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 | flaggedChannels 75-112 |
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44 | flagGrowth 1 |
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45 | growthCut 1.5 |
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46 | flagATrous 1 |
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47 | reconDim 1 |
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48 | scaleMin 1 |
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49 | snrRecon 4 |
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50 | flagFDR 1 |
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51 | alphaFDR 0.1 |
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52 | snrCut 3 |
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53 | threshSpatial 3 |
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54 | threshVelocity 7 |
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55 | \end{verbatim} |
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56 | |
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57 | Note that, as in this example, the flag parameters can be entered as |
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58 | strings (\texttt{true}/\texttt{false}) or integers |
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59 | (\texttt{1}/\texttt{0}). Also, note that it is not necessary to |
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60 | include all these parameters in the file, only those that need to be |
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61 | changed from the defaults (as listed in Appendix~\ref{app-param}), |
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62 | which in this case would be very few. A minimal parameter file might |
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63 | look like: |
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64 | \begin{verbatim} |
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65 | imageFile /home/mduchamp/fountain.fits |
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66 | flagLog false |
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67 | flagATrous 1 |
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68 | snrRecon 3 |
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69 | snrCut 2.5 |
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70 | minChannels 4 |
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71 | \end{verbatim} |
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72 | This will reconstruct the cube with a lower SNR value than the |
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73 | default, select objects at a lower threshold, with a looser minimum |
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74 | channel requirement, and not keep a log of the intermediate |
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75 | detections. |
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76 | |
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77 | The following page demonstrates how the parameters are presented to |
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78 | the user, both on the screen at execution time, and in the output and |
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79 | log files. On each line, there is a description on the parameter, the |
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80 | relevant parameter name that is used in the input file (if there is |
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81 | one that the user can enter), and the value of the parameter being |
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82 | used. |
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83 | |
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84 | \newpage |
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85 | {\scriptsize |
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86 | \begin{verbatim} |
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87 | # ---- Parameters ---- |
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88 | # Image to be analysed.............................[imageFile] = fountain.fits |
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89 | # Intermediate Logfile...............................[logFile] = duchamp-Logfile.txt |
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90 | # Final Results file.................................[outFile] = duchamp-Results.txt |
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91 | # Header for results file.........................[headerFile] = duchamp-Results.hdr |
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92 | # Spectrum file..................................[spectraFile] = duchamp-Spectra.ps |
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93 | # Text file with ascii spectral data.........[spectraTextFile] = duchamp-Spectra.txt |
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94 | # VOTable file.......................................[votFile] = duchamp-Results.xml |
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95 | # Karma annotation file............................[karmaFile] = duchamp-Results.ann |
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96 | # DS9 annotation file................................[ds9File] = duchamp-Results.reg |
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97 | # CASA annotation file..............................[casaFile] = duchamp-Results.crf |
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98 | # 0th Moment Map...................................[momentMap] = duchamp-MomentMap.ps |
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99 | # Detection Map.................................[detectionMap] = duchamp-DetectionMap.ps |
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100 | # Display a map in a pgplot xwindow?.............[flagXOutput] = true |
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101 | # Saving reconstructed cube?.................[flagOutputRecon] = true --> fountain.RECON-1-1-4-1-8-0.005.fits |
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102 | # Saving residuals from reconstruction?......[flagOutputResid] = true --> latestResid.fits |
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103 | # Saving mask cube?...........................[flagOutputMask] = true --> latestmask2.fits |
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104 | # Saving 0th moment to FITS file?........[flagOutputMomentMap] = true --> latestmom0.fits |
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105 | # Saving 0th moment mask to FITS file?..[flagOutputMomentMask] = true --> latestmom0mask.fits |
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106 | # Saving baseline values to FITS file?....[flagOutputBaseline] = false |
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107 | # ------ |
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108 | # Type of searching performed.....................[searchType] = spectral |
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109 | # Blank Pixel Value........................................... = -8.00061 |
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110 | # Trimming Blank Pixels?............................[flagTrim] = false |
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111 | # Searching for Negative features?..............[flagNegative] = false |
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112 | # Channels flagged by user...................[flaggedChannels] = 75-112 |
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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 | # Scales used in reconstruction............[scaleMin-scaleMax] = 1-8 |
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119 | # SNR Threshold within reconstruction...............[snrRecon] = 4 |
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120 | # Residual convergence criterion............[reconConvergence] = 0.005 |
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121 | # Filter being used for reconstruction............[filterCode] = 1 (B3 spline function) |
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122 | # Using Robust statistics?...................[flagRobustStats] = true |
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123 | # Using FDR analysis?................................[flagFDR] = false |
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124 | # SNR Threshold (in sigma)............................[snrCut] = 3.5 |
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125 | # Minimum # Pixels in a detection.....................[minPix] = 5 |
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126 | # Minimum # Channels in a detection..............[minChannels] = 3 |
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127 | # Minimum # Voxels in a detection..................[minVoxels] = 7 |
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128 | # Growing objects after detection?................[flagGrowth] = false |
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129 | # Using Adjacent-pixel criterion?...............[flagAdjacent] = true |
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130 | # Max. velocity separation for merging........[threshVelocity] = 7 |
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131 | # Reject objects before merging?.......[flagRejectBeforeMerge] = false |
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132 | # Merge objects in two stages?...........[flagTwoStageMerging] = false |
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133 | # Method of spectral plotting.................[spectralMethod] = peak |
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134 | # Type of object centre used in results..........[pixelCentre] = centroid |
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135 | # -------------------- |
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136 | \end{verbatim} |
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137 | } |
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138 | %\end{minipage} |
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139 | %\end{sideways} |
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140 | |
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141 | %%% Local Variables: |
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142 | %%% mode: latex |
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143 | %%% TeX-master: "Guide" |
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144 | %%% End: |
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