source: branches/pixel-map-branch/InputComplete @ 254

Last change on this file since 254 was 254, checked in by Matthew Whiting, 17 years ago

Added functionality to use only a subsection in the statistics calculations. This includes:

  • A new Section class.
  • New input parameters.
  • Altering the setCubeStats() function to test for this.
  • Some documentation on the new parameters.
File size: 6.1 KB
Line 
1# FULL PARAMETER LIST
2# -------------------
3#
4# This file contains the full list of user-definable parameters. They are
5#  grouped here according to their use, and the values quoted are the defaults:
6#  if a given parameter is not included in your parameter file, this is the
7#  value it 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 cube exists as a FITS
16#                    file (ie. it has been saved from a previous Duchamp run)
17# reconFile -- the location of the FITS file containing the reconstructed cube
18# flagSmoothExists -- set to true if the smoothed cube exists as a FITS
19#                    file (ie. it has been saved from a previous Duchamp run)
20# smoothFile -- the location of the FITS file containing the smoothed cube
21
22imageFile       your-file-here
23flagSubsection  0
24subsection      [*,*,*]
25flagReconExists 0
26reconFile       your-reconstructed-file-here
27flagReconExists 1
28reconFile       your-smoothed-file-here
29
30# OUTPUT RELATED
31# flagLog -- log the intermediate results?   
32# logfile-- the file to put that in.
33# outFile -- the final output list.
34# spectraFile -- the postscript file of spectra
35# flagOutputSmooth -- whether to save the smoothed arrays as a FITS file
36# flagOutputRecon/Resid -- whether to save the reconstruction & residual arrays
37#                          as FITS files
38# flagVOT -- make a VOTable file of the results? 
39# votFile -- the file to put it in
40# flagKarma -- make a Karma annotation file of the results? 
41# karmaFile -- the file to put it in
42# flagMaps -- save postscript versions of the detection and 0th moment maps?
43# detectionMap, momentMap -- the postscript files produced.
44# flagXOutput -- display the moment map in a pgplot window
45
46flagLog         1
47logFile         duchamp-Logfile.txt
48outFile         duchamp-Results.txt
49spectraFile     duchamp-Spectra.ps
50flagOutputSmooth 0
51flagOutputRecon 0
52flagOutputResid 0
53flagVOT         0
54votFile         duchamp-Results.xml
55flagKarma       0
56karmaFile       duchamp-Results.ann
57flagMaps        1
58detectionMap    duchamp-DetectionMap.ps
59momentMap       duchamp-MomentMap.ps
60flagXOutput     1
61
62# FIXING UP THE CUBE
63# flagBlankPix -- whether to replace & ignore blank pixels.
64# blankPixValue -- what value they should take. This is overridden by
65#                  FITS header information.
66# flagBaseline -- whether to subtract spectral baselines before searching
67# flagMW -- ignore a range of channels (to remove Milky Way emission)?
68# minMW, maxMW -- the first and last channels to be ignored
69
70flagBlankPix    1
71blankPixValue   -8.00061
72flagMW          0
73minMW           75
74maxMW           112
75flagBaseline    0
76
77# GENERAL DETECTION RELATED
78# flagNegative -- Are the features being searched for negative (set to true)
79#                 or positive (false -- the default)?
80# snrCut --  How many sigma above mean is a detection when sigma-clipping
81# threshold -- The threshold flux dividing source and non-source. Used instead
82#              of calculating it from the cube's statistics. If not specified,
83#              it will be calculated.
84# flagGrowth -- Should the detections be "grown" to a lower significance value?
85# growthCut -- The lower threshold used when growing detections
86
87flagStatSec     0
88StatSec         [*,*,*]
89flagNegative    0
90snrCut          3.
91threshold       0.
92flagGrowth      0
93growthCut       2.
94
95# RECONSTRUCTION RELATED
96# flagATrous -- Whether or not to do the reconstruction before searching
97# reconDim -- The number of dimensions in which to perform the reconstruction.
98# scaleMin -- The minimum scale (starts at 1) to be included in the
99#              reconstruction
100# snrRecon -- The threshold used in filtering the wavelet coefficient arrays.
101# filterCode -- The code number for the choice of filter to be used in the
102#               reconstruction:  1 = B3-spline filter, 2 = Triangle function,
103#                                3 = Haar wavelet. Other numbers default to 2.
104
105flagATrous      1
106reconDim        3
107scaleMin        1
108snrRecon        4.
109filterCode      1
110
111# HANNING SMOOTHING
112# flagSmooth -- whether to Hanning-smooth the spectral dimension of the cube.
113# hanningWidth -- the width parameter of the Hanning smoothing function
114
115flagSmooth      false
116hanningWidth    5
117
118# FALSE DISCOVERY RATE METHOD
119# flagFDR -- Whether or not to use the false discovery rate method instead of
120#   simple sigma clipping.
121# alphaFDR -- The "alpha" parameter for the FDR method -- what desired
122#             percentage of discoveries will be false. Expressed as a decimal.
123
124flagFDR         0
125alphaFDR        0.01
126
127# MERGING PARAMETERS
128# flagAdjacent -- Whether to use the "adjacent criterion" to judge if objects
129#                  are to be merged.
130# threshSpatial -- If flagAdjacent=false, this is the maximum spatial
131#                   separation between objects for them to be merged.
132# threshVelocity -- The maximum channel separation between objects for them
133#                   to be merged.
134# minChannels -- The minimum number of consecutive channels an object must have
135#                 for it to be accepted.
136# minPix -- Minimum number of spatial pixels a detected object must have for
137#            it to be counted
138
139flagAdjacent    1
140threshSpatial   3
141threshVelocity  7
142minChannels     3
143minPix          2
144
145# OTHER PARAMETERS
146# verbose -- whether to provide progress indicators on the terminal during
147#             execution
148# drawBorders -- whether to draw borders around the detections on the moment
149#                 maps in the output.
150# drawBlankEdges -- whether to draw an outline around any BLANK regions in the
151#                    moment maps and image cutouts.
152# spectralMethod -- how to plot the spectra in the output -- the spectrum of
153#                    the peak pixel ("peak" -- the default), or integrated over
154#                    all spatial pixels present ("sum")
155# spectralUnits -- what units you want the spectral axis to be plotted in and
156#                   values quoted in (including the units of integrated flux)
157
158verbose         1
159drawBorders     1
160drawBlankEdges  1
161spectralMethod  peak
162spectralUnits   km/s
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