[71] | 1 | # FULL PARAMETER LIST |
---|
| 2 | # ------------------- |
---|
| 3 | # |
---|
[142] | 4 | # This file contains the full list of user-definable parameters. They are |
---|
| 5 | # grouped here according to their use, and the values quoted are the defaults: |
---|
| 6 | # if a given parameter is not included in your parameter file, this is the |
---|
| 7 | # value it will take. |
---|
[71] | 8 | # |
---|
| 9 | # |
---|
[3] | 10 | # INPUT RELATED |
---|
| 11 | # imageFile -- the FITS image. |
---|
| 12 | # flagSubsection -- whether to get a subsection of that image. |
---|
| 13 | # subsection -- the subsection to read in, in format [x1:x2,y1:y2,z1:z2], |
---|
| 14 | # or * to indicate the full range |
---|
[142] | 15 | # flagReconExists -- set to true if the reconstructed image exists as a FITS |
---|
| 16 | # file (ie. it has been saved from a previous Duchamp run) |
---|
[71] | 17 | # reconFile -- the location of the FITS file containing the reconstructed image |
---|
[3] | 18 | |
---|
| 19 | imageFile your-file-here |
---|
[71] | 20 | flagSubsection 0 |
---|
[3] | 21 | subsection [*,*,*] |
---|
[71] | 22 | flagReconExists 0 |
---|
| 23 | reconFile your-reconstructed-file-here |
---|
[3] | 24 | |
---|
| 25 | # OUTPUT RELATED |
---|
[142] | 26 | # flagLog -- log the intermediate results? |
---|
| 27 | # logfile-- the file to put that in. |
---|
[3] | 28 | # outFile -- the final output list. |
---|
| 29 | # spectraFile -- the postscript file of spectra |
---|
[142] | 30 | # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays |
---|
| 31 | # as FITS files |
---|
| 32 | # flagVOT -- make a VOTable file of the results? |
---|
| 33 | # votFile -- the file to put it in |
---|
| 34 | # flagKarma -- make a Karma annotation file of the results? |
---|
| 35 | # karmaFile -- the file to put it in |
---|
[17] | 36 | # flagMaps -- save postscript versions of the detection and 0th moment maps? |
---|
[3] | 37 | # detectionMap, momentMap -- the postscript files produced. |
---|
| 38 | |
---|
| 39 | flagLog 1 |
---|
[87] | 40 | logFile duchamp-Logfile.txt |
---|
| 41 | outFile duchamp-Results.txt |
---|
| 42 | spectraFile duchamp-Spectra.ps |
---|
[3] | 43 | flagOutputRecon 0 |
---|
| 44 | flagOutputResid 0 |
---|
| 45 | flagVOT 0 |
---|
[87] | 46 | votFile duchamp-Results.xml |
---|
[26] | 47 | flagKarma 0 |
---|
[87] | 48 | karmaFile duchamp-Results.ann |
---|
[3] | 49 | flagMaps 1 |
---|
[87] | 50 | detectionMap duchamp-DetectionMap.ps |
---|
| 51 | momentMap duchamp-MomentMap.ps |
---|
[3] | 52 | |
---|
| 53 | # FIXING UP THE CUBE |
---|
| 54 | # flagBlankPix -- whether to replace & ignore blank pixels. |
---|
[142] | 55 | # blankPixValue -- what value they should take. This is overridden by |
---|
| 56 | # FITS header information. |
---|
[3] | 57 | # flagBaseline -- whether to subtract spectral baselines before searching |
---|
[142] | 58 | # flagMW -- ignore a range of channels (to remove Milky Way emission)? |
---|
| 59 | # minMW, maxMW -- the first and last channels to be ignored |
---|
[3] | 60 | |
---|
| 61 | flagBlankPix 1 |
---|
| 62 | blankPixValue -8.00061 |
---|
[71] | 63 | flagMW 0 |
---|
[3] | 64 | minMW 75 |
---|
| 65 | maxMW 112 |
---|
[87] | 66 | flagBaseline 0 |
---|
[3] | 67 | |
---|
| 68 | # GENERAL DETECTION RELATED |
---|
[142] | 69 | # flagNegative -- Are the features being searched for negative (set to true) |
---|
| 70 | # or positive (false -- the default)? |
---|
[3] | 71 | # snrCut -- How many sigma above mean is a detection when sigma-clipping |
---|
| 72 | # flagGrowth -- Should the detections be "grown" to a lower significance value? |
---|
| 73 | # growthCut -- The lower threshold used when growing detections |
---|
| 74 | |
---|
[63] | 75 | flagNegative 0 |
---|
[71] | 76 | snrCut 3. |
---|
[3] | 77 | flagGrowth 0 |
---|
[87] | 78 | growthCut 2. |
---|
[3] | 79 | |
---|
| 80 | # RECONSTRUCTION RELATED |
---|
| 81 | # flagATrous -- Whether or not to do the reconstruction before searching |
---|
[142] | 82 | # reconDim -- The number of dimensions in which to perform the reconstruction. |
---|
| 83 | # scaleMin -- The minimum scale (starts at 1) to be included in the |
---|
| 84 | # reconstruction |
---|
[3] | 85 | # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. |
---|
[142] | 86 | # filterCode -- The code number for the choice of filter to be used in the |
---|
| 87 | # reconstruction: 1 = B3-spline filter, 2 = Triangle function, |
---|
| 88 | # 3 = Haar wavelet. Other numbers default to 2. |
---|
[3] | 89 | |
---|
| 90 | flagATrous 1 |
---|
[103] | 91 | reconDim 3 |
---|
[3] | 92 | scaleMin 1 |
---|
[71] | 93 | snrRecon 4. |
---|
[106] | 94 | filterCode 1 |
---|
[3] | 95 | |
---|
| 96 | # FALSE DISCOVERY RATE METHOD |
---|
| 97 | # flagFDR -- Whether or not to use the false discovery rate method instead of |
---|
| 98 | # simple sigma clipping. |
---|
[142] | 99 | # alphaFDR -- The "alpha" parameter for the FDR method -- what desired |
---|
| 100 | # percentage of discoveries will be false. Expressed as a decimal. |
---|
[3] | 101 | |
---|
| 102 | flagFDR 0 |
---|
[71] | 103 | alphaFDR 0.01 |
---|
[3] | 104 | |
---|
| 105 | # MERGING PARAMETERS |
---|
[142] | 106 | # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects |
---|
| 107 | # are to be merged. |
---|
| 108 | # threshSpatial -- If flagAdjacent=false, this is the maximum spatial |
---|
| 109 | # separation between objects for them to be merged. |
---|
| 110 | # threshVelocity -- The maximum channel separation between objects for them |
---|
| 111 | # to be merged. |
---|
| 112 | # minChannels -- The minimum number of consecutive channels an object must have |
---|
| 113 | # for it to be accepted. |
---|
| 114 | # minPix -- Minimum number of spatial pixels a detected object must have for |
---|
| 115 | # it to be counted |
---|
[3] | 116 | |
---|
| 117 | flagAdjacent 1 |
---|
| 118 | threshSpatial 3 |
---|
| 119 | threshVelocity 7 |
---|
[71] | 120 | minChannels 3 |
---|
| 121 | minPix 2 |
---|
[3] | 122 | |
---|
| 123 | # OTHER PARAMETERS |
---|
[142] | 124 | # verbose -- whether to provide progress indicators on the terminal during |
---|
| 125 | # execution |
---|
| 126 | # drawBorders -- whether to draw borders around the detections on the moment |
---|
| 127 | # maps in the output. |
---|
| 128 | # drawBlankEdges -- whether to draw an outline around any BLANK regions in the |
---|
| 129 | # moment maps and image cutouts. |
---|
| 130 | # spectralMethod -- how to plot the spectra in the output -- the spectrum of |
---|
| 131 | # the peak pixel ("peak" -- the default), or integrated over |
---|
| 132 | # all spatial pixels present ("sum") |
---|
| 133 | # spectralUnits -- what units you want the spectral axis to be plotted in and |
---|
| 134 | # values quoted in (including the units of integrated flux) |
---|
| 135 | |
---|
[3] | 136 | verbose 1 |
---|
| 137 | drawBorders 1 |
---|
[142] | 138 | drawBlankEdges 1 |
---|
[64] | 139 | spectralMethod peak |
---|
[103] | 140 | spectralUnits km/s |
---|