def test_normalize():
w = np.arange(4000., 5000., 10.)
coeff = [1., 0.1, 0.1]
pol = Polynomial(coeff)
obs_spectrum = Spectrum1D.from_array(w, pol(w), dispersion_unit=u.AA)
norm = Normalize(obs_spectrum, npol=3)
model = Spectrum1D.from_array(w, np.ones_like(w), dispersion_unit=u.AA)
fit = norm(model)
npt.assert_allclose(fit.flux, obs_spectrum.flux)
npt.assert_allclose(norm.polynomial(obs_spectrum.wavelength.value),
obs_spectrum.flux)
npt.assert_allclose(norm.polynomial.convert().coef,
np.array(coeff + [0.]), rtol=1e-5, atol=1.e-10)
def test_spectrum1d_fromarray_quantity():
test_spec = Spectrum1D.from_array(np.arange(3000, 9000) * u.angstrom,
np.random.random(6000))
assert hasattr(test_spec, 'wavelength')
assert test_spec.dispersion_unit == u.angstrom
def test_spectrum1d_flux1():
test_spec = Spectrum1D.from_array(np.arange(3000, 9000) * u.angstrom,
np.random.random(6000) * u.erg/u.s,
)
assert not hasattr(test_spec.data, 'unit')
assert test_spec.flux.unit == u.erg / u.s
assert test_spec.unit == u.erg / u.s
def test_interpolate():
obs_spectrum = Spectrum1D.from_array(np.arange(1,26), np.zeros(25),
dispersion_unit='micron',
unit='erg/(cm^2 s Angstrom)')
test_spectrum = Spectrum1D.from_array(np.arange(0.5, 26.5, 1),
np.arange(0.5, 26.5, 1),
dispersion_unit='micron',
unit='erg/(cm^2 s Angstrom)')
interpolate_plugin = Interpolate(obs_spectrum)
interpolated_test_spectrum = interpolate_plugin(test_spectrum)
expected_interpolated_flux = np.arange(1,26)
interpolated_test_flux = interpolated_test_spectrum.flux
npt.assert_array_almost_equal(interpolated_test_flux,
expected_interpolated_flux, decimal=6)
def read_spec(ispec, second_file=None):
'''Parse spectrum out of the input
Parameters:
-----------
ispec: Spectrum1D, str, or tuple
Returns:
-----------
spec: XSpectrum1D
spec_file: str
'''
from specutils import Spectrum1D
from linetools.spectra.utils import XSpectrum1D
#
if isinstance(ispec,basestring):
spec_fil = ispec
spec = lsi.readspec(spec_fil)
# Second file?
if not second_file is None:
spec2 = lsi.readspec(second_file)
if spec2.sig is None:
spec2.sig = np.zeros(spec.flux.size)
# Scale for convenience of plotting
xper1 = xstats.basic.perc(spec.flux, per=0.9)
xper2 = xstats.basic.perc(spec2.flux, per=0.9)
scl = xper1[1]/xper2[1]
# Stitch together
wave3 = np.append(spec.dispersion, spec2.dispersion)
flux3 = np.append(spec.flux, spec2.flux*scl)
sig3 = np.append(spec.sig, spec2.sig*scl)
spec3 = Spectrum1D.from_array(wave3, flux3, uncertainty=StdDevUncertainty(sig3))
# Overwrite
spec = spec3
spec.filename = spec_fil
elif isinstance(ispec,Spectrum1D):
spec = ispec # Assuming Spectrum1D
spec_fil = spec.filename # Grab from Spectrum1D
elif isinstance(ispec,tuple):
# Units
try:
wv_unit = ispec[0].unit
except AttributeError:
wv_unit = u.AA
uwave = u.Quantity(ispec[0], unit=wv_unit)
# Generate
if len(ispec) == 2: # wave, flux
spec = XSpectrum1D.from_array(uwave, u.Quantity(ispec[1]))
else:
spec = XSpectrum1D.from_array(uwave, u.Quantity(ispec[1]),
uncertainty=StdDevUncertainty(ispec[2]))
#
spec_fil = 'none'
spec.filename = spec_fil
else:
raise ValueError('Bad input to read_spec')
# Return
return spec, spec_fil
def __call__(self, spectrum):
wavelength, flux = spectrum.wavelength.value, spectrum.flux
interpolated_flux = np.interp(self.observed.wavelength.value,
wavelength, flux)
return Spectrum1D.from_array(
self.observed.wavelength,
interpolated_flux,
dispersion_unit=self.observed.wavelength.unit,
unit=self.observed.unit)
def test_spectrum1d_fromarray_quantity2():
test_spec = Spectrum1D.from_array(np.arange(3000, 9000) * u.angstrom,
np.random.random(6000), dispersion_unit='nm')
assert hasattr(test_spec, 'wavelength')
assert test_spec.dispersion_unit == u.nm
nptesting.assert_allclose(test_spec.wavelength.value,
np.arange(3000, 9000) / 10.)
def __call__(self, spectrum):
from specutils import extinction
extinction_factor = 10**(-0.4*extinction.extinction_ccm89(
spectrum.wavelength, a_v=self.a_v, r_v=self.r_v))
return Spectrum1D.from_array(
spectrum.wavelength.value,
extinction_factor * spectrum.flux,
dispersion_unit=spectrum.wavelength.unit, unit=spectrum.unit)
def __call__(self, spectrum):
wavelength, flux = spectrum.wavelength.value, spectrum.flux
log_grid_log_wavelength = np.arange(np.log(wavelength.min()),
np.log(wavelength.max()),
self.resolution.to(1).value)
log_grid_wavelength = np.exp(log_grid_log_wavelength)
log_grid_flux = np.interp(log_grid_wavelength, wavelength, flux)
profile = self.rotational_profile()
log_grid_convolved = nd.convolve1d(log_grid_flux, profile)
convolved_flux = np.interp(wavelength, log_grid_wavelength,
log_grid_convolved)
return Spectrum1D.from_array(spectrum.wavelength,
convolved_flux,
dispersion_unit=spectrum.wavelength.unit,
unit=spectrum.unit)
def test_spectrum1d_flux2():
test_spec = Spectrum1D.from_array(np.arange(3000, 9000) * u.angstrom,
np.random.random(6000) * u.erg/u.s,
)
assert not hasattr(test_spec.data, 'unit')
assert test_spec.flux.unit == u.erg / u.s
assert test_spec.unit == u.erg / u.s
new_flux = np.random.random(6000) * u.W
test_spec.flux = new_flux
assert test_spec.flux.unit == u.erg / u.s
nptesting.assert_allclose(new_flux.to(u.erg / u.s).value,
test_spec.data)
def to_spectrum(self):
try:
from specutils import Spectrum1D
except ImportError:
raise ImportError('specutils needed for this functionality')
from xtool.fix_spectrum1d import Spectrum1D
if getattr(self, 'amplitude_uncertainty', None) is None:
uncertainty = None
else:
uncertainty = self.amplitude_uncertainty
spec = Spectrum1D.from_array(
self.wavelength_pixels * u.nm, self.amplitude.value,
uncertainty=uncertainty)
return spec
def get_query_data(self, filter_tuple, plugin,
warning_threshold=1 * u.gigabyte):
"""
Write spectra to disk
:param filter_tuple:
:param models:
:return:
"""
query = self.get_spectrum_query(filter_tuple)
sample_spectrum_row = query.first()
sample_spectrum_flux = plugin(sample_spectrum_row.get_spectrum1d().flux)
no_spectra = query.count()
size_of_spectra = (query.count() *
len(sample_spectrum_flux)) * 8 * u.byte
if size_of_spectra > warning_threshold:
continue_query = raw_input('The size of the spectra are {0:.2f}. '
'Continue [y/N]'.format(
size_of_spectra.to(warning_threshold.unit)))
if continue_query.strip().lower() != 'y':
raise ValueError('Size of requested grid ({:.2f}) to '
'large for user ... aborting'.format(
size_of_spectra.to(warning_threshold.unit)))
fluxes = np.empty((query.count(),
len(sample_spectrum_flux)))
parameters = []
param_names = [item.name
for item in sample_spectrum_row.parameter_set.parameters]
for i, spectrum_row in enumerate(query):
print "{0}/{1}".format(i, no_spectra)
spectrum = spectrum_row.get_spectrum1d()
fluxes[i] = plugin(spectrum.flux)
parameters.append([getattr(spectrum_row.parameter_set, key)
for key in param_names])
parameters = pd.DataFrame(parameters, columns= param_names)
output_sample_spectrum = Spectrum1D.from_array(
plugin.output_wavelength * u.angstrom, sample_spectrum_flux)
return output_sample_spectrum, parameters, fluxes
def __call__(self,spectrum):
R = self.resolution
Lambda = self.central_wavelength.value
wavelength = spectrum.dispersion.value
conversionfactor = 2 * np.sqrt(2 * np.log(2))
deltax = np.mean(wavelength[1:] - wavelength[0:-1])
FWHM = Lambda/R
sigma = (FWHM/deltax)/conversionfactor
flux = spectrum.flux
convolved_flux = gaussian_filter1d(flux, sigma, axis=0, order=0)
return Spectrum1D.from_array(
spectrum.dispersion,
convolved_flux,
dispersion_unit=spectrum.dispersion.unit, unit=spectrum.unit)
def test_export_data(specviz_gui, tmpdir):
fname = str(tmpdir.join('export.ecsv'))
workspace = specviz_gui._workspaces[0]
data_item = workspace.current_item
workspace.export_data_item(data_item, fname, '*.ecsv')
assert os.path.isfile(fname)
exported = Spectrum1D.read(fname, format='ECSV')
original = data_item.data_item.spectrum
assert_quantity_allclose(exported.flux, original.flux)
assert_quantity_allclose(exported.spectral_axis, original.spectral_axis)
if original.uncertainty is None:
assert exported.uncertainty is None
else:
assert_quantity_allclose(exported.uncertainty, original.uncertainty)
def test_convolution():
my_spec = Spectrum1D.from_array(np.linspace(6000, 8000, 2000),
np.ones(2000), dispersion_unit='Angstrom',
unit='erg/(cm^2 s Angstrom)')
my_spec.flux[1000] = 0.0
R = 5000.
central_wavelength = 7000. * u.Angstrom
convolve_plugin = Convolve(R, central_wavelength)
conv_spectrum = convolve_plugin(my_spec)
assert conv_spectrum.flux[999] < 1.
assert conv_spectrum.flux[1000] > 0
integral_pre_convolved = simps(my_spec.flux, my_spec.wavelength.value)
integral_convolved = simps(conv_spectrum.flux,
conv_spectrum.wavelength.value)
npt.assert_allclose(integral_pre_convolved, integral_convolved,
rtol=1.0, atol=0.0002)
def eval(self, teff, logg, feh):
"""
Interpolating on the grid to the necessary parameters
Parameters
----------
teff: float
effective temperature
logg: float
base ten logarithm of surface gravity in cgs
feh: float
[Fe/H]
"""
flux = self.interpolate_grid(teff, logg, feh)
return Spectrum1D.from_array(self.wavelength,
flux,
dispersion_unit=u.angstrom,
unit=u.Unit('erg/ (cm2 s Angstrom)'))
def eval(self, *args):
"""
Interpolating on the grid to the necessary parameters
Parameters
----------
teff: float
effective temperature
logg: float
base ten logarithm of surface gravity in cgs
feh: float
[Fe/H]
"""
flux = self.interpolate_grid(*args)
return Spectrum1D.from_array(self.wavelength.value,
flux,
dispersion_unit=self.wavelength.unit,
unit=self.flux_unit)
def extract_spectrum(self):
"""Extract 1D spectrum from the information provided so far and
createa `~specutils.Spectrum1D` object
"""
try:
from specutils import Spectrum1D
except:
from .spectrum1d import Spectrum1D
if self.wavelength is None:
raise ValueError('wavelength is None')
if self.wavelength_unit is None:
raise ValueError('wavelength_unit is None')
if self.flux is None:
raise ValueError('flux is None')
if self.flux_unit is None:
raise ValueError('flux_unit is None')
wave = self.wavelength * self.wavelength_unit
flux = self.flux * self.flux_unit
return Spectrum1D.from_array(wave, flux)
def __call__(self, model):
rcond = (len(self.observed.flux) *
np.finfo(self.observed.flux.dtype).eps)
# V[:,0]=mfi/e, Vp[:,1]=mfi/e*w, .., Vp[:,npol]=mfi/e*w**npol
V = self._Vp * (model.flux / self.uncertainty)[:,np.newaxis]
# normalizes different powers
scl = np.sqrt((V*V).sum(0))
sol, resids, rank, s = np.linalg.lstsq(V/scl, self.signal_to_noise,
rcond)
sol = (sol.T/scl).T
if rank != self._Vp.shape[-1] - 1:
msg = "The fit may be poorly conditioned"
warnings.warn(msg)
fit = np.dot(V, sol) * self.uncertainty
# keep coefficients in case the outside wants to look at it
self.polynomial = Polynomial(sol, domain=self.domain.value,
window=self.window.value)
return Spectrum1D.from_array(
self.observed.wavelength.value,
fit, unit=self.observed.unit,
dispersion_unit=self.observed.wavelength.unit)
def __call__(self, img, trace_object):
self.last_trace = trace_object
self.last_img = img
if self.apwidth < 1:
raise ValueError('apwidth must be >= 1')
if self.skysep < 1:
raise ValueError('skysep must be >= 1')
if self.skywidth < 1:
raise ValueError('skywidth must be >= 1')
trace_line = trace_object.line
onedspec = np.zeros_like(trace_line)
skysubflux = np.zeros_like(trace_line)
fluxerr = np.zeros_like(trace_line)
for i in range(0, len(trace_line)):
# first do the aperture flux
# juuuust in case the trace gets too close to an edge
widthup = self.apwidth / 2
widthdn = self.apwidth / 2
if (trace_line[i] + widthup > img.shape[0]):
widthup = img.shape[0] - trace_line[i] - 1
if (trace_line[i] - widthdn < 0):
widthdn = trace_line[i] - 1
# simply add up the total flux around the trace_line +/- width
onedspec[i] = np.nansum(
img[int(trace_line[i] - widthdn):int(trace_line[i] + widthup + 1), i]
)
# now do the sky fit
itrace_line = int(trace_line[i])
sky_y = np.append(
np.arange(
itrace_line - self.apwidth - self.skysep - self.skywidth,
itrace_line - self.apwidth - self.skysep
),
np.arange(
itrace_line + self.apwidth + self.skysep + 1,
itrace_line + self.apwidth + self.skysep + self.skywidth + 1
)
)
sky_flux = img[sky_y, i]
if (self.skydeg > 0):
# fit a polynomial to the sky in this column
pfit = np.polyfit(sky_y, sky_flux, self.skydeg)
# define the aperture in this column
ap = np.arange(
trace_line[i] - self.apwidth,
trace_line[i] + self.apwidth + 1
)
# evaluate the polynomial across the aperture, and sum
skysubflux[i] = np.nansum(np.polyval(pfit, ap))
elif (self.skydeg == 0):
skysubflux[i] = np.nanmean(sky_flux) * (self.apwidth * 2.0 + 1)
# finally, compute the error in this pixel
sigma_bkg = np.nanstd(sky_flux) # stddev in the background data
n_bkg = np.float(len(sky_y)) # number of bkgd pixels
n_ap = self.apwidth * 2. + 1 # number of aperture pixels
# based on aperture phot err description by F. Masci, Caltech:
# http://wise2.ipac.caltech.edu/staff/fmasci/ApPhotUncert.pdf
fluxerr[i] = np.sqrt(
np.nansum(onedspec[i] - skysubflux[i]) + (n_ap + n_ap**22 / n_bkg) * (sigma_bkg**2)
)
spec = Spectrum1D(
spectral_axis=np.arange(len(onedspec)) * u.pixel,
flux=onedspec * img.unit,
uncertainty=StdDevUncertainty(fluxerr)
)
skyspec = Spectrum1D(
spectral_axis=np.arange(len(onedspec)) * u.pixel,
flux=skysubflux * img.unit
)
return spec, skyspec
def get_spectrum1d(self):
flux = self._read_flux()
return Spectrum1D.from_array(self.wavelength, flux,
unit=u.Unit(self.flux_unit))
max(mplot2.y[right:]),
num=len(mplot2.x))
y_model = mplot2.y
y_cn = y_model / y_cont
dcontplot = DataPlot()
dcont = Data1D("normalized", mplot.x, y_cn)
dcontplot.prepare(dcont)
dcontplot.plot()
os.chdir(r"/home/dtyler/Desktop/DocumentsDT/outputs/standard_" +
fits_image_filename)
plt.savefig(fits_image_filename[:-4] + "norm_continuum.png")
os.chdir(r"/home/dtyler/Desktop/DocumentsDT/Programs")
###################################
### calculate equivalent width
spectrum = Spectrum1D(flux=y_cn * u.dimensionless_unscaled,
spectral_axis=mplot.x * u.AA)
eqw = equivalent_width(spectrum)
"""print("EW", eqw.value)
print('norm factor', norm_factor)
for par in bmdl.pars:
print(par.fullname, par.val)"""
### print output to file
os.chdir(
r"/home/dtyler/Desktop/DocumentsDT/Analysis/standard_eq_widths")
fil = open(fits_image_filename[:-4] + ".txt", 'w')
fil.write('eqw' + '\t' + str(eqw.value) + '\n')
fil.write('norm' + '\t' + str(norm_factor) + '\n')
for par in bmdl.pars:
from specutils import Spectrum1D
from astropy import units
import numpy as np
dispersion = np.arange(4000, 5000, 0.12)
flux = np.random.randn(len(dispersion))
mySpectrum = Spectrum1D.from_array(dispersion,
flux,
dispersion_unit=units.m)
hBeta = mySpectrum.slice_dispersion(4851.0, 4871.0)
hBeta
def compprep(spectrum, sn_name, z, source):
old_wave = spectrum[:, 0] # wavelengths
old_flux = spectrum[:, 1] # fluxes
try:
old_error = spectrum[:, 2] # check if supernovae has error array
except IndexError:
old_error = np.array([0]) # if not, set default
old_ivar = df.genivar(old_wave, old_flux,
old_error) # generate inverse variance
snr = prep.getsnr(old_flux, old_ivar)
if source == 'cfa': # choosing source dataset
# z = ReadParam()
sne = prep.ReadExtin('extinction.dat')
if source == 'bsnip':
sne = prep.ReadExtin('extinctionbsnip.dat')
if source == 'csp':
sne = prep.ReadExtin('extinctioncsp.dat')
old_wave *= 1 + float(z) # Redshift back
if source == 'uv':
sne = prep.ReadExtin('extinctionuv.dat')
if source == 'other':
sne = prep.ReadExtin('extinctionother.dat')
# host_reddened = ReadExtin('../data/info_files/ryan_av.txt')
newdata = []
old_wave = old_wave * u.Angstrom # wavelengths
old_flux = old_flux * u.Unit('W m-2 angstrom-1 sr-1')
spec1d = Spectrum1D.from_array(old_wave, old_flux)
test_flux = test_dered.dered(
sne, sn_name, spec1d.wavelength, spec1d.flux
) # Deredenning (see if sne in extinction files match the SN name)
# new_flux = host_correction(sne, sn_name, old_wave, new_flux)
# new_flux = old_flux
new_flux = test_flux.value
old_wave = old_wave.value
old_wave = old_wave / (1. + z)
old_flux = np.asarray(old_flux)
new_flux = np.asarray(new_flux)
s = scale_composites_in_range(old_flux, new_flux)
old_flux = s * old_flux
# plt.rc('font', family='serif')
# fig, ax = plt.subplots(1,1)
# fig.set_size_inches(10, 8, forward = True)
# ax.get_yaxis().set_ticks([])
# plt.plot(old_wave, old_flux, linewidth = 2, color = 'r')
# plt.plot(old_wave, new_flux, linewidth = 2, color = '#3F5D7D')
# plt.ylabel('Relative Flux')
# plt.xlabel('Wavelength ' + "($\mathrm{\AA}$)")
# # plt.savefig('../../Paper_Drafts/MW_corr.png', dpi = 300, bbox_inches = 'tight')
# plt.show()
av = .1294 #2006sr
# av = 2.9711 #2005a
name = '2006sr'
# name = '2005a'
host_wave = old_wave * u.Angstrom # wavelengths
host_flux = new_flux * u.Unit('W m-2 angstrom-1 sr-1')
spec1d = Spectrum1D.from_array(host_wave, host_flux)
new_flux_host, new_ivar_host = test_dered.host_correction(
av, 2.5, name, spec1d.wavelength, spec1d.flux, [0])
new_flux = np.asarray(new_flux)
new_flux_host = np.asarray(new_flux_host.value)
s = scale_composites_in_range(new_flux_host, new_flux)
new_flux_host = s * new_flux_host
norm = 1. / np.amax(new_flux_host)
new_flux_host = new_flux_host * norm
new_flux = new_flux * norm
old_flux = old_flux * norm
plt.rc('font', family='serif')
fig, ax = plt.subplots(1, 1)
fig.set_size_inches(10, 8, forward=True)
plt.minorticks_on()
plt.xticks(fontsize=20)
ax.xaxis.set_ticks(
np.arange(np.round(old_wave[0], -3), np.round(old_wave[-1], -3), 1000))
plt.yticks(fontsize=20)
plt.tick_params(which='major',
bottom='on',
top='on',
left='on',
right='on',
length=10)
plt.tick_params(which='minor',
bottom='on',
top='on',
left='on',
right='on',
length=5)
plt.plot(old_wave, old_flux, linewidth=2, color='#d95f02')
plt.plot(old_wave, new_flux, linewidth=2, color='#1b9e77')
plt.plot(host_wave.value, new_flux_host, linewidth=2, color='#7570b3')
plt.ylabel('Relative Flux', fontsize=30)
plt.xlabel('Rest Wavelength ' + "($\mathrm{\AA}$)", fontsize=30)
plt.savefig('../../Paper_Drafts/red_corr.pdf',
dpi=300,
bbox_inches='tight')
# plt.ylim([-.2,1.01])
# plt.savefig('../../Paper_Drafts/red_corr_large.pdf', dpi = 300, bbox_inches = 'tight')
plt.show()
# new_wave = old_wave/(1.+z) # Deredshifting
new_wave = old_wave
new_error = old_error # Placeholder if it needs to be changed
norm = 1. / np.amax(new_flux)
new_flux = new_flux * norm
new_ivar = df.genivar(new_wave, new_flux,
new_error) # generate new inverse variance
#var = new_flux*0+1
newdata = prep.Interpo(new_wave, new_flux,
new_ivar) # Do the interpolation
plt.rc('font', family='serif')
fig, ax = plt.subplots(1, 1)
fig.set_size_inches(10, 8, forward=True)
plt.minorticks_on()
plt.xticks(fontsize=20)
ax.xaxis.set_ticks(
np.arange(np.round(old_wave[0], -3), np.round(old_wave[-1], -3), 1000))
plt.yticks(fontsize=20)
plt.tick_params(which='major',
bottom='on',
top='on',
left='on',
right='on',
length=10)
plt.tick_params(which='minor',
bottom='on',
top='on',
left='on',
right='on',
length=5)
plt.plot(old_wave, new_flux, linewidth=2, color='r')
plt.plot(newdata[0], newdata[1], linewidth=2, color='#3F5D7D')
plt.ylabel('Relative Flux', fontsize=30)
plt.xlabel('Rest Wavelength ' + "($\mathrm{\AA}$)", fontsize=30)
plt.savefig('../../Paper_Drafts/interp.pdf', dpi=300, bbox_inches='tight')
# plt.ylim([-.3,1.])
# plt.savefig('../../Paper_Drafts/interp_large.pdf', dpi = 300, bbox_inches = 'tight')
plt.show()
# print 'new spectra',newdata
return newdata, snr
def mos_niriss_parser(app, data_dir, obs_label=""):
"""
Attempts to parse all data for a NIRISS dataset in the specified
directory, which should include:
- *_direct_*_cal.fits : Direct 2D image
- *_direct_*_cat.ecsv : Source catalog
- *_WFSSR_*_cal.fits : 2D spectra in first orientation
- *_WFSSC_*_cal.fits : 2D spectra in second orientation
- *_WFSSR_*_x1d.fits : 1D spectra in first orientatiom
- *_WFSSC_*_x1d.fits : 1D spectra in second orientatiom
The spectra from the "C" files (horizontal orientation) are showed
in the viewers by default.
"""
p = Path(data_dir)
if not p.is_dir():
raise ValueError("{} is not a valid directory path".format(data_dir))
source_cat = sorted(list(p.glob("{}*_direct_*_cat.ecsv".format(obs_label))))
direct_image = sorted(list(p.glob("{}*_direct_dit1*_i2d.fits".format(obs_label))))
spec2d_r = sorted(list(p.glob("{}*_WFSSR_*_cal.fits".format(obs_label))))
spec2d_c = sorted(list(p.glob("{}*_WFSSC_*_cal.fits".format(obs_label))))
spec1d_r = sorted(list(p.glob("{}*_WFSSR_*_x1d.fits".format(obs_label))))
spec1d_c = sorted(list(p.glob("{}*_WFSSC_*_x1d.fits".format(obs_label))))
file_lists = {
"Source Catalog": source_cat,
"Direct Image": direct_image,
"2D Spectra C": spec2d_c,
"2D Spectra R": spec2d_r,
"1D Spectra C": spec1d_c,
"1D Spectra R": spec1d_r
}
# Convert from pathlib Paths back to strings
for key in file_lists:
file_lists[key] = [str(x) for x in file_lists[key]]
_warn_if_not_found(app, file_lists)
# Parse relevant information from source catalog
cat_fields = ["id", "sky_centroid.ra", "sky_centroid.dec"]
source_ids = []
ras = []
decs = []
image_add = []
pupil_id_dict = {}
# Retrieve source information
for source_catalog_num in range(0, len(file_lists["Source Catalog"])):
cat_file = file_lists["Source Catalog"][source_catalog_num]
parsed_cat_fields = _fields_from_ecsv(cat_file, cat_fields, delimiter=" ")
pupil = [x
for x in cat_file.split("/")[-1].split("_")
if x[0] == "F" or x[0] == "f"][0]
pupil_id_dict[pupil] = {}
for row in parsed_cat_fields:
pupil_id_dict[pupil][int(row[0])] = (row[1], row[2])
# Read in direct image filters
image_dict = {}
filter_wcs = {}
# Set up a dictionary of datasets to add to glue
add_to_glue = {}
print("Loading: Images")
for image_file in file_lists["Direct Image"]:
im_split = image_file.split("/")[-1].split("_")
pupil = [x
for x in image_file.split("/")[-1].split("_")
if x[0] == "F" or x[0] == "f"][0]
image_label = "Image {} {}".format(im_split[0], pupil)
with fits.open(image_file) as file_obj:
data_iter = get_image_data_iterator(app, file_obj, "Image", ext=None)
data_obj = [d[0] for d in data_iter] # We do not use the generated labels
image_data = data_obj[0] # Grab the first one. TODO: Error if multiple found?
with fits.open(image_file) as temp:
filter_wcs[pupil] = temp[1].header
image_data.label = image_label
add_to_glue[image_label] = image_data
image_dict[pupil] = image_label
# Parse 2D spectra
spec_labels_2d = []
for f in ["2D Spectra C", "2D Spectra R"]:
for fname in file_lists[f]:
print(f"Loading: {f} sources")
orientation = f[-1]
filter_name = [x
for x in fname.split("/")[-1].split("_")
if x[0] == "F" or x[0] == "f"][0]
with fits.open(fname, memmap=False) as temp:
sci_hdus = []
wav_hdus = {}
for i in range(len(temp)):
if "EXTNAME" in temp[i].header:
if temp[i].header["EXTNAME"] == "SCI":
sci_hdus.append(i)
wav_hdus[i] = ('WAVELENGTH', temp[i].header['EXTVER'])
# Now get a Spectrum1D object for each SCI HDU
for sci in sci_hdus:
if temp[sci].header["SPORDER"] == 1:
data = temp[sci].data
meta = temp[sci].header
# The wavelength is stored in a WAVELENGTH HDU. This is
# a 2D array, but in order to be able to use Spectrum1D
# we use the average wavelength for all image rows
wav = temp[wav_hdus[sci]].data.mean(axis=0) * u.micron
spec2d = Spectrum1D(data * u.one, spectral_axis=wav, meta=meta)
spec2d.meta['INSTRUME'] = 'NIRISS'
label = "{} Source {} spec2d {}".format(filter_name,
temp[sci].header["SOURCEID"],
orientation
)
ra, dec = pupil_id_dict[filter_name][temp[sci].header["SOURCEID"]]
source_ids.append("Source Catalog: {} Source ID: {}".
format(filter_name, temp[sci].header["SOURCEID"]))
ras.append(ra)
decs.append(dec)
image_add.append(image_dict[filter_name])
spec_labels_2d.append(label)
add_to_glue[label] = spec2d
spec_labels_1d = []
for f in ["1D Spectra C", "1D Spectra R"]:
for fname in file_lists[f]:
print(f"Loading: {f} sources")
with fits.open(fname, memmap=False) as temp:
# TODO: Remove this once valid SRCTYPE values are present in all headers
for hdu in temp:
if "SRCTYPE" in hdu.header and\
(hdu.header["SRCTYPE"] in ["POINT", "EXTENDED"]):
pass
else:
hdu.header["SRCTYPE"] = "EXTENDED"
specs = SpectrumList.read(temp, format="JWST x1d multi")
filter_name = [x
for x in fname.split("/")[-1].split("_")
if x[0] == "F" or x[0] == "f"][0]
# Orientation denoted by "C" or "R"
orientation = f[-1]
for spec in specs:
if spec.meta['header']['SPORDER'] == 1 and\
spec.meta['header']['EXTNAME'] == "EXTRACT1D":
label = "{} Source {} spec1d {}".format(filter_name,
spec.meta['header']['SOURCEID'],
orientation
)
spec_labels_1d.append(label)
add_to_glue[label] = spec
# Add the datasets to glue - we do this in one step so that we can easily
# optimize by avoiding recomputing the full link graph at every add
with app.data_collection.delay_link_manager_update():
for label, data in add_to_glue.items():
app.add_data(data, label, notify_done=False)
# We then populate the table inside this context manager as _add_to_table
# does operations that also trigger link manager updates.
_add_to_table(app, source_ids, "Source ID")
_add_to_table(app, ras, "Right Ascension")
_add_to_table(app, decs, "Declination")
_add_to_table(app, image_add, "Images")
_add_to_table(app, spec_labels_1d, "1D Spectra")
_add_to_table(app, spec_labels_2d, "2D Spectra")
app.get_viewer('table-viewer')._shared_image = True
def compprep(spectrum,
sn_name,
z,
source,
use_old_error=True,
testing=False,
filename=None,
mjd=None,
mjd_max=None):
""" Performs clipping, deredshifting, variance spectrum generation, MW extinction correction,
and interpolation. If testing is True, several plots will be made to assess the quality
of this processing.
"""
old_wave = spectrum[:, 0] # wavelengths
old_flux = spectrum[:, 1] # fluxes
try:
old_error = spectrum[:, 2] # check if supernovae has error array
except IndexError:
old_error = None # if not, set default
if sn_name == '2011fe' and source == 'other':
old_error = np.sqrt(old_error)
if old_error is not None:
old_var = old_error**2.
else:
old_var = None
if old_var is not None:
num_non_zeros = np.count_nonzero(old_var)
if len(old_var) - num_non_zeros > 100:
old_var = None
elif old_var[-1] == 0.:
old_var[-1] = old_var[-2]
elif True in np.isnan(old_var):
nan_inds = np.transpose(np.argwhere(np.isnan(old_var)))[0]
for ind in nan_inds:
if ind != 0:
old_var[ind] = old_var[ind - 1]
else:
old_var[ind] = old_var[ind + 1]
# if testing:
# plt.plot(old_wave, old_flux)
# plt.plot(old_wave/(1.+z), old_flux)
# plt.plot(old_wave*(1.+z), old_flux)
# plt.xlim(5800,6000)
# # plt.show()
# if old_var is not None:
# plt.plot(old_wave, old_var)
# plt.show()
# old_var = None
vexp, SNR = df.find_vexp(old_wave, old_flux, var_y=old_var)
if testing:
print vexp, SNR
if source != 'csp': #already deredshifted
old_wave = old_wave / (1. + z) #deredshift for clipping
old_wave, old_flux, old_var = df.clip(
old_wave, old_flux, old_var, vexp, testing=testing,
filename=filename) #clip emission/absorption lines
old_wave = old_wave * (1. + z) #reredshift for MW extinction correction
temp_ivar, SNR = df.genivar(old_wave,
old_flux,
old_var,
vexp=vexp,
testing=testing,
source=source) # generate inverse variance
#code to save foundation spec for david
# print filename
# plt.plot(old_wave, old_flux)
# plt.show()
# plt.plot(old_wave, temp_ivar)
# plt.show()
# file_path = '../../Foundation/mod_TNS_spec/' + filename.split('.')[0] + '_modified.flm'
# print file_path
# with open(file_path, 'w') as file:
# file.write('# Orginal file name = ' + filename + '\n')
# file.write('# z = ' + str(z) + '\n')
# # file.write('# MJD = ' + str(mjd) + '\n')
# # file.write('# MJD_max = ' + str(mjd_max) + '\n')
# file.write('\n')
# err = np.sqrt(1./np.asarray(temp_ivar))
# data = np.c_[old_wave,old_flux,err]
# table = tabulate(data, headers=['Wavelength', 'Flux', 'Error'],
# tablefmt = 'ascii')
# file.write(table)
if testing:
print SNR
if old_var is not None:
old_ivar = 1. / old_var
else:
old_ivar = temp_ivar
# snr = getsnr(old_flux, old_ivar)
if source == 'cfa': # choosing source dataset
# z = ReadParam()
sne = ReadExtin('extinction.dat')
if source == 'bsnip':
sne = ReadExtin('extinctionbsnip.dat')
if source == 'csp':
sne = ReadExtin('extinctioncsp.dat')
if source == 'uv':
sne = ReadExtin('extinctionuv.dat')
if source == 'other':
sne = ReadExtin('extinctionother.dat')
if source == 'swift_uv':
sne = ReadExtin('extinctionswiftuv.dat')
if source == 'foley_hst':
sne = ReadExtin('extinctionhst.dat')
if source == 'foundation':
sne = ReadExtin('extinctionfoundation.dat')
# host_reddened = ReadExtin('../data/info_files/ryan_av.txt')
newdata = []
old_wave = old_wave * u.Angstrom # wavelengths
old_flux = old_flux * u.Unit('W m-2 angstrom-1 sr-1')
spec1d = Spectrum1D.from_array(old_wave, old_flux)
spec1d_ivar = Spectrum1D.from_array(old_wave, old_ivar)
dered_flux, dered_ivar = test_dered.dered(
sne,
sn_name,
spec1d.wavelength,
spec1d.flux,
spec1d_ivar.flux,
source=source
) # Dereddening (see if sne in extinction files match the SN name)
# new_flux = host_correction(sne, sn_name, old_wave, new_flux)
# new_flux = old_flux
if testing:
new_flux_plot = copy.deepcopy(dered_flux)
new_ivar_plot = copy.deepcopy(dered_ivar)
old_wave_plot = copy.deepcopy(old_wave)
new_flux = dered_flux.value
new_ivar = dered_ivar.value
old_wave = old_wave.value
if testing:
av_specific = 0.2384 #2005lz
av_specific = 0.4089 #2007af
r_v = 2.5
new_flux_host, new_ivar_host = test_dered.host_correction(
av_specific, r_v, sn_name, old_wave_plot, new_flux_plot,
new_ivar_plot)
new_flux_host = new_flux_host.value
old_flux = old_flux.value
s = scale_composites_in_range(new_flux, old_flux)
new_flux_scaled = s * new_flux
s = scale_composites_in_range(new_flux_host, old_flux)
new_flux_host_scaled = s * new_flux_host
valid_data = np.where(old_wave > 4000)
norm = 10. / np.nanmax(new_flux_host_scaled[valid_data])
old_flux_norm = old_flux * norm
new_flux_norm = new_flux_scaled * norm
new_flux_host_norm = new_flux_host_scaled * norm
plt.rc('font', family='serif')
fig, ax = plt.subplots(1, 1)
fig.set_size_inches(10, 8, forward=True)
plt.minorticks_on()
plt.xticks(fontsize=20)
# ax.xaxis.set_ticks(np.arange(np.round(wave[0],-3),np.round(wave[-1],-3),1000))
plt.yticks(fontsize=20)
plt.tick_params(which='major',
bottom='on',
top='on',
left='on',
right='on',
length=10)
plt.tick_params(which='minor',
bottom='on',
top='on',
left='on',
right='on',
length=5)
plt.plot(old_wave,
old_flux_norm,
linewidth=2,
color='#000080',
label='Before Dereddening')
plt.plot(old_wave,
new_flux_norm,
linewidth=2,
color='gold',
label='Milky Way Corrected')
# plt.plot(old_wave, new_flux_host_norm, linewidth = 2, color = '#d95f02', label='Host Corrected')
plt.ylabel('Relative Flux', fontsize=30)
plt.xlabel('Rest Wavelength ' + "($\mathrm{\AA}$)", fontsize=30)
plt.xlim([old_wave[0] - 200, old_wave[-1] + 200])
plt.legend(loc=1, fontsize=20)
# plt.savefig('../../../Paper_Drafts/reprocessing_updated/red_corr.pdf', dpi = 300, bbox_inches = 'tight')
plt.show()
# plt.plot(old_wave, old_ivar)
# plt.plot(old_wave, new_ivar)
# plt.show()
new_wave = old_wave / (1. + z) # Deredshifting
if not use_old_error:
new_var = None
else:
new_var = old_var # Placeholder if it needs to be changed
#var = new_flux*0+1
# newdata = Interpo(new_wave, new_flux, new_ivar) # Do the interpolation
newdata, scale, var_final = Interpo_flux_conserving(new_wave,
new_flux,
new_ivar,
testing=testing)
if testing:
# newdata_test = Interpo(new_wave, new_flux_host_norm, new_ivar)
newdata_test, scale, var_final = Interpo_flux_conserving(
new_wave, new_flux_host_norm, new_ivar)
interp_wave = newdata_test[0, :]
interp_flux = newdata_test[1, :]
plt.rc('font', family='serif')
fig, ax = plt.subplots(1, 1)
fig.set_size_inches(10, 8, forward=True)
plt.minorticks_on()
plt.xticks(fontsize=20)
# ax.xaxis.set_ticks(np.arange(np.round(wave[0],-3),np.round(wave[-1],-3),1000))
plt.yticks(fontsize=20)
plt.tick_params(which='major',
bottom='on',
top='on',
left='on',
right='on',
length=10)
plt.tick_params(which='minor',
bottom='on',
top='on',
left='on',
right='on',
length=5)
plt.plot(new_wave,
2. * new_flux_host_norm,
linewidth=2,
color='#d95f02',
label='Before Interpolation')
plt.plot(interp_wave,
interp_flux,
linewidth=2,
color='darkgreen',
label='After Interpolation')
plt.ylabel('Relative Flux', fontsize=30)
plt.xlabel('Rest Wavelength ' + "($\mathrm{\AA}$)", fontsize=30)
plt.xlim([new_wave[0] - 200, new_wave[-1] + 200])
plt.legend(loc=1, fontsize=20)
# plt.savefig('../../../Paper_Drafts/reprocessing_updated/interp_deredshift.pdf', dpi = 300, bbox_inches = 'tight')
plt.show()
return newdata, SNR
def combine(spectra,
rv,
snr,
wave_range=None,
desired_wavelength_units='angstrom',
flux_unit='W / (m^2 micron)',
fill_value=1.0):
'''Read in some spectra and shift them to rest wavelengths, then
combine them in a weighted average.
Inputs:
------
spectra : list of spectra to input
rv: array of RV values to shift the spectra
snr: signal-to-noise ratio of the spectra
Keywords:
--------
wave_range : the range of wavelengths to have in the final spectrum
Output:
-------
Combined Spectrum1D object
'''
flux_arr = None
#print(len(spectra))
for i in np.arange(len(spectra)):
if os.path.exists(spectra[i]):
#print(spectra[i])
spectrum = read_fits_file.read_fits_file(
spectra[i], desired_wavelength_units=desired_wavelength_units)
wave = spectrum.wavelength.value
flux = spectrum.flux.value
#print(flux)
if flux_arr is None:
if wave_range is not None:
good = np.where((wave >= wave_range[0])
& (wave <= wave_range[1]))[0]
wave_arr = wave[good]
else:
wave_arr = wave
flux_arr = np.ones((len(wave_arr), len(spectra)))
# shift and interpolate wavelengths
shift_wave = wave / (rv[i] / 3e5 + 1.0)
f = interpolate.interp1d(shift_wave,
flux,
fill_value=fill_value,
bounds_error=False)
flux_arr[:, i] = f(wave_arr)
#print(np.shape(flux_arr))
else:
print('file not found:' + spectra[i])
average_flux = np.average(flux_arr, axis=1, weights=snr**2)
ret_spec = Spectrum1D.from_array(
wave_arr,
average_flux,
dispersion_unit=desired_wavelength_units,
unit=flux_unit)
return ret_spec
def vue_fit_model_to_cube(self, *args, **kwargs):
if self._warn_if_no_equation():
return
if self.selected_data in self.app.data_collection.labels:
data = self.app.data_collection[self.selected_data]
else: # User selected some subset from spectrum viewer, just use original cube
data = self.app.data_collection[0]
# First, ensure that the selected data is cube-like. It is possible
# that the user has selected a pre-existing 1d data object.
if data.ndim != 3:
snackbar_message = SnackbarMessage(
f"Selected data {self.selected_data} is not cube-like",
color='error',
sender=self)
self.hub.broadcast(snackbar_message)
return
# Get the primary data component
attribute = data.main_components[0]
component = data.get_component(attribute)
temp_values = data.get_data(attribute)
# Transpose the axis order
values = np.moveaxis(temp_values, 0, -1) * u.Unit(component.units)
# We manually create a Spectrum1D object from the flux information
# in the cube we select
wcs = data.coords.sub([WCSSUB_SPECTRAL])
spec = Spectrum1D(flux=values, wcs=wcs)
# TODO: in vuetify >2.3, timeout should be set to -1 to keep open
# indefinitely
snackbar_message = SnackbarMessage("Fitting model to cube...",
loading=True,
timeout=0,
sender=self)
self.hub.broadcast(snackbar_message)
# Retrieve copy of the models with proper "fixed" dictionaries
models_to_fit = self._reinitialize_with_fixed()
try:
fitted_model, fitted_spectrum = fit_model_to_spectrum(
spec,
models_to_fit,
self.model_equation,
run_fitter=True,
window=self._window)
except ValueError:
snackbar_message = SnackbarMessage("Cube fitting failed",
color='error',
loading=False,
sender=self)
self.hub.broadcast(snackbar_message)
raise
# Save fitted 3D model in a way that the cubeviz
# helper can access it.
for m in fitted_model:
temp_label = "{} ({}, {})".format(self.model_label, m["x"], m["y"])
self.app.fitted_models[temp_label] = m["model"]
# Transpose the axis order back
values = np.moveaxis(fitted_spectrum.flux.value, -1, 0)
count = max(
map(lambda s: int(next(iter(re.findall(r"\d$", s)), 0)),
self.data_collection.labels)) + 1
label = f"{self.model_label} [Cube] {count}"
# Create new glue data object
output_cube = Data(label=label, coords=data.coords)
output_cube['flux'] = values
output_cube.get_component('flux').units = \
fitted_spectrum.flux.unit.to_string()
# Add to data collection
self.app.add_data(output_cube, label)
if self.selected_viewer != 'None':
# replace the contents in the selected viewer with the results from this plugin
self.app.add_data_to_viewer(self.viewer_to_id.get(
self.selected_viewer),
label,
clear_other_data=True)
snackbar_message = SnackbarMessage("Finished cube fitting",
color='success',
loading=False,
sender=self)
self.hub.broadcast(snackbar_message)
sne_name = folder_path.split('/')[-1]
#input command for redshift
redshift = float(input('Input Redshift of SNe:'))
z = 1 + redshift
#turn each file name into array
#apply obs to rest wavelength and flux conversion
#create list of spectrum files, and continuum files
cont_list = []
data = []
for epoch in file_list:
file = np.genfromtxt(fname= epoch)
lamb = (file[:, 0] / z) * u.AA
flux = file[:, 1] * 10 ** -15 * u.Unit('erg cm-2 s-1 AA-1')
spec = Spectrum1D(spectral_axis=lamb, flux=flux)
data.append(spec)
cont_list.append((spec /spec) * fit_generic_continuum(spec)(spec.spectral_axis))
#plot to find the lines to calculate EW
spcplt = data[0]
cntplt = cont_list[0]
f, ax = plt.subplots()
ax.step(spcplt.wavelength, spcplt.flux)
ax.step(cntplt.wavelength, cntplt.flux)
ax.set_xlim(6000*u.AA, 7500*u.AA)
ax.grid(True)
wave = [6563, 6678, 7065, 7155]
for line in wave:
plt.axvline(x = line)
starspectrum_uncert = np.concatenate(
(starspectrum_uncert, single_order_spec.uncertainty.value[::-1]))
starspectrum_flux = np.concatenate(
(starspectrum_flux, single_order_spec.flux.value[::-1]))
starspectrum_wavelength = np.concatenate(
(starspectrum_wavelength,
single_order_spec.wavelength.value[::-1]))
#print allorders_path
#starspectrum = read_fits_file.read_nirspec_dat(allorders_path,desired_wavelength_units='Angstrom',
# wave_range=waveranges)
starspectrum = Spectrum1D.from_array(dispersion=starspectrum_wavelength,
flux=starspectrum_flux,
dispersion_unit=u.angstrom,
uncertainty=starspectrum_uncert)
g = load_grid(
'/u/rbentley/metallicity/grids/phoenix_t2500_6000_w20000_24000_R40000.h5')
w, f = g()
print len(starspectrum.flux.value)
interp1 = Interpolate(starspectrum)
convolve1 = InstrumentConvolveGrating.from_grid(g, R=24000)
rot1 = RotationalBroadening.from_grid(g, vrot=np.array([10.0]))
norm1 = Normalize(starspectrum, 2)
# concatenate the spectral grid (which will have the stellar parameters) with other
# model components that you want to fit
model = g | rot1 | DopplerShift(vrad=0.0) | convolve1 | interp1 | norm1
def vue_fit_model_to_cube(self, *args, **kwargs):
if self._warn_if_no_equation():
return
data = self.app.data_collection[self._selected_data_label]
# First, ensure that the selected data is cube-like. It is possible
# that the user has selected a pre-existing 1d data object.
if data.ndim != 3:
snackbar_message = SnackbarMessage(
f"Selected data {self._selected_data_label} is not cube-like",
color='error',
sender=self)
self.hub.broadcast(snackbar_message)
return
# Get the primary data component
attribute = data.main_components[0]
component = data.get_component(attribute)
temp_values = data.get_data(attribute)
# Transpose the axis order
values = np.moveaxis(temp_values, 0, -1) * u.Unit(component.units)
# We manually create a Spectrum1D object from the flux information
# in the cube we select
wcs = data.coords.sub([WCSSUB_SPECTRAL])
spec = Spectrum1D(flux=values, wcs=wcs)
# TODO: in vuetify >2.3, timeout should be set to -1 to keep open
# indefinitely
snackbar_message = SnackbarMessage("Fitting model to cube...",
loading=True,
timeout=0,
sender=self)
self.hub.broadcast(snackbar_message)
# Retrieve copy of the models with proper "fixed" dictionaries
# TODO: figure out why this was causing the parallel fitting to fail
#models_to_fit = self._reinitialize_with_fixed()
models_to_fit = self._initialized_models.values()
fitted_model, fitted_spectrum = fit_model_to_spectrum(
spec, models_to_fit, self.model_equation, run_fitter=True)
# Save fitted 3D model in a way that the cubeviz
# helper can access it.
self.app._fitted_3d_model = fitted_model
# Transpose the axis order back
values = np.moveaxis(fitted_spectrum.flux.value, -1, 0)
count = max(
map(lambda s: int(next(iter(re.findall("\d$", s)), 0)),
self.data_collection.labels)) + 1
label = f"{self.model_label} [Cube] {count}"
# Create new glue data object
output_cube = Data(label=label, coords=data.coords)
output_cube['flux'] = values
output_cube.get_component('flux').units = \
fitted_spectrum.flux.unit.to_string()
# Add to data collection
self.app.data_collection.append(output_cube)
snackbar_message = SnackbarMessage("Finished cube fitting",
color='success',
loading=False,
sender=self)
self.hub.broadcast(snackbar_message)
masked_data_sl_f = np.delete(starspectrum35.flux.value,sl_mask_indices)
masked_data_sl_w = np.delete(starspectrum35.wavelength.value,sl_mask_indices)
masked_data_sl_u = np.delete(starspectrum35.uncertainty.value,sl_mask_indices)
plt.figure(figsize=(12,10))
#plt.plot(masked_data_sl_w,masked_data_sl_f)
#masked_data_sl = SKSpectrum1D.from_array(wavelength=masked_data_sl_w*u.angstrom, flux=masked_data_sl_f*u.Unit('erg/s/cm^2/angstrom'), uncertainty=masked_data_sl_f*u.Unit('erg/s/cm^2/angstrom'))
masked_data_sl = Spectrum1D.from_array(dispersion=masked_data_sl_w, flux=masked_data_sl_f, dispersion_unit=u.angstrom, uncertainty=masked_data_sl_u) #
interp_sl = Interpolate(masked_data_sl)
convolve_sl = InstrumentConvolveGrating.from_grid(g,R=24000)
rot_sl = RotationalBroadening.from_grid(g,vrot=np.array([10.0]))
norm_sl = Normalize(masked_data_sl,2)
like_sl = Chi2Likelihood(masked_data_sl)
model = g | rot_sl |DopplerShift(vrad=0.0)| convolve_sl | interp_sl | norm_sl
masked_model_sl = model | like_sl
tw,tf = model()
masked_model_sl
#Fits S_lambda masked model
print type(mask_sl_flux), type(masked_data_sl.wavelength.value)
def dered_corr(data_path, template_path, wave_corr, z_lit, z_bound, spec_type):
"""Function to check remaining flexure after flexure correction has been applied.
Parameters
----------
data_path : str
Path to data spectrum file
template_path : str
Path to template spectrum file
wave_corr : tuple
Flexure-corrected wavelength array
z_lit : float
Literature redshift for target object
z_bound : float
Amount to add and subtract from z_lit for redshifts to test
spec_type : str
Indicates if looking at coadded spectrum or single 1D spectrum
Returns
-------
tm_result_corr : float
Best-fitting redshift post flexure-correction
dered_wave : tuple
De-redshifted wavelength array
"""
#Get data
data_wave_full, data_cut_wave, data_flux_full, data_cut_flux, data_noise_full, data_cut_noise = prep_data(data_path,
spec_type)
#Get template
template_wave, smoothed_template_flux, smoothed_template_noise = prep_template(template_path)
#Find redshift of new, corrected spectrum and de-redshift it to match the template
#Continuum-norm over whole blue range
norm_wave_corr, norm_corr_flux, norm_corr_noise = continuum_normalize(np.min(wave_corr), np.max(wave_corr), data_cut_flux,
wave_corr, data_cut_noise)
norm_template_wave, norm_template_flux, norm_template_noise = continuum_normalize(np.min(template_wave),
np.max(template_wave),
smoothed_template_flux, template_wave,
smoothed_template_noise)
#Plot before
plt.figure(figsize=(12,4))
plt.plot(norm_wave_corr, norm_corr_flux, label='observed')
plt.plot(norm_template_wave, norm_template_flux, label='template')
plt.legend()
#Find new redshift of whole spectrum
corr_spec = Spectrum1D(spectral_axis=norm_wave_corr*u.Angstrom, flux=norm_corr_flux*(u.erg/u.s/u.cm**2/u.Angstrom),
uncertainty=StdDevUncertainty(norm_corr_noise))
template_spec = Spectrum1D(spectral_axis=norm_template_wave*u.Angstrom, flux=norm_template_flux*(u.Lsun/u.micron))
pre_redshifts = np.linspace(z_lit-z_bound, z_lit+z_bound, 1000)
tm_result_corr = template_redshift(observed_spectrum=corr_spec, template_spectrum=template_spec, redshift=pre_redshifts)
#Plot after
plt.figure(figsize=(12,4))
plt.plot(corr_spec.spectral_axis, corr_spec.flux, label='observed')
plt.plot(tm_result_corr[2].spectral_axis, tm_result_corr[2].flux, label='redshifted template')
plt.legend()
plt.figure(figsize=(12,4))
plt.plot(template_spec.spectral_axis, template_spec.flux, label='template')
plt.plot(tm_result_corr[2].spectral_axis, tm_result_corr[2].flux, label='redshifted template')
plt.legend()
#De-redshift data
dered_wave = norm_wave_corr/(1+z_lit)
plt.figure(figsize=(12,4))
plt.plot(dered_wave, norm_corr_flux, label='de-redshifted data')
plt.plot(norm_template_wave, norm_template_flux, label='template')
plt.legend()
return tm_result_corr, dered_wave
def centroid_offsets(targ_bounds, data_wave, data_flux, sky_cents):
"""Returns amount by which extracted skylines are offset from model and the nearest wavelength value to each.
Parameters
----------
targ_bounds : tuple
List of tuples defining bounds of region around each skyline to examine
data_wave : tuple
Wavelength array
data_flux : tuple
Flux array
sky_cents : tuple
Skymodel centroids
Returns
-------
nearest_waves : tuple
Nearest wavelength value to centroid
offsets : tuple
Offset between data and skymodel
"""
regions = SpectralRegion(targ_bounds[0][0]*u.Angstrom,targ_bounds[0][-1]*u.Angstrom)
for i in range(1, len(targ_bounds)):
regions += SpectralRegion(targ_bounds[i][0]*u.Angstrom, targ_bounds[i][-1]*u.Angstrom)
#Normalize data
targ_norm_wave, targ_norm_flux, targ_norm_noise = continuum_normalize(np.min(data_wave), np.max(data_wave), data_flux,
data_wave, np.zeros(len(data_flux)))
#Find offsets
target = Spectrum1D(spectral_axis=targ_norm_wave*u.Angstrom, flux=targ_norm_flux*u.ct)
sub_spec = extract_region(target, regions)
offsets = np.zeros(len(sky_cents))
nearest_waves = np.zeros(len(sky_cents))
for i, sub in enumerate(sub_spec):
an_disp = sub.flux.max()
an_ampl = sub.flux.min()
an_mean = sub.spectral_axis[sub.flux.argmax()]
nearest_waves[i] = an_mean.value
an_stdv = np.sqrt(np.sum((sub.spectral_axis - an_mean)**2) / (len(sub.spectral_axis) - 1))
plt.figure()
plt.scatter(an_mean.value, an_disp.value, marker='o', color='#e41a1c', s=100, label='data')
plt.scatter(sky_cents[i], an_disp.value, marker='o', color='k', s=100, label='archive')
plt.vlines([an_mean.value - an_stdv.value, an_mean.value + an_stdv.value],
sub.flux.min().value, sub.flux.max().value,
color='#377eb8', ls='--', lw=2)
g_init = ( models.Const1D(an_disp) +
models.Gaussian1D(amplitude=(an_ampl - an_disp),
mean=an_mean, stddev=an_stdv) )
g_fit = fit_lines(sub, g_init)
line_fit = g_fit(sub.spectral_axis)
plt.plot(sub.spectral_axis, sub.flux, color='#e41a1c', lw=2)
plt.plot(sub.spectral_axis, line_fit, color='#377eb8', lw=2)
plt.axvline(an_mean.value, color='#e41a1c', ls='--', lw=2)
plt.legend()
offsets[i] = an_mean.value - sky_cents[i].value
return nearest_waves, offsets
def chunk_redshift(data_wave, data_flux, data_noise, template_path, z_lit, targ_delta, overhang, z_test, z_bound, position):
"""Returns the bestfit redshift of each chunk.
Parameters
----------
data_wave : tuple
Data wavelength array
data_flux : tuple
Data flux array
data_noise : tuple
Data noise array
template_path : str
Path to template spectrum file
z_lit : float
Literature redshift of target object
targ_delta : float
Wavelength chunk size in Angstroms
overhang : float
Amount of wavelength overhang template chunks should have in Angstroms
z_test : float
Starting redshift for chunks (measured by eye in 1 chunk)
z_bound : float
Amount to add and subtract from z_lit for redshifts to test
position : str
'before' or 'after' to indicate if pre- or post-flexure correction
Results
-------
bestfit_redshift : tuple
Best fitting redshift for each chunk
best_chi2 : tuple
Minimum chi squared for each chunk
redshifted_spectra : tuple
Redshifted chunks
chi2 : tuple
All chi2
"""
#Get data chunks
data_wave_chunks, data_flux_chunks, data_noise_chunks = data_chunks(data_wave, data_flux, data_noise, targ_delta)
#Get template_chunks
temp_wave_chunks, temp_flux_chunks, temp_noise_chunks, temp_central_wavelengths, central_waves = template_chunks(data_wave,
data_flux,
data_noise, template_path,
z_lit, targ_delta,
overhang, position)
#Find redshifts of each chunk
observed_chunks = []
temp_chunks = []
for i in range(len(data_wave_chunks)):
observed_chunks.append(Spectrum1D(spectral_axis=data_wave_chunks[i]*u.Angstrom,
flux=data_flux_chunks[i]*(u.erg/u.s/u.cm**2/u.Angstrom),
uncertainty=InverseVariance(data_noise_chunks[i])))
temp_chunks.append(Spectrum1D(spectral_axis=temp_wave_chunks[i]*u.Angstrom,
flux=temp_flux_chunks[i]*(u.Lsun/u.micron),
uncertainty=StdDevUncertainty(temp_noise_chunks[i])))
redshifts_chunks = np.linspace(z_test-z_bound, z_test+z_bound, 1000)
fitted_redshift_results = []
bestfit_redshift = np.zeros(len(data_wave_chunks))
best_chi2 = np.zeros(len(data_wave_chunks))
redshifted_spectra = []
chi2 = []
for i in range(len(data_wave_chunks)):
fitted_redshift_results.append(template_redshift(observed_spectrum=observed_chunks[i],
template_spectrum=temp_chunks[i],
redshift=redshifts_chunks))
bestfit_redshift[i] = fitted_redshift_results[i][0]
best_chi2[i] = fitted_redshift_results[i][1]
redshifted_spectra.append(fitted_redshift_results[i][2])
chi2.append(fitted_redshift_results[i][3])
return bestfit_redshift, best_chi2, redshifted_spectra, chi2
def sum_order(self, order):
wavelengths = self.es_list[0].get_order(order).wavelength
total_flux = np.sum([spectrum.get_order(order).flux
for spectrum in self.es_list], axis=0)
return Spectrum1D.from_array(wavelengths, total_flux)
def __call__(self,
image,
trace_object,
disp_axis=1,
crossdisp_axis=0,
bkgrd_prof=models.Polynomial1D(2),
variance=None,
mask=None,
unit=None):
"""
Run the Horne calculation on a region of an image and extract a
1D spectrum.
Parameters
----------
image : `~astropy.nddata.NDData` or array-like, required
The input 2D spectrum from which to extract a source. An
NDData object must specify uncertainty and a mask. An array
requires use of the `variance`, `mask`, & `unit` arguments.
trace_object : `~specreduce.tracing.Trace`, required
The associated 1D trace object created for the 2D image.
disp_axis : int, optional
The index of the image's dispersion axis. [default: 1]
crossdisp_axis : int, optional
The index of the image's cross-dispersion axis. [default: 0]
bkgrd_prof : `~astropy.modeling.Model`, optional
A model for the image's background flux.
[default: models.Polynomial1D(2)]
variance : `~numpy.ndarray`, optional
(Only used if `image` is not an NDData object.)
The associated variances for each pixel in the image. Must
have the same dimensions as `image`. [default: None]
mask : `~numpy.ndarray`, optional
(Only used if `image` is not an NDData object.)
Whether to mask each pixel in the image. Must have the same
dimensions as `image`. If blank, all non-NaN pixels are
unmasked. [default: None]
unit : `~astropy.units.core.Unit` or str, optional
(Only used if `image` is not an NDData object.)
The associated unit for the data in `image`. If blank,
fluxes are interpreted as unitless. [default: None]
Returns
-------
spec_1d : `~specutils.Spectrum1D`
The final, Horne extracted 1D spectrum.
"""
# handle image and associated data based on image's type
if isinstance(image, NDData):
img = np.ma.array(image.data, mask=image.mask)
unit = image.unit if image.unit is not None else u.Unit()
if image.uncertainty is not None:
# prioritize NDData's uncertainty over variance argument
if image.uncertainty.uncertainty_type == 'var':
variance = image.uncertainty.array
elif image.uncertainty.uncertainty_type == 'std':
# NOTE: CCDData defaults uncertainties given as pure arrays
# to std and logs a warning saying so upon object creation.
# should we remind users again here?
warnings.warn("image NDData object's uncertainty "
"interpreted as standard deviation. if "
"incorrect, use VarianceUncertainty when "
"assigning image object's uncertainty.")
variance = image.uncertainty.array**2
elif image.uncertainty.uncertainty_type == 'ivar':
variance = 1 / image.uncertainty.array
else:
# other options are InverseVariance and UnknownVariance
raise ValueError(
"image NDData object has unexpected "
"uncertainty type. instead, try "
"VarianceUncertainty or StdDevUncertainty.")
else:
# ignore variance arg to focus on updating NDData object
raise ValueError('image NDData object lacks uncertainty')
else:
if any(arg is None for arg in (variance, mask, unit)):
raise ValueError('if image is a numpy array, the variance, '
'mask, and unit arguments must be specified. '
'consider wrapping that information into one '
'object by instead passing an NDData image.')
if image.shape != variance.shape:
raise ValueError('image and variance shapes must match')
if image.shape != mask.shape:
raise ValueError('image and mask shapes must match')
# fill in non-required arguments if empty
if mask is None:
mask = np.ma.masked_invalid(image)
if isinstance(unit, str):
unit = u.Unit(unit)
else:
unit = unit if unit is not None else u.Unit()
# create image
img = np.ma.array(image, mask=mask)
# co-add signal in each image column
ncols = img.shape[crossdisp_axis]
xd_pixels = np.arange(ncols) # y plot dir / x spec dir
coadd = img.sum(axis=disp_axis) / ncols
# fit source profile, using Gaussian model as a template
# NOTE: could add argument for users to provide their own model
gauss_prof = models.Gaussian1D(amplitude=coadd.max(),
mean=coadd.argmax(),
stddev=2)
# Fit extraction kernel to column with combined gaussian/bkgrd model
ext_prof = gauss_prof + bkgrd_prof
fitter = fitting.LevMarLSQFitter()
fit_ext_kernel = fitter(ext_prof, xd_pixels, coadd)
# use compound model to fit a kernel to each image column
# NOTE: infers Gaussian1D source profile; needs generalization for others
kernel_vals = []
norms = []
for col_pix in range(img.shape[disp_axis]):
# set gaussian model's mean as column's corresponding trace value
fit_ext_kernel.mean_0 = trace_object.trace[col_pix]
# NOTE: support for variable FWHMs forthcoming and would be here
# fit compound model to column
fitted_col = fit_ext_kernel(xd_pixels)
# save result and normalization
kernel_vals.append(fitted_col)
norms.append(fit_ext_kernel.amplitude_0 * fit_ext_kernel.stddev_0 *
np.sqrt(2 * np.pi))
# transform fit-specific information
kernel_vals = np.array(kernel_vals).T
norms = np.array(norms)
# calculate kernel normalization, masking NaNs
g_x = np.ma.sum(kernel_vals**2 / variance, axis=crossdisp_axis)
# sum by column weights
weighted_img = np.ma.divide(img * kernel_vals, variance)
result = np.ma.sum(weighted_img, axis=crossdisp_axis) / g_x
# multiply kernel normalization into the extracted signal
extraction = result * norms
# convert the extraction to a Spectrum1D object
pixels = np.arange(img.shape[disp_axis]) * u.pix
spec_1d = Spectrum1D(spectral_axis=pixels, flux=extraction * unit)
return spec_1d
def __call__(self, spectrum):
doppler_factor = 1. + self.vrad / const.c
return Spectrum1D.from_array(spectrum.wavelength * doppler_factor,
spectrum.flux,
dispersion_unit=spectrum.wavelength.unit)
if __name__ == "__main__":
wline = [185.999]
band = 'R1'
order = int(band[1])
np.random.seed(0)
x = np.linspace(180., 190., 100)
y = 3 * np.exp(-0.5 * (x - 185.999)**2 / 0.1**2)
y += np.random.normal(0., 0.2, x.shape)
y_continuum = 3.2 * np.exp(-0.5 * (x - 5.6)**2 / 4.8**2)
y += y_continuum
#create spectrum to fit
spectrum = Spectrum1D(flux=y * u.Jy, spectral_axis=x * u.um)
noise_region = SpectralRegion(180. * u.um, 184. * u.um)
spectrum = noise_region_uncertainty(spectrum, noise_region)
#line_region = [(185.52059807*u.um, 186.47740193*u.um)]
g1_fit = fit_generic_continuum(spectrum, model=models.Polynomial1D(1))
y_continuum_fitted = g1_fit(x * u.um)
plt.plot(x, y, label='spectrum')
plt.errorbar(x, y, yerr=spectrum.uncertainty.array, color='b')
plt.plot(x, y_continuum_fitted, label='cont_0')
plt.title('Continuum+line Fitting')
plt.grid(True)
line = LineFitterMult(spectrum,
wline,
def mos_spec2d_parser(app, data_obj, data_labels=None, add_to_table=True,
show_in_viewer=False):
"""
Attempts to parse a 2D spectrum object.
Notes
-----
This currently only works with JWST-type data in which the data is in the
second hdu of the fits file.
Parameters
----------
app : `~jdaviz.app.Application`
The application-level object used to reference the viewers.
data_obj : str or list or spectrum-like
File path, list, or spectrum-like object to be read as a new row in
the mosviz table.
data_labels : str, optional
The label applied to the glue data component.
"""
def _parse_as_spectrum1d(path):
# Parse as a FITS file and assume the WCS is correct
with fits.open(path) as hdulist:
data = hdulist[1].data
header = hdulist[1].header
wcs = WCS(header)
return Spectrum1D(data, wcs=wcs)
# Coerce into list-like object
if not isinstance(data_obj, (list, tuple, SpectrumCollection)):
data_obj = [data_obj]
# If we're given a string, repeat it for each object
if isinstance(data_labels, str):
if len(data_obj) > 1:
data_labels = [f"{data_labels} {i}" for i in range(len(data_obj))]
else:
data_labels = [data_labels]
elif data_labels is None:
if len(data_obj) > 1:
data_labels = [f"2D Spectrum {i}" for i in range(len(data_obj))]
else:
data_labels = ['2D Spectrum']
with app.data_collection.delay_link_manager_update():
for index, data in enumerate(data_obj):
# If we got a filepath, first try and parse using the Spectrum1D and
# SpectrumList parsers, and then fall back to parsing it as a generic
# FITS file.
if _check_is_file(data):
try:
data = Spectrum1D.read(data)
except IORegistryError:
try:
data = Spectrum1D.read(data)
except IORegistryError:
data = _parse_as_spectrum1d(data)
# Copy (if present) region to top-level meta object
if ('header' in data.meta and
'S_REGION' in data.meta['header'] and
'S_REGION' not in data.meta):
data.meta['S_REGION'] = data.meta['header']['S_REGION']
# Set the instrument
# TODO: this should not be set to nirspec for all datasets
data.meta['INSTRUME'] = 'nirspec'
# Get the corresponding label for this data product
label = data_labels[index]
app.data_collection[label] = data
if add_to_table:
_add_to_table(app, data_labels, '2D Spectra')
if show_in_viewer:
if len(data_labels) > 1:
raise ValueError("More than one data label provided, unclear " +
"which to show in viewer")
app.add_data_to_viewer("spectrum-2d-viewer", data_labels[0])
from astropy.convolution import Gaussian1DKernel, convolve
INPUT_spec = 'CS31_CNO_0n.spec'
fwhm = 0.20
#SIGMA=8
SIGMA = fwhm / 2.35482 * 100
wl, fl = np.genfromtxt(INPUT_spec, skip_header=2, unpack=True)
wl2, fl2 = np.genfromtxt('fluxCS31_0.norm.nulbad.0.200',
skip_header=2,
unpack=True)
spec1 = Spectrum1D(spectral_axis=wl * u.A, flux=fl * u.Jy)
#spec1_tsmooth = trapezoid_smooth(spec1, width=3)
#spec1_bsmooth = box_smooth(spec1, width=3)
#spec1_msmooth = median_smooth(spec1, width=3)
spec1_gsmooth = gaussian_smooth(spec1, stddev=SIGMA)
g = Gaussian1DKernel(stddev=SIGMA)
# Convolve data
z = convolve(fl, g)
#plt.plot(spec1.spectral_axis, spec1.flux)
plt.plot(wl2, fl2)
plt.plot(wl, z)
def load_aaomega_file(filename, *args, **kwargs):
with read_fileobj_or_hdulist(filename, *args, **kwargs) as fits_file:
fits_header = fits_file[AAOMEGA_SCIENCE_INDEX].header
# fits_file is the hdulist
var_idx = None
rwss_idx = None
for idx, extn in enumerate(fits_file):
if extn.name == "VARIANCE":
var_idx = idx
if extn.name == "RWSS":
rwss_idx = idx
# science data
fits_data = fits_file[AAOMEGA_SCIENCE_INDEX].data
# read in Fibre table data....
ftable = Table(fits_file[AAOMEGA_FIBRE_INDEX].data)
# A SpectrumList to hold all the Spectrum1D objects
sl = SpectrumList()
# the row var contains the pixel data from the science frame
for i, row in enumerate(fits_data):
# Definitely need deepcopy here, otherwise it does *NOT* work!
fib_header = deepcopy(fits_header)
# Adjusting some values from primary header so individual fibre
# spectra have meaningful headers
fib_header["FLDNAME"] = (fits_header["OBJECT"],
"Name of 2dF .fld file")
fib_header["FLDRA"] = (
fits_header["MEANRA"],
"Right Ascension of 2dF field",
)
fib_header["FLDDEC"] = (fits_header["MEANDEC"],
"Declination of 2dF field")
# Now for the fibre specific information from the Fibre Table
# (extension 2)
# Caution: RA and DEC are stored in RADIANS in the FIBRE TABLE!
fib_header["RA"] = (
ftable["RA"][i] * 180.0 / np.pi,
"Right Ascension of fibre from configure .fld file",
)
fib_header["DEC"] = (
ftable["DEC"][i] * 180.0 / np.pi,
"Declination of fibre from configure .fld file",
)
fib_header["OBJECT"] = (
ftable["NAME"][i],
"Name of target observed by fibre",
)
fib_header["OBJCOM"] = (
ftable["COMMENT"][i],
"Comment from configure .fld file for target",
)
fib_header["OBJMAG"] = (
ftable["MAGNITUDE"][i],
"Magnitude of target observed by fibre",
)
fib_header["OBJTYPE"] = (
ftable["TYPE"][i],
"Type of target observed by fibre",
)
fib_header["OBJPIV"] = (
ftable["PIVOT"][i],
"Pivot number used to observe target",
)
fib_header["OBJPID"] = (
ftable["PID"][i],
"Program ID from configure .fld file",
)
fib_header["OBJX"] = (
ftable["X"][i],
"X coord of target observed by fibre (microns)",
)
fib_header["OBJY"] = (
ftable["Y"][i],
"Y coord of target observed by fibre (microns)",
)
fib_header["OBJXERR"] = (
ftable["XERR"][i],
"X coord error of target observed by fibre (microns)",
)
fib_header["OBJYERR"] = (
ftable["YERR"][i],
"Y coord error of target observed by fibre (microns)",
)
fib_header["OBJTHETA"] = (
ftable["THETA"][i],
"Angle of fibre used to observe target",
)
fib_header["OBJRETR"] = (
ftable["RETRACTOR"][i],
"Retractor number used to observe target",
)
# WLEN added around 2005 according to AAOmega obs manual...
# so not always available
if "WLEN" in ftable.colnames:
fib_header["OBJWLEN"] = (
ftable["WLEN"][i],
"Retractor of target observed by fibre",
)
# ftable['TYPE'][i]:
# P == program (science)
# S == sky
# U == unallocated or unused
# F == fiducial (guide) fibre
# N == broken, dead or no fibre
meta = {"header": fib_header}
if ftable["TYPE"][i] == "P":
meta["purpose"] = "reduced"
elif ftable["TYPE"][i] == "S":
meta["purpose"] = "sky"
else:
# Don't include other fibres that are not science or sky
continue
wcs = compute_wcs_from_keys_and_values(fib_header,
**AAOMEGA_2DF_WCS_SETTINGS)
flux = row * AAOMEGA_2DF_FLUX_UNIT
meta["fibre_index"] = i
# Our science spectrum
spectrum = Spectrum1D(wcs=wcs, flux=flux, meta=meta)
# If the VARIANCE spectrum exists, add it as an additional spectrum
# in the meta dict with key 'variance'
if var_idx is not None:
var_data = fits_file[var_idx].data
var_flux = var_data[i] * AAOMEGA_2DF_FLUX_UNIT**2
spectrum.uncertainty = VarianceUncertainty(var_flux)
# If the RWSS spectrum exists, add it as an additional spectrum in
# the meta dict with key 'science_sky'
# This is an optional extension produced by 2dfdr on request: all
# spectra without the average/median sky subtraction
# Useful in case users want to do their own sky subtraction.
if rwss_idx is not None:
rwss_data = fits_file[rwss_idx].data
rwss_flux = rwss_data[i] * AAOMEGA_2DF_FLUX_UNIT
rwss_meta = {"header": fib_header, "purpose": "science_sky"}
spectrum.meta["science_sky"] = Spectrum1D(wcs=wcs,
flux=rwss_flux,
meta=rwss_meta)
# Add our spectrum to the list.
# The additional spectra are accessed using
# spectrum.meta['variance'] and spectrum.meta['science_sky']
sl.append(spectrum)
add_labels(sl)
return sl
def line_fit(spec,
spec_err,
wave_obj,
dwave=10. * u.AA,
dwave_cont=100. * u.AA,
sigmamax=14. * u.AA):
'''
Function to fit a 1D gaussian to a HETDEX spectrum from get_spec.py
Parameters
----------
spec
1D spectrum from a row in the table provided by get_spec.py.
Will assume unit of 10**-17*u.Unit('erg cm-2 s-1 AA-1') if no units
are provided.
spec_err
1D spectral uncertainty from table provided by get_spec.py.
Will assume unit of 10**-17*u.Unit('erg cm-2 s-1 AA-1') if no units
are provided.
wave_obj
wavelength you want to fit, an astropy quantity
dwave
spectral region above and below wave_obj to fit a line, an astropy quantity.
Default is 10.*u.AA
dwave_cont
spectral region to fit continuum. Default is +/- 100.*u.AA
sigmamax
Maximum linewidth (this is sigma/stdev of the gaussian fit) to allow
for a fit. Assumes unit of u.AA if not given
Returns
-------
'''
try:
spectrum = Spectrum1D(flux=spec,
spectral_axis=(2.0 * np.arange(1036) + 3470.) *
u.AA,
uncertainty=StdDevUncertainty(spec_err),
velocity_convention=None)
except ValueError:
spectrum = Spectrum1D(
flux=spec * 10**-17 * u.Unit('erg cm-2 s-1 AA-1'),
spectral_axis=(2.0 * np.arange(1036) + 3470.) * u.AA,
uncertainty=StdDevUncertainty(spec_err * 10**-17 *
u.Unit('erg cm-2 s-1 AA-1')),
velocity_convention=None)
# measure continuum over 2*dwave_cont wide window first:
cont_region = SpectralRegion((wave_obj - dwave_cont),
(wave_obj + dwave_cont))
cont_spectrum = extract_region(spectrum, cont_region)
cont = np.median(cont_spectrum.flux)
if np.isnan(cont):
#set continuum if its NaN
print('Continuum fit is NaN. Setting to 0.0')
cont = 0.0 * cont_spectrum.unit
# now get region to fit the continuum subtracted line
sub_region = SpectralRegion((wave_obj - dwave), (wave_obj + dwave))
sub_spectrum = extract_region(spectrum, sub_region)
try:
line_param = estimate_line_parameters(sub_spectrum - cont,
models.Gaussian1D())
except:
return None
if np.isnan(line_param.amplitude.value):
print('Line fit yields NaN result. Exiting.')
return None
try:
sigma = np.minimum(line_param.stddev, sigmamax)
except ValueError:
sigma = np.minimum(line_param.stddev, sigmamax * u.AA)
if np.isnan(sigma):
sigma = sigmamax
g_init = models.Gaussian1D(amplitude=line_param.amplitude,
mean=line_param.mean,
stddev=sigma)
# lineregion = SpectralRegion((wave_obj-2*sigma), (wave_obj+2*sigma))
# cont = fit_generic_continuum(sub_spectrum, exclude_regions=lineregion,
# model=models.Linear1D(slope=0))
#r1 = SpectralRegion((wave_obj-dwave), (wave_obj-2*sigma))
#r2 = SpectralRegion((wave_obj+2*sigma), (wave_obj+dwave))
#fitcontregion = r1 + r2
#fit_cont_spectrum = extract_region(sub_spectrum, fitcontregion)
#cont = np.mean(np.hstack([fit_cont_spectrum[0].flux, fit_cont_spectrum[1].flux]))
#contspec = cont(sub_spectrum.spectral_axis)
g_fit = fit_lines(sub_spectrum - cont, g_init)
x = np.arange(wave_obj.value - dwave.value, wave_obj.value + dwave.value,
0.5) * u.AA
y_fit = g_fit(x)
line_flux_model = np.sum(y_fit * 0.5 * u.AA)
chi2 = calc_chi2(sub_spectrum - cont, g_fit)
sn = np.sum(np.array(sub_spectrum.flux)) / np.sqrt(
np.sum(sub_spectrum.uncertainty.array**2))
line_flux_data = line_flux(sub_spectrum - cont).to(u.erg * u.cm**-2 *
u.s**-1)
line_flux_data_err = np.sqrt(np.sum(sub_spectrum.uncertainty.array**2))
#fitted_region = SpectralRegion((line_param.mean - 2*sigma),
# (line_param.mean + 2*sigma))
#fitted_spectrum = extract_region(spectrum, fitted_region)
#line_param = estimate_line_parameters(fitted_spectrum, models.Gaussian1D())
#sn = np.sum(np.array(fitted_spectrum.flux)) / np.sqrt(np.sum(
# fitted_spectrum.uncertainty.array**2))
#line_flux_data = line_flux(fitted_spectrum).to(u.erg * u.cm**-2 * u.s**-1)
#line_flux_data_err = np.sqrt(np.sum(fitted_spectrum.uncertainty.array**2))
return line_param, sn, chi2, sigma, line_flux_data, line_flux_model, line_flux_data_err, g_fit, cont
def test_from_spectrum1d(mode):
if mode == 'wcs3d':
# This test is intended to be run with the version of Spectrum1D based
# on NDCube 2.0
pytest.importorskip("ndcube", minversion="1.99")
# Set up simple spatial+spectral WCS
wcs = WCS(naxis=3)
wcs.wcs.ctype = ['RA---TAN', 'DEC--TAN', 'FREQ']
wcs.wcs.set()
flux = np.ones((4, 4, 5))*u.Unit('Jy')
uncertainty = VarianceUncertainty(np.square(flux*0.1))
mask = np.zeros((4, 4, 5))
kwargs = {'wcs': wcs, 'uncertainty': uncertainty, 'mask': mask}
else:
flux = [2, 3, 4, 5] * u.Jy
uncertainty = VarianceUncertainty([0.1, 0.1, 0.1, 0.1] * u.Jy**2)
mask = [False, False, False, False]
if mode == 'wcs1d':
wcs = WCS(naxis=1)
wcs.wcs.ctype = ['FREQ']
wcs.wcs.set()
kwargs = {'wcs': wcs, 'uncertainty': uncertainty, 'mask': mask}
else:
kwargs = {'spectral_axis': [1, 2, 3, 4] * u.Hz,
'uncertainty': uncertainty, 'mask': mask}
spec = Spectrum1D(flux, **kwargs)
data_collection = DataCollection()
data_collection['spectrum'] = spec
data = data_collection['spectrum']
assert isinstance(data, Data)
assert len(data.main_components) == 3
assert data.main_components[0].label == 'flux'
assert_allclose(data['flux'], flux.value)
component = data.get_component('flux')
assert component.units == 'Jy'
# Check uncertainty parsing within glue data object
assert data.main_components[1].label == 'uncertainty'
assert_allclose(data['uncertainty'], uncertainty.array)
component = data.get_component('uncertainty')
assert component.units == 'Jy2'
# Check round-tripping via single attribute reference
spec_new = data.get_object(attribute='flux', statistic=None)
assert isinstance(spec_new, Spectrum1D)
assert_quantity_allclose(spec_new.spectral_axis, [1, 2, 3, 4] * u.Hz)
if mode == 'wcs3d':
assert_quantity_allclose(spec_new.flux, np.ones((5, 4, 4))*u.Unit('Jy'))
else:
assert_quantity_allclose(spec_new.flux, [2, 3, 4, 5] * u.Jy)
assert spec_new.uncertainty is None
# Check complete round-tripping, including uncertainties
spec_new = data.get_object(statistic=None)
assert isinstance(spec_new, Spectrum1D)
assert_quantity_allclose(spec_new.spectral_axis, [1, 2, 3, 4] * u.Hz)
if mode == 'wcs3d':
assert_quantity_allclose(spec_new.flux, np.ones((5, 4, 4))*u.Unit('Jy'))
assert spec_new.uncertainty is not None
print(spec_new.uncertainty)
print(uncertainty)
assert_quantity_allclose(spec_new.uncertainty.quantity,
np.ones((5, 4, 4))*0.01*u.Jy**2)
else:
assert_quantity_allclose(spec_new.flux, [2, 3, 4, 5] * u.Jy)
assert spec_new.uncertainty is not None
assert_quantity_allclose(spec_new.uncertainty.quantity, [0.1, 0.1, 0.1, 0.1] * u.Jy**2)
def test_spectrum1d_2d_data():
# This test makes sure that 2D spectra represented as Spectrum1D round-trip
# Note that Spectrum1D will typically have a 1D spectral WCS even if the
# data is N-dimensional, so we need to pad the WCS before passing it to
# glue and un-pad it when translating back.
# We test both the case where the WCS is 2D and the case where it is 1D
wcs = WCS(naxis=1)
wcs.wcs.ctype = ['FREQ']
wcs.wcs.cdelt = [10]
wcs.wcs.set()
flux = np.ones((3, 2)) * u.Unit('Jy')
spec = Spectrum1D(flux, wcs=wcs, meta={'instrument': 'spamcam'})
assert spec.data.ndim == 2
assert spec.wcs.naxis == 1
data_collection = DataCollection()
data_collection['spectrum'] = spec
data = data_collection['spectrum']
assert isinstance(data, Data)
assert len(data.main_components) == 1
assert data.main_components[0].label == 'flux'
assert_allclose(data['flux'], flux.value)
assert data.coords.pixel_n_dim == 2
assert data.coords.world_n_dim == 2
assert len(data.pixel_component_ids) == 2
assert len(data.world_component_ids) == 2
assert data.coordinate_components[0].label == 'Pixel Axis 0 [y]'
assert data.coordinate_components[1].label == 'Pixel Axis 1 [x]'
assert data.coordinate_components[2].label == 'Offset'
assert data.coordinate_components[3].label == 'Frequency'
assert_equal(data['Offset'], [[0, 0], [1, 1], [2, 2]])
assert_equal(data['Frequency'], [[10, 20], [10, 20], [10, 20]])
s, o = data.coords.pixel_to_world(1, 2)
assert isinstance(s, SpectralCoord)
# Check round-tripping of coordinates
with pytest.warns(AstropyUserWarning, match='No observer defined on WCS'):
px, py = data.coords.world_to_pixel(s, o)
assert_allclose(px, 1)
assert_allclose(py, 2)
# Check round-tripping of translation
spec_new = data.get_object(statistic=None)
assert isinstance(spec_new, Spectrum1D)
# The WCS object should be the same
assert spec_new.wcs.pixel_n_dim == 1
assert spec_new.wcs.world_n_dim == 1
assert spec_new.wcs is spec.wcs
# The metadata should still be present
assert spec_new.meta['instrument'] == 'spamcam'
def EW(specname,name):
lamb, flux= np.genfromtxt(specname, skip_header=1, unpack=True)
flux = flux * u.Unit('J cm-2 s-1 AA-1')
#flux = flux * u.Unit('erg cm-2 s-1 AA-1')
lamb= lamb * u.AA
spec = Spectrum1D(spectral_axis=lamb, flux=flux)
# normalization is not so good
cont_norm_spec = spec / fit_generic_continuum(spec)(spec.spectral_axis)
print('-----------'+name+'------------')
#line A
EWa = equivalent_width(cont_norm_spec, regions=SpectralRegion(8493*u.AA, 8502*u.AA))
#FWHMa = fwhm(cont_norm_spec, regions=SpectralRegion(8493*u.AA, 8502*u.AA))
print('EW A line: '+str(EWa))
#line B
EWb = equivalent_width(cont_norm_spec, regions=SpectralRegion(8533*u.AA, 8551*u.AA))
print('EW B line: '+str(EWb))
#line C
EWc = equivalent_width(cont_norm_spec, regions=SpectralRegion(8655*u.AA, 8670*u.AA))
print('EW C line: '+str(EWc))
#open log file
#nonlinear to metal-poor
V_VHB = -2.0
EWbc= (EWb+EWc)
EWbc= float(EWbc/(1. * u.AA))
EWp = (EWbc)**(-1.5)
#nonlinear to metal-poor
#Wl = float(EWb / (1. * u.AA)) + float(EWc / (1. * u.AA)) + (0.64 * V_VHB)
#FeH= -2.81 + 0.44*Wl
# FeH constants to V-VHB
a=-2.87
b=0.195
c=0.458
d=-0.913
e=0.0155
#float all
FeH = a + b * V_VHB + c * EWbc + d * EWp + e * EWbc * V_VHB
print('[Fe/H]: '+str(FeH))
#change relampled spectrum to noise spectrum
LOG = open('./EWs/EWfile-'+name+'.txt', 'w')
#LOG = open('./EWs/EWfileRE-'+name+'.txt', 'w')
LOG.write('Log file of '+ name +' \n \n')
LOG.write('Input Spectrum: '+ specname +' \n \n')
LOG.write('EW A line: '+ str(EWa) +' \n')
LOG.write('EW B line: '+ str(EWb) +' \n')
LOG.write('EW C line: '+ str(EWc) +' \n')
LOG.write('[Fe/H]_CaT: '+ str(FeH) +' \n')
f1 = plt.figure(figsize=(16,9))
ax = f1.add_subplot(111)
ax.plot(cont_norm_spec.spectral_axis, cont_norm_spec.flux)
ax.set_xlim([8480,8690])
ax.set_ylabel('Flux (J cm-2 s-1 AA-1)')
ax.set_xlabel('Wavelength ( $\AA$ )')
ax.axvspan(8498-float(EWa / (2. * u.AA)) , 8498+float(EWa / (2. * u.AA)) , alpha=0.2, color='red')
ax.axvspan(8542-float(EWb / (2. * u.AA)) , 8542+float(EWb / (2. * u.AA)) , alpha=0.2, color='red')
ax.axvspan(8662-float(EWc / (2. * u.AA)) , 8662+float(EWc / (2. * u.AA)) , alpha=0.2, color='red')
#change relampled spectrum to noise spectrum
plt.savefig('./EWs/EW-figs/EW'+name+'.pdf')
xlims = [4835, 4885]
text_x_offset = 2
text_y_offset = 0.10
text_fontsize = 11
label_fontsize = 10
fig = plt.figure(figsize=(12,6))
fig.subplots_adjust(left=0.05, bottom=0.10, right=0.95, top=0.95)
ax = fig.add_subplot(111)
for i, (accompaning_text, spectrum_filename) in enumerate(zip(accompaning_texts, spectrum_filenames)):
spectrum = Spectrum1D.load(spectrum_filename)
ax.plot(spectrum.disp, spectrum.flux + i, 'k')
#lhs_text, rhs_text = accompaning_text.split('\t')
#ax.text(xlims[0] + text_x_offset, text_y_offset + 1 + i, lhs_text, fontsize=text_fontsize, horizontalalignment='left')
#ax.text(xlims[1] - text_x_offset, text_y_offset + 1 + i, rhs_text, fontsize=text_fontsize, horizontalalignment='right')
ax.text(xlims[0] + text_x_offset, text_y_offset + i + 1, accompaning_text, fontsize=text_fontsize, horizontalalignment='left')
ax.set_xlabel('Wavelength, $\lambda$ (${\AA}$)', fontsize=label_fontsize)
ax.set_ylabel('Flux, $F_\lambda$', fontsize=label_fontsize)
ax.get_yticklabels()[0].set_visible(False)
ax.set_xlim(*xlims)
ax.set_ylim(0, i + 1.5)
for i in range(len(points)):
fit = np.polyfit(wavelengths, values[i], 1)
values[i] = values[i] / (fit[0] * wavelengths + fit[1])
fs = []
for i in vals: #range(len(points)):
removed_points = points[i]
removed_flux = values[i]
grid.fluxes = np.delete(values, i, axis=0)
grid.index = np.delete(points, i, axis=0)
starspectrum = Spectrum1D.from_array(dispersion=wavelengths,
flux=removed_flux,
dispersion_unit=u.angstrom,
uncertainty=removed_flux * (1 / 100.))
interp1 = Interpolate(starspectrum)
norm1 = Normalize(starspectrum, 2)
model = grid | interp1 | norm1
setattr(model, 'teff_0', removed_points[0])
setattr(model, 'logg_0', removed_points[1])
setattr(model, 'mh_0', removed_points[2])
setattr(model, 'alpha_0', removed_points[3])
'''
result = mtf.fit_array(starspectrum, model, R_fixed=25000.)
print result.median
def specviz_spectrum1d_parser(app,
data,
data_label=None,
format=None,
show_in_viewer=True):
"""
Loads a data file or `~specutils.Spectrum1D` object into Specviz.
Parameters
----------
data : str, `~specutils.Spectrum1D`, or `~specutils.SpectrumList`
Spectrum1D, SpectrumList, or path to compatible data file.
data_label : str
The Glue data label found in the ``DataCollection``.
format : str
Loader format specification used to indicate data format in
`~specutils.Spectrum1D.read` io method.
"""
# If no data label is assigned, give it a unique identifier
if not data_label:
data_label = "specviz_data|" + str(
base64.b85encode(uuid.uuid4().bytes), "utf-8")
if isinstance(data, SpectrumCollection):
raise TypeError("SpectrumCollection detected."
" Please provide a Spectrum1D or SpectrumList")
elif isinstance(data, Spectrum1D):
data = [data]
data_label = [data_label]
elif isinstance(data, SpectrumList):
pass
else:
path = pathlib.Path(data)
if path.is_file():
try:
data = [Spectrum1D.read(str(path), format=format)]
data_label = [data_label]
except IORegistryError:
# Multi-extension files may throw a registry error
data = SpectrumList.read(str(path), format=format)
else:
raise FileNotFoundError("No such file: " + str(path))
if isinstance(data, SpectrumList):
if not isinstance(data_label, (list, tuple)):
temp_labels = []
for i in range(len(data)):
temp_labels.append(f"{data_label} {i}")
data_label = temp_labels
elif len(data_label) != len(data):
raise ValueError(
f"Length of data labels list ({len(data_label)}) is different"
f" than length of list of data ({len(data)})")
# If there's already data in the viewer, convert units if needed
current_unit = None
current_spec = app.get_data_from_viewer("spectrum-viewer")
if current_spec != {} and current_spec is not None:
spec_key = list(current_spec.keys())[0]
current_unit = current_spec[spec_key].spectral_axis.unit
with app.data_collection.delay_link_manager_update():
for i in range(len(data)):
spec = data[i]
if current_unit is not None and spec.spectral_axis.unit != current_unit:
spec = Spectrum1D(
flux=spec.flux,
spectral_axis=spec.spectral_axis.to(current_unit))
app.add_data(spec, data_label[i])
# Only auto-show the first spectrum in a list
if i == 0 and show_in_viewer:
app.add_data_to_viewer("spectrum-viewer", data_label[i])
if abs(apogee_res[i])>0.05:
apogee_mask += [apogee_res[i]]
apogee_mask_w += [resampled_apogeew[i]]
apogee_ind += [i]
apogee_ind_s = sorted(apogee_ind, reverse=True)
print 'trimming'
starspectrum_fmasked = np.delete(starspectrum35.flux,apogee_ind_s)
starspectrum_wmasked = np.delete(starspectrum35.wavelength,apogee_ind_s)
starspectrum_umasked = np.delete(starspectrum35.uncertainty,apogee_ind_s)
print len(starspectrum_fmasked), len(apogee_ind)
spectrum_masked = Spectrum1D.from_array(starspectrum_wmasked, starspectrum_fmasked, dispersion_unit=starspectrum35.wavelength.unit, uncertainty=starspectrum_umasked)
#flux_unit=starspectrum35.flux.unit, wavelength_unit=starspectrum35.wavelength.unit)
print starspectrum_fmasked
interp1 = Interpolate(spectrum_masked)
print 'interpolated 2'
convolve1 = InstrumentConvolveGrating.from_grid(g,R=24000)
print 'convolved 2'
rot1 = RotationalBroadening.from_grid(g,vrot=np.array([10.0]))
print 'rot broadend 2'
norm1 = Normalize(spectrum_masked,2)
print 'normalized 2'
# concatenate the spectral grid (which will have the stellar parameters) with other
# model components that you want to fit
model = g | rot1 |DopplerShift(vrad=radv)| convolve1 | interp1 | norm1
print 'model concaten 2'
def read_fits_spectrum1d(filename, dispersion_unit=None, flux_unit=None):
"""
1D reader for spectra in FITS format. This function determines what format
the FITS file is in, and attempts to read the Spectrum. This reader just
uses the primary extension in a FITS file and reads the data and header from
that. It will return a Spectrum1D object if the data is linear, or a list of
Spectrum1D objects if the data format is multi-spec
Parameters
----------
filename : str
FITS filename
dispersion_unit : ~astropy.unit.Unit, optional
unit of the dispersion axis - will overwrite possible information given
in the FITS keywords
default = None
flux_unit : ~astropy.unit.Unit, optional
unit of the flux
Raises
--------
NotImplementedError
If the format can't be read currently
"""
if dispersion_unit:
dispersion_unit = u.Unit(dispersion_unit)
data = fits.getdata(filename)
header = fits.getheader(filename)
wcs_info = FITSWCSSpectrum(header)
if wcs_info.naxis == 1:
wcs = read_fits_wcs_linear1d(wcs_info, dispersion_unit=dispersion_unit)
return Spectrum1D(data, wcs=wcs, unit=flux_unit)
elif wcs_info.naxis == 2 and \
wcs_info.affine_transform_dict['ctype'] == ["MULTISPE", "MULTISPE"]:
multi_wcs = multispec_wcs_reader(wcs_info, dispersion_unit=dispersion_unit)
multispec = []
for spectrum_data, spectrum_wcs in zip(data, multi_wcs.values()):
multispec.append(
Spectrum1D(spectrum_data, wcs=spectrum_wcs, unit=flux_unit))
return multispec
elif wcs_info.naxis == 3 and \
wcs_info.affine_transform_dict['ctype'] == ["LINEAR","LINEAR","LINEAR"]:
wcs = read_fits_wcs_linear1d(wcs_info, dispersion_unit=dispersion_unit)
equispec = []
for i in range(data.shape[0]):
equispec.append(
Spectrum1D(data[i][0], wcs=wcs, unit=flux_unit))
return equispec
elif wcs_info.naxis == 3 and \
wcs_info.affine_transform_dict['ctype'] == ["MULTISPE", "MULTISPE","LINEAR"]:
multi_wcs = multispec_wcs_reader(wcs_info, dispersion_unit=dispersion_unit)
multispec = []
for j in range(data.shape[1]):
equispec = []
for i in range(data.shape[0]):
equispec.append(
Spectrum1D(data[i][j], wcs=list(multi_wcs.values())[j], unit=flux_unit))
multispec.append(equispec)
return multispec
else:
raise NotImplementedError("Either the FITS file does not represent a 1D"
" spectrum or the format isn't supported yet")
def add_single_spectra_to_map(
spectra_map,
*,
header,
data,
spec_info=None,
wcs_info=None,
units_info=None,
purpose_prefix=None,
all_standard_units,
all_keywords,
valid_wcs,
index=None,
):
spec_wcs_info = {}
spec_units_info = {}
if wcs_info is not None:
spec_wcs_info.update(wcs_info)
if units_info is not None:
spec_units_info.update(units_info)
if spec_info is not None:
spec_wcs_info.update(spec_info.get("wcs", {}))
spec_units_info.update(spec_info.get("units", {}))
purpose = spec_info.get("purpose")
else:
purpose = None
purpose = get_purpose(
header,
purpose=purpose,
purpose_prefix=purpose_prefix,
all_keywords=all_keywords,
index=index,
)
if purpose == Purpose.SKIP:
return None
if valid_wcs or not spec_wcs_info:
wcs = WCS(header)
else:
wcs = compute_wcs_from_keys_and_values(header, **spec_wcs_info)
if all_standard_units:
spec_units_info = {"flux_unit_keyword": "BUNIT"}
flux_unit = get_flux_units_from_keys_and_values(header, **spec_units_info)
flux = data * flux_unit
meta = {"header": header, "purpose": PURPOSE_SPECTRA_MAP[purpose]}
if purpose in CREATE_SPECTRA:
spectrum = Spectrum1D(wcs=wcs, flux=flux, meta=meta)
spectra_map[PURPOSE_SPECTRA_MAP[purpose]].append(spectrum)
elif purpose in ERROR_PURPOSES:
try:
spectrum = spectra_map[PURPOSE_SPECTRA_MAP[purpose]][-1]
except IndexError:
raise ValueError(f"No spectra to associate with {purpose}")
aligned_flux = pixel_to_pixel(wcs, spectrum.wcs, flux)
spectrum.uncertainty = UNCERTAINTY_MAP[purpose](aligned_flux)
spectrum.meta["uncertainty_header"] = header
# We never actually want to return something, this just flags it to pylint
# that we know we're breaking out of the function when skip is selected
return None
def to_object(self, data_or_subset, attribute=None, statistic='mean'):
"""
Convert a glue Data object to a Spectrum1D object.
Parameters
----------
data_or_subset : `glue.core.data.Data` or `glue.core.subset.Subset`
The data to convert to a Spectrum1D object
attribute : `glue.core.component_id.ComponentID`
The attribute to use for the Spectrum1D data
statistic : {'minimum', 'maximum', 'mean', 'median', 'sum', 'percentile'}
The statistic to use to collapse the dataset
"""
if isinstance(data_or_subset, Subset):
data = data_or_subset.data
subset_state = data_or_subset.subset_state
else:
data = data_or_subset
subset_state = None
if isinstance(data.coords, WCSCoordinates):
# Find spectral axis
spec_axis = data.coords.wcs.naxis - 1 - data.coords.wcs.wcs.spec
# Find non-spectral axes
axes = tuple(i for i in range(data.ndim) if i != spec_axis)
kwargs = {'wcs': data.coords.wcs.sub([WCSSUB_SPECTRAL])}
elif isinstance(data.coords, SpectralCoordinates):
kwargs = {'spectral_axis': data.coords.spectral_axis}
else:
raise TypeError(
'data.coords should be an instance of WCSCoordinates or SpectralCoordinates'
)
if isinstance(attribute, str):
attribute = data.id[attribute]
elif len(data.main_components) == 0:
raise ValueError('Data object has no attributes.')
elif attribute is None:
if len(data.main_components) == 1:
attribute = data.main_components[0]
else:
raise ValueError(
"Data object has more than one attribute, so "
"you will need to specify which one to use as "
"the flux for the spectrum using the "
"attribute= keyword argument.")
component = data.get_component(attribute)
# Collapse values to profile
if data.ndim > 1:
# Get units and attach to value
values = data.compute_statistic(statistic,
attribute,
axis=axes,
subset_state=subset_state)
mask = None
else:
values = data.get_data(attribute)
if subset_state is None:
mask = None
else:
mask = data.get_mask(subset_state=subset_state)
values = values.copy()
values[~mask] = np.nan
values = values * u.Unit(component.units)
return Spectrum1D(values, mask=mask, **kwargs)
def test_pre_full(data_path, template_path, z_lit, z_bound, spec_type):
"""Returns the full spectrum best-fit redshift and min chi2.
Tests the redshift array on the entire spectrum to ensure bounds are appropriate.
Parameters
----------
data_path : str
Path to data spectrum file
template_path : str
Path to template spectrum file
z_lit : float
Literature redshift for target object
z_bound : float
Amount to add and subtract from z_lit for redshifts to test
spec_type : str
Indicates if looking at coadded spectrum or single 1D spectrum
Returns
-------
tm_result[0] : float
Best-fit redshift
tm_result[1] : float
Minimum chi-squared
"""
#Import data
data_wave_full, data_cut_wave, data_flux_full, data_cut_flux, data_noise_full, data_cut_noise = prep_data(data_path,
spec_type)
#Import smoothed template
template_wave, smoothed_template_flux, smoothed_template_noise = prep_template(template_path)
#Continuum normalize over whole wavelength range
norm_data_wave, norm_data_flux, norm_data_noise = continuum_normalize(np.min(data_cut_wave), np.max(data_cut_wave),
data_cut_flux, data_cut_wave, data_cut_noise)
norm_template_wave, norm_template_flux, norm_template_noise = continuum_normalize(np.min(template_wave),
np.max(template_wave),
smoothed_template_flux, template_wave,
smoothed_template_noise)
#Put spectra into Spectrum1D objects
data_spec = Spectrum1D(spectral_axis=norm_data_wave*u.Angstrom, flux=norm_data_flux*(u.erg/u.s/u.cm**2/u.Angstrom),
uncertainty=StdDevUncertainty(norm_data_noise))
template_spec = Spectrum1D(spectral_axis=norm_template_wave*u.Angstrom, flux=norm_template_flux*(u.Lsun/u.micron))
#Plot before
plt.figure(figsize=(12,4))
plt.plot(data_spec.spectral_axis, data_spec.flux, label='observed')
plt.plot(template_spec.spectral_axis, template_spec.flux, label='template')
plt.legend()
plt.show()
#Fit redshifts
redshifts = np.linspace(z_lit-z_bound, z_lit+z_bound, 1000)
tm_result = template_redshift(observed_spectrum=data_spec, template_spectrum=template_spec, redshift=redshifts)
#Plot after
plt.figure(figsize=(12,4))
plt.plot(data_spec.spectral_axis, data_spec.flux, label='observed')
plt.plot(tm_result[2].spectral_axis, tm_result[2].flux, label='redshifted template')
plt.legend()
plt.show()
plt.figure(figsize=(12,4))
plt.plot(template_spec.spectral_axis, template_spec.flux, label='template')
plt.plot(tm_result[2].spectral_axis, tm_result[2].flux, label='redshifted template')
plt.legend()
plt.show()
return tm_result[0], tm_result[1]
