[1324] | 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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[1330] | 37 | #* logFile [string] {filename} -- The file to put that in. |
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[1324] | 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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[1330] | 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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[1324] | 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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[1328] | 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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[1324] | 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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[1328] | 116 | annotationType borders |
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[1324] | 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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[1328] | 129 | #* flaggedChannels [string] {comma-separated list of channels} -- List of channels to ignore in the source-finding |
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[1324] | 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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[1328] | 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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[1324] | 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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[1328] | 171 | #* snrRecon [float] {> 0} -- The threshold used in filtering the wavelet coefficient arrays. |
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[1324] | 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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