[1319] | 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 no-default |
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| 26 | flagSubsection false |
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| 27 | subsection [*,*,*] |
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| 28 | flagReconExists false |
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| 29 | reconFile your-reconstructed-file-here |
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| 30 | flagSmoothExists false |
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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 | # flagWriteBinaryCatalogue -- whether to create a binary catalogue |
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| 45 | # indicating the pixel locations of |
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| 46 | # detected objects (for later reuse) |
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| 47 | # binaryCatalogue -- the file containing the binary source catalogue |
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| 48 | # flagPlotSpectra -- whether to produce a file showing spectra of each detection |
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| 49 | # spectraFile -- the postscript file of spectra |
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| 50 | # flagPlotIndividualSpectra -- whether to also write individual source |
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| 51 | # spectra postscript files |
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| 52 | # flagTextSpectra -- whether to save a text file detailing the spectra |
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| 53 | # of each source |
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| 54 | # spectraTextFile -- the file in which to save the text-formatted spectra |
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| 55 | # flagOutputBaseline -- whether to save a FITS file containing the cube of baseline values |
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| 56 | # fileOutputBaseline -- the filename for the baseline FITS file. If not given, it defaults |
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| 57 | # to the format shown (for input file image.fits) |
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| 58 | # flagOutputMomentMap -- whether to save a FITS file containing the moment-0 map |
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| 59 | # fileOutputMomentMap -- the filename for the moment-0 FITS file. If not given, it defaults |
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| 60 | # to the format shown (for input file image.fits) |
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| 61 | # flagOutputMomentMask -- whether to save a FITS file containing the |
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| 62 | # moment-0 mask image |
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| 63 | # fileOutputMomentMask -- the filename for the moment-0 mask FITS file. If not given, it defaults |
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| 64 | # to the format shown (for input file image.fits) |
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| 65 | # flagOutputMask -- whether to save a FITS file containing a mask |
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| 66 | # array, showing the locations of detected objects |
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| 67 | # fileOutputMask -- the filename for the mask file. If not given, it defaults |
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| 68 | # to the format shown (for input file image.fits) |
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| 69 | # flagMaskWithObjectNum -- if true, the detected pixels in the mask array have |
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| 70 | # the object ID number, else they all have the value 1. |
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| 71 | # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file |
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| 72 | # fileOutputSmooth -- the filename for the smoothed array file. If not given, it defaults |
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| 73 | # to the format shown (for input file image.fits). See documentation for |
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| 74 | # explanation of format. |
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| 75 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
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| 76 | # as FITS files |
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| 77 | # fileOutputRecon/Resid -- the filename for the reconstruction or residual files. |
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| 78 | # If not given, it defaults to the format shown (for input |
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| 79 | # file image.fits). See documentation for explanation of format. |
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| 80 | # flagVOT -- make a VOTable file of the results? |
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| 81 | # votFile -- the file to put it in |
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| 82 | # flagKarma -- make a Karma annotation file of the results? |
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| 83 | # karmaFile -- the file to put it in |
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| 84 | # flagDS9 -- make a DS9 region file of the results? |
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| 85 | # ds9File -- the file to put it in |
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| 86 | # flagCasa -- make a CASA region file of the results? |
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| 87 | # casaFile -- the file to put it in |
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| 88 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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| 89 | # detectionMap, momentMap -- the postscript files produced. |
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| 90 | # flagXOutput -- display the moment map in a pgplot window |
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| 91 | # newFluxUnits -- brightness units to convert the array values to |
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| 92 | # (eg. from Jy/beam to mJy/beam) |
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| 93 | # precFlux -- Desired precision for Flux value in outputs. |
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| 94 | # precVel -- Desired precision for Velocity/Frequency value in outputs. |
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| 95 | # precSNR -- Desired precision for peak SNR value in ouputs. |
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| 96 | |
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| 97 | flagLog false |
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| 98 | logFile duchamp-Logfile.txt |
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| 99 | outFile duchamp-Results.txt |
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| 100 | flagSeparateHeader false |
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| 101 | headerFile duchamp-Results.hdr |
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| 102 | flagWriteBinaryCatalogue true |
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| 103 | binaryCatalogue duchamp-Catalogue.dpc |
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| 104 | flagPlotSpectra true |
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| 105 | spectraFile duchamp-Spectra.ps |
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| 106 | flagPlotIndividualSpectra false |
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| 107 | flagTextSpectra false |
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| 108 | spectraTextFile duchamp-Spectra.txt |
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| 109 | flagOutputBaseline false |
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| 110 | fileOutputBaseline image.BASE.fits |
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| 111 | flagOutputMomentMap false |
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| 112 | fileOutputMomentMap image.MOM0.fits |
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| 113 | flagOutputMomentMask false |
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| 114 | fileOutputMomentMask image.MOM0MASK.fits |
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| 115 | flagOutputMask false |
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| 116 | fileOutputMask image.MASK.fits |
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| 117 | flagMaskWithObjectNum false |
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| 118 | flagOutputSmooth false |
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| 119 | fileOutputSmooth image.SMOOTH-ND-X.fits |
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| 120 | flagOutputRecon false |
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| 121 | fileOutputRecon image.RECON-A-B-C-D.fits |
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| 122 | flagOutputResid false |
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| 123 | fileOutputResid image.RESID-A-B-C-D.fits |
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| 124 | flagVOT false |
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| 125 | votFile duchamp-Results.xml |
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| 126 | flagKarma false |
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| 127 | karmaFile duchamp-Results.ann |
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| 128 | flagDS9 false |
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| 129 | ds9File duchamp-Results.reg |
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| 130 | flagCasa false |
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| 131 | casaFile duchamp-Results.crf |
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| 132 | flagMaps true |
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| 133 | detectionMap duchamp-DetectionMap.ps |
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| 134 | momentMap duchamp-MomentMap.ps |
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| 135 | flagXOutput true |
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| 136 | newFluxUnits no-default |
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| 137 | precFlux 3 |
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| 138 | precVel 3 |
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| 139 | precSNR 2 |
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| 140 | |
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| 141 | ### MODIFYING THE CUBE |
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| 142 | # flagTrim -- whether to trim blank pixels from the edges of the cube. |
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| 143 | # flagBaseline -- whether to subtract spectral baselines before searching |
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| 144 | # flaggedChannels -- list of channels to ignore in the source-finding |
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| 145 | |
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| 146 | flagTrim false |
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| 147 | flaggedChannels no-default |
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| 148 | flagBaseline false |
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| 149 | |
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| 150 | ### GENERAL DETECTION RELATED |
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| 151 | # flagStatSec -- Whether to only use a subsection of the cube to calculate |
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| 152 | # the statistics. |
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| 153 | # StatSec -- The subsection used for statistics calculations. It has the |
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| 154 | # same format as the pixel subsection. |
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| 155 | # flagRobustStats -- Shall we use robust statistics to characterise |
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| 156 | # the noise in the image? |
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| 157 | # flagNegative -- Are the features being searched for negative (set to true) |
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| 158 | # or positive (false -- the default)? |
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| 159 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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| 160 | # threshold -- The threshold flux dividing source and non-source. Used instead |
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| 161 | # of calculating it from the cube's statistics. If not specified, |
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| 162 | # it will be calculated. |
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| 163 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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| 164 | # growthCut -- The lower threshold used when growing detections |
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| 165 | # growthThreshold -- The lower threshold, used in conjunction with "threshold" |
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| 166 | # beamarea -- the area of the beam in pixels (equivalent to the old beamsize |
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| 167 | # parameter). This value is overridden by the BMAJ, BMIN, BPA header |
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| 168 | # parameters if present. |
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| 169 | # beamFWHM -- the full-width at half-maximum of the beam, in pixels. Where given, |
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| 170 | # it overrides beamarea, but is overridden by the BMAJ, BMIN, BPA |
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| 171 | # headers. |
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| 172 | # searchType -- how the searching is done. Either "spatial", where each 2D map is |
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| 173 | # searched then detections combined, or "spectral", where each 1D |
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| 174 | # spectrum is searched then detections combined. |
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| 175 | |
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| 176 | flagStatSec false |
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| 177 | StatSec [*,*,*] |
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| 178 | flagRobustStats true |
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| 179 | flagNegative false |
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| 180 | snrCut 5. |
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| 181 | threshold 0. |
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| 182 | flagGrowth false |
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| 183 | growthCut 3. |
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| 184 | growthThreshold 0. |
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| 185 | beamArea 0. |
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| 186 | beamFWHM 0. |
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| 187 | searchType spatial |
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| 188 | |
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| 189 | ### RECONSTRUCTION RELATED |
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| 190 | # flagATrous -- Whether or not to do the reconstruction before searching |
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| 191 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
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| 192 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
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| 193 | # reconstruction |
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| 194 | # scaleMax -- The maximum scale to be included in the reconstruction. If it |
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| 195 | # is <=0 then the maximum scale is calculated from the size of |
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| 196 | # the array being reconstructed. |
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| 197 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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| 198 | # reconConvergence -- The relative change in the residual rms must be |
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| 199 | # less than this to stop the a trous iterations. |
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| 200 | # filterCode -- The code number for the choice of filter to be used in the |
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| 201 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
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| 202 | # 3 = Haar wavelet. Other numbers default to 2. |
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| 203 | |
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| 204 | flagATrous false |
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| 205 | reconDim 1 |
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| 206 | scaleMin 1 |
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| 207 | scaleMax 0 |
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| 208 | snrRecon 4. |
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| 209 | reconConvergence 0.005 |
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| 210 | filterCode 1 |
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| 211 | |
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| 212 | ### SMOOTHING |
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| 213 | # flagSmooth -- whether to smooth the cube. |
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| 214 | # smoothType -- either "spectral" or "spatial" |
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| 215 | # hanningWidth -- the width parameter of the Hanning (spectral smoothing) |
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| 216 | # function |
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| 217 | # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian |
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| 218 | # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian |
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| 219 | # kernPA -- the position angle of the major axis of the 2D spatial |
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| 220 | # smoothing gaussian |
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| 221 | # smoothEdgeMethod -- how to deal with the pixels at the edge of the |
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| 222 | # image when using the 2D smoothing algorith. Can |
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| 223 | # be equal, truncate, or scale. |
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| 224 | # spatialSmoothCutoff -- relative cutoff used to determine the width of |
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| 225 | # the 2D smoothing kernel |
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| 226 | |
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| 227 | flagSmooth false |
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| 228 | smoothType spectral |
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| 229 | hanningWidth 5 |
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| 230 | kernMaj 3. |
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| 231 | kernMin -1. |
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| 232 | kernPA 0. |
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| 233 | smoothEdgeMethod equal |
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| 234 | spatialSmoothCutoff 1.e-10 |
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| 235 | |
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| 236 | ### FALSE DISCOVERY RATE METHOD |
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| 237 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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| 238 | # simple sigma clipping. |
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| 239 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
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| 240 | # percentage of discoveries will be false. Expressed as a decimal. |
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| 241 | # FDRnumCorChan -- The number of neighbouring channels that are |
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| 242 | # correlated. This is used in the FDR algorithm |
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| 243 | |
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| 244 | flagFDR false |
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| 245 | alphaFDR 0.01 |
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| 246 | FDRnumCorChan 2 |
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| 247 | |
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| 248 | ### MERGING PARAMETERS |
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| 249 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
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| 250 | # are to be merged. |
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| 251 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
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| 252 | # separation between objects for them to be merged. |
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| 253 | # threshVelocity -- The maximum channel separation between objects for them |
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| 254 | # to be merged. |
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| 255 | # minChannels -- The minimum number of consecutive channels an object must have |
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| 256 | # for it to be accepted. |
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| 257 | # minPix -- Minimum number of spatial pixels a detected object must have for |
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| 258 | # it to be counted |
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| 259 | # minVoxels -- Minimum number of voxels a detected object must have for it to be |
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| 260 | # counted |
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| 261 | # maxChannels -- The maximum number of channels an object must have |
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| 262 | # for it to be accepted. |
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| 263 | # maxPix -- Maximum number of spatial pixels a detected object must have for |
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| 264 | # it to be counted |
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| 265 | # maxVoxels -- Maximum number of voxels a detected object must have for it to be |
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| 266 | # counted |
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| 267 | # flagRejectBeforeMerge -- If true, reject sources for not meeting the above |
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| 268 | # criteria before the merging stage |
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| 269 | # flagTwoStageMerging -- If true, do an initial merge of a new source to the list |
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| 270 | # (that is, merge it with the first source in the list that |
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| 271 | # is close, but stop there) |
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| 272 | |
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| 273 | flagAdjacent true |
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| 274 | threshSpatial 3 |
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| 275 | threshVelocity 7 |
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| 276 | minChannels 3 |
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| 277 | minPix 2 |
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| 278 | minVoxels 4 |
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| 279 | maxChannels -1 |
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| 280 | maxPix -1 |
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| 281 | maxVoxels -1 |
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| 282 | flagRejectBeforeMerge false |
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| 283 | flagTwoStageMerging true |
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| 284 | |
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| 285 | ### WCS PARAMETERS |
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| 286 | # |
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| 287 | # spectralType -- an alternative spectral WCS type to use for spectral |
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| 288 | # transformations. |
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| 289 | # restFrequency -- a value of the rest frequency to override any |
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| 290 | # provided in the FITS header |
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| 291 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
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| 292 | # values quoted in (including the units of integrated flux) |
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| 293 | |
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| 294 | spectralType no-default |
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| 295 | restFrequency -1 |
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| 296 | spectralUnits no-default |
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| 297 | |
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| 298 | ### OTHER PARAMETERS |
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| 299 | # verbose -- whether to provide progress indicators on the terminal during |
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| 300 | # execution |
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| 301 | # drawBorders -- whether to draw borders around the detections on the moment |
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| 302 | # maps in the output. |
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| 303 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
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| 304 | # moment maps and image cutouts. |
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| 305 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
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| 306 | # the peak pixel ("peak" -- the default), or integrated over |
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| 307 | # all spatial pixels present ("sum") |
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| 308 | # pixelCentre -- which option to use for quoting the centre of the detection. |
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| 309 | # Options are: centroid, average, peak. |
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| 310 | # sortingParam -- which parameter to sort the final detection list on. |
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| 311 | # Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50, |
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| 312 | # iflux, pflux, snr. |
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| 313 | |
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| 314 | verbose true |
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| 315 | drawBorders true |
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| 316 | drawBlankEdges true |
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| 317 | spectralMethod peak |
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| 318 | pixelCentre centroid |
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| 319 | sortingParam vel |
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