source: trunk/InputComplete @ 1150

# 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.  THERE IS NO DEFAULT FOR THIS.
# 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
# usePrevious -- whether to read the list of detected objects from a previously-
#                created log file
# objectList -- the list of objects to plot in individual plots: used with usePrevious=true

imageFile       your-file-here
flagSubsection  false
subsection      [*,*,*]
flagReconExists false
reconFile       your-reconstructed-file-here
flagSmoothExists false
smoothFile      your-smoothed-file-here
usePrevious     false
objectList      *

# 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.
# flagWriteBinaryCatalogue -- whether to create a binary catalogue
#                             indicating the pixel locations of
#                             detected objects (for later reuse)
# binaryCatalogue -- the file containing the binary source catalogue
# flagPlotSpectra -- whether to produce a file showing spectra of each detection
# spectraFile -- the postscript file of spectra
# flagPlotIndividualSpectra -- whether to also write individual source
#                              spectra postscript files
# flagTextSpectra -- whether to save a text file detailing the spectra
#                    of each source
# spectraTextFile -- the file in which to save the text-formatted spectra
# flagOutputBaseline -- whether to save a FITS file containing the cube of baseline values
# fileOutputBaseline -- the filename for the baseline FITS file. If not given, it defaults 
#                   to the format shown (for input file image.fits)
# flagOutputMomentMap -- whether to save a FITS file containing the moment-0 map
# fileOutputMomentMap -- the filename for the moment-0 FITS file. If not given, it defaults 
#                   to the format shown (for input file image.fits)
# flagOutputMomentMask -- whether to save a FITS file containing the
#                         moment-0 mask image
# fileOutputMomentMask -- the filename for the moment-0 mask FITS file. If not given, it defaults 
#                   to the format shown (for input file image.fits)
# flagOutputMask -- whether to save a FITS file containing a mask
#                   array, showing the locations of detected objects
# fileOutputMask -- the filename for the mask file. If not given, it defaults 
#                   to the format shown (for input file image.fits)
# flagMaskWithObjectNum -- if true, the detected pixels in the mask array have 
#                          the object ID number, else they all have the value 1.
# flagOutputSmooth -- whether to save the smoothed arrays as a FITS file
# fileOutputSmooth -- 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.
# flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays
#                          as FITS files
# fileOutputRecon/Resid -- 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.
# 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
# flagDS9 -- make a DS9 region file of the results?  
# ds9File -- the file to put it in
# flagCasa -- make a CASA region file of the results?  
# casaFile -- 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         false
logFile         duchamp-Logfile.txt
outFile         duchamp-Results.txt
flagSeparateHeader false
headerFile      duchamp-Results.hdr
flagWriteBinaryCatalogue true
binaryCatalogue duchamp-Catalogue.dpc
flagPlotSpectra true
spectraFile     duchamp-Spectra.ps
flagPlotIndividualSpectra false
flagTextSpectra false
spectraTextFile duchamp-Spectra.txt
flagOutputBaseline  false
fileOutputBaseline  image.BASE.fits
flagOutputMomentMap  false
fileOutputMomentMap  image.MOM0.fits
flagOutputMomentMask  false
fileOutputMomentMask  image.MOM0MASK.fits
flagOutputMask  false
fileOutputMask  image.MASK.fits
flagMaskWithObjectNum false
flagOutputSmooth false
fileOutputSmooth image.SMOOTH-ND-X.fits
flagOutputRecon false
fileOutputRecon image.RECON-A-B-C-D.fits
flagOutputResid false
fileOutputResid image.RESID-A-B-C-D.fits
flagVOT         false
votFile         duchamp-Results.xml
flagKarma       false
karmaFile       duchamp-Results.ann
flagDS9         false
ds9File         duchamp-Results.reg
flagCasa        false
casaFile        duchamp-Results.crf
flagMaps        true
detectionMap    duchamp-DetectionMap.ps
momentMap       duchamp-MomentMap.ps
flagXOutput     true
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        false
flagMW          false
minMW           75
maxMW           112
flagBaseline    false

# 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
# growthThreshold -- The lower threshold, used in conjunction with "threshold"
# beamarea -- 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.
# beamFWHM -- 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.
# searchType -- 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. 

flagStatSec     false
StatSec         [*,*,*]
flagRobustStats true
flagNegative    false
snrCut          5.
threshold       0.
flagGrowth      false
growthCut       3.
growthThreshold 0.
beamArea        0.
beamFWHM        0.
searchType      spatial

# 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.
# reconConvergence -- The relative change in the residual rms must be
#                     less than this to stop the a trous iterations.
# 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.
reconConvergence 0.005
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         -1.
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.
# FDRnumCorChan -- The number of neighbouring channels that are
#                  correlated. This is used in the FDR algorithm

flagFDR         false
alphaFDR        0.01
FDRnumCorChan   2

# 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
# minVoxels -- Minimum number of voxels a detected object must have for it to be 
#              counted
# flagRejectBeforeMerge -- If true, reject sources for not meeting the above 
#                          criteria before the merging stage
# flagTwoStageMerging -- 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)

flagAdjacent           true
threshSpatial          3
threshVelocity         7
minChannels            3
minPix                 2
minVoxels              4
flagRejectBeforeMerge  false
flagTwoStageMerging    true

# WCS PARAMETERS
# 
# spectralType -- an alternative spectral WCS type to use for spectral 
#                 transformations.
# restFrequency -- a value of the rest frequency to override any
#                  provided in the FITS header
# spectralUnits -- what units you want the spectral axis to be plotted in and 
#                   values quoted in (including the units of integrated flux)

spectralType   no-default
restFrequency  -1
spectralUnits  no-default

# 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")
# pixelCentre -- which option to use for quoting the centre of the detection. 
#                 Options are: centroid, average, peak.
# sortingParam -- which parameter to sort the final detection list on.
#                  Options are: xvalue, yvalue, zvalue, ra, dec, vel, w50, 
#                                iflux,  pflux, snr. 

verbose         true
drawBorders     true
drawBlankEdges  true
spectralMethod  peak
pixelCentre     centroid
sortingParam    vel