[71] | 1 | # FULL PARAMETER LIST |
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| 2 | # ------------------- |
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| 3 | # |
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[142] | 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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[71] | 8 | # |
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| 9 | # |
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[3] | 10 | # INPUT RELATED |
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[525] | 11 | # imageFile -- the FITS image. THERE IS NO DEFAULT FOR THIS. |
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[3] | 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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[211] | 15 | # flagReconExists -- set to true if the reconstructed cube exists as a FITS |
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[142] | 16 | # file (ie. it has been saved from a previous Duchamp run) |
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[211] | 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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[483] | 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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[3] | 24 | |
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| 25 | imageFile your-file-here |
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[965] | 26 | flagSubsection false |
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[3] | 27 | subsection [*,*,*] |
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[965] | 28 | flagReconExists false |
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[71] | 29 | reconFile your-reconstructed-file-here |
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[965] | 30 | flagSmoothExists false |
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[447] | 31 | smoothFile your-smoothed-file-here |
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[483] | 32 | usePrevious false |
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| 33 | objectList * |
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[3] | 34 | |
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| 35 | # OUTPUT RELATED |
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[142] | 36 | # flagLog -- log the intermediate results? |
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| 37 | # logfile-- the file to put that in. |
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[3] | 38 | # outFile -- the final output list. |
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[363] | 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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[831] | 44 | # flagPlotSpectra -- whether to produce a file showing spectra of each detection |
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[3] | 45 | # spectraFile -- the postscript file of spectra |
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[425] | 46 | # flagTextSpectra -- whether to save a text file detailing the spectra |
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| 47 | # of each source |
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| 48 | # spectraTextFile -- the file in which to save the text-formatted spectra |
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[1121] | 49 | # flagOutputBaseline -- whether to save a FITS file containing the cube of baseline values |
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| 50 | # fileOutputBaseline -- the filename for the baseline FITS file. If not given, it defaults |
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| 51 | # to the format shown (for input file image.fits) |
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[680] | 52 | # flagOutputMomentMap -- whether to save a FITS file containing the moment-0 map |
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| 53 | # fileOutputMomentMap -- the filename for the moment-0 FITS file. If not given, it defaults |
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| 54 | # to the format shown (for input file image.fits) |
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[386] | 55 | # flagOutputMask -- whether to save a FITS file containing a mask |
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| 56 | # array, showing the locations of detected objects |
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[525] | 57 | # fileOutputMask -- the filename for the mask file. If not given, it defaults |
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| 58 | # to the format shown (for input file image.fits) |
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[521] | 59 | # flagMaskWithObjectNum -- if true, the detected pixels in the mask array have |
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| 60 | # the object ID number, else they all have the value 1. |
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[211] | 61 | # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file |
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[663] | 62 | # fileOutputSmooth -- the filename for the smoothed array file. If not given, it defaults |
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| 63 | # to the format shown (for input file image.fits). See documentation for |
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| 64 | # explanation of format. |
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[142] | 65 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
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| 66 | # as FITS files |
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[525] | 67 | # fileOutputRecon/Resid -- the filename for the reconstruction or residual files. |
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| 68 | # If not given, it defaults to the format shown (for input |
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| 69 | # file image.fits). See documentation for explanation of format. |
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[142] | 70 | # flagVOT -- make a VOTable file of the results? |
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| 71 | # votFile -- the file to put it in |
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| 72 | # flagKarma -- make a Karma annotation file of the results? |
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| 73 | # karmaFile -- the file to put it in |
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[1077] | 74 | # flagDS9 -- make a DS9 region file of the results? |
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| 75 | # ds9File -- the file to put it in |
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[17] | 76 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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[3] | 77 | # detectionMap, momentMap -- the postscript files produced. |
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[195] | 78 | # flagXOutput -- display the moment map in a pgplot window |
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[447] | 79 | # newFluxUnits -- brightness units to convert the array values to |
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| 80 | # (eg. from Jy/beam to mJy/beam) |
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| 81 | # precFlux -- Desired precision for Flux value in outputs. |
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| 82 | # precVel -- Desired precision for Velocity/Frequency value in outputs. |
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| 83 | # precSNR -- Desired precision for peak SNR value in ouputs. |
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[3] | 84 | |
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[965] | 85 | flagLog false |
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[87] | 86 | logFile duchamp-Logfile.txt |
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| 87 | outFile duchamp-Results.txt |
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[965] | 88 | flagSeparateHeader false |
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[363] | 89 | headerFile duchamp-Results.hdr |
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[965] | 90 | flagPlotSpectra true |
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[87] | 91 | spectraFile duchamp-Spectra.ps |
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[965] | 92 | flagTextSpectra false |
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[425] | 93 | spectraTextFile duchamp-Spectra.txt |
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[1121] | 94 | flagOutputBaseline false |
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| 95 | fileOutputBaseline image.BASE.fits |
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[965] | 96 | flagOutputMomentMap false |
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[670] | 97 | fileOutputMomentMap image.MOM0.fits |
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[965] | 98 | flagOutputMask false |
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[525] | 99 | fileOutputMask image.MASK.fits |
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[965] | 100 | flagMaskWithObjectNum false |
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| 101 | flagOutputSmooth false |
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[525] | 102 | fileOutputSmooth image.SMOOTH-ND-X.fits |
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[965] | 103 | flagOutputRecon false |
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[525] | 104 | fileOutputRecon image.RECON-A-B-C-D.fits |
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[965] | 105 | flagOutputResid false |
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[525] | 106 | fileOutputResid image.RESID-A-B-C-D.fits |
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[965] | 107 | flagVOT false |
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[87] | 108 | votFile duchamp-Results.xml |
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[965] | 109 | flagKarma false |
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[87] | 110 | karmaFile duchamp-Results.ann |
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[1077] | 111 | flagDS9 false |
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| 112 | ds9File duchamp-Results.reg |
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[965] | 113 | flagMaps true |
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[87] | 114 | detectionMap duchamp-DetectionMap.ps |
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| 115 | momentMap duchamp-MomentMap.ps |
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[965] | 116 | flagXOutput true |
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[447] | 117 | newFluxUnits no-default |
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| 118 | precFlux 3 |
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| 119 | precVel 3 |
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| 120 | precSNR 2 |
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[3] | 121 | |
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| 122 | # FIXING UP THE CUBE |
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[285] | 123 | # flagTrim -- whether to trim blank pixels from the edges of the cube. |
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[3] | 124 | # flagBaseline -- whether to subtract spectral baselines before searching |
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[142] | 125 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
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| 126 | # minMW, maxMW -- the first and last channels to be ignored |
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[3] | 127 | |
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[965] | 128 | flagTrim false |
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| 129 | flagMW false |
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[3] | 130 | minMW 75 |
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| 131 | maxMW 112 |
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[965] | 132 | flagBaseline false |
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[3] | 133 | |
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| 134 | # GENERAL DETECTION RELATED |
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[258] | 135 | # flagStatSec -- Whether to only use a subsection of the cube to calculate |
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| 136 | # the statistics. |
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| 137 | # StatSec -- The subsection used for statistics calculations. It has the |
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| 138 | # same format as the pixel subsection. |
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[386] | 139 | # flagRobustStats -- Shall we use robust statistics to characterise |
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| 140 | # the noise in the image? |
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[142] | 141 | # flagNegative -- Are the features being searched for negative (set to true) |
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| 142 | # or positive (false -- the default)? |
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[3] | 143 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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[195] | 144 | # threshold -- The threshold flux dividing source and non-source. Used instead |
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| 145 | # of calculating it from the cube's statistics. If not specified, |
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| 146 | # it will be calculated. |
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[3] | 147 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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| 148 | # growthCut -- The lower threshold used when growing detections |
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[483] | 149 | # growthThreshold -- The lower threshold, used in conjunction with "threshold" |
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[738] | 150 | # beamarea -- the area of the beam in pixels (equivalent to the old beamsize |
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| 151 | # parameter). This value is overridden by the BMAJ, BMIN, BPA header |
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| 152 | # parameters if present. |
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| 153 | # beamFWHM -- the full-width at half-maximum of the beam, in pixels. Where given, |
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| 154 | # it overrides beamarea, but is overridden by the BMAJ, BMIN, BPA |
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| 155 | # headers. |
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[686] | 156 | # searchType -- how the searching is done. Either "spatial", where each 2D map is |
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| 157 | # searched then detections combined, or "spectral", where each 1D |
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| 158 | # spectrum is searched then detections combined. |
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[3] | 159 | |
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[965] | 160 | flagStatSec false |
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[258] | 161 | StatSec [*,*,*] |
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[965] | 162 | flagRobustStats true |
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| 163 | flagNegative false |
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[1025] | 164 | snrCut 5. |
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[195] | 165 | threshold 0. |
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[965] | 166 | flagGrowth false |
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| 167 | growthCut 3. |
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[483] | 168 | growthThreshold 0. |
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[801] | 169 | beamArea 0. |
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| 170 | beamFWHM 0. |
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[686] | 171 | searchType spatial |
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[3] | 172 | |
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| 173 | # RECONSTRUCTION RELATED |
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| 174 | # flagATrous -- Whether or not to do the reconstruction before searching |
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[142] | 175 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
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| 176 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
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| 177 | # reconstruction |
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[363] | 178 | # scaleMax -- The maximum scale to be included in the reconstruction. If it |
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| 179 | # is <=0 then the maximum scale is calculated from the size of |
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| 180 | # the array being reconstructed. |
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[3] | 181 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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[1026] | 182 | # reconConvergence -- The relative change in the residual rms must be |
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| 183 | # less than this to stop the a trous iterations. |
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[142] | 184 | # filterCode -- The code number for the choice of filter to be used in the |
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| 185 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
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| 186 | # 3 = Haar wavelet. Other numbers default to 2. |
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[3] | 187 | |
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[279] | 188 | flagATrous false |
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[258] | 189 | reconDim 1 |
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[3] | 190 | scaleMin 1 |
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[363] | 191 | scaleMax 0 |
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[71] | 192 | snrRecon 4. |
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[1026] | 193 | reconConvergence 0.005 |
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[106] | 194 | filterCode 1 |
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[3] | 195 | |
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[275] | 196 | # SMOOTHING |
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| 197 | # flagSmooth -- whether to smooth the cube. |
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| 198 | # smoothType -- either "spectral" or "spatial" |
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| 199 | # hanningWidth -- the width parameter of the Hanning (spectral smoothing) |
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| 200 | # function |
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| 201 | # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian |
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| 202 | # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian |
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| 203 | # kernPA -- the position angle of the major axis of the 2D spatial |
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| 204 | # smoothing gaussian |
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[211] | 205 | |
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| 206 | flagSmooth false |
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[275] | 207 | smoothType spectral |
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[211] | 208 | hanningWidth 5 |
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[275] | 209 | kernMaj 3. |
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[965] | 210 | kernMin -1. |
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[275] | 211 | kernPA 0. |
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[211] | 212 | |
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[3] | 213 | # FALSE DISCOVERY RATE METHOD |
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| 214 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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| 215 | # simple sigma clipping. |
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[142] | 216 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
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| 217 | # percentage of discoveries will be false. Expressed as a decimal. |
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[543] | 218 | # FDRnumCorChan -- The number of neighbouring channels that are |
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| 219 | # correlated. This is used in the FDR algorithm |
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[3] | 220 | |
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[965] | 221 | flagFDR false |
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[71] | 222 | alphaFDR 0.01 |
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[543] | 223 | FDRnumCorChan 2 |
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[3] | 224 | |
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| 225 | # MERGING PARAMETERS |
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[142] | 226 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
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| 227 | # are to be merged. |
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| 228 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
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| 229 | # separation between objects for them to be merged. |
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| 230 | # threshVelocity -- The maximum channel separation between objects for them |
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| 231 | # to be merged. |
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| 232 | # minChannels -- The minimum number of consecutive channels an object must have |
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| 233 | # for it to be accepted. |
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| 234 | # minPix -- Minimum number of spatial pixels a detected object must have for |
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| 235 | # it to be counted |
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[720] | 236 | # minVoxels -- Minimum number of voxels a detected object must have for it to be |
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| 237 | # counted |
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[672] | 238 | # flagRejectBeforeMerge -- If true, reject sources for not meeting the above |
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| 239 | # criteria before the merging stage |
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[691] | 240 | # flagTwoStageMerging -- If true, do an initial merge of a new source to the list |
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| 241 | # (that is, merge it with the first source in the list that |
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| 242 | # is close, but stop there) |
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[3] | 243 | |
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[965] | 244 | flagAdjacent true |
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[691] | 245 | threshSpatial 3 |
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| 246 | threshVelocity 7 |
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| 247 | minChannels 3 |
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| 248 | minPix 2 |
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[720] | 249 | minVoxels 4 |
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[965] | 250 | flagRejectBeforeMerge false |
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| 251 | flagTwoStageMerging true |
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[3] | 252 | |
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[965] | 253 | # WCS PARAMETERS |
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| 254 | # |
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| 255 | # spectralType -- an alternative spectral WCS type to use for spectral |
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| 256 | # transformations. |
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| 257 | # restFrequency -- a value of the rest frequency to override any |
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| 258 | # provided in the FITS header |
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| 259 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
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| 260 | # values quoted in (including the units of integrated flux) |
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| 261 | |
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| 262 | spectralType no-default |
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| 263 | restFrequency -1 |
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| 264 | spectralUnits no-default |
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| 265 | |
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[3] | 266 | # OTHER PARAMETERS |
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[142] | 267 | # verbose -- whether to provide progress indicators on the terminal during |
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| 268 | # execution |
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| 269 | # drawBorders -- whether to draw borders around the detections on the moment |
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| 270 | # maps in the output. |
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| 271 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
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| 272 | # moment maps and image cutouts. |
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| 273 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
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| 274 | # the peak pixel ("peak" -- the default), or integrated over |
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| 275 | # all spatial pixels present ("sum") |
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[285] | 276 | # pixelCentre -- which option to use for quoting the centre of the detection. |
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| 277 | # Options are: centroid, average, peak. |
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[571] | 278 | # sortingParam -- which parameter to sort the final detection list on. |
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[965] | 279 | # Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50, |
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[572] | 280 | # iflux, pflux, snr. |
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[142] | 281 | |
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[965] | 282 | verbose true |
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| 283 | drawBorders true |
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| 284 | drawBlankEdges true |
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[64] | 285 | spectralMethod peak |
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[363] | 286 | pixelCentre centroid |
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[571] | 287 | sortingParam vel |
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