source: branches/fitshead-branch/InputComplete @ 92

Last change on this file since 92 was 92, checked in by Matthew Whiting, 18 years ago

The FitsHeader? class now works fine (and is quicker than before the change!)
Have updated the plotting and param code, as well as the relevant documentation
and the reference to the spectralUnits parameter in InputComplete?.
Have also fixed the code drawing the scale bar in the moment cutout, so that
the length of the bar is indicated.

File size: 4.6 KB
Line 
1# FULL PARAMETER LIST
2# -------------------
3#
4# This file contains the full list of user-definable parameters. They are grouped
5#  here according to their use, and the values quoted are the defaults -- if a
6#  given parameter is not included in your parameter file, this is the value it
7#  will take.
8#
9#
10# INPUT RELATED
11# imageFile -- the FITS image.
12# flagSubsection -- whether to get a subsection of that image.
13# subsection -- the subsection to read in, in format [x1:x2,y1:y2,z1:z2],
14#               or * to indicate the full range
15# flagReconExists -- set to true if the reconstructed image exists as a FITS file
16#                    (ie. it has been saved from a previous run of Duchamp)
17# reconFile -- the location of the FITS file containing the reconstructed image
18
19imageFile       your-file-here
20flagSubsection  0
21subsection      [*,*,*]
22flagReconExists 0
23reconFile       your-reconstructed-file-here
24
25# OUTPUT RELATED
26# flagLog -- log the intermediate results?   logfile-- the file to put that in.
27# outFile -- the final output list.
28# spectraFile -- the postscript file of spectra
29# flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays as FITS files
30# flagVOT -- make a VOTable file of the results?   votFile -- the file to put it in
31# flagKarma -- make a Karma annotation file of the results?  karmaFile -- the file to put it in
32# flagMaps -- save postscript versions of the detection and 0th moment maps?
33# detectionMap, momentMap -- the postscript files produced.
34
35flagLog         1
36logFile         duchamp-Logfile.txt
37outFile         duchamp-Results.txt
38spectraFile     duchamp-Spectra.ps
39flagOutputRecon 0
40flagOutputResid 0
41flagVOT         0
42votFile         duchamp-Results.xml
43flagKarma       0
44karmaFile       duchamp-Results.ann
45flagMaps        1
46detectionMap    duchamp-DetectionMap.ps
47momentMap       duchamp-MomentMap.ps
48
49# FIXING UP THE CUBE
50# flagBlankPix -- whether to replace & ignore blank pixels.
51# blankPixValue -- what value they should take. This is overridden by FITS header information.
52# flagBaseline -- whether to subtract spectral baselines before searching
53# flagMW -- whether to excise a range of channels (to remove Milky Way emission)
54# minMW, maxMW -- the first and last channels to be excised
55
56flagBlankPix    1
57blankPixValue   -8.00061
58flagMW          0
59minMW           75
60maxMW           112
61flagBaseline    0
62
63# GENERAL DETECTION RELATED
64# flagNegative -- Are the features being searched for negative (set to true) or positive (false)?
65# snrCut --  How many sigma above mean is a detection when sigma-clipping
66# flagGrowth -- Should the detections be "grown" to a lower significance value?
67# growthCut -- The lower threshold used when growing detections
68
69flagNegative    0
70snrCut          3.
71flagGrowth      0
72growthCut       2.
73
74# RECONSTRUCTION RELATED
75# flagATrous -- Whether or not to do the reconstruction before searching
76# scaleMin -- The minimum scale (starts at 1) to be included in the reconstruction
77# snrRecon -- The threshold used in filtering the wavelet coefficient arrays.
78# filterCode -- The code number for the choice of filter to be used in the reconstruction:
79# 1 = B3-spline filter, 2 = Triangle function, 3 = Haar wavelet. Other numbers default to 2.
80
81flagATrous      1
82scaleMin        1
83snrRecon        4.
84filterCode      2
85
86# FALSE DISCOVERY RATE METHOD
87# flagFDR -- Whether or not to use the false discovery rate method instead of
88#   simple sigma clipping.
89# alphaFDR -- The "alpha" parameter for the FDR method -- what desired percentage
90#   of discoveries will be false. Expressed as a decimal.
91
92flagFDR         0
93alphaFDR        0.01
94
95# MERGING PARAMETERS
96# flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects are to be merged.
97# threshSpatial -- If flagAdjacent=false, this is the maximum spatial separation between objects
98#    for them to be merged.
99# threshVelocity -- The maximum channel separation between objects for them to be merged.
100# minChannels -- The minimum number of consecutive channels an object must have for it to be accepted.
101# minPix -- Minimum number of spatial pixels for a detected object to be counted
102
103flagAdjacent    1
104threshSpatial   3
105threshVelocity  7
106minChannels     3
107minPix          2
108
109# OTHER PARAMETERS
110# verbose -- whether to provide progress indicators on the terminal during execution
111# drawBorders -- whether to draw borders around the detections on the moment maps in the output.
112# spectralMethod -- how to plot the spectra in the output -- the spectrum of the peak pixel
113#      ("peak" -- the default), or integrated over all spatial pixels present ("sum")
114# spectralUnits -- what units you want the spectral axis to be plotted in and values quoted in
115#      (including the units of integrated flux)
116       
117verbose         1
118drawBorders     1
119spectralMethod  peak
120spectralUnits   km/s
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