Radio Fitting: NH3 CUBE exampleΒΆ

Fit NH3 Cube

Example script to fit all pixels in an NH3 data cube.

This is a bit of a mess, and fairly complicated (intrinsically),
but if you have matched 1-1 + 2-2 + ... NH3 cubes, you should be
able to modify this example and get something useful out.

.. WARNING:: Cube fitting, particularly with a complicated line profile
ammonia, can take a long time.  Test this on a small cube first!

.. TODO:: Turn this example script into a function.  But customizing
    the fit parameters will still require digging into the data manually
    (e.g., excluding bad velocities, or excluding the hyperfine lines from
    the initial guess)
import pyspeckit
import astropy
    import as pyfits
except ImportError:
    import pyfits
import numpy as np
import os
from astropy.convolution import convolve_fft,Gaussian2DKernel

# set up CASA-like shortcuts
F=False; T=True

# Some optional parameters for the script
# (if False, it will try to load an already-stored version
# of the file)
fitcube = True

# Mask out low S/N pixels (to speed things up)
mask = pyfits.getdata('hotclump_11_mask.fits')
mask = np.isfinite(mask) * (mask > 0)

# Load the data using a mask
# Then calibrate the data (the data we're loading in this case are in Janskys,
# but we want surface brightness in Kelvin for the fitting process)
cube11 = pyspeckit.Cube('hotclump_11.cube_r0.5.image.fits', maskmap=mask)
cube11.cube *= (13.6 * (300.0 /
    (pyspeckit.spectrum.models.ammonia.freq_dict['oneone']/1e9))**2 *
    1./cube11.header.get('BMAJ')/3600. * 1./cube11.header.get('BMIN')/3600. )
cube11.unit = "K"
cube22 = pyspeckit.Cube('hotclump_22.cube_r0.5_contsub.image.fits', maskmap=mask)
cube22.cube *= (13.6 * (300.0 /
        (pyspeckit.spectrum.models.ammonia.freq_dict['twotwo']/1e9))**2 *
        1./cube22.header.get('BMAJ')/3600. * 1./cube22.header.get('BMIN')/3600. )
cube22.unit = "K"
cube44 = pyspeckit.Cube('hotclump_44.cube_r0.5_contsub.image.fits', maskmap=mask)
cube44.cube *= (13.6 * (300.0 /
        (pyspeckit.spectrum.models.ammonia.freq_dict['fourfour']/1e9))**2 *
        1./cube44.header.get('BMAJ')/3600. * 1./cube44.header.get('BMIN')/3600. )
cube44.unit = "K"

# Compute an error map.  We use the 1-1 errors for all 3 because they're
# essentially the same, but you could use a different error map for each
# frequency
oneonemomentfn = 'hotclump_11.cube_r0.5_rerun.image.moment_linefree.fits'
errmap11 = (pyfits.getdata(oneonemomentfn).squeeze() * 13.6 *
            (300.0 /
            * 1./cube11.header.get('BMAJ')/3600. *
# Interpolate errors across NaN pixels
errmap11[errmap11 != errmap11] = convolve_fft(errmap11,
                                              interpolate_nan=True)[errmap11 != errmap11]

# Stack the cubes into one big cube.  The X-axis is no longer linear: there
# will be jumps from 1-1 to 2-2 to 4-4.
cubes = pyspeckit.CubeStack([cube11,cube22,cube44], maskmap=mask)
cubes.unit = "K"

# Make a "moment map" to contain the initial guesses
# If you've already fit the cube, just re-load the saved version
# otherwise, re-fit it
if os.path.exists('hot_momentcube.fits'):
    momentcubefile ='hot_momentcube.fits')
    momentcube = momentcubefile[0].data
    # compute the moment at each pixel
    momentcube = cube11.momentcube
    momentcubefile = pyfits.PrimaryHDU(data=momentcube, header=cube11.header)
if astropy.version.major >= 2 or (astropy.version.major==1 and astropy.version.minor>=3):

# Create a "guess cube".  Because we're fitting physical parameters in this
# case, we want to make the initial guesses somewhat reasonable
# As above, we'll just reload the saved version if it exists
guessfn = 'hot_guesscube.fits'
if os.path.exists(guessfn):
    guesscube =
    guesses = guesscube[0].data
    guesses = np.zeros((6,)+cubes.cube.shape[1:])
    guesses[0,:,:] = 20                    # Kinetic temperature
    guesses[1,:,:] = 5                     # Excitation  Temp
    guesses[2,:,:] = 14.5                  # log(column)
    guesses[3,:,:] = momentcube[3,:,:] / 5 # Line width / 5 (the NH3 moment overestimates linewidth)
    guesses[4,:,:] = momentcube[2,:,:]     # Line centroid
    guesses[5,:,:] = 0.5                   # F(ortho) - ortho NH3 fraction (fixed)

    guesscube = pyfits.PrimaryHDU(data=guesses, header=cube11.header)
    if astropy.version.major >= 2 or (astropy.version.major==1 and astropy.version.minor>=3):
        guesscube.writeto(guessfn, overwrite=True)
        guesscube.writeto(guessfn, clobber=True)

# This bit doesn't need to be in an if statment
if fitcube:
    # excise guesses that fall out of the "good" range
    guesses[4,:,:][guesses[4,:,:] > 100] = 100.0
    guesses[4,:,:][guesses[4,:,:] < 91] = 95

    # do the fits
    # signal_cut means ignore any pixel with peak S/N less than this number
    # In this fit, many of the parameters are limited
    # start_from_point selects the pixel coordinates to start from
    # use_nearest_as_guess says that, at each pixel, the input guesses will be
    # set by the fitted parameters from the nearest pixel with a good fit
    # HOWEVER, because this fitting is done in parallel (multicore=12 means
    # 12 parallel fitting processes will run), this actually means that EACH
    # core will have its own sub-set of the cube that it will search for good
    # fits. So if you REALLY want consistency, you need to do the fit in serial.
    cubes.fiteach(fittype='ammonia', multifit=None, guesses=guesses,
            integral=False, verbose_level=3, fixed=[F,F,F,F,F,T], signal_cut=3,
            use_nearest_as_guess=True, start_from_point=(94,250),

    # Save the fitted parameters in a data cube
    fitcubefile = pyfits.PrimaryHDU(data=np.concatenate([cubes.parcube,cubes.errcube]), header=cubes.header)
    fitcubefile.header['PLANE1'] = 'TKIN'
    fitcubefile.header['PLANE2'] = 'TEX'
    fitcubefile.header['PLANE3'] = 'COLUMN'
    fitcubefile.header['PLANE4'] = 'SIGMA'
    fitcubefile.header['PLANE5'] = 'VELOCITY'
    fitcubefile.header['PLANE6'] = 'FORTHO'
    fitcubefile.header['PLANE7'] = 'eTKIN'
    fitcubefile.header['PLANE8'] = 'eTEX'
    fitcubefile.header['PLANE9'] = 'eCOLUMN'
    fitcubefile.header['PLANE10'] = 'eSIGMA'
    fitcubefile.header['PLANE11'] = 'eVELOCITY'
    fitcubefile.header['PLANE12'] = 'eFORTHO'
    fitcubefile.header['CDELT3'] = 1
    fitcubefile.header['CTYPE3'] = 'FITPAR'
    fitcubefile.header['CRVAL3'] = 0
    fitcubefile.header['CRPIX3'] = 1
else: # you can read in a fit you've already done!
    cubes.load_model_fit('hot_fitcube_try6.fits', 6, 'ammonia', _temp_fit_loc=(94,250))
    cubes.specfit.parinfo[5]['fixed'] = True

# Now do some plotting things
import pylab as pl

# Set the map-to-plot to be the line centroid
cubes.mapplot.plane = cubes.parcube[4,:,:]

# Set the reference frequency to be the 1-1 line frequency
cubes.xarr.refX = pyspeckit.spectrum.models.ammonia.freq_dict['oneone']

# If you wanted to view the spectra in velocity units, use this:

# Now replace the cube's plotter with a "special" plotter
# The "special" plotter puts the 1-1, 2-2, and 4-4 lines in their own separate
# windows

cubes.plot_special = pyspeckit.wrappers.fitnh3.plotter_override
cubes.plot_special_kwargs = {'fignum':3, 'vrange':[55,135]}

# make interactive

# At this point, you can click on any pixel in the image and see the spectrum
# with the best-fit ammonia profile overlaid.

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