import _asap class linefinder: """ The class for automated spectral line search in ASAP. Example: fl=linefinder() fl.set_scan(sc) fl.set_options(threshold=3) nlines=fl.find_lines(edge=(50,0)) if nlines!=0: print "Found ",nlines," spectral lines" print fl.get_ranges(False) else: print "No lines found!" sc2=sc.poly_baseline(fl.get_mask(),7) The algorithm involves a simple threshold criterion. The line is considered to be detected if a specified number of consequtive channels (default is 3) is brighter (with respect to the current baseline estimate) than the threshold times the noise level. This criterion is applied in the iterative procedure updating baseline estimate and trying reduced spectral resolutions to detect broad lines as well. The off-line noise level is determined at each iteration as an average of 80% of the lowest variances across the spectrum (i.e. histogram equalization is used to avoid missing weak lines if strong ones are present). For bad baseline shapes it is recommended to increase the threshold and possibly switch the averaging option off (see set_options) to detect strong lines only, fit a high order baseline and repeat the line search. """ def __init__(self): """ Create a line finder object. """ self.finder = _asap.linefinder() return def set_options(self,threshold=1.7320508075688772,min_nchan=3, avg_limit=8,box_size=0.2,noise_box='all',noise_stat='mean80'): """ Set the parameters of the algorithm Parameters: threshold a single channel S/N ratio above which the channel is considered to be a detection Default is sqrt(3), which together with min_nchan=3 gives a 3-sigma criterion min_nchan a minimal number of consequtive channels, which should satisfy a threshold criterion to be a detection. Default is 3. avg_limit A number of consequtive channels not greater than this parameter can be averaged to search for broad lines. Default is 8. box_size A running mean/median box size specified as a fraction of the total spectrum length. Default is 1/5 noise_box Area of the spectrum used to estimate noise stats Both string values and numbers are allowed Allowed string values: 'all' use all the spectrum (default) 'box' noise box is the same as running mean/median box Numeric values are defined as a fraction from the spectrum size. Values should be positive. (noise_box == box_size has the same effect as noise_box = 'box') noise_stat Statistics used to estimate noise, allowed values: 'mean80' use the 80% of the lowest deviations in the noise box (default) 'median' median of deviations in the noise box Note: For bad baselines threshold should be increased, and avg_limit decreased (or even switched off completely by setting this parameter to 1) to avoid detecting baseline undulations instead of real lines. """ if noise_stat.lower() not in ["mean80",'median']: raise RuntimeError, "noise_stat argument in linefinder.set_options can only be mean80 or median" nStat = (noise_stat.lower() == "median") nBox = -1. if isinstance(noise_box,str): if noise_box.lower() not in ['all','box']: raise RuntimeError, "string-valued noise_box in linefinder.set_options can only be all or box" if noise_box.lower() == 'box': nBox = box_size else: nBox = float(noise_box) self.finder.setoptions(threshold,min_nchan,avg_limit,box_size,nBox,nStat) return def set_scan(self, scan): """ Set the 'data' (scantable) to work with. Parameters: scan: a scantable """ if not scan: raise RuntimeError, 'Please give a correct scan' self.finder.setscan(scan) def set_data(self, spectrum): """ Set the 'data' (spectrum) to work with Parameters: a method to allow linefinder work without setting scantable for the purpose of using linefinder inside some method in scantable class. (Dec 22, 2010 by W.Kawasaki) """ if isinstance(spectrum, list) or isinstance(spectrum, tuple): if not isinstance(spectrum[0], float): raise RuntimeError, "Parameter 'spectrum' has to be a list or a tuple of float" else: raise RuntimeError, "Parameter 'spectrum' has to be a list or a tuple of float" self.finder.setdata(spectrum) def find_lines(self,nRow=0,mask=[],edge=(0,0)): """ Search for spectral lines in the scan assigned in set_scan. Parameters: nRow: a row in the scantable to work with mask: an optional mask (e.g. retreived from scantable) edge: an optional number of channels to drop at the edge of the spectrum. If only one value is specified, the same number will be dropped from both sides of the spectrum. Default is to keep all channels A number of lines found will be returned """ if isinstance(edge,int): edge=(edge,) from asap import _is_sequence_or_number as _is_valid if not _is_valid(edge, int): raise RuntimeError, "Parameter 'edge' has to be an integer or \ a pair of integers specified as a tuple" if len(edge)>2: raise RuntimeError, "The edge parameter should have two \ or less elements" return self.finder.findlines(mask,list(edge),nRow) def get_mask(self,invert=False): """ Get the mask to mask out all lines that have been found (default) Parameters: invert if True, only channels belong to lines will be unmasked Note: all channels originally masked by the input mask or dropped out by the edge parameter will still be excluded regardless on the invert option """ return self.finder.getmask(invert) def get_ranges(self,defunits=True): """ Get ranges (start and end channels or velocities) for all spectral lines found. Parameters: defunits if True (default), the range will use the same units as set for the scan (e.g. LSR velocity) if False, the range will be expressed in channels """ if (defunits): return self.finder.getlineranges() else: return self.finder.getlinerangesinchannels()