1 | % ----------------------------------------------------------------------- |
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2 | % outputs.tex: Section detailing the different forms of text- and |
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3 | % plot-based output. |
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4 | % ----------------------------------------------------------------------- |
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5 | % Copyright (C) 2006, Matthew Whiting, ATNF |
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6 | % |
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7 | % This program is free software; you can redistribute it and/or modify it |
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8 | % under the terms of the GNU General Public License as published by the |
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9 | % Free Software Foundation; either version 2 of the License, or (at your |
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10 | % option) any later version. |
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11 | % |
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12 | % Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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13 | % ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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14 | % FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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15 | % for more details. |
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16 | % |
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17 | % You should have received a copy of the GNU General Public License |
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18 | % along with Duchamp; if not, write to the Free Software Foundation, |
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19 | % Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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20 | % |
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21 | % Correspondence concerning Duchamp may be directed to: |
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22 | % Internet email: Matthew.Whiting [at] atnf.csiro.au |
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23 | % Postal address: Dr. Matthew Whiting |
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24 | % Australia Telescope National Facility, CSIRO |
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25 | % PO Box 76 |
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26 | % Epping NSW 1710 |
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27 | % AUSTRALIA |
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28 | % ----------------------------------------------------------------------- |
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29 | \secA{Outputs} |
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30 | \label{sec-output} |
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31 | |
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32 | \secB{During execution} |
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33 | |
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34 | \duchamp provides the user with feedback whilst it is running, to |
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35 | keep the user informed on the progress of the analysis. Most of this |
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36 | consists of self-explanatory messages about the particular stage the |
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37 | program is up to. The relevant parameters are printed to the screen at |
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38 | the start (once the file has been successfully read in), so the user |
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39 | is able to make a quick check that the setup is correct (see |
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40 | Appendix~\ref{app-input} for an example). |
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41 | |
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42 | The extent of memory allocation made at the start is indicated. This |
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43 | will include the arrays needed for the pixel array, the reconstruction |
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44 | or smoothed array, and the 2D detection map, but \emph{not} additional |
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45 | space needed for working within individual algorithms, nor storage |
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46 | needed for the detected objects. |
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47 | |
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48 | \duchamp will report the amount of memory that is allocated when the |
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49 | image is read in. This includes the storage for the array as well as |
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50 | additional storage for the reconstructed/smoothed array and/or the |
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51 | baseline arrays (if these are needed). |
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52 | |
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53 | If the cube is being trimmed (\S\ref{sec-modify}), the resulting |
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54 | dimensions are printed to indicate how much has been trimmed. If a |
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55 | reconstruction is being done, a continually updating message shows |
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56 | either the current iteration and scale, compared to the maximum scale |
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57 | (when \texttt{reconDim = 3}), or a progress bar showing the amount of |
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58 | the cube that has been reconstructed (for smaller values of |
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59 | \texttt{reconDim}). |
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60 | |
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61 | During the searching algorithms, the progress through the search is |
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62 | shown. When completed, the number of objects found is reported (this |
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63 | is the total number found, before any merging is done). |
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64 | |
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65 | In the merging process (where multiple detections of the same object |
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66 | are combined -- see \S\ref{sec-merger}), two stages of output |
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67 | occur. The first is when each object in the list is compared with all |
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68 | others. The output shows two numbers: the first being how far through |
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69 | the list the current object is, and the second being the length of the |
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70 | list. As the algorithm proceeds, the first number should increase and |
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71 | the second should decrease (as objects are combined). When the numbers |
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72 | meet, the whole list has been compared. If the objects are being |
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73 | grown, a similar output is shown, indicating the progress through the |
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74 | list. In the rejection stage, in which objects not meeting the minimum |
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75 | pixels/channels requirements are removed, the total number of objects |
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76 | remaining in the list is shown, which should steadily decrease with |
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77 | each rejection until all have been examined. Note that these steps can |
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78 | be very quick for small numbers of detections. |
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79 | |
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80 | Since this continual printing to screen has some overhead of time and |
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81 | CPU involved, the user can elect to not print this information by |
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82 | setting the parameter \texttt{verbose = false}. In this case, the user |
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83 | is still informed as to the steps being undertaken, but the details of |
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84 | the progress are not shown. |
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85 | |
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86 | There may also be Warning or Error messages printed to screen. The |
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87 | Warning messages occur when something happens that is unexpected (for |
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88 | instance, a desired keyword is not present in the FITS header), but |
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89 | not detrimental to the execution. An Error message is something more |
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90 | serious, and indicates some part of the program was not able to |
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91 | complete its task. This is not necessary fatal, but it may mean the |
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92 | full functionality requested will not be achieved. The message will |
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93 | also indicate which function or subroutine generated it -- this is |
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94 | primarily a tool for debugging, but can be useful in determining what |
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95 | went wrong. |
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96 | |
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97 | \secB{Text-based output files} |
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98 | |
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99 | \secC{Table of results} |
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100 | \label{sec-results} |
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101 | |
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102 | Finally, we get to the results -- the reason for running \duchamp in |
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103 | the first place. Once the detection list is finalised and |
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104 | parameterised according to \S\ref{sec-sourceparam}, it is sorted |
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105 | according to the value of the \texttt{sortingParam}. This can take the |
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106 | value ``xvalue'', ``yvalue'', ``zvalue'', ``ra'', ``dec'', ``vel'', |
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107 | ``w50'', ``iflux'' (for integrated flux), or ``pflux'' (for peak |
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108 | flux), or ``snr''. The default value is ``vel'' (which means the |
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109 | spectral WCS value -- this could be frequency or wavelength depending |
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110 | on the nature of the FITS file). If no good WCS exists, the mean pixel |
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111 | position equivalent is used (``ra'' is replaced by ``xvalue'', ``dec'' |
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112 | by ``yvalue'', ``vel'' and ``w50'' by ``zvalue''). The sense of the |
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113 | sorting will be increasing value with position in the list. To sort in |
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114 | the opposite sense, prepend the parameter name with a '-' (\eg |
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115 | ``-vel'' instead of ``vel''). The object ID number |
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116 | (\S\ref{sec-objectID}) is determined by the order of the list |
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117 | \emph{after} this sorting, so sorting by a different parameter will |
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118 | result in a different object ID for the same object. |
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119 | |
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120 | The results are then printed to the screen and to the output file, |
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121 | given by the \texttt{OutFile} parameter. The output file will contain |
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122 | all calculated parameters, as described in |
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123 | \S\ref{sec-sourceparam}. The results list printed to the screen, |
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124 | however, will leave out certain columns: |
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125 | \begin{itemize} |
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126 | \item The spatial extent columns \texttt{w\_RA \& w\_DEC}. |
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127 | \item The \texttt{w\_20} and \texttt{w\_VEL} spectral width columns. |
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128 | \item The total flux \texttt{F\_tot} (unless there is no good WCS, in |
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129 | which case it is printed instead of \texttt{F\_int}), and the errors |
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130 | on the total and integrated fluxes \texttt{eF\_tot, eF\_int}. |
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131 | \item The explicit columns for the average, centroid and peak pixel |
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132 | locations. The only pixel location columns printed are \texttt{X, Y, |
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133 | Z}, which are determined via the \texttt{pixelCentre} input |
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134 | parameter. |
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135 | \item \textit{If the WCS is no good}, the world-coordinate columns |
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136 | \texttt{RA, DEC, VEL, F\_int} will not be printed either. |
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137 | \end{itemize} |
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138 | |
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139 | The output file consists of two sections. The first section contains |
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140 | the metadata for the search. First, a list of the parameters are |
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141 | printed to the output file, for future reference. Next, the detection |
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142 | threshold that was used is given, so comparison can be made with other |
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143 | searches. The statistics estimating the noise parameters are given |
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144 | (see \S\ref{sec-stats}). Thirdly, the number of detections are |
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145 | reported. |
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146 | |
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147 | All this information, known as the ``header'', can either be written |
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148 | to the start of the output file (denoted by the parameter |
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149 | \texttt{OutFile}), or written to a separate file from the list of |
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150 | detections. This second option is activated by the parameter |
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151 | \texttt{flagSeparateHeader}, and the information is written to the |
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152 | file given by \texttt{HeaderFile}. |
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153 | |
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154 | The second part of the file, however, contains the most interesting |
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155 | part -- the list of detected objects. This is written as an ASCII |
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156 | table, properly spaced so that it is readable. An example is shown in |
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157 | Appendix~\ref{app-output}. |
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158 | |
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159 | The user can specify the precision used to display the flux, spectral |
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160 | location/width and S/Nmax values, by using the input parameters |
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161 | \texttt{precFlux}, \texttt{precVel} and \texttt{precSNR} |
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162 | respectively. These values apply to the tables written to the screen |
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163 | and to the output file, as well as for the VOTable (see below). |
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164 | |
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165 | |
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166 | \secC{VOTable catalogue} |
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167 | \label{sec-votable} |
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168 | |
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169 | Three additional results files can also be requested. One option is a |
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170 | VOTable-format XML file, containing just the RA, Dec, spectral |
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171 | location and the corresponding widths of the detections, as well as |
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172 | the fluxes. The user should set \texttt{flagVOT = true}, and put the |
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173 | desired filename in the parameter \texttt{votFile} -- note that the |
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174 | default is for it not to be produced. An example of VOTable output can |
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175 | be found in Appendix~\ref{app-votable}. This file should be |
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176 | compatible with all Virtual Observatory tools (such as Aladin% |
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177 | \footnote{%Aladin can be found on the web at |
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178 | \href{http://aladin.u-strasbg.fr/}{http://aladin.u-strasbg.fr/}} or |
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179 | TOPCAT\footnote{%Tool for OPerations on Catalogues And Tables: |
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180 | \href{http://www.star.bristol.ac.uk/~mbt/topcat/}% |
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181 | {http://www.star.bristol.ac.uk/~mbt/topcat/}}). |
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182 | |
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183 | \secC{Annotation and region files} |
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184 | \label{sec-annotfiles} |
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185 | |
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186 | A second option are annotation files for use with several |
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187 | visualisation tools, including the Karma toolkit (in particular, with |
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188 | \texttt{kvis}), SAOImage DS9, and \texttt{casaviewer} (and |
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189 | \texttt{casapy} itself). |
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190 | |
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191 | There are three options on how objects are represented, governed by the |
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192 | \texttt{annotationType} parameter. These are: |
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193 | \begin{itemize} |
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194 | \item \texttt{borders} -- a border is drawn around the spatial pixels |
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195 | of the object, in a manner similar to that seen in |
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196 | Fig.~\ref{fig-spect}. Note that Karma/\texttt{kvis} does not always |
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197 | do this perfectly, particularly as you change the zoom, so the lines |
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198 | may not be directly lined up with pixel borders. |
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199 | \item \texttt{circles} -- draws a circle at the position of each |
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200 | detection, scaled by the spatial size of the detection. |
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201 | \item \texttt{ellipses} -- draws an ellipse of size given by the |
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202 | \texttt{MAJ, MIN, PA} source parameters (\S\ref{sec-shape}). |
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203 | \end{itemize} |
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204 | In each case, the object is numbered according to the object ID |
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205 | (\S\ref{sec-objectID}. To make use of this option, the user should set |
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206 | \texttt{flagKarma}, \texttt{flagDS9} or \texttt{flagCasa} to |
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207 | \texttt{true}, and put the desired filename in the parameter |
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208 | \texttt{karmaFile}, \texttt{ds9File} or \texttt{casaFile} -- again, |
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209 | the default is for these not to be produced. Examples of these |
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210 | annotation files are in |
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211 | Appendices~\ref{app-karma},\ref{app-ds9},\ref{app-casa}. |
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212 | |
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213 | \secC{Spectral text file} |
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214 | \label{sec-spectraltext} |
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215 | |
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216 | The final optional results file produced is a simple text file that |
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217 | contains the spectra for each detected object. The format of the file |
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218 | is as follows: the first column has the spectral coordinate, over the |
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219 | full range of values; the remaining columns represent the flux values |
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220 | for each object at the corresponding spectral position. The flux value |
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221 | used is the same as that plotted in the spectral plot detailed below, |
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222 | and governed by the \texttt{spectralMethod} parameter. An example of |
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223 | what a spectral text file might look like is given below: |
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224 | |
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225 | \begin{quote} |
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226 | {\footnotesize |
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227 | \begin{tabular}{lllll} |
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228 | 1405.00219727 &0.01323344 &0.23648241 &0.04202826 &-0.00506790 \\ |
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229 | 1405.06469727 &0.01302835 &0.27393046 &0.04686056 &-0.00471084 \\ |
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230 | 1405.12719727 &0.01583361 &0.27760920 &0.04114933 &-0.01168737 \\ |
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231 | 1405.18969727 &0.01271889 &0.31489247 &0.03307962 &-0.00300790 \\ |
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232 | 1405.25219727 &0.01597644 &0.30401203 &0.05356426 &-0.00551653 \\ |
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233 | 1405.31469727 &0.00773827 &0.30031312 &0.04074831 &-0.00570147 \\ |
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234 | 1405.37719727 &0.00738304 &0.27921870 &0.05272378 &-0.00504959 \\ |
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235 | 1405.43969727 &0.01353923 &0.26132512 &0.03667958 &-0.00151006 \\ |
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236 | 1405.50219727 &0.01119724 &0.28987029 &0.03497849 &-0.00645589 \\ |
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237 | 1405.56469727 &0.00813379 &0.29839963 &0.04711142 &0.00536576 \\ |
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238 | 1405.62719727 &0.00774377 &0.26530230 &0.04620502 &0.00724631 \\ |
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239 | 1405.68969727 &0.00576067 &0.23215000 &0.04995513 &0.00290841 \\ |
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240 | 1405.75219727 &0.00452834 &0.16484940 &0.04261605 &-0.00612812 \\ |
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241 | 1405.81469727 &0.01406293 &0.15989439 &0.03817926 &-0.00758385 \\ |
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242 | 1405.87719727 &0.01116611 &0.11890682 &0.05499069 &-0.00626362 \\ |
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243 | 1405.93969727 &0.00687582 &0.10620256 &0.04743370 &0.00055177 \\ |
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244 | $\vdots$ &$\vdots$ &$\vdots$ &$\vdots$ &$\vdots$ \\ |
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245 | \end{tabular} |
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246 | } |
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247 | \end{quote} |
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248 | |
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249 | \secC{Log file} |
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250 | \label{sec-logfile} |
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251 | |
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252 | In addition to these three files, a log file can also be produced. As |
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253 | the program is running, it also (optionally) records the detections |
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254 | made in each individual spectrum or channel (see \S\ref{sec-detection} |
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255 | for details on this process). This is recorded in the file given by |
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256 | the parameter \texttt{LogFile}. This file does not include the columns |
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257 | \texttt{Name, RA, DEC, w\_RA, w\_DEC, VEL, w\_VEL}. This file is |
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258 | designed primarily for diagnostic purposes: \eg to see if a given set |
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259 | of pixels is detected in, say, one channel image, but does not survive |
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260 | the merging process. The list of pixels (and their fluxes) in the |
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261 | final detection list are also printed to this file, again for |
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262 | diagnostic purposes. The file also records the execution time, as well |
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263 | as the command-line statement used to run \duchamp. The creation of |
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264 | this log file can be prevented by setting \texttt{flagLog = false} |
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265 | (which is the default). |
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266 | |
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267 | \secB{Graphical output} |
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268 | |
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269 | |
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270 | \secC{Spectral plots} |
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271 | |
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272 | As well as the output data file, a postscript file (with the filename |
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273 | given by the \texttt{spectralFile} parameter) is created that shows |
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274 | the spectrum for each detection, together with a small cutout image |
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275 | (the 0th moment) and basic information about the detection (note that |
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276 | any flags are printed after the name of the detection, in the format |
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277 | \texttt{[E]}). If the cube was reconstructed, the spectrum from the |
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278 | reconstruction is shown in red, over the top of the original |
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279 | spectrum. The spectral extent of the detected object is indicated by |
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280 | two dashed blue lines, and the region covered by the ``Milky Way'' |
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281 | channels is shown by a green hashed box. An example detection can be |
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282 | seen in Fig.~\ref{fig-spect}. |
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283 | |
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284 | The spectrum that is plotted is governed by the |
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285 | \texttt{spectralMethod} parameter. It can be either \texttt{peak} (the |
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286 | default), where the spectrum is from the spatial pixel containing the |
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287 | detection's peak flux; or \texttt{sum}, where the spectrum is summed |
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288 | over all spatial pixels, and then corrected for the beam size. If the |
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289 | \texttt{peak} method is used, the detection threshold (and growth |
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290 | threshold, if used) are indicated by dashed (and dotted) lines. These |
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291 | cannot be plotted on the integrated spectrum. The spectral extent of |
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292 | the detection is indicated with blue lines, and a zoom is shown in a |
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293 | separate window. |
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294 | |
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295 | \begin{figure}[t] |
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296 | \begin{center} |
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297 | \includegraphics[width=\textwidth]{example_spectrum} |
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298 | \end{center} |
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299 | \caption{\footnotesize An example of the spectral output. Note |
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300 | several of the features discussed in the text: the red solid lines |
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301 | indicating the reconstructed spectrum; the blue dashed and dotted |
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302 | horizontal lines indicating the detection and growth thresholds |
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303 | respectively; the blue dashed lines indicating the spectral extent |
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304 | of the detection; the green hashed area indicating the Milky Way |
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305 | channels that are ignored by the searching algorithm; the blue |
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306 | border showing its spatial extent on the 0th moment map; the |
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307 | ellipses indicating the size of the object and the beam; and the |
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308 | 15~arcmin-long scale bar.} |
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309 | \label{fig-spect} |
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310 | \end{figure} |
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311 | |
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312 | The cutout image shows a red ellipse indicating the spatial size of the |
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313 | detection (using \texttt{MAJ, MIN, PA} - \S\ref{sec-shape}). Also |
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314 | drawn in green in the corner of the image is an ellipse indicating the |
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315 | beam size (assuming the beam is defined). |
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316 | |
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317 | The cutout image can optionally include a border around the spatial |
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318 | pixels that are in the detection (turned on and off by the |
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319 | \texttt{drawBorders} parameter -- the default is \texttt{true}). It |
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320 | includes a scale bar in the bottom left corner to indicate size -- its |
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321 | length is indicated next to it (the choice of length depends on the |
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322 | size of the image). |
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323 | |
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324 | There may also be one or two extra lines on the image. A yellow line |
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325 | shows the limits of the cube's spatial region: when this is shown, the |
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326 | detected object will lie close to the edge, and the image box will |
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327 | extend outside the region covered by the data. A purple line, however, |
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328 | shows the dividing line between BLANK and non-BLANK pixels. The BLANK |
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329 | pixels will always be shown in black. The first type of line is always |
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330 | drawn, while the second is governed by the parameter |
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331 | \texttt{drawBlankEdges} (whose default is \texttt{true}), and |
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332 | obviously whether there are any BLANK pixel present. |
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333 | |
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334 | Note that the creation of the spectral plots can be prevented by |
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335 | setting \texttt{flagPlotSpectra = false}. |
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336 | |
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337 | When the input image is two-dimensional, with no spectral dimension, |
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338 | this spectral plot would not make much sense. Instead, \duchamp |
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339 | creates a similar postscript file that simply includes the text |
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340 | headers as well as the 0th-moment map of the detection. As for the |
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341 | normal spectral case, this file will be written to the filename given |
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342 | by the \texttt{spectralFile} parameter. |
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343 | |
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344 | When the input image is one-dimensional, the spectral plot is |
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345 | identical save for the absence of the cutout image. |
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346 | |
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347 | In addition to the spectral plot, it is possible to produce plots for |
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348 | each spectrum individually. Set |
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349 | \texttt{flagPlotIndividualSpectra=true}, and a postscript plot will be |
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350 | produced for each object. If the normal spectral output file |
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351 | (determined by the \texttt{spectralFile} input parameter) is called |
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352 | \texttt{duchamp-Spectra.ps}, then the individual files will be called |
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353 | \texttt{duchamp-Spectra-01.ps} etc. |
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354 | |
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355 | |
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356 | \secC{Spatial maps} |
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357 | \label{sec-spatialmaps} |
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358 | |
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359 | \begin{figure}[!t] |
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360 | \begin{center} |
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361 | \includegraphics[width=\textwidth]{example_moment_map} |
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362 | \end{center} |
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363 | \caption{\footnotesize An example of the moment map created by |
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364 | \duchamp. The full extent of the cube is covered, and the 0th moment |
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365 | of each object is shown (integrated individually over all the |
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366 | detected channels). The purple line indicates the limit of the |
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367 | non-BLANK pixels.} |
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368 | \label{fig-moment} |
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369 | \end{figure} |
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370 | |
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371 | Additionally, two types of spatial images are optionally produced: a |
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372 | combined 0th-moment map of the cube, combining just the detected |
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373 | channels in each object, showing the integrated flux in grey-scale; |
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374 | and a ``detection image'', a grey-scale image where the pixel values |
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375 | are the number of channels in which that spatial pixel is |
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376 | detected. These detections include pixels that are subsequently |
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377 | discarded (due to the minimum-size criteria). In both cases, if |
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378 | \texttt{drawBorders = true}, a border is drawn around the spatial |
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379 | extent of each detection, and if \texttt{drawBlankEdges = true}, the |
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380 | purple line dividing BLANK and non-BLANK pixels (as described above) |
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381 | is drawn. An example moment map is shown in Fig.~\ref{fig-moment}. |
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382 | The production or otherwise of these images is governed by the |
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383 | \texttt{flagMaps} parameter. |
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384 | |
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385 | The moment map is also displayed in a PGPlot XWindow (with the |
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386 | \texttt{/xs} display option). This feature can be turned off by |
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387 | setting \texttt{flagXOutput = false} -- this might be useful if |
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388 | running \duchamp on a terminal with no window display capability, or |
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389 | if you have set up a script to run it in a batch mode. |
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390 | |
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391 | If the input image is one-dimensional, such a spatial map is not |
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392 | possible. Instead, the detection map becomes a detection |
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393 | spectrum. This shows the full spectral range, indicating (as for the |
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394 | spectral plots above) the detection and growth thresholds, as well as |
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395 | the `Milky Way' range and every detection that appears in the final |
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396 | catalogue. It also indicates all pixels that were detected, including |
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397 | those subsequently discarded, by thick black lines above the |
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398 | spectrum. An example can be see in |
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399 | Fig.~\ref{fig-1D-detection-spectrum}. Again, this plot is also |
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400 | displayed in a PGPlot XWindow. |
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401 | |
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402 | \begin{figure}[!t] |
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403 | \begin{center} |
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404 | \includegraphics[width=\textwidth]{example_detection_spectrum} |
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405 | \end{center} |
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406 | \caption{\footnotesize An example of the one-dimensional detection |
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407 | spectrum plot, indicating detected sources and detected pixels, |
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408 | including those subsquently discarded due to the minimum-size |
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409 | criteria. The detection threshold is low to show the effect of |
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410 | detecting lots of single-pixel channels, which are then discarded, |
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411 | leaving just the two detections delimited by the blue lines.} |
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412 | \label{fig-1D-detection-spectrum} |
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413 | \end{figure} |
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414 | |
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415 | |
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416 | |
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417 | The purpose of these images is to provide a visual guide to where the |
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418 | detections have been made, and, particularly in the case of the moment |
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419 | map, to provide an indication of the strength of the source. In both |
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420 | cases, the detections are numbered (in the same sense as the output |
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421 | list and as the spectral plots), and the spatial borders are marked |
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422 | out as for the cutout images in the spectra file. Both these images |
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423 | are saved as postscript files (given by the parameters |
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424 | \texttt{momentMap} and \texttt{detectionMap} respectively), with the |
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425 | latter also displayed in a \textsc{pgplot} window (regardless of the |
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426 | state of \texttt{flagMaps}). |
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427 | |
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428 | \secB{FITS output} |
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429 | |
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430 | \secC{Moment map} |
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431 | \label{sec-momentOut} |
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432 | |
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433 | The moment map described above can also be written to a FITS file, so |
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434 | that it can be examined more closely, and have annotation files |
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435 | overlaid. This works in the same way as for the mask image. To create |
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436 | the FITS file, set the input parameter |
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437 | \texttt{flagOutputMomentMap=true}. The file will be named according to |
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438 | the \texttt{fileOutputMomentMap} parameter, or, if this is not given, |
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439 | \texttt{image.MOM0.fits} (where the input image is called |
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440 | \texttt{image.fits}). |
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441 | |
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442 | \secC{Mask images} |
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443 | \label{sec-maskOut} |
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444 | |
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445 | It is also possible to write the mask array to a FITS file, for use in |
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446 | other forms of post-processing. This array is designed to indicate the |
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447 | location of detected objects. The value of the detected pixels is |
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448 | determined by the input parameter \texttt{flagMaskWithObjectNum}: if |
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449 | \texttt{true}, the value of the pixels is given by the corresponding |
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450 | object ID number; if \texttt{false}, they take the value 1 for all |
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451 | objects. Pixels not in a detected object have the value 0. To create |
---|
452 | this FITS file, set the input parameter |
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453 | \texttt{flagOutputMask=true}. The file will be named according to the |
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454 | \texttt{fileOutputMask} parameter, or, if this is not given, |
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455 | \texttt{image.MASK.fits} (where the input image is called |
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456 | \texttt{image.fits}). |
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457 | |
---|
458 | A spatial mask, or moment-0 mask, can also be written. This is simply |
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459 | a two-dimensional image that shows which spatial pixels are detected |
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460 | in one or more channels. Unlike the full mask file above, detected |
---|
461 | pixels can only be recorded as 1 (as a given spatial pixel may appear |
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462 | in multiple objects) -- that is, the parameter |
---|
463 | \texttt{flagMaskWithObjectNum} does not affect the moment-0 mask. To |
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464 | create this FITS file, set the input parameter |
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465 | \texttt{flagOutputMomentMask=true}. The file will be named according |
---|
466 | to the \texttt{fileOutputMomentMask} parameter, or, if this is not |
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467 | given, \texttt{image.MOM0MASK.fits} (where the input image is called |
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468 | \texttt{image.fits}). |
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469 | |
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470 | \secC{Smoothed or Reconstructed image} |
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471 | \label{sec-reconOut} |
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472 | |
---|
473 | As discussed in \S\ref{sec-reconIO}, the reconstructed array, its |
---|
474 | residual, or the smoothed array can be saved to a FITS file. This |
---|
475 | allows examination of them offline, as well as their re-use by |
---|
476 | \duchamp to save the expense of re-calculating. This behaviour is |
---|
477 | controlled by \texttt{flagOutputRecon}, \texttt{flagOutputResid} and |
---|
478 | \texttt{flagOutputSmooth}. Consult \S\ref{sec-reconIO} for further |
---|
479 | details. |
---|
480 | |
---|
481 | \secC{Baseline image} |
---|
482 | \label{sec-baselineOut} |
---|
483 | |
---|
484 | As mentioned in \S\ref{sec-baseline}, the spectral baseline values can |
---|
485 | be saved to a FITS file, allowing examination of them offline. There |
---|
486 | is no scope at present for reloading previously-calculated baselines |
---|
487 | (although the overheads in calculating these are not too |
---|
488 | prohibitive). Saving to a FITS file is controlled by the input |
---|
489 | parameters \texttt{flagOutputBaseline} and |
---|
490 | \texttt{fileOutputBaseline}. If \texttt{fileOutputBaseline} is not |
---|
491 | provided, the file will be named \texttt{image.BASE.fits} (for an |
---|
492 | input image called \texttt{image.fits}). |
---|
493 | |
---|
494 | |
---|
495 | |
---|
496 | \secB{Re-examining previous \duchamp results} |
---|
497 | \label{sec-reuse} |
---|
498 | |
---|
499 | |
---|
500 | \secC{Binary Catalogue} |
---|
501 | \label{sec-bincat} |
---|
502 | |
---|
503 | It is often the case that the bulk of the work in a \duchamp run is in |
---|
504 | the searching for sources. If you are interested in re-doing some of |
---|
505 | the spectral plots, or re-parameterising with different |
---|
506 | \texttt{spectralType} settings, then having to re-run the searching |
---|
507 | can be a bit off-putting. |
---|
508 | |
---|
509 | A solution to this problem exists in the ability to save a binary |
---|
510 | catalogue, containing the information on the individual pixels |
---|
511 | detected in each object. This is sufficient to recreate a set of |
---|
512 | detections and re-do the parameterisation. To enable this mode, set |
---|
513 | \texttt{flagWriteBinaryCatalogue=true}, and provide a filename with |
---|
514 | \texttt{binaryCatalogue} (or use the default of |
---|
515 | \texttt{duchamp-Catalogue.dpc}). The following will be written to the |
---|
516 | catalogue: |
---|
517 | \begin{itemize} |
---|
518 | \item Version of \duchamp. If it is not the same version, a warning is raised. |
---|
519 | \item Current date and time. |
---|
520 | \item The parameter set. Only the parameters affecting the |
---|
521 | pre-processing and searching are stored. Those related to, say, |
---|
522 | graphical output are not. |
---|
523 | \item The measured statistics. |
---|
524 | \item The pixels of each detected object, written using the run-length |
---|
525 | encoding described in \S\ref{sec-scan}. |
---|
526 | \end{itemize} |
---|
527 | These are written in binary format to conserve disk space, and are |
---|
528 | sufficient to recreate the state of \duchamp after the searching has |
---|
529 | taken place. |
---|
530 | |
---|
531 | To re-use this catalogue, set the flag \texttt{usePrevious=true} and |
---|
532 | provide the binary catalogue filename via |
---|
533 | \texttt{binaryCatalogue}. The catalogue will be loaded, and (provided |
---|
534 | it loads correctly) the preprocessing and searching steps will be |
---|
535 | skipped. The post-processing (\ie plotting and catalogue output) steps |
---|
536 | will occur as normal, using the settings provided in the input |
---|
537 | parameter file. |
---|
538 | |
---|
539 | Note that while at this stage this is the only use for the binary |
---|
540 | catalogues, it is anticipated that other functionality will be |
---|
541 | provided in future - for instance, to allow conversion into mask |
---|
542 | images. The binary catalogues are seen as a compact way of storing the |
---|
543 | results of a \duchamp run. |
---|
544 | |
---|
545 | \secC{Selection of objects} |
---|
546 | |
---|
547 | When re-running \duchamp on a previously-generated catalogue, it is |
---|
548 | possible to produce the plots for only a selection of objects. Use the |
---|
549 | \texttt{objectList} parameter to specify a set of objects, listing |
---|
550 | individual object numbers or ranges, for example ``1,3-6,9,11'' means |
---|
551 | objects 1,3,4,5,6,9,11. The output plots will be appropriately |
---|
552 | modified: the spectral plots will only show these objects; the moment |
---|
553 | map plot will only show the contribution from these objects; the |
---|
554 | detection map will show the outlines of only these objects, although |
---|
555 | all detected pixels are still shown in greyscale. |
---|
556 | |
---|
557 | Note that the object numbers here are valid for the catalogue as |
---|
558 | sorted according to the \texttt{sortingParam} specification in the |
---|
559 | parameter file. If you change this, the order of the catalogue may |
---|
560 | change and the specific objects selected by \texttt{objectList} will |
---|
561 | differ. |
---|
562 | |
---|
563 | This option is designed for the case of re-using a catalogue, but can |
---|
564 | be used for a blind search as well. Of course, you may not know what |
---|
565 | numbers the sources will turn out to be. |
---|
566 | |
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567 | %%% Local Variables: |
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568 | %%% mode: latex |
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569 | %%% TeX-master: "Guide" |
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570 | %%% End: |
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