import numpy from asap import rcParams from asap.scantable import scantable from asap.selector import selector from asap._asap import stgrid, stgrid2 import pylab as pl from logging import asaplog class asapgrid_base(object): def __init__( self ): self.outfile = None self.ifno = None self.gridder = None self.infile = None self.scantab = None def setData( self, infile ): raise NotImplementedError('setData is not implemented') def setIF( self, ifno ): """ Set IFNO to be processed. Currently, asapgrid allows to process only one IFNO for one gridding run even if the data contains multiple IFs. If you didn't specify IFNO, default value, which is IFNO in the first spectrum, will be processed. ifno -- IFNO to be processed. """ self.ifno = ifno self.gridder._setif( self.ifno ) def setPolList( self, pollist ): """ Set list of polarization components you want to process. If not specified, all POLNOs will be processed. pollist -- list of POLNOs. """ self.gridder._setpollist( pollist ) def setScanList( self, scanlist ): """ Set list of scans you want to process. If not specified, all scans will be processed. scanlist -- list of SCANNOs. """ self.gridder._setscanlist( scanlist ) def defineImage( self, nx=-1, ny=-1, cellx='', celly='', center='' ): """ Define spatial grid. First two parameters, nx and ny, define number of pixels of the grid. If which of those is not specified, it will be set to the same value as the other. If none of them are specified, it will be determined from map extent and cell size. Next two parameters, cellx and celly, define size of pixel. You should set those parameters as string, which is constructed numerical value and unit, e.g. '0.5arcmin', or numerical value. If those values are specified as numerical value, their units will be assumed to 'arcsec'. If which of those is not specified, it will be set to the same value as the other. If none of them are specified, it will be determined from map extent and number of pixels, or set to '1arcmin' if neither nx nor ny is set. The last parameter, center, define the central coordinate of the grid. You should specify its value as a string, like, 'J2000 05h08m50s -16d23m30s' or 'J2000 05:08:50 -16.23.30' You can omit equinox when you specify center coordinate. In that case, J2000 is assumed. If center is not specified, it will be determined from the observed positions of input data. nx -- number of pixels along x (R.A.) direction. ny -- number of pixels along y (Dec.) direction. cellx -- size of pixel in x (R.A.) direction. celly -- size of pixel in y (Dec.) direction. center -- central position of the grid. """ if not isinstance( cellx, str ): cellx = '%sarcsec'%(cellx) if not isinstance( celly, str ): celly = '%sarcsec'%(celly) self.gridder._defineimage( nx, ny, cellx, celly, center ) def setFunc( self, func='box', convsupport=-1, truncate="-1", gwidth="-1", jwidth="-1" ): """ Set convolution function. Possible options are 'box' (Box-car, default), 'sf' (prolate spheroidal), 'gauss' (Gaussian), and 'gjinc' (Gaussian * Jinc). Width of convolution function can be set using several parameters. For 'box' and 'sf', we have one parameter, convsupport, that specifies a cut-off radius of the convlolution function. By default (-1), convsupport is automatically set depending on each convolution function. Default values for convsupport are: 'box': 1 pixel 'sf': 3 pixels For 'gauss', we have two parameters for convolution function, truncate and gwidth. The truncate is similar to convsupport except that truncate allows to specify its value as float or string consisting of numeric and unit (e.g. '10arcsec' or '3pixel'). Available units are angular units ('arcsec', 'arcmin', 'deg', etc.) and 'pixel'. Default unit is 'pixel' so that if you specify numerical value or string without unit to gwidth, the value will be interpreted as 'pixel'. gwidth is an HWHM of gaussian. It also allows string value. Interpretation of the value for gwidth is same as truncate. Default value for 'gauss' is gwidth: '-1' ---> sqrt(log(2.0)) pixel truncate: '-1' ---> 3*gwidth pixel For 'gjinc', there is an additional parameter jwidth that specifies a width of the jinc function whose functional form is jinc(x) = J_1(pi*x/jwidth) / (pi*x/jwidth) Default values for 'gjinc' is gwidth: '-1' ---> 2.52*sqrt(log(2.0)) pixel jwidth: '-1' ---> 1.55 truncate: '-1' ---> automatically truncate at first null Default values for gwidth and jwidth are taken from Mangum et al. (2007). func -- Function type ('box', 'sf', 'gauss', 'gjinc'). convsupport -- Width of convolution function. Default (-1) is to choose pre-defined value for each convolution function. Effective only for 'box' and 'sf'. truncate -- Truncation radius of the convolution function. Acceptable value is an integer or a float in units of pixel, or a string consisting of numeric plus unit. Default unit for the string is 'pixel'. Default (-1) is to choose pre-defined value for each convolution function. Effective only for 'gauss' and 'gjinc'. gwidth -- The HWHM of the gaussian. Acceptable value is an integer or a float in units of pixel, or a string consisting of numeric plus unit. Default unit for the string is 'pixel'. Default (-1) is to choose pre-defined value for each convolution function. Effective only for 'gauss' and 'gjinc'. jwidth -- The width of the jinc function. Acceptable value is an integer or a float in units of pixel, or a string consisting of numeric plus unit. Default unit for the string is 'pixel'. Default (-1) is to choose pre-defined value for each convolution function. Effective only for 'gjinc'. """ self.gridder._setfunc(func, convsupport=convsupport, truncate=truncate, gwidth=gwidth, jwidth=jwidth) def setWeight( self, weightType='uniform' ): """ Set weight type. Possible options are 'uniform' (default), 'tint' (weight by integration time), 'tsys' (weight by Tsys: 1/Tsys**2), and 'tintsys' (weight by integration time as well as Tsys: tint/Tsys**2). weightType -- weight type ('uniform', 'tint', 'tsys', 'tintsys') """ self.gridder._setweight( weightType ) def enableClip( self ): """ Enable min/max clipping. By default, min/max clipping is disabled so that you should call this method before actual gridding if you want to do clipping. """ self.gridder._enableclip() def disableClip( self ): """ Disable min/max clipping. """ self.gridder._disableclip() def grid( self ): """ Actual gridding which will be done based on several user inputs. """ self.gridder._grid() def plotFunc(self, clear=True): """ Support function to see the shape of current grid function. clear -- clear panel if True. Default is True. """ pl.figure(11) if clear: pl.clf() f = self.gridder._getfunc() convsampling = 100 a = numpy.arange(0,len(f)/convsampling,1./convsampling,dtype=float) pl.plot(a,f,'.-') pl.xlabel('pixel') pl.ylabel('convFunc') def save( self, outfile='' ): raise NotImplementedError('save is not implemented') def plot( self, plotchan=-1, plotpol=-1, plotobs=False, plotgrid=False ): raise NotImplementedError('plot is not implemented') def getResult( self ): raise NotImplementedError('getResult is not implemented') class asapgrid(asapgrid_base): """ The asapgrid class is defined to convolve data onto regular spatial grid. Typical usage is as follows: # create asapgrid instance with two input data g = asapgrid( ['testimage1.asap','testimage2.asap'] ) # set IFNO if necessary g.setIF( 0 ) # set POLNOs if necessary g.setPolList( [0,1] ) # set SCANNOs if necessary g.setScanList( [22,23,24] ) # define image with full specification # you can skip some parameters (see help for defineImage) g.defineImage( nx=12, ny=12, cellx='10arcsec', celly='10arcsec', center='J2000 10h10m10s -5d05m05s' ) # set convolution function g.setFunc( func='sf', convsupport=3 ) # enable min/max clipping g.enableClip() # or, disable min/max clipping #g.disableClip() # actual gridding g.grid() # save result g.save( outfile='grid.asap' ) # plot result g.plot( plotchan=1246, plotpol=-1, plotgrid=True, plotobs=True ) """ def __init__( self, infile ): """ Create asapgrid instance. infile -- input data as a string or string list if you want to grid more than one data at once. """ super(asapgrid,self).__init__() self.gridder = stgrid() self.infile=infile self.setData(infile) def setData( self, infile ): """ Set data to be processed. infile -- input data as a string or string list if you want to grid more than one data at once. """ if isinstance( infile, str ): self.gridder._setin( infile ) else: self.gridder._setfiles( infile ) self.infile = infile def save( self, outfile='' ): """ Save result. By default, output data name will be constructed from first element of input data name list (e.g. 'input.asap.grid'). outfile -- output data name. """ self.outfile = self.gridder._save( outfile ) def plot( self, plotchan=-1, plotpol=-1, plotobs=False, plotgrid=False ): """ Plot gridded data. plotchan -- Which channel you want to plot. Default (-1) is to average all the channels. plotpol -- Which polarization component you want to plot. Default (-1) is to average all the polarization components. plotobs -- Also plot observed position if True. Default is False. Setting True for large amount of spectra might be time consuming. plotgrid -- Also plot grid center if True. Default is False. Setting True for large number of grids might be time consuming. """ import time t0=time.time() # to load scantable on disk storg = rcParams['scantable.storage'] rcParams['scantable.storage'] = 'disk' plotter = _SDGridPlotter( self.infile, self.outfile, self.ifno ) plotter.plot( chan=plotchan, pol=plotpol, plotobs=plotobs, plotgrid=plotgrid ) # back to original setup rcParams['scantable.storage'] = storg t1=time.time() asaplog.push('plot: elapsed time %s sec'%(t1-t0)) asaplog.post('DEBUG','asapgrid.plot') class asapgrid2(asapgrid_base): """ The asapgrid class is defined to convolve data onto regular spatial grid. Typical usage is as follows: # create asapgrid instance with input scantable s = scantable( 'testimage1.asap', average=False ) g = asapgrid( s ) # set IFNO if necessary g.setIF( 0 ) # set POLNOs if necessary g.setPolList( [0,1] ) # set SCANNOs if necessary g.setScanList( [22,23,24] ) # define image with full specification # you can skip some parameters (see help for defineImage) g.defineImage( nx=12, ny=12, cellx='10arcsec', celly='10arcsec', center='J2000 10h10m10s -5d05m05s' ) # set convolution function g.setFunc( func='sf', width=3 ) # enable min/max clipping g.enableClip() # or, disable min/max clipping #g.disableClip() # actual gridding g.grid() # get result as scantable sg = g.getResult() """ def __init__( self, scantab ): """ Create asapgrid instance. scantab -- input data as a scantable or a list of scantables to grid more than one data at once. """ super(asapgrid2,self).__init__() self.gridder = stgrid2() self.scantab = scantab self.setData( scantab ) def setData( self, scantab ): """ Set data to be processed. scantab -- input data as a scantable or a list of scantables to grid more than one data at once. """ if isinstance( scantab, scantable ): self.gridder._setin( scantab ) else: self.gridder._setfiles( scantab ) self.scantab = scantab def getResult( self ): """ Return gridded data as a scantable. """ tp = 0 if rcParams['scantable.storage']=='memory' else 1 return scantable( self.gridder._get( tp ), average=False ) class _SDGridPlotter: def __init__( self, infile, outfile=None, ifno=-1 ): if isinstance( infile, str ): self.infile = [infile] else: self.infile = infile self.outfile = outfile if self.outfile is None: self.outfile = self.infile[0].rstrip('/')+'.grid' self.nx = -1 self.ny = -1 self.nchan = 0 self.npol = 0 self.pollist = [] self.cellx = 0.0 self.celly = 0.0 self.center = [0.0,0.0] self.nonzero = [[0.0],[0.0]] self.ifno = ifno self.tablein = None self.nrow = 0 self.blc = None self.trc = None self.get() def get( self ): s = scantable( self.outfile, average=False ) self.nchan = len(s._getspectrum(0)) nrow = s.nrow() pols = numpy.ones( nrow, dtype=int ) for i in xrange(nrow): pols[i] = s.getpol(i) self.pollist, indices = numpy.unique( pols, return_inverse=True ) self.npol = len(self.pollist) self.pollist = self.pollist[indices[:self.npol]] #print 'pollist=',self.pollist #print 'npol=',self.npol #print 'nrow=',nrow idx = 1 d0 = s.get_direction( 0 ).split()[-2] d = s.get_direction(self.npol*idx) while( d is not None \ and d.split()[-2] != d0): idx += 1 d = s.get_direction(self.npol*idx) self.nx = idx self.ny = nrow / (self.npol * idx ) #print 'nx,ny=',self.nx,self.ny self.blc = s.get_directionval( 0 ) self.trc = s.get_directionval( nrow-self.npol ) #print self.blc #print self.trc if nrow > 1: incrx = s.get_directionval( self.npol ) incry = s.get_directionval( self.nx*self.npol ) else: incrx = [0.0,0.0] incry = [0.0,0.0] self.cellx = abs( self.blc[0] - incrx[0] ) self.celly = abs( self.blc[1] - incry[1] ) #print 'cellx,celly=',self.cellx,self.celly def plot( self, chan=-1, pol=-1, plotobs=False, plotgrid=False ): if pol < 0: opt = 'averaged over pol' else: opt = 'pol %s'%(pol) if type(chan) is list: opt += ', averaged over channel %s-%s'%(chan[0],chan[1]) elif chan < 0: opt += ', averaged over channel' else: opt += ', channel %s'%(chan) data = self.getData( chan, pol ) #data = numpy.fliplr( data ) title = 'Gridded Image (%s)'%(opt) pl.figure(10) pl.clf() # plot grid position if plotgrid: x = numpy.arange(self.blc[0],self.trc[0]+0.5*self.cellx,self.cellx,dtype=float) #print 'len(x)=',len(x) #print 'x=',x ybase = numpy.ones(self.nx,dtype=float)*self.blc[1] #print 'len(ybase)=',len(ybase) incr = self.celly for iy in xrange(self.ny): y = ybase + iy * incr #print y pl.plot(x,y,',',color='blue') # plot observed position if plotobs: for i in xrange(len(self.infile)): self.createTableIn( self.infile[i] ) irow = 0 while ( irow < self.nrow ): chunk = self.getPointingChunk( irow ) #print chunk pl.plot(chunk[0],chunk[1],',',color='green') irow += chunk.shape[1] #print irow # show image extent=[self.trc[0]+0.5*self.cellx, self.blc[0]-0.5*self.cellx, self.blc[1]-0.5*self.celly, self.trc[1]+0.5*self.celly] deccorr = 1.0/numpy.cos(0.5*(self.blc[1]+self.trc[1])) pl.imshow(data,extent=extent,origin='lower',interpolation='nearest') pl.colorbar() pl.xlabel('R.A. [rad]') pl.ylabel('Dec. [rad]') ax = pl.axes() ax.set_aspect(deccorr) pl.title( title ) def createTableIn( self, tab ): del self.tablein self.tablein = scantable( tab, average=False ) if self.ifno < 0: ifno = self.tablein.getif(0) #print 'ifno=',ifno else: ifno = self.ifno sel = selector() sel.set_ifs( ifno ) self.tablein.set_selection( sel ) self.nchan = len(self.tablein._getspectrum(0)) self.nrow = self.tablein.nrow() del sel def getPointingChunk( self, irow ): numchunk = 1000 nrow = min( self.nrow-irow, numchunk ) #print 'nrow=',nrow v = numpy.zeros( (2,nrow), dtype=float ) idx = 0 for i in xrange(irow,irow+nrow): d = self.tablein.get_directionval( i ) v[0,idx] = d[0] v[1,idx] = d[1] idx += 1 return v def getData( self, chan=-1, pol=-1 ): if type(chan) == list: spectra = self.__chanAverage(start=chan[0],end=chan[1]) elif chan == -1: spectra = self.__chanAverage() else: spectra = self.__chanIndex( chan ) data = spectra.reshape( (self.npol,self.ny,self.nx) ) if pol == -1: retval = data.mean(axis=0) else: retval = data[pol] return retval def __chanAverage( self, start=-1, end=-1 ): s = scantable( self.outfile, average=False ) nrow = s.nrow() spectra = numpy.zeros( (self.npol,nrow/self.npol), dtype=float ) irow = 0 sp = [0 for i in xrange(self.nchan)] if start < 0: start = 0 if end < 0: end = self.nchan for i in xrange(nrow/self.npol): for ip in xrange(self.npol): sp = s._getspectrum( irow )[start:end] spectra[ip,i] = numpy.mean( sp ) irow += 1 return spectra def __chanIndex( self, idx ): s = scantable( self.outfile, average=False ) nrow = s.nrow() spectra = numpy.zeros( (self.npol,nrow/self.npol), dtype=float ) irow = 0 sp = [0 for i in xrange(self.nchan)] for i in xrange(nrow/self.npol): for ip in xrange(self.npol): sp = s._getspectrum( irow ) spectra[ip,i] = sp[idx] irow += 1 return spectra