from asap._asap import sdtable from numarray import ones import sys class scantable(sdtable): """ The ASAP container for scans """ def __init__(self, filename): """ Create a scantable from a saved one or make a reference Parameters: filename: the name of an asap table on disk, or [advanced] a refernce to an existing scantable """ self._vb = True self._p = None sdtable.__init__(self, filename) def save(self, name, format='ASAP'): """ Store the scantable on disk. This can be a asap file or SDFITS/MS2. Parameters: name: the name of the outputfile format: an optional file format. Default is ASAP. Alllowed are 'ASAP', 'SDFITS' and 'MS2' Example: scan.save('myscan.asap') scan.save('myscan.sdfits','SDFITS') """ if format == 'ASAP': self._save(name) else: from asap._asap import sdwriter as _sw w = _sw() if format == 'SDFITS': w.write(self, name) return def _verbose(self, *args): """ Set the verbose level True or False, to indicate if output should be printed as well as returned. """ if len(args) == 0: return self._vb elif type(args[0]) is bool: self._vb = args[0] 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: data = open(filename, 'w') data.write(info) data.close() print info def set_selection(self, thebeam=0,theif=0,thepol=0): """ Set the spectrum for individual operations. Parameters: thebeam,theif,thepol: a number Example: scan.set_selection(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_selection(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: out = 'Beam=%d IF=%d Pol=%d '% (i,j,k) print out return i,j,k def stats(self, stat='stddev', mask=None, all=True): """ 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: optional flag to show all or a 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) """ from asap._asap import stats as _stats if mask == None: mask = ones(self.nchan()) if all: out = '' tmp = [] 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) statVal = _stats(self,mask,stat) tmp.append(statVal) # out += 'Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,statVal) # if self._vb: # print out return tmp else: i = self.getbeam() j = self.getif() k = self.getpol() statVal = _stats(self,mask,stat) # out = 'Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,statVal) # if self._vb: # print out return statVal def stddev(self,mask=None, all=True): """ 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 selected spectrum of Beam/IF/Pol Example: scan.set_unit('channel') msk = scan.create_mask([100,200],[500,600]) scan.stddev(mask=m) """ return self.stats(stat='stddev',mask=mask, all=all); def get_tsys(self, all=True): """ 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_selection() [True or False] Returns: a list of Tsys values. """ if all: tmp = [] out = '' 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) ts = self._gettsys() tmp.append(ts) out += 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f\n' % (i,j,k,ts) if self._vb: print out return tmp else: i = self.getbeam() j = self.getif() k = self.getpol() ts = self._gettsys() out = 'TSys: Beam[%d], IF[%d], Pol[%d] = %3.3f' % (i,j,k,ts) if self._vb: print out return ts def get_time(self): """ Get a list of time stamps for the observations. Return a string for each intergration 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_freqframe(self, frame='LSRK'): """ Set the frame type of the Spectral Axis. Parameters: frame: an optional frame type, default 'LSRK'. Examples: scan.set_freqframe('BARY') """ 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_abscissa(self, rowno=0): """ Get the abscissa in the current coordinate setup for the currently selected Beam/IF/Pol Parameters: none Returns: The abscissa values and it's format string. """ absc = self.getabscissa(rowno) lbl = self.getabscissalabel(rowno) return absc, lbl def create_mask(self, *args, **kwargs): """ Compute and return a mask based on [min,max] windows. The specified windows are to be EXCLUDED, when the mask is applied. Parameters: [min,max],[min2,max2],... Pairs of start/end points specifying the regions to be masked invert: return an inverted mask, i.e. the regions specified are not masked (INCLUDED) Example: scan.set_unit('channel') a) msk = scan.set_mask([400,500],[800,900]) # masks the regions between 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 outside 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.getabscissa() msk = ones(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] = 0 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 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. """ validcol = {'Beam':self.nbeam(),'IF':self.nif(),'Pol':self.npol()} validyax = ['spectrum','tsys'] if not self._p: from asap.asaplot import ASAPlot self._p = ASAPlot() # print "Plotting not enabled" # return 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 vb = self._verbose() self._verbose(False) sel = self.get_selection() for i in range(npan): 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_abscissa(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_selection(sel[0],sel[1],sel[2]) self._verbose(vb) return