[158] | 1 | \secA{Example parameter files} |
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| 2 | \label{app-input} |
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| 3 | |
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| 4 | This is what a typical parameter file would look like. |
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| 5 | |
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| 6 | \begin{verbatim} |
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[162] | 7 | imageFile /home/mduchamp/fountain.fits |
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[158] | 8 | logFile logfile.txt |
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| 9 | outFile results.txt |
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| 10 | spectraFile spectra.ps |
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| 11 | flagSubsection false |
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| 12 | flagOutputRecon false |
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| 13 | flagOutputResid 0 |
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| 14 | flagBlankPix 1 |
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| 15 | flagMW 1 |
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| 16 | minMW 75 |
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| 17 | maxMW 112 |
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| 18 | minPix 3 |
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| 19 | flagGrowth 1 |
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| 20 | growthCut 1.5 |
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| 21 | flagATrous 0 |
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| 22 | scaleMin 1 |
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| 23 | snrRecon 4 |
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| 24 | flagFDR 1 |
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| 25 | alphaFDR 0.1 |
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| 26 | numPixPSF 20 |
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| 27 | snrCut 3 |
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| 28 | threshSpatial 3 |
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| 29 | threshVelocity 7 |
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| 30 | \end{verbatim} |
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| 31 | |
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| 32 | Note that, as in this example, the flag parameters can be entered as |
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| 33 | strings (true/false) or integers (1/0). Also, note that it is not |
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| 34 | necessary to include all these parameters in the file, only those that |
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| 35 | need to be changed from the defaults (as listed in |
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| 36 | Appendix~\ref{app-param}), which in this case would be very few. A |
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| 37 | minimal parameter file might look like: |
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| 38 | \begin{verbatim} |
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[162] | 39 | imageFile /home/mduchamp/fountain.fits |
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[158] | 40 | flagLog false |
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| 41 | snrRecon 3 |
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| 42 | snrCut 2.5 |
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| 43 | minChannels 4 |
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| 44 | \end{verbatim} |
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| 45 | This will reconstruct the cube with a lower SNR value than the |
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| 46 | default, select objects at a lower threshold, with a looser minimum |
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| 47 | channel requirement, and not keep a log of the intermediate |
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| 48 | detections. |
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| 49 | |
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| 50 | The following page demonstrates how the parameters are presented to |
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| 51 | the user, both on the screen at execution time, and in the output and |
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| 52 | log files. On each line, there is a description on the parameter, the |
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| 53 | relevant parameter name that is used in the input file (if there is |
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| 54 | one that the user can enter), and the value of the parameter being |
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| 55 | used. |
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| 56 | \newpage |
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| 57 | \begin{landscape} |
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| 58 | Typical presentation of parameters in output and log files: |
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| 59 | \begin{verbatim} |
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| 60 | ---- Parameters ---- |
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[162] | 61 | Image to be analysed.........................[imageFile] = /home/mduchamp/fountain.fits |
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[158] | 62 | Intermediate Logfile...........................[logFile] = duchamp-Logfile.txt |
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| 63 | Final Results file.............................[outFile] = duchamp-Results.txt |
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| 64 | Spectrum file..............................[spectraFile] = duchamp-Spectra.ps |
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| 65 | 0th Moment Map...............................[momentMap] = duchamp-MomentMap.ps |
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| 66 | Detection Map.............................[detectionMap] = duchamp-DetectionMap.ps |
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| 67 | Saving reconstructed cube?.............[flagoutputrecon] = false |
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| 68 | Saving residuals from reconstruction?..[flagoutputresid] = false |
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| 69 | ------ |
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| 70 | Searching for Negative features?..........[flagNegative] = false |
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| 71 | Fixing Blank Pixels?......................[flagBlankPix] = true |
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| 72 | Blank Pixel Value....................................... = -8.00061 |
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| 73 | Removing Milky Way channels?....................[flagMW] = true |
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| 74 | Milky Way Channels.......................[minMW - maxMW] = 75-112 |
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| 75 | Beam Size (pixels)...................................... = 10.1788 |
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| 76 | Removing baselines before search?.........[flagBaseline] = false |
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| 77 | Minimum # Pixels in a detection.................[minPix] = 2 |
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| 78 | Minimum # Channels in a detection..........[minChannels] = 3 |
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| 79 | Growing objects after detection?............[flagGrowth] = false |
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| 80 | Using A Trous reconstruction?...............[flagATrous] = true |
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| 81 | Number of dimensions in reconstruction........[reconDim] = 3 |
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| 82 | Minimum scale in reconstruction...............[scaleMin] = 1 |
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| 83 | SNR Threshold within reconstruction...........[snrRecon] = 4 |
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| 84 | Filter being used for reconstruction........[filterCode] = 1 (B3 spline function) |
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| 85 | Using FDR analysis?............................[flagFDR] = false |
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| 86 | SNR Threshold...................................[snrCut] = 3 |
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| 87 | Using Adjacent-pixel criterion?...........[flagAdjacent] = true |
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| 88 | Max. velocity separation for merging....[threshVelocity] = 7 |
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| 89 | Method of spectral plotting.............[spectralMethod] = peak |
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| 90 | \end{verbatim} |
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