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, average=None, 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 average: average all integrations withinb a scan on read. The default (True) is taken from .asaprc. 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 """ if average is None or type(average) is not bool: average = rcParams['scantable.autoaverage'] varlist = vars() self._vb = rcParams['verbose'] self._p = None if isinstance(filename,sdtable): sdtable.__init__(self, filename) if unit is not None: self.set_fluxunit(unit) else: import os.path if not os.path.exists(filename): print "File '%s' not found." % (filename) return filename = os.path.expandvars(filename) if os.path.isdir(filename): # crude check if asap table if os.path.exists(filename+'/table.info'): sdtable.__init__(self, filename) if unit is not None: self.set_fluxunit(unit) else: print "The given file '%s'is not a valid asap table." % (filename) return else: from asap._asap import sdreader ifSel = -1 beamSel = -1 r = sdreader(filename,ifSel,beamSel) print 'Importing data...' r._read([-1]) tbl = r._getdata() if unit is not None: tbl.set_fluxunit(unit) if average: from asap._asap import average as _av tmp = tuple([tbl]) print 'Auto averaging integrations...' tbl2 = _av(tmp,(),True,'none') sdtable.__init__(self,tbl2) del r,tbl else: sdtable.__init__(self,tbl) self._add_history("scantable", varlist) def save(self, name=None, format=None, stokes=False, 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'). For format "ASCII" this is the root file name (data in 'name'.txt and header in 'name'_header.txt) 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) stokes: Convert to Stokes parameters (only available currently with FITS and ASCII formats. Default is False. overwrite: If the file should be overwritten if it exists. The default False is to return with warning without writing the output. USE WITH CARE. Example: scan.save('myscan.asap') scan.save('myscan.sdfits','SDFITS') """ from os import path 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 name = path.expandvars(name) if path.isfile(name) or path.isdir(name): if not overwrite: print "File %s already exists." % name return format2 = format.upper() if format2 == 'ASAP': self._save(name) else: from asap._asap import sdwriter as _sw w = _sw(format2) w.write(self, name, stokes) 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) elif type(scanid) is list: s = sdtable._getscan(self,scanid) return scantable(s) else: print "Illegal scanid type, use 'int' or 'list' if ints." except RuntimeError: print "Couldn't find any match." def __str__(self): return sdtable._summary(self,True) def summary(self,filename=None, verbose=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 verbose: print extra info such as the frequency table The default (False) is taken from .asaprc """ info = sdtable._summary(self, verbose) if verbose is None: verbose = rcParams['scantable.verbosesummary'] if filename is not None: if filename is "": filename = 'scantable_summary.txt' from os.path import expandvars, isdir filename = expandvars(filename) if not isdir(filename): data = open(filename, 'w') data.write(info) data.close() else: print "Illegal file name '%s'." % (filename) 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 """ varlist = vars() self.setbeam(thebeam) self.setpol(thepol) self.setif(theif) self._add_history("set_cursor",varlist) 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, allaxes=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. allaxes: if True apply to all spectra. Otherwise apply only to the selected (beam/pol/if)spectra only. The default is taken from .asaprc (True if none) Example: scan.set_unit('channel') msk = scan.create_mask([100,200],[500,600]) scan.stats(stat='mean', mask=m) """ if allaxes is None: allaxes = 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'] beamSel,IFSel,polSel = (self.getbeam(),self.getif(),self.getpol()) if allaxes: 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) self.setbeam(beamSel) self.setif(IFSel) self.setpol(polSel) return retval else: 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] ' % (beamSel) if self.nif() > 1: out += ' IF[%d] ' % (IFSel) if self.npol() > 1: out += ' Pol[%d] ' % (polSel) 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, allaxes=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. allaxes: 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 allaxes is None: allaxes = rcParams['scantable.allaxes'] return self.stats(stat='stddev',mask=mask, allaxes=allaxes); def get_tsys(self, allaxes=None): """ Return the System temperatures. Parameters: allaxes: if True apply to all spectra. Otherwise apply only to the selected (beam/pol/if)spectra only. The default is taken from .asaprc (True if none) Returns: a list of Tsys values. """ if allaxes is None: allaxes = rcParams['scantable.allaxes'] from numarray import array,zeros,Float axes = ['Beam','IF','Pol','Time'] if allaxes: 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, row=-1): """ Get a list of time stamps for the observations. Return a string for each integration in the scantable. Parameters: row: row no of integration. Default -1 return all rows Example: none """ out = [] if row == -1: for i in range(self.nrow()): out.append(self._gettime(i)) return out else: if row < self.nrow(): return self._gettime(row) 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', '' """ varlist = vars() if unit in ['','pixel', 'channel']: unit = '' inf = list(self._getcoordinfo()) inf[0] = unit self._setcoordinfo(inf) if self._p: self.plot() self._add_history("set_unit",varlist) def set_instrument(self, instr): """ Set the instrument for subsequent processing Parameters: instr: Select from 'ATPKSMB', 'ATPKSHOH', 'ATMOPRA', 'DSS-43' (Tid), 'CEDUNA', and 'HOBART' """ self._setInstrument(instr) self._add_history("set_instument",vars()) 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' """ varlist = vars() inf = list(self._getcoordinfo()) inf[2] = doppler self._setcoordinfo(inf) if self._p: self.plot() self._add_history("set_doppler",vars()) 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 frame is None: frame = rcParams['scantable.freqframe'] varlist = vars() valid = ['REST','TOPO','LSRD','LSRK','BARY', \ 'GEO','GALACTO','LGROUP','CMB'] if frame in valid: inf = list(self._getcoordinfo()) inf[1] = frame self._setcoordinfo(inf) self._add_history("set_freqframe",varlist) 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 (as a dictionary) """ abc = self._getabcissa(rowno) lbl = self._getabcissalabel(rowno) return abc, lbl #return {'abcissa':abc,'label':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' """ varlist = vars() 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) self._add_history("create_mask", varlist) return msk 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 lines(self): """ Print the list of known spectral lines """ sdtable._lines(self) def set_restfreqs(self, freqs=None, unit='Hz', lines=None, source=None, theif=None): """ Select the restfrequency for the specified source and IF OR replace for all IFs. If the 'freqs' argument holds a scalar, then that rest frequency will be applied to the selected data (and added to the list of available rest frequencies). In this way, you can set a rest frequency for each source and IF combination. If the 'freqs' argument holds a vector, then it MUST be of length the number of IFs (and the available restfrequencies will be replaced by this vector). In this case, *all* data ('source' and 'theif' are ignored) have the restfrequency set per IF according to the corresponding value you give in the 'freqs' vector. E.g. 'freqs=[1e9,2e9]' would mean IF 0 gets restfreq 1e9 and IF 1 gets restfreq 2e9. You can also specify the frequencies via known line names in the argument 'lines'. Use 'freqs' or 'lines'. 'freqs' takes precedence. See the list of known names via function scantable.lines() Parameters: freqs: list of rest frequencies unit: unit for rest frequency (default 'Hz') lines: list of known spectral lines names (alternative to freqs). See possible list via scantable.lines() source: Source name (blank means all) theif: IF (-1 means all) Example: scan.set_restfreqs(freqs=1.4e9, source='NGC253', theif=2) scan.set_restfreqs(freqs=[1.4e9,1.67e9]) """ varlist = vars() if source is None: source = "" if theif is None: theif = -1 t = type(freqs) if t is int or t is float: freqs = [freqs] if freqs is None: freqs = [] t = type(lines) if t is str: lines = [lines] if lines is None: lines = [] sdtable._setrestfreqs(self, freqs, unit, lines, source, theif) self._add_history("set_restfreqs", varlist) 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()): sdtable.setbeam(self, thebeam) sdtable.setif(self, theif) sdtable.setpol(self, thepol) sdtable._flag(self) self._add_history("flag_spectrum", vars()) 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 += "-"*80 out += "\n" print "-"*80 print " ", label print "-"*80 print out def history(self): hist = list(self._gethistory()) print "-"*80 for h in hist: if h.startswith("---"): print h else: items = h.split("##") date = items[0] func = items[1] items = items[2:] print date print "Function: %s\n Parameters:" % (func) for i in items: s = i.split("=") print " %s = %s" % (s[0],s[1]) print "-"*80 return def _add_history(self, funcname, parameters): # create date sep = "##" from datetime import datetime dstr = datetime.now().strftime('%Y/%m/%d %H:%M:%S') hist = dstr+sep hist += funcname+sep#cdate+sep if parameters.has_key('self'): del parameters['self'] for k,v in parameters.iteritems(): if type(v) is dict: for k2,v2 in v.iteritems(): hist += k2 hist += "=" if isinstance(v2,scantable): hist += 'scantable' elif k2 == 'mask': hist += str(self._zip_mask(v2)) else: hist += str(v2) else: hist += k hist += "=" if isinstance(v,scantable): hist += 'scantable' elif k == 'mask': hist += str(self._zip_mask(v)) else: hist += str(v) hist += sep hist = hist[:-2] # remove trailing '##' self._addhistory(hist) def _zip_mask(self, mask): mask = list(mask) i = 0 segments = [] while mask[i:].count(1): i += mask[i:].index(1) if mask[i:].count(0): j = i + mask[i:].index(0) else: j = len(mask) segments.append([i,j]) i = j return segments