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_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()