def jtok_equiv(self, freq):
'''
Return conversion function between Jy/beam to K at the specified
frequency.
The function can be used with the usual astropy.units conversion:
>>> beam = Beam.from_fits_header("header.fits") # doctest: +SKIP
>>> (1.0*u.Jy).to(u.K, beam.jtok_equiv(1.4*u.GHz)) # doctest: +SKIP
Parameters
----------
freq : astropy.units.quantity.Quantity
Frequency to calculate conversion.
Returns
-------
u.brightness_temperature
'''
if not isinstance(freq, u.quantity.Quantity):
raise TypeError("freq must be a Quantity object. "
"Try 'freq*u.Hz' or another equivalent unit.")
try:
return u.brightness_temperature(beam_area=self.sr, frequency=freq)
except TypeError:
# old astropy used ordered arguments
return u.brightness_temperature(self.sr, freq)
def test_brightness_temperature():
omega_B = np.pi * (50 * u.arcsec) ** 2
nu = u.GHz * 5
tb = 7.052587837212582 * u.K
np.testing.assert_almost_equal(
tb.value, (1 * u.Jy).to_value(
u.K, equivalencies=u.brightness_temperature(nu, beam_area=omega_B)))
np.testing.assert_almost_equal(
1.0, tb.to_value(
u.Jy, equivalencies=u.brightness_temperature(nu, beam_area=omega_B)))
def test_brightness_temperature():
omega_B = np.pi * (50 * u.arcsec) ** 2
nu = u.GHz * 5
tb = 7.052590289134352 * u.K
np.testing.assert_almost_equal(
tb.value, (1 * u.Jy).to_value(
u.K, equivalencies=u.brightness_temperature(nu, beam_area=omega_B)))
np.testing.assert_almost_equal(
1.0, tb.to_value(
u.Jy, equivalencies=u.brightness_temperature(nu, beam_area=omega_B)))
def Snu(Te=default_te, nu=95*u.GHz, R=0.1*u.pc, Qlyc=1e45*u.s**-1, beam=4000*u.au,
angular_beam=0.5*u.arcsec):
tb = Tb(Te=Te, nu=nu, EM=EM(R=R, Qlyc=Qlyc))
if beam < R:
return tb.to(u.mJy,
u.brightness_temperature(radio_beam.Beam(angular_beam),
nu))
else:
return (tb * (R/beam)**2).to(u.mJy,
u.brightness_temperature(radio_beam.Beam(angular_beam),
nu))
def to_unit(self, final_unit, barea=None, freq=None):
input_units = self.physical_units
if freq is None:
freq = self.obs_frequency
if barea is None:
beam_area = self.beam_area
else:
beam_area = barea
if self.nmaps == 1:
try:
x = 1.0 * input_units[0]
t = x.to(final_unit,
equivalencies=u.brightness_temperature(
beam_area, freq))
self.data[:] = t * self.data[:]
self.header['TUNIT{0}'.format(1)] = final_unit.to_string()
except UnitConversionError:
try:
x = 1.0 * input_units[0]**(1 / 2)
t = x.to(final_unit,
equivalencies=u.brightness_temperature(
beam_area, freq))
self.data[:] = t * t * self.data[:]
self.header['TUNIT{0}'.format(
1)] = final_unit.to_string() + '^2'
except UnitConversionError:
pass
else:
for jmap in range(self.nmaps):
try:
x = 1.0 * input_units[jmap]
t = x.to(final_unit,
equivalencies=u.brightness_temperature(
beam_area[jmap], freq))
self.data[jmap, :] = t * self.data[jmap, :]
self.header['TUNIT{0}'.format(jmap +
1)] = final_unit.to_string()
except UnitConversionError:
try:
x = 1.0 * input_units[jmap]**(1 / 2)
t = x.to(final_unit,
equivalencies=u.brightness_temperature(
beam_area[jmap], freq))
self.data[jmap, :] = t * t * self.data[jmap, :]
self.header['TUNIT{0}'.format(
jmap + 1)] = '(' + final_unit.to_string() + ')^2'
except UnitConversionError:
pass
def JybeamtoKkms(fluxdict):
intensitylist={}
t_bright={}
dictkeys=fluxdict.keys()
for key in dictkeys:
temptransdict=fluxdict[key]
temptransdictkeys=list(temptransdict.keys())
print(temptransdictkeys)
for i in range(len(temptransdictkeys)):
if 'restfreq' in temptransdictkeys[i]:
continue
else:
temp=(temptransdict[temptransdictkeys[i]]['flux']/linewidth_vel).to('Jy')
#print(temp)
equiv=u.brightness_temperature(temptransdict[temptransdictkeys[i]]['freq'])
#print(equiv)
jy_sr=temp/temptransdict[temptransdictkeys[i]]['beam']
#print(jy_sr)
conversion=jy_sr.to(u.K,equivalencies=equiv)
t_bright.update({temptransdictkeys[i]:conversion})
#print(conversion)
velflux_T=conversion*linewidth_vel
d_velfluxT=(temptransdict[temptransdictkeys[i]]['stddev']/conversion)*velflux_T
intensityerror.append(d_velfluxT)
#print(velflux_T)
#print('\n')
intensitylist.update({temptransdictkeys[i]:velflux_T})
return intensitylist,t_bright
def test_swapped_args_brightness_temperature():
"""
#5173 changes the order of arguments but accepts the old (deprecated) args
"""
omega_B = np.pi * (50 * u.arcsec) ** 2
nu = u.GHz * 5
tb = 7.052587837212582 * u.K
with pytest.warns(AstropyDeprecationWarning) as w:
result = (1*u.Jy).to(
u.K, equivalencies=u.brightness_temperature(omega_B, nu))
roundtrip = result.to(
u.Jy, equivalencies=u.brightness_temperature(omega_B, nu))
assert len(w) == 2
np.testing.assert_almost_equal(tb.value, result.value)
np.testing.assert_almost_equal(roundtrip.value, 1)
def convert_jyperbeam_k(v, bmaj=0., bmin=0., fits_img=None):
"""
calculate the conversion factor from Jy/beam to K
ref: http://docs.astropy.org/en/stable/api/astropy.units.brightness_temperature.html#astropy.units.brightness_temperature
this code give the same results as miriad imstat
:param v: MHz, the freqency of observation
:param bmaj: deg, the beam major angle
:param bmin: deg, the beam minor angle
:param fits_img: optional, the fits image to provide the bmaj and bmin
:return: the conversion factor from Jy/beam to K
"""
if fits_img != None:
fits_open = fits.open(fits_img)
head = fits_open[0].header
bmaj = head['BMAJ']
bmin = head['BMIN']
bmaj = bmaj * u.deg
bmin = bmin * u.deg
fwhm_to_sigma = 1. / (8. * np.log(2.))**0.5
beam_area = 2. * np.pi * (bmaj * bmin * fwhm_to_sigma**2.)
freq = v * u.MHz
equiv = u.brightness_temperature(beam_area, freq)
return u.Jy.to(u.K, equivalencies=equiv)
def scale_values(cat=None, type=None, cubhd=None):
if type == 'imean': # Convert Jy*ch to K km/s
if 'RESTFREQ' in cubhd.keys():
freq = cubhd['RESTFREQ'] * u.Hz
elif 'RESTFRQ' in cubhd.keys():
freq = cubhd['RESTFRQ'] * u.Hz
deltav = cubhd['cdelt3'] / 1000. * u.km / u.s
as2 = 1 * u.arcsec**2
kflux = deltav * as2 * cat['flux'].to(
u.K, equivalencies=u.brightness_temperature(as2, freq))
cat[type] = kflux / cat['area_exact']
cat[type].unit = 'K km / s'
label = 'mean intensity'
elif type == 'v_rms': # Convert m/s to km/s
cat[type] = cat['v_rms'].to(u.km / u.s)
cat[type].unit = 'km / s'
label = 'velocity dispersion'
elif type == 'v_cen': # convert ch number to km/s
cat[type] = 1.e-3 * (cubhd['crval3'] + cubhd['cdelt3'] *
(cat['v_cen'] - cubhd['crpix3']))
cat[type].unit = 'km / s'
label = 'mean velocity'
elif type == 'tmax':
label = 'peak temperature'
else:
label = type
return label
def conversion(v, bmaj, bmin):
'''
v(GHz),bmaj(deg),bmin(deg),retrun(Jy/beam -> K)
'''
if bmaj == bmin:
beam_sigma = bmaj * u.deg
beam_area = 2 * np.pi * (beam_sigma)**2
freq = v * u.GHz
equiv = u.brightness_temperature(beam_area, freq)
else:
bmaj = bmaj * u.deg
bmin = bmin * u.deg
fwhm_to_sigma = 1. / (8 * np.log(2))**0.5
beam_area = 2. * np.pi * (bmaj * bmin * fwhm_to_sigma**2)
freq = v * u.GHz
equiv = u.brightness_temperature(beam_area, freq)
return u.Jy.to(u.K, equivalencies=equiv)
def get_cont(header):
contfn = paths.dpath('W51_te_continuum_best.fits')
beam = radio_beam.Beam.from_fits_header(contfn)
cont_Jy = reproject.reproject_interp(input_data=contfn,
output_projection=header)[0]*u.Jy
cont_K = cont_Jy.to(u.K, u.brightness_temperature(beam,
continuum_frequency))
return cont_K
def convert_to_K(radmc_fits_img, distance=5400*u.pc):
fh = fits.open(radmc_fits_img)
mywcs = wcs.WCS(fh[0].header)
pix_area = np.abs(mywcs.celestial.pixel_scale_matrix.diagonal().prod()) * u.deg**2
conv = u.Jy.to(u.K, equivalencies=u.brightness_temperature(pix_area, mywcs.wcs.crval[2]*u.Hz))
fh[0].data *= conv
fh[0].header['BUNIT'] = 'K'
return fh
def factor_K2JyPixel(self):
"""
Conversion factor from [K] to [Jy/pixel]
"""
pixarea = (self.pixelsize * au.arcsec)**2
freq = self.freq * au.MHz
equiv = au.brightness_temperature(pixarea, freq)
factor = au.K.to(au.Jy, equivalencies=equiv)
return factor
def factor_K2JyPixel(self):
"""
Conversion factor from [K] to [Jy/pixel]
"""
pixarea = (self.pixelsize * au.arcsec) ** 2
freq = self.freq * au.MHz
equiv = au.brightness_temperature(pixarea, freq)
factor = au.K.to(au.Jy, equivalencies=equiv)
return factor
def convert_jy_to_k(hdul):
header = hdul[0].header
beam = radio_beam.Beam.from_fits_header(header)
name = hdul[0].fileinfo()['file'].name
freq = re.search('\d+\.\d+GHz', name).group().rstrip('GHz')
freq = float(freq) * u.GHz
conv = (1 * u.Jy).to(u.K, u.brightness_temperature(beam, freq))
hdul[0].data = hdul[0].data * conv.value
return conv
def convert_jy_kelvin(bmajor,bminor,frequ):
beam_major = bmajor*u.arcsec
beam_minor = bminor*u.arcsec
freq = frequ*u.Hz
fwhm_to_sigma = 1./(8*np.log(2))**0.5
beam_area = 2.*np.pi*(beam_major*beam_minor*fwhm_to_sigma**2)
equiv = u.brightness_temperature(beam_area, freq)
T = (u.Jy.to(u.K, equivalencies=equiv))
return T
def source_line_brightness_temperature(self):
"""
The surface brightness of the source assuming it is observed with a
beam matched to its size and it has ff=1
(this is consistent with the online RADEX calculator)
"""
#return (self.line_flux * beamsize)
# because each line has a different frequency, have to loop it
return ((self.source_line_surfbrightness * u.sr).to(
u.K, u.brightness_temperature(1 * u.sr, self.frequency)))
def test_jtok():
major = 0.1 * u.rad
beam = Beam(major, major, 30 * u.deg)
freq = 1.42 * u.GHz
conv_factor = u.brightness_temperature(beam.sr, freq)
assert_quantity_allclose((1 * u.Jy).to(u.K, equivalencies=conv_factor),
beam.jtok(freq))
def test_jtok():
major = 0.1 * u.rad
beam = Beam(major, major, 30 * u.deg)
freq = 1.42 * u.GHz
conv_factor = u.brightness_temperature(beam.sr, freq)
assert_quantity_allclose((1 * u.Jy).to(u.K, equivalencies=conv_factor),
beam.jtok(freq))
def test_swapped_args_brightness_temperature():
"""
#5173 changes the order of arguments but accepts the old (deprecated) args
"""
omega_B = np.pi * (50 * u.arcsec) ** 2
nu = u.GHz * 5
tb = 7.052590289134352 * u.K
# https://docs.pytest.org/en/latest/warnings.html#ensuring-function-triggers
with warnings.catch_warnings():
warnings.simplefilter('always')
with pytest.warns(DeprecationWarning) as warning_list:
result = (1*u.Jy).to(u.K,
equivalencies=u.brightness_temperature(omega_B,
nu))
roundtrip = result.to(u.Jy,
equivalencies=u.brightness_temperature(omega_B,
nu))
assert len(warning_list) == 2
np.testing.assert_almost_equal(tb.value, result.value)
np.testing.assert_almost_equal(roundtrip.value, 1)
def convert_to_K(radmc_fits_img, distance=5400 * u.pc):
fh = fits.open(radmc_fits_img)
mywcs = wcs.WCS(fh[0].header)
pix_area = np.abs(
mywcs.celestial.pixel_scale_matrix.diagonal().prod()) * u.deg**2
conv = u.Jy.to(u.K,
equivalencies=u.brightness_temperature(
pix_area, mywcs.wcs.crval[2] * u.Hz))
fh[0].data *= conv
fh[0].header['BUNIT'] = 'K'
return fh
def test_swapped_args_brightness_temperature():
"""
#5173 changes the order of arguments but accepts the old (deprecated) args
"""
omega_B = np.pi * (50 * u.arcsec)**2
nu = u.GHz * 5
tb = 7.052590289134352 * u.K
# https://docs.pytest.org/en/latest/warnings.html#ensuring-function-triggers
with warnings.catch_warnings():
warnings.simplefilter('always')
with pytest.warns(DeprecationWarning) as warning_list:
result = (1 * u.Jy).to(u.K,
equivalencies=u.brightness_temperature(
omega_B, nu))
roundtrip = result.to(u.Jy,
equivalencies=u.brightness_temperature(
omega_B, nu))
assert len(warning_list) == 2
np.testing.assert_almost_equal(tb.value, result.value)
np.testing.assert_almost_equal(roundtrip.value, 1)
def source_line_brightness_temperature(self):
"""
The surface brightness of the source assuming it is observed with a
beam matched to its size and it has ff=1
(this is consistent with the online RADEX calculator)
"""
#return (self.line_flux * beamsize)
# because each line has a different frequency, have to loop it
return ((self.source_line_surfbrightness*u.sr).
to(u.K, u.brightness_temperature(1*u.sr,
self.frequency)))
def T2I(temperature, v, bmaj, bmin):
'''
calculate intensity
temperature(K) v(GHz) bmaj(arcsec) bmin(arcsec)
return 1 (Jy/beam)
'''
fwhm_to_sigma = 1. / (8 * np.log(2))**0.5
beam_area = 2. * np.pi * (bmaj * un.arcsec * bmin * un.arcsec *
fwhm_to_sigma**2)
freq = v * u.GHz
equiv = u.brightness_temperature(freq)
return temperature / (u.Jy / beam_area).to(u.K, equivalencies=equiv)
def line_brightness_temperature(self,beamsize):
"""
Return the line surface brightness in kelvins for a given beam area
(Assumes the frequencies are rest frequencies)
"""
#return (self.line_flux * beamsize)
# because each line has a different frequency, have to loop it
try:
return u.Quantity([x.to(u.K, u.brightness_temperature(beamsize, f)).value
for x,f in zip(self.line_flux_density,self.frequency)
],
unit=u.K)
except AttributeError as ex:
raise NotImplementedError("line brightness temperature is not implemented "
"without reference to astropy units yet")
def line_brightness_temperature(self,beamsize):
"""
Return the line surface brightness in kelvins for a given beam area
(Assumes the frequencies are rest frequencies)
"""
#return (self.line_flux * beamsize)
# because each line has a different frequency, have to loop it
try:
return u.Quantity([x.to(u.K, u.brightness_temperature(beamsize, f)).value
for x,f in zip(self.line_flux_density,self.frequency)
],
unit=u.K)
except AttributeError as ex:
raise NotImplementedError("line brightness temperature is not implemented "
"without reference to astropy units yet")
def JybeamtoK(beams,data):
intensitylist=[]
t_bright=[]
for i in range(len(data)):
temp=(data[i]).to('Jy/beam')
#print(temp)
equiv=u.brightness_temperature(data.spectral_axis[i])
#print(equiv)
jy_sr=temp/beams[i]
#print(jy_sr)
conversion=jy_sr.to(u.K,equivalencies=equiv)
t_bright.append(conversion.value)
#print(conversion)
#velflux_T=conversion*lwvel
#print(velflux_T)
#print('\n')
#intensitylist.append(velflux_T)
return t_bright
def Jy_to_Kelvin(flux, freqs):
'''
Convert flux spectrum in Jy/beam to temperature units. Frequency inputs in MHz.
Parameters
----------
flux : 1D Array (float)
Spectrum over frequency band in Jy
freqs : 1D Array (float)
Frequencies (in MHz)
'''
beam_FWHM = 755.0 / (np.mean(freqs * 0.001)) * u.arcsec
beam_area = 2 * np.pi * (beam_FWHM * fwhm_to_sig)**2
freq_MHz = np.mean(freqs) * u.MHz
equiv = u.brightness_temperature(beam_area, freq_MHz)
T = (flux * u.Jy).to(u.K, equivalencies=equiv)
return T, freqs
def get_nhi(sigma, sens, linewidth, beam_maj, beam_min):
"""
Get N_HI sens at sigma level
Inputs:
- sigma: Number, significance level for result
- sens: Quantity, sensitivity matched to linewidth
- linewidth: Quantity, linewidth from N_HI calc
- beam_fwhm: Quantity, beam fwhm
"""
omega_beam = get_beam_area(beam_maj, beam_min)
#hitools, hi freq
#should maybe define globally?
freq = 1420.405752 * u.MHz
#convert to brightness temp
tb = sens.to(u.K, u.brightness_temperature(freq, beam_area=omega_beam))
#convert to N_HI
nhi = 1.823e18 * tb * linewidth / (u.K * u.km / u.s) / (u.cm * u.cm)
nhi_sig = sigma * nhi
return nhi_sig
def k2jysr(temp, freq):
"""
Convert K to Jy/sr.
Parameters
----------
temp: array-like
Brightness temperature in Kelvin
freq: float
Frequency of the map in MHz
Return
------
out: array-like or float
Intensity (brightness) in Jy/sr
"""
ba = 1 * u.sr
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (temp * u.K).to(u.Jy, equivalencies=equiv).value
def k2jysr(temp, freq):
"""
Convert K to Jy/sr.
Parameters
----------
temp: array-like
Brightness temperature in Kelvin
freq: float
Frequency of the map in MHz
Return
------
out: array-like or float
Intensity (brightness) in Jy/sr
"""
ba = 1 * u.sr
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (temp * u.K).to(u.Jy, equivalencies=equiv).value
def jysr2k(intensity, freq):
"""
Convert Jy/sr to K.
Parameters
----------
intensity: array-like
Intensity (brightness) in Jy/sr
freq: float
Frequency of the map in MHz
Return
------
out: array-like or float
Brightness temperature in Kelvin
"""
ba = 1 * u.sr
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (intensity * u.Jy).to(u.K, equivalencies=equiv).value
def jysr2k(intensity, freq):
"""
Convert Jy/sr to K.
Parameters
----------
intensity: array-like
Intensity (brightness) in Jy/sr
freq: float
Frequency of the map in MHz
Return
------
out: array-like or float
Brightness temperature in Kelvin
"""
ba = 1 * u.sr
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (intensity * u.Jy).to(u.K, equivalencies=equiv).value
def convert_to_casa(hdu):
"""
Convert a FITS HDU to casa-compatible units, i.e., Jy/beam
"""
hdu = file_in(hdu)[0].copy()
beam = radio_beam.Beam.from_fits_header(hdu.header)
if hdu.header['BUNIT'] == 'K':
imwcs = wcs.WCS(hdu.header)
cfreq = imwcs.sub([wcs.WCSSUB_SPECTRAL]).wcs_world2pix([0], 0)[0][0]
hdu.data = u.Quantity(hdu.data, unit=u.K).to(
u.Jy, u.brightness_temperature(beam, cfreq * u.Hz)).value
elif u.Unit(hdu.header['BUNIT']).is_equivalent(u.MJy / u.sr):
hdu.data = u.Quantity(hdu.data, u.Unit(hdu.header['BUNIT'])).to(
u.Jy / beam).value
elif hdu.header['BUNIT'] != 'Jy/beam':
raise ValueError("Header BUNIT not recognized")
hdu.header['BUNIT'] = 'Jy/beam'
return hdu
def k2jybeam(temp, freq, beam_width):
"""
Convert K to Jy/beam.
Parameters
----------
temp: array-like
Brightness temperature in Kelvin
freq: float
Frequency of the map in MHz
beam_width: float
The Gaussian FWHM width in degree
Return
------
out: array-like or float
Intensity (brightness) in Jy/beam
"""
ba = beam_area(beam_width) * u.Unit('deg2')
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (temp * u.K).to(u.Jy, equivalencies=equiv).value
def jybeam2k(intensity, freq, beam_width):
"""
Convert Jy/beam to K.
Parameters
----------
intensity: array-like
Intensity (brightness) in Jy/beam
freq: float
Frequency of the map in MHz
beam_width: float
The Gaussian FWHM width in degree
Return
------
out: array-like or float
Brightness temperature in Kelvin
"""
ba = beam_area(beam_width) * u.Unit('deg2')
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (intensity * u.Jy).to(u.K, equivalencies=equiv).value
def jybeam2k(intensity, freq, beam_width):
"""
Convert Jy/beam to K.
Parameters
----------
intensity: array-like
Intensity (brightness) in Jy/beam
freq: float
Frequency of the map in MHz
beam_width: float
The Gaussian FWHM width in degree
Return
------
out: array-like or float
Brightness temperature in Kelvin
"""
ba = beam_area(beam_width) * u.Unit('deg2')
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (intensity * u.Jy).to(u.K, equivalencies=equiv).value
def k2jybeam(temp, freq, beam_width):
"""
Convert K to Jy/beam.
Parameters
----------
temp: array-like
Brightness temperature in Kelvin
freq: float
Frequency of the map in MHz
beam_width: float
The Gaussian FWHM width in degree
Return
------
out: array-like or float
Intensity (brightness) in Jy/beam
"""
ba = beam_area(beam_width) * u.Unit('deg2')
equiv = u.brightness_temperature(ba, freq * u.MHz)
return (temp * u.K).to(u.Jy, equivalencies=equiv).value
def dendrogram_downaddmom_cube(*args, **kwargs):
datacube_dt, datacube_dt_header = downsample_addnoise_and_momentmask(*args)
datacube_dt_wcs = wcs.wcs.WCS(datacube_dt_header)
beam_size = 1/8 * u.deg
frequency = 115 * u.GHz
d = astrodendro.Dendrogram.compute(datacube_dt, wcs=datacube_dt_wcs, **kwargs)
v_scale = datacube_dt_header['cdelt3']
v_unit = u.km / u.s
l_scale = datacube_dt_header['cdelt1']
b_scale = datacube_dt_header['cdelt2']
metadata = {}
metadata['data_unit'] = u.K
metadata['spatial_scale'] = b_scale * u.deg
metadata['velocity_scale'] = v_scale * v_unit
metadata['wavelength'] = frequency
metadata['beam_major'] = beam_size
metadata['beam_minor'] = beam_size
metadata['vaxis'] = 0 # keep it this way if you think the (post-downsample/transposed) input data is (l, b, v)
metadata['wcs'] = datacube_dt_wcs
catalog = astrodendro.ppv_catalog(d, metadata, verbose=True)
flux = u.Quantity(catalog['flux'])
area_exact = catalog['area_exact'].unit*catalog['area_exact'].data
# average brightness temperature integrated over area_exact
flux_kelvin = flux.to('K', equivalencies=u.brightness_temperature(area_exact, frequency))
# flux integrated over area and velocity
flux_kelvin_kms_deg2 = flux_kelvin * metadata['velocity_scale'] * area_exact
catalog.add_column(astropy.table.Column(data=flux_kelvin_kms_deg2, name='flux_kelvin_kms_deg2'))
return d, catalog, datacube_dt_header, metadata
def jy_to_ksr(freqs):
"""
Calculate multiplicative factors to convert [Jy] to [K sr].
Parameters
----------
freqs : :class:`astropy.Quantity` or array_like of float (Deprecated)
Frequencies, assumed to be in Hz if not a Quantity.
Returns
-------
Quantity
Conversion factor(s) to go from [Jy] to [K sr]. Shape equal to shape of freqs.
"""
freqs = np.atleast_1d(freqs)
if not isinstance(freqs, Quantity):
freqs = freqs * units.Hz
equiv = units.brightness_temperature(freqs, beam_area=1 * units.sr)
conv_factor = (1 * units.Jy).to(units.K,
equivalencies=equiv) * units.sr / units.Jy
return conv_factor
def to_temperature(self,
bmaj: Optional[u.Quantity] = None,
bmin: Optional[u.Quantity] = None) -> u.Quantity:
"""Obtain the intensity axis in temperature units.
Args:
bmaj: optional; beam major axis.
bmin: optional; beam minor axis.
Returns:
The intensity axis in temperature units.
"""
# Beam
if bmaj is not None and bmin is not None:
beam = Beam(bmaj, bmin)
elif self.beam is not None:
beam = self.beam
else:
raise ValueError('Cannot convert to temperature units')
# Convert
equiv = u.brightness_temperature(self.spectral_axis, beam_area=beam)
return self.intensity.to(u.K, equivalencies=equiv)
def jtok_equiv(self, freq):
'''
Return conversion function between Jy/beam to K at the specified
frequency.
The function can be used with the usual astropy.units conversion:
>>> (1.0*u.Jy).to(u.K, self.jtok_equiv(1.4*u.GHz))
Parameters
----------
freq : astropy.units.quantity.Quantity
Frequency to calculate conversion.
Returns
-------
u.brightness_temperature
'''
if not isinstance(freq, u.quantity.Quantity):
raise TypeError("freq must be a Quantity object. "
"Try 'freq*u.Hz' or another equivalent unit.")
return u.brightness_temperature(self.sr, freq)
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
def density_distribution(densarr, distr, moleculecolumn, tauthresh=0.8,
opr=None, line_ids=[], mincol=None, Radex=Radex,
**kwargs):
"""
Compute the LVG model for a single zone with an assumed density
*distribution* but other properties fixed.
Parameters
----------
dendarr : array
Array of densities corresponding to the distribution function
distr : array
The density distribution corresponding to the density array
moleculecolumn : quantity
The total column density of the molecule in question. It will be
redistributed across the appropriate densities. Units: cm^-2
[this is wrong - each density will assume a too-low optical depth]
"""
try:
np.testing.assert_almost_equal(distr.sum(), 1)
except AssertionError:
raise ValueError("The distribution must be normalized.")
if not line_ids:
raise ValueError("Specify at least one line ID")
meandens = (densarr*distr).mean()
if opr is None:
collider_densities = {'H2': meandens}
else:
fortho = opr/(1+opr)
collider_densities = {'oH2':meandens*fortho,'pH2':meandens*(1-fortho)}
# Test whether the multi-slab model is reasonable by checking:
# if the column was all at the mean density, would any lines be
# optically thick?
R = Radex(collider_densities=collider_densities, column=moleculecolumn, **kwargs)
R.run_radex()
if np.any(R.tau > tauthresh):
warnings.warn(("At least one line optical depth is >{tauthresh}. "
"Smoothing may be invalid.").format(tauthresh=tauthresh))
# set the optical depth from the *mean* density assuming the *total* column
tau = R.tau
print("Mean density: {0} Optical Depth: {1}".format(meandens, tau[line_ids]))
_thc = (2 * constants.h * constants.c).cgs / u.sr
_fk = (constants.h * constants.c / constants.k_B).cgs
_thc_value = _thc.value
_fk_value = _fk.value
_u_brightness = (u.erg * u.s**-1 * u.cm**-2 * u.Hz**-1 * u.sr**-1)
xnu = R.frequency.to(u.cm**-1, u.spectral()).value
linestrengths = []
texs = []
for dens,prob in zip(densarr,distr):
if opr is None:
collider_densities = {'H2':dens}
else:
collider_densities = {'oH2':dens*fortho,'pH2':dens*(1-fortho)}
R.density = collider_densities
try:
R.column = moleculecolumn * prob
if mincol is not None and R.column < mincol:
R.column = mincol
R.run_radex()
except ValueError as ex:
if ex.args[0] == "Extremely low or extremely high column.":
if R.column > u.Quantity(1e20, u.cm**-2):
raise ex
else:
texs.append(np.zeros_like(line_ids)+2.73)
linestrengths.append(np.zeros_like(line_ids))
continue
else:
raise ex
if hasattr(R, 'radex'):
R.radex.radi.taul[:len(tau)] = tau
elif hasattr(R, '_data_dict'):
R._data_dict['tau'] = tau
fk = _fk_value
thc = _thc_value
with QuantityOff():
ftau = np.exp(-tau)
xt = xnu**3
earg = fk*xnu/R.tex
bnutex = thc*xt/(np.exp(earg)-1.0)
toti_nounit = R.background_brightness*ftau+bnutex*(1.0-ftau)
toti = u.Quantity(toti_nounit, _u_brightness)
totK = ((toti*u.sr).to(u.K, u.brightness_temperature(1*u.sr,
R.frequency)))
linestrengths.append(totK[line_ids])
texs.append(R.tex[line_ids])
linestrengths = np.array(linestrengths)
texs = np.array(texs)
return R, linestrengths, linestrengths.sum(axis=0), texs, tau[line_ids]
import mpl_plot_templates
import numpy as np
from agpy import fit_a_line
import astropy.units as u
import common_constants
from common_constants import h2co11freq, h2co22freq, etamb_77, rrl, aobeamarea, gbbeamarea
from paths import datapath, fpath
import matplotlib
matplotlib.rc_file("pubfiguresrc")
pl.mpl.rcParams["axes.color_cycle"] = [
"#" + x for x in "348ABD, 7A68A6, A60628, 467821, CF4457, 188487, E24A33".split(", ")
]
# Have to convert to Jy to compare fairly
ktojy111 = (1 * u.K).to(u.Jy, u.brightness_temperature(aobeamarea, h2co11freq))
ktojy77 = (1 * u.K).to(u.Jy, u.brightness_temperature(gbbeamarea, h2co22freq))
aofn = os.path.join(datapath, "W51_Halpha_6cm_cube_supersampled.fits")
h112i = (
fits.getdata(os.path.join(datapath, "H110a_integral.fits")) * ktojy111
) # ,aofn.replace("cube","integrated"))) * ktojy111
h112a = fits.getdata(os.path.join(datapath, "H110a_amplitude.fits")) * ktojy111
h112a.value[h112a == 0] = np.nan
h112c = fits.getdata(os.path.join(datapath, "W51_Halpha_6cm_cube_supersampled_continuum.fits")) * ktojy111
h112c.value[h112c == 0] = np.nan
h112h = fits.getheader(os.path.join(datapath, "W51_Halpha_6cm_cube_supersampled_continuum.fits"))
h77iname = os.path.join(datapath, "H77a_integral.fits") #'W51_h77a_pyproc_integrated_supersampled.fits')
h77aname = os.path.join(datapath, "H77a_amplitude.fits") #'W51_h77a_pyproc_integrated_supersampled.fits')
h77i = fits.getdata(h77iname) * ktojy77 / etamb_77
def compute_catalog(d, header):
"""
Computes a catalog on a dendrogram.
Parameters
----------
d : astrodendro.dendrogram.Dendrogram
Dendrogram on which to compute a catalog
header : astropy.io.fits.header.Header
Header corresponding exactly to `d.data`.
Used for unit and scaling information to calculate flux and
world coordinates.
Returns
-------
catalog : astropy.table.table.Table
Catalog describing the structures in dendrogram `d`
using units provided in `header`.
metadata : dict
Explicitly lists unit properties used in `catalog`
"""
# rough average of North and South telescopes:
# see Dame et al. 2001, p. 794.
# "The Northern telescope... has a beamwidth of 8'.4 +/- 0'.2....
# The Southern telescope has nearly the same beamwidth to within
# the uncertainties: 8'.8 +/- 0'.2"
beam_size = 8.5 * u.arcmin
frequency = 115.27 * u.GHz # http://www.cv.nrao.edu/php/splat/
# Remember: by this point, the data ought to be in (v, b, l), with FITS header order opposite that
if 'vel' not in header['ctype3'].lower():
raise ValueError("CTYPE3 must be velocity - check that the data were permuted correctly")
v_scale = header['cdelt3']
v_unit = u.km / u.s
l_scale = header['cdelt1']
b_scale = header['cdelt2']
metadata = {}
metadata['data_unit'] = u.K
metadata['spatial_scale'] = b_scale * u.deg
metadata['velocity_scale'] = v_scale * v_unit
metadata['wavelength'] = frequency # formerly: (c.c / frequency).to('mm') but now compute_flux can handle frequency in spectral equivalency
metadata['beam_major'] = beam_size
metadata['beam_minor'] = beam_size
metadata['vaxis'] = 0 # keep it this way if you think the (post-downsample/transposed) input data is (l, b, v)
metadata['wcs'] = d.wcs
catalog = astrodendro.ppv_catalog(d, metadata, verbose=True)
if catalog['flux'].unit.is_equivalent('Jy'):
# Workaround because flux is computed wrong (see https://github.com/dendrograms/astrodendro/issues/107)
flux = u.Quantity(catalog['flux'])
area_exact = u.Quantity(catalog['area_exact']) #.unit*catalog['area_exact'].data
# average brightness temperature integrated over area_exact
flux_kelvin = flux.to('K', equivalencies=u.brightness_temperature(area_exact, frequency))
# flux integrated over area and velocity
flux_kelvin_kms_sr = flux_kelvin * metadata['velocity_scale'] * area_exact.to(u.steradian)
catalog['flux_true'] = flux_kelvin_kms_sr
background_flux_array = np.zeros_like(catalog['flux_true'])
# do a clipping --
# this uses the approximation that any given structure's background is well-represented by its lowest-valued pixel, which can get messy sometimes.
for i, row in enumerate(catalog):
background_kelvins = d[i].vmin * u.K
background_flux = background_kelvins * d[i].get_npix() * metadata['velocity_scale'] * metadata['spatial_scale']**2
background_flux_array[i] = background_flux.to(u.K * u.km/u.s * u.steradian).value
catalog['flux_clipped'] = catalog['flux_true'] - background_flux_array
return catalog, metadata
'Dec': u.deg,
}
results = photometry(data, mywcs, regs, beam)
for name in results:
rslt_dict = {line+"_"+key: value
for key,value in results[name].items()}
if name in all_results:
all_results[name].update(rslt_dict)
else:
all_results[name] = rslt_dict
restfrq = header['RESTFRQ'] * u.Hz
tbmax = (results[name]['peak']*u.Jy).to(u.K,
u.brightness_temperature(results[name]['beam_area'],
restfrq))
all_results[name][line+'_peak_brightness'] = tbmax
all_results[name][line+"_freq"] = restfrq
# invert the table to make it parseable by astropy...
# (this shouldn't be necessary....)
results_inv = {'name':{}}
columns = {'name':[]}
colnames = {'name'} # set
for k,v in all_results.items():
results_inv['name'][k] = k
columns['name'].append(k)
for kk,vv in v.items():
colnames.add(kk)
if kk in results_inv:
def test_surfacebrightness():
sb = 50*u.MJy/u.sr
k = sb.to(u.K, u.brightness_temperature(50*u.GHz))
np.testing.assert_almost_equal(k.value, 0.650965, 5)
assert k.unit.is_equivalent(u.K)
#ax3.set_ylabel("Number of sources")
#pl.legend(loc='best')
#fig2.savefig(paths.fpath('coreplots/mass_histograms.png'))
#peak_plot[0].set_visible(False)
#H,L,P = ax3.hist(cores_merge['peak_cont_mass'], bins=bins, color='b',
# facecolor='none', histtype='step', label='M($20$K)',
# linewidth=2, alpha=0.5)
#ax3.set_xlim(0,7)
#fig2.savefig(paths.fpath('coreplots/mass_histograms_low.png'))
#
#
#
#
# beam area is for the continuum data
beam_area = u.Quantity(np.array(dendro_merge['beam_area']), u.sr)
jy_to_k = (1*u.Jy).to(u.K, u.brightness_temperature(beam_area,
220*u.GHz)).mean()
m20kconv = float(dendro_merge.meta['keywords']['mass_conversion_factor']['value'].split()[1])
def m20ktickfunc(x):
return ["{0:0.0f}".format(y*m20kconv) for y in x]
fig4 = pl.figure(4)
fig4.clf()
ax5 = fig4.gca()
#for species in np.unique(dendro_merge['PeakLineSpecies']):
# if species != 'NONE':
# mask = species == dendro_merge['PeakLineSpecies']
# ax5.plot(dendro_merge['cont_flux0p4arcsec'][mask]-dendro_merge['cont_flux0p2arcsec'][mask],
# dendro_merge['peak_cont_flux'][mask], 's', label=species)
ax5.plot(dendro_merge['cont_flux0p4arcsec']-dendro_merge['cont_flux0p2arcsec'],
dendro_merge['peak_cont_flux'], 'ks', alpha=0.75, label='')
import FITS_tools
import os
import aplpy
import numpy as np
from astropy import units as u
import pylab as pl
#lawfile = os.path.join(datapath,'GCCBand_Brick_zoom_crop.fits')
lawfile = os.path.join(datapath,'GCCBand_lb.2.fits')
lawdata = fits.getdata(lawfile).squeeze()
law_hdr = FITS_tools.strip_headers.flatten_header(fits.getheader(lawfile))
fwhm = np.sqrt(8*np.log(2))
beam = (2*np.pi*u.deg**2*(4.241274E-02)**2/fwhm**2)
kperjy = (1*u.Jy).to(u.K, equivalencies=u.brightness_temperature(beam,4.829*u.GHz))
lawdata = lawdata * kperjy.value
ccontfile = os.path.join(datapath,'LimaBean_H2CO11_cube_continuum.fits')
ccontdata = fits.getdata(ccontfile).squeeze()
#ccontdata -= np.nanmin(ccontdata) # HACK
ccont_hdr = fits.getheader(ccontfile)
brick_mask = fits.getdata(datapath+'brick_mask11.fits').astype('bool')
okimg = np.isfinite(ccontdata).astype('float')
resampled_law = FITS_tools.hcongrid.hcongrid(lawdata, law_hdr, ccont_hdr)
xok = (np.isfinite(ccontdata) * (ccontdata != 0)).max(axis=0)
yok = (np.isfinite(ccontdata) * (ccontdata != 0)).max(axis=1)
def K2JyPixel(self):
pixarea = (self._pixelsize * au.arcsec) ** 2
equiv = au.brightness_temperature(pixarea, self._freq*au.MHz)
return au.K.to(au.Jy, equivalencies=equiv)
Column(data=([cubes[name].wcs.wcs.restfrq for name in cube_names]*u.Hz).to(u.GHz),
name='Frequency'),
Column(data=[dv[name].to(u.km/u.s).value for name in cube_names]*u.km/u.s,
name='Channel Width'),
Column(data=[errors[name].to(u.mJy).value for name in
cube_names]*u.mJy/u.beam, name='RMS'),
Column(data=[beams[name].major.to(u.arcsec).value for name in
cube_names]*u.arcsec, name='BMAJ'),
Column(data=[beams[name].minor.to(u.arcsec).value for name in
cube_names]*u.arcsec, name='BMIN'),
Column(data=[beams[name].pa.to(u.deg).value for name in
cube_names]*u.deg, name='BPA'),
]
)
tbl.add_column(Column(data=[(1*u.Jy).to(u.K, u.brightness_temperature(bm.sr,
freq*u.GHz,)).value
for bm,freq in zip(beams.values(),
tbl['Frequency'])
],
name='Jy-Kelvin'))
tbl.add_column(Column(data=((tbl['RMS']*u.beam).to(u.Jy).value*tbl['Jy-Kelvin'])*u.K,
name='RMS$_K$'), index=4)
tbl.sort(['Frequency'])
latexdict['header_start'] = '\label{tab:cubes}'
latexdict['caption'] = 'Spectral Cubes'
latexdict['tablefoot'] = ('\par\nJy-Kelvin gives the conversion factor from Jy '
'to Kelvin given the synthesized beam size and '
'observation frequency.')
latexdict['col_align'] = 'l'*len(tbl.columns)
#latexdict['tabletype'] = 'longtable'
centroid_par='shift',
)
myclass.__name__ = "ch3cn_absorption"
return myclass
pyspeckit.spectrum.fitters.default_Registry.add_fitter('ch3cn_absorption',ch3cn_absorption_fitter(),5)
if __name__ == "__main__" and False:
import paths
cube = SpectralCube.read(paths.dpath('longbaseline/W51e2e_CH3CN_cutout.fits'))
sp_ = cube[:,43,43]
hdr = sp_.header
hdr['BUNIT'] = 'K'
sphdu = fits.PrimaryHDU(data=sp_.to(u.K, u.brightness_temperature(cube.beam,
cube.wcs.wcs.restfrq*u.Hz)).value,
header=hdr)
sp = pyspeckit.Spectrum.from_hdu(sphdu)
sp.data -= np.percentile(sp.data, 25)
sp.plotter()
sp.specfit(fittype='ch3cn', guesses=[62, 2, 500, 1e16])
# do it again, excluding k=0 and k=1
sp2 = sp[:400]
sp2.plotter()
sp2.specfit(fittype='ch3cn', guesses=[62, 2, 500, 1e16])
F = False
T = True
sp.specfit(fittype='ch3cn_spw', guesses=[62, 2,]+[100]*14 + [0],
"""
A 1 mJy source will have T_B = 811.6665408856167 K at 4.9 GHz
The upper size limit for a 10^4 K source is 0.030297250253506165 arcsec,or 0.7946490089788438 mpc = 163.9081238701842 AU
"""
import numpy as np
from astropy.io import fits
from astropy import units as u
import radio_beam
import paths
from common_constants import distance
header = fits.getheader(paths.dpath("W51C_ACarray_continuum_4096_both_uniform_contsplit.clean.image.fits"))
beam = radio_beam.Beam.from_fits_header(header)
mJytoK = (1*u.mJy).to(u.K, u.brightness_temperature(beam, 4.9*u.GHz))
print("A 1 mJy source will have T_B = {0} at 4.9 GHz".format(mJytoK))
sizelim = (((mJytoK/(1e4*u.K) * (beam.sr))/(2.*np.pi))**0.5).to(u.arcsec)
print("The upper size limit for a 10^4 K source is {0},"
"or {1} = {2}".format(sizelim, (sizelim*distance).to(u.mpc,
u.dimensionless_angles()),
(sizelim*distance).to(u.au,
u.dimensionless_angles())
))
w = wcs.WCS(header).sub([wcs.WCSSUB_CELESTIAL])
mask = noisereg.get_mask(header=w.to_header(), shape=im[0].data.squeeze().shape)
noise_est[ep] = im[0].data.squeeze()[mask].std() * 1000
peak[ep] = im[0].data.max()*1000
obstbl = Table([Column(data=[ep.split()[-1] for ep in beams], name='Epoch'),
Column(data=[float(ep.split()[0]) for ep in beams]*u.GHz, name='Frequency'),
Column(data=[bm.major.to(u.arcsec).value for bm in beams.values()]*u.arcsec, name='BMAJ'),
Column(data=[bm.minor.to(u.arcsec).value for bm in beams.values()]*u.arcsec, name='BMIN'),
Column(data=[bm.pa.to(u.deg).value for bm in beams.values()]*u.deg, name='BPA'),
Column(data=[noise_est[ep] for ep in beams]*u.mJy/u.beam, name='Noise Estimate'),
Column(data=[peak[ep]/noise_est[ep] for ep in beams], name='Dynamic Range'),
])
obstbl.add_column(Column(data=[(1*u.Jy).to(u.K,
u.brightness_temperature(bm.sr, freq*u.GHz,)
).value
for bm,freq in zip(beams.values(),
obstbl['Frequency'])
],
name='Jy-Kelvin'
)
)
obstbl.sort(['Frequency', 'Epoch'])
latexdict['header_start'] = '\label{tab:observations}'
latexdict['caption'] = 'Observations'
latexdict['tablefoot'] = ('\par\nJy-Kelvin gives the conversion factor from Jy '
'to Kelvin given the synthesized beam size and '
'observation frequency.')
#latexdict['col_align'] = 'lllrr'
results_inv['name'][k] = k
columns['name'].append(k)
for kk,vv in v.items():
if kk in results_inv:
results_inv[kk][k] = vv
columns[kk].append(vv)
else:
results_inv[kk] = {k:vv}
columns[kk] = [vv]
for c in columns:
if c in units:
columns[c] = u.Quantity(columns[c], units[c])
tbl = Table([Column(data=columns[k],
name=k)
for k in ['name', 'RA', 'Dec', 'peak', 'sum', 'npix', 'beam_area',
'bgmad',
'peak_90GHz', 'sum_90GHz', 'bgmad_90GHz',
'peak_100GHz', 'sum_100GHz', 'bgmad_100GHz',
'peak_mass_20K', 'peak_col_20K']])
peak_brightness = (tbl['peak']*u.beam).to(u.K,
u.brightness_temperature(tbl['beam_area'],
masscalc.centerfreq))
tbl.add_column(Column(data=peak_brightness, name='peak_K', unit=u.K))
tbl.sort('peak_mass_20K')
tbl.write(paths.tpath("continuum_photometry.ipac"), format='ascii.ipac',
overwrite=True)
from astropy.io import fits
from astropy import units as u
import numpy as np
from paths import dpath
#f = fits.open('H2CO_11_speccube.fits')
f = fits.open(dpath('H2CO_11_speccube_contsub17_big_uniform.image.fits'))
beam = (np.pi*f[0].header['BMAJ']*f[0].header['BMAJ']*u.deg**2)
cont_offset = (2.7315*u.K).to(u.Jy,u.brightness_temperature(beam, 4.82966*u.GHz))
# try to fix NANs.... this definitely makes everything technically wrong, but more aesthetically useful
extra_cont_offset = 0.10
# 0.05 arbitrarily selected to get a decent match...
#cont = (f[0].data[0,100:300,:,:].sum(axis=0) + f[0].data[0,600:900,:,:].sum(axis=0)) / 500. + 0.05
cont = fits.getdata(dpath('H2CO_11_speccube_cont_16_18_big_uniform.image.fits')).squeeze() + cont_offset.value + extra_cont_offset
cspec = f[0].data[:70,:,:]
cspec[cspec > 0] = 0
spec = cspec + cont
# try to "subtract out" the negative continuum...
spec[:,cont<0] -= cont[cont<0]
cont[cont<0] = cont_offset.value + extra_cont_offset
# avoid huge NAN splotches
#spec[spec<0] = cont_offset.value
tau = -np.log((spec/cont))
tau[0,:,:] = cont # just so we have it... that first channel sucked anyway
dd = ds9.ds9()
cubes = {name: SpectralCube.read(dpath(fn)) for name,fn in cube_names.items()}
vcubes = {name: cube.with_spectral_unit(u.km/u.s, velocity_convention='radio')
for name,cube in cubes.items()}
beams = {name: radio_beam.Beam.from_fits_header(cube.header)
for name,cube in vcubes.items()}
for cube in vcubes.values():
cube._unit = u.Jy
vkcubes = {name: cube.with_flux_unit(u.K,
u.brightness_temperature(beams[name],
cube.wcs.wcs.restfrq*u.Hz))
for name,cube in vcubes.items()}
for name,vc in vkcubes.items():
vc._header['OBJECT'] = name
vc.to_ds9(dd.id, newframe=True)
dd.set('tile yes')
dd.set('frame frameno 1')
dd.set('frame delete')
dd.set('scale limits -300 300')
dd.set('wcs fk5')
dd.set('lock frame wcs')
dd.set('lock slice wcs')
dd.set('lock scale yes')
dd.set('lock color yes')
#ln selfcal_allspw_selfcal_4ampphase_mfs_tclean_deeper_5mJy.image.pbcor.fits W51_te_continuum_best.fits
#ln selfcal_allspw_selfcal_4ampphase_mfs_tclean_deeper_5mJy.residual.fits W51_te_continuum_best_residual.fits
contfile = fits.open(paths.dpath('W51_te_continuum_best.fits'))
data = u.Quantity(contfile[0].data, unit=contfile[0].header['BUNIT'])
mywcs = wcs.WCS(contfile[0].header)
beam = radio_beam.Beam.from_fits_header(contfile[0].header)
pixel_scale = np.abs(mywcs.pixel_scale_matrix.diagonal().prod())**0.5 * u.deg
pixel_scale_as = pixel_scale.to(u.arcsec).value
ppbeam = (beam.sr/(pixel_scale**2)).decompose().value / u.beam
#pl.hist(data[np.isfinite(data)], bins=np.linspace(1e-4,0.1,100))
# over what threshold are we including flux when measuring total masses?
threshold = 10*u.mJy/u.beam
# threshold above which 20 K is very thick
thick_threshold = (20*u.K).to(u.mJy, u.brightness_temperature(beam, masscalc.centerfreq)) / u.beam
threshold_column = (threshold * u.beam/u.Jy * masscalc.col_conversion_factor(beam)).to(u.cm**-2)
threshold_column = masscalc.dust.colofsnu(nu=masscalc.centerfreq,
snu=threshold*u.beam,
beamomega=beam.sr).to(u.cm**-2,
u.dimensionless_angles())
threshold_density = (masscalc.mass_conversion_factor(20) * (threshold*u.beam).to(u.mJy).value /
(4/3.*np.pi) /
(beam.sr.value*masscalc.distance**2)**(1.5) /
(2.8*constants.m_p)).to(1/u.cm**3)
definitely_signal = data > threshold
definitely_thick_if_20K = data > thick_threshold
total_signal = data[definitely_signal].sum() / ppbeam
print("Total pixels > 10mJy/beam: {0} = {1}; r_eff = {2}"
.format(definitely_signal.sum(), definitely_signal.sum()/ppbeam,
((definitely_signal.sum()*(pixel_scale*masscalc.distance)**2)**0.5).to(u.pc,