| 1 | import _asap
|
|---|
| 2 |
|
|---|
| 3 | class linefinder:
|
|---|
| 4 | """
|
|---|
| 5 | The class for automated spectral line search in ASAP.
|
|---|
| 6 |
|
|---|
| 7 | Example:
|
|---|
| 8 | fl=linefinder()
|
|---|
| 9 | fl.set_scan(sc)
|
|---|
| 10 | fl.set_options(threshold=3)
|
|---|
| 11 | nlines=fl.find_lines(edge=(50,0))
|
|---|
| 12 | if nlines!=0:
|
|---|
| 13 | print "Found ",nlines," spectral lines"
|
|---|
| 14 | print fl.get_ranges(False)
|
|---|
| 15 | else:
|
|---|
| 16 | print "No lines found!"
|
|---|
| 17 | sc2=sc.poly_baseline(fl.get_mask(),7)
|
|---|
| 18 |
|
|---|
| 19 | The algorithm involves a simple threshold criterion. The line is
|
|---|
| 20 | considered to be detected if a specified number of consequtive
|
|---|
| 21 | channels (default is 3) is brighter (with respect to the current baseline
|
|---|
| 22 | estimate) than the threshold times the noise level. This criterion is
|
|---|
| 23 | applied in the iterative procedure updating baseline estimate and trying
|
|---|
| 24 | reduced spectral resolutions to detect broad lines as well. The off-line
|
|---|
| 25 | noise level is determined at each iteration as an average of 80% of the
|
|---|
| 26 | lowest variances across the spectrum (i.e. histogram equalization is
|
|---|
| 27 | used to avoid missing weak lines if strong ones are present). For
|
|---|
| 28 | bad baseline shapes it is recommended to increase the threshold and
|
|---|
| 29 | possibly switch the averaging option off (see set_options) to
|
|---|
| 30 | detect strong lines only, fit a high order baseline and repeat the line
|
|---|
| 31 | search.
|
|---|
| 32 |
|
|---|
| 33 | """
|
|---|
| 34 |
|
|---|
| 35 | def __init__(self):
|
|---|
| 36 | """
|
|---|
| 37 | Create a line finder object.
|
|---|
| 38 | """
|
|---|
| 39 | self.finder = _asap.linefinder()
|
|---|
| 40 | return
|
|---|
| 41 |
|
|---|
| 42 | def set_options(self,threshold=1.7320508075688772,min_nchan=3,
|
|---|
| 43 | avg_limit=8,box_size=0.2,noise_box='all',noise_stat='mean80'):
|
|---|
| 44 | """
|
|---|
| 45 | Set the parameters of the algorithm
|
|---|
| 46 | Parameters:
|
|---|
| 47 | threshold a single channel S/N ratio above which the
|
|---|
| 48 | channel is considered to be a detection
|
|---|
| 49 | Default is sqrt(3), which together with
|
|---|
| 50 | min_nchan=3 gives a 3-sigma criterion
|
|---|
| 51 | min_nchan a minimal number of consequtive channels,
|
|---|
| 52 | which should satisfy a threshold criterion to
|
|---|
| 53 | be a detection. Default is 3.
|
|---|
| 54 | avg_limit A number of consequtive channels not greater than
|
|---|
| 55 | this parameter can be averaged to search for
|
|---|
| 56 | broad lines. Default is 8.
|
|---|
| 57 | box_size A running mean/median box size specified as a fraction
|
|---|
| 58 | of the total spectrum length. Default is 1/5
|
|---|
| 59 | noise_box Area of the spectrum used to estimate noise stats
|
|---|
| 60 | Both string values and numbers are allowed
|
|---|
| 61 | Allowed string values:
|
|---|
| 62 | 'all' use all the spectrum (default)
|
|---|
| 63 | 'box' noise box is the same as running mean/median
|
|---|
| 64 | box
|
|---|
| 65 | Numeric values are defined as a fraction from the
|
|---|
| 66 | spectrum size. Values should be positive.
|
|---|
| 67 | (noise_box == box_size has the same effect as
|
|---|
| 68 | noise_box = 'box')
|
|---|
| 69 | noise_stat Statistics used to estimate noise, allowed values:
|
|---|
| 70 | 'mean80' use the 80% of the lowest deviations
|
|---|
| 71 | in the noise box (default)
|
|---|
| 72 | 'median' median of deviations in the noise box
|
|---|
| 73 |
|
|---|
| 74 | Note: For bad baselines threshold should be increased,
|
|---|
| 75 | and avg_limit decreased (or even switched off completely by
|
|---|
| 76 | setting this parameter to 1) to avoid detecting baseline
|
|---|
| 77 | undulations instead of real lines.
|
|---|
| 78 | """
|
|---|
| 79 | if noise_stat.lower() not in ["mean80",'median']:
|
|---|
| 80 | raise RuntimeError, "noise_stat argument in linefinder.set_options can only be mean80 or median"
|
|---|
| 81 | nStat = (noise_stat.lower() == "median")
|
|---|
| 82 | nBox = -1.
|
|---|
| 83 | if isinstance(noise_box,str):
|
|---|
| 84 | if noise_box.lower() not in ['all','box']:
|
|---|
| 85 | raise RuntimeError, "string-valued noise_box in linefinder.set_options can only be all or box"
|
|---|
| 86 | if noise_box.lower() == 'box':
|
|---|
| 87 | nBox = box_size
|
|---|
| 88 | else:
|
|---|
| 89 | nBox = float(noise_box)
|
|---|
| 90 | self.finder.setoptions(threshold,min_nchan,avg_limit,box_size,nBox,nStat)
|
|---|
| 91 | return
|
|---|
| 92 |
|
|---|
| 93 | def set_scan(self, scan):
|
|---|
| 94 | """
|
|---|
| 95 | Set the 'data' (scantable) to work with.
|
|---|
| 96 | Parameters:
|
|---|
| 97 | scan: a scantable
|
|---|
| 98 | """
|
|---|
| 99 | if not scan:
|
|---|
| 100 | raise RuntimeError, 'Please give a correct scan'
|
|---|
| 101 | self.finder.setscan(scan)
|
|---|
| 102 |
|
|---|
| 103 | def find_lines(self,nRow=0,mask=[],edge=(0,0)):
|
|---|
| 104 | """
|
|---|
| 105 | Search for spectral lines in the scan assigned in set_scan.
|
|---|
| 106 | Parameters:
|
|---|
| 107 | nRow: a row in the scantable to work with
|
|---|
| 108 | mask: an optional mask (e.g. retreived from scantable)
|
|---|
| 109 | edge: an optional number of channels to drop at
|
|---|
| 110 | the edge of the spectrum. If only one value is
|
|---|
| 111 | specified, the same number will be dropped from
|
|---|
| 112 | both sides of the spectrum. Default is to keep
|
|---|
| 113 | all channels
|
|---|
| 114 | A number of lines found will be returned
|
|---|
| 115 | """
|
|---|
| 116 | if isinstance(edge,int):
|
|---|
| 117 | edge=(edge,)
|
|---|
| 118 |
|
|---|
| 119 | from asap import _is_sequence_or_number as _is_valid
|
|---|
| 120 |
|
|---|
| 121 | if not _is_valid(edge, int):
|
|---|
| 122 | raise RuntimeError, "Parameter 'edge' has to be an integer or \
|
|---|
| 123 | a pair of integers specified as a tuple"
|
|---|
| 124 |
|
|---|
| 125 | if len(edge)>2:
|
|---|
| 126 | raise RuntimeError, "The edge parameter should have two \
|
|---|
| 127 | or less elements"
|
|---|
| 128 | return self.finder.findlines(mask,list(edge),nRow)
|
|---|
| 129 | def get_mask(self,invert=False):
|
|---|
| 130 | """
|
|---|
| 131 | Get the mask to mask out all lines that have been found (default)
|
|---|
| 132 |
|
|---|
| 133 | Parameters:
|
|---|
| 134 | invert if True, only channels belong to lines will be unmasked
|
|---|
| 135 |
|
|---|
| 136 | Note: all channels originally masked by the input mask or
|
|---|
| 137 | dropped out by the edge parameter will still be excluded
|
|---|
| 138 | regardless on the invert option
|
|---|
| 139 | """
|
|---|
| 140 | return self.finder.getmask(invert)
|
|---|
| 141 | def get_ranges(self,defunits=True):
|
|---|
| 142 | """
|
|---|
| 143 | Get ranges (start and end channels or velocities) for all spectral
|
|---|
| 144 | lines found.
|
|---|
| 145 |
|
|---|
| 146 | Parameters:
|
|---|
| 147 | defunits if True (default), the range will use the same units
|
|---|
| 148 | as set for the scan (e.g. LSR velocity)
|
|---|
| 149 | if False, the range will be expressed in channels
|
|---|
| 150 | """
|
|---|
| 151 | if (defunits):
|
|---|
| 152 | return self.finder.getlineranges()
|
|---|
| 153 | else:
|
|---|
| 154 | return self.finder.getlinerangesinchannels()
|
|---|
