source: trunk/InputComplete @ 16

# 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 

imageFile       your-file-here
flagSubsection  1
subsection      [*,*,*]

# 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
# flagMaps -- save postscript versions of the detection and 1st moment maps?
# detectionMap, momentMap -- the postscript files produced.

flagLog         1
logFile         logfile.txt
outFile         results.txt
spectraFile     spectra.ps
flagOutputRecon 0
flagOutputResid 0
flagVOT         0
votFile         results.xml
flagMaps        1
detectionMap    latest-detection-map.ps
momentMap       latest-moment-map.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
flagBaseline    1
flagMW          1
minMW           75
maxMW           112

# GENERAL DETECTION RELATED
# minPix -- Minimum number of pixels for a detected object to be counted
# 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

minPix          3
snrCut          2.5
flagGrowth      0
growthCut       1.5

# 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        5.
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        0.05

# 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.

flagAdjacent    1
threshSpatial   3
threshVelocity  7
minChannels     4

# 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.
verbose         1
drawBorders     1