source: trunk/python/scantable.py @ 340

from asap._asap import sdtable
from asap import rcParams
from numarray import ones,zeros
import sys

class scantable(sdtable):
    """
        The ASAP container for scans
    """
    
    def __init__(self, filename, unit=None):
        """
        Create a scantable from a saved one or make a reference
        Parameters:
            filename:    the name of an asap table on disk
                         or
                         the name of a rpfits/sdfits/ms file
                         (integrations within scans are auto averaged
                         and the whole file is read)
                         or
                         [advanced] a reference to an existing
                         scantable
           unit:         brightness unit; must be consistent with K or Jy.
                         Over-rides the default selected by the reader
                         (input rpfits/sdfits/ms) or replaces the value
                         in existing scantables
        """
        self._vb = rcParams['verbose']
        self._p = None
        from os import stat as st
        import stat
        if isinstance(filename,sdtable):
            sdtable.__init__(self, filename)            
            if unit is not None:
                print 'Setting brightness unit to ', unit
                sdtable.set_fluxunit(unit)                       
        else:
            try:
                mode = st(filename)[stat.ST_MODE]
            except OSError:
                print "File not found"
                return
            if stat.S_ISDIR(mode):
                # crude check if asap table
                if stat.S_ISREG(st(filename+'/table.info')[stat.ST_MODE]):
                    sdtable.__init__(self, filename)
                    if unit is not None:
                        print 'Setting brightness unit to ', unit
                        self.set_fluxunit(unit)                       
                else:
                    print 'The given file is not a valid asap table'
                    return
            else:
                autoav = rcParams['scantable.autoaverage']

                from asap._asap import sdreader
                ifSel = -1
                beamSel = -1
                if unit is None:
                    unit = ""
                r = sdreader(filename,unit,ifSel,beamSel)
                print 'Importing data...'
                r.read([-1])
                tbl = r.getdata()
                if autoav:
                    from asap._asap import average
                    tmp = tuple([tbl])
                    print 'Auto averaging integrations...'
                    tbl2 = average(tmp,(),True,'none')
                    sdtable.__init__(self,tbl2)
                    del r,tbl
                else:
                    sdtable.__init__(self,tbl)

    def save(self, name=None, format=None, overwrite=False):
        """
        Store the scantable on disk. This can be an asap (aips++) Table, SDFITS, 
        Image FITS or MS2 format.
        Parameters:
            name:        the name of the outputfile. For format="FITS" this
                         is the directory file name into which all the files will
                         be written (default is 'asap_FITS')
            format:      an optional file format. Default is ASAP.
                         Allowed are - 'ASAP' (save as ASAP [aips++] Table),
                                       'SDFITS' (save as SDFITS file)
                                       'FITS' (saves each row as a FITS Image) 
                                       'ASCII' (saves as ascii text file)
                                       'MS2' (saves as an aips++
                                              MeasurementSet V2)
            overwrite:   if the file should be overwritten if it exists.
                         The default False is to return with warning
                         without writing the output
        Example:
            scan.save('myscan.asap')
            scan.save('myscan.sdfits','SDFITS')
        """
        if format is None: format = rcParams['scantable.save']
        suffix = '.'+format.lower()
        if name is None or name =="":
            name = 'scantable'+suffix
            print "No filename given. Using default name %s..." % name
        from os import path
        if path.isfile(name) or path.isdir(name):
            if not overwrite:
                print "File %s already exists." % name
                return
        if format == 'ASAP':
            self._save(name)
        else:
            from asap._asap import sdwriter as _sw
            w = _sw(format)
            w.write(self, name)
        return

    def copy(self):
        """
        Return a copy of this scantable.
        Parameters:
            none
        Example:
            copiedscan = scan.copy()
        """
        sd = scantable(sdtable._copy(self))
        return sd

    def get_scan(self, scanid=None):
        """
        Return a specific scan (by scanno) or collection of scans (by
        source name) in a new scantable.
        Parameters:
            scanid:    a scanno or a source name
        Example:
            scan.get_scan('323p459')
            # gets all scans containing the source '323p459'
        """
        if scanid is None:
            print "Please specify a scan no or name to retrieve from the scantable"
        try:
            if type(scanid) is str:
                s = sdtable._getsource(self,scanid)
                return scantable(s)
            elif type(scanid) is int:
                s = sdtable._getscan(self,scanid)
                return scantable(s)
        except RuntimeError:
            print "Couldn't find any match."

    def __str__(self):
        return sdtable._summary(self)

    def summary(self,filename=None):
        """
        Print a summary of the contents of this scantable.
        Parameters:
            filename:    the name of a file to write the putput to
                         Default - no file output
        """
        info = sdtable._summary(self)
        if filename is not None:
            if filename is "":
                filename = 'scantable_summary.txt'
            data = open(filename, 'w')
            data.write(info)
            data.close()
        print info

    def set_cursor(self, thebeam=0,theif=0,thepol=0):
        """
        Set the spectrum for individual operations.
        Parameters:
            thebeam,theif,thepol:    a number
        Example:
            scan.set_cursor(0,0,1)
            pol1sig = scan.stats(all=False) # returns std dev for beam=0
                                            # if=0, pol=1
        """
        self.setbeam(thebeam)
        self.setpol(thepol)
        self.setif(theif)
        return

    def get_cursor(self):
        """
        Return/print a the current 'cursor' into the Beam/IF/Pol cube.
        Parameters:
            none
        Returns:
            a list of values (currentBeam,currentIF,currentPol)
        Example:
            none
        """
        i = self.getbeam()
        j = self.getif()
        k = self.getpol()
        if self._vb:
            print "--------------------------------------------------"
            print " Cursor position"
            print "--------------------------------------------------"
            out = 'Beam=%d IF=%d Pol=%d ' % (i,j,k)
            print out
        return i,j,k

    def stats(self, stat='stddev', mask=None, all=None):
        """
        Determine the specified statistic of the current beam/if/pol
        Takes a 'mask' as an optional parameter to specify which
        channels should be excluded.
        Parameters:
            stat:    'min', 'max', 'sumsq', 'sum', 'mean'
                     'var', 'stddev', 'avdev', 'rms', 'median'
            mask:    an optional mask specifying where the statistic
                     should be determined.
            all:     if true show all (default or .asaprc) rather
                     that the cursor selected spectrum of Beam/IF/Pol

        Example:
            scan.set_unit('channel')
            msk = scan.create_mask([100,200],[500,600])
            scan.stats(stat='mean', mask=m)
        """
        if all is None: all = rcParams['scantable.allaxes']
        from asap._asap import stats as _stats
        from numarray import array,zeros,Float
        if mask == None:
            mask = ones(self.nchan())
        axes = ['Beam','IF','Pol','Time']

        if all:
            n = self.nbeam()*self.nif()*self.npol()*self.nrow()
            shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
            arr = array(zeros(n),shape=shp,type=Float)

            for i in range(self.nbeam()):
                self.setbeam(i)
                for j in range(self.nif()):
                    self.setif(j)
                    for k in range(self.npol()):
                        self.setpol(k)
                        arr[i,j,k,:] = _stats(self,mask,stat,-1)
            retval = {'axes': axes, 'data': arr, 'cursor':None}
            tm = [self._gettime(val) for val in range(self.nrow())]
            if self._vb:
                self._print_values(retval,stat,tm)
            return retval

        else:
            i,j,k = (self.getbeam(),self.getif(),self.getpol())
            statval = _stats(self,mask,stat,-1)
            out = ''
            for l in range(self.nrow()):
                tm = self._gettime(l)
                out += 'Time[%s]:\n' % (tm)
                if self.nbeam() > 1: out +=  ' Beam[%d] ' % (i)
                if self.nif() > 1: out +=  ' IF[%d] ' % (j)
                if self.npol() > 1: out +=  ' Pol[%d] ' % (k)
                out += '= %3.3f\n' % (statval[l])
                out +=  "--------------------------------------------------\n"

            if self._vb:
                print "--------------------------------------------------"
                print " ",stat
                print "--------------------------------------------------"
                print out
            retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
            return retval

    def stddev(self,mask=None, all=None):
        """
        Determine the standard deviation of the current beam/if/pol
        Takes a 'mask' as an optional parameter to specify which
        channels should be excluded.
        Parameters:
            mask:    an optional mask specifying where the standard
                     deviation should be determined.
            all:     optional flag to show all or a cursor selected
                     spectrum of Beam/IF/Pol. Default is all or taken
                     from .asaprc

        Example:
            scan.set_unit('channel')
            msk = scan.create_mask([100,200],[500,600])
            scan.stddev(mask=m)
        """
        if all is None: all = rcParams['scantable.allaxes']
        return self.stats(stat='stddev',mask=mask, all=all);

    def get_tsys(self, all=None):
        """
        Return the System temperatures.
        Parameters:
            all:    optional parameter to get the Tsys values for all
                    Beams/IFs/Pols (default) or just the one selected
                    with scantable.set_cursor()
                    [True or False]
        Returns:
            a list of Tsys values.
        """
        if all is None: all = rcParams['scantable.allaxes']
        from numarray import array,zeros,Float
        axes = ['Beam','IF','Pol','Time']

        if all:
            n = self.nbeam()*self.nif()*self.npol()*self.nrow()
            shp = [self.nbeam(),self.nif(),self.npol(),self.nrow()]
            arr = array(zeros(n),shape=shp,type=Float)

            for i in range(self.nbeam()):
                self.setbeam(i)
                for j in range(self.nif()):
                    self.setif(j)
                    for k in range(self.npol()):
                        self.setpol(k)
                        arr[i,j,k,:] = self._gettsys()
            retval = {'axes': axes, 'data': arr, 'cursor':None}
            tm = [self._gettime(val) for val in range(self.nrow())]
            if self._vb:
                self._print_values(retval,'Tsys',tm)
            return retval

        else:
            i,j,k = (self.getbeam(),self.getif(),self.getpol())
            statval = self._gettsys()
            out = ''
            for l in range(self.nrow()):
                tm = self._gettime(l)
                out += 'Time[%s]:\n' % (tm)
                if self.nbeam() > 1: out +=  ' Beam[%d] ' % (i)
                if self.nif() > 1: out +=  ' IF[%d] ' % (j)
                if self.npol() > 1: out +=  ' Pol[%d] ' % (k)
                out += '= %3.3f\n' % (statval[l])
                out +=  "--------------------------------------------------\n"

            if self._vb:
                print "--------------------------------------------------"
                print " TSys"
                print "--------------------------------------------------"
                print out
            retval = {'axes': axes, 'data': array(statval), 'cursor':(i,j,k)}
            return retval
        
    def get_time(self):
        """
        Get a list of time stamps for the observations.
        Return a string for each integration in the scantable.
        Parameters:
            none
        Example:
            none
        """
        out = []
        for i in range(self.nrow()):
            out.append(self._gettime(i))
        return out

    def set_unit(self, unit='channel'):
        """
        Set the unit for all following operations on this scantable
        Parameters:
            unit:    optional unit, default is 'channel'
                     one of '*Hz','km/s','channel', ''
        """

        if unit in ['','pixel', 'channel']:
            unit = ''
        inf = list(self._getcoordinfo())
        inf[0] = unit
        self._setcoordinfo(inf)
        if self._p: self.plot()

    def set_doppler(self, doppler='RADIO'):
        """
        Set the doppler for all following operations on this scantable.
        Parameters:
            doppler:    One of 'RADIO', 'OPTICAL', 'Z', 'BETA', 'GAMMA'
        """

        inf = list(self._getcoordinfo())
        inf[2] = doppler
        self._setcoordinfo(inf)
        if self._p: self.plot()

    def set_freqframe(self, frame=None):
        """
        Set the frame type of the Spectral Axis.
        Parameters:
            frame:   an optional frame type, default 'LSRK'.
        Examples:
            scan.set_freqframe('BARY')
        """
        if not frame: frame = rcParams['scantable.freqframe']
        valid = ['REST','TOPO','LSRD','LSRK','BARY', \
                   'GEO','GALACTO','LGROUP','CMB']
        if frame in valid:
            inf = list(self._getcoordinfo())
            inf[1] = frame
            self._setcoordinfo(inf)
        else:
            print "Please specify a valid freq type. Valid types are:\n",valid
            
    def get_unit(self):
        """
        Get the default unit set in this scantable
        Parameters:
        Returns:
            A unit string
        """
        inf = self._getcoordinfo()
        unit = inf[0]
        if unit == '': unit = 'channel'
        return unit

    def get_abcissa(self, rowno=0):
        """
        Get the abcissa in the current coordinate setup for the currently
        selected Beam/IF/Pol
        Parameters:
            rowno:    an optional row number in the scantable. Default is the
                      first row, i.e. rowno=0
        Returns:
            The abcissa values and it's format string.
        """
        abc = self._getabcissa(rowno)
        lbl = self._getabcissalabel(rowno)
        return abc, lbl

    def create_mask(self, *args, **kwargs):
        """
        Compute and return a mask based on [min,max] windows.
        The specified windows are to be INCLUDED, when the mask is
        applied.
        Parameters:
            [min,max],[min2,max2],...
                Pairs of start/end points specifying the regions
                to be masked
            invert:     optional argument. If specified as True,
                        return an inverted mask, i.e. the regions
                        specified are EXCLUDED
        Example:
            scan.set_unit('channel')

            a)
            msk = scan.set_mask([400,500],[800,900])
            # masks everything outside 400 and 500
            # and 800 and 900 in the unit 'channel'

            b)
            msk = scan.set_mask([400,500],[800,900], invert=True)
            # masks the regions between 400 and 500
            # and 800 and 900 in the unit 'channel'
           
        """
        u = self._getcoordinfo()[0]
        if self._vb:
            if u == "": u = "channel"
            print "The current mask window unit is", u
        n = self.nchan()
        data = self._getabcissa()
        msk = zeros(n)
        for  window in args:
            if (len(window) != 2 or window[0] > window[1] ):
                print "A window needs to be defined as [min,max]"
                return
            for i in range(n):
                if data[i] >= window[0] and data[i] < window[1]:
                    msk[i] = 1
        if kwargs.has_key('invert'):
            if kwargs.get('invert'):
                from numarray import logical_not
                msk = logical_not(msk)
        return msk
    
    def set_restfreqs(self, freqs, unit='Hz'):
        """
        Set the restfrequency(s) for this scantable.
        Parameters:
            freqs:    one or more frequencies
            unit:     optional 'unit', default 'Hz'
        Example:
            scan.set_restfreqs([1000000000.0])
        """
        if type(freqs) is float or int:
            freqs = (freqs)
        sdtable._setrestfreqs(self,freqs, unit)
        return
    def get_restfreqs(self):
        """
        Get the restfrequency(s) stored in this scantable.
        The return value(s) are always of unit 'Hz'
        Parameters:
            none
        Returns:
            a list of doubles
        """
        return list(self._getrestfreqs())

    def flag_spectrum(self, thebeam, theif, thepol):
        """
        This flags a selected spectrum in the scan 'for good'.
        USE WITH CARE - not reversible.
        Use masks for non-permanent exclusion of channels.
        Parameters:
            thebeam,theif,thepol:    all have to be explicitly
                                     specified
        Example:
            scan.flag_spectrum(0,0,1)
            flags the spectrum for Beam=0, IF=0, Pol=1
        """
        if (thebeam < self.nbeam() and  theif < self.nif() and thepol < self.npol()):
            stable.setbeam(thebeam)
            stable.setif(theif)
            stable.setpol(thepol)
            stable._flag(self)
        else:
            print "Please specify a valid (Beam/IF/Pol)"
        return

    def plot(self, what='spectrum',col='Pol', panel=None):
        """
        Plot the spectra contained in the scan. Alternatively you can also
        Plot Tsys vs Time
        Parameters:
            what:     a choice of 'spectrum' (default) or 'tsys'
            col:      which out of Beams/IFs/Pols should be colour stacked
            panel:    set up multiple panels, currently not working.
        """
        print "Warning! Not fully functional. Use plotter.plot() instead"
        
        validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()}

        validyax = ['spectrum','tsys']
        from asap.asaplot import ASAPlot
        if not self._p:
            self._p = ASAPlot()
            #print "Plotting not enabled"
            #return
        if self._p.is_dead:
            del self._p
            self._p = ASAPlot()
        npan = 1
        x = None
        if what == 'tsys':
            n = self.nrow()
            if n < 2:
                print "Only one integration. Can't plot."
                return
        self._p.hold()
        self._p.clear()
        if panel == 'Time':
            npan = self.nrow()
            self._p.set_panels(rows=npan)
        xlab,ylab,tlab = None,None,None
        self._vb = False
        sel = self.get_cursor()        
        for i in range(npan):
            if npan > 1:
                self._p.subplot(i)
            for j in range(validcol[col]):
                x = None
                y = None
                m = None
                tlab = self._getsourcename(i)
                import re
                tlab = re.sub('_S','',tlab)
                if col == 'Beam':
                    self.setbeam(j)
                elif col == 'IF':
                    self.setif(j)
                elif col == 'Pol':
                    self.setpol(j)
                if what == 'tsys':
                    x = range(self.nrow())
                    xlab = 'Time [pixel]'
                    m = list(ones(len(x)))
                    y = []
                    ylab = r'$T_{sys}$'
                    for k in range(len(x)):
                        y.append(self._gettsys(k))
                else:
                    x,xlab = self.get_abcissa(i)
                    y = self._getspectrum(i)
                    ylab = r'Flux'
                    m = self._getmask(i)
                llab = col+' '+str(j)
                self._p.set_line(label=llab)
                self._p.plot(x,y,m)
            self._p.set_axes('xlabel',xlab)
            self._p.set_axes('ylabel',ylab)
            self._p.set_axes('title',tlab)
        self._p.release()
        self.set_cursor(sel[0],sel[1],sel[2])
        self._vb = rcParams['verbose']
        return

        print out 

    def _print_values(self, dat, label='', timestamps=[]):
        d = dat['data']
        a = dat['axes']
        shp = d.getshape()
        out = ''
        for i in range(shp[3]):
            out += '%s [%s]:\n' % (a[3],timestamps[i])
            t = d[:,:,:,i]
            for j in range(shp[0]):
                if shp[0] > 1: out +=  ' %s[%d] ' % (a[0],j)
                for k in range(shp[1]):
                    if shp[1] > 1: out +=  ' %s[%d] ' % (a[1],k)
                    for l in range(shp[2]):
                        if shp[2] > 1: out +=  ' %s[%d] ' % (a[2],l)
                        out += '= %3.3f\n' % (t[j,k,l])
            out += "--------------------------------------------------\n"
        print "--------------------------------------------------"
        print " ", label
        print "--------------------------------------------------"
        print out