az/el based on pointing |
---|
854 | \end{verbatim} |
---|
855 | |
---|
856 | Gain-elevation curves for some telescopes and frequencies are known to |
---|
857 | ASAP (currently only for Tidbinbilla at 20~GHz). In these cases |
---|
858 | making gain-corrections is simple. If the gain curve for your data is |
---|
859 | not known, the user can supply either a gain polynomial or text file |
---|
860 | tabulating gain factors at a range of elevations (see \cmd{help |
---|
861 | scantable.gain\_el}). |
---|
862 | |
---|
863 | Examples: |
---|
864 | |
---|
865 | \begin{verbatim} |
---|
866 | ASAP> scans.gain_el() # If gain table known |
---|
867 | ASAP> scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) |
---|
868 | \end{verbatim} |
---|
869 | |
---|
870 | \index{Opacity}Opacity corrections can be made with the global |
---|
871 | function \cmd{opacity}. This should work on all telescopes as long as |
---|
872 | a measurement of the opacity factor was made during the observation. |
---|
873 | |
---|
874 | \begin{verbatim} |
---|
875 | ASAP> scans.opacity(0.083) |
---|
876 | \end{verbatim} |
---|
877 | |
---|
878 | Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, |
---|
879 | which takes opacity effects into account (to first order). ASAP |
---|
880 | opacity corrections should not be used for Mopra 3-mm data. |
---|
881 | |
---|
882 | \subsection{Frequency Frame Alignment} |
---|
883 | \label{sec:freqalign} |
---|
884 | |
---|
885 | \index{Frequency alignment}\index{Velicity alignment}When time |
---|
886 | averaging a series of scans together, it is possible that the velocity |
---|
887 | scales are not exactly aligned. This may be for many reasons such as |
---|
888 | not Doppler tracking the observations, errors in the Doppler tracking |
---|
889 | etc. This mostly affects very long integrations or integrations |
---|
890 | averaged together from different days. Before averaging such data |
---|
891 | together, they should be frequency aligned using \cmd{freq\_align}. |
---|
892 | |
---|
893 | E.g.: |
---|
894 | |
---|
895 | \begin{verbatim} |
---|
896 | ASAP> scans.freq_align() |
---|
897 | ASAP> av = average_time(scans) |
---|
898 | \end{verbatim} |
---|
899 | |
---|
900 | {\em A Global freq\_align command will be made eventually} |
---|
901 | |
---|
902 | To average together data taken on different days, which are in |
---|
903 | different scantables, each scantable must aligned to a common |
---|
904 | reference time then the scantables averaged. The simplest way of |
---|
905 | doing this is to allow ASAP to choose the reference time for the first |
---|
906 | scantable then using this time for the subsequent scantables. |
---|
907 | |
---|
908 | \begin{verbatim} |
---|
909 | ASAP> scans1.freq_align() # Copy the refeference Epoch from the output |
---|
910 | ASAP> scans2.freq_align(reftime='2004/11/23/18:43:35') |
---|
911 | ASAP> scans3.freq_align(reftime='2004/11/23/18:43:35') |
---|
912 | ASAP> av = average_time(scans1, scans2, scans3) |
---|
913 | \end{verbatim} |
---|
914 | |
---|
915 | \section{Scantable manipulation} |
---|
916 | |
---|
917 | \index{Scantable!manipulation}While it is very useful to have many |
---|
918 | independent sources within one scantable, it is often inconvenient for |
---|
919 | data processing. The \cmd{get\_scan} function can be used to create a |
---|
920 | new scantable with a selection of scans from a scantable. The |
---|
921 | selection can either be on the source name, with simple wildcard |
---|
922 | matching or set of scan ids. Internally this uses the selector object, |
---|
923 | so for more complicated selection the selector should be used directly |
---|
924 | instead. |
---|
925 | |
---|
926 | For example: |
---|
927 | |
---|
928 | \begin{verbatim} |
---|
929 | ASAP> ss = scans.get_scan(10) # Get the 11th scan (zero based) |
---|
930 | ASAP> ss = scans.get_scan(range(10)) # Get the first 10 scans |
---|
931 | ASAP> ss = scans.get_scan(range(10,20)) # Get the next 10 scans |
---|
932 | ASAP> ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans |
---|
933 | |
---|
934 | ASAP> ss = scans.get_scan('345p407') # Get a specific source |
---|
935 | ASAP> ss = scans.get_scan('345*') # Get a few sources |
---|
936 | |
---|
937 | ASAP> r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra) |
---|
938 | ASAP> s = scans.get_scan('*_S') # Get all program sources (Parkes/Mopra) |
---|
939 | ASAP> r = scans.get_scan('*[ew]') # Get all reference sources (Tid) |
---|
940 | ASAP> s = scans.get_scan('*[^ew]') # Get all program sources (Tid) |
---|
941 | |
---|
942 | \end{verbatim} |
---|
943 | |
---|
944 | To copy a scantable the following does not work: |
---|
945 | |
---|
946 | \begin{verbatim} |
---|
947 | ASAP> ss = scans |
---|
948 | \end{verbatim} |
---|
949 | |
---|
950 | as this just creates a reference to the original scantable. Any |
---|
951 | changes made to \cmd{ss} are also seen in \cmd{scans}. To duplicate a |
---|
952 | scantable, use the copy function. |
---|
953 | |
---|
954 | \begin{verbatim} |
---|
955 | ASAP> ss = scans.copy() |
---|
956 | \end{verbatim} |
---|
957 | |
---|
958 | \section{Data Output} |
---|
959 | |
---|
960 | \index{Scantable!save}\index{Saving data}ASAP can save scantables in a |
---|
961 | variety of formats, suitable for reading into other packages. The |
---|
962 | formats are: |
---|
963 | |
---|
964 | \begin{itemize} |
---|
965 | \item[ASAP] This is the internal format used for ASAP. It is the only |
---|
966 | format that allows the user to restore the data, fits etc. without |
---|
967 | loosing any information. As mentioned before, the ASAP scantable is |
---|
968 | an AIPS++ Table (a memory-based table). This function just converts |
---|
969 | it to a disk-based Table. You can the access that Table with the |
---|
970 | AIPS++ Table browser or any other AIPS++ tool. |
---|
971 | |
---|
972 | \item[SDFITS] The Single Dish FITS format. This format was designed to |
---|
973 | for interchange between packages, but few packages actually can read |
---|
974 | it. |
---|
975 | |
---|
976 | %\item[FITS] This uses simple ``image'' fits to save the data, each row |
---|
977 | % being written to a separate fits file. This format is suitable for |
---|
978 | % importing the data into CLASS. |
---|
979 | |
---|
980 | \item[ASCII] A simple text based format suitable for the user to |
---|
981 | processing using Perl or, Python, gnuplot etc. |
---|
982 | |
---|
983 | \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. |
---|
984 | You can also access this with the Table browser and other AIPS++ |
---|
985 | tools. |
---|
986 | |
---|
987 | \end{itemize} |
---|
988 | |
---|
989 | The default output format can be set in the users {\tt .asaprc} file. |
---|
990 | Typical usages are: |
---|
991 | |
---|
992 | \begin{verbatim} |
---|
993 | ASAP> scans.save('myscans') # Save in default format |
---|
994 | ASAP> scans.save('myscans', 'FITS') # Save as FITS for exporting into CLASS |
---|
995 | ASAP> scans.save('myscans', overwrite=True) # Overwrite an existing file |
---|
996 | \end{verbatim} |
---|
997 | |
---|
998 | |
---|
999 | \section{Plotter} |
---|
1000 | |
---|
1001 | \index{Plotter}Scantable spectra can be plotted at any time. An asapplotter object is |
---|
1002 | used for plotting, meaning multiple plot windows can be active at the |
---|
1003 | same time. On start up a default asapplotter object is created called |
---|
1004 | ``plotter''. This would normally be used for standard plotting. |
---|
1005 | |
---|
1006 | The plotter, optionally, will run in a multipanel mode and contain |
---|
1007 | multiple plots per panel. The user must tell the plotter how they want |
---|
1008 | the data distributed. This is done using the set\_mode function. The |
---|
1009 | default can be set in the users {\tt .asaprc} file. The units (and frame |
---|
1010 | etc) of the abscissa will be whatever has previously been set by |
---|
1011 | \cmd{set\_unit}, \cmd{set\_freqframe} etc. |
---|
1012 | |
---|
1013 | Typical plotter usage would be: |
---|
1014 | |
---|
1015 | \begin{verbatim} |
---|
1016 | ASAP> scans.set_unit('km/s') |
---|
1017 | ASAP> plotter.set_mode(stacking='p',panelling='t') |
---|
1018 | ASAP> plotter.plot(scans) |
---|
1019 | \end{verbatim} |
---|
1020 | |
---|
1021 | This will plot multiple polarisation within each plot panel and each |
---|
1022 | scan row in a separate panel. |
---|
1023 | |
---|
1024 | Other possibilities include: |
---|
1025 | |
---|
1026 | \begin{verbatim} |
---|
1027 | # Plot multiple IFs per panel |
---|
1028 | ASAP> plotter.set_mode(stacking='i',panelling='t') |
---|
1029 | |
---|
1030 | # Plot multiple beams per panel |
---|
1031 | ASAP> plotter.set_mode(stacking='b',panelling='t') |
---|
1032 | |
---|
1033 | # Plot one IF per panel, time stacked |
---|
1034 | ASAP> plotter.set_mode('t', 'i') |
---|
1035 | |
---|
1036 | # Plot each scan in a seperate panel |
---|
1037 | ASAP> plotter.set_mode('t', 's') |
---|
1038 | |
---|
1039 | \end{verbatim} |
---|
1040 | |
---|
1041 | \subsection{Plot Selection} |
---|
1042 | \label{sec:plotter_cursor} |
---|
1043 | |
---|
1044 | \index{Plotter!selection}The plotter can plot up to 25 panels and |
---|
1045 | stacked spectra per panel. If you have data larger than this (or for |
---|
1046 | your own sanity) you need to select a subset of this data. This is |
---|
1047 | particularly true for multibeam or multi IF data. The selector object |
---|
1048 | should be used for this purpose. Selection can either be applied to |
---|
1049 | the scantable or directly to the plotter, the end result is the same. |
---|
1050 | You don't have to reset the scantable slection though, if you set |
---|
1051 | the selection on the plotter. |
---|
1052 | |
---|
1053 | Examples: |
---|
1054 | |
---|
1055 | \begin{verbatim} |
---|
1056 | ASAP> selection = selector() |
---|
1057 | # Select second IF |
---|
1058 | ASAP> selection.set_ifs(1) |
---|
1059 | ASAP> plotter.set_selection(selection) |
---|
1060 | |
---|
1061 | # Select first 4 beams |
---|
1062 | ASAP> selection.set_beams([0,1,2,3]) |
---|
1063 | ASAP> plotter.set_selection(selection) |
---|
1064 | |
---|
1065 | # Select a few scans |
---|
1066 | ASAP> selection.set_scans([2,4,6,10]) |
---|
1067 | ASAP> plotter.set_selection(selection) |
---|
1068 | |
---|
1069 | # Multiple selection |
---|
1070 | ASAP> selection.set_ifs(1) |
---|
1071 | ASAP> selection.set_scans([2,4,6,10]) |
---|
1072 | ASAP> plotter.set_selection(selection) |
---|
1073 | |
---|
1074 | \end{verbatim} |
---|
1075 | |
---|
1076 | \subsection{Plot Control} |
---|
1077 | |
---|
1078 | \index{Plotter!control}The plotter window has a row of buttons on the |
---|
1079 | lower left. These can be used to control the plotter (mostly for |
---|
1080 | zooming the individual plots). From left to right: |
---|
1081 | |
---|
1082 | \begin{itemize} |
---|
1083 | |
---|
1084 | \item[Home] This will unzoom the plots to the original zoom factor |
---|
1085 | |
---|
1086 | \item[Plot history] (left and right arrow). The plotter keeps a |
---|
1087 | history of zoom settings. The left arrow sets the plot zoom to the |
---|
1088 | previous value. The right arrow returns back again. This allows you, |
---|
1089 | for example, to zoom in on one feature then return the plot to how it |
---|
1090 | was previously. |
---|
1091 | |
---|
1092 | \item[Pan] (The Cross) This sets the cursor to pan, or scroll mode |
---|
1093 | allowing you to shift the plot within the window. Useful when |
---|
1094 | zoomed in on a feature. |
---|
1095 | |
---|
1096 | \item[Zoom] (the letter with the magnifying glass) lets you draw a |
---|
1097 | rectangle around a region of interest then zooms in on that |
---|
1098 | region. Use the plot history to unzoom again. |
---|
1099 | |
---|
1100 | \item[Adjust] (rectangle with 4 arrows) adjust subplot paramaters |
---|
1101 | (space at edge of plots) |
---|
1102 | |
---|
1103 | \item[Save] (floppy disk). Save the plot as a postscript or .png file |
---|
1104 | |
---|
1105 | You can also type ``g'' in the plot window to toggle on and off grid |
---|
1106 | lines. Typing 'l' turns on and off logarithmic Y-axis. |
---|
1107 | |
---|
1108 | \end{itemize} |
---|
1109 | |
---|
1110 | \subsection{Other control} |
---|
1111 | |
---|
1112 | The plotter has a number of functions to describe the layout of the |
---|
1113 | plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. |
---|
1114 | |
---|
1115 | To set the exact velocity or channel range to be plotted use the |
---|
1116 | \cmd{set\_range} function. To reset to the default value, call |
---|
1117 | \cmd{set\_range} with no arguments. E.g. |
---|
1118 | |
---|
1119 | \begin{verbatim} |
---|
1120 | ASAP> scans.set_unit('km/s') |
---|
1121 | ASAP> plotter.plot(scans) |
---|
1122 | ASAP> plotter.set_range(-150,-50) |
---|
1123 | ASAP> plotter.set_range() # To reset |
---|
1124 | \end{verbatim} |
---|
1125 | |
---|
1126 | Both the range of the ``x'' and ``y'' axis can be set at once, if desired: |
---|
1127 | |
---|
1128 | \begin{verbatim} |
---|
1129 | ASAP> plotter.set_range(-10,30,-1,6.6) |
---|
1130 | \end{verbatim} |
---|
1131 | |
---|
1132 | To save a hardcopy of the current plot, use the save function, e.g. |
---|
1133 | |
---|
1134 | \begin{verbatim} |
---|
1135 | ASAP> plotter.save('myplot.ps') |
---|
1136 | ASAP> plotter.save('myplot.png', dpi=80) |
---|
1137 | \end{verbatim} |
---|
1138 | |
---|
1139 | \section{Fitting} |
---|
1140 | |
---|
1141 | \index{Fitting}Currently multicomponent Gaussian function is |
---|
1142 | available. This is done by creating a fitting object, setting up the |
---|
1143 | fit and actually fitting the data. Fitting can either be done on a |
---|
1144 | single scantable selection or on an entire scantable using the |
---|
1145 | \cmd{auto\_fit} function. If single value fitting is used, and the |
---|
1146 | current selection includes multiple spectra (beams, IFs, scans etc) |
---|
1147 | then the first spectrum in the scantable will be used for fitting. |
---|
1148 | |
---|
1149 | \begin{verbatim} |
---|
1150 | ASAP> f = fitter() |
---|
1151 | ASAP> f.set_function(gauss=2) # Fit two Gaussians |
---|
1152 | ASAP> f.set_scan(scans) |
---|
1153 | ASAP> selection = selector() |
---|
1154 | ASAP> selection.set_polarisations(1) # Fit the second polarisation |
---|
1155 | ASAP> scans.set_selection(selection) |
---|
1156 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
---|
1157 | ASAP> f.fit(1) # Run the fit on the second row in the table |
---|
1158 | ASAP> f.plot() # Show fit in a plot window |
---|
1159 | ASAP> f.get_parameters() # Return the fit paramaters |
---|
1160 | \end{verbatim} |
---|
1161 | |
---|
1162 | This auto-guesses the initial values of the fit and works well for data |
---|
1163 | without extra confusing features. Note that the fit is performed in |
---|
1164 | whatever unit the abscissa is set to. |
---|
1165 | |
---|
1166 | If you want to confine the fitting to a smaller range (e.g. to avoid |
---|
1167 | band edge effects or RFI you must set a mask. |
---|
1168 | |
---|
1169 | \begin{verbatim} |
---|
1170 | ASAP> f = fitter() |
---|
1171 | ASAP> f.set_function(gauss=2) |
---|
1172 | ASAP> scans.set_unit('km/s') # Set the mask in channel units |
---|
1173 | ASAP> msk = s.create_mask([1800,2200]) |
---|
1174 | ASAP> scans.set_unit('km/s') # Make fit in velocity units |
---|
1175 | ASAP> f.set_scan(s,msk) |
---|
1176 | ASAP> f.fit() |
---|
1177 | ASAP> f.plot() |
---|
1178 | ASAP> f.get_parameters() |
---|
1179 | \end{verbatim} |
---|
1180 | |
---|
1181 | If you wish, the initial parameter guesses can be specified and |
---|
1182 | specific parameters can be fixed: |
---|
1183 | |
---|
1184 | \begin{verbatim} |
---|
1185 | ASAP> f = fitter() |
---|
1186 | ASAP> f.set_function(gauss=2) |
---|
1187 | ASAP> f.set_scan(s,msk) |
---|
1188 | ASAP> f.fit() # Fit using auto-estimates |
---|
1189 | # Set Peak, centre and fwhm for the second gaussian. |
---|
1190 | # Force the centre to be fixed |
---|
1191 | ASAP> f.set_gauss_parameters(0.4,450,150,0,1,0,component=1) |
---|
1192 | ASAP> f.fit() # Re-run the fit |
---|
1193 | \end{verbatim} |
---|
1194 | |
---|
1195 | The fitter \cmd{plot} function has a number of options to either view |
---|
1196 | the fit residuals or the individual components (by default it plots |
---|
1197 | the sum of the model components). |
---|
1198 | |
---|
1199 | Examples: |
---|
1200 | |
---|
1201 | \begin{verbatim} |
---|
1202 | # Plot the residual |
---|
1203 | ASAP> f.plot(residual=True) |
---|
1204 | |
---|
1205 | # Plot the first 2 componentsa |
---|
1206 | ASAP> f.plot(components=[0,1]) |
---|
1207 | |
---|
1208 | # Plot the first and third component plus the model sum |
---|
1209 | ASAP> f.plot(components=[-1,0,2]) # -1 means the compoment sum |
---|
1210 | \end{verbatim} |
---|
1211 | |
---|
1212 | \subsection{Fit saving} |
---|
1213 | |
---|
1214 | \index{Fitter!Fit saving}One you are happy with your fit, it is |
---|
1215 | possible to store it as part of the scantable. |
---|
1216 | |
---|
1217 | \begin{verbatim} |
---|
1218 | ASAP> f.storefit() |
---|
1219 | \end{verbatim} |
---|
1220 | |
---|
1221 | This will be saved to disk with the data, if the ``ASAP'' file format |
---|
1222 | is selected. Multiple fits to the same data can be stored in the |
---|
1223 | scantable. |
---|
1224 | |
---|
1225 | The scantable function \cmd{get\_fit} can be used to retrieve the |
---|
1226 | stored fits. Currently the fit parameters are just printed to the |
---|
1227 | screen. |
---|
1228 | |
---|
1229 | \begin{verbatim} |
---|
1230 | ASAP> scans.get_fit(4) # Print fits for row 4 |
---|
1231 | \end{verbatim} |
---|
1232 | |
---|
1233 | \section{Polarisation} |
---|
1234 | |
---|
1235 | \index{Polarisation}Currently ASAP only supports polarmetric analysis |
---|
1236 | on linearly polarised feeds and the cross polarisation products |
---|
1237 | measured. Other cases will be added on an as needed basis. |
---|
1238 | |
---|
1239 | Conversions of linears to Stokes or Circular polarisations are done |
---|
1240 | ``on-the-fly''. Leakage cannot be corrected for nor are there routines |
---|
1241 | to calibrate position angle offsets. |
---|
1242 | |
---|
1243 | \subsection{Simple Calibration} |
---|
1244 | |
---|
1245 | \index{Polarisation!calibration}It is possible that there is a phase |
---|
1246 | offset between polarisation which will effect the phase of the cross |
---|
1247 | polarisation correlation, and so give rise to spurious |
---|
1248 | polarisation. \cmd{rotate\_xyphase} can be used to correct for this |
---|
1249 | error. At this point, the user must know how to determine the size of |
---|
1250 | the phase offset themselves. |
---|
1251 | |
---|
1252 | \begin{verbatim} |
---|
1253 | ASAP> scans.rotate_xyphase(10.5) # Degrees |
---|
1254 | \end{verbatim} |
---|
1255 | |
---|
1256 | Note that if this function is run twice, the sum of the two values is |
---|
1257 | applied because it is done in-situ. |
---|
1258 | |
---|
1259 | A correction for the receiver parallactic angle may need to be made, |
---|
1260 | generally because of how it is mounted. Use \cmd{rotate\_linpolphase} |
---|
1261 | to correct the position angle. Running this function twice results in |
---|
1262 | the sum of the corrections being applied because it is applied |
---|
1263 | in-situ. |
---|
1264 | |
---|
1265 | \begin{verbatim} |
---|
1266 | ASAP> scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting |
---|
1267 | \end{verbatim} |
---|
1268 | |
---|
1269 | If the sign of the complex correlation is wrong (this can happen |
---|
1270 | depending on the correlator configuration), use \cmd{invert\_phase} to |
---|
1271 | change take the complex conjugate of the complex correlation |
---|
1272 | term. This is always performed in-situ. |
---|
1273 | |
---|
1274 | \begin{verbatim} |
---|
1275 | ASAP> scans.invert_phase() |
---|
1276 | \end{verbatim} |
---|
1277 | |
---|
1278 | Depending on how the correlator is configured, ``BA'' may be |
---|
1279 | correlated insead of ``AB''. Use \cmd{swap\_linears} to correct for |
---|
1280 | this problem: |
---|
1281 | |
---|
1282 | \begin{verbatim} |
---|
1283 | ASAP> scans.swap_linears() |
---|
1284 | \end{verbatim} |
---|
1285 | |
---|
1286 | \subsection{Conversion} |
---|
1287 | \label{sec:polconv} |
---|
1288 | |
---|
1289 | Data can be permanently converted between linear and circular |
---|
1290 | polarisations and stokes. |
---|
1291 | |
---|
1292 | \begin{verbatim} |
---|
1293 | ASAP> stokescans = linearscans.convert_pol("stokes") |
---|
1294 | \end{verbatim} |
---|
1295 | |
---|
1296 | |
---|
1297 | \subsection{Plotting} |
---|
1298 | \label{sec:polplot} |
---|
1299 | |
---|
1300 | \index{Polarisation!plotting}To plot Stokes values, a selector object |
---|
1301 | must be created and the set\_polarisation function used to select the |
---|
1302 | desired polarisation products. |
---|
1303 | |
---|
1304 | The values which can be plotted include a selection of [I,Q,U,V], [I, |
---|
1305 | Plinear, Pangle, V], [RR, LL] or [XX, YY, Real(XY), |
---|
1306 | Imaginary(XY)]. (Plinear and Pangle are the percentage and position |
---|
1307 | angle of linear polarisation). |
---|
1308 | |
---|
1309 | Example: |
---|
1310 | |
---|
1311 | \begin{verbatim} |
---|
1312 | ASAP> selection = selector() |
---|
1313 | |
---|
1314 | ASAP> selection.set_polarisations(``I Q U V'') |
---|
1315 | ASAP plotter.set_selection(selection); # Select I, Q, U \& V |
---|
1316 | |
---|
1317 | ASAP> selection.set_polarisations(``I Q'') |
---|
1318 | ASAP plotter.set_selection(selection); # Select just I \& Q |
---|
1319 | |
---|
1320 | ASAP> selection.set_polarisations(``RR LL'') |
---|
1321 | ASAP plotter.set_selection(selection); # Select just RR \& LL |
---|
1322 | |
---|
1323 | ASAP> selection.set_polarisations(``XX YY'') |
---|
1324 | ASAP plotter.set_selection(selection); # Select linears |
---|
1325 | |
---|
1326 | ASAP> selection.set_polarisations(``I Plinear'') |
---|
1327 | ASAP plotter.set_selection(selection); # Fractional linear |
---|
1328 | |
---|
1329 | ASAP> selection.set_polarisations(``Pangle'') |
---|
1330 | ASAP plotter.set_selection(selection); # Position angle |
---|
1331 | |
---|
1332 | \end{verbatim} |
---|
1333 | |
---|
1334 | Scan, beam and IF selection are also available in the selector object as |
---|
1335 | describe in section~\ref{sec:selection}. |
---|
1336 | |
---|
1337 | \subsection{Saving} |
---|
1338 | |
---|
1339 | \index{Polarisation!saving}When saving data using the \cmd{save} |
---|
1340 | function, the \cmd{stokes} argument can be used to save the data as |
---|
1341 | Stoke values when saving in FITS format. |
---|
1342 | |
---|
1343 | Example: |
---|
1344 | |
---|
1345 | \begin{verbatim} |
---|
1346 | ASAP> scans.save('myscan.sdfits', 'SDFITS', stokes=True) |
---|
1347 | \end{verbatim} |
---|
1348 | |
---|
1349 | \section{Scantable Mathematics} |
---|
1350 | |
---|
1351 | \index{Scantable!maths}It is possible to to simple mathematics |
---|
1352 | directly on scantables from the command line using the \cmd{+, -, *, |
---|
1353 | /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works |
---|
1354 | between a scantable and a float. (Note that it does |
---|
1355 | not work for integers). |
---|
1356 | |
---|
1357 | {\em Currently mathematics between two scantables is not available } |
---|
1358 | |
---|
1359 | % ASAP> sum = scan1+scan2 |
---|
1360 | \begin{verbatim} |
---|
1361 | ASAP> scan2 = scan1+2.0 |
---|
1362 | ASAP> scan *= 1.05 |
---|
1363 | \end{verbatim} |
---|
1364 | |
---|
1365 | \section{Scripting} |
---|
1366 | |
---|
1367 | \index{Scripting}Because asap is based on python, it easy for the user |
---|
1368 | write their own scripts and functions to process data. This is highly |
---|
1369 | recommended as most processing of user data could then be done in a |
---|
1370 | couple of steps using a few simple user defined functions. A Python |
---|
1371 | primer is beyond the scope of this userguide. See the asap home pages |
---|
1372 | for a scripting tutorial or the main python website for comprehensive |
---|
1373 | documentation. |
---|
1374 | |
---|
1375 | \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials |
---|
1376 | |
---|
1377 | \hspace{1cm} http://www.python.org/doc/Introduction.html |
---|
1378 | |
---|
1379 | \subsection{Running scripts} |
---|
1380 | |
---|
1381 | The asap global function \cmd{execfile} reads the named text file and |
---|
1382 | executes the contained python code. This file can either contain |
---|
1383 | function definitions which will be used in subsequent processing or |
---|
1384 | just a set of commands to process a specific dataset. |
---|
1385 | |
---|
1386 | \subsection{asapuserfuncs.py} |
---|
1387 | |
---|
1388 | The file $\sim$/.asap/asapuserfuncs.py is automatically read in when |
---|
1389 | asap is started. The user can use this to define a set of user |
---|
1390 | functions which are automatically available each time asap is |
---|
1391 | used. The \cmd{execfile} function can be called from within this file. |
---|
1392 | |
---|
1393 | \section{Worked examples} |
---|
1394 | |
---|
1395 | In the following section a few examples of end-to-end processing of |
---|
1396 | some data in asap are given. |
---|
1397 | |
---|
1398 | \subsection{Mopra} |
---|
1399 | \index{Mopra} |
---|
1400 | |
---|
1401 | The following example is of some dual polarisation, position switched |
---|
1402 | data from Mopra. The source has been observed mulitple times split |
---|
1403 | into a number of seperate rpfits files. To make the processing easier, |
---|
1404 | the first step is to \cmd{cat} the seeprate rpfits files together and |
---|
1405 | load as a whole (future versions of asap will make this unnecessary). |
---|
1406 | |
---|
1407 | |
---|
1408 | \begin{verbatim} |
---|
1409 | # get a list of the individual rpfits files in the current directory |
---|
1410 | myfiles = list_files() |
---|
1411 | |
---|
1412 | # Load the data into a scantable |
---|
1413 | data = scantable(myfiles) |
---|
1414 | print data |
---|
1415 | |
---|
1416 | # Form the quotient spectra |
---|
1417 | q = data.auto_quotient() |
---|
1418 | print q |
---|
1419 | |
---|
1420 | # Look at the spectra |
---|
1421 | plotter.plot(q) |
---|
1422 | |
---|
1423 | # Set unit and reference frame |
---|
1424 | q.set_unit('km/s') |
---|
1425 | q.set_freqframe('LSRK') |
---|
1426 | |
---|
1427 | # Average all scans in time, aligning in velocity |
---|
1428 | av = q.average_time(align=True) |
---|
1429 | plotter.plot(av) |
---|
1430 | |
---|
1431 | # Remove the baseline |
---|
1432 | msk = av.create_mask([100,130],[160,200]) |
---|
1433 | av.poly_baseline(msk,2) |
---|
1434 | |
---|
1435 | # Average the two polarisations together |
---|
1436 | iav = av.average_pol() |
---|
1437 | print iav |
---|
1438 | plotter.plot(iav) |
---|
1439 | |
---|
1440 | # Set a sensible velocity range on the plot |
---|
1441 | plotter.set_range(85,200) |
---|
1442 | |
---|
1443 | # Smooth the data a little |
---|
1444 | av.smooth('gauss',4) |
---|
1445 | plotter.plot() |
---|
1446 | |
---|
1447 | # Fit a guassian to the emission |
---|
1448 | f = fitter() |
---|
1449 | f.set_function(gauss=1) |
---|
1450 | f.set_scan(av) |
---|
1451 | f.fit() |
---|
1452 | |
---|
1453 | # View the fit |
---|
1454 | f.plot() |
---|
1455 | |
---|
1456 | # Get the fit parameters |
---|
1457 | f.get_parameters() |
---|
1458 | |
---|
1459 | \end{verbatim} |
---|
1460 | |
---|
1461 | |
---|
1462 | \subsection{Parkes Polarimetry} |
---|
1463 | |
---|
1464 | \index{Parkes}\index{Polarisation}The following example is processing |
---|
1465 | of some Parkes polarmetric observations of OH masers at |
---|
1466 | 1.6~GHz. Because digital filters where used in the backend, the |
---|
1467 | baselines are stable enough not to require a quotient spectra. The |
---|
1468 | 4~MHz bandwidth is wide enough to observe both the 1665 and 1667~MHz |
---|
1469 | OH maser transitions. Each source was observed once for about 10 |
---|
1470 | minutes. Tsys information was not written to the rpfits file (a |
---|
1471 | nominal 25K values was used), so the amplitudes need to be adjusted |
---|
1472 | based on a separate log file. A simple user function is used to |
---|
1473 | simplify this, contained in a file called mypol.py: |
---|
1474 | |
---|
1475 | \begin{verbatim} |
---|
1476 | def xyscale(data,xtsys=1.0,ytsys=1.0,nomtsys=25.0) : |
---|
1477 | |
---|
1478 | selection = selector() |
---|
1479 | selection.set_polarisations(0) |
---|
1480 | data.set_selection(selection) |
---|
1481 | data.scale(xtsys/nomtsys) |
---|
1482 | |
---|
1483 | selection.set_polarisations(1) |
---|
1484 | data.set_selection(selection) |
---|
1485 | data.scale(ytsys/nomtsys) |
---|
1486 | |
---|
1487 | selection.set_polarisations(0) |
---|
1488 | data.set_selection(selection) |
---|
1489 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
1490 | |
---|
1491 | selection.set_polarisations(0) |
---|
1492 | data.set_selection(selection) |
---|
1493 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
1494 | \end{verbatim} |
---|
1495 | |
---|
1496 | The typical asap session would be |
---|
1497 | |
---|
1498 | \begin{verbatim} |
---|
1499 | |
---|
1500 | # Remind ourself the name of the rpfits files |
---|
1501 | ls |
---|
1502 | |
---|
1503 | # Load data from an rpfits file |
---|
1504 | d1665 = scantable('2005-10-27_0154-P484.rpf') |
---|
1505 | |
---|
1506 | # Check what we have just loaded |
---|
1507 | d1665.summary() |
---|
1508 | |
---|
1509 | # View the data in velocity |
---|
1510 | d1665.set_unit('km/s') |
---|
1511 | d1665.set_freqframe('LSRK') |
---|
1512 | |
---|
1513 | # Correct for the known phase offset in the crosspol data |
---|
1514 | d1665.rotate_xyphase(-4) |
---|
1515 | |
---|
1516 | # Create a copy of the data and set the rest frequency to the 1667 MHz |
---|
1517 | # transition |
---|
1518 | d1667 = d1665.copy() |
---|
1519 | d1667.set_restfreqs([1667.3590], 'MHz') |
---|
1520 | d1667.summary() |
---|
1521 | |
---|
1522 | # Copy out the scan we wish to process |
---|
1523 | g351_5 = d1665.get_scan('351p160') |
---|
1524 | g351_7 = d1667.get_scan('351p160') |
---|
1525 | |
---|
1526 | # Baseline both |
---|
1527 | msk = g351_5.create_mask([-30,-25],[-5,0]) |
---|
1528 | g351_5.poly_baseline(msk,order=1) |
---|
1529 | msk = g351_7.create_mask([-30,-25],[-5,0]) |
---|
1530 | g351_7.poly_baseline(msk,order=1) |
---|
1531 | |
---|
1532 | |
---|
1533 | # Plot the data. The plotter can only plot a single scantable |
---|
1534 | # So we must merge the two tables first |
---|
1535 | |
---|
1536 | plotscans = merge(g351_5, g351_7) |
---|
1537 | |
---|
1538 | plotter.plot(plotscans) # Only shows one panel |
---|
1539 | |
---|
1540 | # Tell the plotter to stack polarisation and panel scans |
---|
1541 | plotter.set_mode('p','s') |
---|
1542 | |
---|
1543 | # Correct for the Tsys using our predefined function |
---|
1544 | execfile('mypol.py') # Read in the function xyscale |
---|
1545 | xyscale(g351_5,23.2,22.7) # Execute it on the data |
---|
1546 | xyscale(g351_7,23.2,22.7) |
---|
1547 | |
---|
1548 | # Only plot the velocity range of interest |
---|
1549 | plotter.set_range(-30,10) |
---|
1550 | |
---|
1551 | # Update the plot with the baselined data |
---|
1552 | plotter.plot() |
---|
1553 | |
---|
1554 | # Look at the various polarisation products |
---|
1555 | selection = selector() |
---|
1556 | selection.set_polarisations(``RR LL'') |
---|
1557 | plotter.set_selection(selection) |
---|
1558 | selection.set_polarisations(``I Plinear'') |
---|
1559 | plotter.set_selection(selection) |
---|
1560 | selection.set_polarisations(``I Q U V'') |
---|
1561 | plotter.set_selection(selection) |
---|
1562 | |
---|
1563 | # Save the plot as postscript |
---|
1564 | plotter.save('g351_stokes.ps') |
---|
1565 | |
---|
1566 | # Save the process spectra |
---|
1567 | plotscans.save('g351.asap') |
---|
1568 | |
---|
1569 | \end{verbatim} |
---|
1570 | |
---|
1571 | \subsection{Tidbinbilla} |
---|
1572 | |
---|
1573 | \index{Tidbinbilla}The following example is processing of some |
---|
1574 | Tidbinbilla observations of NH$_3$ at 12~mm. Tidbinbilla has (at the |
---|
1575 | time of observations) a single polarisation, but can process two IFs |
---|
1576 | simultaneously. In the example, the first half of the observation was |
---|
1577 | observing the (1,1) and (2,2) transitions simultaneously). The second |
---|
1578 | half observed only the (4,4) transition due to bandwidth |
---|
1579 | limitations. The data is position switched, observing first an |
---|
1580 | reference to the west, then the source twice and finally reference to |
---|
1581 | the east. |
---|
1582 | |
---|
1583 | \begin{verbatim} |
---|
1584 | |
---|
1585 | # Load the rpfits file and inspect |
---|
1586 | d = scantable('2003-03-16_082048_t0002.rpf') |
---|
1587 | print d |
---|
1588 | |
---|
1589 | # Make the quotient spectra |
---|
1590 | q = d.auto_quotient() |
---|
1591 | print q |
---|
1592 | |
---|
1593 | del d |
---|
1594 | |
---|
1595 | # Plot/select in velocity |
---|
1596 | q.set_freqframe('LSRK') |
---|
1597 | q.set_unit('km/s') |
---|
1598 | |
---|
1599 | # Correct for gain/el effects |
---|
1600 | |
---|
1601 | q.recalc_azel() # Tid does not write the elevation |
---|
1602 | q.gain_el() |
---|
1603 | q.opacity(0.05) |
---|
1604 | |
---|
1605 | # Seperate data from the (1,1)&(2,2) and (4,4) transitions |
---|
1606 | g1 = q.get_scan(range(6)) # scans 0..5 |
---|
1607 | g2 = q.get_scan(range(6,12)) # scans 6..11 |
---|
1608 | |
---|
1609 | # Align data in velocity |
---|
1610 | g1.freq_align() |
---|
1611 | g2.freq_align() |
---|
1612 | |
---|
1613 | # Average individual scans |
---|
1614 | a1 = g1.average_time() |
---|
1615 | a2 = g2.average_time() |
---|
1616 | |
---|
1617 | # Rpfits file only contains a single rest frequency. Set both |
---|
1618 | a1.set_restfreqs([23694.4700e6,23722.6336e6]) |
---|
1619 | |
---|
1620 | plotter.plot(a1) |
---|
1621 | plotter.set_mode('i','t') |
---|
1622 | |
---|
1623 | a1.auto_poly_baseline() |
---|
1624 | |
---|
1625 | plotter.plot() |
---|
1626 | |
---|
1627 | a1.smooth('gauss',5) |
---|
1628 | plotter.plot() |
---|
1629 | |
---|
1630 | |
---|
1631 | \end{verbatim} |
---|
1632 | |
---|
1633 | \newpage |
---|
1634 | |
---|
1635 | \section{Appendix} |
---|
1636 | |
---|
1637 | \subsection{Function Summary} |
---|
1638 | |
---|
1639 | \index{Functions!summary}% |
---|
1640 | \begin{verbatim} |
---|
1641 | ASAP> commands() |
---|
1642 | [The scan container] |
---|
1643 | scantable - a container for integrations/scans |
---|
1644 | (can open asap/rpfits/sdfits and ms files) |
---|
1645 | copy - returns a copy of a scan |
---|
1646 | get_scan - gets a specific scan out of a scantable |
---|
1647 | (by name or number) |
---|
1648 | set_selection - set a new subselection of the data |
---|
1649 | get_selection - get the current selection object |
---|
1650 | summary - print info about the scantable contents |
---|
1651 | stats - get specified statistic of the spectra in |
---|
1652 | the scantable |
---|
1653 | stddev - get the standard deviation of the spectra |
---|
1654 | in the scantable |
---|
1655 | get_tsys - get the TSys |
---|
1656 | get_time - get the timestamps of the integrations |
---|
1657 | get_sourcename - get the source names of the scans |
---|
1658 | get_azimuth - get the azimuth of the scans |
---|
1659 | get_elevation - get the elevation of the scans |
---|
1660 | get_parangle - get the parallactic angle of the scans |
---|
1661 | get_unit - get the current unit |
---|
1662 | set_unit - set the abcissa unit to be used from this |
---|
1663 | point on |
---|
1664 | get_abcissa - get the abcissa values and name for a given |
---|
1665 | row (time) |
---|
1666 | set_freqframe - set the frame info for the Spectral Axis |
---|
1667 | (e.g. 'LSRK') |
---|
1668 | set_doppler - set the doppler to be used from this point on |
---|
1669 | set_dirframe - set the frame for the direction on the sky |
---|
1670 | set_instrument - set the instrument name |
---|
1671 | get_fluxunit - get the brightness flux unit |
---|
1672 | set_fluxunit - set the brightness flux unit |
---|
1673 | create_mask - return an mask in the current unit |
---|
1674 | for the given region. The specified regions |
---|
1675 | are NOT masked |
---|
1676 | get_restfreqs - get the current list of rest frequencies |
---|
1677 | set_restfreqs - set a list of rest frequencies |
---|
1678 | flag_spectrum - flag data |
---|
1679 | save - save the scantable to disk as either 'ASAP' |
---|
1680 | or 'SDFITS' |
---|
1681 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
1682 | nscan - the number of scans in the scantable |
---|
1683 | nrow - te number of spectra in the scantable |
---|
1684 | history - print the history of the scantable |
---|
1685 | get_fit - get a fit which has been stored witnh the data |
---|
1686 | average_time - return the (weighted) time average of a scan |
---|
1687 | or a list of scans |
---|
1688 | average_pol - average the polarisations together. |
---|
1689 | The dimension won't be reduced and |
---|
1690 | all polarisations will contain the |
---|
1691 | averaged spectrum. |
---|
1692 | convert_pol - convert to a different polarisation type |
---|
1693 | auto_quotient - return the on/off quotient with |
---|
1694 | automatic detection of the on/off scans |
---|
1695 | (matched pairs and 1 off - n on) |
---|
1696 | scale - return a scan scaled by a given factor |
---|
1697 | add - return a scan with given value added |
---|
1698 | bin - return a scan with binned channels |
---|
1699 | resample - return a scan with resampled channels |
---|
1700 | smooth - return the spectrally smoothed scan |
---|
1701 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
1702 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
1703 | recalc_azel - recalculate azimuth and elevation based on |
---|
1704 | the pointing |
---|
1705 | gain_el - apply gain-elevation correction |
---|
1706 | opacity - apply opacity correction |
---|
1707 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
1708 | units |
---|
1709 | freq_align - align spectra in frequency frame |
---|
1710 | rotate_xyphase - rotate XY phase of cross correlation |
---|
1711 | rotate_linpolphase - rotate the phase of the complex |
---|
1712 | polarization O=Q+iU correlation |
---|
1713 | freq_switch - perform frequency switching on the data |
---|
1714 | stats - Determine the specified statistic, e.g. 'min' |
---|
1715 | 'max', 'rms' etc. |
---|
1716 | stddev - Determine the standard deviation of the current |
---|
1717 | beam/if/pol |
---|
1718 | |
---|
1719 | [Math] Mainly functions which operate on more than one scantable |
---|
1720 | |
---|
1721 | average_time - return the (weighted) time average |
---|
1722 | of a list of scans |
---|
1723 | quotient - return the on/off quotient |
---|
1724 | simple_math - simple mathematical operations on two scantables, |
---|
1725 | 'add', 'sub', 'mul', 'div' |
---|
1726 | [Fitting] |
---|
1727 | fitter |
---|
1728 | auto_fit - return a scan where the function is |
---|
1729 | applied to all Beams/IFs/Pols. |
---|
1730 | commit - return a new scan where the fits have been |
---|
1731 | commited. |
---|
1732 | fit - execute the actual fitting process |
---|
1733 | store_fit - store the fit parameters in the data (scantable) |
---|
1734 | get_chi2 - get the Chi^2 |
---|
1735 | set_scan - set the scantable to be fit |
---|
1736 | set_function - set the fitting function |
---|
1737 | set_parameters - set the parameters for the function(s), and |
---|
1738 | set if they should be held fixed during fitting |
---|
1739 | set_gauss_parameters - same as above but specialised for individual |
---|
1740 | gaussian components |
---|
1741 | get_parameters - get the fitted parameters |
---|
1742 | plot - plot the resulting fit and/or components and |
---|
1743 | residual |
---|
1744 | [Plotter] |
---|
1745 | asapplotter - a plotter for asap, default plotter is |
---|
1746 | called 'plotter' |
---|
1747 | plot - plot a scantable |
---|
1748 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
1749 | set_mode - set the state of the plotter, i.e. |
---|
1750 | what is to be plotted 'colour stacked' |
---|
1751 | and what 'panelled' |
---|
1752 | set_selection - only plot a selected part of the data |
---|
1753 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
---|
1754 | set_legend - specify user labels for the legend indeces |
---|
1755 | set_title - specify user labels for the panel indeces |
---|
1756 | set_abcissa - specify a user label for the abcissa |
---|
1757 | set_ordinate - specify a user label for the ordinate |
---|
1758 | set_layout - specify the multi-panel layout (rows,cols) |
---|
1759 | set_colors - specify a set of colours to use |
---|
1760 | set_linestyles - specify a set of linestyles to use if only |
---|
1761 | using one color |
---|
1762 | set_mask - set a plotting mask for a specific polarization |
---|
1763 | |
---|
1764 | [Reading files] |
---|
1765 | reader - access rpfits/sdfits files |
---|
1766 | open - attach reader to a file |
---|
1767 | close - detach reader from file |
---|
1768 | read - read in integrations |
---|
1769 | summary - list info about all integrations |
---|
1770 | |
---|
1771 | [General] |
---|
1772 | commands - this command |
---|
1773 | print - print details about a variable |
---|
1774 | list_scans - list all scantables created bt the user |
---|
1775 | list_files - list all files readable by asap (default rpf) |
---|
1776 | del - delete the given variable from memory |
---|
1777 | range - create a list of values, e.g. |
---|
1778 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
1779 | help - print help for one of the listed functions |
---|
1780 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
1781 | list_rcparameters - print out a list of possible values to be |
---|
1782 | put into $HOME/.asaprc |
---|
1783 | mask_and,mask_or, |
---|
1784 | mask_not - boolean operations on masks created with |
---|
1785 | scantable.create_mask |
---|
1786 | |
---|
1787 | Note: |
---|
1788 | How to use this with help: |
---|
1789 | # function 'summary' |
---|
1790 | [xxx] is just a category |
---|
1791 | Every 'sub-level' in this list should be replaces by a '.' Period when |
---|
1792 | using help |
---|
1793 | Example: |
---|
1794 | ASAP> help scantable # to get info on ths scantable |
---|
1795 | ASAP> help scantable.summary # to get help on the scantable's |
---|
1796 | ASAP> help average_time |
---|
1797 | |
---|
1798 | |
---|
1799 | \end{verbatim} |
---|
1800 | |
---|
1801 | \subsection{ASCII output format} |
---|
1802 | |
---|
1803 | \subsection{.asaprc settings} |
---|
1804 | \index{.asaprc} |
---|
1805 | \asaprc{verbose}{{\bf True}/False}{Print verbose output, good to disable in scripts} |
---|
1806 | |
---|
1807 | \asaprc{insitu}{{\bf True}/False}{Apply operations on the input |
---|
1808 | scantable or return new one} |
---|
1809 | |
---|
1810 | % plotting |
---|
1811 | |
---|
1812 | \asaprc{useplotter}{{\bf True}/False}{Preload a default plotter} |
---|
1813 | |
---|
1814 | \asaprc{plotter.gui}{{\bf True}/False}{Do we want a GUI or plot to a |
---|
1815 | file} |
---|
1816 | |
---|
1817 | \asaprc{plotter.stacking}{{\bf Pol} Beam IF Scan Time}{Default mode for |
---|
1818 | colour stacking} |
---|
1819 | |
---|
1820 | \asaprc{plotter.panelling}{Pol Beam IF {\bf Scan} Time}{Default mode |
---|
1821 | for panelling} |
---|
1822 | |
---|
1823 | \asaprc{plotter.ganged}{{\bf True}/False}{Push panels together, to |
---|
1824 | share axislabels} |
---|
1825 | |
---|
1826 | \asaprc{plotter.decimate}{True/{\bf False}}{Decimate the number of |
---|
1827 | points plotted by a factor of nchan/1024} |
---|
1828 | |
---|
1829 | % default colours/linestyles |
---|
1830 | %\asaprc{plotter.colours}{.}{.} |
---|
1831 | %\asaprc{plotter.linestyles{.}{.} |
---|
1832 | |
---|
1833 | % scantable |
---|
1834 | \asaprc{scantable.save}{{\bf ASAP} SDFITS FITS ASCII MS2}{Default output |
---|
1835 | format when saving} |
---|
1836 | |
---|
1837 | \asaprc{scantable.autoaverage}{{\bf True}/False}{Auto averaging on |
---|
1838 | read} |
---|
1839 | |
---|
1840 | \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default |
---|
1841 | frequency frame to set when function scantable.set\_freqframe is |
---|
1842 | called or the data is imported} |
---|
1843 | |
---|
1844 | \subsection{Installation} |
---|
1845 | |
---|
1846 | \index{Installation}ASAP depends on a number of third-party libraries which you must |
---|
1847 | have installed before attempting to build ASAP. These are: |
---|
1848 | |
---|
1849 | \begin{itemize} |
---|
1850 | \item AIPS++ |
---|
1851 | \item Boost |
---|
1852 | \item Matplotlib |
---|
1853 | \item python/ipython |
---|
1854 | \end{itemize} |
---|
1855 | |
---|
1856 | Debian Linux is currently supported and we intend also |
---|
1857 | to support other popular Linux flavours, Solaris and Mac. |
---|
1858 | |
---|
1859 | Of the dependencies, AIPS++ is the most complex to install. |
---|
1860 | |
---|
1861 | \printindex |
---|
1862 | |
---|
1863 | \end{document} |
---|
1864 | |
---|