# FULL PARAMETER LIST # ------------------- # # This file contains the full list of user-definable parameters. They are # grouped here according to their use, and the values quoted are the defaults: # if a given parameter is not included in your parameter file, this is the # value it will take. # # # INPUT RELATED # imageFile -- the FITS image. # flagSubsection -- whether to get a subsection of that image. # subsection -- the subsection to read in, in format [x1:x2,y1:y2,z1:z2], # or * to indicate the full range # flagReconExists -- set to true if the reconstructed cube exists as a FITS # file (ie. it has been saved from a previous Duchamp run) # reconFile -- the location of the FITS file containing the reconstructed cube # flagSmoothExists -- set to true if the smoothed cube exists as a FITS # file (ie. it has been saved from a previous Duchamp run) # smoothFile -- the location of the FITS file containing the smoothed # cube # beamsize -- the size of the beam in pixels. This value is overridden # by the BMAJ, BMIN, BPA header parameters if present. imageFile your-file-here flagSubsection 0 subsection [*,*,*] flagReconExists 0 reconFile your-reconstructed-file-here flagSmoothExists 1 smoothFile your-smoothed-file-here beamsize 10. # OUTPUT RELATED # flagLog -- log the intermediate results? # logfile-- the file to put that in. # outFile -- the final output list. # flagSeparateHeader -- 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). # headerFile -- the file to write the header information to. # spectraFile -- the postscript file of spectra # flagTextSpectra -- whether to save a text file detailing the spectra # of each source # spectraTextFile -- the file in which to save the text-formatted spectra # flagOutputMask -- whether to save a FITS file containing a mask # array, showing the locations of detected objects # flagOutputSmooth -- whether to save the smoothed arrays as a FITS file # flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays # as FITS files # flagVOT -- make a VOTable file of the results? # votFile -- the file to put it in # flagKarma -- make a Karma annotation file of the results? # karmaFile -- the file to put it in # flagMaps -- save postscript versions of the detection and 0th moment maps? # detectionMap, momentMap -- the postscript files produced. # flagXOutput -- display the moment map in a pgplot window # newFluxUnits -- brightness units to convert the array values to # (eg. from Jy/beam to mJy/beam) # precFlux -- Desired precision for Flux value in outputs. # precVel -- Desired precision for Velocity/Frequency value in outputs. # precSNR -- Desired precision for peak SNR value in ouputs. flagLog 0 logFile duchamp-Logfile.txt outFile duchamp-Results.txt flagSeparateHeader 0 headerFile duchamp-Results.hdr spectraFile duchamp-Spectra.ps flagTextSpectra 0 spectraTextFile duchamp-Spectra.txt flagOutputMask 0 flagOutputSmooth 0 flagOutputRecon 0 flagOutputResid 0 flagVOT 0 votFile duchamp-Results.xml flagKarma 0 karmaFile duchamp-Results.ann flagMaps 1 detectionMap duchamp-DetectionMap.ps momentMap duchamp-MomentMap.ps flagXOutput 1 newFluxUnits no-default precFlux 3 precVel 3 precSNR 2 # FIXING UP THE CUBE # flagTrim -- whether to trim blank pixels from the edges of the cube. # flagBaseline -- whether to subtract spectral baselines before searching # flagMW -- ignore a range of channels (to remove Milky Way emission)? # minMW, maxMW -- the first and last channels to be ignored flagTrim 0 flagMW 0 minMW 75 maxMW 112 flagBaseline 0 # GENERAL DETECTION RELATED # flagStatSec -- Whether to only use a subsection of the cube to calculate # the statistics. # StatSec -- The subsection used for statistics calculations. It has the # same format as the pixel subsection. # flagRobustStats -- Shall we use robust statistics to characterise # the noise in the image? # flagNegative -- Are the features being searched for negative (set to true) # or positive (false -- the default)? # snrCut -- How many sigma above mean is a detection when sigma-clipping # threshold -- 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. # flagGrowth -- Should the detections be "grown" to a lower significance value? # growthCut -- The lower threshold used when growing detections flagStatSec 0 StatSec [*,*,*] flagRobustStats 1 flagNegative 0 snrCut 3. threshold 0. flagGrowth 0 growthCut 2. # RECONSTRUCTION RELATED # flagATrous -- Whether or not to do the reconstruction before searching # reconDim -- The number of dimensions in which to perform the reconstruction. # scaleMin -- The minimum scale (starts at 1) to be included in the # reconstruction # scaleMax -- 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. # snrRecon -- The threshold used in filtering the wavelet coefficient arrays. # filterCode -- 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 2. flagATrous false reconDim 1 scaleMin 1 scaleMax 0 snrRecon 4. filterCode 1 # SMOOTHING # flagSmooth -- whether to smooth the cube. # smoothType -- either "spectral" or "spatial" # hanningWidth -- the width parameter of the Hanning (spectral smoothing) # function # kernMaj -- the FWHM of the major axis of the 2D spatial smoothing gaussian # kernMin -- the FWHM of the minor axis of the 2D spatial smoothing gaussian # kernPA -- the position angle of the major axis of the 2D spatial # smoothing gaussian flagSmooth false smoothType spectral hanningWidth 5 kernMaj 3. kernMin 3. kernPA 0. # FALSE DISCOVERY RATE METHOD # flagFDR -- Whether or not to use the false discovery rate method instead of # simple sigma clipping. # alphaFDR -- The "alpha" parameter for the FDR method -- what desired # percentage of discoveries will be false. Expressed as a decimal. flagFDR 0 alphaFDR 0.01 # MERGING PARAMETERS # flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects # are to be merged. # threshSpatial -- If flagAdjacent=false, this is the maximum spatial # separation between objects for them to be merged. # threshVelocity -- The maximum channel separation between objects for them # to be merged. # minChannels -- The minimum number of consecutive channels an object must have # for it to be accepted. # minPix -- Minimum number of spatial pixels a detected object must have for # it to be counted flagAdjacent 1 threshSpatial 3 threshVelocity 7 minChannels 3 minPix 2 # OTHER PARAMETERS # verbose -- whether to provide progress indicators on the terminal during # execution # drawBorders -- whether to draw borders around the detections on the moment # maps in the output. # drawBlankEdges -- whether to draw an outline around any BLANK regions in the # moment maps and image cutouts. # spectralMethod -- 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") # spectralUnits -- what units you want the spectral axis to be plotted in and # values quoted in (including the units of integrated flux) # pixelCentre -- which option to use for quoting the centre of the detection. # Options are: centroid, average, peak. verbose 1 drawBorders 1 drawBlankEdges 1 spectralMethod peak spectralUnits km/s pixelCentre centroid