source: trunk/python/asaplinefind.py @ 371

import _asap

class linefinder:
    """
    The class for automated spectral line search in ASAP.

    Example:
       fl=linefinder()
       fl.set_scan(sc,edge=(50,))
       fl.set_options(threshold=3)
       nlines=fl.find_lines()
       if nlines!=0:
          print "Found ",nlines," spectral lines"
          print fl.get_ranges(False)
       else:
          print "No lines found!"
       sc2=poly_baseline(sc,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 reccommended 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):
        """
        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 box size specified as a fraction
                          of the total spectrum length. Default is 1/5
        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.  
        """
        self.finder.setoptions(threshold,min_nchan,avg_limit,box_size)
        return
             
    def set_scan(self,scan,mask=None,edge=(0,0)):
        """
        Set the 'data' (scantable) to work with.
        Parameters:
             scan:    a scantable
             mask:       an optional mask retreived from scantable
             edge:       an optional number of channel to drop at
                         the edge of 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
        """
        if not scan:
           raise RuntimeError, 'Please give a correct scan'
        if len(edge)>2:
           raise RuntimeError, "The edge parameter should have two \
           or less elements"
        if mask is None:
            from numarray import ones
            self.finder.setscan(scan,ones(scan.nchan()),edge)
        else:    
            self.finder.setscan(scan,mask,edge)
        return 
    def find_lines(self,nRow=0):
        """
        Search for spectral lines in the scan assigned in set_scan.
        Current Beam/IF/Pol is used, Row is specified by parameter
        A number of lines found will be returned
        """
        return self.finder.findlines(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()

def auto_poly_baseline(scan, mask=None, edge=(0,0), order=0,
    threshold=3,insitu=None):
    """
    Return a scan which has been baselined (all rows) by a polynomial.
    Spectral lines are detected first using linefinder and masked out
    to avoid them affecting the baseline solution.

    Parameters:
        scan:    a scantable
        mask:       an optional mask retreived from scantable
        edge:       an optional number of channel to drop at
                    the edge of 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
        order:      the order of the polynomial (default is 0)
        threshold:  the threshold used by line finder. It is better to
                    keep it large as only strong lines affect the
                    baseline solution.
        insitu:     if False a new scantable is returned.
                    Otherwise, the scaling is done in-situ
                    The default is taken from .asaprc (False)

    Example:
        sc2=auto_poly_baseline(sc,order=7)
    """
    from asap.asapfitter import fitter
    from asap import scantable

    # setup fitter

    f = fitter()
    f._verbose(True)
    f.set_function(poly=order)

    # setup line finder

    fl=linefinder()
    fl.set_options(threshold=threshold)

    if not insitu:
        workscan=scan.copy()
    else:
        workscan=scan

    vb=workscan._vb
    # remember the verbose parameter and selection
    workscan._vb=False
    sel=workscan.get_cursor()
    rows=range(workscan.nrow()) 
    for i in range(workscan.nbeam()):
        workscan.setbeam(i)
        for j in range(workscan.nif()):
            workscan.setif(j)
            for k in range(workscan.npol()):
                workscan.setpol(k)
                if f._vb:
                   print "Processing:"
                   print 'Beam[%d], IF[%d], Pol[%d]' % (i,j,k)
                for iRow in rows:
                   fl.set_scan(workscan,mask,edge)
                   fl.find_lines(iRow)
                   f.set_scan(workscan, fl.get_mask())
                   f.x=workscan._getabcissa(iRow)
                   f.y=workscan._getspectrum(iRow)
                   f.data=None
                   f.fit()
                   x=f.get_parameters()
                   workscan._setspectrum(f.fitter.getresidual(),iRow)
    workscan.set_cursor(sel[0],sel[1],sel[2])
    workscan._vb = vb
    if not insitu:
       return workscan