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 |
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5 | # grouped here according to their use, and the values quoted are the defaults: |
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6 | # if a given parameter is not included in your parameter file, this is the |
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7 | # value it 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. THERE IS NO DEFAULT FOR THIS. |
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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 cube exists as a FITS |
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16 | # file (ie. it has been saved from a previous Duchamp run) |
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17 | # reconFile -- the location of the FITS file containing the reconstructed cube |
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18 | # flagSmoothExists -- set to true if the smoothed cube exists as a FITS |
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19 | # file (ie. it has been saved from a previous Duchamp run) |
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20 | # smoothFile -- the location of the FITS file containing the smoothed cube |
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21 | # usePrevious -- whether to read the list of detected objects from a previously- |
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22 | # created log file |
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23 | # objectList -- the list of objects to plot in individual plots: used with usePrevious=true |
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24 | |
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25 | imageFile your-file-here |
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26 | flagSubsection 0 |
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27 | subsection [*,*,*] |
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28 | flagReconExists 0 |
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29 | reconFile your-reconstructed-file-here |
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30 | flagSmoothExists 1 |
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31 | smoothFile your-smoothed-file-here |
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32 | usePrevious false |
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33 | objectList * |
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34 | |
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35 | # OUTPUT RELATED |
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36 | # flagLog -- log the intermediate results? |
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37 | # logfile-- the file to put that in. |
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38 | # outFile -- the final output list. |
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39 | # flagSeparateHeader -- whether to write the header information |
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40 | # (i.e. parameters, statistics and number of detections) |
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41 | # to a separate file from the outFile (so that the |
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42 | # outFile just contains the table of detections). |
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43 | # headerFile -- the file to write the header information to. |
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44 | # spectraFile -- the postscript file of spectra |
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45 | # flagTextSpectra -- whether to save a text file detailing the spectra |
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46 | # of each source |
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47 | # spectraTextFile -- the file in which to save the text-formatted spectra |
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48 | # flagOutputMomentMap -- whether to save a FITS file containing the moment-0 map |
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49 | # fileOutputMomentMap -- the filename for the moment-0 FITS file. If not given, it defaults |
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50 | # to the format shown (for input file image.fits) |
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51 | # flagOutputMask -- whether to save a FITS file containing a mask |
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52 | # array, showing the locations of detected objects |
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53 | # fileOutputMask -- the filename for the mask file. If not given, it defaults |
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54 | # to the format shown (for input file image.fits) |
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55 | # flagMaskWithObjectNum -- if true, the detected pixels in the mask array have |
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56 | # the object ID number, else they all have the value 1. |
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57 | # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file |
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58 | # fileOutputSmooth -- the filename for the smoothed array file. If not given, it defaults |
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59 | # to the format shown (for input file image.fits). See documentation for |
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60 | # explanation of format. |
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61 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
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62 | # as FITS files |
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63 | # fileOutputRecon/Resid -- the filename for the reconstruction or residual files. |
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64 | # If not given, it defaults to the format shown (for input |
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65 | # file image.fits). See documentation for explanation of format. |
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66 | # flagVOT -- make a VOTable file of the results? |
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67 | # votFile -- the file to put it in |
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68 | # flagKarma -- make a Karma annotation file of the results? |
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69 | # karmaFile -- the file to put it in |
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70 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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71 | # detectionMap, momentMap -- the postscript files produced. |
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72 | # flagXOutput -- display the moment map in a pgplot window |
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73 | # newFluxUnits -- brightness units to convert the array values to |
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74 | # (eg. from Jy/beam to mJy/beam) |
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75 | # precFlux -- Desired precision for Flux value in outputs. |
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76 | # precVel -- Desired precision for Velocity/Frequency value in outputs. |
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77 | # precSNR -- Desired precision for peak SNR value in ouputs. |
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78 | |
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79 | flagLog 0 |
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80 | logFile duchamp-Logfile.txt |
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81 | outFile duchamp-Results.txt |
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82 | flagSeparateHeader 0 |
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83 | headerFile duchamp-Results.hdr |
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84 | spectraFile duchamp-Spectra.ps |
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85 | flagTextSpectra 0 |
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86 | spectraTextFile duchamp-Spectra.txt |
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87 | flagOutputMomentMap 0 |
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88 | fileOutputMomentMap image.MOM0.fits |
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89 | flagOutputMask 0 |
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90 | fileOutputMask image.MASK.fits |
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91 | flagMaskWithObjectNum 0 |
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92 | flagOutputSmooth 0 |
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93 | fileOutputSmooth image.SMOOTH-ND-X.fits |
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94 | flagOutputRecon 0 |
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95 | fileOutputRecon image.RECON-A-B-C-D.fits |
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96 | flagOutputResid 0 |
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97 | fileOutputResid image.RESID-A-B-C-D.fits |
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98 | flagVOT 0 |
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99 | votFile duchamp-Results.xml |
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100 | flagKarma 0 |
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101 | karmaFile duchamp-Results.ann |
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102 | flagMaps 1 |
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103 | detectionMap duchamp-DetectionMap.ps |
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104 | momentMap duchamp-MomentMap.ps |
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105 | flagXOutput 1 |
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106 | newFluxUnits no-default |
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107 | precFlux 3 |
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108 | precVel 3 |
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109 | precSNR 2 |
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110 | |
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111 | # FIXING UP THE CUBE |
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112 | # flagTrim -- whether to trim blank pixels from the edges of the cube. |
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113 | # flagBaseline -- whether to subtract spectral baselines before searching |
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114 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
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115 | # minMW, maxMW -- the first and last channels to be ignored |
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116 | |
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117 | flagTrim 0 |
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118 | flagMW 0 |
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119 | minMW 75 |
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120 | maxMW 112 |
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121 | flagBaseline 0 |
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122 | |
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123 | # GENERAL DETECTION RELATED |
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124 | # flagStatSec -- Whether to only use a subsection of the cube to calculate |
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125 | # the statistics. |
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126 | # StatSec -- The subsection used for statistics calculations. It has the |
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127 | # same format as the pixel subsection. |
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128 | # flagRobustStats -- Shall we use robust statistics to characterise |
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129 | # the noise in the image? |
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130 | # flagNegative -- Are the features being searched for negative (set to true) |
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131 | # or positive (false -- the default)? |
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132 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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133 | # threshold -- The threshold flux dividing source and non-source. Used instead |
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134 | # of calculating it from the cube's statistics. If not specified, |
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135 | # it will be calculated. |
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136 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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137 | # growthCut -- The lower threshold used when growing detections |
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138 | # growthThreshold -- The lower threshold, used in conjunction with "threshold" |
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139 | # beamsize -- the size of the beam in pixels. This value is overridden |
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140 | # by the BMAJ, BMIN, BPA header parameters if present. |
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141 | # searchType -- how the searching is done. Either "spatial", where each 2D map is |
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142 | # searched then detections combined, or "spectral", where each 1D |
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143 | # spectrum is searched then detections combined. |
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144 | |
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145 | flagStatSec 0 |
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146 | StatSec [*,*,*] |
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147 | flagRobustStats 1 |
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148 | flagNegative 0 |
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149 | snrCut 3. |
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150 | threshold 0. |
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151 | flagGrowth 0 |
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152 | growthCut 2. |
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153 | growthThreshold 0. |
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154 | beamArea -1. |
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155 | beamFWHM 3. |
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156 | searchType spatial |
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157 | |
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158 | # RECONSTRUCTION RELATED |
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159 | # flagATrous -- Whether or not to do the reconstruction before searching |
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160 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
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161 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
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162 | # reconstruction |
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163 | # scaleMax -- The maximum scale to be included in the reconstruction. If it |
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164 | # is <=0 then the maximum scale is calculated from the size of |
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165 | # the array being reconstructed. |
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166 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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167 | # filterCode -- The code number for the choice of filter to be used in the |
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168 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
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169 | # 3 = Haar wavelet. Other numbers default to 2. |
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170 | |
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171 | flagATrous false |
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172 | reconDim 1 |
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173 | scaleMin 1 |
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174 | scaleMax 0 |
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175 | snrRecon 4. |
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176 | filterCode 1 |
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177 | |
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178 | # SMOOTHING |
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179 | # flagSmooth -- whether to smooth the cube. |
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180 | # smoothType -- either "spectral" or "spatial" |
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181 | # hanningWidth -- the width parameter of the Hanning (spectral smoothing) |
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182 | # function |
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183 | # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian |
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184 | # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian |
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185 | # kernPA -- the position angle of the major axis of the 2D spatial |
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186 | # smoothing gaussian |
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187 | |
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188 | flagSmooth false |
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189 | smoothType spectral |
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190 | hanningWidth 5 |
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191 | kernMaj 3. |
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192 | kernMin 3. |
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193 | kernPA 0. |
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194 | |
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195 | # FALSE DISCOVERY RATE METHOD |
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196 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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197 | # simple sigma clipping. |
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198 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
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199 | # percentage of discoveries will be false. Expressed as a decimal. |
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200 | # FDRnumCorChan -- The number of neighbouring channels that are |
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201 | # correlated. This is used in the FDR algorithm |
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202 | |
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203 | flagFDR 0 |
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204 | alphaFDR 0.01 |
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205 | FDRnumCorChan 2 |
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206 | |
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207 | # MERGING PARAMETERS |
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208 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
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209 | # are to be merged. |
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210 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
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211 | # separation between objects for them to be merged. |
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212 | # threshVelocity -- The maximum channel separation between objects for them |
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213 | # to be merged. |
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214 | # minChannels -- The minimum number of consecutive channels an object must have |
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215 | # for it to be accepted. |
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216 | # minPix -- Minimum number of spatial pixels a detected object must have for |
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217 | # it to be counted |
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218 | # flagRejectBeforeMerge -- If true, reject sources for not meeting the above |
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219 | # criteria before the merging stage |
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220 | # flagTwoStageMerging -- If true, do an initial merge of a new source to the list |
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221 | # (that is, merge it with the first source in the list that |
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222 | # is close, but stop there) |
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223 | |
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224 | flagAdjacent 1 |
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225 | threshSpatial 3 |
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226 | threshVelocity 7 |
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227 | minChannels 3 |
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228 | minPix 2 |
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229 | flagRejectBeforeMerge 0 |
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230 | flagTwoStageMerging 1 |
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231 | |
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232 | # OTHER PARAMETERS |
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233 | # verbose -- whether to provide progress indicators on the terminal during |
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234 | # execution |
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235 | # drawBorders -- whether to draw borders around the detections on the moment |
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236 | # maps in the output. |
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237 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
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238 | # moment maps and image cutouts. |
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239 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
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240 | # the peak pixel ("peak" -- the default), or integrated over |
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241 | # all spatial pixels present ("sum") |
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242 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
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243 | # values quoted in (including the units of integrated flux) |
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244 | # pixelCentre -- which option to use for quoting the centre of the detection. |
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245 | # Options are: centroid, average, peak. |
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246 | # sortingParam -- which parameter to sort the final detection list on. |
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247 | # Options are: x-value, y-value, z-value, ra, dec, vel, w50, |
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248 | # iflux, pflux, snr. |
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249 | |
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250 | verbose 1 |
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251 | drawBorders 1 |
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252 | drawBlankEdges 1 |
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253 | spectralMethod peak |
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254 | spectralUnits km/s |
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255 | pixelCentre centroid |
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256 | sortingParam vel |
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