| 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,edge=(50,))
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| 10 | fl.set_options(threshold=3)
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| 11 | nlines=fl.find_lines()
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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=poly_baseline(sc,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 reccommended 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,mask=None,edge=(0,0)):
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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 | mask: an optional mask retreived from scantable
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| 73 | edge: an optional number of channel to drop at
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| 74 | the edge of spectrum. If only one value is
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| 75 | specified, the same number will be dropped from
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| 76 | both sides of the spectrum. Default is to keep
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| 77 | all channels
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| 78 | """
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| 79 | if not scan:
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| 80 | raise RuntimeError, 'Please give a correct scan'
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| 81 | if len(edge)>2:
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| 82 | raise RuntimeError, "The edge parameter should have two \
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| 83 | or less elements"
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| 84 | if mask is None:
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| 85 | from numarray import ones
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| 86 | self.finder.setscan(scan,ones(scan.nchan()),edge)
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| 87 | else:
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| 88 | self.finder.setscan(scan,mask,edge)
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| 89 | return
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| 90 | def find_lines(self,nRow=0):
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| 91 | """
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| 92 | Search for spectral lines in the scan assigned in set_scan.
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| 93 | Current Beam/IF/Pol is used, Row is specified by parameter
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| 94 | A number of lines found will be returned
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| 95 | """
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| 96 | return self.finder.findlines(nRow)
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| 97 | def get_mask(self,invert=False):
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| 98 | """
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| 99 | Get the mask to mask out all lines that have been found (default)
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| 100 |
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| 101 | Parameters:
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| 102 | invert if True, only channels belong to lines will be unmasked
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| 103 |
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| 104 | Note: all channels originally masked by the input mask or
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| 105 | dropped out by the edge parameter will still be excluded
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| 106 | regardless on the invert option
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| 107 | """
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| 108 | return self.finder.getmask(invert)
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| 109 | def get_ranges(self,defunits=True):
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| 110 | """
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| 111 | Get ranges (start and end channels or velocities) for all spectral
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| 112 | lines found.
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| 113 |
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| 114 | Parameters:
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| 115 | defunits if True (default), the range will use the same units
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| 116 | as set for the scan (e.g. LSR velocity)
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| 117 | if False, the range will be expressed in channels
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| 118 | """
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| 119 | if (defunits):
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| 120 | return self.finder.getlineranges()
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| 121 | else:
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| 122 | return self.finder.getlinerangesinchannels()
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| 123 |
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| 124 | def auto_poly_baseline(scan, mask=None, edge=(0,0), order=0,
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| 125 | threshold=3,insitu=None):
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| 126 | """
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| 127 | Return a scan which has been baselined (all rows) by a polynomial.
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| 128 | Spectral lines are detected first using linefinder and masked out
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| 129 | to avoid them affecting the baseline solution.
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| 130 |
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| 131 | Parameters:
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| 132 | scan: a scantable
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| 133 | mask: an optional mask retreived from scantable
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| 134 | edge: an optional number of channel to drop at
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| 135 | the edge of spectrum. If only one value is
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| 136 | specified, the same number will be dropped from
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| 137 | both sides of the spectrum. Default is to keep
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| 138 | all channels
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| 139 | order: the order of the polynomial (default is 0)
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| 140 | threshold: the threshold used by line finder. It is better to
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| 141 | keep it large as only strong lines affect the
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| 142 | baseline solution.
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| 143 | insitu: if False a new scantable is returned.
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| 144 | Otherwise, the scaling is done in-situ
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| 145 | The default is taken from .asaprc (False)
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| 146 |
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| 147 | Example:
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| 148 | sc2=auto_poly_baseline(sc,order=7)
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| 149 | """
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| 150 | from asap.asapfitter import fitter
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| 151 | from asap import scantable
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| 152 |
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| 153 | # setup fitter
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| 154 |
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| 155 | f = fitter()
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| 156 | f._verbose(True)
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| 157 | f.set_function(poly=order)
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| 158 |
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| 159 | # setup line finder
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| 160 |
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| 161 | fl=linefinder()
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| 162 | fl.set_options(threshold=threshold)
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| 163 |
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| 164 | if not insitu:
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| 165 | workscan=scan.copy()
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| 166 | else:
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| 167 | workscan=scan
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| 168 |
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| 169 | vb=workscan._vb
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| 170 | # remember the verbose parameter and selection
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| 171 | workscan._vb=False
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| 172 | sel=workscan.get_cursor()
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| 173 | rows=range(workscan.nrow())
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| 174 | for i in range(workscan.nbeam()):
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| 175 | workscan.setbeam(i)
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| 176 | for j in range(workscan.nif()):
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| 177 | workscan.setif(j)
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| 178 | for k in range(workscan.npol()):
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| 179 | workscan.setpol(k)
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| 180 | if f._vb:
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| 181 | print "Processing:"
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| 182 | print 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k)
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| 183 | for iRow in rows:
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| 184 | fl.set_scan(workscan,mask,edge)
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| 185 | fl.find_lines(iRow)
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| 186 | f.set_scan(workscan, fl.get_mask())
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| 187 | f.x=workscan._getabcissa(iRow)
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| 188 | f.y=workscan._getspectrum(iRow)
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| 189 | f.data=None
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| 190 | f.fit()
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| 191 | x=f.get_parameters()
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| 192 | workscan._setspectrum(f.fitter.getresidual(),iRow)
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| 193 | workscan.set_cursor(sel[0],sel[1],sel[2])
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| 194 | workscan._vb = vb
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| 195 | if not insitu:
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| 196 | return workscan
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