[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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| 11 | # imageFile -- the FITS image. |
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| 12 | # flagSubsection -- whether to get a subsection of that image. |
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| 13 | # subsection -- the subsection to read in, in format [x1:x2,y1:y2,z1:z2], |
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| 14 | # or * to indicate the full range |
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[142] | 15 | # flagReconExists -- set to true if the reconstructed image exists as a FITS |
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| 16 | # file (ie. it has been saved from a previous Duchamp run) |
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[71] | 17 | # reconFile -- the location of the FITS file containing the reconstructed image |
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[3] | 18 | |
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| 19 | imageFile your-file-here |
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[71] | 20 | flagSubsection 0 |
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[3] | 21 | subsection [*,*,*] |
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[71] | 22 | flagReconExists 0 |
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| 23 | reconFile your-reconstructed-file-here |
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[3] | 24 | |
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| 25 | # OUTPUT RELATED |
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[142] | 26 | # flagLog -- log the intermediate results? |
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| 27 | # logfile-- the file to put that in. |
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[3] | 28 | # outFile -- the final output list. |
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| 29 | # spectraFile -- the postscript file of spectra |
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[142] | 30 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
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| 31 | # as FITS files |
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| 32 | # flagVOT -- make a VOTable file of the results? |
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| 33 | # votFile -- the file to put it in |
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| 34 | # flagKarma -- make a Karma annotation file of the results? |
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| 35 | # karmaFile -- the file to put it in |
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[17] | 36 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
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[3] | 37 | # detectionMap, momentMap -- the postscript files produced. |
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[195] | 38 | # flagXOutput -- display the moment map in a pgplot window |
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[3] | 39 | |
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| 40 | flagLog 1 |
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[87] | 41 | logFile duchamp-Logfile.txt |
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| 42 | outFile duchamp-Results.txt |
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| 43 | spectraFile duchamp-Spectra.ps |
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[3] | 44 | flagOutputRecon 0 |
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| 45 | flagOutputResid 0 |
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| 46 | flagVOT 0 |
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[87] | 47 | votFile duchamp-Results.xml |
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[26] | 48 | flagKarma 0 |
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[87] | 49 | karmaFile duchamp-Results.ann |
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[3] | 50 | flagMaps 1 |
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[87] | 51 | detectionMap duchamp-DetectionMap.ps |
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| 52 | momentMap duchamp-MomentMap.ps |
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[195] | 53 | flagXOutput 1 |
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[3] | 54 | |
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| 55 | # FIXING UP THE CUBE |
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| 56 | # flagBlankPix -- whether to replace & ignore blank pixels. |
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[142] | 57 | # blankPixValue -- what value they should take. This is overridden by |
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| 58 | # FITS header information. |
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[3] | 59 | # flagBaseline -- whether to subtract spectral baselines before searching |
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[142] | 60 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
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| 61 | # minMW, maxMW -- the first and last channels to be ignored |
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[3] | 62 | |
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| 63 | flagBlankPix 1 |
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| 64 | blankPixValue -8.00061 |
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[71] | 65 | flagMW 0 |
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[3] | 66 | minMW 75 |
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| 67 | maxMW 112 |
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[87] | 68 | flagBaseline 0 |
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[3] | 69 | |
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| 70 | # GENERAL DETECTION RELATED |
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[142] | 71 | # flagNegative -- Are the features being searched for negative (set to true) |
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| 72 | # or positive (false -- the default)? |
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[3] | 73 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
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[195] | 74 | # threshold -- The threshold flux dividing source and non-source. Used instead |
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| 75 | # of calculating it from the cube's statistics. If not specified, |
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| 76 | # it will be calculated. |
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[3] | 77 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
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| 78 | # growthCut -- The lower threshold used when growing detections |
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| 79 | |
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[63] | 80 | flagNegative 0 |
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[71] | 81 | snrCut 3. |
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[195] | 82 | threshold 0. |
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[3] | 83 | flagGrowth 0 |
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[87] | 84 | growthCut 2. |
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[3] | 85 | |
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| 86 | # RECONSTRUCTION RELATED |
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| 87 | # flagATrous -- Whether or not to do the reconstruction before searching |
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[142] | 88 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
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| 89 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
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| 90 | # reconstruction |
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[3] | 91 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
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[142] | 92 | # filterCode -- The code number for the choice of filter to be used in the |
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| 93 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
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| 94 | # 3 = Haar wavelet. Other numbers default to 2. |
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[3] | 95 | |
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| 96 | flagATrous 1 |
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[103] | 97 | reconDim 3 |
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[3] | 98 | scaleMin 1 |
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[71] | 99 | snrRecon 4. |
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[106] | 100 | filterCode 1 |
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[3] | 101 | |
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| 102 | # FALSE DISCOVERY RATE METHOD |
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| 103 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
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| 104 | # simple sigma clipping. |
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[142] | 105 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
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| 106 | # percentage of discoveries will be false. Expressed as a decimal. |
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[3] | 107 | |
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| 108 | flagFDR 0 |
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[71] | 109 | alphaFDR 0.01 |
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[3] | 110 | |
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| 111 | # MERGING PARAMETERS |
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[142] | 112 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
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| 113 | # are to be merged. |
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| 114 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
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| 115 | # separation between objects for them to be merged. |
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| 116 | # threshVelocity -- The maximum channel separation between objects for them |
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| 117 | # to be merged. |
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| 118 | # minChannels -- The minimum number of consecutive channels an object must have |
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| 119 | # for it to be accepted. |
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| 120 | # minPix -- Minimum number of spatial pixels a detected object must have for |
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| 121 | # it to be counted |
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[3] | 122 | |
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| 123 | flagAdjacent 1 |
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| 124 | threshSpatial 3 |
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| 125 | threshVelocity 7 |
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[71] | 126 | minChannels 3 |
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| 127 | minPix 2 |
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[3] | 128 | |
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| 129 | # OTHER PARAMETERS |
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[142] | 130 | # verbose -- whether to provide progress indicators on the terminal during |
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| 131 | # execution |
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| 132 | # drawBorders -- whether to draw borders around the detections on the moment |
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| 133 | # maps in the output. |
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| 134 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
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| 135 | # moment maps and image cutouts. |
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| 136 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
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| 137 | # the peak pixel ("peak" -- the default), or integrated over |
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| 138 | # all spatial pixels present ("sum") |
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| 139 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
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| 140 | # values quoted in (including the units of integrated flux) |
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| 141 | |
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[3] | 142 | verbose 1 |
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| 143 | drawBorders 1 |
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[142] | 144 | drawBlankEdges 1 |
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[64] | 145 | spectralMethod peak |
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[103] | 146 | spectralUnits km/s |
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