1 | % ----------------------------------------------------------------------- |
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2 | % app-paramEx.tex: Example input parameter files, and how the |
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3 | % parameters are listed in the 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{Example parameter files} |
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30 | \label{app-input} |
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31 | |
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32 | This is what a typical parameter file would look like. |
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33 | |
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34 | \begin{verbatim} |
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35 | imageFile /home/mduchamp/fountain.fits |
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36 | logFile logfile.txt |
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37 | outFile results.txt |
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38 | spectraFile spectra.ps |
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39 | flagSubsection false |
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40 | flagOutputRecon false |
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41 | flagOutputResid 0 |
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42 | flagTrim 1 |
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43 | flagMW 1 |
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44 | minMW 75 |
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45 | maxMW 112 |
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46 | flagGrowth 1 |
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47 | growthCut 1.5 |
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48 | flagATrous 1 |
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49 | reconDim 1 |
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50 | scaleMin 1 |
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51 | snrRecon 4 |
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52 | flagFDR 1 |
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53 | alphaFDR 0.1 |
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54 | snrCut 3 |
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55 | threshSpatial 3 |
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56 | threshVelocity 7 |
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57 | \end{verbatim} |
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58 | |
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59 | Note that, as in this example, the flag parameters can be entered as |
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60 | strings (\texttt{true}/\texttt{false}) or integers |
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61 | (\texttt{1}/\texttt{0}). Also, note that it is not necessary to |
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62 | include all these parameters in the file, only those that need to be |
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63 | changed from the defaults (as listed in Appendix~\ref{app-param}), |
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64 | which in this case would be very few. A minimal parameter file might |
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65 | look like: |
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66 | \begin{verbatim} |
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67 | imageFile /home/mduchamp/fountain.fits |
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68 | flagLog false |
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69 | flagATrous 1 |
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70 | snrRecon 3 |
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71 | snrCut 2.5 |
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72 | minChannels 4 |
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73 | \end{verbatim} |
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74 | This will reconstruct the cube with a lower SNR value than the |
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75 | default, select objects at a lower threshold, with a looser minimum |
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76 | channel requirement, and not keep a log of the intermediate |
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77 | detections. |
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78 | |
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79 | The following page demonstrates how the parameters are presented to |
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80 | the user, both on the screen at execution time, and in the output and |
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81 | log files. On each line, there is a description on the parameter, the |
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82 | relevant parameter name that is used in the input file (if there is |
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83 | one that the user can enter), and the value of the parameter being |
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84 | used. |
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85 | |
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86 | \newpage |
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87 | {\scriptsize |
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88 | \begin{verbatim} |
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89 | ---- Parameters ---- |
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90 | Image to be analysed.........................[imageFile] = fountain.fits |
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91 | Intermediate Logfile...........................[logFile] = duchamp-Logfile.txt |
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92 | Final Results file.............................[outFile] = duchamp-Results.txt |
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93 | Header for results file.....................[headerFile] = duchamp-Results.hdr |
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94 | Spectrum file..............................[spectraFile] = duchamp-Spectra.ps |
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95 | Text file with ascii spectral data.....[spectraTextFile] = duchamp-Spectra.txt |
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96 | VOTable file...................................[votFile] = duchamp-Results.xml |
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97 | Karma annotation file........................[karmaFile] = duchamp-Results.ann |
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98 | DS9 annotation file............................[ds9File] = duchamp-Results.reg |
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99 | 0th Moment Map...............................[momentMap] = duchamp-MomentMap.ps |
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100 | Detection Map.............................[detectionMap] = duchamp-DetectionMap.ps |
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101 | Display a map in a pgplot xwindow?.........[flagXOutput] = true |
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102 | Saving reconstructed cube?.............[flagOutputRecon] = false |
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103 | Saving residuals from reconstruction?..[flagOutputResid] = false |
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104 | Saving mask cube?.......................[flagOutputMask] = false |
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105 | Saving 0th moment to FITS file?.........[flagOutputMask] = false |
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106 | ------ |
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107 | Type of searching performed.................[searchType] = spectral |
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108 | Blank Pixel Value....................................... = -8.00061 |
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109 | Trimming Blank Pixels?........................[flagTrim] = false |
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110 | Searching for Negative features?..........[flagNegative] = false |
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111 | Removing Milky Way channels?....................[flagMW] = true |
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112 | Milky Way Channels.......................[minMW - maxMW] = 75-113 |
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113 | Area of Beam (pixels)................................... = 14.6848 (beam: 3.6 x 3.6 pixels) |
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114 | Removing baselines before search?.........[flagBaseline] = false |
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115 | Smoothing data prior to searching?..........[flagSmooth] = false |
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116 | Using A Trous reconstruction?...............[flagATrous] = true |
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117 | Number of dimensions in reconstruction........[reconDim] = 1 |
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118 | Minimum scale in reconstruction...............[scaleMin] = 1 |
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119 | SNR Threshold within reconstruction...........[snrRecon] = 3 |
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120 | Filter being used for reconstruction........[filterCode] = 1 (B3 spline function) |
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121 | Using Robust statistics?...............[flagRobustStats] = true |
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122 | Using FDR analysis?............................[flagFDR] = false |
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123 | SNR Threshold (in sigma)........................[snrCut] = 3 |
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124 | Minimum # Pixels in a detection.................[minPix] = 5 |
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125 | Minimum # Channels in a detection..........[minChannels] = 3 |
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126 | Minimum # Voxels in a detection..............[minVoxels] = 7 |
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127 | Growing objects after detection?............[flagGrowth] = false |
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128 | Using Adjacent-pixel criterion?...........[flagAdjacent] = true |
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129 | Max. velocity separation for merging....[threshVelocity] = 7 |
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130 | Reject objects before merging?...[flagRejectBeforeMerge] = false |
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131 | Merge objects in two stages?.......[flagTwoStageMerging] = false |
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132 | Method of spectral plotting.............[spectralMethod] = sum |
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133 | Type of object centre used in results......[pixelCentre] = centroid |
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134 | -------------------- |
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135 | \end{verbatim} |
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136 | } |
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137 | %\end{minipage} |
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138 | %\end{sideways} |
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