def test40(self): '''cvel2 40: test effect of sign of width parameter: radio velocity mode, width negative''' self.setUp_vis_b() myvis = vis_b os.system('ln -sf ' + myvis + ' myinput.ms') mytb.open('myinput.ms/SPECTRAL_WINDOW') a = mytb.getcell('CHAN_FREQ') c = qa.constants('c')['value'] mytb.close() restf = a[0] bv1 = c * (restf - a[3]) / restf bv2 = c * (restf - a[4]) / restf wv = abs(bv2 - bv1) b = numpy.array([a[3], a[4], a[5]]) rval = cvel2(vis='myinput.ms', outputvis=outfile, mode='velocity', veltype='radio', nchan=3, start=str(bv1) + 'm/s', width="-" + str(wv) + 'm/s', restfreq=str(restf) + 'Hz') self.assertNotEqual(rval, False) ret = verify_ms(outfile, 1, 3, 0, b) self.assertTrue(ret[0], ret[1])
def test42(self): '''cvel2 42: test effect of sign of width parameter: optical velocity mode, width negative''' self.setUp_vis_b() myvis = vis_b os.system('ln -sf ' + myvis + ' myinput.ms') mytb.open('myinput.ms/SPECTRAL_WINDOW') a = mytb.getcell('CHAN_FREQ') c = qa.constants('c')['value'] mytb.close() restf = a[0] bv1 = c * (restf - a[5]) / a[5] bv2 = c * (restf - a[4]) / a[4] wv = abs(bv2 - bv1 + 1.) bv2 = bv1 + wv bv3 = bv2 + wv a4 = restf / (bv2 / c + 1.) a3 = restf / (bv3 / c + 1.) b = numpy.array([a3, a4, a[5]]) rval = cvel2(vis='myinput.ms', outputvis=outfile, mode='velocity', veltype='optical', nchan=3, start=str(bv3) + 'm/s', width='-' + str(wv) + 'm/s', restfreq=str(restf) + 'Hz') self.assertNotEqual(rval, False) ret = verify_ms(outfile, 1, 3, 0, b) self.assertTrue(ret[0], ret[1])
def test41(self): '''cvel2 41: test effect of sign of width parameter: optical velocity mode, width positive''' self.setUp_vis_b() myvis = vis_b os.system('ln -sf ' + myvis + ' myinput.ms') mytb.open('myinput.ms/SPECTRAL_WINDOW') a = mytb.getcell('CHAN_FREQ') c = qa.constants('c')['value'] mytb.close() restf = a[0] bv1 = c * (restf-a[5])/a[5] bv2 = c * (restf-a[4])/a[4] wv = abs(bv2-bv1+1.) bv2 = bv1 + wv bv3 = bv2 + wv a4 = restf/(bv2/c+1.) a3 = restf/(bv3/c+1.) b = numpy.array([a3, a4, a[5]]) rval = cvel2( vis = 'myinput.ms', outputvis = outfile, mode = 'velocity', veltype = 'optical', nchan = 3, start = str(bv1)+'m/s', width=str(wv)+'m/s', restfreq=str(restf)+'Hz' ) self.assertNotEqual(rval,False) ret = verify_ms(outfile, 1, 3, 0, b) self.assertTrue(ret[0],ret[1])
def test40(self): '''cvel2 40: test effect of sign of width parameter: radio velocity mode, width negative''' self.setUp_vis_b() myvis = vis_b os.system('ln -sf ' + myvis + ' myinput.ms') mytb.open('myinput.ms/SPECTRAL_WINDOW') a = mytb.getcell('CHAN_FREQ') c = qa.constants('c')['value'] mytb.close() restf = a[0] bv1 = c * (restf-a[3])/restf bv2 = c * (restf-a[4])/restf wv = abs(bv2-bv1) b = numpy.array([a[3], a[4], a[5]]) rval = cvel2( vis = 'myinput.ms', outputvis = outfile, mode = 'velocity', veltype = 'radio', nchan = 3, start = str(bv1)+'m/s', width="-"+str(wv)+'m/s', restfreq=str(restf)+'Hz' ) self.assertNotEqual(rval,False) ret = verify_ms(outfile, 1, 3, 0, b) self.assertTrue(ret[0],ret[1])
restfreq = None plot_profile_map(image, figfile, pol, spectralaxis, restfreq, title, linecolor, linestyle, linewidth, separatepanel, plotmasked, maskedcolor, showaxislabel, showtick, showticklabel, parsed_size, nx, ny, transparent, plotrange) except Exception, e: casalog.post('Error: %s'%(str(e)), priority='SEVERE') import traceback casalog.post(traceback.format_exc(), priority='DEBUG') raise e finally: pass NoData = -32767.0 NoDataThreshold = NoData + 10000.0 LightSpeedQuantity = qa.constants('c') LightSpeed = qa.convert(LightSpeedQuantity, 'km/s')['value'] # speed of light in km/s DPIDetail = 130 dsyb = '$^\circ$' hsyb = ':' msyb = ':' def Deg2HMS(x, arrowance): # Transform degree to HHMMSS.sss format xx = x % 360 + arrowance h = int(xx / 15) m = int((xx % 15) * 4) s = ((xx % 15) * 4 - m) * 60.0 return (h, m, s)
def imreg(vis=None, ephem=None, msinfo=None, imagefile=None, timerange=None, reftime=None, fitsfile=None, beamfile=None, offsetfile=None, toTb=None, sclfactor=1.0, verbose=False, p_ang=False, overwrite=True, usephacenter=True, deletehistory=False, subregion=[], docompress=False): ''' main routine to register CASA images Required Inputs: vis: STRING. CASA measurement set from which the image is derived imagefile: STRING or LIST. name of the input CASA image timerange: STRING or LIST. timerange used to generate the CASA image, must have the same length as the input images. Each element should be in CASA standard time format, e.g., '2012/03/03/12:00:00~2012/03/03/13:00:00' Optional Inputs: msinfo: DICTIONARY. CASA MS information, output from read_msinfo. If not provided, generate one from the supplied vis ephem: DICTIONARY. solar ephem, output from read_horizons. If not provided, query JPL Horizons based on time info of the vis (internet connection required) fitsfile: STRING or LIST. name of the output registered fits files reftime: STRING or LIST. Each element should be in CASA standard time format, e.g., '2012/03/03/12:00:00' offsetfile: optionally provide an offset with a series of solar x and y offsets with timestamps toTb: Bool. Convert the default Jy/beam to brightness temperature? sclfactor: scale the image values up by its value (to compensate VLA 20 dB attenuator) verbose: Bool. Show more diagnostic info if True. usephacenter: Bool -- if True, correct for the RA and DEC in the ms file based on solar empheris. Otherwise assume the phasecenter is correctly pointed to the solar disk center (EOVSA case) subregion: Region selection. See 'help par.region' for details. Usage: >>> from suncasa.utils import helioimage2fits as hf >>> hf.imreg(vis='mydata.ms', imagefile='myimage.image', fitsfile='myimage.fits', timerange='2017/08/21/20:21:10~2017/08/21/20:21:18') The output fits file is 'myimage.fits' History: BC (sometime in 2014): function was first wrote, followed by a number of edits by BC and SY BC (2019-07-16): Added checks for stokes parameter. Verified that for converting from Jy/beam to brightness temperature, the convention of 2*k_b*T should always be used. I.e., for unpolarized source, stokes I, RR, LL, XX, YY, etc. in the output CASA images from (t)clean should all have same values of radio intensity (in Jy/beam) and brightness temperature (in K). ''' if deletehistory: ms_clearhistory(vis) if not imagefile: raise ValueError('Please specify input image') if not timerange: raise ValueError('Please specify timerange of the input image') if type(imagefile) == str: imagefile = [imagefile] if type(timerange) == str: timerange = [timerange] if not fitsfile: fitsfile = [img + '.fits' for img in imagefile] if type(fitsfile) == str: fitsfile = [fitsfile] nimg = len(imagefile) if len(timerange) != nimg: raise ValueError( 'Number of input images does not equal to number of timeranges!') if len(fitsfile) != nimg: raise ValueError( 'Number of input images does not equal to number of output fits files!' ) nimg = len(imagefile) if verbose: print(str(nimg) + ' images to process...') if reftime: # use as reference time to find solar disk RA and DEC to register the image, but not the actual timerange associated with the image if type(reftime) == str: reftime = [reftime] * nimg if len(reftime) != nimg: raise ValueError( 'Number of reference times does not match that of input images!' ) helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=reftime, usephacenter=usephacenter) else: # use the supplied timerange to register the image helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=timerange, usephacenter=usephacenter) if toTb: (bmajs, bmins, bpas, beamunits, bpaunits) = getbeam(imagefile=imagefile, beamfile=beamfile) for n, img in enumerate(imagefile): if verbose: print('processing image #' + str(n) + ' ' + img) fitsf = fitsfile[n] timeran = timerange[n] # obtain duration of the image as FITS header exptime try: [tbg0, tend0] = timeran.split('~') tbg_d = qa.getvalue(qa.convert(qa.totime(tbg0), 'd'))[0] tend_d = qa.getvalue(qa.convert(qa.totime(tend0), 'd'))[0] tdur_s = (tend_d - tbg_d) * 3600. * 24. dateobs = qa.time(qa.quantity(tbg_d, 'd'), form='fits', prec=10)[0] except: print('Error in converting the input timerange: ' + str(timeran) + '. Proceeding to the next image...') continue hel = helio[n] if not os.path.exists(img): warnings.warn('{} does not existed!'.format(img)) else: if os.path.exists(fitsf) and not overwrite: raise ValueError( 'Specified fits file already exists and overwrite is set to False. Aborting...' ) else: p0 = hel['p0'] tb.open(img + '/logtable', nomodify=False) nobs = tb.nrows() tb.removerows([i + 1 for i in range(nobs - 1)]) tb.close() ia.open(img) imr = ia.rotate(pa=str(-p0) + 'deg') if subregion is not []: imr = imr.subimage(region=subregion) imr.tofits(fitsf, history=False, overwrite=overwrite) imr.close() imsum = ia.summary() ia.close() ia.done() # construct the standard fits header # RA and DEC of the reference pixel crpix1 and crpix2 (imra, imdec) = (imsum['refval'][0], imsum['refval'][1]) # find out the difference of the image center to the CASA phase center # RA and DEC difference in arcseconds ddec = degrees((imdec - hel['dec_fld'])) * 3600. dra = degrees((imra - hel['ra_fld']) * cos(hel['dec_fld'])) * 3600. # Convert into image heliocentric offsets prad = -radians(hel['p0']) dx = (-dra) * cos(prad) - ddec * sin(prad) dy = (-dra) * sin(prad) + ddec * cos(prad) if offsetfile: try: offset = np.load(offsetfile) except: raise ValueError( 'The specified offsetfile does not exist!') reftimes_d = offset['reftimes_d'] xoffs = offset['xoffs'] yoffs = offset['yoffs'] timg_d = hel['reftime'] ind = bisect.bisect_left(reftimes_d, timg_d) xoff = xoffs[ind - 1] yoff = yoffs[ind - 1] else: xoff = hel['refx'] yoff = hel['refy'] if verbose: print( 'offset of image phase center to visibility phase center (arcsec): dx={0:.2f}, dy={1:.2f}' .format(dx, dy)) print( 'offset of visibility phase center to solar disk center (arcsec): dx={0:.2f}, dy={1:.2f}' .format(xoff, yoff)) (crval1, crval2) = (xoff + dx, yoff + dy) # update the fits header to heliocentric coordinates hdu = pyfits.open(fitsf, mode='update') hdu[0].verify('fix') header = hdu[0].header dshape = hdu[0].data.shape ndim = hdu[0].data.ndim (cdelt1, cdelt2) = (-header['cdelt1'] * 3600., header['cdelt2'] * 3600. ) # Original CDELT1, 2 are for RA and DEC in degrees header['cdelt1'] = cdelt1 header['cdelt2'] = cdelt2 header['cunit1'] = 'arcsec' header['cunit2'] = 'arcsec' header['crval1'] = crval1 header['crval2'] = crval2 header['ctype1'] = 'HPLN-TAN' header['ctype2'] = 'HPLT-TAN' header['date-obs'] = dateobs # begin time of the image if not p_ang: hel['p0'] = 0 try: # this works for pyfits version of CASA 4.7.0 but not CASA 4.6.0 if tdur_s: header.set('exptime', tdur_s) else: header.set('exptime', 1.) header.set('p_angle', hel['p0']) header.set('hgln_obs', 0.) header.set('rsun_ref', sun.constants.radius.value) if sunpyver <= 1: header.set( 'dsun_obs', sun.sunearth_distance(Time(dateobs)).to(u.meter).value) header.set( 'rsun_obs', sun.solar_semidiameter_angular_size( Time(dateobs)).value) header.set( 'hglt_obs', sun.heliographic_solar_center(Time(dateobs))[1].value) else: header.set( 'dsun_obs', sun.earth_distance(Time(dateobs)).to(u.meter).value) header.set('rsun_obs', sun.angular_radius(Time(dateobs)).value) header.set('hglt_obs', sun.L0(Time(dateobs)).value) except: # this works for astropy.io.fits if tdur_s: header.append(('exptime', tdur_s)) else: header.append(('exptime', 1.)) header.append(('p_angle', hel['p0'])) header.append(('hgln_obs', 0.)) header.append(('rsun_ref', sun.constants.radius.value)) if sunpyver <= 1: header.append( ('dsun_obs', sun.sunearth_distance(Time(dateobs)).to( u.meter).value)) header.append(('rsun_obs', sun.solar_semidiameter_angular_size( Time(dateobs)).value)) header.append(('hglt_obs', sun.heliographic_solar_center( Time(dateobs))[1].value)) else: header.append( ('dsun_obs', sun.earth_distance(Time(dateobs)).to(u.meter).value)) header.append( ('rsun_obs', sun.angular_radius(Time(dateobs)).value)) header.append(('hglt_obs', sun.L0(Time(dateobs)).value)) # check if stokes parameter exist exist_stokes = False stokes_mapper = { 'I': 1, 'Q': 2, 'U': 3, 'V': 4, 'RR': -1, 'LL': -2, 'RL': -3, 'LR': -4, 'XX': -5, 'YY': -6, 'XY': -7, 'YX': -8 } if 'CRVAL3' in header.keys(): if header['CTYPE3'] == 'STOKES': stokenum = header['CRVAL3'] exist_stokes = True if 'CRVAL4' in header.keys(): if header['CTYPE4'] == 'STOKES': stokenum = header['CRVAL4'] exist_stokes = True if exist_stokes: if stokenum in stokes_mapper.values(): stokesstr = list(stokes_mapper.keys())[list( stokes_mapper.values()).index(stokenum)] else: print('Stokes parameter {0:d} not recognized'.format( stokenum)) if verbose: print('This image is in Stokes ' + stokesstr) else: print( 'STOKES Information does not seem to exist! Assuming Stokes I' ) stokenum = 1 # intensity units to brightness temperature if toTb: # get restoring beam info bmaj = bmajs[n] bmin = bmins[n] beamunit = beamunits[n] data = hdu[ 0].data # remember the data order is reversed due to the FITS convension keys = list(header.keys()) values = list(header.values()) # which axis is frequency? faxis = keys[values.index('FREQ')][-1] faxis_ind = ndim - int(faxis) # find out the polarization of this image k_b = qa.constants('k')['value'] c_l = qa.constants('c')['value'] # Always use 2*kb for all polarizations const = 2. * k_b / c_l**2 if header['BUNIT'].lower() == 'jy/beam': header['BUNIT'] = 'K' header['BTYPE'] = 'Brightness Temperature' for i in range(dshape[faxis_ind]): nu = header['CRVAL' + faxis] + header['CDELT' + faxis] * ( i + 1 - header['CRPIX' + faxis]) if header['CUNIT' + faxis] == 'KHz': nu *= 1e3 if header['CUNIT' + faxis] == 'MHz': nu *= 1e6 if header['CUNIT' + faxis] == 'GHz': nu *= 1e9 if len(bmaj) > 1: # multiple (per-plane) beams bmajtmp = bmaj[i] bmintmp = bmin[i] else: # one single beam bmajtmp = bmaj[0] bmintmp = bmin[0] if beamunit == 'arcsec': bmaj0 = np.radians(bmajtmp / 3600.) bmin0 = np.radians(bmintmp / 3600.) if beamunit == 'arcmin': bmaj0 = np.radians(bmajtmp / 60.) bmin0 = np.radians(bmintmp / 60.) if beamunit == 'deg': bmaj0 = np.radians(bmajtmp) bmin0 = np.radians(bmintmp) if beamunit == 'rad': bmaj0 = bmajtmp bmin0 = bmintmp beam_area = bmaj0 * bmin0 * np.pi / (4. * log(2.)) factor = const * nu**2 # SI unit jy_to_si = 1e-26 # print(nu/1e9, beam_area, factor) factor2 = sclfactor # if sclfactor: # factor2 = 100. if faxis == '3': data[:, i, :, :] *= jy_to_si / beam_area / factor * factor2 if faxis == '4': data[ i, :, :, :] *= jy_to_si / beam_area / factor * factor2 header = fu.headerfix(header) hdu.flush() hdu.close() if ndim - np.count_nonzero(np.array(dshape) == 1) > 3: docompress = False ''' Caveat: only 1D, 2D, or 3D images are currently supported by the astropy fits compression. If a n-dimensional image data array does not have at least n-3 single-dimensional entries, force docompress to be False ''' print( 'warning: The fits data contains more than 3 non squeezable dimensions. Skipping fits compression..' ) if docompress: fitsftmp = fitsf + ".tmp.fits" os.system("mv {} {}".format(fitsf, fitsftmp)) hdu = pyfits.open(fitsftmp) hdu[0].verify('fix') header = hdu[0].header data = hdu[0].data fu.write_compressed_image_fits(fitsf, data, header, compression_type='RICE_1', quantize_level=4.0) os.system("rm -rf {}".format(fitsftmp)) if deletehistory: ms_restorehistory(vis) return fitsfile
def imreg(vis=None, ephem=None, msinfo=None, reftime=None, imagefile=None, fitsfile=None, beamfile=None, \ offsetfile=None, toTb=None, scl100=None, verbose=False, p_ang = False, overwrite = True, usephacenter=False): ia = iatool() if not imagefile: raise ValueError, 'Please specify input image' if not reftime: raise ValueError, 'Please specify reference time corresponding to the input image' if not fitsfile: fitsfile = [img + '.fits' for img in imagefile] if len(imagefile) != len(reftime): raise ValueError, 'Number of input images does not equal to number of helio coord headers!' if len(imagefile) != len(fitsfile): raise ValueError, 'Number of input images does not equal to number of output fits files!' nimg = len(imagefile) if verbose: print str(nimg) + ' images to process...' helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=reftime, usephacenter=usephacenter) for n, img in enumerate(imagefile): if verbose: print 'processing image #' + str(n) fitsf = fitsfile[n] hel = helio[n] if not os.path.exists(img): raise ValueError, 'Please specify input image' if os.path.exists(fitsf) and not overwrite: raise ValueError, 'Specified fits file already exists and overwrite is set to False. Aborting...' else: p0 = hel['p0'] ia.open(img) imr = ia.rotate(pa=str(-p0) + 'deg') imr.tofits(fitsf, history=False, overwrite=overwrite) imr.close() sum = ia.summary() ia.close() # construct the standard fits header # RA and DEC of the reference pixel crpix1 and crpix2 (imra, imdec) = (sum['refval'][0], sum['refval'][1]) # find out the difference of the image center to the CASA phase center # RA and DEC difference in arcseconds ddec = degrees((imdec - hel['dec_fld'])) * 3600. dra = degrees((imra - hel['ra_fld']) * cos(hel['dec_fld'])) * 3600. # Convert into image heliocentric offsets prad = -radians(hel['p0']) dx = (-dra) * cos(prad) - ddec * sin(prad) dy = (-dra) * sin(prad) + ddec * cos(prad) if offsetfile: try: offset = np.load(offsetfile) except: raise ValueError, 'The specified offsetfile does not exist!' reftimes_d = offset['reftimes_d'] xoffs = offset['xoffs'] yoffs = offset['yoffs'] timg_d = hel['reftime'] ind = bisect.bisect_left(reftimes_d, timg_d) xoff = xoffs[ind - 1] yoff = yoffs[ind - 1] else: xoff = hel['refx'] yoff = hel['refy'] if verbose: print 'offset of image phase center to visibility phase center (arcsec): ', dx, dy print 'offset of visibility phase center to solar disk center (arcsec): ', xoff, yoff (crval1, crval2) = (xoff + dx, yoff + dy) # update the fits header to heliocentric coordinates hdu = pyfits.open(fitsf, mode='update') header = hdu[0].header (cdelt1, cdelt2) = (-header['cdelt1'] * 3600., header['cdelt2'] * 3600. ) # Original CDELT1, 2 are for RA and DEC in degrees header['cdelt1'] = cdelt1 header['cdelt2'] = cdelt2 header['cunit1'] = 'arcsec' header['cunit2'] = 'arcsec' header['crval1'] = crval1 header['crval2'] = crval2 header['ctype1'] = 'HPLN-TAN' header['ctype2'] = 'HPLT-TAN' header['date-obs'] = hel['date-obs'] #begin time of the image if not p_ang: hel['p0'] = 0 try: # this works for pyfits version of CASA 4.7.0 but not CASA 4.6.0 header.update('exptime', hel['exptime']) header.update('p_angle', hel['p0']) header.update( 'dsun_obs', sun.sunearth_distance(Time(hel['date-obs'])).to(u.meter).value) header.update( 'rsun_obs', sun.solar_semidiameter_angular_size(Time( hel['date-obs'])).value) header.update('rsun_ref', sun.constants.radius.value) header.update('hgln_obs', 0.) header.update( 'hglt_obs', sun.heliographic_solar_center(Time(hel['date-obs']))[1].value) except: # this works for astropy.io.fits header.append(('exptime', hel['exptime'])) header.append(('p_angle', hel['p0'])) header.append( ('dsun_obs', sun.sunearth_distance(Time(hel['date-obs'])).to( u.meter).value)) header.append(('rsun_obs', sun.solar_semidiameter_angular_size( Time(hel['date-obs'])).value)) header.append(('rsun_ref', sun.constants.radius.value)) header.append(('hgln_obs', 0.)) header.append(('hglt_obs', sun.heliographic_solar_center(Time( hel['date-obs']))[1].value)) # header.update('comment', 'Fits header updated to heliocentric coordinates by Bin Chen') # update intensity units, i.e. to brightness temperature? if toTb: # get restoring beam info (bmajs, bmins, bpas, beamunits, bpaunits) = getbeam(imagefile=imagefile, beamfile=beamfile) bmaj = bmajs[n] bmin = bmins[n] beamunit = beamunits[n] data = hdu[ 0].data # remember the data order is reversed due to the FITS convension dim = data.ndim sz = data.shape keys = header.keys() values = header.values() # which axis is frequency? faxis = keys[values.index('FREQ')][-1] faxis_ind = dim - int(faxis) if header['BUNIT'].lower() == 'jy/beam': header['BUNIT'] = 'K' for i in range(sz[faxis_ind]): nu = header['CRVAL' + faxis] + header['CDELT' + faxis] * \ (i + 1 - header['CRPIX' + faxis]) if header['CUNIT' + faxis] == 'KHz': nu *= 1e3 if header['CUNIT' + faxis] == 'MHz': nu *= 1e6 if header['CUNIT' + faxis] == 'GHz': nu *= 1e9 if len(bmaj) > 1: # multiple (per-plane) beams bmajtmp = bmaj[i] bmintmp = bmin[i] else: # one single beam bmajtmp = bmaj[0] bmintmp = bmin[0] if beamunit == 'arcsec': bmaj0 = np.radians(bmajtmp / 3600.) bmin0 = np.radians(bmajtmp / 3600.) if beamunit == 'arcmin': bmaj0 = np.radians(bmajtmp / 60.) bmin0 = np.radians(bmintmp / 60.) if beamunit == 'deg': bmaj0 = np.radians(bmajtmp) bmin0 = np.radians(bmintmp) if beamunit == 'rad': bmaj0 = bmajtmp bmin0 = bmintmp beam_area = bmaj0 * bmin0 * np.pi / (4. * log(2.)) k_b = qa.constants('k')['value'] c_l = qa.constants('c')['value'] factor = 2. * k_b * nu**2 / c_l**2 # SI unit jy_to_si = 1e-26 # print nu/1e9, beam_area, factor factor2 = 1. if scl100: factor2 = 100. if faxis == '3': data[:, i, :, :] *= jy_to_si / beam_area / factor * factor2 if faxis == '4': data[ i, :, :, :] *= jy_to_si / beam_area / factor * factor2 hdu.flush() hdu.close()
def plotcomp(compdict, showplot=True, wantdict=False, symb=',', include0amp=False, include0bl=False, blunit='', bl0flux=0.0): """ Given a dict including {'clist': component list, 'objname': objname, 'epoch': epoch, 'shape': component shape dict, including direction. 'freqs (GHz)': pl.array of frequencies, 'antennalist': An array configuration file as used by simdata, 'savedfig': False or, if specified, the filename to save the plot to, 'standard': setjy fluxstandard type}, and symb: One of matplotlib's codes for plot symbols: .:,o^v<>s+xDd234hH|_ default: ',': The smallest points I could find, make a plot of visibility amplitude vs. baseline length for clist at epoch. If antennalist is not found as is, it will look for antennalist in os.getenv('CASAPATH').split(' ')[0] + '/data/alma/simmos/'. showplot: Whether or not to show the plot on screen. If wantdict is True, it returns a dictionary with the amplitudes and baselines on success. Otherwise, it returns True or False as its estimated success value. include0amp: Force the lower limit of the amplitude axis to 0. include0bl: Force the lower limit of the baseline length axis to 0. blunit: unit of the baseline length (='' used the unit in the data or klambda) bl0flux: Zero baseline flux """ def failval(): """ Returns an appropriate failure value. Note that mydict.update(plotcomp(wantdict=True, ...)) would give a confusing error message if plotcomp returned False. """ retval = False if wantdict: retval = {} return retval retval = failval() # Default try: clist = compdict['clist'] objname = compdict['objname'] epoch = compdict['epoch'] epstr = mepoch_to_str(epoch) antennalist = compdict['antennalist'] # Read the configuration info. if not antennalist: print "compdict['antennalist'] must be set!" print "Try something in", os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/" return failval() # Try repodir if raw antennalist doesn't work. if not os.path.exists(antennalist): repodir = os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/" antennalist = repodir + antennalist su = simutil("") stnx, stny, stnz, diam, padnames, telescopename, obsmeas = su.readantenna(antennalist) #print "telescopename:", telescopename # Check that the source is up. myme = metool() posobs = myme.observatory(telescopename) #print "posobs:", posobs myme.doframe(epoch) myme.doframe(posobs) azel = myme.measure(compdict['shape']['direction'], 'azel') azeldegs = tuple([qa.convert(azel[m], 'deg')['value'] for m in ('m0', 'm1')]) casalog.post("(az, el): (%.2f, %.2f) degrees" % azeldegs) # riseset blabs to the logger, so introduce it now. casalog.post('Rise and set times of ' + objname + " from " + telescopename + ':') approx = '' if 'JPL' in compdict.get('standard', 'JPL'): # The object is in the Solar System or not known to be extragalactic. approx = "APPROXIMATE. The times do not account for the apparent motion of "\ + objname + "." casalog.post(" (" + approx + ")") riset = myme.riseset(compdict['shape']['direction']) msg = '' if riset['rise'] == 'above': msg = objname + " is circumpolar" elif riset['rise'] == 'below': msg = objname + ' is not visible from ' + telescopename if msg: if approx: msg += ' around ' + mepoch_to_str(epoch) casalog.post(msg) else: for t in riset: riset[t]['str'] = mepoch_to_str(riset[t]['utc']) casalog.post(objname + " rises at %s and sets at %s." % (riset['rise']['str'], riset['set']['str'])) tmeridian=(riset['rise']['utc']['m0']['value']+riset['set']['utc']['m0']['value'])/2. casalog.post(objname + ': meridian passage at ' + qa.time(str(tmeridian)+'d')[0]) if approx: riset['NOTE'] = approx if not azel['m1']['value'] > 0.0: casalog.post(objname + " is not visible from " + telescopename + " at " + epstr, 'SEVERE') if wantdict: return riset else: return False # Start a temp MS. workingdir = os.path.abspath(os.path.dirname(clist.rstrip('/'))) tempms = tempfile.mkdtemp(prefix=objname, dir=workingdir) mysm = smtool() mysm.open(tempms) su.setcfg(mysm, telescopename, stnx, stny, stnz, diam, padnames, posobs) #print "cfg set" # Only 1 polarization is wanted for now. stokes, feeds = su.polsettings(telescopename, 'RR') casalog.post("stokes, feeds: %s, %s" % (stokes, feeds)) fband = su.bandname(compdict['freqs (GHz)'][0]) chaninc = 1.0 nchan = len(compdict['freqs (GHz)']) if nchan > 1: chaninc = (compdict['freqs (GHz)'][-1] - compdict['freqs (GHz)'][0]) / (nchan - 1) mysm.setspwindow(spwname=fband, freq=str(compdict['freqs (GHz)'][0]) + 'GHz', deltafreq=str(chaninc) + 'GHz', freqresolution='1Hz', nchannels=nchan, refcode="LSRK", stokes=stokes) mysm.setfeed(mode=feeds, pol=['']) mysm.setlimits(shadowlimit=0.01, elevationlimit='10deg') mysm.setauto(0.0) mysm.setfield(sourcename=objname, sourcedirection=compdict['shape']['direction'], calcode="OBJ", distance='0m') mysm.settimes(integrationtime="1s", usehourangle=False, referencetime=epoch) # this only creates blank uv entries mysm.observe(sourcename=objname, spwname=fband, starttime="-0.5s", stoptime="0.5s", project=objname) mysm.setdata(fieldid=[0]) mysm.setvp() casalog.post("done setting up simulation parameters") mysm.predict(complist=clist) # do actual calculation of visibilities: mysm.close() casalog.post("Simulation finished.") mytb = tbtool() mytb.open(tempms) data = mytb.getcol('DATA')[0] # Again, only 1 polarization for now. data = abs(data) baselines = mytb.getcol('UVW')[:2,:] # Drop w. datablunit = mytb.getcolkeywords('UVW')['QuantumUnits'] mytb.close() #print "Got the data and baselines" shutil.rmtree(tempms) if datablunit[1] != datablunit[0]: casalog.post('The baseline units are mismatched!: %s' % datablunit, 'SEVERE') return failval() datablunit = datablunit[0] # uv dist unit in klambda or m if datablunit == 'm' and blunit=='klambda': kl = qa.constants('C')['value']/(compdict['freqs (GHz)'][0]*1e6) blunit = 'k$\lambda$' else: blunit = datablunit kl = 1.0 pl.ioff() #baselines = pl.hypot(baselines[0]/kl, baselines[1]/kl) baselines = pl.hypot(baselines[0], baselines[1]) #if not showplot: # casalog.post('Sorry, not showing the plot is not yet implemented', # 'WARN') if showplot: pl.ion() pl.clf() pl.ioff() nfreqs = len(compdict['freqs (GHz)']) for freqnum in xrange(nfreqs): freq = compdict['freqs (GHz)'][freqnum] casalog.post("Plotting " + str(freq) + " GHz.") pl.plot(baselines/kl, data[freqnum], symb, label="%.3g GHz" % freq) #pl.plot(baselines, data[freqnum], symb, label="%.3g GHz" % freq) pl.xlabel("Baseline length (" + blunit + ")") pl.ylabel("Visibility amplitude (Jy)") if include0amp: pl.ylim(ymin=0.0) if include0bl: pl.xlim(xmin=0.0) pl.suptitle(objname + " (predicted by %s)" % compdict['standard'], fontsize=14) #pl.suptitle(objname + " (predicted)", fontsize=14) # Unlike compdict['antennalist'], antennalist might have had repodir # prefixed to it. pl.title('at ' + epstr + ' for ' + os.path.basename(compdict['antennalist']), fontsize=10) titletxt='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs # for comparison of old and new models - omit azeldegs as all in az~0 if bl0flux > 0.0: if len(compdict['freqs (GHz)']) == 1: titletxt+='\n bl0 flux:%.3f Jy' % bl0flux else: titletxt+='\n bl0 flux:%.3f Jy @ %s GHz' % (bl0flux, compdict['freqs (GHz)'][0]) pl.legend(loc='best', title=titletxt) #pl.legend(loc='best', title='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs) y_formatter=matplotlib.ticker.ScalarFormatter(useOffset=False) pl.axes().yaxis.set_major_formatter(y_formatter) if showplot: pl.ion() pl.draw() if compdict.get('savedfig'): pl.savefig(compdict.get('savedfig')) casalog.post("Saved plot to " + str(compdict.get('savedfig'))) if wantdict: retval = {'amps': data, 'antennalist': antennalist, # Absolute path, now. 'azel': azel, 'baselines': baselines, 'blunit': blunit, 'riseset': riset, 'savedfig': compdict.get('savedfig')} else: retval = True except Exception, instance: casalog.post(str(instance), 'SEVERE') if os.path.isdir(tempms): shutil.rmtree(tempms)
def imreg(vis=None, ephem=None, msinfo=None, imagefile=None, timerange=None, reftime=None, fitsfile=None, beamfile=None, offsetfile=None, toTb=None, scl100=None, verbose=False, p_ang=False, overwrite=True, usephacenter=True, deletehistory=False): ''' main routine to register CASA images Required Inputs: vis: STRING. CASA measurement set from which the image is derived imagefile: STRING or LIST. name of the input CASA image timerange: STRING or LIST. timerange used to generate the CASA image, must have the same length as the input images. Each element should be in CASA standard time format, e.g., '2012/03/03/12:00:00~2012/03/03/13:00:00' Optional Inputs: msinfo: DICTIONARY. CASA MS information, output from read_msinfo. If not provided, generate one from the supplied vis ephem: DICTIONARY. solar ephem, output from read_horizons. If not provided, query JPL Horizons based on time info of the vis (internet connection required) fitsfile: STRING or LIST. name of the output registered fits files reftime: STRING or LIST. Each element should be in CASA standard time format, e.g., '2012/03/03/12:00:00' offsetfile: optionally provide an offset with a series of solar x and y offsets with timestamps toTb: Bool. Convert the default Jy/beam to brightness temperature? scl100: Bool. If True, scale the image values up by 100 (to compensate VLA 20 dB attenuator) verbose: Bool. Show more diagnostic info if True. usephacenter: Bool -- if True, correct for the RA and DEC in the ms file based on solar empheris. Otherwise assume the phasecenter is correctly pointed to the solar disk center (EOVSA case) ''' ia = iatool() if deletehistory: msclearhistory(vis) if verbose: import time t0 = time.time() prtidx = 1 print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 if not imagefile: raise ValueError, 'Please specify input image' if not timerange: raise ValueError, 'Please specify timerange of the input image' if type(imagefile) == str: imagefile = [imagefile] if type(timerange) == str: timerange = [timerange] if not fitsfile: fitsfile = [img + '.fits' for img in imagefile] if type(fitsfile) == str: fitsfile = [fitsfile] nimg = len(imagefile) if len(timerange) != nimg: raise ValueError, 'Number of input images does not equal to number of timeranges!' if len(fitsfile) != nimg: raise ValueError, 'Number of input images does not equal to number of output fits files!' nimg = len(imagefile) if verbose: print str(nimg) + ' images to process...' if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 if reftime: # use as reference time to find solar disk RA and DEC to register the image, but not the actual timerange associated with the image if type(reftime) == str: reftime = [reftime] * nimg if len(reftime) != nimg: raise ValueError, 'Number of reference times does not match that of input images!' helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=reftime, usephacenter=usephacenter) else: # use the supplied timerange to register the image helio = ephem_to_helio(vis, ephem=ephem, msinfo=msinfo, reftime=timerange, usephacenter=usephacenter) if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 for n, img in enumerate(imagefile): if verbose: print 'processing image #' + str(n) fitsf = fitsfile[n] timeran = timerange[n] # obtain duration of the image as FITS header exptime try: [tbg0, tend0] = timeran.split('~') tbg_d = qa.getvalue(qa.convert(qa.totime(tbg0), 'd'))[0] tend_d = qa.getvalue(qa.convert(qa.totime(tend0), 'd'))[0] tdur_s = (tend_d - tbg_d) * 3600. * 24. dateobs = qa.time(qa.quantity(tbg_d, 'd'), form='fits', prec=10)[0] except: print 'Error in converting the input timerange: ' + str( timeran) + '. Proceeding to the next image...' continue if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 hel = helio[n] if not os.path.exists(img): raise ValueError, 'Please specify input image' if os.path.exists(fitsf) and not overwrite: raise ValueError, 'Specified fits file already exists and overwrite is set to False. Aborting...' else: p0 = hel['p0'] ia.open(img) imr = ia.rotate(pa=str(-p0) + 'deg') imr.tofits(fitsf, history=False, overwrite=overwrite) imr.close() imsum = ia.summary() ia.close() if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 # construct the standard fits header # RA and DEC of the reference pixel crpix1 and crpix2 (imra, imdec) = (imsum['refval'][0], imsum['refval'][1]) # find out the difference of the image center to the CASA phase center # RA and DEC difference in arcseconds ddec = degrees((imdec - hel['dec_fld'])) * 3600. dra = degrees((imra - hel['ra_fld']) * cos(hel['dec_fld'])) * 3600. # Convert into image heliocentric offsets prad = -radians(hel['p0']) dx = (-dra) * cos(prad) - ddec * sin(prad) dy = (-dra) * sin(prad) + ddec * cos(prad) if offsetfile: try: offset = np.load(offsetfile) except: raise ValueError, 'The specified offsetfile does not exist!' reftimes_d = offset['reftimes_d'] xoffs = offset['xoffs'] yoffs = offset['yoffs'] timg_d = hel['reftime'] ind = bisect.bisect_left(reftimes_d, timg_d) xoff = xoffs[ind - 1] yoff = yoffs[ind - 1] else: xoff = hel['refx'] yoff = hel['refy'] if verbose: print 'offset of image phase center to visibility phase center (arcsec): ', dx, dy print 'offset of visibility phase center to solar disk center (arcsec): ', xoff, yoff (crval1, crval2) = (xoff + dx, yoff + dy) # update the fits header to heliocentric coordinates if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 hdu = pyfits.open(fitsf, mode='update') if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 header = hdu[0].header (cdelt1, cdelt2) = (-header['cdelt1'] * 3600., header['cdelt2'] * 3600. ) # Original CDELT1, 2 are for RA and DEC in degrees header['cdelt1'] = cdelt1 header['cdelt2'] = cdelt2 header['cunit1'] = 'arcsec' header['cunit2'] = 'arcsec' header['crval1'] = crval1 header['crval2'] = crval2 header['ctype1'] = 'HPLN-TAN' header['ctype2'] = 'HPLT-TAN' header['date-obs'] = dateobs # begin time of the image if not p_ang: hel['p0'] = 0 try: # this works for pyfits version of CASA 4.7.0 but not CASA 4.6.0 if tdur_s: header.set('exptime', tdur_s) else: header.set('exptime', 1.) header.set('p_angle', hel['p0']) header.set('dsun_obs', sun.sunearth_distance(Time(dateobs)).to(u.meter).value) header.set( 'rsun_obs', sun.solar_semidiameter_angular_size(Time(dateobs)).value) header.set('rsun_ref', sun.constants.radius.value) header.set('hgln_obs', 0.) header.set('hglt_obs', sun.heliographic_solar_center(Time(dateobs))[1].value) except: # this works for astropy.io.fits if tdur_s: header.append(('exptime', tdur_s)) else: header.append(('exptime', 1.)) header.append(('p_angle', hel['p0'])) header.append( ('dsun_obs', sun.sunearth_distance(Time(dateobs)).to(u.meter).value)) header.append( ('rsun_obs', sun.solar_semidiameter_angular_size(Time(dateobs)).value)) header.append(('rsun_ref', sun.constants.radius.value)) header.append(('hgln_obs', 0.)) header.append( ('hglt_obs', sun.heliographic_solar_center(Time(dateobs))[1].value)) if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 # update intensity units, i.e. to brightness temperature? if toTb: # get restoring beam info (bmajs, bmins, bpas, beamunits, bpaunits) = getbeam(imagefile=imagefile, beamfile=beamfile) bmaj = bmajs[n] bmin = bmins[n] beamunit = beamunits[n] data = hdu[ 0].data # remember the data order is reversed due to the FITS convension dim = data.ndim sz = data.shape keys = header.keys() values = header.values() # which axis is frequency? faxis = keys[values.index('FREQ')][-1] faxis_ind = dim - int(faxis) if header['BUNIT'].lower() == 'jy/beam': header['BUNIT'] = 'K' header['BTYPE'] = 'Brightness Temperature' for i in range(sz[faxis_ind]): nu = header['CRVAL' + faxis] + header['CDELT' + faxis] * ( i + 1 - header['CRPIX' + faxis]) if header['CUNIT' + faxis] == 'KHz': nu *= 1e3 if header['CUNIT' + faxis] == 'MHz': nu *= 1e6 if header['CUNIT' + faxis] == 'GHz': nu *= 1e9 if len(bmaj) > 1: # multiple (per-plane) beams bmajtmp = bmaj[i] bmintmp = bmin[i] else: # one single beam bmajtmp = bmaj[0] bmintmp = bmin[0] if beamunit == 'arcsec': bmaj0 = np.radians(bmajtmp / 3600.) bmin0 = np.radians(bmajtmp / 3600.) if beamunit == 'arcmin': bmaj0 = np.radians(bmajtmp / 60.) bmin0 = np.radians(bmintmp / 60.) if beamunit == 'deg': bmaj0 = np.radians(bmajtmp) bmin0 = np.radians(bmintmp) if beamunit == 'rad': bmaj0 = bmajtmp bmin0 = bmintmp beam_area = bmaj0 * bmin0 * np.pi / (4. * log(2.)) k_b = qa.constants('k')['value'] c_l = qa.constants('c')['value'] factor = 2. * k_b * nu**2 / c_l**2 # SI unit jy_to_si = 1e-26 # print nu/1e9, beam_area, factor factor2 = 1. if scl100: factor2 = 100. if faxis == '3': data[:, i, :, :] *= jy_to_si / beam_area / factor * factor2 if faxis == '4': data[ i, :, :, :] *= jy_to_si / beam_area / factor * factor2 if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1 hdu.flush() hdu.close() if verbose: print('point {}: {}'.format(prtidx, time.time() - t0)) prtidx += 1
def plotcomp(compdict, showplot=True, wantdict=False, symb=',', include0amp=False, include0bl=False, blunit='', bl0flux=0.0): """ Given a dict including {'clist': component list, 'objname': objname, 'epoch': epoch, 'shape': component shape dict, including direction. 'freqs (GHz)': pl.array of frequencies, 'antennalist': An array configuration file as used by simdata, 'savedfig': False or, if specified, the filename to save the plot to, 'standard': setjy fluxstandard type}, and symb: One of matplotlib's codes for plot symbols: .:,o^v<>s+xDd234hH|_ default: ',': The smallest points I could find, make a plot of visibility amplitude vs. baseline length for clist at epoch. If antennalist is not found as is, it will look for antennalist in os.getenv('CASAPATH').split(' ')[0] + '/data/alma/simmos/'. showplot: Whether or not to show the plot on screen. If wantdict is True, it returns a dictionary with the amplitudes and baselines on success. Otherwise, it returns True or False as its estimated success value. include0amp: Force the lower limit of the amplitude axis to 0. include0bl: Force the lower limit of the baseline length axis to 0. blunit: unit of the baseline length (='' used the unit in the data or klambda) bl0flux: Zero baseline flux """ def failval(): """ Returns an appropriate failure value. Note that mydict.update(plotcomp(wantdict=True, ...)) would give a confusing error message if plotcomp returned False. """ retval = False if wantdict: retval = {} return retval retval = failval() # Default try: clist = compdict['clist'] objname = compdict['objname'] epoch = compdict['epoch'] epstr = mepoch_to_str(epoch) antennalist = compdict['antennalist'] # Read the configuration info. if not antennalist: print "compdict['antennalist'] must be set!" print "Try something in", os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/" return failval() # Try repodir if raw antennalist doesn't work. if not os.path.exists(antennalist): repodir = os.getenv("CASAPATH").split(' ')[0] + "/data/alma/simmos/" antennalist = repodir + antennalist su = simutil("") stnx, stny, stnz, diam, padnames, nant, telescopename = su.readantenna(antennalist) #print "telescopename:", telescopename # Check that the source is up. myme = metool() posobs = myme.observatory(telescopename) #print "posobs:", posobs myme.doframe(epoch) myme.doframe(posobs) azel = myme.measure(compdict['shape']['direction'], 'azel') azeldegs = tuple([qa.convert(azel[m], 'deg')['value'] for m in ('m0', 'm1')]) casalog.post("(az, el): (%.2f, %.2f) degrees" % azeldegs) # riseset blabs to the logger, so introduce it now. casalog.post('Rise and set times of ' + objname + " from " + telescopename + ':') approx = '' if 'JPL' in compdict.get('standard', 'JPL'): # The object is in the Solar System or not known to be extragalactic. approx = "APPROXIMATE. The times do not account for the apparent motion of "\ + objname + "." casalog.post(" (" + approx + ")") riset = myme.riseset(compdict['shape']['direction']) msg = '' if riset['rise'] == 'above': msg = objname + " is circumpolar" elif riset['rise'] == 'below': msg = objname + ' is not visible from ' + telescopename if msg: if approx: msg += ' around ' + mepoch_to_str(epoch) casalog.post(msg) else: for t in riset: riset[t]['str'] = mepoch_to_str(riset[t]['utc']) casalog.post(objname + " rises at %s and sets at %s." % (riset['rise']['str'], riset['set']['str'])) tmeridian=(riset['rise']['utc']['m0']['value']+riset['set']['utc']['m0']['value'])/2. casalog.post(objname + ': meridian passage at ' + qa.time(str(tmeridian)+'d')[0]) if approx: riset['NOTE'] = approx if not azel['m1']['value'] > 0.0: casalog.post(objname + " is not visible from " + telescopename + " at " + epstr, 'SEVERE') if wantdict: return riset else: return False # Start a temp MS. workingdir = os.path.abspath(os.path.dirname(clist.rstrip('/'))) tempms = tempfile.mkdtemp(prefix=objname, dir=workingdir) mysm = smtool() mysm.open(tempms) su.setcfg(mysm, telescopename, stnx, stny, stnz, diam, padnames, posobs) #print "cfg set" # Only 1 polarization is wanted for now. stokes, feeds = su.polsettings(telescopename, 'RR') casalog.post("stokes, feeds: %s, %s" % (stokes, feeds)) fband = su.bandname(compdict['freqs (GHz)'][0]) chaninc = 1.0 nchan = len(compdict['freqs (GHz)']) if nchan > 1: chaninc = (compdict['freqs (GHz)'][-1] - compdict['freqs (GHz)'][0]) / (nchan - 1) mysm.setspwindow(spwname=fband, freq=str(compdict['freqs (GHz)'][0]) + 'GHz', deltafreq=str(chaninc) + 'GHz', freqresolution='1Hz', nchannels=nchan, refcode="LSRK", stokes=stokes) mysm.setfeed(mode=feeds, pol=['']) mysm.setlimits(shadowlimit=0.01, elevationlimit='10deg') mysm.setauto(0.0) mysm.setfield(sourcename=objname, sourcedirection=compdict['shape']['direction'], calcode="OBJ", distance='0m') mysm.settimes(integrationtime="1s", usehourangle=False, referencetime=epoch) # this only creates blank uv entries mysm.observe(sourcename=objname, spwname=fband, starttime="-0.5s", stoptime="0.5s", project=objname) mysm.setdata(fieldid=[0]) mysm.setvp() casalog.post("done setting up simulation parameters") mysm.predict(complist=clist) # do actual calculation of visibilities: mysm.close() casalog.post("Simulation finished.") mytb = tbtool() mytb.open(tempms) data = mytb.getcol('DATA')[0] # Again, only 1 polarization for now. data = abs(data) baselines = mytb.getcol('UVW')[:2,:] # Drop w. datablunit = mytb.getcolkeywords('UVW')['QuantumUnits'] mytb.close() #print "Got the data and baselines" shutil.rmtree(tempms) if datablunit[1] != datablunit[0]: casalog.post('The baseline units are mismatched!: %s' % datablunit, 'SEVERE') return failval() datablunit = datablunit[0] # uv dist unit in klambda or m if datablunit == 'm' and blunit=='klambda': kl = qa.constants('C')['value']/(compdict['freqs (GHz)'][0]*1e6) blunit = 'k$\lambda$' else: blunit = datablunit kl = 1.0 pl.ioff() #baselines = pl.hypot(baselines[0]/kl, baselines[1]/kl) baselines = pl.hypot(baselines[0], baselines[1]) #if not showplot: # casalog.post('Sorry, not showing the plot is not yet implemented', # 'WARN') if showplot: pl.ion() pl.clf() pl.ioff() nfreqs = len(compdict['freqs (GHz)']) for freqnum in xrange(nfreqs): freq = compdict['freqs (GHz)'][freqnum] casalog.post("Plotting " + str(freq) + " GHz.") pl.plot(baselines/kl, data[freqnum], symb, label="%.3g GHz" % freq) #pl.plot(baselines, data[freqnum], symb, label="%.3g GHz" % freq) pl.xlabel("Baseline length (" + blunit + ")") pl.ylabel("Visibility amplitude (Jy)") if include0amp: pl.ylim(ymin=0.0) if include0bl: pl.xlim(xmin=0.0) pl.suptitle(objname + " (predicted by %s)" % compdict['standard'], fontsize=14) #pl.suptitle(objname + " (predicted)", fontsize=14) # Unlike compdict['antennalist'], antennalist might have had repodir # prefixed to it. pl.title('at ' + epstr + ' for ' + os.path.basename(compdict['antennalist']), fontsize=10) titletxt='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs # for comparison of old and new models - omit azeldegs as all in az~0 if bl0flux > 0.0: if len(compdict['freqs (GHz)']) == 1: titletxt+='\n bl0 flux:%.3f Jy' % bl0flux else: titletxt+='\n bl0 flux:%.3f Jy @ %s GHz' % (bl0flux, compdict['freqs (GHz)'][0]) pl.legend(loc='best', title=titletxt) #pl.legend(loc='best', title='($%.0f^\circ$ az, $%.0f^\circ$ el)' % azeldegs) y_formatter=matplotlib.ticker.ScalarFormatter(useOffset=False) pl.axes().yaxis.set_major_formatter(y_formatter) if showplot: pl.ion() pl.draw() if compdict.get('savedfig'): pl.savefig(compdict.get('savedfig')) casalog.post("Saved plot to " + str(compdict.get('savedfig'))) if wantdict: retval = {'amps': data, 'antennalist': antennalist, # Absolute path, now. 'azel': azel, 'baselines': baselines, 'blunit': blunit, 'riseset': riset, 'savedfig': compdict.get('savedfig')} else: retval = True except Exception, instance: casalog.post(str(instance), 'SEVERE') if os.path.isdir(tempms): shutil.rmtree(tempms)
linecolor, linestyle, linewidth, separatepanel, plotmasked, maskedcolor, showaxislabel, showtick, showticklabel, parsed_size, nx, ny, transparent, plotrange) except Exception, e: casalog.post('Error: %s' % (str(e)), priority='SEVERE') import traceback casalog.post(traceback.format_exc(), priority='DEBUG') raise e finally: pass NoData = -32767.0 NoDataThreshold = NoData + 10000.0 LightSpeedQuantity = qa.constants('c') LightSpeed = qa.convert(LightSpeedQuantity, 'km/s')['value'] # speed of light in km/s DPIDetail = 130 dsyb = '$^\circ$' hsyb = ':' msyb = ':' def Deg2HMS(x, arrowance): # Transform degree to HHMMSS.sss format xx = x % 360 + arrowance h = int(xx / 15) m = int((xx % 15) * 4) s = ((xx % 15) * 4 - m) * 60.0