source: branches/Release-1-fixes/python/asaplinefind.py@ 1859

Last change on this file since 1859 was 522, checked in by vor010, 20 years ago

Line finder - edge parameter workaround

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File size: 4.7 KB
Line 
1import _asap
2
3class linefinder:
4 """
5 The class for automated spectral line search in ASAP.
6
7 Example:
8 fl=linefinder()
9 fl.set_scan(sc,edge=(50,))
10 fl.set_options(threshold=3)
11 nlines=fl.find_lines()
12 if nlines!=0:
13 print "Found ",nlines," spectral lines"
14 print fl.get_ranges(False)
15 else:
16 print "No lines found!"
17 sc2=sc.poly_baseline(fl.get_mask(),7)
18
19 The algorithm involves a simple threshold criterion. The line is
20 considered to be detected if a specified number of consequtive
21 channels (default is 3) is brighter (with respect to the current baseline
22 estimate) than the threshold times the noise level. This criterion is
23 applied in the iterative procedure updating baseline estimate and trying
24 reduced spectral resolutions to detect broad lines as well. The off-line
25 noise level is determined at each iteration as an average of 80% of the
26 lowest variances across the spectrum (i.e. histogram equalization is
27 used to avoid missing weak lines if strong ones are present). For
28 bad baseline shapes it is reccommended to increase the threshold and
29 possibly switch the averaging option off (see set_options) to
30 detect strong lines only, fit a high order baseline and repeat the line
31 search.
32
33 """
34
35 def __init__(self):
36 """
37 Create a line finder object.
38 """
39 self.finder = _asap.linefinder()
40 return
41
42 def set_options(self,threshold=1.7320508075688772,min_nchan=3,
43 avg_limit=8,box_size=0.2):
44 """
45 Set the parameters of the algorithm
46 Parameters:
47 threshold a single channel S/N ratio above which the
48 channel is considered to be a detection
49 Default is sqrt(3), which together with
50 min_nchan=3 gives a 3-sigma criterion
51 min_nchan a minimal number of consequtive channels,
52 which should satisfy a threshold criterion to
53 be a detection. Default is 3.
54 avg_limit A number of consequtive channels not greater than
55 this parameter can be averaged to search for
56 broad lines. Default is 8.
57 box_size A running mean box size specified as a fraction
58 of the total spectrum length. Default is 1/5
59 Note: For bad baselines threshold should be increased,
60 and avg_limit decreased (or even switched off completely by
61 setting this parameter to 1) to avoid detecting baseline
62 undulations instead of real lines.
63 """
64 self.finder.setoptions(threshold,min_nchan,avg_limit,box_size)
65 return
66
67 def set_scan(self,scan,mask=None,edge=(0,0)):
68 """
69 Set the 'data' (scantable) to work with.
70 Parameters:
71 scan: a scantable
72 mask: an optional mask retreived from scantable
73 edge: an optional number of channel to drop at
74 the edge of spectrum. If only one value is
75 specified, the same number will be dropped from
76 both sides of the spectrum. Default is to keep
77 all channels
78 """
79 if not scan:
80 raise RuntimeError, 'Please give a correct scan'
81
82 if isinstance(edge,int):
83 edge=(edge,)
84
85 from asap import _is_sequence_or_number as _is_valid
86
87 if not _is_valid(edge, int):
88 raise RuntimeError, "Parameter 'edge' has to be an integer or \
89 a pair of integers specified as a tuple"
90
91 if len(edge)>2:
92 raise RuntimeError, "The edge parameter should have two \
93 or less elements"
94 if mask is None:
95 from numarray import ones
96 self.finder.setscan(scan,ones(scan.nchan()),tuple(edge))
97 else:
98 self.finder.setscan(scan,mask,tuple(edge))
99 return
100 def find_lines(self,nRow=0):
101 """
102 Search for spectral lines in the scan assigned in set_scan.
103 Current Beam/IF/Pol is used, Row is specified by parameter
104 A number of lines found will be returned
105 """
106 return self.finder.findlines(nRow)
107 def get_mask(self,invert=False):
108 """
109 Get the mask to mask out all lines that have been found (default)
110
111 Parameters:
112 invert if True, only channels belong to lines will be unmasked
113
114 Note: all channels originally masked by the input mask or
115 dropped out by the edge parameter will still be excluded
116 regardless on the invert option
117 """
118 return self.finder.getmask(invert)
119 def get_ranges(self,defunits=True):
120 """
121 Get ranges (start and end channels or velocities) for all spectral
122 lines found.
123
124 Parameters:
125 defunits if True (default), the range will use the same units
126 as set for the scan (e.g. LSR velocity)
127 if False, the range will be expressed in channels
128 """
129 if (defunits):
130 return self.finder.getlineranges()
131 else:
132 return self.finder.getlinerangesinchannels()
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