[71] | 1 | # FULL PARAMETER LIST |
---|
| 2 | # ------------------- |
---|
| 3 | # |
---|
[142] | 4 | # This file contains the full list of user-definable parameters. They are |
---|
| 5 | # grouped here according to their use, and the values quoted are the defaults: |
---|
| 6 | # if a given parameter is not included in your parameter file, this is the |
---|
| 7 | # value it will take. |
---|
[71] | 8 | # |
---|
| 9 | # |
---|
[3] | 10 | # INPUT RELATED |
---|
[525] | 11 | # imageFile -- the FITS image. THERE IS NO DEFAULT FOR THIS. |
---|
[3] | 12 | # flagSubsection -- whether to get a subsection of that image. |
---|
| 13 | # subsection -- the subsection to read in, in format [x1:x2,y1:y2,z1:z2], |
---|
| 14 | # or * to indicate the full range |
---|
[211] | 15 | # flagReconExists -- set to true if the reconstructed cube exists as a FITS |
---|
[142] | 16 | # file (ie. it has been saved from a previous Duchamp run) |
---|
[211] | 17 | # reconFile -- the location of the FITS file containing the reconstructed cube |
---|
| 18 | # flagSmoothExists -- set to true if the smoothed cube exists as a FITS |
---|
| 19 | # file (ie. it has been saved from a previous Duchamp run) |
---|
[483] | 20 | # smoothFile -- the location of the FITS file containing the smoothed cube |
---|
| 21 | # usePrevious -- whether to read the list of detected objects from a previously- |
---|
| 22 | # created log file |
---|
| 23 | # objectList -- the list of objects to plot in individual plots: used with usePrevious=true |
---|
[3] | 24 | |
---|
| 25 | imageFile your-file-here |
---|
[965] | 26 | flagSubsection false |
---|
[3] | 27 | subsection [*,*,*] |
---|
[965] | 28 | flagReconExists false |
---|
[71] | 29 | reconFile your-reconstructed-file-here |
---|
[965] | 30 | flagSmoothExists false |
---|
[447] | 31 | smoothFile your-smoothed-file-here |
---|
[483] | 32 | usePrevious false |
---|
| 33 | objectList * |
---|
[3] | 34 | |
---|
| 35 | # OUTPUT RELATED |
---|
[142] | 36 | # flagLog -- log the intermediate results? |
---|
| 37 | # logfile-- the file to put that in. |
---|
[3] | 38 | # outFile -- the final output list. |
---|
[363] | 39 | # flagSeparateHeader -- whether to write the header information |
---|
| 40 | # (i.e. parameters, statistics and number of detections) |
---|
| 41 | # to a separate file from the outFile (so that the |
---|
| 42 | # outFile just contains the table of detections). |
---|
| 43 | # headerFile -- the file to write the header information to. |
---|
[831] | 44 | # flagPlotSpectra -- whether to produce a file showing spectra of each detection |
---|
[3] | 45 | # spectraFile -- the postscript file of spectra |
---|
[425] | 46 | # flagTextSpectra -- whether to save a text file detailing the spectra |
---|
| 47 | # of each source |
---|
| 48 | # spectraTextFile -- the file in which to save the text-formatted spectra |
---|
[680] | 49 | # flagOutputMomentMap -- whether to save a FITS file containing the moment-0 map |
---|
| 50 | # fileOutputMomentMap -- the filename for the moment-0 FITS file. If not given, it defaults |
---|
| 51 | # to the format shown (for input file image.fits) |
---|
[386] | 52 | # flagOutputMask -- whether to save a FITS file containing a mask |
---|
| 53 | # array, showing the locations of detected objects |
---|
[525] | 54 | # fileOutputMask -- the filename for the mask file. If not given, it defaults |
---|
| 55 | # to the format shown (for input file image.fits) |
---|
[521] | 56 | # flagMaskWithObjectNum -- if true, the detected pixels in the mask array have |
---|
| 57 | # the object ID number, else they all have the value 1. |
---|
[211] | 58 | # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file |
---|
[663] | 59 | # fileOutputSmooth -- the filename for the smoothed array file. If not given, it defaults |
---|
| 60 | # to the format shown (for input file image.fits). See documentation for |
---|
| 61 | # explanation of format. |
---|
[142] | 62 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
---|
| 63 | # as FITS files |
---|
[525] | 64 | # fileOutputRecon/Resid -- the filename for the reconstruction or residual files. |
---|
| 65 | # If not given, it defaults to the format shown (for input |
---|
| 66 | # file image.fits). See documentation for explanation of format. |
---|
[142] | 67 | # flagVOT -- make a VOTable file of the results? |
---|
| 68 | # votFile -- the file to put it in |
---|
| 69 | # flagKarma -- make a Karma annotation file of the results? |
---|
| 70 | # karmaFile -- the file to put it in |
---|
[1077] | 71 | # flagDS9 -- make a DS9 region file of the results? |
---|
| 72 | # ds9File -- the file to put it in |
---|
[17] | 73 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
---|
[3] | 74 | # detectionMap, momentMap -- the postscript files produced. |
---|
[195] | 75 | # flagXOutput -- display the moment map in a pgplot window |
---|
[447] | 76 | # newFluxUnits -- brightness units to convert the array values to |
---|
| 77 | # (eg. from Jy/beam to mJy/beam) |
---|
| 78 | # precFlux -- Desired precision for Flux value in outputs. |
---|
| 79 | # precVel -- Desired precision for Velocity/Frequency value in outputs. |
---|
| 80 | # precSNR -- Desired precision for peak SNR value in ouputs. |
---|
[3] | 81 | |
---|
[965] | 82 | flagLog false |
---|
[87] | 83 | logFile duchamp-Logfile.txt |
---|
| 84 | outFile duchamp-Results.txt |
---|
[965] | 85 | flagSeparateHeader false |
---|
[363] | 86 | headerFile duchamp-Results.hdr |
---|
[965] | 87 | flagPlotSpectra true |
---|
[87] | 88 | spectraFile duchamp-Spectra.ps |
---|
[965] | 89 | flagTextSpectra false |
---|
[425] | 90 | spectraTextFile duchamp-Spectra.txt |
---|
[965] | 91 | flagOutputMomentMap false |
---|
[670] | 92 | fileOutputMomentMap image.MOM0.fits |
---|
[965] | 93 | flagOutputMask false |
---|
[525] | 94 | fileOutputMask image.MASK.fits |
---|
[965] | 95 | flagMaskWithObjectNum false |
---|
| 96 | flagOutputSmooth false |
---|
[525] | 97 | fileOutputSmooth image.SMOOTH-ND-X.fits |
---|
[965] | 98 | flagOutputRecon false |
---|
[525] | 99 | fileOutputRecon image.RECON-A-B-C-D.fits |
---|
[965] | 100 | flagOutputResid false |
---|
[525] | 101 | fileOutputResid image.RESID-A-B-C-D.fits |
---|
[965] | 102 | flagVOT false |
---|
[87] | 103 | votFile duchamp-Results.xml |
---|
[965] | 104 | flagKarma false |
---|
[87] | 105 | karmaFile duchamp-Results.ann |
---|
[1077] | 106 | flagDS9 false |
---|
| 107 | ds9File duchamp-Results.reg |
---|
[965] | 108 | flagMaps true |
---|
[87] | 109 | detectionMap duchamp-DetectionMap.ps |
---|
| 110 | momentMap duchamp-MomentMap.ps |
---|
[965] | 111 | flagXOutput true |
---|
[447] | 112 | newFluxUnits no-default |
---|
| 113 | precFlux 3 |
---|
| 114 | precVel 3 |
---|
| 115 | precSNR 2 |
---|
[3] | 116 | |
---|
| 117 | # FIXING UP THE CUBE |
---|
[285] | 118 | # flagTrim -- whether to trim blank pixels from the edges of the cube. |
---|
[3] | 119 | # flagBaseline -- whether to subtract spectral baselines before searching |
---|
[142] | 120 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
---|
| 121 | # minMW, maxMW -- the first and last channels to be ignored |
---|
[3] | 122 | |
---|
[965] | 123 | flagTrim false |
---|
| 124 | flagMW false |
---|
[3] | 125 | minMW 75 |
---|
| 126 | maxMW 112 |
---|
[965] | 127 | flagBaseline false |
---|
[3] | 128 | |
---|
| 129 | # GENERAL DETECTION RELATED |
---|
[258] | 130 | # flagStatSec -- Whether to only use a subsection of the cube to calculate |
---|
| 131 | # the statistics. |
---|
| 132 | # StatSec -- The subsection used for statistics calculations. It has the |
---|
| 133 | # same format as the pixel subsection. |
---|
[386] | 134 | # flagRobustStats -- Shall we use robust statistics to characterise |
---|
| 135 | # the noise in the image? |
---|
[142] | 136 | # flagNegative -- Are the features being searched for negative (set to true) |
---|
| 137 | # or positive (false -- the default)? |
---|
[3] | 138 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
---|
[195] | 139 | # threshold -- The threshold flux dividing source and non-source. Used instead |
---|
| 140 | # of calculating it from the cube's statistics. If not specified, |
---|
| 141 | # it will be calculated. |
---|
[3] | 142 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
---|
| 143 | # growthCut -- The lower threshold used when growing detections |
---|
[483] | 144 | # growthThreshold -- The lower threshold, used in conjunction with "threshold" |
---|
[738] | 145 | # beamarea -- the area of the beam in pixels (equivalent to the old beamsize |
---|
| 146 | # parameter). This value is overridden by the BMAJ, BMIN, BPA header |
---|
| 147 | # parameters if present. |
---|
| 148 | # beamFWHM -- the full-width at half-maximum of the beam, in pixels. Where given, |
---|
| 149 | # it overrides beamarea, but is overridden by the BMAJ, BMIN, BPA |
---|
| 150 | # headers. |
---|
[686] | 151 | # searchType -- how the searching is done. Either "spatial", where each 2D map is |
---|
| 152 | # searched then detections combined, or "spectral", where each 1D |
---|
| 153 | # spectrum is searched then detections combined. |
---|
[3] | 154 | |
---|
[965] | 155 | flagStatSec false |
---|
[258] | 156 | StatSec [*,*,*] |
---|
[965] | 157 | flagRobustStats true |
---|
| 158 | flagNegative false |
---|
[1025] | 159 | snrCut 5. |
---|
[195] | 160 | threshold 0. |
---|
[965] | 161 | flagGrowth false |
---|
| 162 | growthCut 3. |
---|
[483] | 163 | growthThreshold 0. |
---|
[801] | 164 | beamArea 0. |
---|
| 165 | beamFWHM 0. |
---|
[686] | 166 | searchType spatial |
---|
[3] | 167 | |
---|
| 168 | # RECONSTRUCTION RELATED |
---|
| 169 | # flagATrous -- Whether or not to do the reconstruction before searching |
---|
[142] | 170 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
---|
| 171 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
---|
| 172 | # reconstruction |
---|
[363] | 173 | # scaleMax -- The maximum scale to be included in the reconstruction. If it |
---|
| 174 | # is <=0 then the maximum scale is calculated from the size of |
---|
| 175 | # the array being reconstructed. |
---|
[3] | 176 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
---|
[1026] | 177 | # reconConvergence -- The relative change in the residual rms must be |
---|
| 178 | # less than this to stop the a trous iterations. |
---|
[142] | 179 | # filterCode -- The code number for the choice of filter to be used in the |
---|
| 180 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
---|
| 181 | # 3 = Haar wavelet. Other numbers default to 2. |
---|
[3] | 182 | |
---|
[279] | 183 | flagATrous false |
---|
[258] | 184 | reconDim 1 |
---|
[3] | 185 | scaleMin 1 |
---|
[363] | 186 | scaleMax 0 |
---|
[71] | 187 | snrRecon 4. |
---|
[1026] | 188 | reconConvergence 0.005 |
---|
[106] | 189 | filterCode 1 |
---|
[3] | 190 | |
---|
[275] | 191 | # SMOOTHING |
---|
| 192 | # flagSmooth -- whether to smooth the cube. |
---|
| 193 | # smoothType -- either "spectral" or "spatial" |
---|
| 194 | # hanningWidth -- the width parameter of the Hanning (spectral smoothing) |
---|
| 195 | # function |
---|
| 196 | # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian |
---|
| 197 | # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian |
---|
| 198 | # kernPA -- the position angle of the major axis of the 2D spatial |
---|
| 199 | # smoothing gaussian |
---|
[211] | 200 | |
---|
| 201 | flagSmooth false |
---|
[275] | 202 | smoothType spectral |
---|
[211] | 203 | hanningWidth 5 |
---|
[275] | 204 | kernMaj 3. |
---|
[965] | 205 | kernMin -1. |
---|
[275] | 206 | kernPA 0. |
---|
[211] | 207 | |
---|
[3] | 208 | # FALSE DISCOVERY RATE METHOD |
---|
| 209 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
---|
| 210 | # simple sigma clipping. |
---|
[142] | 211 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
---|
| 212 | # percentage of discoveries will be false. Expressed as a decimal. |
---|
[543] | 213 | # FDRnumCorChan -- The number of neighbouring channels that are |
---|
| 214 | # correlated. This is used in the FDR algorithm |
---|
[3] | 215 | |
---|
[965] | 216 | flagFDR false |
---|
[71] | 217 | alphaFDR 0.01 |
---|
[543] | 218 | FDRnumCorChan 2 |
---|
[3] | 219 | |
---|
| 220 | # MERGING PARAMETERS |
---|
[142] | 221 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
---|
| 222 | # are to be merged. |
---|
| 223 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
---|
| 224 | # separation between objects for them to be merged. |
---|
| 225 | # threshVelocity -- The maximum channel separation between objects for them |
---|
| 226 | # to be merged. |
---|
| 227 | # minChannels -- The minimum number of consecutive channels an object must have |
---|
| 228 | # for it to be accepted. |
---|
| 229 | # minPix -- Minimum number of spatial pixels a detected object must have for |
---|
| 230 | # it to be counted |
---|
[720] | 231 | # minVoxels -- Minimum number of voxels a detected object must have for it to be |
---|
| 232 | # counted |
---|
[672] | 233 | # flagRejectBeforeMerge -- If true, reject sources for not meeting the above |
---|
| 234 | # criteria before the merging stage |
---|
[691] | 235 | # flagTwoStageMerging -- If true, do an initial merge of a new source to the list |
---|
| 236 | # (that is, merge it with the first source in the list that |
---|
| 237 | # is close, but stop there) |
---|
[3] | 238 | |
---|
[965] | 239 | flagAdjacent true |
---|
[691] | 240 | threshSpatial 3 |
---|
| 241 | threshVelocity 7 |
---|
| 242 | minChannels 3 |
---|
| 243 | minPix 2 |
---|
[720] | 244 | minVoxels 4 |
---|
[965] | 245 | flagRejectBeforeMerge false |
---|
| 246 | flagTwoStageMerging true |
---|
[3] | 247 | |
---|
[965] | 248 | # WCS PARAMETERS |
---|
| 249 | # |
---|
| 250 | # spectralType -- an alternative spectral WCS type to use for spectral |
---|
| 251 | # transformations. |
---|
| 252 | # restFrequency -- a value of the rest frequency to override any |
---|
| 253 | # provided in the FITS header |
---|
| 254 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
---|
| 255 | # values quoted in (including the units of integrated flux) |
---|
| 256 | |
---|
| 257 | spectralType no-default |
---|
| 258 | restFrequency -1 |
---|
| 259 | spectralUnits no-default |
---|
| 260 | |
---|
[3] | 261 | # OTHER PARAMETERS |
---|
[142] | 262 | # verbose -- whether to provide progress indicators on the terminal during |
---|
| 263 | # execution |
---|
| 264 | # drawBorders -- whether to draw borders around the detections on the moment |
---|
| 265 | # maps in the output. |
---|
| 266 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
---|
| 267 | # moment maps and image cutouts. |
---|
| 268 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
---|
| 269 | # the peak pixel ("peak" -- the default), or integrated over |
---|
| 270 | # all spatial pixels present ("sum") |
---|
[285] | 271 | # pixelCentre -- which option to use for quoting the centre of the detection. |
---|
| 272 | # Options are: centroid, average, peak. |
---|
[571] | 273 | # sortingParam -- which parameter to sort the final detection list on. |
---|
[965] | 274 | # Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50, |
---|
[572] | 275 | # iflux, pflux, snr. |
---|
[142] | 276 | |
---|
[965] | 277 | verbose true |
---|
| 278 | drawBorders true |
---|
| 279 | drawBlankEdges true |
---|
[64] | 280 | spectralMethod peak |
---|
[363] | 281 | pixelCentre centroid |
---|
[571] | 282 | sortingParam vel |
---|