1 | % ----------------------------------------------------------------------- |
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2 | % app-param.tex: Section listing all the possible input parameters and |
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3 | % their defaults. |
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4 | % ----------------------------------------------------------------------- |
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5 | % Copyright (C) 2006, Matthew Whiting, ATNF |
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6 | % |
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7 | % This program is free software; you can redistribute it and/or modify it |
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8 | % under the terms of the GNU General Public License as published by the |
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9 | % Free Software Foundation; either version 2 of the License, or (at your |
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10 | % option) any later version. |
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11 | % |
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12 | % Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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13 | % ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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14 | % FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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15 | % for more details. |
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16 | % |
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17 | % You should have received a copy of the GNU General Public License |
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18 | % along with Duchamp; if not, write to the Free Software Foundation, |
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19 | % Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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20 | % |
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21 | % Correspondence concerning Duchamp may be directed to: |
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22 | % Internet email: Matthew.Whiting [at] atnf.csiro.au |
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23 | % Postal address: Dr. Matthew Whiting |
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24 | % Australia Telescope National Facility, CSIRO |
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25 | % PO Box 76 |
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26 | % Epping NSW 1710 |
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27 | % AUSTRALIA |
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28 | % ----------------------------------------------------------------------- |
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29 | \secA{Available parameters} |
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30 | \label{app-param} |
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31 | |
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32 | The full list of parameters that can be listed in the input file are |
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33 | given here. Following each parameter name are listed three things: the |
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34 | default parameter taken when not provided in the input file; the data |
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35 | type that should be provided; and some indication (where applicable) |
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36 | of the range of values required or the type of information expected. |
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37 | Since the order of the parameters in the input file does not matter, |
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38 | they are grouped here in logical sections. |
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39 | |
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40 | \secB*{Input related} |
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41 | \begin{Lentry} |
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42 | \item[{ImageFile [no default | string | filename]}] The filename of |
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43 | the data cube to be analysed. |
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44 | \item[{flagSubsection [false | bool | true/false/1/0]}] A flag to |
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45 | indicate whether one wants a subsection of the requested image. |
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46 | \item[{Subsection [full field | string | Subsection string]}] The |
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47 | requested subsection -- see \S\ref{sec-input} for details on the |
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48 | subsection format. If the full range of a dimension is required, |
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49 | use a \texttt{*} (thus the default is the full cube). |
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50 | \item[{flagReconExists [false | bool | true/false/1/0]}] A flag to |
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51 | indicate whether the reconstructed array has been saved by a |
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52 | previous run of \duchamp. If set true, the reconstructed array will |
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53 | be read from the file given by \texttt{reconFile}, rather than |
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54 | calculated directly. |
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55 | \item[{reconFile [no default | string | filename]}] The FITS file that |
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56 | contains the reconstructed array. If \texttt{flagReconExists} is |
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57 | true and this parameter is not defined, the default file that is |
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58 | looked for will be determined by the \atrous parameters (see |
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59 | \S\ref{sec-recon}). |
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60 | \item[{flagSmoothExists [false | bool | true/false/1/0]}] A flag to |
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61 | indicate whether the Hanning-smoothed array has been saved by a |
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62 | previous run of \duchamp. If set true, the smoothed array will be |
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63 | read from the file given by \texttt{smoothFile}, rather than |
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64 | calculated directly. |
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65 | \item[{smoothFile [no default | string | filename]}] The FITS file |
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66 | that has a previously smoothed array. If \texttt{flagSmoothExists} |
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67 | is true and this parameter is not defined, the default file that is |
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68 | looked for will be determined by the smoothing parameters (see |
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69 | \S\ref{sec-smoothing}). |
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70 | \item[{usePrevious [false | bool | true/false/1/0]}] A flag to |
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71 | indicate that \duchamp should read the list of objects from a |
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72 | previously-created log file, rather than doing the searching |
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73 | itself. The set of outputs will be created according to the flags in |
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74 | the following section. |
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75 | \item[{objectList [no default | string | comma-separated list]}] When |
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76 | \texttt{usePrevious=true}, this list is used to output individual |
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77 | spectral plots, as well as a postscript file for all spectral plots |
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78 | as given by \texttt{SpectraFile}. The filenames of the plots will be |
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79 | the same as \texttt{SpectraFile}, but with -XX at the end, where XX |
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80 | is the object number (\eg \texttt{duchamp-Spectra-07.ps}). The |
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81 | format of the parameter value should be a string listing individual |
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82 | objects or object ranges: \eg 1,2,4-7,8,14. |
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83 | \end{Lentry} |
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84 | |
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85 | \secB*{Output related} |
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86 | \begin{Lentry} |
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87 | \item[{OutFile [duchamp-\\Results.txt | string | filename]}] The file |
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88 | containing the final list of detections. This also records the list |
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89 | of input parameters. |
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90 | \item[{flagSeparateHeader [false | bool | true/false/1/0]}] A flag to |
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91 | indicate that the header information that would normally be printed |
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92 | at the start of the results file (containing information on the |
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93 | parameters, image statistics and number of detections) should |
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94 | instead be written to a separate file. |
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95 | \item[{HeaderFile [duchamp-\\Results.hdr | string | filename]}] The |
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96 | file to which the header information should be written when |
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97 | \texttt{flagSeparateHeader=true}. |
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98 | \item[{flagWriteBinaryCatalogue [true | bool | true/false/1/0]}] |
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99 | Whether to write a binary catalogue of the detections, for later |
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100 | re-use (see \S\ref{sec-reuse} for details). |
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101 | \item[{binaryCatalogue [duchamp-Catalogue.dpc | string | filename]}] |
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102 | The filename for the binary catalogue. |
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103 | \item[{flagPlotSpectra [true | bool | true/false/1/0]}] Whether to |
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104 | produce a postscript file containing spectra of all detected |
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105 | objects. If PGPlot has not been enabled, this parameter defaults to |
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106 | \texttt{false}. |
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107 | \item[{SpectraFile [duchamp-\\Spectra.ps | string | filename]}] The |
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108 | postscript file that contains the resulting integrated spectra and |
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109 | images of the detections. |
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110 | \item[{flagPlotIndividualSpectra [false | bool | true/false/1/0]}] |
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111 | Whether to produce individual spectral plots for listed sources. |
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112 | \item[{flagTextSpectra [false | bool | true/false/1/0]}] A flag to say |
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113 | whether the spectra should be saved in text form in a single |
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114 | file. See below for a description. |
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115 | \item[{spectraTextFile [duchamp-\\Spectra.txt | string | filename]}] |
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116 | The file containing the spectra of each object in ascii format. This |
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117 | file will have a column showing the spectral coordinates, and one |
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118 | column for each of the detected objects, showing the flux values as |
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119 | plotted in the graphical output of \texttt{spectraFile}. |
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120 | \item[{flagLog [false | bool | true/false/1/0]}] A flag to indicate |
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121 | whether the details of intermediate detections should be logged. |
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122 | \item[{LogFile [duchamp-\\Logfile.txt | string | filename]}] The file |
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123 | in which intermediate detections and the pixel content of the final |
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124 | list of detections are logged. These are detections that have not |
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125 | been merged. This is primarily for use in debugging and diagnostic |
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126 | purposes: normal use of the program will probably not require it. |
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127 | \item[{flagOutputMomentMap [false | bool | true/false/1/0]}] A flag to |
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128 | say whether or not to save a FITS file containing the moment-0 map. |
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129 | \item[fileOutputMomentMap{ [see text | string | filename]}] The file |
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130 | to which the moment-0 array is written. If left blank (the default), |
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131 | the naming scheme detailed in \S\ref{sec-momentOut} is used. |
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132 | \item[{flagOutputMomentMask [false | bool | true/false/1/0]}] A flag |
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133 | to say whether or not to save a FITS file containing the moment-0 |
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134 | mask (a mask showing which spatial pixels are detected in one or |
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135 | more channels). |
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136 | \item[fileOutputMomentMask{ [see text | string | filename]}] The file |
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137 | to which the moment-0 mask is written. If left blank (the default), |
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138 | the naming scheme detailed in \S\ref{sec-maskOut} is used. |
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139 | \item[{flagOutputMask [false | bool | true/false/1/0]}] A flag to say |
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140 | whether or not to save a FITS file containing a mask array, with |
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141 | values 1 where there is a detected object and 0 elsewhere. |
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142 | \item[fileOutputMask{ [see text | string | filename]}] The file to |
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143 | which the mask array is written. If left blank (the default), the |
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144 | naming scheme detailed in \S\ref{sec-maskOut} is used. |
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145 | \item[{flagMaskWithObjectNum [false | bool | true/false/1/0]}] If this |
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146 | flag is true, the detected pixels in the mask image have the |
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147 | corresponding object ID as their value. If false, they have the |
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148 | value 1. All non-detected pixels have the value 0. |
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149 | \item[{flagOutputRecon [false | bool | true/false/1/0]}] A flag to say |
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150 | whether or not to save the reconstructed cube as a FITS file. |
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151 | \item[fileOutputRecon{ [see text | string | filename]}] The file to |
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152 | which the reconstructed array is written. If left blank (the |
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153 | default), the naming scheme detailed in \S\ref{sec-reconIO} is used. |
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154 | \item[{flagOutputResid [false | bool | true/false/1/0]}] As for |
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155 | \texttt{flagOutputRecon}, but for the residual array -- the |
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156 | difference between the original cube and the reconstructed cube. |
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157 | \item[fileOutputResid{ [see text | string | filename]}] The file to |
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158 | which the residual array is written. If left blank (the default), |
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159 | the naming scheme detailed in \S\ref{sec-reconIO} is used. |
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160 | \item[{flagOutputSmooth [false | bool | true/false/1/0]}] A flag to |
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161 | say whether or not to save the smoothed cube as a FITS file. |
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162 | \item[fileOutputSmooth{ [see text | string | filename]}] The file to |
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163 | which the smoothed array is written. If left blank (the default), |
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164 | the naming scheme detailed in \S\ref{sec-reconIO} is used. |
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165 | \item[{flagOutputBaseline [false | bool | true/false/1/0]}] A flag to |
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166 | say whether or not to save the cube of spectral baseline values as a |
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167 | FITS file. |
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168 | \item[fileOutputBaseline{ [see text | string | filename]}] The file to |
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169 | which the baseline values are written. If left blank (the default), |
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170 | the naming scheme detailed in \S\ref{sec-baselineOut} is used. |
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171 | \item[{flagVOT [false | bool | true/false/1/0]}] A flag to say whether |
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172 | to create a VOTable file with the detection information. This will |
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173 | be an XML file in the Virtual Observatory VOTable format. |
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174 | \item[{votFile [duchamp-\\Results.xml | string | filename]}] The |
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175 | VOTable file with the list of final detections. Some input |
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176 | parameters are also recorded. |
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177 | \item[{flagKarma [false | bool | true/false/1/0]}] A flag to say |
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178 | whether to create a Karma annotation file corresponding to the |
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179 | information in \texttt{outfile}. This can be used as an overlay in |
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180 | Karma programs such as \texttt{kvis}. |
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181 | \item[{karmaFile [duchamp-\\Results.ann | string | filename]}] The |
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182 | Karma annotation file showing the list of final detections. |
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183 | \item[{flagDS9 [false | bool | true/false/1/0]}] A flag to say whether |
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184 | to create a DS9 region file corresponding to the information in |
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185 | \texttt{outfile}. This can be used as an overlay in SAOImage DS9 or |
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186 | casaviewer. |
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187 | \item[{ds9File [duchamp-\\Results.ann | string | filename]}] The DS9 |
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188 | region file showing the list of final detections. |
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189 | \item[{flagCasa [false | bool | true/false/1/0]}] A flag to say |
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190 | whether to create a CASA region file corresponding to the |
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191 | information in \texttt{outfile}. This can be used as an overlay in |
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192 | casaviewer (when this functionality is available) or import into |
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193 | casapy. |
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194 | \item[{casaFile [duchamp-\\Results.crf | string | filename]}] The CASA |
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195 | region file showing the list of final detections. |
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196 | \item[{annotationType [borders | string | borders/circles/ellipses]}] |
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197 | Which type of annotation plot to use. Specifying ``borders'' gives |
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198 | an outline around the detected spatial pixels, ``circles'' gives a |
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199 | circle centred on the centre of the object with radius large enough |
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200 | to encompass all spatial pixels, and ``ellipses'' gives an ellipse |
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201 | centred on the centre of the object of size given by the MAJ, MIN \& |
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202 | PA values. |
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203 | \item[{flagMaps [true | bool | true/false/1/0]}] A flag to say whether |
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204 | to save postscript files showing the 0th moment map of the whole |
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205 | cube (\texttt{momentMap}) and the detection image |
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206 | (\texttt{detectionMap}). If PGPlot has not been enabled, this |
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207 | parameter defaults to \texttt{false}. |
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208 | \item[{momentMap [duchamp-\\MomentMap.ps | string | filename]}] A |
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209 | postscript file containing a map of the 0th moment of the detected |
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210 | sources, as well as pixel and WCS coordinates. |
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211 | \item[{detectionMap [duchamp-\\DetectionMap.ps | string | filename]}] |
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212 | A postscript file with a map showing each of the detected objects, |
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213 | coloured in greyscale by the number of detected channels in each |
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214 | spatial pixel. Also shows pixel and WCS coordinates. |
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215 | \item[{flagXOutput [true | bool | true/false/1/0]}] A flag to say |
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216 | whether to display a 0th moment map in a PGPlot X-window. This will |
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217 | be in addition to any that are saved to a file. This parameter can |
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218 | be overridden by the use of the \texttt{-x} command-line option, |
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219 | which disables the X-windows output. If PGPlot has not been enabled, |
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220 | this parameter defaults to \texttt{false}. |
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221 | \item[{newFluxUnits [no default | string | units string]}] Flux units |
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222 | that the pixel values should be converted into. These should be |
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223 | directly compatible with the units in the FITS header, given by the |
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224 | BUNIT keyword. |
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225 | \item[{precFlux [3 | int | $> 0$]}] The desired precision (\ie number |
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226 | of decimal places) for flux values given in the output files and |
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227 | tables. |
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228 | \item[{precVel [3 | int | $> 0$]}] The desired precision (\ie number |
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229 | of decimal places) for velocity/frequency values given in the output |
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230 | files and tables. |
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231 | \item[{precSNR [2 | int | $> 0$]}] The desired precision (\ie number |
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232 | of decimal places) for the peak SNR value given in the output files |
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233 | and tables. |
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234 | \end{Lentry} |
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235 | |
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236 | \secB*{Modifying the cube} |
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237 | \begin{Lentry} |
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238 | \item[{flagTrim [false | bool | true/false/1/0]}] A flag to say |
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239 | whether to trim BLANK pixels from the edges of the cube -- these are |
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240 | typically pixels set to some particular value because they fall |
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241 | outside the imaged area, and trimming them can help speed up the |
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242 | execution. |
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243 | \item[{flaggedChannels [no default | string | comma-separated list]}] |
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244 | Channels that are to be ignored by the source-finding. These should |
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245 | be specified by a comma-separated list of single values and ranges, |
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246 | such as 1,3,6-12,18. Channel numbers are zero-based, so that the |
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247 | first channel in the cube has value 0. |
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248 | \item[{flagBaseline [false | bool | true/false/1/0]}] A flag to say |
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249 | whether to remove the baseline from each spectrum in the cube for |
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250 | the purposes of reconstruction and detection. |
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251 | \item[{baselineType [atrous | string | atrous/median]}] The algorithm |
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252 | used to calculate the spectral baseline. Only \texttt{atrous} or |
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253 | \texttt{median} are accepted. |
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254 | \item[{baselineBoxWidth [51 | int | odd integer $> 0$]}] The box width |
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255 | used by the \texttt{median} baseline algorithm. Needs to be odd - if |
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256 | even, it will be incremented by one. |
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257 | \end{Lentry} |
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258 | |
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259 | \secB*{Detection related} |
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260 | |
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261 | \secC*{General detection} |
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262 | \begin{Lentry} |
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263 | \item[{searchType [spatial | string | spectral/spatial]}] How the |
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264 | searches are done. Only ``spatial'' and ``spectral'' are accepted. A |
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265 | value of ``spatial'' means each 2D channel map is searched, whereas |
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266 | ``spectral'' means each 1D spectrum is searched. |
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267 | \item[{flagStatSec [false | bool | true/false/1/0]}] A flag indicating |
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268 | whether the statistics should be calculated on a subsection of the |
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269 | cube, rather than the full cube. Note that this only applies to the |
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270 | statistics used to determine the threshold, and not for other |
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271 | statistical calculations (such as those in the reconstruction |
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272 | phase). |
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273 | \item[{StatSec [full field | string | Subsection string]}] The |
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274 | subsection of the cube used for calculating statistics -- see |
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275 | \S\ref{sec-input} for details on the subsection format. Only used if |
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276 | \texttt{flagStatSec=true}. |
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277 | \item[{flagRobustStats [true | bool | true/false/1/0]}] A flag |
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278 | indicating whether to use the robust statistics (median and MADFM) |
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279 | to estimate the noise parameters of the cube, rather than the mean |
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280 | and rms. See \S\ref{sec-stats} for details. |
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281 | \item[{flagNegative [false | bool | true/false/1/0]}] A flag |
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282 | indicating that the features of interest are negative. The cube is |
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283 | inverted prior to searching. |
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284 | \item[{snrCut [5. | float | any]}] The threshold, in multiples of |
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285 | $\sigma$ above the mean. |
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286 | \item[{threshold [no default | float | any]}] The actual value of the |
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287 | threshold. Normally the threshold is calculated from the cube's |
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288 | statistics, but the user can manually specify a value to be used |
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289 | that overrides the calculated value. If this is not specified, the |
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290 | calculated value is used, but this value will take precedence over |
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291 | other means of calculating the threshold (\ie via \texttt{snrCut} or |
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292 | the FDR method). |
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293 | \item[{flagGrowth [false | bool | true/false/1/0]}] A flag indicating |
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294 | whether or not to grow the detected objects to a smaller threshold. |
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295 | \item[{growthCut [3. | float | any]}] The smaller threshold using in |
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296 | growing detections. In units of $\sigma$ above the mean. |
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297 | \item[{growthThreshold [no default | float | any]}] Alternatively, the |
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298 | threshold to which detections are grown can be specified in flux |
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299 | units (in the same manner as the \texttt{threshold} parameter). When |
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300 | the \texttt{threshold} parameter is given, this option \textbf{must} |
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301 | be used instead of \texttt{growthCut}. |
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302 | \item[{beamFWHM [0. | float | $> 0.$]}] The full-width at half maximum |
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303 | of the beam, in pixels. If the header keywords BMAJ and BMIN are |
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304 | present, then these will be used to calculate the beam area, and |
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305 | this parameter will be ignored. This will take precedence over |
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306 | \texttt{beamArea} (but is ignored if not specified). |
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307 | \item[{beamArea [0. | float | $> 0.$]}] The \textbf{area} of the beam |
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308 | in pixels (\ie how many pixel does the beam cover?). As above, if |
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309 | the header keywords BMAJ and BMIN are present, then these will be |
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310 | used to calculate the beam area, and this parameter will be ignored. |
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311 | \end{Lentry} |
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312 | |
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313 | \secC*{\Atrous reconstruction} |
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314 | \begin{Lentry} |
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315 | \item[{flagATrous [false | bool | true/false/1/0]}] A flag indicating |
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316 | whether or not to reconstruct the cube using the \atrous wavelet |
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317 | reconstruction. See \S\ref{sec-recon} for details. |
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318 | \item[{reconDim [1 | int | 1, 2 or 3]}] The number of dimensions to use in |
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319 | the reconstruction. 1 means reconstruct each spectrum separately, 2 |
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320 | means each channel map is done separately, and 3 means do the whole |
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321 | cube in one go. |
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322 | \item[{scaleMin [1 | int | $> 0$]}] The minimum wavelet scale to be |
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323 | used in the reconstruction. A value of 1 means ``use all scales''. |
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324 | \item[{scaleMax [0 | int | any]}] The maximum wavelet scale to be used |
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325 | in the reconstruction. If the value is $\le0$ then the maximum scale |
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326 | is calculated from the size of the input array. Similarly, if the |
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327 | value given is larger than this calculated value, the calculated |
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328 | value is used instead. |
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329 | \item[{snrRecon [4 | float | $> 0$]}] The thresholding cutoff used in |
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330 | the reconstruction -- only wavelet coefficients at least this many |
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331 | $\sigma$ above the mean are included in the reconstruction. |
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332 | \item[{reconConvergence [0.005 | float | $> 0.$]}] The convergence |
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333 | criterion used in the reconstruction. The \atrous algorithm iterates |
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334 | until the relative change in the standard deviation of the residuals |
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335 | is less than this amount. |
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336 | \item[{filterCode [1 | int | 1/2/3]}] The code number of the filter to |
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337 | use in the reconstruction. The options are: |
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338 | \begin{itemize} |
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339 | \item \textbf{1:} B$_3$-spline filter: coefficients = |
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340 | $(\frac{1}{16}, \frac{1}{4}, \frac{3}{8}, \frac{1}{4}, \frac{1}{16})$ |
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341 | \item \textbf{2:} Triangle filter: coefficients = |
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342 | $(\frac{1}{4}, \frac{1}{2}, \frac{1}{4})$ |
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343 | \item \textbf{3:} Haar wavelet: coefficients = |
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344 | $(0, \frac{1}{2}, \frac{1}{2})$ |
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345 | \end{itemize} |
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346 | \end{Lentry} |
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347 | |
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348 | \secC*{Smoothing the cube} |
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349 | \begin{Lentry} |
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350 | \item[{flagSmooth [false | bool | true/false/1/0]}] A flag indicating whether to |
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351 | smooth the cube. See \S\ref{sec-smoothing} for details. |
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352 | \item[{smoothType [spectral | string | spectral/spatial]}] The |
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353 | smoothing method used: either ``spectral'' (with a 1D Hanning |
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354 | filter) or ``spatial'' (with a 2D Gaussian filter). |
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355 | \item[{hanningWidth [5 | int | $> 0$]}] The width of the Hanning |
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356 | smoothing kernel. |
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357 | \item[{kernMaj [3 | float | $> 0.$]}] The full-width-half-maximum |
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358 | (FWHM), in pixels, of the 2D Gaussian smoothing kernel's major axis. |
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359 | \item[{kernMin [3 | float | $> 0.$]}] The FWHM (in pixels) of the 2D Gaussian smoothing kernel's |
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360 | minor axis. |
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361 | \item[{kernPA [0 | float | any]}] The position angle, in degrees, |
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362 | anticlockwise from vertical (\ie usually East of North). |
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363 | \item[{smoothEdgeMethod [equal | string | equal/truncate/scale]}] What |
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364 | method to use for dealing with pixels on the edge of the spatial |
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365 | image (\ie within the width of the kernel). Can be one of |
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366 | \texttt{equal, truncate, scale}. See \S\ref{sec-smoothing} for |
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367 | details. |
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368 | \item[{spatialSmoothCutoff [1.e-10 | float | $> 0.$]}] The cutoff |
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369 | value for determining the width of the smoothing kernel. See |
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370 | \S\ref{sec-smoothing} for details. |
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371 | \end{Lentry} |
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372 | |
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373 | \secC*{FDR method} |
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374 | \begin{Lentry} |
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375 | \item[{flagFDR [false | bool | true/false/1/0]}] A flag indicating whether or not to use |
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376 | the False Discovery Rate method in thresholding the pixels. |
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377 | \item[{alphaFDR [0.01 | float | $0. - 1.$]}] The $\alpha$ parameter used in the FDR |
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378 | analysis. The average number of false detections, as a fraction of |
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379 | the total number, will be less than $\alpha$ (see |
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380 | \S\ref{sec-detection}). |
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381 | \item[{FDRnumCorChan [2 | int | $> 0$]}] The number of neighbouring spectral |
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382 | channels that are assumed to be correlated. This is needed by the |
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383 | FDR algorithm to calculate the normalisation constant $c_N$ (see |
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384 | \S\ref{sec-detection}). |
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385 | \end{Lentry} |
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386 | |
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387 | \secC*{Merging detections} |
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388 | \begin{Lentry} |
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389 | \item[{minPix [2 | int | $> 0$]}] The minimum number of spatial pixels for a |
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390 | single detection to be counted. |
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391 | \item[{minChannels [3 | int | $> 0$]}] At least one contiguous set of this many |
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392 | channels must be present in the detection for it to be accepted. |
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393 | \item[{minVoxels [minPix$+$minChannels$-$1 | int | $> 0$]}] The minimum size of |
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394 | the object, in terms of the total number of voxels, for it to be |
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395 | accepted. This will be \textit{at least} minPix$+$minChannels$-$1, |
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396 | but can be set higher. |
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397 | \item[{maxPix [$-1$ | int | any]}] The maximum number of spatial pixels an object |
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398 | can have. No check is made if the value is negative. |
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399 | \item[{maxChannels [-1 | int | any]}] The maximum number of channels an object can |
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400 | have. No check is made if the value is negative. |
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401 | \item[{maxVoxels [$-1$ | int | any]}] The maximum size of |
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402 | the object, in terms of the total number of voxels, for it to be |
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403 | accepted. No check is made if the value is negative. |
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404 | \item[{flagRejectBeforeMerge [false | bool | true/false/1/0]}] A flag |
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405 | indicating whether to reject sources that fail to meet the |
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406 | \texttt{minPix} or \texttt{minChannels} criteria \textbf{before} the |
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407 | merging stage. Default behaviour is to do the rejection last. |
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408 | \item[{flagTwoStageMerging [true | bool | true/false/1/0]}] A flag |
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409 | indicating whether to do an initial merge of newly-detected sources |
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410 | into the source list as they are found. If \texttt{false}, new |
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411 | sources are simply added to the end of the list for later merging. |
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412 | \item[{flagAdjacent [true | bool | true/false/1/0]}] A flag indicating |
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413 | whether to use the ``adjacent pixel'' criterion to decide whether to |
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414 | merge objects. If not, the next two parameters are used to determine |
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415 | whether objects are within the necessary thresholds. |
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416 | \item[{threshSpatial [$3.$ | float | $\ge 0$]}] The maximum allowed |
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417 | minimum spatial separation (in pixels) between two detections for |
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418 | them to be merged into one. Only used if \texttt{flagAdjacent = |
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419 | false}. |
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420 | \item[{threshVelocity [$7.$ | float | $\ge 0$]}] The maximum allowed |
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421 | minimum channel separation between two detections for them to be |
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422 | merged into one. |
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423 | \end{Lentry} |
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424 | |
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425 | \secC*{WCS parameters} |
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426 | \begin{Lentry} |
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427 | \item[{spectralType ["" | string | A valid WCS type]}] The user can |
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428 | specify an alternative WCS spectral type that the spectral axis can |
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429 | be expressed in. This specification should conform to the standards |
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430 | described in \citet{greisen06}, although it is possible to provide |
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431 | just the first four letters (the ``S-type'', \eg 'VELO'). |
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432 | \item[{restFrequency [-1 | float | any]}] If provided, this will be used in |
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433 | preference to the rest frequency given in the FITS header to |
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434 | calculate velocities and related quantities. A negative value (such |
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435 | as the default) will mean this is not used and the FITS header |
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436 | value, if present, is used instead. |
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437 | \item[{spectralUnits ["" | string | A valid units string]}] The user |
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438 | can specify the units of the spectral axis, overriding those given |
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439 | in the FITS header. If the spectral type is being changed, these |
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440 | units should be appropriate for that quantity. If not provided, the |
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441 | FITS header information is used. |
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442 | \end{Lentry} |
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443 | |
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444 | \secC*{Other parameters} |
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445 | \begin{Lentry} |
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446 | \item[{spectralMethod [peak | string | peak/sum]}] This indicates |
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447 | which method is used to plot the output spectra: \texttt{peak} means |
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448 | plot the spectrum containing the detection's peak pixel; |
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449 | \texttt{sum} means sum the spectra of each detected spatial pixel, |
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450 | and correct for the beam size. Any other choice defaults to |
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451 | \texttt{peak}. |
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452 | \item[{pixelCentre [centroid | string | centroid/peak/average]}] Which |
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453 | of the three ways of expressing the ``centre'' of a detection (see |
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454 | \S\ref{sec-results} for a description of the options) to use for the |
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455 | X, Y, \& Z columns in the output list. Alternatives are: |
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456 | \texttt{centroid, peak, average}. |
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457 | \item[{sortingParam [vel | string | see text for options]}] The |
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458 | parameter on which to sort the output list of detected |
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459 | objects. Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50, |
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460 | iflux, pflux (integrated and peak flux respectively), or snr. If the |
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461 | parameter begins with a '-' (\eg '-vel'), the order of the sort is |
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462 | reversed. |
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463 | \item[{drawBorders [true | bool | true/false/1/0]}] A flag indicating whether to draw |
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464 | borders around the detected objects in the moment maps included in |
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465 | the output (see for example Fig.~\ref{fig-spect}). |
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466 | \item[{drawBlankEdges [true | bool | true/false/1/0]}] A flag indicating whether to |
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467 | draw the dividing line between BLANK and non-BLANK pixels on the |
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468 | 2D images (see for example Fig.~\ref{fig-moment}). |
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469 | \item[{verbose [true | bool | true/false/1/0]}] A flag indicating whether to print the |
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470 | progress of any computationally intensive algorithms (\eg |
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471 | reconstruction, searching or merging algorithms) to the screen. |
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472 | \end{Lentry} |
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473 | |
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474 | |
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475 | %%% Local Variables: |
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476 | %%% mode: latex |
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477 | %%% TeX-master: "Guide" |
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478 | %%% End: |
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