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_light_ray_non_cosmo_from_dataset():
"""
This test generates a non-cosmological light ray created from an already
loaded dataset
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = data_dir_load(COSMO_PLUS_SINGLE)
lr = LightRay(ds)
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')
ds = load('lightray.h5')
compare_light_ray_solutions(lr, ds)
# 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_non_cosmo_sph():
"""
This test generates an absorption spectrum from a simple light ray on a
particle dataset
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = load(GIZMO_PLUS_SINGLE)
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=[('gas', 'temperature'),
('gas', 'H_number_density')],
data_filename='lightray.h5')
sp = AbsorptionSpectrum(1200.0, 1300.0, 10001)
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)
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__ = "{}_non_cosmo_sph".format(key)
test = GenericArrayTest(None, func)
test_absorption_spectrum_non_cosmo_sph.__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_equivalent_width_conserved():
"""
This tests that the equivalent width of the optical depth is conserved
regardless of the bin width employed in wavelength space.
Unresolved lines should still deposit optical depth into the spectrum.
"""
# 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')
my_label = 'HI Lya'
field = 'H_number_density'
wave = 1215.6700 # Angstroms
f_value = 4.164E-01
gamma = 6.265e+08
mass = 1.00794
lambda_min = 1200
lambda_max = 1300
lambda_bin_widths = [1e-3, 1e-2, 1e-1, 1e0, 1e1]
total_tau = []
for lambda_bin_width in lambda_bin_widths:
n_lambda = ((lambda_max - lambda_min) / lambda_bin_width) + 1
sp = AbsorptionSpectrum(lambda_min=lambda_min,
lambda_max=lambda_max,
n_lambda=n_lambda)
sp.add_line(my_label, field, wave, f_value, gamma, mass)
wavelength, flux = sp.make_spectrum('lightray.h5')
total_tau.append((lambda_bin_width * sp.tau_field).sum())
# assure that the total tau values are all within 1e-3 of each other
for tau in total_tau:
assert_almost_equal(tau, total_tau[0], 3)
# 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_light_ray_cosmo_nonperiodic():
"""
This test generates a cosmological light ray using non-periodic segments
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
lr = LightRay(COSMO_PLUS, 'Enzo', 0.0, 0.03)
lr.make_light_ray(seed=1234567, periodic=False,
fields=['temperature', 'density', 'H_number_density'],
data_filename='lightray.h5')
ds = load('lightray.h5')
compare_light_ray_solutions(lr, ds)
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
def test_light_ray_cosmo_nested():
"""
This test generates a cosmological light ray confing the ray to a subvolume
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
left = np.ones(3) * 0.25
right = np.ones(3) * 0.75
lr = LightRay(COSMO_PLUS, 'Enzo', 0.0, 0.03)
lr.make_light_ray(seed=1234567, left_edge=left, right_edge=right,
fields=['temperature', 'density', 'H_number_density'],
data_filename='lightray.h5')
ds = load('lightray.h5')
compare_light_ray_solutions(lr, ds)
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
import os
import yt
from yt.analysis_modules.cosmological_observation.api import \
LightRay
ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030")
lr = LightRay(ds)
# With a single dataset, a start_position and
# end_position or trajectory must be given.
# These positions can be defined as xyz coordinates,
# but here we just use the two opposite corners of the
# simulation box. Alternatively, trajectory should
# be given as (r, theta, phi)
lr.make_light_ray(start_position=ds.domain_left_edge,
end_position=ds.domain_right_edge,
solution_filename='lightraysolution.txt',
data_filename='lightray.h5',
fields=['temperature', 'density'])
# Optionally, we can now overplot this ray on a projection of the source
# dataset
p = yt.ProjectionPlot(ds, 'z', 'density')
p.annotate_ray(lr)
p.save()
def test_absorption_spectrum_with_zero_field():
"""
This test generates an absorption spectrum with some
particle dataset
"""
# Set up in a temp dir
tmpdir = tempfile.mkdtemp()
curdir = os.getcwd()
os.chdir(tmpdir)
ds = load(FIRE)
lr = LightRay(ds)
# Define species and associated parameters to add to continuum
# Parameters used for both adding the transition to the spectrum
# and for fitting
# Note that for single species that produce multiple lines
# (as in the OVI doublet), 'numLines' will be equal to the number
# of lines, and f,gamma, and wavelength will have multiple values.
HI_parameters = {
'name': 'HI',
'field': 'H_number_density',
'f': [.4164],
'Gamma': [6.265E8],
'wavelength': [1215.67],
'mass': 1.00794,
'numLines': 1,
'maxN': 1E22, 'minN': 1E11,
'maxb': 300, 'minb': 1,
'maxz': 6, 'minz': 0,
'init_b': 30,
'init_N': 1E14
}
species_dicts = {'HI': HI_parameters}
# Get all fields that need to be added to the light ray
fields = [('gas','temperature')]
for s, params in species_dicts.items():
fields.append(params['field'])
# With a single dataset, a start_position and
# end_position or trajectory must be given.
# Trajectory should be given as (r, theta, phi)
lr.make_light_ray(
start_position=ds.arr([0., 0., 0.], 'unitary'),
end_position=ds.arr([1., 1., 1.], 'unitary'),
solution_filename='test_lightraysolution.txt',
data_filename='test_lightray.h5',
fields=fields)
# Create an AbsorptionSpectrum object extending from
# lambda = 900 to lambda = 1800, with 10000 pixels
sp = AbsorptionSpectrum(900.0, 1400.0, 50000)
# Iterate over species
for s, params in species_dicts.items():
# Iterate over transitions for a single species
for i in range(params['numLines']):
# Add the lines to the spectrum
sp.add_line(
s, params['field'],
params['wavelength'][i], params['f'][i],
params['Gamma'][i], params['mass'],
label_threshold=1.e10)
# Make and save spectrum
wavelength, flux = sp.make_spectrum(
'test_lightray.h5',
output_file='test_spectrum.h5',
line_list_file='test_lines.txt',
use_peculiar_velocity=True)
# clean up
os.chdir(curdir)
shutil.rmtree(tmpdir)
import os
import sys
import yt
from yt.analysis_modules.cosmological_observation.api import \
LightRay
# Create a directory for the light rays
if not os.path.isdir("LR"):
os.mkdir('LR')
# Create a LightRay object extending from z = 0 to z = 0.1
# and use only the redshift dumps.
lr = LightRay("enzo_tiny_cosmology/32Mpc_32.enzo",
'Enzo',
0.0,
0.1,
use_minimum_datasets=True,
time_data=False)
# Make a light ray, and set njobs to -1 to use one core
# per dataset.
lr.make_light_ray(seed=123456789,
solution_filename='LR/lightraysolution.txt',
data_filename='LR/lightray.h5',
fields=['temperature', 'density'],
get_los_velocity=True,
njobs=-1)
import os
import yt
from yt.analysis_modules.cosmological_observation.api import \
LightRay
fn = "IsolatedGalaxy/galaxy0030/galaxy0030"
lr = LightRay(fn)
# With a single dataset, a start_position and
# end_position or trajectory must be given.
# Trajectory should be given as (r, theta, phi)
lr.make_light_ray(start_position=[0., 0., 0.],
end_position=[1., 1., 1.],
solution_filename='lightraysolution.txt',
data_filename='lightray.h5',
fields=['temperature', 'density'],
get_los_velocity=True)
# Optionally, we can now overplot this ray on a projection of the source
# dataset
ds = yt.load(fn)
p = yt.ProjectionPlot(ds, 'z', 'density')
p.annotate_ray(lr)
p.save()
import os
import yt
from yt.analysis_modules.cosmological_observation.api import \
LightRay
fn = "IsolatedGalaxy/galaxy0030/galaxy0030"
lr = LightRay(fn)
# With a single dataset, a start_position and
# end_position or trajectory must be given.
# Trajectory should be given as (r, theta, phi)
lr.make_light_ray(start_position=[0., 0., 0.],
end_position=[1., 1., 1.],
solution_filename='lightraysolution.txt',
data_filename='lightray.h5',
fields=['temperature', 'density'],
get_los_velocity=True)
# Optionally, we can now overplot this ray on a projection of the source
# dataset
ds = yt.load(fn)
p = yt.ProjectionPlot(ds, 'z', 'density')
p.annotate_ray(lr)
p.save()
import os
import yt
from yt.analysis_modules.cosmological_observation.api import \
LightRay
# Create a directory for the light rays
if not os.path.isdir("LR"):
os.mkdir('LR')
# Create a LightRay object extending from z = 0 to z = 0.1
# and use only the redshift dumps.
lr = LightRay("enzo_tiny_cosmology/32Mpc_32.enzo",
'Enzo', 0.0, 0.1,
use_minimum_datasets=True,
time_data=False)
# Make a light ray, and set njobs to -1 to use one core
# per dataset.
lr.make_light_ray(seed=123456789,
solution_filename='LR/lightraysolution.txt',
data_filename='LR/lightray.h5',
fields=['temperature', 'density'],
get_los_velocity=True,
njobs=-1)
# Optionally, we can now overplot the part of this ray that intersects
# one output from the source dataset in a ProjectionPlot
ds = yt.load('enzo_tiny_cosmology/RD0004/RD0004')
p = yt.ProjectionPlot(ds, 'z', 'density')
p.annotate_ray(lr)
p.save()