source: trunk/python/asaplinefind.py@ 369

Last change on this file since 369 was 369, checked in by vor010, 20 years ago

SDLineFinder: bug corrections, setOption method
has been added + fitting baseline at each iterations to cope with bad
baselines

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 3.0 KB
Line 
1import _asap
2
3class linefinder:
4 """
5 The class for automated spectral line search in ASAP.
6 """
7
8 def __init__(self):
9 """
10 Create a line finder object.
11 """
12 self.finder = _asap.linefinder()
13 return
14
15 def set_options(self,threshold=1.7320508075688772,min_nchan=3,
16 avg_limit=8,box_size=0.2):
17 """
18 Set the parameters of the algorithm
19 Parameters:
20 threshold a single channel S/N ratio above which the
21 channel is considered to be a detection
22 Default is sqrt(3), which together with
23 min_nchan=3 gives a 3-sigma criterion
24 min_nchan a minimal number of consequtive channels,
25 which should satisfy a threshold criterion to
26 be a detection. Default is 3.
27 avg_limit A number of consequtive channels not greater than
28 this parameter can be averaged to search for
29 broad lines. Default is 8.
30 box_size A running mean box size specified as a fraction
31 of the total spectrum length. Default is 1/5
32 Note: For bad baselines threshold should be increased,
33 and avg_limit decreased (or even switched off completely by
34 setting this parameter to 1) to avoid detecting baseline
35 undulations instead of real lines.
36 """
37 self.finder.setoptions(threshold,min_nchan,avg_limit,box_size)
38 return
39
40 def set_scan(self,scan,mask=None,edge=(0,0)):
41 """
42 Set the 'data' (scantable) to work with.
43 Parameters:
44 scan: a scantable
45 mask: an optional mask retreived from scantable
46 edge: an optional number of channel to drop at
47 the edge of spectrum. If only one value is
48 specified, the same number will be dropped from
49 both sides of the spectrum. Default is to keep
50 all channels
51 """
52 if not scan:
53 raise RuntimeError, 'Please give a correct scan'
54 if len(edge)>2:
55 raise RuntimeError, "The edge parameter should have two \
56 or less elements"
57 if mask is None:
58 from numarray import ones
59 self.finder.setscan(scan,ones(scan.nchan()),edge)
60 else:
61 self.finder.setscan(scan,mask,edge)
62 return
63 def find_lines(self):
64 """
65 Search for spectral lines in the scan assigned in set_scan.
66 A number of lines found will be returned
67 """
68 return self.finder.findlines()
69 def get_mask(self,invert=False):
70 """
71 Get the mask to mask out all lines that have been found (default)
72
73 Parameters:
74 invert if True, only channels belong to lines will be unmasked
75
76 Note: all channels originally masked by the input mask or
77 dropped out by the edge parameter will still be excluded
78 regardless on the invert option
79 """
80 return self.finder.getmask(invert)
81 def get_ranges(self,defunits=True):
82 """
83 Get ranges (start and end channels or velocities) for all spectral
84 lines found.
85
86 Parameters:
87 defunits if True (default), the range will use the same units
88 as set for the scan (e.g. LSR velocity)
89 if False, the range will be expressed in channels
90 """
91 return self.finder.getlineranges(defunits)
Note: See TracBrowser for help on using the repository browser.