def gen_spec(model_params):
"""
Generate a synthetic spectrum
model_params = [Tkin, Tex, Ntot, width]
"""
xarr11 = SpectroscopicAxis(np.linspace(-40, 40, 1000) * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['oneone']).as_unit(u.GHz)
xarr22 = SpectroscopicAxis(np.linspace(-40, 40, 1000) * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['twotwo']).as_unit(u.GHz)
xarr = SpectroscopicAxes([xarr11, xarr22])
tkin = model_params[0]
tex = model_params[1]
ntot = model_params[2]
width = model_params[3]
fortho = 0.0
synthspec = pyspeckit.spectrum.models.ammonia.cold_ammonia(xarr,
tkin=tkin,
tex=tex,
ntot=ntot,
width=width,
fortho=fortho)
spectrum = pyspeckit.Spectrum(xarr=xarr, data=synthspec)
return spectrum
def toy_observation(snr=2,
debug=False,
seed=0,
v1=10,
v2=70,
nchan=1000,
truth_narrow=[4, 40, 1.0],
truth_wide=[2, 41, 3.0]):
np.random.seed(seed)
if debug: # <CheatMode>
log.setLevel('DEBUG')
# initialize the spectral axis
xunit, bunit = 'km/s', 'K'
refX = 120 * u.GHz
log.debug("Genarating a spactral axis instance from {}"
" to {} {}".format(v1, v2, xunit))
xarr = SpectroscopicAxis(np.linspace(v1, v2, nchan) * u.Unit(xunit),
refX=refX,
velocity_convention='radio')
# generate a spectrum approximated by a gaussian
log.debug("Gaussian parameters for the"
" narrow component: {}".format(truth_narrow))
log.debug("Gaussian parameters for the"
" wide component: {}".format(truth_wide))
true_data_narrow = gaussian(xarr, *truth_narrow)
true_data_wide = gaussian(xarr, *truth_wide)
true_total = true_data_narrow + true_data_wide
signal_peak = true_total.max()
log.debug("For a signal-to-noise ratio of {} the square root of noise"
" variance is {:.2f} {}.".format(snr, signal_peak / snr, bunit))
noise = np.random.normal(loc=0, scale=signal_peak / snr, size=xarr.size)
observed = true_total + noise
log.setLevel('INFO') # <\CheatMode>
# make a spectrum class instance in Tmb units
xarr._make_header()
sp = Spectrum(xarr=xarr, data=observed, unit=u.Unit(bunit), header={})
sp.header['NPEAKS'] = 2
sp.header['NOISERMS'] = round(signal_peak / snr, 4)
for comp, name in zip([truth_narrow, truth_wide], ['1', '2']):
sp.header['AMP_' + name] = comp[0]
sp.header['XOFF_' + name] = comp[1]
sp.header['SIG_' + name] = comp[2]
return sp
def highres_xarr(xarr, N_res, refX):
# make sure the 11 and 22 cubes are in GHz
xarr.convert_to_unit(u.GHz)
xnparr = np.linspace(xarr.min(), xarr.max(), N_res)
xarr_hires = SpectroscopicAxis(xarr=xnparr,
refX=refX,
velocity_convention="radio")
return xarr_hires
def get_singv_tau11(singv_para):
'''
Take a GAS DR1 parameter maps and return optical depth of the 1-1 line.
Parameters
----------
sigv_para : str or ndarray
The GAS DR1 parameter cube (i.e., maps), either as a file name or as a 3D ndarray cube.
Returns
-------
tau11 : ndarray
A map of model optical depths for ammonia (1-1)
'''
# Note: the efficiency could benifit from multi-core processing
if type(singv_para) == str:
parcube = fits.getdata(singv_para)
else:
parcube = singv_para
# Create a dummy spectral-axis in km/s as a place holder to acquire tau
xarr = np.linspace(0.0, 10.0, 10, endpoint=True)
xarr = SpectroscopicAxis(xarr * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['oneone'] * u.Hz).as_unit(u.GHz)
# set ntot elements with zero values to NaN
parcube[:, parcube[2] == 0.0] = np.nan
yy, xx = np.indices(parcube.shape[1:])
nanvals = np.any(~np.isfinite(parcube), axis=0)
isvalid = np.any(parcube, axis=0) & ~nanvals
valid_pixels = zip(xx[isvalid], yy[isvalid])
tau11 = np.zeros(parcube.shape[1:])
def model_a_pixel(xy):
x, y = int(xy[0]), int(xy[1])
kwargs = {
'tkin': parcube[0, y, x],
'tex': parcube[1, y, x],
'ntot': parcube[2, y, x],
'width': parcube[3, y, x],
'xoff_v': parcube[4, y, x],
'fortho': parcube[5, y, x],
'return_tau': True,
}
tau = ammonia.cold_ammonia(xarr, **kwargs)
tau11[y, x] = tau['oneone']
for xy in ProgressBar(list(valid_pixels)):
model_a_pixel(xy)
return tau11
def test_convert_to_unit(run_with_assert=False):
for from_unit, to_unit, _, __ in u.doppler_optical(1 * u.Hz):
sp = SpectroscopicAxis(
np.linspace(-100, 100, 100), unit=from_unit, refX=23.2 * u.Hz, velocity_convention="optical"
)
sp.convert_to_unit(to_unit)
if run_with_assert:
assert sp.unit == to_unit
for from_unit, to_unit, _, __ in u.doppler_radio(1 * u.eV):
sp = SpectroscopicAxis(
np.linspace(-100, 100, 100), unit=from_unit, refX=23.2 * u.Hz, velocity_convention="optical"
)
sp.convert_to_unit(to_unit)
if run_with_assert:
assert sp.unit == to_unit
for from_unit, to_unit, _, __ in u.doppler_relativistic(1 * u.Angstrom):
sp = SpectroscopicAxis(
np.linspace(-100, 100, 100), unit=from_unit, refX=23.2 * u.Hz, velocity_convention="relativistic"
)
sp.convert_to_unit(to_unit)
if run_with_assert:
assert sp.unit == to_unit
def test_moments():
xvals = np.linspace(-100, 100, 200) * u.km / u.s
# Some models will fail without a center frequency and a velocity convention
xarr = SpectroscopicAxis(xvals,
velocity_convention='radio',
center_frequency=100 * u.GHz)
# creating the random data
rawdata = np.random.randn(xarr.size)
# creating a sample Spectrum from a .fits file
sp = Spectrum('test.fits')
for model_name in sp.specfit.Registry.multifitters.keys():
print('testing:', model_name)
model = sp.specfit.Registry.multifitters[model_name]
params = model.moments(xarr, rawdata, vheight=False)
print('params from moments:', params)
assert len(params) == model.npars
# if this call does not raise an Exception then moments() produced
# the correct number of parameters
model.n_modelfunc(pars=params)(xarr)
def load_spectrum(j=6, object='w51e2-tot',
npix=1,
headerfile='../W51-25GHzcont.map.image.fits',
fntemplate='spec-{object}-{j}{j2}-pb.txt',):
# convert 6 -> 'six' for use below
linename = ammonia_constants.num_to_name[j] * 2
# the beam size is important for determining the brighntess conversion
bm = radio_beam.Beam.from_fits_header(headerfile)
# read in the file (dumped to text)
xx,yy=np.loadtxt(fntemplate.format(object=object, j=j, j2=j if j < 10 else ""),
comments="#").T
# we want MEAN flux, not SUM
yy = yy / npix
# x units are in km/s, reference is in Hz
xarr = SpectroscopicAxis(xx*u.km/u.s,
refX=ammonia.freq_dict[linename]*u.Hz,
velocity_convention='radio')
sp = pyspeckit.Spectrum(xarr=xarr, data=yy)
sp.unit = 'Jy'
# compute the typical noise over the -10 to 10 km/s region
mean_error = sp.stats((-10,10))['std']
sp.error[:] = mean_error
sp.specname = '{0} {1}'.format(object, linename)
# Copy the spectrum so we can convert it to Kelvins
spK = sp.copy()
jytok = ((1*u.Jy).to(u.K, u.brightness_temperature(bm, sp.xarr.refX)).value)
sp.header['JYTOK'] = jytok
spK.unit = 'K'
spK.data = sp.data * jytok
spK.error = sp.error * jytok
mean_error_k = mean_error * jytok
return sp, spK, mean_error, mean_error_k
import numpy as np
import pyspeckit
from astropy import units as u
from pyspeckit.spectrum.models import ammonia_constants, ammonia, ammonia_hf
from pyspeckit.spectrum.models.ammonia_constants import freq_dict
from pyspeckit.spectrum.units import SpectroscopicAxis, SpectroscopicAxes
# Step 1. Generate a synthetic spectrum. Already have a real spectrum? Skip
# to step 2!
# Generate a synthetic spectrum based off of 3 NH3 lines
# Note that they are converted to GHz first
xarr11 = SpectroscopicAxis(np.linspace(-30, 30, 100) * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['oneone']).as_unit(u.GHz)
xarr22 = SpectroscopicAxis(np.linspace(-40, 40, 100) * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['twotwo']).as_unit(u.GHz)
xarr33 = SpectroscopicAxis(np.linspace(-50, 50, 100) * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['threethree']).as_unit(u.GHz)
# Merge the three X-axes into a single axis
xarr = SpectroscopicAxes([xarr11, xarr22, xarr33])
# Compute a synthetic model that is made of two temperature components with
# identical velocities
synthspec = (
ammonia.ammonia(xarr, tkin=20, ntot=15, fortho=0.5, xoff_v=0.0,
width=1.0) +
ammonia.ammonia(xarr, tkin=50, ntot=14, fortho=0.5, xoff_v=0.0, width=1.0))
# Create the Spectrum object
def hmm1_cubefit(vmin=3.4,
vmax=5.0,
tk_ave=10.,
do_plot=False,
snr_min=5.0,
multicore=1,
do_thin=False):
"""
Fit NH3(1,1) and (2,2) cubes for H-MM1.
It fits all pixels with SNR larger than requested.
Initial guess is based on moment maps and neighboring pixels.
The fitting can be done in parallel mode using several cores,
however, this is dangerous for large regions, where using a
good initial guess is important.
It stores the result in a FITS cube.
TODO:
-convert FITS cube into several FITS files
-Improve initial guess
Parameters
----------
vmin : numpy.float
Minimum centroid velocity to plot, in km/s.
vmax : numpy.float
Maximum centroid velocity to plot, in km/s.
tk_ave : numpy.float
Mean kinetic temperature of the region, in K.
do_plot : bool
If True, then a map of the region to map is shown.
snr_min : numpy.float
Minimum signal to noise ratio of the spectrum to be fitted.
multicore : int
Numbers of cores to use for parallel processing.
"""
cube11sc = SpectralCube.read(OneOneFile)
cube22sc = SpectralCube.read(TwoTwoFile)
cube11_v = cube11sc.with_spectral_unit(u.km / u.s,
velocity_convention='radio',
rest_value=freq11)
cube22_v = cube22sc.with_spectral_unit(u.km / u.s,
velocity_convention='radio',
rest_value=freq22)
from pyspeckit.spectrum.units import SpectroscopicAxis
spec11 = SpectroscopicAxis(cube11_v.spectral_axis,
refX=freq11,
velocity_convention='radio')
spec22 = SpectroscopicAxis(cube22_v.spectral_axis,
refX=freq22,
velocity_convention='radio')
errmap11 = fits.getdata(RMSFile_11)
errmap22 = fits.getdata(RMSFile_22)
errmap_K = errmap11 #[errmap11, errmap22]
Tpeak11 = fits.getdata(OneOnePeak)
moment1 = fits.getdata(OneOneMom1)
moment2 = (fits.getdata(OneOneMom2))**0.5
snr = cube11sc.filled_data[:].value / errmap11
peaksnr = Tpeak11 / errmap11
planemask = (peaksnr > snr_min) # *(errmap11 < 0.15)
planemask = remove_small_objects(planemask, min_size=40)
planemask = opening(planemask, disk(1))
#planemask = (peaksnr>20) * (errmap11 < 0.2)
mask = (snr > 3) * planemask
maskcube = cube11sc.with_mask(mask.astype(bool))
maskcube = maskcube.with_spectral_unit(u.km / u.s,
velocity_convention='radio')
slab = maskcube.spectral_slab(vmax * u.km / u.s, vmin * u.km / u.s)
w11 = slab.moment(order=0, axis=0).value
peakloc = np.nanargmax(w11)
ymax, xmax = np.unravel_index(peakloc, w11.shape)
moment2[np.isnan(moment2)] = 0.2
moment2[moment2 < 0.2] = 0.2
## Load FITS files
cube11 = pyspeckit.Cube(OneOneFile, maskmap=planemask)
cube22 = pyspeckit.Cube(TwoTwoFile, maskmap=planemask)
# Stack files
cubes = pyspeckit.CubeStack([cube11, cube22], maskmap=planemask)
cubes.unit = "K"
# Define initial guess
guesses = np.zeros((6, ) + cubes.cube.shape[1:])
moment1[moment1 < vmin] = vmin + 0.2
moment1[moment1 > vmax] = vmax - 0.2
guesses[0, :, :] = tk_ave # Kinetic temperature
guesses[1, :, :] = 7 # Excitation Temp
guesses[2, :, :] = 14.5 # log(column)
guesses[
3, :, :] = moment2 # Line width / 5 (the NH3 moment overestimates linewidth)
guesses[4, :, :] = moment1 # Line centroid
guesses[5, :, :] = 0.5 # F(ortho) - ortho NH3 fraction (fixed)
if do_plot:
import matplotlib.pyplot as plt
plt.imshow(w11 * planemask, origin='lower')
plt.show()
print('start fit')
cubes.specfit.Registry.add_fitter('cold_ammonia',
ammonia.cold_ammonia_model(), 6)
if do_thin:
file_out = "{0}H-MM1_cold_parameter_maps_snr{1}_thin_v1.fits".format(
fit_dir, snr_min)
else:
file_out = "{0}H-MM1_cold_parameter_maps_snr{1}_thick_v1.fits".format(
fit_dir, snr_min)
cubes.fiteach(fittype='cold_ammonia',
guesses=guesses,
integral=False,
verbose_level=3,
fixed=[do_thin, False, False, False, False, True],
signal_cut=2,
limitedmax=[True, False, False, False, True, True],
maxpars=[20, 15, 20, 0.4, vmax, 1],
limitedmin=[True, True, True, True, True, True],
minpars=[5, 2.8, 12.0, 0.05, vmin, 0],
start_from_point=(xmax, ymax),
use_neighbor_as_guess=True,
position_order=1 / peaksnr,
errmap=errmap_K,
multicore=multicore)
# Store fits into FITS cube
fitcubefile = fits.PrimaryHDU(data=np.concatenate(
[cubes.parcube, cubes.errcube]),
header=cubes.header)
fitcubefile.header.set('PLANE1', 'TKIN')
fitcubefile.header.set('PLANE2', 'TEX')
fitcubefile.header.set('PLANE3', 'COLUMN')
fitcubefile.header.set('PLANE4', 'SIGMA')
fitcubefile.header.set('PLANE5', 'VELOCITY')
fitcubefile.header.set('PLANE6', 'FORTHO')
fitcubefile.header.set('PLANE7', 'eTKIN')
fitcubefile.header.set('PLANE8', 'eTEX')
fitcubefile.header.set('PLANE9', 'eCOLUMN')
fitcubefile.header.set('PLANE10', 'eSIGMA')
fitcubefile.header.set('PLANE11', 'eVELOCITY')
fitcubefile.header.set('PLANE12', 'eFORTHO')
fitcubefile.header.set('CDELT3', 1)
fitcubefile.header.set('CTYPE3', 'FITPAR')
fitcubefile.header.set('CRVAL3', 0)
fitcubefile.header.set('CRPIX3', 1)
fitcubefile.writeto(file_out, overwrite=True)
def test_convert_to_unit(run_with_assert=False):
for from_unit, to_unit, _, __ in u.doppler_optical(1 * u.Hz):
sp = SpectroscopicAxis(np.linspace(-100, 100, 100),
unit=from_unit,
refX=23.2 * u.Hz,
velocity_convention='optical')
sp.convert_to_unit(to_unit)
if (run_with_assert):
assert sp.unit == to_unit
for from_unit, to_unit, _, __ in u.doppler_radio(1 * u.eV):
sp = SpectroscopicAxis(np.linspace(-100, 100, 100),
unit=from_unit,
refX=23.2 * u.Hz,
velocity_convention='optical')
sp.convert_to_unit(to_unit)
if (run_with_assert):
assert sp.unit == to_unit
for from_unit, to_unit, _, __ in u.doppler_relativistic(1 * u.Angstrom):
sp = SpectroscopicAxis(np.linspace(-100, 100, 100),
unit=from_unit,
refX=23.2 * u.Hz,
velocity_convention='relativistic')
sp.convert_to_unit(to_unit)
if (run_with_assert):
assert sp.unit == to_unit
def get_SNR(paraname, savename=None, rms=0.15, n_comp=2, linename='oneone'):
'''
Take a multiple velocity componet fit and produce a signal to noise ratio of the two velocity components
:param paraname:
:param savename:
:param rms:
:param n_comp:
:return:
'''
para, hdr = fits.getdata(paraname, header=True)
n_para = n_comp * 4
# remove the error components
para = para[:n_para]
assert para.shape[0] == n_para
yy, xx = np.indices(para.shape[1:])
nanvals = np.any(~np.isfinite(para), axis=0)
isvalid = np.any(para, axis=0) & ~nanvals
valid_pixels = zip(xx[isvalid], yy[isvalid])
# Create a synthetic X-dimension in km/s
vres = 0.07
vpad = 0.5
vmax, vmin = np.argmax([para[0], para[4]]), np.argmin([para[0], para[4]])
vmax = vmax + vpad
vmin = vmin - vpad
n_samp = (vmax - vmin) / vres
xarr = np.linspace(vmin, vmax, int(n_samp) + 1, endpoint=True)
xarr = SpectroscopicAxis(xarr * u.km / u.s,
velocity_convention='radio',
refX=freq_dict[linename] * u.Hz).as_unit(u.GHz)
peakT = np.zeros((n_comp, para.shape[1], para.shape[2]))
def model_a_pixel(xy):
x, y = int(xy[0]), int(xy[1])
models = [
ammonia._ammonia_spectrum(xarr.as_unit('GHz'),
tex=tex,
tau_dict={linename: tau},
width=width,
xoff_v=vel,
fortho=0.0,
line_names=[linename])
for vel, width, tex, tau in zip(para[::4, y, x], para[1::4, y, x],
para[2::4, y, x], para[3::4, y, x])
]
peakT[:, y, x] = np.nanmax(models, axis=1)
for xy in ProgressBar(list(valid_pixels)):
print int(xy[0]), int(xy[1])
model_a_pixel(xy)
if savename != None:
for i in np.arange(n_comp * 8) + 1:
key = 'PLANE{0}'.format(i)
if key in hdr:
hdr.remove(key)
newfits = fits.PrimaryHDU(data=peakT / rms, header=hdr)
newfits.header.set('CDELT3', 1)
newfits.header.set('CTYPE3', 'FITPAR')
newfits.header.set('PLANE1', 'SNR_0')
newfits.header.set('PLANE2', 'SNR_1')
newfits.header.set('NAXIS3', n_comp * 8)
newfits.writeto(savename, overwrite=True)
return peakT / rms
from astropy.table import Table
import numpy as np
import matplotlib.pyplot as plt
import scipy.interpolate as interp
import astropy.units as u
from pyspeckit.spectrum.units import SpectroscopicAxis
from pyspeckit.spectrum.models.h2co_mm import h2co_mm_radex
import mmh2co_model as model
t = Table.read('ph2cogrid.fits.gz',format='fits')
bundle = model.H2COModel(t)
nu = SpectroscopicAxis(np.linspace(218e9,219e9,1000)*u.Hz)
spec = h2co_mm_radex(nu,gridbundle=bundle,verbose=True,Temperature=15,width=1.0)
plt.plot(nu.as_unit('GHz'),spec)
plt.show()
def spec_curve_fit(bin_num, map_name=map_column_dens):
# following loop has not good style. One should build in some break statements or error messages
# if files repeatedly appear in loop.
for one_file in files:
if 'NH3_11' in one_file:
file_name_NH3_11 = one_file
if 'NH3_22' in one_file:
file_name_NH3_22 = one_file
if 'NH3_33' in one_file:
file_name_NH3_33 = one_file
y, x, med = binning(bin_width, bin_num)
s11, _, offset_velocity11, sp_av11 = averaging_over_dopplervel(
file_name_NH3_11, y, x)
s22, _, offset_velocity22, sp_av22 = averaging_over_dopplervel(
file_name_NH3_22, y, x)
s33, _, offset_velocity33, sp_av33 = averaging_over_dopplervel(
file_name_NH3_33, y, x)
xarr11 = SpectroscopicAxis(offset_velocity11 * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['oneone']).as_unit(u.GHz)
xarr22 = SpectroscopicAxis(offset_velocity22 * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['twotwo']).as_unit(u.GHz)
xarr33 = SpectroscopicAxis(offset_velocity33 * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['threethree']).as_unit(u.GHz)
sp11 = psk.Spectrum(data=s11,
xarr=xarr11,
xarrkwargs={'unit': 'km/s'},
unit='K')
sp22 = psk.Spectrum(data=s22,
xarr=xarr22,
xarrkwargs={'unit': 'km/s'},
unit='K')
sp33 = psk.Spectrum(data=s33,
xarr=xarr33,
xarrkwargs={'unit': 'km/s'},
unit='K')
# This joins all the spectra together into one object.
allspec = psk.Spectra([sp11, sp22, sp33])
allspec.xarr.as_unit('Hz', velocity_convention='radio')
# This add the cold_ammonia model to the list of things we can use for fitting
allspec.specfit.Registry.add_fitter('cold_ammonia',
ammonia.cold_ammonia_model(), 6)
# This does the fit. The values of the guess are
# Kinetic Temperature (usually about 15 to 25 K)
# Excitation Temperature (between 2.73 K and the excitation temperature)
# Log Column Density of ammonia
# Line width (~1 km/s)
# Offset velocity (you will usually use 0 instead of 8.5)
# Ortho fraction (leave at 0)
allspec.specfit(fittype='cold_ammonia', guesses=[23, 5, 13.1, 1, 0, 0])
# You can make a plot here.
fig = plt.figure()
allspec.plotter()
allspec.specfit.plot_fit(lw=1, components=True)
plt.xlim((23.692, 23.697))
# plt.xlim((23.72,23.725))
# plt.xlim((23.8692, 23.8708))
# plt.savefig("OrionA:pyspeckit_fit_bin_width=%rthis_bin=%r.ps" %(bin_width, this_bin))
plt.savefig("Map=%r:bin_num=%r_pyspeckit_fit_NH3_11TEST.ps" %
(map_name, bin_num))
plt.show()
# returns the values of the fitted parameters: T_K, T_ex, N, sigma, v, F_0
return allspec.specfit.parinfo, allspec.specfit.parinfo.errors
import pkgutil
import os
import importlib
from pyspeckit.spectrum.models.inherited_gaussfitter import gaussian_fitter
from pyspeckit.spectrum.units import SpectroscopicAxis
import numpy as np
import pyspeckit.spectrum.models as models
models_path = os.path.dirname(models.__file__)
xarr = np.linspace(-100, 100, 200)
names = [name for _, name, _ in pkgutil.iter_modules([models_path])]
for name in names:
try:
model_name = 'pyspeckit.spectrum.models.' + name
model_module = importlib.import_module(model_name)
model = getattr(model_module, name + '_model')
model_instance = model()
moments = getattr(model, 'moments')
rawdata = np.random.randn(xarr.size)
params = model_instance.moments(xarr, rawdata)
print 'params:', params
xarr = SpectroscopicAxis(xarr)
# if moments() returns wrong number of parameters this should fail
print model_instance.n_modelfunc(pars=params)(xarr)
except Exception as e:
print e
mg=1,
isg1=1,
isg2=1)
for j in np.arange(nts):
T11 = T11_thy + np.random.randn(len(v_axis)) * rms
T22 = T22_thy + np.random.randn(len(v_axis)) * rms
# ------------ hf Trot ---------------
S11_mg = np.sum(T11[i11_m] * cw)
S11_isg = np.sum(T11[i11_isg0]) * cw + np.sum(T11[i11_isg1]) * cw
S11_osg = np.sum(T11[i11_osg0]) * cw + np.sum(T11[i11_osg1]) * cw
S22_mg = np.sum(T22[i22_mg] * cw)
S22_isg = np.sum(T22[i22_isg0]) * cw + np.sum(T22[i22_isg1]) * cw
Tex_hf = Tex_main(S11_mg, S11_isg, S11_osg, S22_mg, S22_isg, dv=dv)
# ----------- speckit Tex ------------
xarr11 = SpectroscopicAxis(v_axis * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['oneone']).as_unit(u.GHz)
xarr22 = SpectroscopicAxis(v_axis * u.km / u.s,
velocity_convention='radio',
refX=freq_dict['twotwo']).as_unit(u.GHz)
xarr = SpectroscopicAxes([xarr11, xarr22])
synthspec = np.hstack((T11, T22))
nh3_sp = pyspeckit.Spectrum(xarr=xarr, data=synthspec, header={})
# nh3_sp.plotter(axis=nh3_sp.plotter.axis,clear=True)
# trot=20, tex=None, ntot=14.8, width=1, xoff_v=0.0, fortho=0.5
# nh3_sp.plotter(axis=ax1, clear=False) # axis=ax1
nh3_sp.specfit(
fittype='ammonia_tau',
guesses=[Tex_ini, Tex_ini - 10, tau_1 / 2, dv / d2s, 0, 0.5],
fixed=[0, 1, 0, 1, 1, 1])
Tex_kit = nh3_sp.specfit.parinfo[0]['value']
from __future__ import print_function
import numpy as np
from pyspeckit import SpectralCube
from pyspeckit.spectrum.units import SpectroscopicAxis
from pyspeckit.spectrum.models.inherited_gaussfitter import gaussian_fitter
from astropy import units as u
import matplotlib.pyplot as plt
import pytest
from astropy import log
xarr = SpectroscopicAxis(np.linspace(-100, 100, 50),
unit=u.dimensionless_unscaled)
gf = gaussian_fitter()
params = [1.0, 2.0, 5.0]
parameter_error_amplitude = [50., 5., 5.]
assertion_list = []
passes = {'passes': [0, 0, 0], 'avg_difference': [0, 0, 0]}
fails = {'fails': [0, 0, 0], 'avg_difference': [0, 0, 0]}
@pytest.mark.parametrize(("rawdata", "noise"), [(gf.n_modelfunc(pars=params)(
xarr.value), np.random.randn(xarr.value.size) / 100.)])
def test_fiteach(rawdata, noise):
for i in range(1):
passed = True
parameter_noise = [
params[0] + abs(np.random.randn()) * parameter_error_amplitude[0],
params[1] + abs(np.random.randn()) * parameter_error_amplitude[1],
params[2] + abs(np.random.randn()) * parameter_error_amplitude[2]
]
guesses = np.array(params) + parameter_noise
T0 = (const.h * rest_freq / const.k_B).decompose().value
def J_nu(T, T_nu):
''' Brightness temperature calculated in the R-J regime
'''
return T_nu / (np.exp(T_nu / T) - 1)
#
#
rms_thin = 0.001
rms_thick = 0.3
#
xarr = SpectroscopicAxis(
np.linspace(93164661398.45563, 93182630148.45563, num=921) * u.Hz,
refX=rest_freq)
# thin
signal_thin = pyspeckit.models.n2hp.n2hp_vtau.hyperfine(xarr,
Tex=9.0,
tau=0.01,
xoff_v=0.0,
width=0.3)
signal_thin += rms_thin * np.random.randn(len(signal_thin))
signal_thin = np.float32(signal_thin)
# thick
signal_thick = pyspeckit.models.n2hp.n2hp_vtau.hyperfine(xarr,
Tex=9.0,
tau=9.0,
xoff_v=0.0,
width=0.3)
try:
import scipy
scipyOK = True
except ImportError:
scipyOK = False
if scipyOK:
import numpy as np
import pyspeckit.spectrum.models.inherited_voigtfitter as IV
from pyspeckit.spectrum.units import SpectroscopicAxis
xarr = SpectroscopicAxis(np.linspace(-100, 100, 1000))
dx = np.diff(xarr).mean()
V1 = IV.voigt(xarr, 1, 0, 1, 1, normalized=False)
V2 = IV.voigt(xarr, 1, 0, 1, 1, normalized=True)
assert np.sqrt(2 * np.pi) - 0.05 < V1.sum() * dx.value < np.sqrt(
2 * np.pi) + 0.05
assert 0.99 < V2.sum() * dx.value < 1.01
else:
print("Skipped Voigt test because scipy could not be imported")