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: 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: 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,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