def _get_milky_way_foreground(self, filename=None):
"""
Read in MW spectrum and return an interpolated version.
Interpolated version for fitting the desired wavelength interval and
binning.
Source data come from Charles Danforth and are a median-combination of
92 normalized COS/G130M+G160M AGN spectra valid from 1130-1800A.
"""
if filename is None:
filename = os.path.join(trident_path(), "data",
"spectral_templates",
"mw_foreground_COS.txt")
data = np.loadtxt(filename)
MW_lambda = YTArray(data[:, 0], 'angstrom')
MW_flux = data[:, 1]
index = np.digitize(self.lambda_field, MW_lambda)
np.clip(index, 1, MW_lambda.size - 1, out=index)
slope = (MW_flux[index] - MW_flux[index - 1]) / \
(MW_lambda[index] - MW_lambda[index - 1])
my_flux = slope * (self.lambda_field -
MW_lambda[index]) + MW_flux[index]
# just set values that go beyond the data to 1
my_flux[self.lambda_field > 1799.9444] = 1.0
return my_flux
def _get_qso_spectrum(self,
emitting_redshift,
observing_redshift,
filename=None):
"""
Read in QSO spectrum and return an interpolated version. Interpolated
version for fitting the desired wavelength interval and binning.
"""
if observing_redshift is None:
observing_redshift = self.observing_redshift
if emitting_redshift is None:
emitting_redshift = 0.
# Following Hogg (2000) eq. 13 for the effective redshift z12 of
# observing at z1 redshift light emitted at z2:
# 1 + z12 = (1 + z2) / (1 + z1)
redshift_eff = (1 + emitting_redshift) / (1 + observing_redshift) - 1
if filename is None:
filename = os.path.join(trident_path(), "data",
"spectral_templates",
"qso_background_COS_HST.txt")
data = np.loadtxt(filename)
qso_lambda = YTArray(data[:, 0], 'angstrom')
qso_lambda += qso_lambda * redshift_eff
qso_flux = data[:, 1]
index = np.digitize(self.lambda_field, qso_lambda)
np.clip(index, 1, qso_lambda.size - 1, out=index)
slope = (qso_flux[index] - qso_flux[index - 1]) / \
(qso_lambda[index] - qso_lambda[index - 1])
my_flux = slope * (self.lambda_field -
qso_lambda[index]) + qso_flux[index]
return my_flux
def __init__(self, function=None, width=None, filename=None):
self.kernel = []
self.filename = filename
self.function = function
self.width = width
# if filename is defined, use it
if filename is not None:
# Check to see if the file is in the local dir
if os.path.isfile(filename):
lsf_file = open(filename, 'r')
# otherwise use the file in the lsf_kernels dir
else:
filename2 = os.path.join(trident_path(), "data", \
"lsf_kernels", filename)
if os.path.isfile(filename2):
lsf_file = open(filename2, 'r')
else:
raise RuntimeError(
"LSF filename not found in current " +
"directory or in %s/data/lsf_kernels directory" %
trident_path())
for line in lsf_file:
self.kernel.append(float(line.split()[1]))
lsf_file.close()
self.kernel = np.array(self.kernel)
self.width = self.kernel.size
elif function is not None and width is not None:
if function == 'boxcar':
if width % 2 == 0:
mylog.warn(
"LSF kernel must have an odd length. Reducing kernel size by 1."
)
width -= 1
self.kernel = np.ones(width) / width
elif function == 'gaussian':
from astropy.convolution import Gaussian1DKernel
self.kernel = Gaussian1DKernel(width)
else:
raise RuntimeError(
"Either LSF filename OR function+width must be specified.")
def load_line_list_from_file(self, filename):
"""
Load a line list from a file into the LineDatabase.
Line list file is a tab-delimited text file in the format:
element, ion_state, wavelength, gamma, f_value, (name)
H, I, 1215.67, 4.69e8, 4.16e-1, Ly a
**Parameters**
filename : string
The filename of the list to add. First looks in
trident.__path__/data/line_lists directory, then in cwd.
"""
# check to see if file exists in trident/data/line_lists
# if not, look in cwd
filename = os.path.join(trident_path(), "data", "line_lists", filename)
if not os.path.isfile(filename):
filename = filename.split(os.sep)[-1]
if not os.path.isfile(filename):
raise RuntimeError("line_list %s is not found in local "
"directory or in trident/data/line_lists " %
(filename.split(os.sep)[-1]))
# Step through each line of text in file and add to database
for line in open(filename).readlines():
online = line.rstrip().split()
if line.startswith("#") or len(online) < 5:
continue
element, ion_state, wavelength, gamma, f_value = online[:5]
# optional identifier should be added if existent
if len(online) > 5:
identifier = " ".join(online[5:])
else:
identifier = None
self.add_line(element,
ion_state,
wavelength,
gamma,
f_value,
identifier=identifier)
Line
from trident.lsf import \
LSF
from trident.plotting import \
plot_spectrum
from trident.spectrum_generator import \
SpectrumGenerator, \
valid_instruments, \
load_spectrum
from trident.utilities import \
make_onezone_dataset, \
make_onezone_ray
from trident.ray_generator import \
make_simple_ray, \
make_compound_ray
from trident.roman import \
to_roman, \
from_roman
from trident.light_ray import \
LightRay
# Making installation path global
path = trident_path()
def test_line_database_from_local_file():
line_file = os.path.join(trident_path(), 'data/line_lists/lines.txt')
copyfile(line_file, 'test_lines.txt')
ld = LineDatabase('test_lines.txt')
print(ld)
os.remove('test_lines.txt')
def test_path():
"""
Tests that the trident path is working ok.
"""
trident_path()
