[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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[1322] | 39 | \item[{ImageFile [no default | string | filename]}] The filename of |
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| 40 | the data cube to be analysed. |
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| 41 | \item[{flagSubsection [false | bool | true/false/1/0]}] A flag to |
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| 42 | indicate whether one wants a subsection of the requested image. |
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| 43 | \item[{Subsection [full field | string | Subsection string]}] The |
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| 44 | requested subsection -- see \S\ref{sec-input} for details on the |
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| 45 | subsection format. If the full range of a dimension is required, |
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| 46 | use a \texttt{*} (thus the default is the full cube). |
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| 47 | \item[{flagReconExists [false | bool | true/false/1/0]}] A flag to |
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| 48 | indicate whether the reconstructed array has been saved by a |
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| 49 | previous run of \duchamp. If set true, the reconstructed array will |
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| 50 | be read from the file given by \texttt{reconFile}, rather than |
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| 51 | calculated directly. |
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| 52 | \item[{reconFile [no default | string | filename]}] The FITS file that |
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| 53 | contains the reconstructed array. If \texttt{flagReconExists} is |
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| 54 | true and this parameter is not defined, the default file that is |
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| 55 | looked for will be determined by the \atrous parameters (see |
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| 56 | \S\ref{sec-recon}). |
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| 57 | \item[{flagSmoothExists [false | bool | true/false/1/0]}] A flag to |
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| 58 | indicate whether the Hanning-smoothed array has been saved by a |
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| 59 | previous run of \duchamp. If set true, the smoothed array will be |
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| 60 | read from the file given by \texttt{smoothFile}, rather than |
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| 61 | calculated directly. |
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| 62 | \item[{smoothFile [no default | string | filename]}] The FITS file |
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| 63 | that has a previously smoothed array. If \texttt{flagSmoothExists} |
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[306] | 64 | is true and this parameter is not defined, the default file that is |
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| 65 | looked for will be determined by the smoothing parameters (see |
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[208] | 66 | \S\ref{sec-smoothing}). |
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[1322] | 67 | \item[{usePrevious [false | bool | true/false/1/0]}] A flag to |
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| 68 | indicate that \duchamp should read the list of objects from a |
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| 69 | previously-created log file, rather than doing the searching |
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| 70 | itself. The set of outputs will be created according to the flags in |
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| 71 | the following section. |
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| 72 | \item[{objectList [no default | string | comma-separated list]}] When |
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| 73 | \texttt{usePrevious=true}, this list is used to output individual |
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| 74 | spectral plots, as well as a postscript file for all spectral plots |
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| 75 | as given by \texttt{SpectraFile}. The filenames of the plots will be |
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| 76 | the same as \texttt{SpectraFile}, but with -XX at the end, where XX |
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| 77 | is the object number (\eg \texttt{duchamp-Spectra-07.ps}). The |
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| 78 | format of the parameter value should be a string listing individual |
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| 79 | objects or object ranges: \eg 1,2,4-7,8,14. |
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[306] | 80 | \end{Lentry} |
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[208] | 81 | |
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| 82 | \secB*{Output related} |
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[306] | 83 | \begin{Lentry} |
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[1322] | 84 | \item[{OutFile [duchamp-\\Results.txt | string | filename]}] The file |
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| 85 | containing the final list of detections. This also records the list |
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| 86 | of input parameters. |
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| 87 | \item[{flagSeparateHeader [false | bool | true/false/1/0]}] A flag to |
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| 88 | indicate that the header information that would normally be printed |
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| 89 | at the start of the results file (containing information on the |
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| 90 | parameters, image statistics and number of detections) should |
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| 91 | instead be written to a separate file. |
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| 92 | \item[{HeaderFile [duchamp-\\Results.hdr | string | filename]}] The |
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| 93 | file to which the header information should be written when |
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[364] | 94 | \texttt{flagSeparateHeader=true}. |
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[1322] | 95 | \item[{flagWriteBinaryCatalogue [true | bool | true/false/1/0]}] |
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| 96 | Whether to write a binary catalogue of the detections, for later |
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| 97 | re-use (see \S\ref{sec-reuse} for details). |
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| 98 | \item[{binaryCatalogue [duchamp-Catalogue.dpc | string | filename]}] |
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| 99 | The filename for the binary catalogue. |
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| 100 | \item[{flagPlotSpectra [true | bool | true/false/1/0]}] Whether to |
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| 101 | produce a postscript file containing spectra of all detected |
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| 102 | objects. If PGPlot has not been enabled, this parameter defaults to |
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| 103 | \texttt{false}. |
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| 104 | \item[{SpectraFile [duchamp-\\Spectra.ps | string | filename]}] The |
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| 105 | postscript file that contains the resulting integrated spectra and |
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| 106 | images of the detections. |
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| 107 | \item[{flagPlotIndividualSpectra [false | bool | true/false/1/0]}] |
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| 108 | Whether to produce individual spectral plots for listed sources. |
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| 109 | \item[{flagTextSpectra [false | bool | true/false/1/0]}] A flag to say |
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| 110 | whether the spectra should be saved in text form in a single |
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| 111 | file. See below for a description. |
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| 112 | \item[{spectraTextFile [duchamp-\\Spectra.txt | string | filename]}] |
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| 113 | The file containing the spectra of each object in ascii format. This |
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| 114 | file will have a column showing the spectral coordinates, and one |
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| 115 | column for each of the detected objects, showing the flux values as |
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| 116 | plotted in the graphical output of \texttt{spectraFile}. |
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| 117 | \item[{flagLog [false | bool | true/false/1/0]}] A flag to indicate |
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| 118 | whether the details of intermediate detections should be logged. |
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| 119 | \item[{LogFile [duchamp-\\Logfile.txt | string | filename]}] The file |
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| 120 | in which intermediate detections and the pixel content of the final |
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| 121 | list of detections are logged. These are detections that have not |
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| 122 | been merged. This is primarily for use in debugging and diagnostic |
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[1021] | 123 | purposes: normal use of the program will probably not require it. |
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[1322] | 124 | \item[{flagOutputMomentMap [false | bool | true/false/1/0]}] A flag to |
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| 125 | say whether or not to save a FITS file containing the moment-0 map. |
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| 126 | \item[fileOutputMomentMap{ [see text | string | filename]}] The file |
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| 127 | to which the moment-0 array is written. If left blank (the default), |
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| 128 | the naming scheme detailed in \S\ref{sec-momentOut} is used. |
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| 129 | \item[{flagOutputMomentMask [false | bool | true/false/1/0]}] A flag |
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| 130 | to say whether or not to save a FITS file containing the moment-0 |
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| 131 | mask (a mask showing which spatial pixels are detected in one or |
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| 132 | more channels). |
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| 133 | \item[fileOutputMomentMask{ [see text | string | filename]}] The file |
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| 134 | to which the moment-0 mask is written. If left blank (the default), |
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| 135 | the naming scheme detailed in \S\ref{sec-maskOut} is used. |
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| 136 | \item[{flagOutputMask [false | bool | true/false/1/0]}] A flag to say |
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| 137 | whether or not to save a FITS file containing a mask array, with |
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| 138 | values 1 where there is a detected object and 0 elsewhere. |
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| 139 | \item[fileOutputMask{ [see text | string | filename]}] The file to |
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| 140 | which the mask array is written. If left blank (the default), the |
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| 141 | naming scheme detailed in \S\ref{sec-maskOut} is used. |
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| 142 | \item[{flagMaskWithObjectNum [false | bool | true/false/1/0]}] If this |
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| 143 | flag is true, the detected pixels in the mask image have the |
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| 144 | corresponding object ID as their value. If false, they have the |
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| 145 | value 1. All non-detected pixels have the value 0. |
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| 146 | \item[{flagOutputRecon [false | bool | true/false/1/0]}] A flag to say |
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| 147 | whether or not to save the reconstructed cube as a FITS file. |
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| 148 | \item[fileOutputRecon{ [see text | string | filename]}] The file to |
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| 149 | which the reconstructed array is written. If left blank (the |
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| 150 | default), the naming scheme detailed in \S\ref{sec-reconIO} is used. |
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| 151 | \item[{flagOutputResid [false | bool | true/false/1/0]}] As for |
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[158] | 152 | \texttt{flagOutputRecon}, but for the residual array -- the |
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[525] | 153 | difference between the original cube and the reconstructed cube. |
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[1322] | 154 | \item[fileOutputResid{ [see text | string | filename]}] The file to |
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| 155 | which the residual array is written. If left blank (the default), |
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| 156 | the naming scheme detailed in \S\ref{sec-reconIO} is used. |
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| 157 | \item[{flagOutputSmooth [false | bool | true/false/1/0]}] A flag to |
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| 158 | say whether or not to save the smoothed cube as a FITS file. |
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| 159 | \item[fileOutputSmooth{ [see text | string | filename]}] The file to |
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| 160 | which the smoothed array is written. If left blank (the default), |
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| 161 | the naming scheme detailed in \S\ref{sec-reconIO} is used. |
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| 162 | \item[{flagOutputBaseline [false | bool | true/false/1/0]}] A flag to |
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| 163 | say whether or not to save the cube of spectral baseline values as a |
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| 164 | FITS file. |
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| 165 | \item[fileOutputBaseline{ [see text | string | filename]}] The file to |
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| 166 | which the baseline values are written. If left blank (the default), |
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| 167 | the naming scheme detailed in \S\ref{sec-baselineOut} is used. |
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| 168 | \item[{flagVOT [false | bool | true/false/1/0]}] A flag to say whether |
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| 169 | to create a VOTable file with the detection information. This will |
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| 170 | be an XML file in the Virtual Observatory VOTable format. |
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| 171 | \item[{votFile [duchamp-\\Results.xml | string | filename]}] The |
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| 172 | VOTable file with the list of final detections. Some input |
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| 173 | parameters are also recorded. |
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| 174 | \item[{flagKarma [false | bool | true/false/1/0]}] A flag to say |
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| 175 | whether to create a Karma annotation file corresponding to the |
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| 176 | information in \texttt{outfile}. This can be used as an overlay in |
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| 177 | Karma programs such as \texttt{kvis}. |
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| 178 | \item[{karmaFile [duchamp-\\Results.ann | string | filename]}] The |
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| 179 | Karma annotation file showing the list of final detections. |
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| 180 | \item[{flagDS9 [false | bool | true/false/1/0]}] A flag to say whether |
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| 181 | to create a DS9 region file corresponding to the information in |
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[1078] | 182 | \texttt{outfile}. This can be used as an overlay in SAOImage DS9 or |
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[1322] | 183 | casaviewer. |
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| 184 | \item[{ds9File [duchamp-\\Results.ann | string | filename]}] The DS9 |
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| 185 | region file showing the list of final detections. |
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| 186 | \item[{flagCasa [false | bool | true/false/1/0]}] A flag to say |
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| 187 | whether to create a CASA region file corresponding to the |
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| 188 | information in \texttt{outfile}. This can be used as an overlay in |
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| 189 | casaviewer (when this functionality is available) or import into |
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| 190 | casapy. |
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| 191 | \item[{casaFile [duchamp-\\Results.crf | string | filename]}] The CASA |
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| 192 | region file showing the list of final detections. |
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| 193 | \item[{annotationType [borders | string | borders/circles/ellipses]}] |
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| 194 | Which type of annotation plot to use. Specifying ``borders'' gives |
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| 195 | an outline around the detected spatial pixels, ``circles'' gives a |
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| 196 | circle centred on the centre of the object with radius large enough |
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| 197 | to encompass all spatial pixels, and ``ellipses'' gives an ellipse |
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| 198 | centred on the centre of the object of size given by the MAJ, MIN \& |
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| 199 | PA values. |
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| 200 | \item[{flagMaps [true | bool | true/false/1/0]}] A flag to say whether |
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| 201 | to save postscript files showing the 0th moment map of the whole |
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| 202 | cube (\texttt{momentMap}) and the detection image |
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[840] | 203 | (\texttt{detectionMap}). If PGPlot has not been enabled, this |
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| 204 | parameter defaults to \texttt{false}. |
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[1322] | 205 | \item[{momentMap [duchamp-\\MomentMap.ps | string | filename]}] A |
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| 206 | postscript file containing a map of the 0th moment of the detected |
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| 207 | sources, as well as pixel and WCS coordinates. |
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| 208 | \item[{detectionMap [duchamp-\\DetectionMap.ps | string | filename]}] |
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| 209 | A postscript file with a map showing each of the detected objects, |
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| 210 | coloured in greyscale by the number of detected channels in each |
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| 211 | spatial pixel. Also shows pixel and WCS coordinates. |
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| 212 | \item[{flagXOutput [true | bool | true/false/1/0]}] A flag to say |
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| 213 | whether to display a 0th moment map in a PGPlot X-window. This will |
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| 214 | be in addition to any that are saved to a file. This parameter can |
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| 215 | be overridden by the use of the \texttt{-x} command-line option, |
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| 216 | which disables the X-windows output. If PGPlot has not been enabled, |
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| 217 | this parameter defaults to \texttt{false}. |
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| 218 | \item[{newFluxUnits [no default | string | units string]}] Flux units |
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| 219 | that the pixel values should be converted into. These should be |
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| 220 | directly compatible with the units in the FITS header, given by the |
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| 221 | BUNIT keyword. |
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| 222 | \item[{precFlux [3 | int | $> 0$]}] The desired precision (\ie number |
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| 223 | of decimal places) for flux values given in the output files and |
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[447] | 224 | tables. |
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[1322] | 225 | \item[{precVel [3 | int | $> 0$]}] The desired precision (\ie number |
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| 226 | of decimal places) for velocity/frequency values given in the output |
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| 227 | files and tables. |
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| 228 | \item[{precSNR [2 | int | $> 0$]}] The desired precision (\ie number |
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| 229 | of decimal places) for the peak SNR value given in the output files |
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| 230 | and tables. |
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[306] | 231 | \end{Lentry} |
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[158] | 232 | |
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| 233 | \secB*{Modifying the cube} |
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[306] | 234 | \begin{Lentry} |
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[1322] | 235 | \item[{flagTrim [false | bool | true/false/1/0]}] A flag to say |
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| 236 | whether to trim BLANK pixels from the edges of the cube -- these are |
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| 237 | typically pixels set to some particular value because they fall |
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| 238 | outside the imaged area, and trimming them can help speed up the |
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| 239 | execution. |
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| 240 | \item[{flaggedChannels [no default | string | comma-separated list]}] |
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| 241 | Channels that are to be ignored by the source-finding. These should |
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| 242 | be specified by a comma-separated list of single values and ranges, |
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| 243 | such as 1,3,6-12,18. Channel numbers are zero-based, so that the |
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| 244 | first channel in the cube has value 0. |
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| 245 | \item[{flagBaseline [false | bool | true/false/1/0]}] A flag to say |
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| 246 | whether to remove the baseline from each spectrum in the cube for |
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| 247 | the purposes of reconstruction and detection. |
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| 248 | \item[{baselineType [atrous | string | atrous/median]}] The algorithm |
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| 249 | used to calculate the spectral baseline. Only \texttt{atrous} or |
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| 250 | \texttt{median} are accepted. |
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| 251 | \item[{baselineBoxWidth [51 | int | odd integer $> 0$]}] The box width |
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| 252 | used by the \texttt{median} baseline algorithm. Needs to be odd - if |
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| 253 | even, it will be incremented by one. |
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[306] | 254 | \end{Lentry} |
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[158] | 255 | |
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| 256 | \secB*{Detection related} |
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| 257 | |
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| 258 | \secC*{General detection} |
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[306] | 259 | \begin{Lentry} |
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[1322] | 260 | \item[{searchType [spatial | string | spectral/spatial]}] How the |
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| 261 | searches are done. Only ``spatial'' and ``spectral'' are accepted. A |
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| 262 | value of ``spatial'' means each 2D channel map is searched, whereas |
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| 263 | ``spectral'' means each 1D spectrum is searched. |
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| 264 | \item[{flagStatSec [false | bool | true/false/1/0]}] A flag indicating |
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| 265 | whether the statistics should be calculated on a subsection of the |
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| 266 | cube, rather than the full cube. Note that this only applies to the |
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| 267 | statistics used to determine the threshold, and not for other |
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| 268 | statistical calculations (such as those in the reconstruction |
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| 269 | phase). |
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| 270 | \item[{StatSec [full field | string | Subsection string]}] The |
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| 271 | subsection of the cube used for calculating statistics -- see |
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| 272 | \S\ref{sec-input} for details on the subsection format. Only used if |
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| 273 | \texttt{flagStatSec=true}. |
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| 274 | \item[{flagRobustStats [true | bool | true/false/1/0]}] A flag |
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| 275 | indicating whether to use the robust statistics (median and MADFM) |
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| 276 | to estimate the noise parameters of the cube, rather than the mean |
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| 277 | and rms. See \S\ref{sec-stats} for details. |
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| 278 | \item[{flagNegative [false | bool | true/false/1/0]}] A flag |
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| 279 | indicating that the features of interest are negative. The cube is |
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| 280 | inverted prior to searching. |
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| 281 | \item[{snrCut [5. | float | any]}] The threshold, in multiples of |
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| 282 | $\sigma$ above the mean. |
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| 283 | \item[{threshold [no default | float | any]}] The actual value of the |
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[194] | 284 | threshold. Normally the threshold is calculated from the cube's |
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| 285 | statistics, but the user can manually specify a value to be used |
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| 286 | that overrides the calculated value. If this is not specified, the |
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[462] | 287 | calculated value is used, but this value will take precedence over |
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| 288 | other means of calculating the threshold (\ie via \texttt{snrCut} or |
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| 289 | the FDR method). |
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[1322] | 290 | \item[{flagGrowth [false | bool | true/false/1/0]}] A flag indicating |
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| 291 | whether or not to grow the detected objects to a smaller threshold. |
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| 292 | \item[{growthCut [3. | float | any]}] The smaller threshold using in |
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| 293 | growing detections. In units of $\sigma$ above the mean. |
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| 294 | \item[{growthThreshold [no default | float | any]}] Alternatively, the |
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| 295 | threshold to which detections are grown can be specified in flux |
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| 296 | units (in the same manner as the \texttt{threshold} parameter). When |
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| 297 | the \texttt{threshold} parameter is given, this option \textbf{must} |
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| 298 | be used instead of \texttt{growthCut}. |
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| 299 | \item[{beamFWHM [0. | float | $> 0.$]}] The full-width at half maximum |
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| 300 | of the beam, in pixels. If the header keywords BMAJ and BMIN are |
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| 301 | present, then these will be used to calculate the beam area, and |
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| 302 | this parameter will be ignored. This will take precedence over |
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| 303 | \texttt{beamArea} (but is ignored if not specified). |
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| 304 | \item[{beamArea [0. | float | $> 0.$]}] The \textbf{area} of the beam |
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| 305 | in pixels (\ie how many pixel does the beam cover?). As above, if |
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| 306 | the header keywords BMAJ and BMIN are present, then these will be |
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| 307 | used to calculate the beam area, and this parameter will be ignored. |
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[306] | 308 | \end{Lentry} |
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[158] | 309 | |
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[258] | 310 | \secC*{\Atrous reconstruction} |
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[306] | 311 | \begin{Lentry} |
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[1322] | 312 | \item[{flagATrous [false | bool | true/false/1/0]}] A flag indicating |
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| 313 | whether or not to reconstruct the cube using the \atrous wavelet |
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[158] | 314 | reconstruction. See \S\ref{sec-recon} for details. |
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[1322] | 315 | \item[{reconDim [1 | int | $> 0$]}] The number of dimensions to use in |
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| 316 | the reconstruction. 1 means reconstruct each spectrum separately, 2 |
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[158] | 317 | means each channel map is done separately, and 3 means do the whole |
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| 318 | cube in one go. |
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[1322] | 319 | \item[{scaleMin [1 | int | $> 0$]}] The minimum wavelet scale to be |
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| 320 | used in the reconstruction. A value of 1 means ``use all scales''. |
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| 321 | \item[{scaleMax [0 | int | any]}] The maximum wavelet scale to be used |
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| 322 | in the reconstruction. If the value is $\le0$ then the maximum scale |
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| 323 | is calculated from the size of the input array. Similarly, if the |
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| 324 | value given is larger than this calculated value, the calculated |
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| 325 | value is used instead. |
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| 326 | \item[{snrRecon [4 | float | $> 0$]}] The thresholding cutoff used in |
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| 327 | the reconstruction -- only wavelet coefficients at least this many |
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| 328 | $\sigma$ above the mean are included in the reconstruction. |
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| 329 | \item[{reconConvergence [0.005 | float | $> 0.$]}] The convergence |
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| 330 | criterion used in the reconstruction. The \atrous algorithm iterates |
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| 331 | until the relative change in the standard deviation of the residuals |
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| 332 | is less than this amount. |
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| 333 | \item[{filterCode [1 | int | 1/2/3]}] The code number of the filter to |
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| 334 | use in the reconstruction. The options are: |
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[158] | 335 | \begin{itemize} |
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| 336 | \item \textbf{1:} B$_3$-spline filter: coefficients = |
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| 337 | $(\frac{1}{16}, \frac{1}{4}, \frac{3}{8}, \frac{1}{4}, \frac{1}{16})$ |
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| 338 | \item \textbf{2:} Triangle filter: coefficients = |
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| 339 | $(\frac{1}{4}, \frac{1}{2}, \frac{1}{4})$ |
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| 340 | \item \textbf{3:} Haar wavelet: coefficients = |
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| 341 | $(0, \frac{1}{2}, \frac{1}{2})$ |
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| 342 | \end{itemize} |
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[306] | 343 | \end{Lentry} |
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[158] | 344 | |
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[208] | 345 | \secC*{Smoothing the cube} |
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[306] | 346 | \begin{Lentry} |
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[1322] | 347 | \item[{flagSmooth [false | bool | true/false/1/0]}] A flag indicating whether to |
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[275] | 348 | smooth the cube. See \S\ref{sec-smoothing} for details. |
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[1322] | 349 | \item[{smoothType [spectral | string | spectral/spatial]}] The |
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| 350 | smoothing method used: either ``spectral'' (with a 1D Hanning |
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| 351 | filter) or ``spatial'' (with a 2D Gaussian filter). |
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| 352 | \item[{hanningWidth [5 | int | $> 0$]}] The width of the Hanning |
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| 353 | smoothing kernel. |
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| 354 | \item[{kernMaj [3 | float | $> 0.$]}] The full-width-half-maximum |
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| 355 | (FWHM), in pixels, of the 2D Gaussian smoothing kernel's major axis. |
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| 356 | \item[{kernMin [3 | float | $> 0.$]}] The FWHM (in pixels) of the 2D Gaussian smoothing kernel's |
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[306] | 357 | minor axis. |
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[1322] | 358 | \item[{kernPA [0 | float | any]}] The position angle, in degrees, |
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[1280] | 359 | anticlockwise from vertical (\ie usually East of North). |
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[1322] | 360 | \item[{smoothEdgeMethod [equal | string | equal/truncate/scale]}] What |
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| 361 | method to use for dealing with pixels on the edge of the spatial |
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| 362 | image (\ie within the width of the kernel). Can be one of |
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| 363 | \texttt{equal, truncate, scale}. See \S\ref{sec-smoothing} for |
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| 364 | details. |
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| 365 | \item[{spatialSmoothCutoff [1.e-10 | float | $> 0.$]}] The cutoff |
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| 366 | value for determining the width of the smoothing kernel. See |
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[1280] | 367 | \S\ref{sec-smoothing} for details. |
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[306] | 368 | \end{Lentry} |
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[208] | 369 | |
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[158] | 370 | \secC*{FDR method} |
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[306] | 371 | \begin{Lentry} |
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[1322] | 372 | \item[{flagFDR [false | bool | true/false/1/0]}] A flag indicating whether or not to use |
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[158] | 373 | the False Discovery Rate method in thresholding the pixels. |
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[1322] | 374 | \item[{alphaFDR [0.01 | float | $0. - 1.$]}] The $\alpha$ parameter used in the FDR |
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[306] | 375 | analysis. The average number of false detections, as a fraction of |
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| 376 | the total number, will be less than $\alpha$ (see |
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[543] | 377 | \S\ref{sec-detection}). |
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[1322] | 378 | \item[{FDRnumCorChan [2 | int | $> 0$]}] The number of neighbouring spectral |
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[543] | 379 | channels that are assumed to be correlated. This is needed by the |
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| 380 | FDR algorithm to calculate the normalisation constant $c_N$ (see |
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[306] | 381 | \S\ref{sec-detection}). |
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| 382 | \end{Lentry} |
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[158] | 383 | |
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| 384 | \secC*{Merging detections} |
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[306] | 385 | \begin{Lentry} |
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[1322] | 386 | \item[{minPix [2 | int | $> 0$]}] The minimum number of spatial pixels for a |
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[158] | 387 | single detection to be counted. |
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[1322] | 388 | \item[{minChannels [3 | int | $> 0$]}] At least one contiguous set of this many |
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[306] | 389 | channels must be present in the detection for it to be accepted. |
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[1322] | 390 | \item[{minVoxels [minPix$+$minChannels$-$1 | int | $> 0$]}] The minimum size of |
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[964] | 391 | the object, in terms of the total number of voxels, for it to be |
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| 392 | accepted. This will be \textit{at least} minPix$+$minChannels$-$1, |
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| 393 | but can be set higher. |
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[1322] | 394 | \item[{maxPix [$-1$ | int | any]}] The maximum number of spatial pixels an object |
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[1262] | 395 | can have. No check is made if the value is negative. |
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[1322] | 396 | \item[{maxChannels [-1 | int | any]}] The maximum number of channels an object can |
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[1262] | 397 | have. No check is made if the value is negative. |
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[1322] | 398 | \item[{maxVoxels [$-1$ | int | any]}] The maximum size of |
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[1262] | 399 | the object, in terms of the total number of voxels, for it to be |
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| 400 | accepted. No check is made if the value is negative. |
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[1322] | 401 | \item[{flagRejectBeforeMerge [false | bool | true/false/1/0]}] A flag |
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| 402 | indicating whether to reject sources that fail to meet the |
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| 403 | \texttt{minPix} or \texttt{minChannels} criteria \textbf{before} the |
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| 404 | merging stage. Default behaviour is to do the rejection last. |
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| 405 | \item[{flagTwoStageMerging [true | bool | true/false/1/0]}] A flag |
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| 406 | indicating whether to do an initial merge of newly-detected sources |
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| 407 | into the source list as they are found. If \texttt{false}, new |
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| 408 | sources are simply added to the end of the list for later merging. |
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| 409 | \item[{flagAdjacent [true | bool | true/false/1/0]}] A flag indicating |
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| 410 | whether to use the ``adjacent pixel'' criterion to decide whether to |
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| 411 | merge objects. If not, the next two parameters are used to determine |
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[158] | 412 | whether objects are within the necessary thresholds. |
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[1322] | 413 | \item[{threshSpatial [$3.$ | float | $\ge 0$]}] The maximum allowed |
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| 414 | minimum spatial separation (in pixels) between two detections for |
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| 415 | them to be merged into one. Only used if \texttt{flagAdjacent = |
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| 416 | false}. |
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| 417 | \item[{threshVelocity [$7.$ | float | $\ge 0$]}] The maximum allowed |
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| 418 | minimum channel separation between two detections for them to be |
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| 419 | merged into one. |
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[306] | 420 | \end{Lentry} |
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[158] | 421 | |
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[964] | 422 | \secC*{WCS parameters} |
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| 423 | \begin{Lentry} |
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[1322] | 424 | \item[{spectralType ["" | string | A valid WCS type]}] The user can |
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| 425 | specify an alternative WCS spectral type that the spectral axis can |
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| 426 | be expressed in. This specification should conform to the standards |
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| 427 | described in \citet{greisen06}, although it is possible to provide |
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| 428 | just the first four letters (the ``S-type'', \eg 'VELO'). |
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| 429 | \item[{restFrequency [-1 | float | any]}] If provided, this will be used in |
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[964] | 430 | preference to the rest frequency given in the FITS header to |
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| 431 | calculate velocities and related quantities. A negative value (such |
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| 432 | as the default) will mean this is not used and the FITS header |
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| 433 | value, if present, is used instead. |
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[1322] | 434 | \item[{spectralUnits ["" | string | A valid units string]}] The user |
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| 435 | can specify the units of the spectral axis, overriding those given |
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| 436 | in the FITS header. If the spectral type is being changed, these |
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| 437 | units should be appropriate for that quantity. If not provided, the |
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| 438 | FITS header information is used. |
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[964] | 439 | \end{Lentry} |
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| 440 | |
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[158] | 441 | \secC*{Other parameters} |
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[306] | 442 | \begin{Lentry} |
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[1322] | 443 | \item[{spectralMethod [peak | string | peak/sum]}] This indicates |
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| 444 | which method is used to plot the output spectra: \texttt{peak} means |
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| 445 | plot the spectrum containing the detection's peak pixel; |
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| 446 | \texttt{sum} means sum the spectra of each detected spatial pixel, |
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| 447 | and correct for the beam size. Any other choice defaults to |
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| 448 | \texttt{peak}. |
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| 449 | \item[{pixelCentre [centroid | string | centroid/peak/average]}] Which |
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| 450 | of the three ways of expressing the ``centre'' of a detection (see |
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| 451 | \S\ref{sec-results} for a description of the options) to use for the |
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| 452 | X, Y, \& Z columns in the output list. Alternatives are: |
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| 453 | \texttt{centroid, peak, average}. |
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| 454 | \item[{sortingParam [vel | string | see text for options]}] The |
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| 455 | parameter on which to sort the output list of detected |
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| 456 | objects. Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50, |
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| 457 | iflux, pflux (integrated and peak flux respectively), or snr. If the |
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| 458 | parameter begins with a '-' (\eg '-vel'), the order of the sort is |
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| 459 | reversed. |
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| 460 | \item[{drawBorders [true | bool | true/false/1/0]}] A flag indicating whether to draw |
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[306] | 461 | borders around the detected objects in the moment maps included in |
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| 462 | the output (see for example Fig.~\ref{fig-spect}). |
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[1322] | 463 | \item[{drawBlankEdges [true | bool | true/false/1/0]}] A flag indicating whether to |
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[306] | 464 | draw the dividing line between BLANK and non-BLANK pixels on the |
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| 465 | 2D images (see for example Fig.~\ref{fig-moment}). |
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[1322] | 466 | \item[{verbose [true | bool | true/false/1/0]}] A flag indicating whether to print the |
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[306] | 467 | progress of any computationally intensive algorithms (\eg |
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[231] | 468 | reconstruction, searching or merging algorithms) to the screen. |
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[306] | 469 | \end{Lentry} |
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[158] | 470 | |
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[964] | 471 | |
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| 472 | %%% Local Variables: |
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| 473 | %%% mode: latex |
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| 474 | %%% TeX-master: "Guide" |
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| 475 | %%% End: |
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