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