1 | \documentclass[11pt]{article} |
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2 | \usepackage{a4} |
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14 | |
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15 | \title{ATNF Spectral Analysis Package\\User Guide v2.1\\DRAFT } |
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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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29 | } |
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33 | \begin{minipage}[t]{\textwidth-47mm}#2 \\ \tt #3\end{minipage} |
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34 | } |
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35 | |
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36 | \makeindex |
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37 | |
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38 | \begin{document} |
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39 | |
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40 | \maketitle |
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41 | |
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42 | \section{Introduction} |
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43 | |
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44 | ASAP is a single dish spectral line processing package currently being |
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45 | developed by the ATNF. It is intended to process data from all ATNF |
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46 | antennas, and can probably be used for other antennas if they can |
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47 | produce ``Single Dish FITS'' format. It is based on the AIPS++ |
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48 | package. |
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49 | |
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50 | This userguide has been updated for the ASAP 2.1. Please report any |
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51 | mistakes you find. |
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52 | |
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53 | \section{Installation and Running} |
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54 | |
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55 | Currently there are installations running on Linux machines at |
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56 | |
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57 | \begin{itemize} |
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58 | \item Epping - use hosts {\tt draco} or {\tt hydra} |
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59 | \item Narrabri - use host {\tt kaputar} |
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60 | \item Parkes - use host {\tt bourbon} |
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61 | \item Mopra - use host {\tt minos} |
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62 | \end{itemize} |
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63 | |
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64 | Or use your own Linux desktop. |
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65 | |
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66 | {\em Note. ASAP2.1 only runs on ATNF Linux machines which have been |
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67 | updated to Debian Sarge and are using the ``DEBIANSarge'' |
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68 | /usr/local. If your favourite machine has not been upgraded, send a |
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69 | request to your friendly IT support. At the time of writing asap 2.1 |
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70 | does not run on hydra, bourbon or kaputar.} |
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71 | |
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72 | \index{Running}To start asap log onto one of these Linux hosts and enter |
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73 | |
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74 | \begin{verbatim} |
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75 | > cd /my/data/directory |
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76 | > asap |
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77 | \end{verbatim} |
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78 | |
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79 | This starts ASAP. To quit, you need to type \verb+^+-d (control-d) or |
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80 | type \cmd{\%Exit}. |
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81 | |
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82 | \section{Interface} |
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83 | |
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84 | \index{Interface}ASAP is written in C++ and python. The user interface |
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85 | uses the ``ipython'' interactive shell, which is a simple interactive |
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86 | interface to python. The user does not need to understand python to |
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87 | use this, but certain aspects python affect what the user can do. The |
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88 | current interface is object oriented. |
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89 | |
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90 | \subsection {Integer Indices are 0-relative} |
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91 | |
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92 | Please note, all integer indices in ASAP and iPython are {\bf 0-relative}. |
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93 | |
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94 | \subsection{Objects} |
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95 | \index{objects} |
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96 | The ASAP interface is based around a number of ``objects'' which the |
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97 | user deals with. Objects range from the data which have been read from |
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98 | disk, to tools used for fitting functions to the data. The following |
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99 | main objects are used : |
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100 | |
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101 | \begin{tabular}{ll} |
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102 | |
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103 | \cmd{scantable} & \parbox[t]{0.7\textwidth}{The data container (actual |
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104 | spectra and header information)} \\ |
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105 | \cmd{selector} & \parbox[t]{0.80\textwidth}{Allows the user to select |
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106 | a subsection of the data, such as a specified or range of beam |
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107 | numbers, IFs, etc.} \\ |
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108 | \cmd{plotter} & A tool used to plot the spectral line data \\ |
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109 | \cmd{fitter} & A tool used to fit functions to the spectral data \\ |
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110 | \cmd{reader} & \parbox[t]{0.8\textwidth}{A tool which can be used to |
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111 | read data from disks into a scantable object (advanced use).}\\ |
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112 | \end{tabular} |
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113 | |
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114 | There can be many objects of the same type. Each object is referred to |
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115 | by a variable name made by the user. The name of this variable is not |
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116 | important and can be set to whatever the user prefers (i.e. ``s'' and |
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117 | ``ParkesHOH-20052002'' are equivalent). However, having a simple and |
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118 | consistent naming convention will help you a lot. |
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119 | |
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120 | \subsection{Member Functions (functions)} |
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121 | |
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122 | \index{Functions!member}Following the object oriented approach, |
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123 | objects have associated ``member functions'' which can either be used |
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124 | to modify the data in some way or change global properties of the |
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125 | object. In this document member functions will be referred to simply |
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126 | as functions. From the command line, the user can execute these |
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127 | functions using the syntax: |
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128 | \begin{verbatim} |
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129 | ASAP>out = object.function(arguments) |
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130 | \end{verbatim} |
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131 | |
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132 | Where \cmd{out} is the name of the returned variable (could be a new |
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133 | scantable object, or a vector of data, or a status return), |
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134 | \cmd{object} is the object variable name (set by the user), |
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135 | \cmd{function} is the name of the member function and \cmd{arguments} |
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136 | is a list of arguments to the function. The arguments can be provided |
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137 | either though position or \cmd{name=}. A mix of the two can be used. |
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138 | E.g. |
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139 | |
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140 | \begin{verbatim} |
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141 | ASAP>av = scans.average_time(msk,weight='tsys') |
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142 | ASAP>av = scans.average_time(mask=msk,weight='tsys') |
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143 | ASAP>av = scans.average_time(msk,tsys) |
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144 | ASAP>scans.poly_baseline(mask=msk, order=0, insitu=True) |
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145 | ASAP>scans.poly_baseline(msk,0,True) |
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146 | ASAP>scans.poly_baseline(mask, insitu=True) |
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147 | \end{verbatim} |
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148 | |
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149 | \subsection{Global Functions} |
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150 | |
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151 | \index{Functions!global}It does not make sense to implement some functions as member |
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152 | functions, typically functions which operate on more than one |
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153 | scantable (e.g. time averaging of many scans). These functions will |
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154 | always be referred to as global functions. |
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155 | |
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156 | \subsection{Interactive environment} |
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157 | |
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158 | \index{ipython!environment}ipython has a number of useful interactive |
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159 | features and a few things to be aware of for the new user. |
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160 | |
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161 | \subsubsection{String completion} |
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162 | |
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163 | \index{ipython!string completion}Tab completion is enabled for all |
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164 | function names. If you type the first few letters of a function name, |
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165 | then type {\tt <TAB>} the function name will be auto completed if it |
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166 | is un-ambiguous, or a list of possibilities will be |
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167 | given. Auto-completion works for the user object names as well as |
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168 | function names. It does not work for filenames, nor for function |
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169 | arguments. |
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170 | |
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171 | Example |
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172 | \begin{verbatim} |
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173 | ASAP>scans = scantable('MyData.rpf') |
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174 | ASAP>scans.se<TAB> |
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175 | ASAP>scans.set_in<TAB> |
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176 | scans.set_cursor scans.set_freqframe scans.set_selection |
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177 | scans.set_doppler scans.set_instrument scans.set_unit |
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178 | scans.set_fluxunit scans.set_restfreqs |
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179 | |
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180 | ASAP>scans.set_instrument() |
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181 | \end{verbatim} |
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182 | |
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183 | \subsubsection{Leading Spaces} |
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184 | |
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185 | \index{ipython!leading space}Python uses leading space to mark blocks |
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186 | of code. This means that it you start a command line with a space, the |
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187 | command generally will fail with an syntax error. |
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188 | |
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189 | \subsubsection{Variable Names} |
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190 | |
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191 | \index{ipython!variable names}During normal data processing, the user |
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192 | will have to create named variables to hold spectra etc. These must |
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193 | conform to the normal python syntax, specifically they cannot contain |
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194 | ``special'' characters such as \@ \$ etc and cannot start with a |
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195 | number (but can contain numbers). Variable (and function) names are |
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196 | case sensitive. |
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197 | |
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198 | \subsubsection{Unix Interaction} |
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199 | |
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200 | \index{ipython!unix interaction}Basic unix shell commands (\cmd{pwd}, |
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201 | \cmd{ls}, \cmd{cd} etc) can be issued from within ASAP. This allows |
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202 | the user to do things like look at files in the current directory. The |
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203 | shell command ``\cmd{cd}'' works within ASAP, allowing the user to |
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204 | change between data directories. Unix programs cannot be run this way, |
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205 | but the shell escape ``$!$'' can be used to run arbitrary |
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206 | programs. E.g. |
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207 | |
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208 | \begin{verbatim} |
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209 | ASAP>pwd |
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210 | ASAP>ls |
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211 | ASAP>cd /my/data/directory |
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212 | ASAP>! mozilla& |
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213 | \end{verbatim} |
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214 | |
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215 | \subsection{Help} |
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216 | |
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217 | \index{Help}ASAP has built in help for all functions. To get a list of |
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218 | functions type: |
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219 | |
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220 | \begin{verbatim} |
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221 | ASAP>commands() |
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222 | \end{verbatim} |
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223 | |
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224 | To get help on specific functions, the built in help needs to be given |
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225 | the object and function name. E.g. |
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226 | |
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227 | \begin{verbatim} |
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228 | ASAP>help scantable.get_scan # or help(scantable.get_scan) |
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229 | ASAP>help scantable.stats |
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230 | ASAP>help plotter.plot |
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231 | ASAP>help fitter.plot |
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232 | |
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233 | ASAP>scans = scantable('mydata.asap') |
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234 | ASAP>help scans.get_scan # Same as above |
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235 | \end{verbatim} |
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236 | |
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237 | Global functions just need their name |
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238 | |
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239 | \begin{verbatim} |
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240 | ASAP>help average_time |
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241 | \end{verbatim} |
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242 | |
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243 | Note that if you just type \cmd{help} the internal ipython help is |
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244 | invoked, which is probably {\em not} what you want. Type \verb+^+-d |
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245 | (control-d) to escape from this. |
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246 | |
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247 | \subsection{Customisation - .asaprc} |
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248 | |
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249 | \index{.asaprc}ASAP use an \cmd{.asaprc} file to control the user's |
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250 | preference of default values for various functions arguments. This |
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251 | includes the defaults for arguments such as \cmd{insitu}, scantable |
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252 | \cmd{freqframe} and the plotters \cmd{set\_mode} values. The help on |
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253 | individual functions says which arguments can be set default values |
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254 | from the \cmd{.asaprc} file. To get a sample contents for the |
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255 | \cmd{.asaprc} file use the command \cmd{list\_rcparameters}. |
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256 | |
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257 | Common values include: |
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258 | \begin{verbatim} |
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259 | # apply operations on the input scantable or return new one |
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260 | insitu : False |
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261 | |
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262 | # default output format when saving scantable |
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263 | scantable.save : ASAP |
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264 | |
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265 | # default frequency frame to set when function |
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266 | # scantable.set_freqframe is called |
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267 | scantable.freqframe : LSRK |
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268 | |
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269 | # auto averaging on read |
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270 | scantable.autoaverage : True |
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271 | \end{verbatim} |
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272 | |
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273 | For a complete list of \cmd{.asaprc} values, see the Appendix. |
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274 | |
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275 | \section{Scantables} |
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276 | \index{Scantables} |
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277 | \subsection {Description} |
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278 | |
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279 | \subsubsection {Basic Structure} |
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280 | |
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281 | \index{Scantable!structure}ASAP data handling works on objects called |
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282 | scantables. A scantable holds your data, and also provides functions |
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283 | to operate upon it. |
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284 | |
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285 | The building block of a scantable is an integration, which is a single |
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286 | row of a scantable. Each row contains just one spectrum for each beam, |
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287 | IF and polarisation. For example Parkes OH-multibeam data would |
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288 | normally contain 13 beams, 1 IF and 2 polarisations, Parkes |
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289 | methanol-multibeam data would contain 7 beams, 2 IFs and 2 |
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290 | polarisations while the Mopra 8-GHz MOPS filterbank will produce one |
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291 | beam, many IFs, and 2-4 polarisations. |
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292 | |
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293 | All of the combinations of Beams/IFs an Polarisations are |
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294 | contained in separate rows. These rows are grouped in cycles (same time stamp). |
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295 | |
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296 | A collection of cycles for one source is termed a scan (and each scan |
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297 | has a unique numeric identifier, the SCANNO). A scantable is then a |
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298 | collection of one or more scans. If you have scan-averaged your data |
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299 | in time, i.e. you have averaged all cycles within a scan, then each |
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300 | scan would hold just one (averaged) integration. |
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301 | |
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302 | Many of the functions which work on scantables can either return a new |
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303 | scantable with modified data or change the scantable insitu. Which |
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304 | method is used depends on the users preference. The default can be |
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305 | changed via the {\tt .asaprc} resource file. |
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306 | |
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307 | For example a Mopra scan with a 4s integration time, two IFs and |
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308 | dual polarisations has two (2s) cycles. |
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309 | \begin{verbatim} |
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310 | SCANNO CYCLENO BEAMNO IFNO POLNO |
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311 | 0 0 0 0 0 |
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312 | 0 0 0 0 1 |
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313 | 0 0 0 1 0 |
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314 | 0 0 0 1 1 |
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315 | 0 1 0 0 0 |
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316 | 0 1 0 0 1 |
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317 | 0 1 0 1 0 |
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318 | 0 1 0 1 1 |
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319 | \end{verbatim} |
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320 | |
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321 | |
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322 | \subsubsection {Contents} |
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323 | |
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324 | \index{Scantable!contents}A scantable has header information and data |
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325 | (a scantable is actually an AIPS++ Table and it is generally stored in |
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326 | memory when you are manipulating it with ASAP. You can save it to |
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327 | disk and then browse it with the AIPS++ Table browser if you know how |
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328 | to do that !). |
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329 | |
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330 | The data are stored in columns (the length of a column is the number of |
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331 | rows/spectra of course). |
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332 | |
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333 | Two important columns are those that describe the frequency setup. We mention |
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334 | them explicitly here because you need to be able to understand the presentation |
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335 | of the frequency information and possibly how to manipulate it. |
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336 | |
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337 | These columns are called FREQ\_ID and MOLECULE\_ID. They contain indices, for |
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338 | each IF, pointing into tables with all of the frequency and rest-frequency |
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339 | information for that integration. |
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340 | |
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341 | There are of course many other columns which contain the actual spectra, |
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342 | the flags, the Tsys, the source names and so on. |
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343 | |
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344 | There is also a function \cmd{summary} to list a summary of the scantable. |
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345 | You will find this very useful. |
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346 | |
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347 | Example: |
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348 | |
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349 | \begin{verbatim} |
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350 | ASAP>scans = scantable('MyData.rpf') |
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351 | ASAP>scans.summary() # Brief listing |
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352 | |
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353 | # Equivalent to brief summary function call |
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354 | ASAP>print scan |
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355 | \end{verbatim} |
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356 | |
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357 | The summary function gives you a scan-based summary, presenting the |
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358 | scantable as a cascading view of Beams and IFs. Note that the output |
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359 | of summary is redirected into your current pager specified by the |
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360 | \$PAGER environment variable. If you find the screen is reset to the |
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361 | original state when summary is finished (i.e. the output from summary |
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362 | disappears), you may need to set the \$LESS environment variable to |
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363 | include the \cmd{-X} option. |
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364 | |
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365 | \subsection{Data Selection} |
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366 | \label{sec:selection} |
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367 | |
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368 | ASAP contains flexible data selection. Data can be selected based on |
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369 | IF, beam, polarisation, scan number as well as values such as |
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370 | Tsys. Advanced users can also make use of the AIPS++ TAQL language to |
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371 | create selections based on almost any of the values recorded. |
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372 | |
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373 | Selection is based on a \cmd{selector} object. This object is created |
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374 | and various selection functions applied to it (\cmd{set\_ifs}, |
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375 | \cmd{set\_beams} etc). The selection object then must be applied to a |
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376 | scantable using the \cmd{set\_selection} function. A single selection |
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377 | object can be created and setup then applied to multiple scantables. |
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378 | |
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379 | Once a selection has been applied, all following functions will only |
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380 | ``see'' the selected spectra (including functions such as |
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381 | \cmd{summary}). The selection can then be reset and all spectra are |
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382 | visible. Note that if functions such as \cmd{copy} are run on a |
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383 | scantable with active selection, only the selected spectra are copied. |
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384 | |
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385 | The common selection functions are: |
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386 | |
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387 | \begin{tabular}{ll} |
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388 | |
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389 | \cmd{set\_beams} & Select beams by index number \\ |
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390 | \cmd{set\_ifs} & Select ifs by index number \\ |
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391 | \cmd{set\_name} & Select by source name. Can contain ``*'' as a |
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392 | wildcard, e.g. ``Orion*\_R''. \\ |
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393 | \cmd{set\_ifs} & Select IFs by index number \\ |
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394 | |
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395 | \cmd{set\_polarisation} & \parbox[t]{0.73\textwidth}{Select by |
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396 | polarisation index or name. If polarisation names are given, the data |
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397 | will be on-the-fly onverted (for example from linears to Stokes). }\\ |
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398 | |
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399 | \cmd{set\_query} & Set query directly. For power users only! \\ |
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400 | \cmd{set\_tsys} & Select data based on Tsys. Also example of user |
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401 | definable query. \\ |
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402 | \cmd{reset} & Reset the selection to include all spectra. \\ |
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403 | |
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404 | \end{tabular} |
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405 | |
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406 | Note that all indices are zero based. |
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407 | |
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408 | Examples: |
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409 | |
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410 | \begin{verbatim} |
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411 | ASAP>selection = selector() # Create selection object |
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412 | ASAP>selection.set_ifs(0) # Just select the first IF |
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413 | ASAP>scans.set_selection(selection) # Apply the selection |
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414 | ASAP>print scans # Will just show the first IF |
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415 | |
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416 | ASAP>selection.set_ifs([0,1]) # Select the first two IFs |
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417 | ASAP>selection.set_beams([1,3,5]) # Also select three of the beams |
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418 | ASAP>scans.set_selection(selection) # Apply the selection |
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419 | |
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420 | ASAP>selection.set_name('G308*') # Select by source name |
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421 | |
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422 | ASAP>selection.reset() # Turn off selection |
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423 | ASAP>scans.set_selection(selection) # Apply the reset selection |
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424 | |
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425 | \end{verbatim} |
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426 | |
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427 | \subsection{State} |
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428 | |
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429 | \index{Scantable!state}Each scantable contains "state"; these are |
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430 | properties applying to all of the data in the scantable. |
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431 | |
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432 | Examples are the selection of beam, IF and polarisation, spectral unit |
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433 | (e.g. km/s), frequency reference frame (e.g. BARY) and velocity Doppler |
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434 | type (e.g. RADIO). |
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435 | |
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436 | \subsubsection{Units, Doppler and Frequency Reference Frame} |
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437 | |
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438 | The information describing the frequency setup for each integration |
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439 | is stored fundamentally in frequency in the reference frame |
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440 | of observation (E.g. TOPO). |
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441 | |
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442 | When required, this is converted to the desired reference frame |
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443 | (e.g. LSRK), Doppler (e.g. OPTICAL) and unit (e.g. km/s) on-the-fly. |
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444 | This is important, for example, when you are displaying the data or |
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445 | fitting to it. The reference frame is set on file read to the value |
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446 | set in the user \cmd{.asaprc} file. |
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447 | |
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448 | For units, the user has the choice of frequency, velocity or channel. |
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449 | The \cmd{set\_unit} function is used to set the current unit for a |
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450 | scantable. All functions will (where relevant) work with the selected |
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451 | unit until this changes. This is mainly important for fitting (the fits |
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452 | can be computed in any of these units), plotting and mask creation. |
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453 | |
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454 | The velocity definition can be changed with the \cmd{set\_doppler} |
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455 | function, and the frequency reference frame can be changed with the |
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456 | \cmd{set\_freqframe} function. |
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457 | |
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458 | Example usage: |
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459 | |
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460 | \begin{verbatim} |
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461 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf') # Read in the data |
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462 | ASAP>scans.set_freqframe('LSRK') # Use the LSR velocity frame |
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463 | ASAP>scans.set_unit('km/s') # Use velocity for plots etc from now on |
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464 | ASAP>scans.set_doppler('OPTICAL') # Use the optical velocity convention |
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465 | ASAP>scans.set_unit('MHz') # Use frequency in MHz from now on |
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466 | \end{verbatim} |
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467 | |
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468 | |
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469 | \subsubsection{Rest Frequency} |
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470 | |
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471 | \index{Scantable!rest frequency}ASAP reads the line rest frequency |
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472 | from the RPFITS file when reading the data. The values stored in the |
---|
473 | RPFITS file are not always correct and so there is a function |
---|
474 | \cmd{set\_restfreq} to set the rest frequencies for the currently |
---|
475 | selected data. |
---|
476 | |
---|
477 | For each integration, there is a rest-frequency per IF (the rest |
---|
478 | frequencies are just stored as a list with an index into them). |
---|
479 | There are a few ways to set the rest frequencies with this function. |
---|
480 | |
---|
481 | If you specify just one rest frequency, then it is set for all IF. |
---|
482 | |
---|
483 | \begin{verbatim} |
---|
484 | # Set all IFs |
---|
485 | ASAP>scans.set_restfreqs(freqs=1.667359e9) |
---|
486 | \end{verbatim} |
---|
487 | |
---|
488 | If set a rest frequency for each IF, specify a list of frequencies (of |
---|
489 | length the number of IFs). Regardless of the source, the rest |
---|
490 | frequency will be set for each IF to the corresponding value in the |
---|
491 | provided list. |
---|
492 | |
---|
493 | \begin{verbatim} |
---|
494 | # Set rest frequency for all IFs |
---|
495 | ASAP>scans.set_restfreqs(freqs=[1.6654018e9,1.667359e9,]) |
---|
496 | |
---|
497 | \end{verbatim} |
---|
498 | |
---|
499 | A predetermined ``line catalog'' can be used to set the rest |
---|
500 | frequency. See section \S \ref{sec:linecat}. |
---|
501 | |
---|
502 | |
---|
503 | \subsubsection{Masks} |
---|
504 | |
---|
505 | \index{Masks}\index{Scantable!masks} |
---|
506 | |
---|
507 | Many tasks (fitting, baseline subtraction, statistics etc) should only |
---|
508 | be run on range of channels. Depending on the current ``unit'' setting |
---|
509 | this range is set directly as channels, velocity or frequency |
---|
510 | ranges. Internally these are converted into a simple boolean mask for |
---|
511 | each channel of the abscissa. This means that if the unit setting is |
---|
512 | later changed, previously created mask are still valid. (This is not |
---|
513 | true for functions which change the shape or shift the frequency |
---|
514 | axis). You create masks with the function \cmd{create\_mask} and this |
---|
515 | specified the channels to be included in the selection. When setting |
---|
516 | the mask in velocity, the conversion from velocity to channels is |
---|
517 | based on the current selection, specified row and selected frequency |
---|
518 | reference frame. |
---|
519 | |
---|
520 | |
---|
521 | Note that for multi IF data with different number of channels per IF a |
---|
522 | single mask cannot be applied to different IFs. To use a mask on such |
---|
523 | data the selector should be applied to select all IFs with the same |
---|
524 | number of channels. |
---|
525 | |
---|
526 | Example : |
---|
527 | \begin{verbatim} |
---|
528 | |
---|
529 | # Select channel range for baselining |
---|
530 | ASAP>scans.set_unit('channels') |
---|
531 | ASAP>msk = scans.create_mask([100,400],[600,800]) |
---|
532 | |
---|
533 | # Select velocity range for fitting |
---|
534 | ASAP>scans.set_unit('km/s') |
---|
535 | ASAP>msk = scans.create_mask([-30,-10]) |
---|
536 | \end{verbatim} |
---|
537 | |
---|
538 | Sometimes it is more convenient to specify the channels to be |
---|
539 | excluded, rather included. You can do this with the ``invert'' |
---|
540 | argument. |
---|
541 | |
---|
542 | Example : |
---|
543 | \begin{verbatim} |
---|
544 | ASAP>scans.set_unit('channels') |
---|
545 | ASAP>msk = scans.create_mask([0,100],[900-1023], invert=True) |
---|
546 | \end{verbatim} |
---|
547 | |
---|
548 | By default \cmd{create\_mask} uses the frequency setup of the first row |
---|
549 | to convert velocities into a channel mask. If the rows in the data |
---|
550 | cover different velocity ranges, the scantable row to use should be |
---|
551 | specified: |
---|
552 | |
---|
553 | \begin{verbatim} |
---|
554 | ASAP>scans.set_unit('km/s') |
---|
555 | ASAP>msk = q.create_mask([-30,-10], row=5) |
---|
556 | \end{verbatim} |
---|
557 | |
---|
558 | Because the mask is stored in a simple python variable, the users is |
---|
559 | able to combine masks using simple arithmetic. To create a mask |
---|
560 | excluding the edge channels, a strong maser feature and a birdie in |
---|
561 | the middle of the band: |
---|
562 | |
---|
563 | \begin{verbatim} |
---|
564 | ASAP>scans.set_unit('channels') |
---|
565 | ASAP>msk1 = q.create_mask([0,100],[511,511],[900,1023],invert=True) |
---|
566 | ASAP>scans.set_unit('km/s') |
---|
567 | ASAP>msk2 = q.create_mask([-20,-10],invert=True) |
---|
568 | |
---|
569 | ASAP>mask = msk1 and msk2 |
---|
570 | \end{verbatim} |
---|
571 | |
---|
572 | |
---|
573 | \subsection{Management} |
---|
574 | |
---|
575 | \index{Scantable!management}During processing it is possible to create |
---|
576 | a large number of scan tables. These all consume memory, so it is best |
---|
577 | to periodically remove unneeded scan tables. Use \cmd{list\_scans} to |
---|
578 | print a list of all scantables and \cmd{del} to remove unneeded ones. |
---|
579 | |
---|
580 | Example: |
---|
581 | |
---|
582 | \begin{verbatim} |
---|
583 | ASAP>list_scans() |
---|
584 | The user created scantables are: |
---|
585 | ['s', 'scans', 'av', 's2', 'ss'] |
---|
586 | |
---|
587 | ASAP>del s2 |
---|
588 | ASAP>del ss |
---|
589 | \end{verbatim} |
---|
590 | |
---|
591 | \section{Data Input} |
---|
592 | |
---|
593 | \index{Reading data}Data can be loaded in one of two ways; using the |
---|
594 | reader object or via the scantable constructor. The scantable method |
---|
595 | is simpler but the reader allows the user more control on what is read. |
---|
596 | |
---|
597 | \subsection{Scantable constructor} |
---|
598 | |
---|
599 | \index{Scantable constructor}\index{Scantable!constructor}This loads |
---|
600 | all of the data from filename into the scantable object scans and |
---|
601 | averages all the data within a scan (i.e. the resulting scantable |
---|
602 | will have one row per scan). The recognised input file formats are |
---|
603 | RPFITS, SDFITS (singledish fits), ASAP's scantable format and aips++ |
---|
604 | MeasurementSet2 format. |
---|
605 | |
---|
606 | Example usage: |
---|
607 | |
---|
608 | \begin{verbatim} |
---|
609 | ASAP>scan = scantable('2004-11-23_1841-P484.rpf') |
---|
610 | |
---|
611 | # Don't scan average the data |
---|
612 | ASAP>scan = scantable('2004-11-23_1841-P484.rpf', average=False) |
---|
613 | \end{verbatim} |
---|
614 | |
---|
615 | |
---|
616 | \subsection{Reader object} |
---|
617 | |
---|
618 | \index{Reader object}\index{Scantable!reader object}For more control |
---|
619 | when reading data into ASAP, the reader object should be used. This |
---|
620 | has the option of only reading in a range of integrations, only a |
---|
621 | specified beam or IF and does not perform any scan averaging of the |
---|
622 | data, allowing analysis of the individual integrations. Note that due |
---|
623 | to limitation of the RPFITS library, only one reader object can be |
---|
624 | open at one time reading RPFITS files. To read multiple RPFITS files, |
---|
625 | the old reader must be destroyed before the new file is opened. |
---|
626 | However, multiple readers can be created and attached to SDFITS files. |
---|
627 | |
---|
628 | |
---|
629 | Example usage: |
---|
630 | |
---|
631 | \begin{verbatim} |
---|
632 | ASAP>r = reader('2003-03-16_082048_t0002.rpf') |
---|
633 | ASAP>r.summary() |
---|
634 | ASAP>scan = r.read() |
---|
635 | ASAP>del r |
---|
636 | \end{verbatim} |
---|
637 | |
---|
638 | \section{Basic Processing} |
---|
639 | |
---|
640 | In the following section, a simple data reduction to form a quotient |
---|
641 | spectrum of a single source is followed. It has been assume that the |
---|
642 | \cmd{.asaprc} file has {\em not} been used to change the \cmd{insitu} |
---|
643 | default value from \cmd{True}. |
---|
644 | |
---|
645 | \subsection{Auto quotient} |
---|
646 | \index{Auto quotient}Quotients can be computed ``automatically''. This |
---|
647 | requires the data to have matching source/reference pairs or one |
---|
648 | reference for multiple sources. Auto quotient assumes reference scans |
---|
649 | have a trailing ``\_R'' in the source name for data from Parkes and |
---|
650 | Mopra, and a trailing ``e'' or ``w'' for data fro, Tidbinbilla. |
---|
651 | |
---|
652 | \begin{verbatim} |
---|
653 | ASAP>q = s.auto_quotient() |
---|
654 | \end{verbatim} |
---|
655 | |
---|
656 | By default the quotient spectra is calculated |
---|
657 | to preserve continuum emission. If you wish to remove the continuum |
---|
658 | contribution, use the \cmd{preserve} argument: |
---|
659 | |
---|
660 | \begin{verbatim} |
---|
661 | ASAP>q = s.auto_quotient(preserve=True) |
---|
662 | \end{verbatim} |
---|
663 | |
---|
664 | If this is not sufficient the following alternative method can be used. |
---|
665 | |
---|
666 | \subsection{Separate reference and source observations} |
---|
667 | |
---|
668 | \index{Quotient spectra}Most data from ATNF observatories |
---|
669 | distinguishes on and off source data using the file name. This makes |
---|
670 | it easy to create two scantables with the source and reference |
---|
671 | data. As long as there was exactly one reference observation for each |
---|
672 | on source observation for following method will work. |
---|
673 | |
---|
674 | For Mopra and Parkes data: |
---|
675 | \begin{verbatim} |
---|
676 | ASAP>r = scans.get_scan('*_R') |
---|
677 | ASAP>s = scans.get_scan('*_S') |
---|
678 | \end{verbatim} |
---|
679 | |
---|
680 | For Tidbinbilla data |
---|
681 | \begin{verbatim} |
---|
682 | ASAP>r = scans.get_scan('*_[ew]') |
---|
683 | ASAP>s = scans.get_scan('*_[^ew]') |
---|
684 | \end{verbatim} |
---|
685 | |
---|
686 | \subsection{Make the quotient spectra} |
---|
687 | |
---|
688 | Use the quotient function |
---|
689 | |
---|
690 | \begin{verbatim} |
---|
691 | ASAP>q = s.quotient(r) |
---|
692 | \end{verbatim} |
---|
693 | |
---|
694 | This uses the rows in scantable \cmd{r} as reference spectra for the |
---|
695 | rows in scantable \cmd{s}. Scantable \cmd{r} must have either 1 row |
---|
696 | (which is applied to all rows in \cmd{s}) or both scantables must have |
---|
697 | the same number of rows. |
---|
698 | |
---|
699 | \subsection{Time average separate scans} |
---|
700 | |
---|
701 | \index{Time average}If you have observed the source with multiple |
---|
702 | source/reference cycles you will want to scan-average the quotient |
---|
703 | spectra together. |
---|
704 | |
---|
705 | \begin{verbatim} |
---|
706 | ASAP>av = q.average_time() |
---|
707 | \end{verbatim} |
---|
708 | |
---|
709 | If for some you want to average multiple sets of scantables together |
---|
710 | you can: |
---|
711 | |
---|
712 | \begin{verbatim} |
---|
713 | ASAP>av = average_time(q1, q2, q3) |
---|
714 | \end{verbatim} |
---|
715 | |
---|
716 | The default is to use integration time weighting. The alternative is |
---|
717 | to use none, variance, Tsys weighting, Tsys \& integration time or |
---|
718 | median averaging. |
---|
719 | |
---|
720 | \begin{verbatim} |
---|
721 | ASAP>av = average_time(q, weight='tintsys') |
---|
722 | \end{verbatim} |
---|
723 | |
---|
724 | To use variance based weighting, you need to supply a mask saying which |
---|
725 | channel range you want it to calculate the variance from. |
---|
726 | |
---|
727 | \begin{verbatim} |
---|
728 | ASAP>msk = scans.create_mask([200,400],[600,800]) |
---|
729 | ASAP>av = average_time(scans, mask=msk, weight='var') |
---|
730 | \end{verbatim} |
---|
731 | |
---|
732 | If you have not observed your data with Doppler tracking (or run |
---|
733 | \cmd{freq\_align} explicitly) you should align the data in frequency |
---|
734 | before averaging. |
---|
735 | |
---|
736 | \begin{verbatim} |
---|
737 | ASAP>av = scans.average_time(align=True) |
---|
738 | \end{verbatim} |
---|
739 | |
---|
740 | Note that, if needed, you should run \cmd{gain\_el} and \cmd{opacity} |
---|
741 | before you average the data in time (\S \ref{sec:gainel} \& |
---|
742 | \ref{sec:freqalign}). |
---|
743 | |
---|
744 | \subsection{Baseline fitting} |
---|
745 | |
---|
746 | \index{Baseline fitting}To make a baseline fit, you must first create |
---|
747 | a mask of channels to use in the baseline fit. |
---|
748 | |
---|
749 | \begin{verbatim} |
---|
750 | ASAP>msk = scans.create_mask([100,400],[600,900]) |
---|
751 | ASAP>scans.poly_baseline(msk, order=1) |
---|
752 | \end{verbatim} |
---|
753 | |
---|
754 | This will fit a first order polynomial to the selected channels and subtract |
---|
755 | this polynomial from the full spectra. |
---|
756 | |
---|
757 | \subsubsection{Auto-baselining} |
---|
758 | |
---|
759 | \index{Auto-baseline}The function \cmd{auto\_poly\_baseline} can be used to automatically |
---|
760 | baseline your data without having to specify channel ranges for the |
---|
761 | line free data. It automatically figures out the line-free emission |
---|
762 | and fits a polynomial baseline to that data. The user can use masks to |
---|
763 | fix the range of channels or velocity range for the fit as well as |
---|
764 | mark the band edge as invalid. |
---|
765 | |
---|
766 | Simple example |
---|
767 | |
---|
768 | \begin{verbatim} |
---|
769 | ASAP>scans.auto_poly_baseline(order=2,threshold=5) |
---|
770 | \end{verbatim} |
---|
771 | |
---|
772 | \cmd{order} is the polynomial order for the fit. \cmd{threshold} is |
---|
773 | the SNR threshold to use to deliminate line emission from |
---|
774 | signal. Generally the value of threshold is not too critical, however |
---|
775 | making this too large will compromise the fit (as it will include |
---|
776 | strong line features) and making it too small will mean it cannot find |
---|
777 | enough line free channels. |
---|
778 | |
---|
779 | |
---|
780 | Other examples: |
---|
781 | |
---|
782 | \begin{verbatim} |
---|
783 | # Don't try and fit the edge of the bandpass which is noisier |
---|
784 | ASAP>scans.auto_poly_baseline(edge=(500,450),order=3,threshold=3) |
---|
785 | |
---|
786 | # Only fit a given region around the line |
---|
787 | ASAP>scans.set_unit('km/s') |
---|
788 | ASAP>msk = scans.create_mask([-60,-20]) |
---|
789 | ASAP>scans.auto_poly_baseline(mask=msk,order=3,threshold=3) |
---|
790 | |
---|
791 | \end{verbatim} |
---|
792 | |
---|
793 | \subsection{Average the polarisations} |
---|
794 | |
---|
795 | \index{average\_pol}If you are just interested in the highest SNR for total intensity you |
---|
796 | will want to average the parallel polarisations together. |
---|
797 | |
---|
798 | \begin{verbatim} |
---|
799 | ASAP>scans.average_pol() |
---|
800 | \end{verbatim} |
---|
801 | |
---|
802 | \subsection{Calibration} |
---|
803 | |
---|
804 | \index{Calibration}For most uses, calibration happens transparently as the input data |
---|
805 | contains the Tsys measurements taken during observations. The nominal |
---|
806 | ``Tsys'' values may be in Kelvin or Jansky. The user may wish to |
---|
807 | supply a Tsys correction or apply gain-elevation and opacity |
---|
808 | corrections. |
---|
809 | |
---|
810 | \subsubsection{Brightness Units} |
---|
811 | |
---|
812 | \index{Brightness Units}RPFITS files do not contain any information as |
---|
813 | to whether the telescope calibration was in units of Kelvin or |
---|
814 | Janskys. On reading the data a default value is set depending on the |
---|
815 | telescope and frequency of observation. If this default is incorrect |
---|
816 | (you can see it in the listing from the \cmd{summary} function) the |
---|
817 | user can either override this value on reading the data or later. |
---|
818 | E.g: |
---|
819 | |
---|
820 | \begin{verbatim} |
---|
821 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf', unit='Jy') |
---|
822 | # Or in two steps |
---|
823 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf') |
---|
824 | ASAP>scans.set_fluxunit('Jy') |
---|
825 | \end{verbatim} |
---|
826 | |
---|
827 | \subsubsection{Feed Polarisation} |
---|
828 | |
---|
829 | \index{Brightness Units}The RPFITS files also do not contain any |
---|
830 | information as to the feed polarisation. ASAP will set a default based |
---|
831 | on the antenna, but this will often be wrong the data has been read, |
---|
832 | the default can be changed using the \cmd{set\_feedtype} function with |
---|
833 | an argument of \cmd{'linear'} or \cmd{'circular'}. |
---|
834 | |
---|
835 | E.g: |
---|
836 | |
---|
837 | \begin{verbatim} |
---|
838 | ASAP>scans = scantable('2004-11-23_1841-P484.rpf') |
---|
839 | ASAP>scans.set_feedtype('circular') |
---|
840 | \end{verbatim} |
---|
841 | |
---|
842 | \subsubsection{Tsys scaling} |
---|
843 | |
---|
844 | \index{Tsys scaling}Sometime the nominal Tsys measurement at the |
---|
845 | telescope is wrong due to an incorrect noise diode calibration. This |
---|
846 | can easily be corrected for with the scale function. By default, |
---|
847 | \cmd{scale} only scans the spectra and not the corresponding Tsys. |
---|
848 | |
---|
849 | \begin{verbatim} |
---|
850 | ASAP>scans.scale(1.05, tsys=True) |
---|
851 | \end{verbatim} |
---|
852 | |
---|
853 | \subsubsection{Unit Conversion} |
---|
854 | |
---|
855 | \index{Unit conversion}To convert measurements in Kelvin to Jy (and |
---|
856 | vice versa) the global function \cmd{convert\_flux} is needed. This |
---|
857 | converts and scales the data from K to Jy or vice-versa depending on |
---|
858 | what the current brightness unit is set to. The function knows the |
---|
859 | basic parameters for some frequencies and telescopes, but the user may |
---|
860 | need to supply the aperture efficiency, telescope diameter or the Jy/K |
---|
861 | factor. |
---|
862 | |
---|
863 | \begin{verbatim} |
---|
864 | ASAP>scans.convert_flux() # If efficency known |
---|
865 | ASAP>scans.convert_flux(eta=0.48) # If telescope diameter known |
---|
866 | ASAP>scans.convert_flux(eta=0.48,d=35) # Unknown telescope |
---|
867 | ASAP>scans.convert_flux(jypk=15) # Alternative |
---|
868 | \end{verbatim} |
---|
869 | |
---|
870 | \subsubsection{Gain-Elevation and Opacity Corrections} |
---|
871 | \label{sec:gainel} |
---|
872 | |
---|
873 | \index{Gain-elevation}As higher frequencies (particularly $>$20~GHz) |
---|
874 | it is important to make corrections for atmospheric opacity and |
---|
875 | gain-elevation effects. |
---|
876 | |
---|
877 | Note that currently the elevation is not written correctly into |
---|
878 | Tidbinbilla rpfits files. This means that gain-elevation and opacity |
---|
879 | corrections will not work unless these get recalculated. |
---|
880 | |
---|
881 | \begin{verbatim} |
---|
882 | ASAP>scans.recalc_azel() # recalculate az/el based on pointing |
---|
883 | \end{verbatim} |
---|
884 | |
---|
885 | Gain-elevation curves for some telescopes and frequencies are known to |
---|
886 | ASAP (currently only for Tidbinbilla at 20~GHz). In these cases |
---|
887 | making gain-corrections is simple. If the gain curve for your data is |
---|
888 | not known, the user can supply either a gain polynomial or text file |
---|
889 | tabulating gain factors at a range of elevations (see \cmd{help |
---|
890 | scantable.gain\_el}). |
---|
891 | |
---|
892 | Examples: |
---|
893 | |
---|
894 | \begin{verbatim} |
---|
895 | ASAP>scans.gain_el() # If gain table known |
---|
896 | ASAP>scans.gain_el(poly=[3.58788e-1,2.87243e-2,-3.219093e-4]) |
---|
897 | \end{verbatim} |
---|
898 | |
---|
899 | \index{Opacity}Opacity corrections can be made with the global |
---|
900 | function \cmd{opacity}. This should work on all telescopes as long as |
---|
901 | a measurement of the opacity factor was made during the observation. |
---|
902 | |
---|
903 | \begin{verbatim} |
---|
904 | ASAP>scans.opacity(0.083) |
---|
905 | \end{verbatim} |
---|
906 | |
---|
907 | Note that at 3~mm Mopra uses a paddle wheel for Tsys calibration, |
---|
908 | which takes opacity effects into account (to first order). ASAP |
---|
909 | opacity corrections should not be used for Mopra 3-mm data. |
---|
910 | |
---|
911 | \subsection{Frequency Frame Alignment} |
---|
912 | \label{sec:freqalign} |
---|
913 | |
---|
914 | \index{Frequency alignment}\index{Velocity alignment}When time |
---|
915 | averaging a series of scans together, it is possible that the velocity |
---|
916 | scales are not exactly aligned. This may be for many reasons such as |
---|
917 | not Doppler tracking the observations, errors in the Doppler tracking |
---|
918 | etc. This mostly affects very long integrations or integrations |
---|
919 | averaged together from different days. Before averaging such data |
---|
920 | together, they should be frequency aligned using \cmd{freq\_align}. |
---|
921 | |
---|
922 | E.g.: |
---|
923 | |
---|
924 | \begin{verbatim} |
---|
925 | ASAP>scans.freq_align() |
---|
926 | ASAP>av = average_time(scans) |
---|
927 | \end{verbatim} |
---|
928 | |
---|
929 | {\em A Global freq\_align command will be made eventually} |
---|
930 | |
---|
931 | To average together data taken on different days, which are in |
---|
932 | different scantables, each scantable must aligned to a common |
---|
933 | reference time then the scantables averaged. The simplest way of |
---|
934 | doing this is to allow ASAP to choose the reference time for the first |
---|
935 | scantable then using this time for the subsequent scantables. |
---|
936 | |
---|
937 | \begin{verbatim} |
---|
938 | ASAP>scans1.freq_align() # Copy the refeference Epoch from the output |
---|
939 | ASAP>scans2.freq_align(reftime='2004/11/23/18:43:35') |
---|
940 | ASAP>scans3.freq_align(reftime='2004/11/23/18:43:35') |
---|
941 | ASAP>av = average_time(scans1, scans2, scans3) |
---|
942 | \end{verbatim} |
---|
943 | |
---|
944 | \section{Scantable manipulation} |
---|
945 | |
---|
946 | \index{Scantable!manipulation}While it is very useful to have many |
---|
947 | independent sources within one scantable, it is often inconvenient for |
---|
948 | data processing. The \cmd{get\_scan} function can be used to create a |
---|
949 | new scantable with a selection of scans from a scantable. The |
---|
950 | selection can either be on the source name, with simple wildcard |
---|
951 | matching or set of scan ids. Internally this uses the selector object, |
---|
952 | so for more complicated selection the selector should be used directly |
---|
953 | instead. |
---|
954 | |
---|
955 | For example: |
---|
956 | |
---|
957 | \begin{verbatim} |
---|
958 | ASAP>ss = scans.get_scan(10) # Get the 11th scan (zero based) |
---|
959 | ASAP>ss = scans.get_scan(range(10)) # Get the first 10 scans |
---|
960 | ASAP>ss = scans.get_scan(range(10,20)) # Get the next 10 scans |
---|
961 | ASAP>ss = scans.get_scan([2,4,6,8,10]) # Get a selection of scans |
---|
962 | |
---|
963 | ASAP>ss = scans.get_scan('345p407') # Get a specific source |
---|
964 | ASAP>ss = scans.get_scan('345*') # Get a few sources |
---|
965 | |
---|
966 | ASAP>r = scans.get_scan('*_R') # Get all reference sources (Parkes/Mopra) |
---|
967 | ASAP>s = scans.get_scan('*_S') # Get all program sources (Parkes/Mopra) |
---|
968 | ASAP>r = scans.get_scan('*[ew]') # Get all reference sources (Tid) |
---|
969 | ASAP>s = scans.get_scan('*[^ew]') # Get all program sources (Tid) |
---|
970 | |
---|
971 | \end{verbatim} |
---|
972 | |
---|
973 | To copy a scantable the following does not work: |
---|
974 | |
---|
975 | \begin{verbatim} |
---|
976 | ASAP>ss = scans |
---|
977 | \end{verbatim} |
---|
978 | |
---|
979 | as this just creates a reference to the original scantable. Any |
---|
980 | changes made to \cmd{ss} are also seen in \cmd{scans}. To duplicate a |
---|
981 | scantable, use the copy function. |
---|
982 | |
---|
983 | \begin{verbatim} |
---|
984 | ASAP>ss = scans.copy() |
---|
985 | \end{verbatim} |
---|
986 | |
---|
987 | \section{Data Output} |
---|
988 | |
---|
989 | \index{Scantable!save}\index{Saving data}ASAP can save scantables in a |
---|
990 | variety of formats, suitable for reading into other packages. The |
---|
991 | formats are: |
---|
992 | |
---|
993 | \begin{itemize} |
---|
994 | \item[ASAP] This is the internal format used for ASAP. It is the only |
---|
995 | format that allows the user to restore the data, fits etc. without |
---|
996 | loosing any information. As mentioned before, the ASAP scantable is |
---|
997 | an AIPS++ Table (a memory-based table). This function just converts |
---|
998 | it to a disk-based Table. You can the access that Table with the |
---|
999 | AIPS++ Table browser or any other AIPS++ tool. |
---|
1000 | |
---|
1001 | \item[SDFITS] The Single Dish FITS format. This format was designed to |
---|
1002 | for interchange between packages, but few packages actually can read |
---|
1003 | it. |
---|
1004 | |
---|
1005 | %\item[FITS] This uses simple ``image'' fits to save the data, each row |
---|
1006 | % being written to a separate fits file. This format is suitable for |
---|
1007 | % importing the data into CLASS. |
---|
1008 | |
---|
1009 | \item[ASCII] A simple text based format suitable for the user to |
---|
1010 | processing using Perl or, Python, gnuplot etc. |
---|
1011 | |
---|
1012 | \item[MS2] Saves the data in an aips++ MeasurementSet V2 format. |
---|
1013 | You can also access this with the Table browser and other AIPS++ |
---|
1014 | tools. |
---|
1015 | |
---|
1016 | \end{itemize} |
---|
1017 | |
---|
1018 | The default output format can be set in the users {\tt .asaprc} file. |
---|
1019 | Typical usages are: |
---|
1020 | |
---|
1021 | \begin{verbatim} |
---|
1022 | ASAP>scans.save('myscans') # Save in default format |
---|
1023 | ASAP>scans.save('myscans', overwrite=True) # Overwrite an existing file |
---|
1024 | \end{verbatim} |
---|
1025 | |
---|
1026 | \section{Plotter} |
---|
1027 | |
---|
1028 | \index{Plotter}Scantable spectra can be plotted at any time. An |
---|
1029 | asapplotter object is used for plotting, meaning multiple plot windows |
---|
1030 | can be active at the same time. On start up a default asapplotter |
---|
1031 | object is created called ``plotter''. This would normally be used for |
---|
1032 | standard plotting. |
---|
1033 | |
---|
1034 | The plotter, optionally, will run in a multi-panel mode and contain |
---|
1035 | multiple plots per panel. The user must tell the plotter how they want |
---|
1036 | the data distributed. This is done using the set\_mode function. The |
---|
1037 | default can be set in the users {\tt .asaprc} file. The units (and frame |
---|
1038 | etc) of the abscissa will be whatever has previously been set by |
---|
1039 | \cmd{set\_unit}, \cmd{set\_freqframe} etc. |
---|
1040 | |
---|
1041 | Typical plotter usage would be: |
---|
1042 | |
---|
1043 | \begin{verbatim} |
---|
1044 | ASAP>scans.set_unit('km/s') |
---|
1045 | ASAP>plotter.set_mode(stacking='p',panelling='t') |
---|
1046 | ASAP>plotter.plot(scans) |
---|
1047 | \end{verbatim} |
---|
1048 | |
---|
1049 | This will plot multiple polarisation within each plot panel and each |
---|
1050 | scan row in a separate panel. |
---|
1051 | |
---|
1052 | Other possibilities include: |
---|
1053 | |
---|
1054 | \begin{verbatim} |
---|
1055 | # Plot multiple IFs per panel |
---|
1056 | ASAP>plotter.set_mode(stacking='i',panelling='t') |
---|
1057 | |
---|
1058 | # Plot multiple beams per panel |
---|
1059 | ASAP>plotter.set_mode(stacking='b',panelling='t') |
---|
1060 | |
---|
1061 | # Plot one IF per panel, time stacked |
---|
1062 | ASAP>plotter.set_mode('t', 'i') |
---|
1063 | |
---|
1064 | # Plot each scan in a seperate panel |
---|
1065 | ASAP>plotter.set_mode('t', 's') |
---|
1066 | |
---|
1067 | \end{verbatim} |
---|
1068 | |
---|
1069 | \subsection{Plot Selection} |
---|
1070 | \label{sec:plotter_cursor} |
---|
1071 | |
---|
1072 | \index{Plotter!selection}The plotter can plot up to 25 panels and |
---|
1073 | stacked spectra per panel. If you have data larger than this (or for |
---|
1074 | your own sanity) you need to select a subset of this data. This is |
---|
1075 | particularly true for multibeam or multi IF data. The selector object |
---|
1076 | should be used for this purpose. Selection can either be applied to |
---|
1077 | the scantable or directly to the plotter, the end result is the same. |
---|
1078 | You don't have to reset the scantable selection though, if you set |
---|
1079 | the selection on the plotter. |
---|
1080 | |
---|
1081 | Examples: |
---|
1082 | |
---|
1083 | \begin{verbatim} |
---|
1084 | ASAP>selection = selector() |
---|
1085 | # Select second IF |
---|
1086 | ASAP>selection.set_ifs(1) |
---|
1087 | ASAP>plotter.set_selection(selection) |
---|
1088 | |
---|
1089 | # Select first 4 beams |
---|
1090 | ASAP>selection.set_beams([0,1,2,3]) |
---|
1091 | ASAP>plotter.set_selection(selection) |
---|
1092 | |
---|
1093 | # Select a few scans |
---|
1094 | ASAP>selection.set_scans([2,4,6,10]) |
---|
1095 | ASAP>plotter.set_selection(selection) |
---|
1096 | |
---|
1097 | # Multiple selection |
---|
1098 | ASAP>selection.set_ifs(1) |
---|
1099 | ASAP>selection.set_scans([2,4,6,10]) |
---|
1100 | ASAP>plotter.set_selection(selection) |
---|
1101 | |
---|
1102 | \end{verbatim} |
---|
1103 | |
---|
1104 | \subsection{Plot Control} |
---|
1105 | |
---|
1106 | \index{Plotter!control}The plotter window has a row of buttons on the |
---|
1107 | lower left. These can be used to control the plotter (mostly for |
---|
1108 | zooming the individual plots). From left to right: |
---|
1109 | |
---|
1110 | \begin{tabular}{ll} |
---|
1111 | |
---|
1112 | Home & This will unzoom the plots to the original zoom factor \\ |
---|
1113 | |
---|
1114 | Plot history & \parbox[t]{0.8\textwidth}{(left and right arrow) The |
---|
1115 | plotter keeps a history of zoom settings. The left arrow sets the plot |
---|
1116 | zoom to the previous value. The right arrow returns back again. This |
---|
1117 | allows you, for example, to zoom in on one feature then return the |
---|
1118 | plot to how it was previously. }\\ |
---|
1119 | |
---|
1120 | Pan & \parbox[t]{0.8\textwidth}{(The Cross) This sets the cursor to |
---|
1121 | pan, or scroll mode allowing you to shift the plot within the |
---|
1122 | window. Useful when zoomed in on a feature. }\\ |
---|
1123 | |
---|
1124 | Zoom & \parbox[t]{0.8\textwidth}{(the letter with the magnifying |
---|
1125 | glass) lets you draw a rectangle around a region of interest then |
---|
1126 | zooms in on that region. Use the plot history to unzoom again.}\\ |
---|
1127 | |
---|
1128 | Adjust & \parbox[t]{0.8\textwidth}{(rectangle with 4 arrows) adjust |
---|
1129 | subplot parameters (space at edge of plots)}\\ |
---|
1130 | |
---|
1131 | Save & \parbox[t]{0.8\textwidth}{(floppy disk). Save the plot as a |
---|
1132 | postscript or .png file}\\ |
---|
1133 | |
---|
1134 | \end{tabular} |
---|
1135 | |
---|
1136 | You can also type ``g'' in the plot window to toggle on and off grid |
---|
1137 | lines. Typing 'l' turns on and off logarithmic Y-axis. |
---|
1138 | |
---|
1139 | \subsection{Other control} |
---|
1140 | |
---|
1141 | The plotter has a number of functions to describe the layout of the |
---|
1142 | plot. These include \cmd{set\_legend}, \cmd{set\_layout} and \cmd{set\_title}. |
---|
1143 | |
---|
1144 | To set the exact velocity or channel range to be plotted use the |
---|
1145 | \cmd{set\_range} function. To reset to the default value, call |
---|
1146 | \cmd{set\_range} with no arguments. E.g. |
---|
1147 | |
---|
1148 | \begin{verbatim} |
---|
1149 | ASAP>scans.set_unit('km/s') |
---|
1150 | ASAP>plotter.plot(scans) |
---|
1151 | ASAP>plotter.set_range(-150,-50) |
---|
1152 | ASAP>plotter.set_range() # To reset |
---|
1153 | \end{verbatim} |
---|
1154 | |
---|
1155 | Both the range of the ``x'' and ``y'' axis can be set at once, if desired: |
---|
1156 | |
---|
1157 | \begin{verbatim} |
---|
1158 | ASAP>plotter.set_range(-10,30,-1,6.6) |
---|
1159 | \end{verbatim} |
---|
1160 | |
---|
1161 | To save a hardcopy of the current plot, use the save function, e.g. |
---|
1162 | |
---|
1163 | \begin{verbatim} |
---|
1164 | ASAP>plotter.save('myplot.ps') |
---|
1165 | ASAP>plotter.save('myplot.png', dpi=80) |
---|
1166 | \end{verbatim} |
---|
1167 | |
---|
1168 | \subsection{Plotter Customisation} |
---|
1169 | |
---|
1170 | The plotter allows the user to change most properties such as text |
---|
1171 | size and colour. The \cmd{commands} function and {\cmd help\ |
---|
1172 | asapplotter} list all the possible commands that can be used with the |
---|
1173 | plotter. |
---|
1174 | |
---|
1175 | \commanddef{set\_colors}{Change the default colours used for line |
---|
1176 | plotting. Colours can be given either by name, using the html standard |
---|
1177 | (e.g. red, blue or hotpink), or hexadecimal code (e.g. for black |
---|
1178 | \#000000). If less colours are specified than lines plotted , the |
---|
1179 | plotter cycles through the colours. Example:} {ASAP> |
---|
1180 | plotter.set\_colors('red blue green')\\ ASAP> |
---|
1181 | plotter.set\_colors(`\#0000 blue \#FF00FF')\\ } |
---|
1182 | |
---|
1183 | \commanddef{set\_linestyles}{Change the line styles used for |
---|
1184 | plots. Allowable values are 'line', 'dashed', 'dotted', 'dashdot', |
---|
1185 | 'dashdotdot' and 'dashdashdot. Example: }{ |
---|
1186 | ASAP>plotter.set\_linestyles('line dash cotted datshot.)\\ |
---|
1187 | ASAP>plotter.set\_font(size=10)\\ |
---|
1188 | } |
---|
1189 | |
---|
1190 | \commanddef{set\_font}{Change the font style and size. Example}{ |
---|
1191 | ASAP>plotter.set\_font(weight='bold')\\ |
---|
1192 | ASAP>plotter.set\_font(size=10)\\ |
---|
1193 | ASAP>plotter.set\_font(style='italic')\\ |
---|
1194 | } |
---|
1195 | |
---|
1196 | \commanddef{set\_layout}{Change the multi-panel layout, i.e. now many |
---|
1197 | rows and columns}{ |
---|
1198 | ASAP>plotter.set\_layout(3,2) |
---|
1199 | } |
---|
1200 | |
---|
1201 | \commanddef{set\_legend}{Set the position, size and optional value of the legend}{ |
---|
1202 | ASAP>plotter.set\_legend(fontsize=16)\\ |
---|
1203 | ASAP>plotter.set\_legend(mode=0) \# ASAP chooses where to put the legend\\ |
---|
1204 | ASAP>plotter.set\_legend(mode=4) \# Put legend on lower right\\ |
---|
1205 | ASAP>plotter.set\_legend(mode=-1) \# No legend\\ |
---|
1206 | ASAP>plotter.set\_legend(mp=['RR','LL']) \# Specify legend labels\\ |
---|
1207 | ASAP>plotter.set\_legend(mp=[r'\$\^\{12\}CO\$',r'\$\^\{13\}CO\$']) \# Latex labels |
---|
1208 | } |
---|
1209 | |
---|
1210 | \commanddef{set\_title}{Set the plot title. If multiple panels are |
---|
1211 | plotted, multiple titles have to be specified}{ |
---|
1212 | ASAP>plotter.set\_title(`G323.12$-$1.79`)\\ |
---|
1213 | ASAP>plotter.set\_title([`SiO`, 'Methanol'], fontsize=18)\\ |
---|
1214 | } |
---|
1215 | |
---|
1216 | \subsection{Plotter Annotations} |
---|
1217 | |
---|
1218 | The plotter allows various annotations (lines, arrows, text and |
---|
1219 | ``spans'') to be added to the plot. These annotations are |
---|
1220 | ``temporary'', when the plotter is next refreshed |
---|
1221 | (e.g. \cmd{plotter.plot} or \cmd{plotter.set\_range}) the annotations |
---|
1222 | will be removed. |
---|
1223 | |
---|
1224 | \bigcommanddef{arrow(x,y,x+dx,y+dy)}{Draw an arrow from a specified |
---|
1225 | \cmd{(x,y)} position to \cmd{(x+dx, y+dy)}. The values are in world |
---|
1226 | coordinates. Addition arguments which must be passed are {\cmd head\_width} and \cmd{head\_length}}{ |
---|
1227 | ASAP>plotter.arrow(-40,7,35,0,head\_width=0.2, head\_length=10) |
---|
1228 | } |
---|
1229 | |
---|
1230 | \bigcommanddef{axhline(y, xmin, xmax)}{Draw a horizontal line at the |
---|
1231 | specified \cmd{y} position (in world coordinates) between xmin and xmax |
---|
1232 | (in relative coordinates, i.e. 0.0 is the left hand edge of the plot |
---|
1233 | while 1.0 is the right side of the plot).}{ |
---|
1234 | ASAP>plotter.axhline(6.0,0.2,0.8) |
---|
1235 | } |
---|
1236 | |
---|
1237 | \bigcommanddef{avhline(x, ymin, ymax)}{Draw a vertical line at the |
---|
1238 | specified \cmd{x} position (in world coordinates) between \cmd{ymin} |
---|
1239 | and \cmd{ymax} (in relative coordinates, i.e. 0.0 is the left hand edge |
---|
1240 | of the plot while 1.0 is the right side of the plot).}{ |
---|
1241 | ASAP>plotter.axvline(-50.0,0.1,1.0) |
---|
1242 | } |
---|
1243 | |
---|
1244 | \bigcommanddef{axhspan(ymin, ymax, \\ \hspace*{20mm}xmin, |
---|
1245 | xmax)}{Overlay a transparent colour rectangle. \cmd{ymin} and |
---|
1246 | \cmd{ymax} are given in world coordinates while \cmd{xmin} and |
---|
1247 | \cmd{xmax} are given in relative coordinates}{ |
---|
1248 | ASAP>plotter.axhspan(2,4,0.25,0.75) |
---|
1249 | } |
---|
1250 | |
---|
1251 | \bigcommanddef{axvspan(xmin, xmax, \\ \hspace*{20mm} ymin, |
---|
1252 | ymax)}{Overlay a transparent colour rectangle. \cmd{ymin} and |
---|
1253 | \cmd{ymax} are given in relative coordinates while \cmd{xmin} and |
---|
1254 | \cmd{xmax} are given in world coordinates}{ |
---|
1255 | ASAP>plotter.axvspan(-50,60,0.2,0.5) |
---|
1256 | } |
---|
1257 | |
---|
1258 | \bigcommanddef{text(x, y, str)}{Place the string \cmd{str} at the |
---|
1259 | given \cmd{(x,y)} position in world coordinates.}{ |
---|
1260 | ASAP>plotter.text(-10,7,"CO") |
---|
1261 | } |
---|
1262 | |
---|
1263 | These functions all take a set of \cmd{kwargs} commands. These can be |
---|
1264 | used to set colour, linewidth fontsize etc. These are standard |
---|
1265 | matplotlib settings. Common ones include: |
---|
1266 | |
---|
1267 | \begin{tabular}{ll} |
---|
1268 | \tt color, facecolor, edgecolor \\ |
---|
1269 | \tt width, linewidth \\ |
---|
1270 | \tt fontsize \\ |
---|
1271 | \tt fontname & Sans, Helvetica, Courier, Times etc\\ |
---|
1272 | \tt rotation & Text rotation (horizontal, vertical) \\ |
---|
1273 | \tt alpha & The alpha transparency on 0-1 scale\\ |
---|
1274 | \end{tabular} |
---|
1275 | |
---|
1276 | Examples: |
---|
1277 | \begin{verbatim} |
---|
1278 | ASAP>plotter.axhline(6.0,0.2,0.8, color='red', linewidth=3) |
---|
1279 | ASAP>plotter.text(-10,7,"CO", fontsize=20) |
---|
1280 | \end{verbatim} |
---|
1281 | |
---|
1282 | \section{Line Catalog} |
---|
1283 | \label{sec:linecat} |
---|
1284 | \index{Linecatalog}ASAP can load and manipulate line catlogs to |
---|
1285 | retrieve rest frequencies for \cmd{set\_restfreqs} and for line |
---|
1286 | identification in the plotter. All line catalogs are loaded into a ``linecatalog'' object. |
---|
1287 | |
---|
1288 | No line catalogs are built into ASAP, the user must load a ASCII based |
---|
1289 | table (which can optionally be saved in an internal format) either of |
---|
1290 | the users own creation or a standard line catalog such as the JPL line |
---|
1291 | catalog or Lovas. The ATNF asap ftp area as copies of the JPL and |
---|
1292 | Lovas catalog in the appropriate format: |
---|
1293 | |
---|
1294 | \hspace{1cm}\cmd{ftp://ftp.atnf.csiro.au/pub/software/asap/data} |
---|
1295 | |
---|
1296 | |
---|
1297 | \subsection{Loading a Line Catalog} |
---|
1298 | |
---|
1299 | \index{Linecatalog!loading}The ASCII text line catalog must have at |
---|
1300 | least 4 columns. The first four columns must contain (in order): |
---|
1301 | Molecule name, frequency in MHz, frequency error and ``intensity'' |
---|
1302 | (any units). If the molecule name contains any spaces, they must be |
---|
1303 | wrapped in quotes \verb+""+. |
---|
1304 | |
---|
1305 | A sample from the JPL line catalog: |
---|
1306 | |
---|
1307 | \begin{verbatim} |
---|
1308 | H2D+ 3955.2551 228.8818 -7.1941 |
---|
1309 | H2D+ 12104.7712 177.1558 -6.0769 |
---|
1310 | H2D+ 45809.2731 118.3223 -3.9494 |
---|
1311 | CH 701.6811 .0441 -7.1641 |
---|
1312 | CH 724.7709 .0456 -7.3912 |
---|
1313 | CH 3263.7940 .1000 -6.3501 |
---|
1314 | CH 3335.4810 .1000 -6.0304 |
---|
1315 | \end{verbatim} |
---|
1316 | |
---|
1317 | To load a line catalog then save it in the internal format: |
---|
1318 | |
---|
1319 | \begin{verbatim} |
---|
1320 | ASAP>jpl = linecatalog('jpl_pruned.txt') |
---|
1321 | ASAP>jpl.save('jpl.tbl') |
---|
1322 | \end{verbatim} |
---|
1323 | |
---|
1324 | Later the saved line catalog can reloaded: |
---|
1325 | |
---|
1326 | \begin{verbatim} |
---|
1327 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
1328 | \end{verbatim} |
---|
1329 | |
---|
1330 | {\em NOTE:} Due to a bug in ipython, if you do not \cmd{del} the |
---|
1331 | linecatalog table before quiting asap, you will be left with temporary |
---|
1332 | files. It is safe to delete these once asap has finished. |
---|
1333 | |
---|
1334 | \subsection{Line selection} |
---|
1335 | |
---|
1336 | \index{Linecatalog!line selection}The linecatalog has a number of |
---|
1337 | selection functions to select a range of lines from a larger catalog |
---|
1338 | (the JPL catalog has $>$180000 lines for |
---|
1339 | example). \cmd{set\_frequency\_limits} selects on frequency range, |
---|
1340 | \cmd{set\_strength\_limits} selects on intensity while \cmd{set\_name} |
---|
1341 | selects on molecule name (wild cards allowed). The \cmd{summary} |
---|
1342 | function lists the currently selected lines. |
---|
1343 | |
---|
1344 | \begin{verbatim} |
---|
1345 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
1346 | ASAP>jpl.set_frequency_limits(80,115,'GHz') # Lines for 3mm receiver |
---|
1347 | ASAP>jpl.set_name('*OH') # Select all alcohols |
---|
1348 | ASAP>jpl.set_name('OH') # Select only OH molecules |
---|
1349 | ASAP>jpl.summary() |
---|
1350 | |
---|
1351 | ASAP>jpl.reset() # Selections are accumulative |
---|
1352 | ASAP>jpl.set_frequency_limits(80,115,'GHz') |
---|
1353 | ASAP>jpl.set_strength_limits(-2,10) # Select brightest lines |
---|
1354 | ASAP>jpl.summary() |
---|
1355 | \end{verbatim} |
---|
1356 | |
---|
1357 | \subsection{Using Linecatalog} |
---|
1358 | |
---|
1359 | The line catalogs can be used for line overlays on the plotter or with |
---|
1360 | \cmd{set\_restfreq}. |
---|
1361 | |
---|
1362 | \subsubsection{Plotting linecatalog} |
---|
1363 | |
---|
1364 | \index{Linecatalog!plotting} |
---|
1365 | |
---|
1366 | The plotter \cmd{plot\_lines} function takes a line catalog as an |
---|
1367 | argument and overlays the lines on the spectrum. {\em Currently this |
---|
1368 | only works when plotting in units of frequency (Hz, GHz etc).} If a |
---|
1369 | large line catalog has been loaded (e.g. JPL) it is highly recommended |
---|
1370 | that you use the selection functions to narrow down the number of |
---|
1371 | lines. By default the line catalog overlay is plotted assuming a line |
---|
1372 | velocity of 0.0. This can be set using the \cmd{doppler} argument (in |
---|
1373 | km/s). Each time \cmd{plot\_lines} is called the new lines are added |
---|
1374 | to any existing line catalog annotations. These are all removed after |
---|
1375 | the next call to \cmd{plotter.plot()}. |
---|
1376 | |
---|
1377 | \begin{verbatim} |
---|
1378 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
1379 | ASAP>jpl.set_frequency_limits(23,24,'GHz') |
---|
1380 | ASAP>data.set_unit('GHz') # Only works with freq axis currently |
---|
1381 | ASAP>plotter.plot(data) |
---|
1382 | ASAP>plotter.plot_lines(jpl) |
---|
1383 | |
---|
1384 | ASAP>plotter.plot() # Reset plotter |
---|
1385 | ASAP>plotter.plot_lines(jpl,doppler=-10,location='Top') |
---|
1386 | # On top with -10 km/s velocity |
---|
1387 | \end{verbatim} |
---|
1388 | |
---|
1389 | \subsubsection{Setting Rest Frequencies} |
---|
1390 | |
---|
1391 | \index{Linecatalog!set\_restfreq}A linecatalog can be used as an |
---|
1392 | argument for \cmd{set\_restfreqs}. If a personal line catalog has been |
---|
1393 | used (which has the same size as the number of number of IFs) or |
---|
1394 | linecatalog selection has been used to reduce the number of entries, |
---|
1395 | the line catalog can be used directly as an argument to |
---|
1396 | \cmd{set\_restfreqs}, e.g.: |
---|
1397 | \begin{verbatim} |
---|
1398 | ASAP>jpl = linecatalog('jpl.tbl') |
---|
1399 | ASAP>jpl.set_frequency_limits(23.66,23.75,'GHz') |
---|
1400 | ASAP>data = scantable('data.rpf') |
---|
1401 | ASAP>data.set_restfreqs(jpl) |
---|
1402 | \end{verbatim} |
---|
1403 | |
---|
1404 | If a larger linecatalog is used, individual elements can be used. Use |
---|
1405 | the \cmd{summary} to get the index number of the rest frequency you |
---|
1406 | wish to use. E.g.: |
---|
1407 | |
---|
1408 | \begin{verbatim} |
---|
1409 | ASAP>jpl.summary() |
---|
1410 | ASAP>data.set_restfreqs([jpl[11],[jpl[21]]) |
---|
1411 | \end{verbatim} |
---|
1412 | |
---|
1413 | For data with many IFs, such as from MOPS, the user it is recommended |
---|
1414 | that the user creates their own line cstalog for the data and use this |
---|
1415 | to set the rest frequency for each IF. |
---|
1416 | |
---|
1417 | \section{Fitting} |
---|
1418 | |
---|
1419 | \index{Fitting}Currently multicomponent Gaussian function is |
---|
1420 | available. This is done by creating a fitting object, setting up the |
---|
1421 | fit and actually fitting the data. Fitting can either be done on a |
---|
1422 | single scantable selection or on an entire scantable using the |
---|
1423 | \cmd{auto\_fit} function. If single value fitting is used, and the |
---|
1424 | current selection includes multiple spectra (beams, IFs, scans etc) |
---|
1425 | then the first spectrum in the scantable will be used for fitting. |
---|
1426 | |
---|
1427 | \begin{verbatim} |
---|
1428 | ASAP>f = fitter() |
---|
1429 | ASAP>f.set_function(gauss=2) # Fit two Gaussians |
---|
1430 | ASAP>f.set_scan(scans) |
---|
1431 | ASAP>selection = selector() |
---|
1432 | ASAP>selection.set_polarisations(1) # Fit the second polarisation |
---|
1433 | ASAP>scans.set_selection(selection) |
---|
1434 | ASAP>scans.set_unit('km/s') # Make fit in velocity units |
---|
1435 | ASAP>f.fit(1) # Run the fit on the second row in the table |
---|
1436 | ASAP>f.plot() # Show fit in a plot window |
---|
1437 | ASAP>f.get_parameters() # Return the fit paramaters |
---|
1438 | \end{verbatim} |
---|
1439 | |
---|
1440 | This auto-guesses the initial values of the fit and works well for data |
---|
1441 | without extra confusing features. Note that the fit is performed in |
---|
1442 | whatever unit the abscissa is set to. |
---|
1443 | |
---|
1444 | If you want to confine the fitting to a smaller range (e.g. to avoid |
---|
1445 | band edge effects or RFI you must set a mask. |
---|
1446 | |
---|
1447 | \begin{verbatim} |
---|
1448 | ASAP>f = fitter() |
---|
1449 | ASAP>f.set_function(gauss=2) |
---|
1450 | ASAP>scans.set_unit('km/s') # Set the mask in channel units |
---|
1451 | ASAP>msk = s.create_mask([1800,2200]) |
---|
1452 | ASAP>scans.set_unit('km/s') # Make fit in velocity units |
---|
1453 | ASAP>f.set_scan(s,msk) |
---|
1454 | ASAP>f.fit() |
---|
1455 | ASAP>f.plot() |
---|
1456 | ASAP>f.get_parameters() |
---|
1457 | \end{verbatim} |
---|
1458 | |
---|
1459 | If you wish, the initial parameter guesses can be specified and |
---|
1460 | specific parameters can be fixed: |
---|
1461 | |
---|
1462 | \begin{verbatim} |
---|
1463 | ASAP>f = fitter() |
---|
1464 | ASAP>f.set_function(gauss=2) |
---|
1465 | ASAP>f.set_scan(s,msk) |
---|
1466 | ASAP>f.fit() # Fit using auto-estimates |
---|
1467 | # Set Peak, centre and fwhm for the second gaussian. |
---|
1468 | # Force the centre to be fixed |
---|
1469 | ASAP>f.set_gauss_parameters(0.4,450,150,0,1,0,component=1) |
---|
1470 | ASAP>f.fit() # Re-run the fit |
---|
1471 | \end{verbatim} |
---|
1472 | |
---|
1473 | The fitter \cmd{plot} function has a number of options to either view |
---|
1474 | the fit residuals or the individual components (by default it plots |
---|
1475 | the sum of the model components). |
---|
1476 | |
---|
1477 | Examples: |
---|
1478 | |
---|
1479 | \begin{verbatim} |
---|
1480 | # Plot the residual |
---|
1481 | ASAP>f.plot(residual=True) |
---|
1482 | |
---|
1483 | # Plot the first 2 componentsa |
---|
1484 | ASAP>f.plot(components=[0,1]) |
---|
1485 | |
---|
1486 | # Plot the first and third component plus the model sum |
---|
1487 | ASAP>f.plot(components=[-1,0,2]) # -1 means the compoment sum |
---|
1488 | \end{verbatim} |
---|
1489 | |
---|
1490 | \subsection{Fit saving} |
---|
1491 | |
---|
1492 | \index{Fitter!Fit saving}One you are happy with your fit, it is |
---|
1493 | possible to store it as part of the scantable. |
---|
1494 | |
---|
1495 | \begin{verbatim} |
---|
1496 | ASAP>f.store_fit() |
---|
1497 | \end{verbatim} |
---|
1498 | |
---|
1499 | This will be saved to disk with the data, if the ``ASAP'' file format |
---|
1500 | is selected. Multiple fits to the same data can be stored in the |
---|
1501 | scantable. |
---|
1502 | |
---|
1503 | The scantable function \cmd{get\_fit} can be used to retrieve the |
---|
1504 | stored fits. Currently the fit parameters are just printed to the |
---|
1505 | screen. |
---|
1506 | |
---|
1507 | \begin{verbatim} |
---|
1508 | ASAP>scans.get_fit(4) # Print fits for row 4 |
---|
1509 | \end{verbatim} |
---|
1510 | |
---|
1511 | A fit can also be exported to an ASCII file using the \cmd{store\_fit} |
---|
1512 | function. Simply give the name of the output file requires as an |
---|
1513 | argument. |
---|
1514 | |
---|
1515 | \begin{verbatim} |
---|
1516 | ASAP>f.store_fit('myfit.txt') |
---|
1517 | \end{verbatim} |
---|
1518 | |
---|
1519 | \section{Polarisation} |
---|
1520 | |
---|
1521 | \index{Polarisation}Currently ASAP only supports polarmetric analysis |
---|
1522 | on linearly polarised feeds and the cross polarisation products |
---|
1523 | measured. Other cases will be added on an as needed basis. |
---|
1524 | |
---|
1525 | Conversions of linears to Stokes or Circular polarisations are done |
---|
1526 | ``on-the-fly''. Leakage cannot be corrected for nor are there routines |
---|
1527 | to calibrate position angle offsets. |
---|
1528 | |
---|
1529 | \subsection{Simple Calibration} |
---|
1530 | |
---|
1531 | \index{Polarisation!calibration}It is possible that there is a phase |
---|
1532 | offset between polarisation which will effect the phase of the cross |
---|
1533 | polarisation correlation, and so give rise to spurious |
---|
1534 | polarisation. \cmd{rotate\_xyphase} can be used to correct for this |
---|
1535 | error. At this point, the user must know how to determine the size of |
---|
1536 | the phase offset themselves. |
---|
1537 | |
---|
1538 | \begin{verbatim} |
---|
1539 | ASAP>scans.rotate_xyphase(10.5) # Degrees |
---|
1540 | \end{verbatim} |
---|
1541 | |
---|
1542 | Note that if this function is run twice, the sum of the two values is |
---|
1543 | applied because it is done in-situ. |
---|
1544 | |
---|
1545 | A correction for the receiver parallactic angle may need to be made, |
---|
1546 | generally because of how it is mounted. Use \cmd{rotate\_linpolphase} |
---|
1547 | to correct the position angle. Running this function twice results in |
---|
1548 | the sum of the corrections being applied because it is applied |
---|
1549 | in-situ. |
---|
1550 | |
---|
1551 | \begin{verbatim} |
---|
1552 | ASAP>scans.rotate_linpolphase(-45) # Degrees; correct for receiver mounting |
---|
1553 | \end{verbatim} |
---|
1554 | |
---|
1555 | If the sign of the complex correlation is wrong (this can happen |
---|
1556 | depending on the correlator configuration), use \cmd{invert\_phase} to |
---|
1557 | change take the complex conjugate of the complex correlation |
---|
1558 | term. This is always performed in-situ. |
---|
1559 | |
---|
1560 | \begin{verbatim} |
---|
1561 | ASAP>scans.invert_phase() |
---|
1562 | \end{verbatim} |
---|
1563 | |
---|
1564 | Depending on how the correlator is configured, ``BA'' may be |
---|
1565 | correlated instead of ``AB''. Use \cmd{swap\_linears} to correct for |
---|
1566 | this problem: |
---|
1567 | |
---|
1568 | \begin{verbatim} |
---|
1569 | ASAP>scans.swap_linears() |
---|
1570 | \end{verbatim} |
---|
1571 | |
---|
1572 | \subsection{Conversion} |
---|
1573 | \label{sec:polconv} |
---|
1574 | |
---|
1575 | Data can be permanently converted between linear and circular |
---|
1576 | polarisations and stokes. |
---|
1577 | |
---|
1578 | \begin{verbatim} |
---|
1579 | ASAP>stokescans = linearscans.convert_pol("stokes") |
---|
1580 | \end{verbatim} |
---|
1581 | |
---|
1582 | |
---|
1583 | \subsection{Plotting} |
---|
1584 | \label{sec:polplot} |
---|
1585 | |
---|
1586 | \index{Polarisation!plotting}To plot Stokes values, a selector object |
---|
1587 | must be created and the set\_polarisation function used to select the |
---|
1588 | desired polarisation products. |
---|
1589 | |
---|
1590 | The values which can be plotted include a selection of [I,Q,U,V], [I, |
---|
1591 | Plinear, Pangle, V], [RR, LL] or [XX, YY, Real(XY), |
---|
1592 | Imaginary(XY)]. (Plinear and Pangle are the percentage and position |
---|
1593 | angle of linear polarisation). |
---|
1594 | |
---|
1595 | Example: |
---|
1596 | |
---|
1597 | \begin{verbatim} |
---|
1598 | ASAP>selection = selector() |
---|
1599 | |
---|
1600 | ASAP>selection.set_polarisations(``I Q U V'') |
---|
1601 | ASAP plotter.set_selection(selection); # Select I, Q, U \& V |
---|
1602 | |
---|
1603 | ASAP>selection.set_polarisations(``I Q'') |
---|
1604 | ASAP plotter.set_selection(selection); # Select just I \& Q |
---|
1605 | |
---|
1606 | ASAP>selection.set_polarisations(``RR LL'') |
---|
1607 | ASAP plotter.set_selection(selection); # Select just RR \& LL |
---|
1608 | |
---|
1609 | ASAP>selection.set_polarisations(``XX YY'') |
---|
1610 | ASAP plotter.set_selection(selection); # Select linears |
---|
1611 | |
---|
1612 | ASAP>selection.set_polarisations(``I Plinear'') |
---|
1613 | ASAP plotter.set_selection(selection); # Fractional linear |
---|
1614 | |
---|
1615 | ASAP>selection.set_polarisations(``Pangle'') |
---|
1616 | ASAP plotter.set_selection(selection); # Position angle |
---|
1617 | |
---|
1618 | \end{verbatim} |
---|
1619 | |
---|
1620 | Scan, beam and IF selection are also available in the selector object as |
---|
1621 | describe in section~\ref{sec:selection}. |
---|
1622 | |
---|
1623 | \section{Specialised Processing} |
---|
1624 | |
---|
1625 | \subsection{Multibeam MX mode} |
---|
1626 | |
---|
1627 | MX mode is a specific observing approach with a multibeam where a |
---|
1628 | single source is observed cycling through each beam. The scans when |
---|
1629 | the beam is off source is used as a reference for the on-source |
---|
1630 | scan. The function \cmd{mx\_quotient} is used to make a quotient |
---|
1631 | spectrum from an MX cycle. This works averaging the ``off-source'' |
---|
1632 | scans for each beam (either a median average or mean) and using this |
---|
1633 | as a reference scan in a normal quotient (for each beam). The final |
---|
1634 | spectrum for each beam is returned on a new scantable containing |
---|
1635 | single scan (it the scan numbers are re-labelled to be the same). Note |
---|
1636 | that the current version of \cmd{mx\_quotient} only handles a single |
---|
1637 | MX cycle, i.e. if each beam has observed the source multiple times you |
---|
1638 | will need to use the selector object multiple times to select a single |
---|
1639 | MX cycle, run \cmd{mx\_quotient} for each cycle then merge the |
---|
1640 | resulting scan tables back together. |
---|
1641 | |
---|
1642 | Example: |
---|
1643 | |
---|
1644 | \begin{verbatim} |
---|
1645 | ASAP>scans = scantable('mydata.rpf') |
---|
1646 | ASAP>q = scans.mx_quotient() |
---|
1647 | ASAP>plotter.plot(q) |
---|
1648 | \end{verbatim} |
---|
1649 | |
---|
1650 | The function \cmd{average\_beam} averages multiple beam data |
---|
1651 | together. This is need if MX mode has been used to make a long |
---|
1652 | integration on a single source. E.g. |
---|
1653 | |
---|
1654 | \begin{verbatim} |
---|
1655 | ASAP>av = q.average_beam() |
---|
1656 | \end{verbatim} |
---|
1657 | |
---|
1658 | \subsection{Frequency Switching} |
---|
1659 | |
---|
1660 | {\em FILL ME IN} |
---|
1661 | |
---|
1662 | \subsection{Disk Based Processing} |
---|
1663 | \index{Scantable!disk based} |
---|
1664 | |
---|
1665 | Normally scantables exist entirely in memory during an ASAP |
---|
1666 | session. This has the advantage of speed, but causes limits on the |
---|
1667 | size of the dataset which can be loaded. ASAP can use ``disk based'' |
---|
1668 | scan tables which cache the bulk of the scantable on disk and require |
---|
1669 | significantly less memory usage. |
---|
1670 | |
---|
1671 | To use disk based tables you either need to change the default in your |
---|
1672 | \cmd{.asapr} file, e.g. |
---|
1673 | \begin{verbatim} |
---|
1674 | scantable.storage : disk |
---|
1675 | \end{verbatim} |
---|
1676 | |
---|
1677 | or use set the ``\cmd{rc}'' value while running asap to change this |
---|
1678 | on-the-fly. E.g. |
---|
1679 | \begin{verbatim} |
---|
1680 | ASAP>rc('scantable',storage='disk') |
---|
1681 | ASAP>data = scantable('data.rpf') # Loaded using disk based table |
---|
1682 | ASAP>rc('scantable',storage='memory') # Memory tables will be used now |
---|
1683 | \end{verbatim} |
---|
1684 | |
---|
1685 | Changing the ``\cmd{rc}'' value affects the next time the |
---|
1686 | \cmd{scantable} constructor is called. |
---|
1687 | |
---|
1688 | {\bf NOTE: } Currently a bug in ipython means temporary files are not |
---|
1689 | cleaned up properly when you exit ASAP. If you use disk based scan |
---|
1690 | tables your directory will be left with 'tabXXXXX\_X' directories. These can |
---|
1691 | be safely removed if ASAP is not running. |
---|
1692 | |
---|
1693 | \section{Scantable Mathematics} |
---|
1694 | |
---|
1695 | \index{Scantable!maths}It is possible to to simple mathematics |
---|
1696 | directly on scantables from the command line using the \cmd{+, -, *, |
---|
1697 | /} operators as well as their cousins \cmd{+=, -= *=, /=}. This works |
---|
1698 | between a scantable and a float. (Note that it does |
---|
1699 | not work for integers). |
---|
1700 | |
---|
1701 | {\em Currently mathematics between two scantables is not available } |
---|
1702 | |
---|
1703 | % ASAP>sum = scan1+scan2 |
---|
1704 | \begin{verbatim} |
---|
1705 | ASAP>scan2 = scan1+2.0 |
---|
1706 | ASAP>scan *= 1.05 |
---|
1707 | \end{verbatim} |
---|
1708 | |
---|
1709 | \section{Scripting} |
---|
1710 | |
---|
1711 | \index{Scripting}Because ASAP is based on python, it easy for the user |
---|
1712 | write their own scripts and functions to process data. This is highly |
---|
1713 | recommended as most processing of user data could then be done in a |
---|
1714 | couple of steps using a few simple user defined functions. A Python |
---|
1715 | primer is beyond the scope of this userguide. See the ASAP home pages |
---|
1716 | for a scripting tutorial or the main python website for comprehensive |
---|
1717 | documentation. |
---|
1718 | |
---|
1719 | \hspace{1cm} http://www.atnf.csiro.au/computing/software/asap/tutorials |
---|
1720 | |
---|
1721 | \hspace{1cm} http://www.python.org/doc/Introduction.html |
---|
1722 | |
---|
1723 | \subsection{Running scripts} |
---|
1724 | |
---|
1725 | The ASAP global function \cmd{execfile} reads the named text file and |
---|
1726 | executes the contained python code. This file can either contain |
---|
1727 | function definitions which will be used in subsequent processing or |
---|
1728 | just a set of commands to process a specific dataset. |
---|
1729 | |
---|
1730 | \subsection{asapuserfuncs.py} |
---|
1731 | |
---|
1732 | The file $\sim$/.asap/asapuserfuncs.py is automatically read in when |
---|
1733 | ASAP is started. The user can use this to define a set of user |
---|
1734 | functions which are automatically available each time ASAP is |
---|
1735 | used. The \cmd{execfile} function can be called from within this file. |
---|
1736 | |
---|
1737 | \section{Worked examples} |
---|
1738 | |
---|
1739 | In the following section a few examples of end-to-end processing of |
---|
1740 | some data in ASAP are given. |
---|
1741 | |
---|
1742 | \subsection{Mopra} |
---|
1743 | \index{Mopra} |
---|
1744 | |
---|
1745 | The following example is of some dual polarisation, position switched |
---|
1746 | data from Mopra. The source has been observed multiple times split |
---|
1747 | into a number of separate RPFITS files. To make the processing easier, |
---|
1748 | the first step is to \cmd{cat} the separate RPFITS files together and |
---|
1749 | load as a whole (future versions of ASAP will make this unnecessary). |
---|
1750 | |
---|
1751 | |
---|
1752 | \begin{verbatim} |
---|
1753 | # get a list of the individual rpfits files in the current directory |
---|
1754 | myfiles = list_files() |
---|
1755 | |
---|
1756 | # Load the data into a scantable |
---|
1757 | data = scantable(myfiles) |
---|
1758 | print data |
---|
1759 | |
---|
1760 | # Form the quotient spectra |
---|
1761 | q = data.auto_quotient() |
---|
1762 | print q |
---|
1763 | |
---|
1764 | # Look at the spectra |
---|
1765 | plotter.plot(q) |
---|
1766 | |
---|
1767 | # Set unit and reference frame |
---|
1768 | q.set_unit('km/s') |
---|
1769 | q.set_freqframe('LSRK') |
---|
1770 | |
---|
1771 | # Average all scans in time, aligning in velocity |
---|
1772 | av = q.average_time(align=True) |
---|
1773 | plotter.plot(av) |
---|
1774 | |
---|
1775 | # Remove the baseline |
---|
1776 | msk = av.create_mask([100,130],[160,200]) |
---|
1777 | av.poly_baseline(msk,2) |
---|
1778 | |
---|
1779 | # Average the two polarisations together |
---|
1780 | iav = av.average_pol() |
---|
1781 | print iav |
---|
1782 | plotter.plot(iav) |
---|
1783 | |
---|
1784 | # Set a sensible velocity range on the plot |
---|
1785 | plotter.set_range(85,200) |
---|
1786 | |
---|
1787 | # Smooth the data a little |
---|
1788 | av.smooth('gauss',4) |
---|
1789 | plotter.plot() |
---|
1790 | |
---|
1791 | # Fit a guassian to the emission |
---|
1792 | f = fitter() |
---|
1793 | f.set_function(gauss=1) |
---|
1794 | f.set_scan(av) |
---|
1795 | f.fit() |
---|
1796 | |
---|
1797 | # View the fit |
---|
1798 | f.plot() |
---|
1799 | |
---|
1800 | # Get the fit parameters |
---|
1801 | f.get_parameters() |
---|
1802 | |
---|
1803 | \end{verbatim} |
---|
1804 | |
---|
1805 | |
---|
1806 | \subsection{Parkes Polarimetry} |
---|
1807 | |
---|
1808 | \index{Parkes}\index{Polarisation}The following example is processing |
---|
1809 | of some Parkes polarimetric observations of OH masers at |
---|
1810 | 1.6~GHz. Because digital filters where used in the backend, the |
---|
1811 | baselines are stable enough not to require a quotient spectra. The |
---|
1812 | 4~MHz bandwidth is wide enough to observe both the 1665 and 1667~MHz |
---|
1813 | OH maser transitions. Each source was observed once for about 10 |
---|
1814 | minutes. Tsys information was not written to the RPFITS file (a |
---|
1815 | nominal 25K values was used), so the amplitudes need to be adjusted |
---|
1816 | based on a separate log file. A simple user function is used to |
---|
1817 | simplify this, contained in a file called mypol.py: |
---|
1818 | |
---|
1819 | \begin{verbatim} |
---|
1820 | def xyscale(data,xtsys=1.0,ytsys=1.0,nomtsys=25.0) : |
---|
1821 | |
---|
1822 | selection = selector() |
---|
1823 | selection.set_polarisations(0) |
---|
1824 | data.set_selection(selection) |
---|
1825 | data.scale(xtsys/nomtsys) |
---|
1826 | |
---|
1827 | selection.set_polarisations(1) |
---|
1828 | data.set_selection(selection) |
---|
1829 | data.scale(ytsys/nomtsys) |
---|
1830 | |
---|
1831 | selection.set_polarisations(0) |
---|
1832 | data.set_selection(selection) |
---|
1833 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
1834 | |
---|
1835 | selection.set_polarisations(0) |
---|
1836 | data.set_selection(selection) |
---|
1837 | data.scale((xtsys+ytsys)/(2*nomtsys)) |
---|
1838 | \end{verbatim} |
---|
1839 | |
---|
1840 | The typical ASAP session would be |
---|
1841 | |
---|
1842 | \begin{verbatim} |
---|
1843 | |
---|
1844 | # Remind ourself the name of the rpfits files |
---|
1845 | ls |
---|
1846 | |
---|
1847 | # Load data from an rpfits file |
---|
1848 | d1665 = scantable('2005-10-27_0154-P484.rpf') |
---|
1849 | |
---|
1850 | # Check what we have just loaded |
---|
1851 | d1665.summary() |
---|
1852 | |
---|
1853 | # View the data in velocity |
---|
1854 | d1665.set_unit('km/s') |
---|
1855 | d1665.set_freqframe('LSRK') |
---|
1856 | |
---|
1857 | # Correct for the known phase offset in the crosspol data |
---|
1858 | d1665.rotate_xyphase(-4) |
---|
1859 | |
---|
1860 | # Create a copy of the data and set the rest frequency to the 1667 MHz |
---|
1861 | # transition |
---|
1862 | d1667 = d1665.copy() |
---|
1863 | d1667.set_restfreqs([1667.3590], 'MHz') |
---|
1864 | d1667.summary() |
---|
1865 | |
---|
1866 | # Copy out the scan we wish to process |
---|
1867 | g351_5 = d1665.get_scan('351p160') |
---|
1868 | g351_7 = d1667.get_scan('351p160') |
---|
1869 | |
---|
1870 | # Baseline both |
---|
1871 | msk = g351_5.create_mask([-30,-25],[-5,0]) |
---|
1872 | g351_5.poly_baseline(msk,order=1) |
---|
1873 | msk = g351_7.create_mask([-30,-25],[-5,0]) |
---|
1874 | g351_7.poly_baseline(msk,order=1) |
---|
1875 | |
---|
1876 | |
---|
1877 | # Plot the data. The plotter can only plot a single scantable |
---|
1878 | # So we must merge the two tables first |
---|
1879 | |
---|
1880 | plotscans = merge(g351_5, g351_7) |
---|
1881 | |
---|
1882 | plotter.plot(plotscans) # Only shows one panel |
---|
1883 | |
---|
1884 | # Tell the plotter to stack polarisation and panel scans |
---|
1885 | plotter.set_mode('p','s') |
---|
1886 | |
---|
1887 | # Correct for the Tsys using our predefined function |
---|
1888 | execfile('mypol.py') # Read in the function xyscale |
---|
1889 | xyscale(g351_5,23.2,22.7) # Execute it on the data |
---|
1890 | xyscale(g351_7,23.2,22.7) |
---|
1891 | |
---|
1892 | # Only plot the velocity range of interest |
---|
1893 | plotter.set_range(-30,10) |
---|
1894 | |
---|
1895 | # Update the plot with the baselined data |
---|
1896 | plotter.plot() |
---|
1897 | |
---|
1898 | # Look at the various polarisation products |
---|
1899 | selection = selector() |
---|
1900 | selection.set_polarisations(``RR LL'') |
---|
1901 | plotter.set_selection(selection) |
---|
1902 | selection.set_polarisations(``I Plinear'') |
---|
1903 | plotter.set_selection(selection) |
---|
1904 | selection.set_polarisations(``I Q U V'') |
---|
1905 | plotter.set_selection(selection) |
---|
1906 | |
---|
1907 | # Save the plot as postscript |
---|
1908 | plotter.save('g351_stokes.ps') |
---|
1909 | |
---|
1910 | # Save the process spectra |
---|
1911 | plotscans.save('g351.asap') |
---|
1912 | |
---|
1913 | \end{verbatim} |
---|
1914 | |
---|
1915 | \subsection{Tidbinbilla} |
---|
1916 | |
---|
1917 | \index{Tidbinbilla}The following example is processing of some |
---|
1918 | Tidbinbilla observations of NH$_3$ at 12~mm. Tidbinbilla has (at the |
---|
1919 | time of observations) a single polarisation, but can process two IFs |
---|
1920 | simultaneously. In the example, the first half of the observation was |
---|
1921 | observing the (1,1) and (2,2) transitions simultaneously). The second |
---|
1922 | half observed only the (4,4) transition due to bandwidth |
---|
1923 | limitations. The data is position switched, observing first an |
---|
1924 | reference to the west, then the source twice and finally reference to |
---|
1925 | the east. |
---|
1926 | |
---|
1927 | \begin{verbatim} |
---|
1928 | |
---|
1929 | # Load the rpfits file and inspect |
---|
1930 | d = scantable('2003-03-16_082048_t0002.rpf') |
---|
1931 | print d |
---|
1932 | |
---|
1933 | # Make the quotient spectra |
---|
1934 | q = d.auto_quotient() |
---|
1935 | print q |
---|
1936 | |
---|
1937 | del d |
---|
1938 | |
---|
1939 | # Plot/select in velocity |
---|
1940 | q.set_freqframe('LSRK') |
---|
1941 | q.set_unit('km/s') |
---|
1942 | |
---|
1943 | # Correct for gain/el effects |
---|
1944 | |
---|
1945 | q.recalc_azel() # Tid does not write the elevation |
---|
1946 | q.gain_el() |
---|
1947 | q.opacity(0.05) |
---|
1948 | |
---|
1949 | # Seperate data from the (1,1)&(2,2) and (4,4) transitions |
---|
1950 | g1 = q.get_scan(range(6)) # scans 0..5 |
---|
1951 | g2 = q.get_scan(range(6,12)) # scans 6..11 |
---|
1952 | |
---|
1953 | # Align data in velocity |
---|
1954 | g1.freq_align() |
---|
1955 | g2.freq_align() |
---|
1956 | |
---|
1957 | # Average individual scans |
---|
1958 | a1 = g1.average_time() |
---|
1959 | a2 = g2.average_time() |
---|
1960 | |
---|
1961 | # Rpfits file only contains a single rest frequency. Set both |
---|
1962 | a1.set_restfreqs([23694.4700e6,23722.6336e6]) |
---|
1963 | |
---|
1964 | plotter.plot(a1) |
---|
1965 | plotter.set_mode('i','t') |
---|
1966 | |
---|
1967 | a1.auto_poly_baseline() |
---|
1968 | |
---|
1969 | plotter.plot() |
---|
1970 | |
---|
1971 | a1.smooth('gauss',5) |
---|
1972 | plotter.plot() |
---|
1973 | |
---|
1974 | |
---|
1975 | \end{verbatim} |
---|
1976 | |
---|
1977 | \newpage |
---|
1978 | |
---|
1979 | \section{Appendix} |
---|
1980 | |
---|
1981 | \subsection{Function Summary} |
---|
1982 | |
---|
1983 | \index{Functions!summary}% |
---|
1984 | \begin{verbatim} |
---|
1985 | [The scan container] |
---|
1986 | scantable - a container for integrations/scans |
---|
1987 | (can open asap/rpfits/sdfits and ms files) |
---|
1988 | copy - returns a copy of a scan |
---|
1989 | get_scan - gets a specific scan out of a scantable |
---|
1990 | (by name or number) |
---|
1991 | drop_scan - drops a specific scan out of a scantable |
---|
1992 | (by number) |
---|
1993 | set_selection - set a new subselection of the data |
---|
1994 | get_selection - get the current selection object |
---|
1995 | summary - print info about the scantable contents |
---|
1996 | stats - get specified statistic of the spectra in |
---|
1997 | the scantable |
---|
1998 | stddev - get the standard deviation of the spectra |
---|
1999 | in the scantable |
---|
2000 | get_tsys - get the TSys |
---|
2001 | get_time - get the timestamps of the integrations |
---|
2002 | get_sourcename - get the source names of the scans |
---|
2003 | get_azimuth - get the azimuth of the scans |
---|
2004 | get_elevation - get the elevation of the scans |
---|
2005 | get_parangle - get the parallactic angle of the scans |
---|
2006 | get_unit - get the current unit |
---|
2007 | set_unit - set the abcissa unit to be used from this |
---|
2008 | point on |
---|
2009 | get_abcissa - get the abcissa values and name for a given |
---|
2010 | row (time) |
---|
2011 | get_column_names - get the names of the columns in the scantable |
---|
2012 | for use with selector.set_query |
---|
2013 | set_freqframe - set the frame info for the Spectral Axis |
---|
2014 | (e.g. 'LSRK') |
---|
2015 | set_doppler - set the doppler to be used from this point on |
---|
2016 | set_dirframe - set the frame for the direction on the sky |
---|
2017 | set_instrument - set the instrument name |
---|
2018 | set_feedtype - set the feed type |
---|
2019 | get_fluxunit - get the brightness flux unit |
---|
2020 | set_fluxunit - set the brightness flux unit |
---|
2021 | create_mask - return an mask in the current unit |
---|
2022 | for the given region. The specified regions |
---|
2023 | are NOT masked |
---|
2024 | get_restfreqs - get the current list of rest frequencies |
---|
2025 | set_restfreqs - set a list of rest frequencies |
---|
2026 | flag - flag selected channels in the data |
---|
2027 | save - save the scantable to disk as either 'ASAP', |
---|
2028 | 'SDFITS' or 'ASCII' |
---|
2029 | nbeam,nif,nchan,npol - the number of beams/IFs/Pols/Chans |
---|
2030 | nscan - the number of scans in the scantable |
---|
2031 | nrow - te number of spectra in the scantable |
---|
2032 | history - print the history of the scantable |
---|
2033 | get_fit - get a fit which has been stored witnh the data |
---|
2034 | average_time - return the (weighted) time average of a scan |
---|
2035 | or a list of scans |
---|
2036 | average_pol - average the polarisations together. |
---|
2037 | average_beam - average the beams together. |
---|
2038 | convert_pol - convert to a different polarisation type |
---|
2039 | auto_quotient - return the on/off quotient with |
---|
2040 | automatic detection of the on/off scans (closest |
---|
2041 | in time off is selected) |
---|
2042 | mx_quotient - Form a quotient using MX data (off beams) |
---|
2043 | scale, *, / - return a scan scaled by a given factor |
---|
2044 | add, +, - - return a scan with given value added |
---|
2045 | bin - return a scan with binned channels |
---|
2046 | resample - return a scan with resampled channels |
---|
2047 | smooth - return the spectrally smoothed scan |
---|
2048 | poly_baseline - fit a polynomial baseline to all Beams/IFs/Pols |
---|
2049 | auto_poly_baseline - automatically fit a polynomial baseline |
---|
2050 | recalc_azel - recalculate azimuth and elevation based on |
---|
2051 | the pointing |
---|
2052 | gain_el - apply gain-elevation correction |
---|
2053 | opacity - apply opacity correction |
---|
2054 | convert_flux - convert to and from Jy and Kelvin brightness |
---|
2055 | units |
---|
2056 | freq_align - align spectra in frequency frame |
---|
2057 | invert_phase - Invert the phase of the cross-correlation |
---|
2058 | swap_linears - Swap XX and YY |
---|
2059 | rotate_xyphase - rotate XY phase of cross correlation |
---|
2060 | rotate_linpolphase - rotate the phase of the complex |
---|
2061 | polarization O=Q+iU correlation |
---|
2062 | freq_switch - perform frequency switching on the data |
---|
2063 | stats - Determine the specified statistic, e.g. 'min' |
---|
2064 | 'max', 'rms' etc. |
---|
2065 | stddev - Determine the standard deviation of the current |
---|
2066 | beam/if/pol |
---|
2067 | [Selection] |
---|
2068 | selector - a selection object to set a subset of a scantable |
---|
2069 | set_cycles - set (a list of) cycles by index |
---|
2070 | set_beams - set (a list of) beamss by index |
---|
2071 | set_ifs - set (a list of) ifs by index |
---|
2072 | set_polarisations - set (a list of) polarisations by name |
---|
2073 | or by index |
---|
2074 | set_names - set a selection by name (wildcards allowed) |
---|
2075 | set_tsys - set a selection by tsys thresholds |
---|
2076 | set_query - set a selection by SQL-like query, e.g. BEAMNO==1 |
---|
2077 | reset - unset all selections |
---|
2078 | + - merge to selections |
---|
2079 | |
---|
2080 | [Math] Mainly functions which operate on more than one scantable |
---|
2081 | |
---|
2082 | average_time - return the (weighted) time average |
---|
2083 | of a list of scans |
---|
2084 | quotient - return the on/off quotient |
---|
2085 | simple_math - simple mathematical operations on two scantables, |
---|
2086 | 'add', 'sub', 'mul', 'div' |
---|
2087 | quotient - build quotient of the given on and off scans |
---|
2088 | (matched pairs and 1 off/n on are valid) |
---|
2089 | merge - merge a list of scantables |
---|
2090 | |
---|
2091 | [Line Catalog] |
---|
2092 | linecatalog - a linecatalog wrapper, taking an ASCII or |
---|
2093 | internal format table |
---|
2094 | summary - print a summary of the current selection |
---|
2095 | set_name - select a subset by name pattern, e.g. '*OH*' |
---|
2096 | set_strength_limits - select a subset by line strength limits |
---|
2097 | set_frequency_limits - select a subset by frequency limits |
---|
2098 | reset - unset all selections |
---|
2099 | save - save the current subset to a table (internal |
---|
2100 | format) |
---|
2101 | get_row - get the name and frequency from a specific |
---|
2102 | row in the table |
---|
2103 | [Fitting] |
---|
2104 | fitter |
---|
2105 | auto_fit - return a scan where the function is |
---|
2106 | applied to all Beams/IFs/Pols. |
---|
2107 | commit - return a new scan where the fits have been |
---|
2108 | commited. |
---|
2109 | fit - execute the actual fitting process |
---|
2110 | store_fit - store the fit parameters in the data (scantable) |
---|
2111 | get_chi2 - get the Chi^2 |
---|
2112 | set_scan - set the scantable to be fit |
---|
2113 | set_function - set the fitting function |
---|
2114 | set_parameters - set the parameters for the function(s), and |
---|
2115 | set if they should be held fixed during fitting |
---|
2116 | set_gauss_parameters - same as above but specialised for individual |
---|
2117 | gaussian components |
---|
2118 | get_parameters - get the fitted parameters |
---|
2119 | plot - plot the resulting fit and/or components and |
---|
2120 | residual |
---|
2121 | [Plotter] |
---|
2122 | asapplotter - a plotter for asap, default plotter is |
---|
2123 | called 'plotter' |
---|
2124 | plot - plot a scantable |
---|
2125 | plot_lines - plot a linecatalog overlay |
---|
2126 | save - save the plot to a file ('png' ,'ps' or 'eps') |
---|
2127 | set_mode - set the state of the plotter, i.e. |
---|
2128 | what is to be plotted 'colour stacked' |
---|
2129 | and what 'panelled' |
---|
2130 | set_selection - only plot a selected part of the data |
---|
2131 | set_range - set a 'zoom' window [xmin,xmax,ymin,ymax] |
---|
2132 | set_legend - specify user labels for the legend indeces |
---|
2133 | set_title - specify user labels for the panel indeces |
---|
2134 | set_abcissa - specify a user label for the abcissa |
---|
2135 | set_ordinate - specify a user label for the ordinate |
---|
2136 | set_layout - specify the multi-panel layout (rows,cols) |
---|
2137 | set_colors - specify a set of colours to use |
---|
2138 | set_linestyles - specify a set of linestyles to use if only |
---|
2139 | using one color |
---|
2140 | set_font - set general font properties, e.g. 'family' |
---|
2141 | set_histogram - plot in historam style |
---|
2142 | set_mask - set a plotting mask for a specific polarization |
---|
2143 | text - draw text annotations either in data or relative |
---|
2144 | coordinates |
---|
2145 | arrow - draw arrow annotations either in data or relative |
---|
2146 | coordinates |
---|
2147 | axhline,axvline - draw horizontal/vertical lines |
---|
2148 | axhspan,axvspan - draw horizontal/vertical regions |
---|
2149 | |
---|
2150 | xyplotter - matplotlib/pylab plotting functions |
---|
2151 | |
---|
2152 | [Reading files] |
---|
2153 | reader - access rpfits/sdfits files |
---|
2154 | arrow - draw arrow annotations either in data or relative |
---|
2155 | coordinates |
---|
2156 | axhline,axvline - draw horizontal/vertical lines |
---|
2157 | axhspan,axvspan - draw horizontal/vertical regions |
---|
2158 | |
---|
2159 | xyplotter - matplotlib/pylab plotting functions |
---|
2160 | |
---|
2161 | [Reading files] |
---|
2162 | reader - access rpfits/sdfits files |
---|
2163 | open - attach reader to a file |
---|
2164 | close - detach reader from file |
---|
2165 | read - read in integrations |
---|
2166 | summary - list info about all integrations |
---|
2167 | |
---|
2168 | [General] |
---|
2169 | commands - this command |
---|
2170 | print - print details about a variable |
---|
2171 | list_scans - list all scantables created bt the user |
---|
2172 | list_files - list all files readable by asap (default rpf) |
---|
2173 | del - delete the given variable from memory |
---|
2174 | range - create a list of values, e.g. |
---|
2175 | range(3) = [0,1,2], range(2,5) = [2,3,4] |
---|
2176 | help - print help for one of the listed functions |
---|
2177 | execfile - execute an asap script, e.g. execfile('myscript') |
---|
2178 | list_rcparameters - print out a list of possible values to be |
---|
2179 | put into .asaprc |
---|
2180 | rc - set rc parameters from within asap |
---|
2181 | mask_and,mask_or, |
---|
2182 | mask_not - boolean operations on masks created with |
---|
2183 | scantable.create_mask |
---|
2184 | \end{verbatim} |
---|
2185 | |
---|
2186 | \subsection{ASCII output format} |
---|
2187 | |
---|
2188 | \subsection{.asaprc settings} |
---|
2189 | \index{.asaprc} |
---|
2190 | \asaprc{verbose}{{\bf True}/False}{Print verbose output, good to disable in scripts} |
---|
2191 | |
---|
2192 | \asaprc{insitu}{{\bf True}/False}{Apply operations on the input |
---|
2193 | scantable or return new one} |
---|
2194 | |
---|
2195 | \asaprc{useplotter}{{\bf True}/False}{Preload a default plotter} |
---|
2196 | |
---|
2197 | \asaprc{plotter.gui}{{\bf True}/False}{Do we want a GUI or plot to a |
---|
2198 | file} |
---|
2199 | |
---|
2200 | \asaprc{plotter.stacking}{{\bf Pol} Beam IF Scan Time}{Default mode for |
---|
2201 | colour stacking} |
---|
2202 | |
---|
2203 | \asaprc{plotter.panelling}{Pol Beam IF {\bf Scan} Time}{Default mode |
---|
2204 | for panelling} |
---|
2205 | |
---|
2206 | \asaprc{plotter.ganged}{{\bf True}/False}{Push panels together, to |
---|
2207 | share axislabels} |
---|
2208 | |
---|
2209 | \asaprc{plotter.decimate}{True/{\bf False}}{Decimate the number of |
---|
2210 | points plotted by a factor of nchan/1024} |
---|
2211 | |
---|
2212 | \asaprc{plotter.histogram}{True/{\bf False}}{Plot spectrum using |
---|
2213 | histogram rather than lines.} |
---|
2214 | |
---|
2215 | \asaprc{plotter.colours}{}{Set default colours for plotting} |
---|
2216 | |
---|
2217 | \asaprc{plotter.colours}{}{Set default line styles} |
---|
2218 | |
---|
2219 | \asaprc{plotter.papersze}{{\bf A4}}{} |
---|
2220 | |
---|
2221 | % scantable |
---|
2222 | \asaprc{scantable.save}{{\bf ASAP} SDFITS ASCII MS2}{Default output |
---|
2223 | format when saving} |
---|
2224 | |
---|
2225 | \asaprc{scantable.autoaverage}{{\bf True}/False}{Auto averaging on |
---|
2226 | read} |
---|
2227 | |
---|
2228 | \asaprc{scantable.freqframe}{{\bf LSRK} TOPO BARY etc}{default |
---|
2229 | frequency frame to set when function scantable.set\_freqframe is |
---|
2230 | called or the data is imported} |
---|
2231 | |
---|
2232 | \asaprc{scantable.verbosesummary}{True/{\bf False}}{Control the level |
---|
2233 | of information printed by summary} |
---|
2234 | |
---|
2235 | \asaprc{scantable.storage}{{\bf memory}/disk}{Storage of scantables in |
---|
2236 | memory of via based disk tables} |
---|
2237 | |
---|
2238 | \subsection{Installation} |
---|
2239 | |
---|
2240 | \index{Installation} |
---|
2241 | |
---|
2242 | Please refer to the asap wiki for instructions on downloading and/or |
---|
2243 | building asap from source. |
---|
2244 | |
---|
2245 | \hspace{1cm}\cmd{http://www.atnf.csiro.au/computing/software/asap/} |
---|
2246 | |
---|
2247 | \printindex |
---|
2248 | |
---|
2249 | \end{document} |
---|
2250 | |
---|