Difference between revisions of "Fit a Gaussian to Visibility data and plot it over the data"

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plt.show()
 
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The result--
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[[File:Example.jpg]]

Revision as of 13:27, 24 July 2015

  • DRAFT*

B.Mason, K.Ward-Duong, & J.Patience July 2015 developed in CASA 4.2.2

This CASA guide illustrates how to run UVMODELFIT to fit a single Gaussian component to UV data (i.e. the raw visibilities); and subsequently how to make a plot of the binned, "azimuthally" averaged (in UV space) UV data together with the fitted model. In broad outlines, the steps required are:

  1 Estimate the peak location of emission. shift the phase center here if desired.
  2 Estimate starting values for the gaussian component fit
  3 do the fit.
  4 run ft() to put the results of the fit in the MS explicitly (as a MODEL column).
  5 Extract MODEL and DATA, make the plot

PHASE SHIFT:

fixvis(vis="J04292165_cont.ms",outputvis="J04292165_cont_recenter.ms",field="",refcode="",reuse=True,phasecenter="J2000 4h29m21.66s +27d01m25.72s",datacolumn="all")

(note: not done in this example)

do the fit -- this is for all spws together:

default uvmodelfit
vis=myvis
field='0'
comptype='G'
sourcepar=[0.006,0.1,-0.05,0.4,0.3,0.0]
varypar=[]
outfile='J04292165_cont_allspw.uv.cl'
inp
go

in this example we had not phase shifted.

run FT -- you must have usescratch=True

default ft
vis=myvis
complist='J04292165_cont_allspw.uv.cl'
usescratch=True
inp
go

# did that work?
plotms(vis=myvis,xaxis='uvwave',yaxis='real',ydatacolumn='model')
# yes it did.

Finally, use VISSTAT() to extract model and data values in bins of uv-radius:

import numpy as np
import matplotlib.pyplot as plt
import glob

testms = 'J04292165_cont.ms'

# set the uvrange in kilo lambda
#  NB: take care that the bin width and uvmin/max ranges ensure
#   you get no bins without data! the appropriate values may change
#   if you, e.g., change the SPW you are looking at
uvmin = 0
#uvmax = 1200
uvmax = 800
 # define steps in klambda
duv=40

uvsteps = np.arange(uvmin, uvmax, duv)

avg_amps = [] # define an empty list in which to put the averaged amplitudes

stddev_amps = [] # define an empty list in which to put the amp stddev

numpoints = []

uvpoints = uvsteps[:-1] + np.diff(uvsteps)/2 # get array of uvmidpoints over which avg taken

model_amps = [] # define list to get model amplitudes after fourier transforming into the model data column

# iterate over the uvrange:
for ii in range(len(uvsteps[:-1])):
        tmp = visstat(vis = testms,axis = 'real',
                      uvrange = str(uvsteps[ii]) + '~' + str(uvsteps[ii+1]) + 'klambda',
                      datacolumn = 'data')
        print str(uvsteps[ii]) + '~' + str(uvsteps[ii+1]) + 'klambda'
        avg_amps.append(tmp['DATA']['mean'])
        stddev_amps.append(tmp['DATA']['stddev'])
        numpoints.append(tmp['DATA']['npts'])


for ii in range(len(uvsteps[:-1])):
        tmp = visstat(vis = testms,
                        axis = 'real', # you may want to change this to real...?
                        uvrange = str(uvsteps[ii]) + '~' + str(uvsteps[ii+1]) + 'klambda',
                        datacolumn = 'model')
        print str(uvsteps[ii]) + '~' + str(uvsteps[ii+1]) + 'klambda, from the model column'
        #avg_amps.append(tmp['DATA']['mean'])
        #stddev_amps.append(tmp['DATA']['stddev'])
        #numpoints.append(tmp['DATA']['npts'])
        model_amps.append(tmp['MODEL']['mean'])

error_amps = stddev_amps/(np.sqrt(numpoints) - 1)

plt.clf()
plt.cla()

avg_amps_mjy = [x * 1000 for x in avg_amps]
model_amps_mjy = [x * 1000 for x in model_amps]
error_amps_mjy = [x * 1000 for x in error_amps]

plt.errorbar(uvpoints, avg_amps_mjy, yerr = error_amps_mjy, mfc='k', fmt='o', label='data')
plt.plot(uvpoints, model_amps_mjy, 'r-', label=r'model from $uvmodelfit$')

plt.legend(loc = 3, numpoints = 1)

plt.xlabel(r'UV Distance (k$\lambda$)')
plt.ylabel('Real Visibility (mJy)')

plt.show()

The result--

File:Example.jpg