[303] | 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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[158] | 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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[162] | 35 | imageFile /home/mduchamp/fountain.fits |
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[158] | 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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[285] | 42 | flagTrim 1 |
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[158] | 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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[285] | 48 | flagATrous 1 |
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| 49 | reconDim 1 |
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[158] | 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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[298] | 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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[158] | 66 | \begin{verbatim} |
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[162] | 67 | imageFile /home/mduchamp/fountain.fits |
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[158] | 68 | flagLog false |
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[279] | 69 | flagATrous 1 |
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[158] | 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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[231] | 85 | |
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[992] | 86 | \newpage |
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[231] | 87 | {\scriptsize |
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[158] | 88 | \begin{verbatim} |
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| 89 | ---- Parameters ---- |
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[285] | 90 | Image to be analysed.........................[imageFile] = fountain.fits |
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[158] | 91 | Intermediate Logfile...........................[logFile] = duchamp-Logfile.txt |
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| 92 | Final Results file.............................[outFile] = duchamp-Results.txt |
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[992] | 93 | Header for results file.....................[headerFile] = duchamp-Results.hdr |
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[285] | 94 | Spectrum file..............................[spectraFile] = duchamp-Spectra.ps |
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[992] | 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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[158] | 98 | 0th Moment Map...............................[momentMap] = duchamp-MomentMap.ps |
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| 99 | Detection Map.............................[detectionMap] = duchamp-DetectionMap.ps |
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[285] | 100 | Display a map in a pgplot xwindow?.........[flagXOutput] = true |
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[992] | 101 | Saving reconstructed cube?.............[flagOutputRecon] = false |
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| 102 | Saving residuals from reconstruction?..[flagOutputResid] = false |
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| 103 | Saving mask cube?.......................[flagOutputMask] = false |
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| 104 | Saving 0th moment to FITS file?.........[flagOutputMask] = false |
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[158] | 105 | ------ |
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[992] | 106 | Type of searching performed.................[searchType] = spectral |
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[285] | 107 | Blank Pixel Value....................................... = -8.00061 |
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[992] | 108 | Trimming Blank Pixels?........................[flagTrim] = false |
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[158] | 109 | Searching for Negative features?..........[flagNegative] = false |
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| 110 | Removing Milky Way channels?....................[flagMW] = true |
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[992] | 111 | Milky Way Channels.......................[minMW - maxMW] = 75-113 |
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| 112 | Area of Beam (pixels)................................... = 14.6848 (beam: 3.6 x 3.6 pixels) |
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[158] | 113 | Removing baselines before search?.........[flagBaseline] = false |
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[992] | 114 | Smoothing data prior to searching?..........[flagSmooth] = false |
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[158] | 115 | Using A Trous reconstruction?...............[flagATrous] = true |
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[285] | 116 | Number of dimensions in reconstruction........[reconDim] = 1 |
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[158] | 117 | Minimum scale in reconstruction...............[scaleMin] = 1 |
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[992] | 118 | SNR Threshold within reconstruction...........[snrRecon] = 3 |
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[158] | 119 | Filter being used for reconstruction........[filterCode] = 1 (B3 spline function) |
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[992] | 120 | Using Robust statistics?...............[flagRobustStats] = true |
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[158] | 121 | Using FDR analysis?............................[flagFDR] = false |
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[285] | 122 | SNR Threshold (in sigma)........................[snrCut] = 3 |
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[992] | 123 | Minimum # Pixels in a detection.................[minPix] = 5 |
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[285] | 124 | Minimum # Channels in a detection..........[minChannels] = 3 |
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[992] | 125 | Minimum # Voxels in a detection..............[minVoxels] = 7 |
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[285] | 126 | Growing objects after detection?............[flagGrowth] = false |
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[158] | 127 | Using Adjacent-pixel criterion?...........[flagAdjacent] = true |
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| 128 | Max. velocity separation for merging....[threshVelocity] = 7 |
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[992] | 129 | Reject objects before merging?...[flagRejectBeforeMerge] = false |
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| 130 | Merge objects in two stages?.......[flagTwoStageMerging] = false |
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| 131 | Method of spectral plotting.............[spectralMethod] = sum |
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[285] | 132 | Type of object centre used in results......[pixelCentre] = centroid |
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| 133 | -------------------- |
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[158] | 134 | \end{verbatim} |
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[231] | 135 | } |
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| 136 | %\end{minipage} |
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| 137 | %\end{sideways} |
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