def test_absorption_spectrum_cosmo_sph():
"""
This test generates an absorption spectrum from a compound light ray on a
particle dataset
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
lr = LightRay(GIZMO_PLUS, 'Gadget', 0.0, 0.01)
lr.make_light_ray(seed=1234567,
fields=[('gas', 'temperature'),
('gas', 'H_number_density')],
data_filename='lightray.h5')
sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
my_label = 'HI Lya'
field = ('gas', 'H_number_density')
wavelength = 1215.6700 # Angstroms
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794
sp.add_line(my_label,
field,
wavelength,
f_value,
gamma,
mass,
label_threshold=1.e10)
my_label = 'HI Lya'
field = ('gas', 'H_number_density')
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0
sp.add_continuum(my_label, field, wavelength, normalization, index)
wavelength, flux = sp.make_spectrum('lightray.h5',
output_file='spectrum.h5',
line_list_file='lines.txt',
use_peculiar_velocity=True)
# load just-generated hdf5 file of spectral data (for consistency)
data = h5.File('spectrum.h5', 'r')
for key in data.keys():
func = lambda x=key: data[x][:]
func.__name__ = "{}_cosmo_sph".format(key)
test = GenericArrayTest(None, func)
test_absorption_spectrum_cosmo_sph.__name__ = test.description
yield test
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_absorption_spectrum_with_continuum():
"""
This test generates an absorption spectrum from a simple light ray on a
grid dataset and adds Lyman alpha and Lyman continuum to it
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = load(ISO_GALAXY)
lr = LightRay(ds)
ray_start = ds.domain_left_edge
ray_end = ds.domain_right_edge
lr.make_light_ray(start_position=ray_start, end_position=ray_end,
fields=['temperature', 'density', 'H_number_density'],
data_filename='lightray.h5')
sp = AbsorptionSpectrum(800.0, 1300.0, 5001)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 1215.6700 # Angstromss
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794
sp.add_line(my_label, field, wavelength, f_value,
gamma, mass, label_threshold=1.e10)
my_label = 'Ly C'
field = 'H_number_density'
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0
sp.add_continuum(my_label, field, wavelength, normalization, index)
wavelength, flux = sp.make_spectrum('lightray.h5',
output_file='spectrum.h5',
line_list_file='lines.txt',
use_peculiar_velocity=True)
# load just-generated hdf5 file of spectral data (for consistency)
data = h5.File('spectrum.h5', 'r')
for key in data.keys():
func = lambda x=key: data[x][:]
func.__name__ = "{}_continuum".format(key)
test = GenericArrayTest(None, func)
test_absorption_spectrum_with_continuum.__name__ = test.description
yield test
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_absorption_spectrum_fits():
"""
This test is simply following the description in the docs for how to
generate an absorption spectrum from a cosmological light ray for one
of the sample datasets. Outputs to fits file if astropy is installed.
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
lr = LightRay(COSMO_PLUS, 'Enzo', 0.0, 0.1)
lr.make_light_ray(seed=1234567,
fields=['temperature', 'density', 'H_number_density'],
get_los_velocity=True,
data_filename='lightray.h5')
sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 1215.6700 # Angstromss
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794
sp.add_line(my_label,
field,
wavelength,
f_value,
gamma,
mass,
label_threshold=1.e10)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0
sp.add_continuum(my_label, field, wavelength, normalization, index)
wavelength, flux = sp.make_spectrum('lightray.h5',
output_file='spectrum.fits',
line_list_file='lines.txt',
use_peculiar_velocity=True)
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_absorption_spectrum_fits():
"""
This test generates an absorption spectrum and saves it as a fits file.
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
lr = LightRay(COSMO_PLUS_SINGLE)
ray_start = [0, 0, 0]
ray_end = [1, 1, 1]
lr.make_light_ray(start_position=ray_start,
end_position=ray_end,
fields=['temperature', 'density', 'H_number_density'],
data_filename='lightray.h5')
sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 1215.6700 # Angstroms
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794
sp.add_line(my_label,
field,
wavelength,
f_value,
gamma,
mass,
label_threshold=1.e10)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0
sp.add_continuum(my_label, field, wavelength, normalization, index)
wavelength, flux = sp.make_spectrum('lightray.h5',
output_file='spectrum.fits',
line_list_file='lines.txt',
use_peculiar_velocity=True)
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_absorption_spectrum_fits():
"""
This test is simply following the description in the docs for how to
generate an absorption spectrum from a cosmological light ray for one
of the sample datasets. Outputs to fits file if astropy is installed.
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
lr = LightRay(COSMO_PLUS, 'Enzo', 0.0, 0.1)
lr.make_light_ray(seed=1234567,
fields=['temperature', 'density', 'H_number_density'],
get_los_velocity=True,
data_filename='lightray.h5')
sp = AbsorptionSpectrum(900.0, 1800.0, 10000)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 1215.6700 # Angstromss
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794
sp.add_line(my_label, field, wavelength, f_value,
gamma, mass, label_threshold=1.e10)
my_label = 'HI Lya'
field = 'H_number_density'
wavelength = 912.323660 # Angstroms
normalization = 1.6e17
index = 3.0
sp.add_continuum(my_label, field, wavelength, normalization, index)
wavelength, flux = sp.make_spectrum('lightray.h5',
output_file='spectrum.fits',
line_list_file='lines.txt',
use_peculiar_velocity=True)
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
