source: tags/release-0.9.2/InputComplete

# 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 image exists as a FITS file
#                    (ie. it has been saved from a previous run of Duchamp)
# reconFile -- the location of the FITS file containing the reconstructed image

imageFile       your-file-here
flagSubsection  0
subsection      [*,*,*]
flagReconExists 0
reconFile       your-reconstructed-file-here

# OUTPUT RELATED
# flagLog -- log the intermediate results?   logfile-- the file to put that in.
# outFile -- the final output list. 
# spectraFile -- the postscript file of spectra
# 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.

flagLog         1
logFile         duchamp-Logfile.txt
outFile         duchamp-Results.txt
spectraFile     duchamp-Spectra.ps
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

# FIXING UP THE CUBE
# flagBlankPix -- whether to replace & ignore blank pixels. 
# blankPixValue -- what value they should take. This is overridden by FITS header information.
# flagBaseline -- whether to subtract spectral baselines before searching
# flagMW -- whether to excise a range of channels (to remove Milky Way emission)
# minMW, maxMW -- the first and last channels to be excised

flagBlankPix    1
blankPixValue   -8.00061
flagMW          0
minMW           75
maxMW           112
flagBaseline    0

# GENERAL DETECTION RELATED
# flagNegative -- Are the features being searched for negative (set to true) or positive (false)?
# snrCut --  How many sigma above mean is a detection when sigma-clipping
# flagGrowth -- Should the detections be "grown" to a lower significance value?
# growthCut -- The lower threshold used when growing detections

flagNegative    0
snrCut          3.
flagGrowth      0
growthCut       2.

# RECONSTRUCTION RELATED
# flagATrous -- Whether or not to do the reconstruction before searching
# scaleMin -- The minimum scale (starts at 1) to be included in the reconstruction
# 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      1
scaleMin        1
snrRecon        4.
filterCode      2

# 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 for a detected object 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.
# 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")
        
verbose         1
drawBorders     1
spectralMethod  peak