| 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 | return
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| 76 | def find_lines(self,nRow=0,mask=None,edge=(0,0)):
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| 77 | """
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| 78 | Search for spectral lines in the scan assigned in set_scan.
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| 79 | Parameters:
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| 80 | nRow: a row in the scantable to work with
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| 81 | mask: an optional mask (e.g. retreived from scantable)
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| 82 | edge: an optional number of channels to drop at
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| 83 | the edge of the spectrum. If only one value is
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| 84 | specified, the same number will be dropped from
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| 85 | both sides of the spectrum. Default is to keep
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| 86 | all channels
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| 87 | A number of lines found will be returned
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| 88 | """
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| 89 | if isinstance(edge,int):
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| 90 | edge=(edge,)
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| 91 |
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| 92 | from asap import _is_sequence_or_number as _is_valid
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| 93 |
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| 94 | if not _is_valid(edge, int):
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| 95 | raise RuntimeError, "Parameter 'edge' has to be an integer or \
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| 96 | a pair of integers specified as a tuple"
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| 97 |
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| 98 | if len(edge)>2:
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| 99 | raise RuntimeError, "The edge parameter should have two \
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| 100 | or less elements"
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| 101 | if mask is None:
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| 102 | from numarray import ones
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| 103 | return self.finder.findlines(ones(scan.nchan(nRow)),list(edge),nRow)
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| 104 | else:
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| 105 | return self.finder.setscan(mask,list(edge),nRow)
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| 106 | def get_mask(self,invert=False):
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| 107 | """
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| 108 | Get the mask to mask out all lines that have been found (default)
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| 109 |
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| 110 | Parameters:
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| 111 | invert if True, only channels belong to lines will be unmasked
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| 112 |
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| 113 | Note: all channels originally masked by the input mask or
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| 114 | dropped out by the edge parameter will still be excluded
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| 115 | regardless on the invert option
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| 116 | """
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| 117 | return self.finder.getmask(invert)
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| 118 | def get_ranges(self,defunits=True):
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| 119 | """
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| 120 | Get ranges (start and end channels or velocities) for all spectral
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| 121 | lines found.
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| 122 |
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| 123 | Parameters:
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| 124 | defunits if True (default), the range will use the same units
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| 125 | as set for the scan (e.g. LSR velocity)
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| 126 | if False, the range will be expressed in channels
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| 127 | """
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| 128 | if (defunits):
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| 129 | return self.finder.getlineranges()
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| 130 | else:
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| 131 | return self.finder.getlinerangesinchannels()
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