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. |
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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 | |
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22 | imageFile your-file-here |
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23 | flagSubsection 0 |
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24 | subsection [*,*,*] |
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25 | flagReconExists 0 |
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26 | reconFile your-reconstructed-file-here |
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27 | flagReconExists 1 |
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28 | reconFile your-smoothed-file-here |
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29 | |
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30 | # OUTPUT RELATED |
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31 | # flagLog -- log the intermediate results? |
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32 | # logfile-- the file to put that in. |
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33 | # outFile -- the final output list. |
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34 | # flagSeparateHeader -- whether to write the header information |
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35 | # (i.e. parameters, statistics and number of detections) |
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36 | # to a separate file from the outFile (so that the |
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37 | # outFile just contains the table of detections). |
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38 | # headerFile -- the file to write the header information to. |
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39 | # spectraFile -- the postscript file of spectra |
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40 | # flagTextSpectra -- whether to save a text file detailing the spectra |
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41 | # of each source |
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42 | # spectraTextFile -- the file in which to save the text-formatted spectra |
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43 | # flagOutputMask -- whether to save a FITS file containing a mask |
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44 | # array, showing the locations of detected objects |
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45 | # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file |
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46 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
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47 | # as FITS files |
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48 | # flagVOT -- make a VOTable file of the results? |
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49 | # votFile -- the file to put it in |
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50 | # flagKarma -- make a Karma annotation file of the results? |
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51 | # karmaFile -- the file to put it in |
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52 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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53 | # detectionMap, momentMap -- the postscript files produced. |
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54 | # flagXOutput -- display the moment map in a pgplot window |
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55 | |
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56 | flagLog 0 |
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57 | logFile duchamp-Logfile.txt |
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58 | outFile duchamp-Results.txt |
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59 | flagSeparateHeader 0 |
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60 | headerFile duchamp-Results.hdr |
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61 | spectraFile duchamp-Spectra.ps |
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62 | flagTextSpectra 0 |
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63 | spectraTextFile duchamp-Spectra.txt |
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64 | flagOutputMask 0 |
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65 | flagOutputSmooth 0 |
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66 | flagOutputRecon 0 |
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67 | flagOutputResid 0 |
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68 | flagVOT 0 |
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69 | votFile duchamp-Results.xml |
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70 | flagKarma 0 |
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71 | karmaFile duchamp-Results.ann |
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72 | flagMaps 1 |
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73 | detectionMap duchamp-DetectionMap.ps |
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74 | momentMap duchamp-MomentMap.ps |
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75 | flagXOutput 1 |
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76 | |
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77 | # FIXING UP THE CUBE |
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78 | # flagTrim -- whether to trim blank pixels from the edges of the cube. |
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79 | # blankPixValue -- what value they should take. This is overridden by |
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80 | # FITS header information. |
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81 | # flagBaseline -- whether to subtract spectral baselines before searching |
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82 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
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83 | # minMW, maxMW -- the first and last channels to be ignored |
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84 | |
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85 | flagTrim 0 |
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86 | blankPixValue -8.00061 |
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87 | flagMW 0 |
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88 | minMW 75 |
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89 | maxMW 112 |
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90 | flagBaseline 0 |
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91 | |
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92 | # GENERAL DETECTION RELATED |
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93 | # flagStatSec -- Whether to only use a subsection of the cube to calculate |
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94 | # the statistics. |
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95 | # StatSec -- The subsection used for statistics calculations. It has the |
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96 | # same format as the pixel subsection. |
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97 | # flagRobustStats -- Shall we use robust statistics to characterise |
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98 | # the noise in the image? |
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99 | # flagNegative -- Are the features being searched for negative (set to true) |
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100 | # or positive (false -- the default)? |
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101 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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102 | # threshold -- The threshold flux dividing source and non-source. Used instead |
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103 | # of calculating it from the cube's statistics. If not specified, |
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104 | # it will be calculated. |
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105 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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106 | # growthCut -- The lower threshold used when growing detections |
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107 | |
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108 | flagStatSec 0 |
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109 | StatSec [*,*,*] |
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110 | flagRobustStats 1 |
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111 | flagNegative 0 |
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112 | snrCut 3. |
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113 | threshold 0. |
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114 | flagGrowth 0 |
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115 | growthCut 2. |
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116 | |
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117 | # RECONSTRUCTION RELATED |
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118 | # flagATrous -- Whether or not to do the reconstruction before searching |
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119 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
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120 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
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121 | # reconstruction |
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122 | # scaleMax -- The maximum scale to be included in the reconstruction. If it |
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123 | # is <=0 then the maximum scale is calculated from the size of |
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124 | # the array being reconstructed. |
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125 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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126 | # filterCode -- The code number for the choice of filter to be used in the |
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127 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
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128 | # 3 = Haar wavelet. Other numbers default to 2. |
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129 | |
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130 | flagATrous false |
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131 | reconDim 1 |
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132 | scaleMin 1 |
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133 | scaleMax 0 |
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134 | snrRecon 4. |
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135 | filterCode 1 |
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136 | |
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137 | # SMOOTHING |
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138 | # flagSmooth -- whether to smooth the cube. |
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139 | # smoothType -- either "spectral" or "spatial" |
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140 | # hanningWidth -- the width parameter of the Hanning (spectral smoothing) |
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141 | # function |
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142 | # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian |
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143 | # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian |
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144 | # kernPA -- the position angle of the major axis of the 2D spatial |
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145 | # smoothing gaussian |
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146 | |
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147 | flagSmooth false |
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148 | smoothType spectral |
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149 | hanningWidth 5 |
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150 | kernMaj 3. |
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151 | kernMin 3. |
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152 | kernPA 0. |
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153 | |
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154 | # FALSE DISCOVERY RATE METHOD |
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155 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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156 | # simple sigma clipping. |
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157 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
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158 | # percentage of discoveries will be false. Expressed as a decimal. |
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159 | |
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160 | flagFDR 0 |
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161 | alphaFDR 0.01 |
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162 | |
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163 | # MERGING PARAMETERS |
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164 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
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165 | # are to be merged. |
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166 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
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167 | # separation between objects for them to be merged. |
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168 | # threshVelocity -- The maximum channel separation between objects for them |
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169 | # to be merged. |
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170 | # minChannels -- The minimum number of consecutive channels an object must have |
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171 | # for it to be accepted. |
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172 | # minPix -- Minimum number of spatial pixels a detected object must have for |
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173 | # it to be counted |
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174 | |
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175 | flagAdjacent 1 |
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176 | threshSpatial 3 |
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177 | threshVelocity 7 |
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178 | minChannels 3 |
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179 | minPix 2 |
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180 | |
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181 | # OTHER PARAMETERS |
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182 | # verbose -- whether to provide progress indicators on the terminal during |
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183 | # execution |
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184 | # drawBorders -- whether to draw borders around the detections on the moment |
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185 | # maps in the output. |
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186 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
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187 | # moment maps and image cutouts. |
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188 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
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189 | # the peak pixel ("peak" -- the default), or integrated over |
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190 | # all spatial pixels present ("sum") |
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191 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
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192 | # values quoted in (including the units of integrated flux) |
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193 | # pixelCentre -- which option to use for quoting the centre of the detection. |
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194 | # Options are: centroid, average, peak. |
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195 | |
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196 | verbose 1 |
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197 | drawBorders 1 |
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198 | drawBlankEdges 1 |
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199 | spectralMethod peak |
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200 | spectralUnits km/s |
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201 | pixelCentre centroid |
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