Ticket #60: input

#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

imageFile       ../../image/M33.fits
flagSubsection  1
Subsection      [*,141:396,6:68]
flagReconExists 0
reconFile       your-reconstructed-file-here
flagSmoothExists        0
reconFile       your-smoothed-file-here

# 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

flagLog         0
logFile         M33_Log.txt
outFile         M33_Results.txt
flagSeparateHeader 0
headerFile      M33_Results.hdr
spectraFile     M33_Spectra.ps
flagTextSpectra 1
spectraTextFile M33_Spectra.txt
flagOutputMask  0
flagOutputSmooth 0
flagOutputRecon 0
flagOutputResid 0
flagVOT         0
votFile         M33_Results.xml
flagKarma       0
karmaFile       M33_Results.ann
flagMaps        1
detectionMap    M33_DetectionMap.ps
momentMap       M33_MomentMap.ps
flagXOutput     0

# FIXING UP THE CUBE
# flagTrim -- whether to trim blank pixels from the edges of the cube.
# blankPixValue -- what value they should take. This is overridden by 
#                  FITS header information.
# 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           241
maxMW           400
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         [100,100,241:300]
flagRobustStats 1
flagNegative    0
snrCut          3
#threshold      0.4
flagGrowth      0
growthCut       2.8
beamSize        3.4

# 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
# 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      true
reconDim        1
scaleMin        1
snrRecon        3.
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    0
threshSpatial   3
threshVelocity  2
minChannels     3
minPix          14

# 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  sum
spectralUnits   km/s
pixelCentre     centroid

#Use Prvious Paramters
usePrevious     true