1 | # FULL PARAMETER LIST |
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2 | # ------------------- |
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3 | # |
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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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8 | # |
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9 | # In the comments at the start of each section, each parameter is listed followed |
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10 | # by its datatype (in []) and, where applicable, a description of the allowed range |
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11 | # of values or types of inputs accepted (in {}), followed by a more verbose description. |
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12 | # |
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13 | # |
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14 | ### INPUT RELATED |
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15 | #* imageFile [string] {filename (must exist)} -- The FITS image. THERE IS NO DEFAULT FOR THIS. |
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16 | #* flagSubsection [bool] {true or false, or 1 or 0} -- Whether to get a subsection of that image. |
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17 | #* subsection [string] {Subsection specification like [x1:x2,y1:y2,z1:z2]} -- The subsection to read in, in format [x1:x2,y1:y2,z1:z2], or * to indicate the full range |
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18 | #* flagReconExists [bool] {true or false, or 1 or 0} -- Set to true if the reconstructed cube exists as a FITS file (ie. it has been saved from a previous Duchamp run) |
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19 | #* reconFile [string] {filename (must exist)} -- The location of the FITS file containing the reconstructed cube |
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20 | #* flagSmoothExists [bool] {true or false, or 1 or 0} -- Set to true if the smoothed cube exists as a FITS file (ie. it has been saved from a previous Duchamp run) |
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21 | #* smoothFile [string] {filename (must exist)} -- The location of the FITS file containing the smoothed cube |
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22 | #* usePrevious [bool] {true or false, or 1 or 0} -- Whether to read the list of detected objects from a previously-created log file |
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23 | #* objectList [string] {comma-separated list of object numbers (integers)} -- The list of objects to plot in individual plots: used with usePrevious=true |
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24 | |
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25 | imageFile your-file-here |
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26 | flagSubsection false |
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27 | subsection "" |
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28 | flagReconExists false |
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29 | reconFile your-reconstructed-file-here |
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30 | flagSmoothExists false |
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31 | smoothFile your-smoothed-file-here |
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32 | usePrevious false |
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33 | objectList * |
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34 | |
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35 | ### OUTPUT RELATED |
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36 | #* flagLog [bool] {true or false, or 1 or 0} -- Log the intermediate results? |
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37 | #* logFile [string] {filename} -- The file to put that in. |
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38 | #* outFile [string] {filename} -- The final output list. |
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39 | #* flagSeparateHeader [bool] {true or false, or 1 or 0} -- Whether to write the header information (i.e. parameters, statistics and number of detections) to a separate file from the outFile (so that the outFile just contains the table of detections). |
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40 | #* headerFile [string] {filename} -- The file to write the header information to. |
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41 | #* flagWriteBinaryCatalogue [bool] {true or false, or 1 or 0} -- Whether to create a binary catalogue indicating the pixel locations of detected objects (for later reuse) |
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42 | #* binaryCatalogue [string] {filename} -- The file containing the binary source catalogue |
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43 | #* flagPlotSpectra [bool] {true or false, or 1 or 0} -- Whether to produce a file showing spectra of each detection |
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44 | #* spectraFile [string] {filename} -- The postscript file of spectra |
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45 | #* flagPlotIndividualSpectra [bool] {true or false, or 1 or 0} -- Whether to also write individual source spectra postscript files |
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46 | #* flagTextSpectra [bool] {true or false, or 1 or 0} -- Whether to save a text file detailing the spectra of each source |
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47 | #* spectraTextFile [string] {filename} -- The file in which to save the text-formatted spectra |
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48 | #* flagOutputBaseline [bool] {true or false, or 1 or 0} -- Whether to save a FITS file containing the cube of baseline values |
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49 | #* fileOutputBaseline [string] {filename} -- The filename for the baseline FITS file. If not given, it defaults to the format shown (for input file image.fits) |
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50 | #* flagOutputMomentMap [bool] {true or false, or 1 or 0} -- Whether to save a FITS file containing the moment-0 map |
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51 | #* fileOutputMomentMap [string] {filename} -- The filename for the moment-0 FITS file. If not given, it defaults to the format shown (for input file image.fits) |
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52 | #* flagOutputMomentMask [bool] {true or false, or 1 or 0} -- Whether to save a FITS file containing the moment-0 mask image |
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53 | #* fileOutputMomentMask [string] {filename} -- The filename for the moment-0 mask FITS file. If not given, it defaults to the format shown (for input file image.fits) |
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54 | #* flagOutputMask [bool] {true or false, or 1 or 0} -- Whether to save a FITS file containing a mask array, showing the locations of detected objects |
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55 | #* fileOutputMask [string] {filename} -- The filename for the mask file. If not given, it defaults to the format shown (for input file image.fits) |
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56 | #* flagMaskWithObjectNum [bool] {true or false, or 1 or 0} -- If true, the detected pixels in the mask array have the object ID number, else they all have the value 1. |
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57 | #* flagOutputSmooth [bool] {true or false, or 1 or 0} -- Whether to save the smoothed arrays as a FITS file |
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58 | #* fileOutputSmooth [string] {filename} -- The filename for the smoothed array file. If not given, it defaults to the format shown (for input file image.fits). See documentation for explanation of format. |
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59 | #* flagOutputRecon [bool] {true or false, or 1 or 0} -- Whether to save the reconstruction & residual arrays as FITS files |
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60 | #* fileOutputRecon [string] {filename} -- The filename for the reconstruction or residual files. If not given, it defaults to the format shown (for input file image.fits). See documentation for explanation of format. |
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61 | #* flagOutputResid [bool] {true or false, or 1 or 0} -- Whether to save the reconstruction & residual arrays as FITS files |
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62 | #* fileOutputResid [string] {filename} -- The filename for the reconstruction or residual files. If not given, it defaults to the format shown (for input file image.fits). See documentation for explanation of format. |
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63 | #* flagVOT [bool] {true or false, or 1 or 0} -- Make a VOTable file of the results? |
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64 | #* votFile [string] {filename} -- The file to put it in |
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65 | #* flagKarma [bool] {true or false, or 1 or 0} -- Make a Karma annotation file of the results? |
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66 | #* karmaFile [string] {filename} -- The file to put it in |
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67 | #* flagDS9 [bool] {true or false, or 1 or 0} -- Make a DS9 region file of the results? |
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68 | #* ds9File [string] {filename} -- The file to put it in |
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69 | #* flagCasa [bool] {true or false, or 1 or 0} -- Make a CASA region file of the results? |
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70 | #* casaFile [string] {filename} -- The file to put it in |
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71 | #* annotationType [string] {borders/circles/ellipses} -- Which type of annotation plot to use. Options are: borders = outline around detected pixels; circles = circle centred on object with radius encompassing all detected pixels; ellipses = ellipse centred on object with size given by MAJ, MIN, PA |
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72 | #* flagMaps [bool] {true or false, or 1 or 0} -- Save postscript versions of the detection and 0th moment maps? |
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73 | #* detectionMap [string] {filename} -- The postscript file containing the detection map |
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74 | #* momentMap [string] {filename} -- The postscript files containing the 0th-moment map |
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75 | #* flagXOutput [bool] {true or false, or 1 or 0} -- Display the moment map in a pgplot window |
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76 | #* newFluxUnits [string] {units, convertible from FITS file units} -- Brightness units to convert the array values to (eg. from Jy/beam to mJy/beam) |
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77 | #* precFlux [int] {>=0} -- Desired precision for Flux value in outputs. |
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78 | #* precVel [int] {>=0} -- Desired precision for Velocity/Frequency value in outputs. |
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79 | #* precSNR [int] {>=0} -- Desired precision for peak SNR value in ouputs. |
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80 | |
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81 | flagLog false |
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82 | logFile duchamp-Logfile.txt |
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83 | outFile duchamp-Results.txt |
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84 | flagSeparateHeader false |
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85 | headerFile duchamp-Results.hdr |
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86 | flagWriteBinaryCatalogue true |
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87 | binaryCatalogue duchamp-Catalogue.dpc |
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88 | flagPlotSpectra true |
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89 | spectraFile duchamp-Spectra.ps |
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90 | flagPlotIndividualSpectra false |
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91 | flagTextSpectra false |
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92 | spectraTextFile duchamp-Spectra.txt |
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93 | flagOutputBaseline false |
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94 | fileOutputBaseline image.BASE.fits |
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95 | flagOutputMomentMap false |
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96 | fileOutputMomentMap image.MOM0.fits |
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97 | flagOutputMomentMask false |
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98 | fileOutputMomentMask image.MOM0MASK.fits |
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99 | flagOutputMask false |
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100 | fileOutputMask image.MASK.fits |
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101 | flagMaskWithObjectNum false |
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102 | flagOutputSmooth false |
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103 | fileOutputSmooth image.SMOOTH-ND-X.fits |
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104 | flagOutputRecon false |
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105 | fileOutputRecon image.RECON-A-B-C-D.fits |
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106 | flagOutputResid false |
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107 | fileOutputResid image.RESID-A-B-C-D.fits |
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108 | flagVOT false |
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109 | votFile duchamp-Results.xml |
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110 | flagKarma false |
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111 | karmaFile duchamp-Results.ann |
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112 | flagDS9 false |
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113 | ds9File duchamp-Results.reg |
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114 | flagCasa false |
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115 | casaFile duchamp-Results.crf |
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116 | annotationType borders |
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117 | flagMaps true |
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118 | detectionMap duchamp-DetectionMap.ps |
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119 | momentMap duchamp-MomentMap.ps |
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120 | flagXOutput true |
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121 | newFluxUnits no-default |
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122 | precFlux 3 |
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123 | precVel 3 |
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124 | precSNR 2 |
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125 | |
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126 | ### MODIFYING THE CUBE |
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127 | #* flagTrim [bool] {true or false, or 1 or 0} -- Whether to trim blank pixels from the edges of the cube. |
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128 | #* flagBaseline [bool] {true or false, or 1 or 0} -- Whether to subtract spectral baselines before searching |
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129 | #* flaggedChannels [string] {comma-separated list of channels} -- List of channels to ignore in the source-finding |
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130 | #* baselineType [string] {either 'atrous' or 'median'} -- Which type of baseline estimation to use. Only 'atrous' or 'median' modes accepted. |
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131 | #* baselineBoxWidth [int] {odd integer > 0} -- Box width used by the median baseline algorithm |
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132 | |
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133 | flagTrim false |
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134 | flaggedChannels "" |
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135 | flagBaseline false |
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136 | baselineType atrous |
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137 | baselineBoxWidth 51 |
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138 | |
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139 | ### GENERAL DETECTION RELATED |
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140 | #* flagStatSec [bool] {true or false, or 1 or 0} -- Whether to only use a subsection of the cube to calculate the statistics. |
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141 | #* StatSec [string] {Subsection specification like [x1:x2,y1:y2,z1:z2]} -- The subsection used for statistics calculations. It has the same format as the pixel subsection. |
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142 | #* flagRobustStats [bool] {true or false, or 1 or 0} -- Shall we use robust statistics to characterise the noise in the image? |
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143 | #* flagNegative [bool] {true or false, or 1 or 0} -- Are the features being searched for negative (set to true) or positive (false -- the default)? |
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144 | #* snrCut [float] {any} -- How many sigma above mean is a detection when sigma-clipping |
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145 | #* threshold [float] {any} -- The threshold flux dividing source and non-source. Used instead of calculating it from the cube's statistics. If not specified, it will be calculated. |
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146 | #* flagGrowth [bool] {true or false, or 1 or 0} -- Should the detections be "grown" to a lower significance value? |
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147 | #* growthCut [float] {any} -- The lower threshold used when growing detections |
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148 | #* growthThreshold [float] {any} -- The lower threshold, used in conjunction with "threshold" |
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149 | #* beamarea [float] {> 0.} -- The area of the beam in pixels (equivalent to the old beamsize parameter). This value is overridden by the BMAJ, BMIN, BPA header parameters if present. |
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150 | #* beamFWHM [float] {> 0.} -- The full-width at half-maximum of the beam, in pixels. Where given, it overrides beamarea, but is overridden by the BMAJ, BMIN, BPA headers. |
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151 | #* searchType [string] {either 'spatial' or 'spectral'} -- How the searching is done. Either "spatial", where each 2D map is searched then detections combined, or "spectral", where each 1D spectrum is searched then detections combined. |
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152 | |
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153 | flagStatSec false |
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154 | StatSec "" |
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155 | flagRobustStats true |
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156 | flagNegative false |
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157 | snrCut 5. |
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158 | threshold 0. |
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159 | flagGrowth false |
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160 | growthCut 3. |
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161 | growthThreshold 0. |
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162 | beamArea 0. |
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163 | beamFWHM 0. |
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164 | searchType spatial |
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165 | |
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166 | ### RECONSTRUCTION RELATED |
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167 | #* flagATrous [bool] {true or false, or 1 or 0} -- Whether or not to do the reconstruction before searching |
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168 | #* reconDim [int] {> 0} -- The number of dimensions in which to perform the reconstruction. |
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169 | #* scaleMin [int] {> 0} -- The minimum scale (starts at 1) to be included in the reconstruction |
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170 | #* scaleMax [int] {any} -- The maximum scale to be included in the reconstruction. If it is <=0 then the maximum scale is calculated from the size of the array being reconstructed. |
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171 | #* snrRecon [float] {> 0} -- The threshold used in filtering the wavelet coefficient arrays. |
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172 | #* reconConvergence [float] {> 0.} -- The relative change in the residual rms must be less than this to stop the a trous iterations. |
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173 | #* filterCode [int] {one of 1,2,3} -- The code number for the choice of filter to be used in the reconstruction: 1 = B3-spline filter, 2 = Triangle function, 3 = Haar wavelet. Other numbers default to 1. |
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174 | |
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175 | flagATrous false |
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176 | reconDim 1 |
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177 | scaleMin 1 |
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178 | scaleMax 0 |
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179 | snrRecon 4. |
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180 | reconConvergence 0.005 |
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181 | filterCode 1 |
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182 | |
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183 | ### SMOOTHING |
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184 | #* flagSmooth [bool] {true or false, or 1 or 0} -- Whether to smooth the cube. |
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185 | #* smoothType [string] {either 'spectral' or 'spatial'} -- The type of smoothing to use, either "spectral" or "spatial" |
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186 | #* hanningWidth [int] {> 0} -- The width parameter of the Hanning (spectral smoothing) function |
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187 | #* kernMaj [float] {> 0.} -- The FWHM (in pixels) of the major axis of the 2D spatial smoothing gaussian |
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188 | #* kernMin [float] {> 0.} -- The FWHM (in pixels) of the minor axis of the 2D spatial smoothing gaussian |
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189 | #* kernPA [float] {any} -- The position angle (in degrees) of the major axis of the 2D spatial smoothing gaussian |
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190 | #* smoothEdgeMethod [string] {one of 'equal', 'truncate' or 'scale'} -- How to deal with the pixels at the edge of the image when using the 2D smoothing algorith. Can be equal, truncate, or scale. |
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191 | #* spatialSmoothCutoff [float] {> 0.} -- Relative cutoff used to determine the width of the 2D smoothing kernel |
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192 | |
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193 | flagSmooth false |
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194 | smoothType spectral |
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195 | hanningWidth 5 |
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196 | kernMaj 3. |
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197 | kernMin -1. |
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198 | kernPA 0. |
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199 | smoothEdgeMethod equal |
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200 | spatialSmoothCutoff 1.e-10 |
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201 | |
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202 | ### FALSE DISCOVERY RATE METHOD |
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203 | #* flagFDR [bool] {true or false, or 1 or 0} -- Whether or not to use the false discovery rate method instead of simple sigma clipping. |
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204 | #* alphaFDR [float] {0. - 1.} -- The "alpha" parameter for the FDR method -- what desired fraction of discoveries will be false. Expressed as a decimal. |
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205 | #* FDRnumCorChan [int] {>0} -- The number of neighbouring channels that are correlated. This is used only in the FDR algorithm |
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206 | |
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207 | flagFDR false |
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208 | alphaFDR 0.01 |
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209 | FDRnumCorChan 2 |
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210 | |
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211 | ### MERGING PARAMETERS |
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212 | #* flagAdjacent [bool] {true or false, or 1 or 0} -- Whether to use the "adjacent criterion" to judge if objects are to be merged. |
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213 | #* threshSpatial [float] {>= 0.} -- If flagAdjacent=false, this is the maximum spatial separation between objects for them to be merged. |
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214 | #* threshVelocity [float] {>= 0.} -- The maximum channel separation between objects for them to be merged. |
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215 | #* minChannels [int] {> 0} -- The minimum number of consecutive channels an object must have for it to be accepted. |
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216 | #* minPix [int] {> 0} -- Minimum number of spatial pixels a detected object must have for it to be counted |
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217 | #* minVoxels [int] {> 0} -- Minimum number of voxels a detected object must have for it to be counted |
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218 | #* maxChannels [int] {any} -- The maximum number of channels an object must have for it to be accepted. |
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219 | #* maxPix [int] {any} -- Maximum number of spatial pixels a detected object must have for it to be counted |
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220 | #* maxVoxels [int] {any} -- Maximum number of voxels a detected object must have for it to be counted |
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221 | #* flagRejectBeforeMerge [bool] {true or false, or 1 or 0} -- If true, reject sources for not meeting the above criteria before the merging stage |
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222 | #* flagTwoStageMerging [bool] {true or false, or 1 or 0} -- If true, do an initial merge of a new source to the list (that is, merge it with the first source in the list that is close, but stop there) |
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223 | |
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224 | flagAdjacent true |
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225 | threshSpatial 3 |
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226 | threshVelocity 7 |
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227 | minChannels 3 |
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228 | minPix 2 |
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229 | minVoxels 4 |
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230 | maxChannels -1 |
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231 | maxPix -1 |
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232 | maxVoxels -1 |
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233 | flagRejectBeforeMerge false |
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234 | flagTwoStageMerging true |
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235 | |
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236 | ### WCS PARAMETERS |
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237 | #* spectralType [string] {a valid WCS type} -- An alternative spectral WCS type to use for spectral transformations. |
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238 | #* restFrequency [float] {any} -- A value of the rest frequency to override any provided in the FITS header. Negative values will be ignored. |
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239 | #* spectralUnits [string] {valid units string} -- What units you want the spectral axis to be plotted in and values quoted in (including the units of integrated flux) |
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240 | |
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241 | spectralType "" |
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242 | restFrequency -1 |
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243 | spectralUnits "" |
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244 | |
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245 | ### OTHER PARAMETERS |
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246 | #* verbose [bool] {true or false, or 1 or 0} -- Whether to provide progress indicators on the terminal during execution |
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247 | #* drawBorders [bool] {true or false, or 1 or 0} -- Whether to draw borders around the detections on the moment maps in the output. |
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248 | #* drawBlankEdges [bool] {true or false, or 1 or 0} -- Whether to draw an outline around any BLANK regions in the moment maps and image cutouts. |
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249 | #* spectralMethod [string] {either 'peak' or 'sum'} -- How to plot the spectra in the output -- the spectrum of the peak pixel ("peak" -- the default), or integrated over all spatial pixels present ("sum") |
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250 | #* pixelCentre [string] {one of 'centroid', 'average' or 'peak'} -- Which option to use for quoting the centre of the detection. Options are: centroid (flux-weighted average position), average (simple average with no weighting), peak (brightest pixel). |
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251 | #* sortingParam [string] {one of 'xvalue', 'yvalue', 'zvalue', 'ra', 'dec', 'vel', 'w50', 'iflux', 'pflux', 'snr'} -- The parameter by which the final detection list is sorted |
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252 | |
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253 | verbose true |
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254 | drawBorders true |
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255 | drawBlankEdges true |
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256 | spectralMethod peak |
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257 | pixelCentre centroid |
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258 | sortingParam vel |
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