[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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[1249] | 43 | flaggedChannels 75-112 |
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[158] | 44 | flagGrowth 1 |
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| 45 | growthCut 1.5 |
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[285] | 46 | flagATrous 1 |
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| 47 | reconDim 1 |
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[158] | 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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[298] | 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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[158] | 64 | \begin{verbatim} |
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[162] | 65 | imageFile /home/mduchamp/fountain.fits |
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[158] | 66 | flagLog false |
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[279] | 67 | flagATrous 1 |
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[158] | 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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[231] | 83 | |
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[992] | 84 | \newpage |
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[231] | 85 | {\scriptsize |
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[158] | 86 | \begin{verbatim} |
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[1276] | 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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[158] | 136 | \end{verbatim} |
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[231] | 137 | } |
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| 138 | %\end{minipage} |
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| 139 | %\end{sideways} |
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[1249] | 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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