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