1 | # FULL PARAMETER LIST |
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2 | # ------------------- |
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3 | # |
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4 | # This file contains the full list of user-definable parameters. They are grouped |
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5 | # here according to their use, and the values quoted are the defaults -- if a |
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6 | # given parameter is not included in your parameter file, this is the value it |
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7 | # will take. |
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8 | # |
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9 | # |
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10 | # INPUT RELATED |
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11 | # imageFile -- the FITS image. |
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12 | # flagSubsection -- whether to get a subsection of that image. |
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13 | # subsection -- the subsection to read in, in format [x1:x2,y1:y2,z1:z2], |
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14 | # or * to indicate the full range |
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15 | # flagReconExists -- set to true if the reconstructed image exists as a FITS file |
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16 | # (ie. it has been saved from a previous run of Duchamp) |
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17 | # reconFile -- the location of the FITS file containing the reconstructed image |
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18 | |
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19 | imageFile your-file-here |
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20 | flagSubsection 0 |
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21 | subsection [*,*,*] |
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22 | flagReconExists 0 |
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23 | reconFile your-reconstructed-file-here |
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24 | |
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25 | # OUTPUT RELATED |
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26 | # flagLog -- log the intermediate results? logfile-- the file to put that in. |
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27 | # outFile -- the final output list. |
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28 | # spectraFile -- the postscript file of spectra |
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29 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays as FITS files |
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30 | # flagVOT -- make a VOTable file of the results? votFile -- the file to put it in |
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31 | # flagKarma -- make a Karma annotation file of the results? karmaFile -- the file to put it in |
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32 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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33 | # detectionMap, momentMap -- the postscript files produced. |
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34 | |
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35 | flagLog 1 |
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36 | logFile duchamp-Logfile.txt |
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37 | outFile duchamp-Results.txt |
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38 | spectraFile duchamp-Spectra.ps |
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39 | flagOutputRecon 0 |
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40 | flagOutputResid 0 |
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41 | flagVOT 0 |
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42 | votFile duchamp-Results.xml |
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43 | flagKarma 0 |
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44 | karmaFile duchamp-Results.ann |
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45 | flagMaps 1 |
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46 | detectionMap duchamp-DetectionMap.ps |
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47 | momentMap duchamp-MomentMap.ps |
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48 | |
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49 | # FIXING UP THE CUBE |
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50 | # flagBlankPix -- whether to replace & ignore blank pixels. |
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51 | # blankPixValue -- what value they should take. This is overridden by FITS header information. |
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52 | # flagBaseline -- whether to subtract spectral baselines before searching |
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53 | # flagMW -- whether to excise a range of channels (to remove Milky Way emission) |
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54 | # minMW, maxMW -- the first and last channels to be excised |
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55 | |
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56 | flagBlankPix 1 |
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57 | blankPixValue -8.00061 |
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58 | flagMW 0 |
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59 | minMW 75 |
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60 | maxMW 112 |
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61 | flagBaseline 0 |
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62 | |
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63 | # GENERAL DETECTION RELATED |
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64 | # flagNegative -- Are the features being searched for negative (set to true) or positive (false)? |
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65 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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66 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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67 | # growthCut -- The lower threshold used when growing detections |
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68 | |
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69 | flagNegative 0 |
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70 | snrCut 3. |
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71 | flagGrowth 0 |
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72 | growthCut 2. |
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73 | |
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74 | # RECONSTRUCTION RELATED |
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75 | # flagATrous -- Whether or not to do the reconstruction before searching |
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76 | # reconDim -- The number of dimensions with which to perform the reconstruction. |
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77 | # scaleMin -- The minimum scale (starts at 1) to be included in the reconstruction |
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78 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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79 | # filterCode -- The code number for the choice of filter to be used in the reconstruction: |
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80 | # 1 = B3-spline filter, 2 = Triangle function, 3 = Haar wavelet. Other numbers default to 2. |
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81 | |
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82 | flagATrous 1 |
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83 | reconDim 3 |
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84 | scaleMin 1 |
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85 | snrRecon 4. |
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86 | filterCode 2 |
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87 | |
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88 | # FALSE DISCOVERY RATE METHOD |
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89 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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90 | # simple sigma clipping. |
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91 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired percentage |
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92 | # of discoveries will be false. Expressed as a decimal. |
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93 | |
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94 | flagFDR 0 |
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95 | alphaFDR 0.01 |
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96 | |
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97 | # MERGING PARAMETERS |
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98 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects are to be merged. |
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99 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial separation between objects |
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100 | # for them to be merged. |
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101 | # threshVelocity -- The maximum channel separation between objects for them to be merged. |
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102 | # minChannels -- The minimum number of consecutive channels an object must have for it to be accepted. |
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103 | # minPix -- Minimum number of spatial pixels for a detected object to be counted |
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104 | |
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105 | flagAdjacent 1 |
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106 | threshSpatial 3 |
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107 | threshVelocity 7 |
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108 | minChannels 3 |
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109 | minPix 2 |
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110 | |
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111 | # OTHER PARAMETERS |
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112 | # verbose -- whether to provide progress indicators on the terminal during execution |
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113 | # drawBorders -- whether to draw borders around the detections on the moment maps in the output. |
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114 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of the peak pixel |
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115 | # ("peak" -- the default), or integrated over all spatial pixels present ("sum") |
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116 | # spectralUnits -- what units you want the spectral axis to be plotted in and values quoted in |
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117 | # (including the units of integrated flux) |
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118 | |
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119 | verbose 1 |
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120 | drawBorders 1 |
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121 | spectralMethod peak |
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122 | spectralUnits km/s |
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