[303] | 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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[158] | 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. If not listed, they take the default value given in |
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| 34 | parentheses. Since the order of the parameters in the input file does |
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| 35 | not matter, they are grouped here in logical sections. |
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| 36 | |
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[208] | 37 | \secB*{Input related} |
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[306] | 38 | \begin{Lentry} |
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| 39 | \item[{ImageFile [no default]}] The filename of the |
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| 40 | data cube to be analysed. |
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| 41 | \item[{flagSubsection [false]}] A flag to indicate whether one |
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[158] | 42 | wants a subsection of the requested image. |
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[306] | 43 | \item[{Subsection [ [*,*,*] ]}] The requested subsection |
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[258] | 44 | -- see \S\ref{sec-input} for details on the subsection format. If |
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| 45 | the full range of a dimension is required, use a \texttt{*} (thus the |
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| 46 | default is the full cube). |
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[306] | 47 | \item[{flagReconExists [false]}] A flag to indicate whether the |
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[158] | 48 | reconstructed array has been saved by a previous run of \duchamp. If |
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| 49 | set true, the reconstructed array will be read from the file given |
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| 50 | by \texttt{reconFile}, rather than calculated directly. |
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[306] | 51 | \item[{reconFile [no default]}] The FITS file that contains the |
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[158] | 52 | reconstructed array. If \texttt{flagReconExists} is true and this |
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[231] | 53 | parameter is not defined, the default file that is looked for will |
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[258] | 54 | be determined by the \atrous parameters (see \S\ref{sec-recon}). |
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[306] | 55 | \item[{flagSmoothExists [false]}] A flag to indicate whether the |
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[208] | 56 | Hanning-smoothed array has been saved by a previous run of \duchamp. If |
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| 57 | set true, the smoothed array will be read from the file given |
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| 58 | by \texttt{smoothFile}, rather than calculated directly. |
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[306] | 59 | \item[{smoothFile [no default]}] The FITS file that has |
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| 60 | a previously smoothed array. If \texttt{flagSmoothExists} |
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| 61 | is true and this parameter is not defined, the default file that is |
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| 62 | looked for will be determined by the smoothing parameters (see |
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[208] | 63 | \S\ref{sec-smoothing}). |
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[480] | 64 | \item[{usePrevious [false]}] A flag to indicate that \duchamp should |
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| 65 | read the list of objects from a previously-created log file, rather |
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| 66 | than doing the searching itself. The set of outputs will be created |
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| 67 | according to the flags in the following section. |
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| 68 | \item[{objectList [no default]}] When \texttt{usePrevious=true}, this |
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| 69 | list is used to output individual spectral plots, as well as a |
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| 70 | postscript file for all spectral plots as given by |
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| 71 | \texttt{SpectraFile}. The filenames of the plots will be the same as |
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| 72 | \texttt{SpectraFile}, but with -XX at the end, where XX is the |
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| 73 | object number (\eg \texttt{duchamp-Spectra-07.ps}). The format of |
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| 74 | the parameter value should be a string listing individual objects or |
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| 75 | object ranges: \eg 1,2,4-7,8,14. |
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[306] | 76 | \end{Lentry} |
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[208] | 77 | |
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| 78 | \secB*{Output related} |
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[306] | 79 | \begin{Lentry} |
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| 80 | \item[{OutFile [duchamp-\\Results.txt]}] The file containing the |
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[158] | 81 | final list of detections. This also records the list of input |
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[364] | 82 | parameters. |
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| 83 | \item[{flagSeparateHeader [false]}] A flag to indicate that the header |
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| 84 | information that would normally be printed at the start of the |
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| 85 | results file (containing information on the parameters, image |
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| 86 | statistics and number of detections) should instead be written to a |
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| 87 | separate file. |
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| 88 | \item[{HeaderFile [duchamp-\\Results.hdr]}] The file to which the |
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[373] | 89 | header information should be written when |
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[364] | 90 | \texttt{flagSeparateHeader=true}. |
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[306] | 91 | \item[{SpectraFile [duchamp-\\Spectra.ps]}] The postscript file |
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[158] | 92 | containing the resulting integrated spectra and images of the |
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[425] | 93 | detections. |
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| 94 | \item[{flagTextSpectra [false]}] A flag to say whether the spectra |
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| 95 | should be saved in text form in a single file. See below for a |
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| 96 | description. |
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| 97 | \item[{spectraTextFile [duchamp-\\Spectra.txt]}] The file containing |
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| 98 | the spectra of each object in ascii format. This file will have a |
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| 99 | column showing the spectral coordinates, and one column for each of |
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| 100 | the detected objects, showing the flux values as plotted in the |
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| 101 | graphical output of \texttt{spectraFile}. |
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[306] | 102 | \item[{flagLog [false]}] A flag to indicate whether the |
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[231] | 103 | details of intermediate detections should be logged. |
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[306] | 104 | \item[{LogFile [duchamp-\\Logfile.txt]}] The file in which |
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[158] | 105 | intermediate detections are logged. These are detections that have |
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| 106 | not been merged. This is primarily for use in debugging and |
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[306] | 107 | diagnostic purposes: normal use of the program will probably not |
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| 108 | require it. |
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[670] | 109 | \item[{flagOutputMomentMap [false]}] A flag to say whether or not to save a |
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| 110 | FITS file containing the moment-0 map. |
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| 111 | \item[fileOutputMomentMap{ [see text]}] The file to which the moment-0 array is |
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| 112 | written. If left blank (the default), the naming scheme detailed in |
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| 113 | Section~\ref{sec-maskOut} is used. |
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[380] | 114 | \item[{flagOutputMask [false]}] A flag to say whether or not to save a |
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| 115 | FITS file containing a mask array, with values 1 where there is a |
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[525] | 116 | detected object and 0 elsewhere. |
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| 117 | \item[fileOutputMask{ [see text]}] The file to which the mask array is |
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| 118 | written. If left blank (the default), the naming scheme detailed in |
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| 119 | Section~\ref{sec-maskOut} is used. |
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[522] | 120 | \item[{flagMaskWithObjectNum [false]}] If this flag is true, the |
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| 121 | detected pixels in the mask image have the corresponding object ID |
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| 122 | as their value. If false, they have the value 1. All non-detected |
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| 123 | pixels have the value 0. |
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[306] | 124 | \item[{flagOutputRecon [false]}] A flag to say whether or not |
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[525] | 125 | to save the reconstructed cube as a FITS file. |
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| 126 | \item[fileOutputRecon{ [see text]}] The file to which the reconstructed array |
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| 127 | is written. If left blank (the default), the naming scheme detailed |
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| 128 | in Section~\ref{sec-reconIO} is used. |
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[306] | 129 | \item[{flagOutputResid [false]}] As for |
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[158] | 130 | \texttt{flagOutputRecon}, but for the residual array -- the |
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[525] | 131 | difference between the original cube and the reconstructed cube. |
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| 132 | \item[fileOutputResid{ [see text]}] The file to which the residual array |
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| 133 | is written. If left blank (the default), the naming scheme detailed |
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| 134 | in Section~\ref{sec-reconIO} is used. |
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[306] | 135 | \item[{flagOutputSmooth [false]}] A flag to say whether or not |
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[525] | 136 | to save the smoothed cube as a FITS file. |
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| 137 | \item[fileOutputSmooth{ [see text]}] The file to which the smoothed array |
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| 138 | is written. If left blank (the default), the naming scheme detailed |
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| 139 | in Section~\ref{sec-reconIO} is used. |
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[306] | 140 | \item[{flagVOT [false]}] A flag to say whether to create a |
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| 141 | VOTable file with the detection information. This will be an XML |
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| 142 | file in the Virtual Observatory VOTable format. |
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| 143 | \item[{votFile [duchamp-\\Results.xml]}] The VOTable file with |
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[158] | 144 | the list of final detections. Some input parameters are also |
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[306] | 145 | recorded. |
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| 146 | \item[{flagKarma [false]}] A flag to say whether to create a |
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[158] | 147 | Karma annotation file corresponding to the information in |
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[306] | 148 | \texttt{outfile}. This can be used as an overlay in Karma |
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[158] | 149 | programs such as \texttt{kvis}. |
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[306] | 150 | \item[{karmaFile [duchamp-\\Results.ann]}] The Karma annotation |
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[447] | 151 | file showing the list of final detections. |
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| 152 | \item[{annotationType [borders]}] Which type of annotation plot to |
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| 153 | use. Specifying ``borders'' gives an outline around the detected |
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| 154 | spatial pixels, while ``circles'' gives a circle centred on the |
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| 155 | centre of the object with radius large enough to encompass all |
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| 156 | spatial pixels. |
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[306] | 157 | \item[{flagMaps [true]}] A flag to say whether to save |
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[158] | 158 | postscript files showing the 0th moment map of the whole cube |
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| 159 | (parameter \texttt{momentMap}) and the detection image |
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| 160 | (\texttt{detectionMap}). |
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[306] | 161 | \item[{momentMap [duchamp-\\MomentMap.ps]}] A postscript file |
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[158] | 162 | containing a map of the 0th moment of the detected sources, as well |
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| 163 | as pixel and WCS coordinates. |
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[306] | 164 | \item[{detectionMap [duchamp-\\DetectionMap.ps]}] A postscript |
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| 165 | file with a map showing each of the detected objects, coloured in |
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| 166 | greyscale by the number of detected channels in each spatial |
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| 167 | pixel. Also shows pixel and WCS coordinates. |
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| 168 | \item[{flagXOutput [true]}] A flag to say whether to display a |
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[294] | 169 | 0th moment map in a PGPlot X-window. This will be in addition to any |
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| 170 | that are saved to a file. This parameter can be overridden by the |
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| 171 | use of the \texttt{-x} command-line option, which disables the |
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| 172 | X-windows output. |
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[447] | 173 | \item[{newFluxUnits [no default]}] Flux units that the pixel values |
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| 174 | should be converted into. These should be directly compatible with |
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| 175 | the existing units, given by the BUNIT keyword. |
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| 176 | \item[{precFlux [3]}] The desired precision (\ie number of decimal |
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| 177 | places) for flux values given in the output files and tables. |
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| 178 | \item[{precVel [3]}] The desired precision (\ie number of decimal |
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| 179 | places) for velocity/frequency values given in the output files and |
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| 180 | tables. |
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| 181 | \item[{precSNR [2]}] The desired precision (\ie number of decimal |
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| 182 | places) for the peak SNR value given in the output files and tables. |
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[306] | 183 | \end{Lentry} |
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[158] | 184 | |
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| 185 | \secB*{Modifying the cube} |
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[306] | 186 | \begin{Lentry} |
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| 187 | \item[{flagTrim [false]}] A flag to say whether to trim |
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[285] | 188 | BLANK pixels from the edges of the cube -- these are typically |
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| 189 | pixels set to some particular value because they fall outside the |
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| 190 | imaged area, and trimming them can help speed up the execution. |
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[306] | 191 | \item[{flagMW [false]}] A flag to say whether to ignore |
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[158] | 192 | channels contaminated by Milky Way (or other) emission -- the |
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| 193 | searching algorithms will not look at these channels. |
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[306] | 194 | \item[{maxMW [112]}] The maximum channel number that contains |
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[673] | 195 | ``Milky Way'' emission. This is the channel number in the original |
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| 196 | cube, before any subsection is applied. |
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| 197 | \item[{minMW [75]}] The minimum channel number that contains ``Milky |
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| 198 | Way'' emission. This is the channel number in the original cube, |
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| 199 | before any subsection is applied. Note that the range specified by |
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[158] | 200 | \texttt{maxMW} and \texttt{minMW} is inclusive. |
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[306] | 201 | \item[{flagBaseline [false]}] A flag to say whether to remove |
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[158] | 202 | the baseline from each spectrum in the cube for the purposes of |
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| 203 | reconstruction and detection. |
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[306] | 204 | \end{Lentry} |
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[158] | 205 | |
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| 206 | \secB*{Detection related} |
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| 207 | |
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| 208 | \secC*{General detection} |
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[306] | 209 | \begin{Lentry} |
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| 210 | \item[{flagStatSec [false]}] A flag indicating whether the |
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[258] | 211 | statistics should be calculated on a subsection of the cube, rather |
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[265] | 212 | than the full cube. Note that this only applies to the statistics |
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| 213 | used to determine the threshold, and not for other statistical |
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| 214 | calculations (such as those in the reconstruction phase). |
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[306] | 215 | \item[{StatSec [ [*,*,*] ]}] The subsection of the cube used |
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[258] | 216 | for calculating statistics -- see \S\ref{sec-input} for details on |
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| 217 | the subsection format. Only used if \texttt{flagStatSec=true}. |
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[386] | 218 | \item[{flagRobustStats [true]}] A flag indicating whether to use the |
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| 219 | robust statistics (median and MADFM) to estimate the noise |
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| 220 | parameters, rather than the mean and rms. See \S\ref{sec-stats} for |
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| 221 | details. |
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[306] | 222 | \item[{flagNegative [false]}] A flag indicating that the |
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| 223 | features of interest are negative. The cube is inverted prior to |
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| 224 | searching. |
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| 225 | \item[{snrCut [3.]}] The threshold, in multiples of $\sigma$ above |
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| 226 | the mean. |
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| 227 | \item[{threshold [no default]}] The actual value of the |
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[194] | 228 | threshold. Normally the threshold is calculated from the cube's |
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| 229 | statistics, but the user can manually specify a value to be used |
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| 230 | that overrides the calculated value. If this is not specified, the |
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[462] | 231 | calculated value is used, but this value will take precedence over |
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| 232 | other means of calculating the threshold (\ie via \texttt{snrCut} or |
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| 233 | the FDR method). |
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[306] | 234 | \item[{flagGrowth [false]}] A flag indicating whether or not to |
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[158] | 235 | grow the detected objects to a smaller threshold. |
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[462] | 236 | \item[{growthCut [3.]}] The smaller threshold using in growing |
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[158] | 237 | detections. In units of $\sigma$ above the mean. |
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[462] | 238 | \item[{growthThreshold [no default]}] Alternatively, the threshold to |
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| 239 | which detections are grown can be specified in flux units (in the |
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| 240 | same manner as the \texttt{threshold} parameter). When the |
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| 241 | \texttt{threshold} parameter is given, this option \textbf{must} be |
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| 242 | used instead of \texttt{growthCut}. |
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[675] | 243 | \item[{beamFWHM [-1.]}] The full-width at half maximum of the beam, in |
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| 244 | pixels. If the header keywords BMAJ and BMIN are present, then |
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| 245 | these will be used to calculate the beam area, and this parameter |
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| 246 | will be ignored. This will take precedence over \texttt{beamArea} |
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| 247 | (but is ignored if not specified). |
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| 248 | \item[{beamArea [10.]}] The \textbf{area} of the beam in pixels (\ie |
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| 249 | how many pixel does the beam cover?). As above, if the header |
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| 250 | keywords BMAJ and BMIN are present, then these will be used to |
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| 251 | calculate the beam area, and this parameter will be ignored. |
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[306] | 252 | \end{Lentry} |
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[158] | 253 | |
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[258] | 254 | \secC*{\Atrous reconstruction} |
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[306] | 255 | \begin{Lentry} |
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| 256 | \item[{flagATrous [false]}] A flag indicating whether or not to |
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[258] | 257 | reconstruct the cube using the \atrous wavelet |
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[158] | 258 | reconstruction. See \S\ref{sec-recon} for details. |
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[306] | 259 | \item[{reconDim [1]}] The number of dimensions to use in the |
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[158] | 260 | reconstruction. 1 means reconstruct each spectrum separately, 2 |
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| 261 | means each channel map is done separately, and 3 means do the whole |
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| 262 | cube in one go. |
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[306] | 263 | \item[{scaleMin [1]}] The minimum wavelet scale to be used in the |
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[158] | 264 | reconstruction. A value of 1 means ``use all scales''. |
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[364] | 265 | \item[{scaleMax [0]}] The maximum wavelet scale to be used in the |
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| 266 | reconstruction. If the value is $\le0$ then the maximum scale is |
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| 267 | calculated from the size of the input array. Similarly, if the value |
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| 268 | given is larger than this calculated value, the calculated value is |
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| 269 | used instead. |
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[306] | 270 | \item[{snrRecon [4]}] The thresholding cutoff used in the |
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[158] | 271 | reconstruction -- only wavelet coefficients this many $\sigma$ above |
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| 272 | the mean (or greater) are included in the reconstruction. |
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[306] | 273 | \item[{filterCode [1]}] The code number of the filter to use in |
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[158] | 274 | the reconstruction. The options are: |
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| 275 | \begin{itemize} |
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| 276 | \item \textbf{1:} B$_3$-spline filter: coefficients = |
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| 277 | $(\frac{1}{16}, \frac{1}{4}, \frac{3}{8}, \frac{1}{4}, \frac{1}{16})$ |
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| 278 | \item \textbf{2:} Triangle filter: coefficients = |
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| 279 | $(\frac{1}{4}, \frac{1}{2}, \frac{1}{4})$ |
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| 280 | \item \textbf{3:} Haar wavelet: coefficients = |
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| 281 | $(0, \frac{1}{2}, \frac{1}{2})$ |
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| 282 | \end{itemize} |
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[306] | 283 | \end{Lentry} |
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[158] | 284 | |
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[208] | 285 | \secC*{Smoothing the cube} |
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[306] | 286 | \begin{Lentry} |
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| 287 | \item[{flagSmooth [false]}] A flag indicating whether to |
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[275] | 288 | smooth the cube. See \S\ref{sec-smoothing} for details. |
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[306] | 289 | \item[{smoothType [spectral]}] The smoothing method used: either |
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| 290 | ``spectral'' (with a 1D Hanning filter) or ``spatial'' (with a 2D |
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| 291 | Gaussian filter). |
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| 292 | \item[{hanningWidth [5]}] The width of the Hanning smoothing |
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| 293 | kernel. |
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| 294 | \item[{kernMaj [3]}] The full-width-half-maximum (FWHM) of the |
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| 295 | 2D Gaussian smoothing kernel's major axis. |
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| 296 | \item[{kernMin [3]}] The FWHM of the 2D Gaussian smoothing kernel's |
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| 297 | minor axis. |
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| 298 | \item[{kernPA [0]}] The position angle, in degrees, |
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| 299 | anticlockwise from vertical (\ie usually East of North). |
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| 300 | \end{Lentry} |
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[208] | 301 | |
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[158] | 302 | \secC*{FDR method} |
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[306] | 303 | \begin{Lentry} |
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| 304 | \item[{flagFDR [false]}] A flag indicating whether or not to use |
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[158] | 305 | the False Discovery Rate method in thresholding the pixels. |
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[306] | 306 | \item[{alphaFDR [0.01]}] The $\alpha$ parameter used in the FDR |
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| 307 | analysis. The average number of false detections, as a fraction of |
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| 308 | the total number, will be less than $\alpha$ (see |
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[543] | 309 | \S\ref{sec-detection}). |
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| 310 | \item[{FDRnumCorChan [2]}] The number of neighbouring spectral |
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| 311 | channels that are assumed to be correlated. This is needed by the |
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| 312 | FDR algorithm to calculate the normalisation constant $c_N$ (see |
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[306] | 313 | \S\ref{sec-detection}). |
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| 314 | \end{Lentry} |
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[158] | 315 | |
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| 316 | \secC*{Merging detections} |
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[306] | 317 | \begin{Lentry} |
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| 318 | \item[{minPix [2]}] The minimum number of spatial pixels for a |
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[158] | 319 | single detection to be counted. |
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[306] | 320 | \item[{minChannels [3]}] At least one contiguous set of this many |
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| 321 | channels must be present in the detection for it to be accepted. |
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[672] | 322 | \item[{flagRejectBeforeMerge [false]}] A flag indicating whether to |
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| 323 | reject sources that fail to meet the \texttt{minPix} or |
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| 324 | \texttt{minChannels} criteria \textbf{before} the merging |
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| 325 | stage. Default behaviour is to do the rejection last. |
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[306] | 326 | \item[{flagAdjacent [true]}] A flag indicating whether to use |
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[158] | 327 | the ``adjacent pixel'' criterion to decide whether to merge |
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| 328 | objects. If not, the next two parameters are used to determine |
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| 329 | whether objects are within the necessary thresholds. |
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[306] | 330 | \item[{threshSpatial [3.]}] The maximum allowed minimum spatial |
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[158] | 331 | separation (in pixels) between two detections for them to be merged |
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| 332 | into one. Only used if \texttt{flagAdjacent = false}. |
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[306] | 333 | \item[{threshVelocity [7.]}] The maximum allowed minimum channel |
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[158] | 334 | separation between two detections for them to be merged into |
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| 335 | one. |
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[306] | 336 | \end{Lentry} |
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[158] | 337 | |
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| 338 | \secC*{Other parameters} |
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[306] | 339 | \begin{Lentry} |
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| 340 | \item[{spectralMethod [peak]}] This indicates which method is used |
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[158] | 341 | to plot the output spectra: \texttt{peak} means plot the spectrum |
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| 342 | containing the detection's peak pixel; \texttt{sum} means sum the |
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| 343 | spectra of each detected spatial pixel, and correct for the beam |
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| 344 | size. Any other choice defaults to \texttt{peak}. |
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[306] | 345 | \item[{spectralUnits [km/s]}] The user can specify the units of |
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[158] | 346 | the spectral axis. Assuming the WCS of the FITS file is valid, the |
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| 347 | spectral axis is transformed into velocity, and put into these units |
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| 348 | for all output and for calculations such as the integrated flux of a |
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| 349 | detection. |
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[306] | 350 | \item[{pixelCentre [centroid]}] Which of the three ways of |
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[285] | 351 | expressing the ``centre'' of a detection (see \S\ref{sec-results} |
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| 352 | for a description of the options) to use for the X, Y, \& Z |
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| 353 | columns in the output list. Alternatives are: \texttt{centroid, peak, |
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[571] | 354 | average}. |
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| 355 | \item[{sortingParam [vel]}] The parameter on which to sort the output |
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| 356 | list of detected objects. Options are: x-value, y-value, z-value, |
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| 357 | ra, dec, vel, w50, iflux, pflux (integrated and peak flux |
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[572] | 358 | respectively), or snr. |
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[306] | 359 | \item[{drawBorders [true]}] A flag indicating whether to draw |
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| 360 | borders around the detected objects in the moment maps included in |
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| 361 | the output (see for example Fig.~\ref{fig-spect}). |
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| 362 | \item[{drawBlankEdges [true]}] A flag indicating whether to |
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| 363 | draw the dividing line between BLANK and non-BLANK pixels on the |
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| 364 | 2D images (see for example Fig.~\ref{fig-moment}). |
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| 365 | \item[{verbose [true]}] A flag indicating whether to print the |
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| 366 | progress of any computationally intensive algorithms (\eg |
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[231] | 367 | reconstruction, searching or merging algorithms) to the screen. |
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[306] | 368 | \end{Lentry} |
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[158] | 369 | |
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