[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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[71] | 26 | flagSubsection 0 |
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[3] | 27 | subsection [*,*,*] |
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[71] | 28 | flagReconExists 0 |
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| 29 | reconFile your-reconstructed-file-here |
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[447] | 30 | flagSmoothExists 1 |
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| 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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[3] | 44 | # spectraFile -- the postscript file of spectra |
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[425] | 45 | # flagTextSpectra -- whether to save a text file detailing the spectra |
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| 46 | # of each source |
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| 47 | # spectraTextFile -- the file in which to save the text-formatted spectra |
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[386] | 48 | # flagOutputMask -- whether to save a FITS file containing a mask |
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| 49 | # array, showing the locations of detected objects |
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[525] | 50 | # fileOutputMask -- the filename for the mask file. If not given, it defaults |
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| 51 | # to the format shown (for input file image.fits) |
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[521] | 52 | # flagMaskWithObjectNum -- if true, the detected pixels in the mask array have |
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| 53 | # the object ID number, else they all have the value 1. |
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[211] | 54 | # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file |
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[525] | 55 | # fileOutputMask -- the filename for the smoothed array file. If not given, it defaults |
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| 56 | # to the format shown (for input file image.fits). See documentation for |
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| 57 | # explanation of format. |
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[142] | 58 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
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| 59 | # as FITS files |
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[525] | 60 | # fileOutputRecon/Resid -- the filename for the reconstruction or residual files. |
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| 61 | # If not given, it defaults to the format shown (for input |
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| 62 | # file image.fits). See documentation for explanation of format. |
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[142] | 63 | # flagVOT -- make a VOTable file of the results? |
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| 64 | # votFile -- the file to put it in |
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| 65 | # flagKarma -- make a Karma annotation file of the results? |
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| 66 | # karmaFile -- the file to put it in |
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[17] | 67 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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[3] | 68 | # detectionMap, momentMap -- the postscript files produced. |
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[195] | 69 | # flagXOutput -- display the moment map in a pgplot window |
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[447] | 70 | # newFluxUnits -- brightness units to convert the array values to |
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| 71 | # (eg. from Jy/beam to mJy/beam) |
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| 72 | # precFlux -- Desired precision for Flux value in outputs. |
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| 73 | # precVel -- Desired precision for Velocity/Frequency value in outputs. |
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| 74 | # precSNR -- Desired precision for peak SNR value in ouputs. |
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[3] | 75 | |
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[280] | 76 | flagLog 0 |
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[87] | 77 | logFile duchamp-Logfile.txt |
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| 78 | outFile duchamp-Results.txt |
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[363] | 79 | flagSeparateHeader 0 |
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| 80 | headerFile duchamp-Results.hdr |
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[87] | 81 | spectraFile duchamp-Spectra.ps |
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[425] | 82 | flagTextSpectra 0 |
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| 83 | spectraTextFile duchamp-Spectra.txt |
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[386] | 84 | flagOutputMask 0 |
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[525] | 85 | fileOutputMask image.MASK.fits |
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[521] | 86 | flagMaskWithObjectNum 0 |
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[211] | 87 | flagOutputSmooth 0 |
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[525] | 88 | fileOutputSmooth image.SMOOTH-ND-X.fits |
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[3] | 89 | flagOutputRecon 0 |
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[525] | 90 | fileOutputRecon image.RECON-A-B-C-D.fits |
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[3] | 91 | flagOutputResid 0 |
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[525] | 92 | fileOutputResid image.RESID-A-B-C-D.fits |
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[3] | 93 | flagVOT 0 |
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[87] | 94 | votFile duchamp-Results.xml |
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[26] | 95 | flagKarma 0 |
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[87] | 96 | karmaFile duchamp-Results.ann |
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[3] | 97 | flagMaps 1 |
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[87] | 98 | detectionMap duchamp-DetectionMap.ps |
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| 99 | momentMap duchamp-MomentMap.ps |
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[195] | 100 | flagXOutput 1 |
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[447] | 101 | newFluxUnits no-default |
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| 102 | precFlux 3 |
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| 103 | precVel 3 |
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| 104 | precSNR 2 |
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[3] | 105 | |
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| 106 | # FIXING UP THE CUBE |
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[285] | 107 | # flagTrim -- whether to trim blank pixels from the edges of the cube. |
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[3] | 108 | # flagBaseline -- whether to subtract spectral baselines before searching |
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[142] | 109 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
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| 110 | # minMW, maxMW -- the first and last channels to be ignored |
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[3] | 111 | |
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[285] | 112 | flagTrim 0 |
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[71] | 113 | flagMW 0 |
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[3] | 114 | minMW 75 |
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| 115 | maxMW 112 |
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[87] | 116 | flagBaseline 0 |
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[3] | 117 | |
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| 118 | # GENERAL DETECTION RELATED |
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[258] | 119 | # flagStatSec -- Whether to only use a subsection of the cube to calculate |
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| 120 | # the statistics. |
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| 121 | # StatSec -- The subsection used for statistics calculations. It has the |
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| 122 | # same format as the pixel subsection. |
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[386] | 123 | # flagRobustStats -- Shall we use robust statistics to characterise |
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| 124 | # the noise in the image? |
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[142] | 125 | # flagNegative -- Are the features being searched for negative (set to true) |
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| 126 | # or positive (false -- the default)? |
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[3] | 127 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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[195] | 128 | # threshold -- The threshold flux dividing source and non-source. Used instead |
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| 129 | # of calculating it from the cube's statistics. If not specified, |
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| 130 | # it will be calculated. |
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[3] | 131 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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| 132 | # growthCut -- The lower threshold used when growing detections |
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[483] | 133 | # growthThreshold -- The lower threshold, used in conjunction with "threshold" |
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| 134 | # beamsize -- the size of the beam in pixels. This value is overridden |
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| 135 | # by the BMAJ, BMIN, BPA header parameters if present. |
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[3] | 136 | |
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[258] | 137 | flagStatSec 0 |
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| 138 | StatSec [*,*,*] |
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[386] | 139 | flagRobustStats 1 |
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[63] | 140 | flagNegative 0 |
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[71] | 141 | snrCut 3. |
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[195] | 142 | threshold 0. |
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[3] | 143 | flagGrowth 0 |
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[87] | 144 | growthCut 2. |
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[483] | 145 | growthThreshold 0. |
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| 146 | beamsize 10. |
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[3] | 147 | |
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| 148 | # RECONSTRUCTION RELATED |
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| 149 | # flagATrous -- Whether or not to do the reconstruction before searching |
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[142] | 150 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
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| 151 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
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| 152 | # reconstruction |
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[363] | 153 | # scaleMax -- The maximum scale to be included in the reconstruction. If it |
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| 154 | # is <=0 then the maximum scale is calculated from the size of |
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| 155 | # the array being reconstructed. |
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[3] | 156 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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[142] | 157 | # filterCode -- The code number for the choice of filter to be used in the |
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| 158 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
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| 159 | # 3 = Haar wavelet. Other numbers default to 2. |
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[3] | 160 | |
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[279] | 161 | flagATrous false |
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[258] | 162 | reconDim 1 |
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[3] | 163 | scaleMin 1 |
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[363] | 164 | scaleMax 0 |
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[71] | 165 | snrRecon 4. |
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[106] | 166 | filterCode 1 |
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[3] | 167 | |
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[275] | 168 | # SMOOTHING |
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| 169 | # flagSmooth -- whether to smooth the cube. |
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| 170 | # smoothType -- either "spectral" or "spatial" |
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| 171 | # hanningWidth -- the width parameter of the Hanning (spectral smoothing) |
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| 172 | # function |
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| 173 | # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian |
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| 174 | # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian |
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| 175 | # kernPA -- the position angle of the major axis of the 2D spatial |
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| 176 | # smoothing gaussian |
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[211] | 177 | |
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| 178 | flagSmooth false |
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[275] | 179 | smoothType spectral |
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[211] | 180 | hanningWidth 5 |
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[275] | 181 | kernMaj 3. |
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| 182 | kernMin 3. |
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| 183 | kernPA 0. |
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[211] | 184 | |
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[3] | 185 | # FALSE DISCOVERY RATE METHOD |
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| 186 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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| 187 | # simple sigma clipping. |
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[142] | 188 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
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| 189 | # percentage of discoveries will be false. Expressed as a decimal. |
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[543] | 190 | # FDRnumCorChan -- The number of neighbouring channels that are |
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| 191 | # correlated. This is used in the FDR algorithm |
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[3] | 192 | |
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| 193 | flagFDR 0 |
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[71] | 194 | alphaFDR 0.01 |
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[543] | 195 | FDRnumCorChan 2 |
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[3] | 196 | |
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| 197 | # MERGING PARAMETERS |
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[142] | 198 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
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| 199 | # are to be merged. |
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| 200 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
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| 201 | # separation between objects for them to be merged. |
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| 202 | # threshVelocity -- The maximum channel separation between objects for them |
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| 203 | # to be merged. |
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| 204 | # minChannels -- The minimum number of consecutive channels an object must have |
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| 205 | # for it to be accepted. |
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| 206 | # minPix -- Minimum number of spatial pixels a detected object must have for |
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| 207 | # it to be counted |
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[3] | 208 | |
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| 209 | flagAdjacent 1 |
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| 210 | threshSpatial 3 |
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| 211 | threshVelocity 7 |
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[71] | 212 | minChannels 3 |
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| 213 | minPix 2 |
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[3] | 214 | |
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| 215 | # OTHER PARAMETERS |
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[142] | 216 | # verbose -- whether to provide progress indicators on the terminal during |
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| 217 | # execution |
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| 218 | # drawBorders -- whether to draw borders around the detections on the moment |
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| 219 | # maps in the output. |
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| 220 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
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| 221 | # moment maps and image cutouts. |
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| 222 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
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| 223 | # the peak pixel ("peak" -- the default), or integrated over |
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| 224 | # all spatial pixels present ("sum") |
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| 225 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
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| 226 | # values quoted in (including the units of integrated flux) |
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[285] | 227 | # pixelCentre -- which option to use for quoting the centre of the detection. |
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| 228 | # Options are: centroid, average, peak. |
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[142] | 229 | |
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[3] | 230 | verbose 1 |
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| 231 | drawBorders 1 |
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[142] | 232 | drawBlankEdges 1 |
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[64] | 233 | spectralMethod peak |
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[103] | 234 | spectralUnits km/s |
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[363] | 235 | pixelCentre centroid |
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