def test_dlambda_extra_wide(self):
"""
Compare auto velocity against setting same dlambda with
min and max set extra wide.
"""
sg_auto = SpectrumGenerator(lambda_min='auto',
lambda_max='auto',
dlambda=1.0,
bin_space='velocity')
sg_auto.make_spectrum("ray.h5",
lines=self.line_list,
store_observables=True)
sg_comp = SpectrumGenerator(lambda_min=sg_auto.lambda_field[0],
lambda_max=sg_auto.lambda_field[-1],
n_lambda=sg_auto.lambda_field.size,
bin_space='velocity')
sg_comp.make_spectrum("ray.h5",
lines=self.line_list,
store_observables=True)
assert_allclose(
sg_auto.tau_field.sum(),
sg_comp.tau_field.sum(),
rtol=1e-7,
err_msg='Total tau disagrees with extra wide spectrum.')
def test_setting_lambda_max(self):
"""
Test setting an arbitrary lambda_max with auto-lambda.
"""
sg_auto = SpectrumGenerator(lambda_min='auto',
lambda_max='auto',
dlambda=1.0,
bin_space='velocity')
sg_auto.make_spectrum("ray.h5",
lines=self.line_list,
ly_continuum=False)
sg_comp = SpectrumGenerator(lambda_min='auto',
lambda_max=-10000.,
dlambda=1.0,
bin_space='velocity')
sg_comp.make_spectrum("ray.h5",
lines=self.line_list,
ly_continuum=False)
comp_lambda = sg_auto.lambda_field <= sg_comp.lambda_field[-1]
assert_allclose(sg_auto.tau_field[comp_lambda].sum(),
sg_comp.tau_field.sum())
def test_n_lambda(self):
"""
Compare auto velocity against setting same min, max, and n_lambda
"""
sg_auto = SpectrumGenerator(
lambda_min='auto', lambda_max='auto',
dlambda=1.0, bin_space='velocity')
sg_auto.make_spectrum("ray.h5", lines=self.line_list,
store_observables=True)
sg_comp = SpectrumGenerator(
lambda_min=sg_auto.lambda_field[0],
lambda_max=sg_auto.lambda_field[-1],
n_lambda=sg_auto.lambda_field.size,
bin_space='velocity')
sg_comp.make_spectrum("ray.h5", lines=self.line_list,
store_observables=True)
compare_spectra(sg_auto, sg_comp, 'manually setting n_lambda')
def test_dlambda(self):
"""
Compare auto wavelength against setting same min, max, and dlambda
"""
sg_auto = SpectrumGenerator(lambda_min='auto',
lambda_max='auto',
dlambda=0.01)
sg_auto.make_spectrum("ray.h5",
lines=self.line_list,
store_observables=True)
sg_comp = SpectrumGenerator(lambda_min=sg_auto.lambda_field[0],
lambda_max=sg_auto.lambda_field[-1],
dlambda=sg_auto.bin_width)
sg_comp.make_spectrum("ray.h5",
lines=self.line_list,
store_observables=True)
compare_spectra(sg_auto, sg_comp, 'manually setting dlambda')
def test_setting_lambda_min(self):
"""
Test setting an arbitrary lambda_min with auto-lambda.
"""
sg_auto = SpectrumGenerator(lambda_min='auto',
lambda_max='auto',
dlambda=0.01)
sg_auto.make_spectrum("ray.h5",
lines=self.line_list,
ly_continuum=False)
sg_comp = SpectrumGenerator(lambda_min=1100,
lambda_max='auto',
dlambda=0.01)
sg_comp.make_spectrum("ray.h5",
lines=self.line_list,
ly_continuum=False)
comp_lambda = sg_auto.lambda_field >= sg_comp.lambda_field[0]
assert_allclose(sg_auto.tau_field[comp_lambda].sum(),
sg_comp.tau_field.sum())
def test_empty_spectrum(self):
"""
Test we can make an empty spectrum without crashing.
"""
sg = SpectrumGenerator(lambda_min=3000,
lambda_max='auto',
dlambda=1.0,
bin_space='velocity')
sg.make_spectrum("ray.h5", lines=['H I 1216'],
output_file='blank.h5',
output_absorbers_file='blank.txt',
store_observables=True, ly_continuum=True)
sg.plot_spectrum('spec_blank.png')
assert sg.lambda_field is None
assert sg.tau_field is None
assert sg.flux_field is None
def test_absorption_spectrum_with_continuum(self):
"""
This test generates an absorption spectrum then does a default fit.
Uses the example in the docs as a template:
https://trident.readthedocs.io/en/latest/absorption_spectrum_fit.html
"""
ds = load(ISO_GALAXY)
line_list = ['O VI']
ray = make_simple_ray(ds,
start_position=ds.domain_left_edge,
end_position=ds.domain_right_edge,
data_filename='ray.h5',
lines=line_list,
ftype='gas')
sg = SpectrumGenerator('COS')
sg.make_spectrum(ray, lines=line_list)
wavelength = sg.lambda_field
flux = sg.flux_field
OVI_parameters = {
'name': 'OVI',
'f': [.1325, .06580],
'Gamma': [4.148E8, 4.076E8],
'wavelength': [1031.9261, 1037.6167],
'numLines': 2,
'maxN': 1E17,
'minN': 1E11,
'maxb': 300,
'minb': 1,
'maxz': 6,
'minz': 0,
'init_b': 20,
'init_N': 1E12
}
speciesDicts = {'OVI': OVI_parameters}
orderFits = ['OVI']
fitted_lines, fitted_flux = generate_total_fit(wavelength, flux,
orderFits, speciesDicts)
def test_enzo_small_simple(self):
"""
This is an answer test, which compares the results of this test
against answers generated from a previous version of the code.
This test generates a COS spectrum from a single Enzo dataset
using a simple ray and compare the ray and spectral output data
against a known answer.
"""
# Set the dataset filename, load it into yt and define the trajectory
# of the LightRay to cross the box from one corner to the other.
ds = load(os.path.join(enzo_small, 'RD0009/RD0009'))
ray_start = ds.domain_left_edge
ray_end = ds.domain_right_edge
# Make a LightRay object including all necessary fields so you can add
# all H, C, N, O, and Mg fields to the resulting spectrum from your dataset.
# Save LightRay to ray.h5 and use it locally as ray object.
ray_fn = 'enzo_small_simple_ray.h5'
ray = make_simple_ray(ds,
start_position=ray_start,
end_position=ray_end,
data_filename=ray_fn,
lines=['H', 'C', 'N', 'O', 'Mg'],
ftype='gas')
# Now use the ray object to actually generate an absorption spectrum
# Use the settings (spectral range, LSF, and spectral resolution) for COS
# And save it as an output hdf5 file and plot it to an image.
sg = SpectrumGenerator('COS')
sg.make_spectrum(ray, lines=['H', 'C', 'N', 'O', 'Mg'])
raw_file = 'enzo_small_simple_spec_raw.h5'
raw_file_compare = os.path.join(test_results_dir, raw_file)
sg.save_spectrum(raw_file)
sg.plot_spectrum('enzo_small_simple_spec_raw.png')
# "Final" spectrum with added quasar, MW background, applied line-spread
# function, and added gaussian noise (SNR=30)
# Save as a text file and plot it to an image.
sg.add_qso_spectrum()
sg.add_milky_way_foreground()
sg.apply_lsf()
sg.add_gaussian_noise(30, seed=1)
final_file = 'enzo_small_simple_spec_final.h5'
final_file_compare = os.path.join(test_results_dir, final_file)
sg.save_spectrum(final_file)
sg.plot_spectrum('enzo_small_simple_spec_final.png')
if generate_results:
os.rename(raw_file, raw_file_compare)
os.rename(final_file, final_file_compare)
else:
old_spec = h5py.File(raw_file_compare, 'r')
new_spec = h5py.File(raw_file, 'r')
for key in old_spec.keys():
assert_almost_equal(new_spec[key].value, old_spec[key].value, \
decimal=err_precision,
err_msg='Raw spectrum array does not match '+\
'for enzo_small_simple answer test')
old_spec.close()
new_spec.close()
old_spec = h5py.File(final_file_compare, 'r')
new_spec = h5py.File(final_file, 'r')
for key in old_spec.keys():
assert_almost_equal(new_spec[key].value, old_spec[key].value, \
decimal=err_precision,
err_msg='Final spectrum array does not match '+\
'for enzo_small_simple answer test')
old_spec.close()
new_spec.close()
def test_enzo_small_compound(self):
"""
This is an answer test, which compares the results of this test
against answers generated from a previous version of the code.
This test generates a COS spectrum from a single Enzo dataset
using a compound ray and compare the ray and spectral output data
against a known answer.
"""
# Set the dataset filename, the redshift range to be covered, and the
# ions in which we're interested, and give the random number generator
# a seed (for determining the ray trajectory). Use these to create a
# compound ray spanning multiple datasets to cover the desired redshift
# range.
fn = os.path.join(enzo_small, 'AMRCosmology.enzo')
redshift_start = 0.00
redshift_end = 0.015
lines = ['H', 'C', 'N', 'O', 'Mg']
seed = 1
ray_fn = 'enzo_small_compound_ray.h5'
ray = make_compound_ray(fn,
'Enzo',
redshift_start,
redshift_end,
lines=lines,
seed=seed,
ftype='gas',
data_filename=ray_fn)
# Now use the ray object to actually generate an absorption spectrum
# Use the settings (spectral range, LSF, and spectral resolution) for COS
# And save it as an output hdf5 file and plot it to an image.
sg = SpectrumGenerator('COS')
sg.make_spectrum(ray, lines=lines)
raw_file = 'enzo_small_compound_spec_raw.h5'
raw_file_compare = os.path.join(test_results_dir, raw_file)
sg.save_spectrum(raw_file)
sg.plot_spectrum('enzo_small_compound_spec_raw.png')
# "Final" spectrum with added quasar, MW background, applied line-spread
# function, and added gaussian noise (SNR=30)
# Save as a text file and plot it to an image.
sg.add_qso_spectrum()
sg.add_milky_way_foreground()
sg.apply_lsf()
sg.add_gaussian_noise(30, seed=1)
final_file = 'enzo_small_compound_spec_final.h5'
sg.save_spectrum(final_file)
final_file_compare = os.path.join(test_results_dir, final_file)
sg.plot_spectrum('enzo_small_compound_spec_final.png')
if generate_results:
os.rename(raw_file, raw_file_compare)
os.rename(final_file, final_file_compare)
else:
old_spec = h5py.File(raw_file_compare, 'r')
new_spec = h5py.File(raw_file, 'r')
for key in old_spec.keys():
assert_almost_equal(new_spec[key].value, old_spec[key].value, \
decimal=err_precision,
err_msg='Raw spectrum array does not match '+\
'for enzo_small_compound answer test')
old_spec.close()
new_spec.close()
old_spec = h5py.File(final_file_compare, 'r')
new_spec = h5py.File(final_file, 'r')
for key in old_spec.keys():
assert_almost_equal(new_spec[key].value, old_spec[key].value, \
decimal=err_precision,
err_msg='Final spectrum array does not match '+\
'for enzo_small_compound answer test')
old_spec.close()
new_spec.close()