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