def test_log_to_list_origin2():
with log.log_to_list(filter_origin='astropy.wcs') as log_list:
log.error("Error message")
log.warning("Warning message")
assert len(log_list) == 0
def test_log_to_list_level():
with log.log_to_list(filter_level='ERROR') as log_list:
log.error("Error message")
log.warning("Warning message")
assert len(log_list) == 1 and log_list[0].levelname == 'ERROR'
def test_log_to_list_level():
with log.log_to_list(filter_level='ERROR') as log_list:
log.error("Error message")
log.warning("Warning message")
assert len(log_list) == 1 and log_list[0].levelname == 'ERROR'
def test_log_to_list_origin2():
with log.log_to_list(filter_origin='astropy.wcs') as log_list:
log.error("Error message")
log.warning("Warning message")
assert len(log_list) == 0
def test_infol_logged_if_unit_in_fits_header(ccd_data, tmpdir):
tmpfile = tmpdir.join('temp.fits')
ccd_data.write(tmpfile.strpath)
log.setLevel('INFO')
explicit_unit_name = "photon"
with log.log_to_list() as log_list:
ccd_from_disk = CCDData.read(tmpfile.strpath, unit=explicit_unit_name)
assert explicit_unit_name in log_list[0].message
def test_infol_logged_if_unit_in_fits_header(ccd_data, tmpdir):
tmpfile = tmpdir.join('temp.fits')
ccd_data.write(tmpfile.strpath)
log.setLevel('INFO')
explicit_unit_name = "photon"
with log.log_to_list() as log_list:
ccd_from_disk = CCDData.read(tmpfile.strpath, unit=explicit_unit_name)
assert explicit_unit_name in log_list[0].message
def test_warnings_logging():
# Without warnings logging
with catch_warnings() as warn_list:
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
assert len(log_list) == 0
assert len(warn_list) == 1
assert warn_list[0].message.args[0] == "This is a warning"
# With warnings logging
with catch_warnings() as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 0
assert log_list[0].levelname == 'WARNING'
assert log_list[0].message.startswith('This is a warning')
assert log_list[0].origin == 'astropy.tests.test_logger'
# With warnings logging (differentiate between Astropy and non-Astropy)
with catch_warnings() as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
warnings.warn("This is another warning, not from Astropy")
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 1
assert log_list[0].levelname == 'WARNING'
assert log_list[0].message.startswith('This is a warning')
assert log_list[0].origin == 'astropy.tests.test_logger'
assert warn_list[0].message.args[
0] == "This is another warning, not from Astropy"
# Without warnings logging
with catch_warnings() as warn_list:
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
assert len(log_list) == 0
assert len(warn_list) == 1
assert warn_list[0].message.args[0] == "This is a warning"
def test_warnings_logging():
# Without warnings logging
with catch_warnings() as warn_list:
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
assert len(log_list) == 0
assert len(warn_list) == 1
assert warn_list[0].message.args[0] == "This is a warning"
# With warnings logging
with catch_warnings() as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 0
assert log_list[0].levelname == 'WARNING'
assert log_list[0].message.startswith('This is a warning')
assert log_list[0].origin == 'astropy.tests.test_logger'
# With warnings logging (differentiate between Astropy and non-Astropy)
with catch_warnings() as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
warnings.warn("This is another warning, not from Astropy")
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 1
assert log_list[0].levelname == 'WARNING'
assert log_list[0].message.startswith('This is a warning')
assert log_list[0].origin == 'astropy.tests.test_logger'
assert warn_list[0].message.args[0] == "This is another warning, not from Astropy"
# Without warnings logging
with catch_warnings() as warn_list:
with log.log_to_list() as log_list:
warnings.warn("This is a warning", AstropyUserWarning)
assert len(log_list) == 0
assert len(warn_list) == 1
assert warn_list[0].message.args[0] == "This is a warning"
def test_exception_logging():
# Without exception logging
try:
with log.log_to_list() as log_list:
raise Exception("This is an Exception")
except Exception as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0] == "This is an Exception"
else:
assert False # exception should have been raised
assert len(log_list) == 0
# With exception logging
try:
log.enable_exception_logging()
with log.log_to_list() as log_list:
raise Exception("This is an Exception")
except Exception as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0] == "This is an Exception"
else:
assert False # exception should have been raised
assert len(log_list) == 1
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message.startswith('Exception: This is an Exception')
assert log_list[0].origin == 'astropy.tests.test_logger'
# Without exception logging
log.disable_exception_logging()
try:
with log.log_to_list() as log_list:
raise Exception("This is an Exception")
except Exception as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0] == "This is an Exception"
else:
assert False # exception should have been raised
assert len(log_list) == 0
def test_exception_logging():
# Without exception logging
try:
with log.log_to_list() as log_list:
raise Exception("This is an Exception")
except Exception as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0] == "This is an Exception"
else:
assert False # exception should have been raised
assert len(log_list) == 0
# With exception logging
try:
log.enable_exception_logging()
with log.log_to_list() as log_list:
raise Exception("This is an Exception")
except Exception as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0] == "This is an Exception"
else:
assert False # exception should have been raised
assert len(log_list) == 1
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message.startswith('Exception: This is an Exception')
assert log_list[0].origin == 'astropy.tests.test_logger'
# Without exception logging
log.disable_exception_logging()
try:
with log.log_to_list() as log_list:
raise Exception("This is an Exception")
except Exception as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0] == "This is an Exception"
else:
assert False # exception should have been raised
assert len(log_list) == 0
def test_log_to_list(level):
orig_level = log.level
try:
if level is not None:
log.setLevel(level)
with log.log_to_list() as log_list:
log.error("Error message")
log.warning("Warning message")
log.info("Information message")
log.debug("Debug message")
finally:
log.setLevel(orig_level)
if level is None:
# The log level *should* be set to whatever it was in the config
level = conf.log_level
# Check list length
if level == 'DEBUG':
assert len(log_list) == 4
elif level == 'INFO':
assert len(log_list) == 3
elif level == 'WARN':
assert len(log_list) == 2
elif level == 'ERROR':
assert len(log_list) == 1
# Check list content
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message.startswith('Error message')
assert log_list[0].origin == 'astropy.tests.test_logger'
if len(log_list) >= 2:
assert log_list[1].levelname == 'WARNING'
assert log_list[1].message.startswith('Warning message')
assert log_list[1].origin == 'astropy.tests.test_logger'
if len(log_list) >= 3:
assert log_list[2].levelname == 'INFO'
assert log_list[2].message.startswith('Information message')
assert log_list[2].origin == 'astropy.tests.test_logger'
if len(log_list) >= 4:
assert log_list[3].levelname == 'DEBUG'
assert log_list[3].message.startswith('Debug message')
assert log_list[3].origin == 'astropy.tests.test_logger'
def test_log_to_list(level):
orig_level = log.level
try:
if level is not None:
log.setLevel(level)
with log.log_to_list() as log_list:
log.error("Error message")
log.warning("Warning message")
log.info("Information message")
log.debug("Debug message")
finally:
log.setLevel(orig_level)
if level is None:
# The log level *should* be set to whatever it was in the config
level = conf.log_level
# Check list length
if level == 'DEBUG':
assert len(log_list) == 4
elif level == 'INFO':
assert len(log_list) == 3
elif level == 'WARN':
assert len(log_list) == 2
elif level == 'ERROR':
assert len(log_list) == 1
# Check list content
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message.startswith('Error message')
assert log_list[0].origin == 'astropy.tests.test_logger'
if len(log_list) >= 2:
assert log_list[1].levelname == 'WARNING'
assert log_list[1].message.startswith('Warning message')
assert log_list[1].origin == 'astropy.tests.test_logger'
if len(log_list) >= 3:
assert log_list[2].levelname == 'INFO'
assert log_list[2].message.startswith('Information message')
assert log_list[2].origin == 'astropy.tests.test_logger'
if len(log_list) >= 4:
assert log_list[3].levelname == 'DEBUG'
assert log_list[3].message.startswith('Debug message')
assert log_list[3].origin == 'astropy.tests.test_logger'
def test_warnings_logging_with_custom_class():
class CustomAstropyWarningClass(AstropyWarning):
pass
# With warnings logging
with catch_warnings() as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
warnings.warn("This is a warning", CustomAstropyWarningClass)
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 0
assert log_list[0].levelname == 'WARNING'
assert log_list[0].message.startswith('CustomAstropyWarningClass: This is a warning')
assert log_list[0].origin == 'astropy.tests.test_logger'
def test_warning_logging_with_io_votable_warning():
from astropy.io.votable.exceptions import W02, vo_warn
with pytest.warns(None) as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
vo_warn(W02, ('a', 'b'))
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 0
assert log_list[0].levelname == 'WARNING'
x = log_list[0].message.startswith("W02: ?:?:?: W02: a attribute 'b' is "
"invalid. Must be a standard XML id")
assert x
assert log_list[0].origin == 'astropy.tests.test_logger'
def test_warnings_logging_with_custom_class():
class CustomAstropyWarningClass(AstropyWarning):
pass
# With warnings logging
with pytest.warns(None) as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
warnings.warn("This is a warning", CustomAstropyWarningClass)
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 0
assert log_list[0].levelname == 'WARNING'
assert log_list[0].message.startswith('CustomAstropyWarningClass: This is a warning')
assert log_list[0].origin == 'astropy.tests.test_logger'
def test_warning_logging_with_io_votable_warning():
from astropy.io.votable.exceptions import W02, vo_warn
with catch_warnings() as warn_list:
log.enable_warnings_logging()
with log.log_to_list() as log_list:
vo_warn(W02, ('a', 'b'))
log.disable_warnings_logging()
assert len(log_list) == 1
assert len(warn_list) == 0
assert log_list[0].levelname == 'WARNING'
x = log_list[0].message.startswith(("W02: ?:?:?: W02: a attribute 'b' is "
"invalid. Must be a standard XML id"))
assert x
assert log_list[0].origin == 'astropy.tests.test_logger'
def test_exception_logging_argless_exception():
"""
Regression test for a crash that occurred on Python 3 when logging an
exception that was instantiated with no arguments (no message, etc.)
Regression test for https://github.com/astropy/astropy/pull/4056
"""
try:
log.enable_exception_logging()
with log.log_to_list() as log_list:
raise Exception()
except Exception:
sys.excepthook(*sys.exc_info())
else:
assert False # exception should have been raised
assert len(log_list) == 1
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message == 'Exception [astropy.tests.test_logger]'
assert log_list[0].origin == 'astropy.tests.test_logger'
def test_exception_logging_argless_exception():
"""
Regression test for a crash that occurred on Python 3 when logging an
exception that was instantiated with no arguments (no message, etc.)
Regression test for https://github.com/astropy/astropy/pull/4056
"""
try:
log.enable_exception_logging()
with log.log_to_list() as log_list:
raise Exception()
except Exception as exc:
sys.excepthook(*sys.exc_info())
else:
assert False # exception should have been raised
assert len(log_list) == 1
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message == 'Exception [astropy.tests.test_logger]'
assert log_list[0].origin == 'astropy.tests.test_logger'
def test_exception_logging_origin():
# The point here is to get an exception raised from another location
# and make sure the error's origin is reported correctly
from astropy.utils.collections import HomogeneousList
l = HomogeneousList(int)
try:
log.enable_exception_logging()
with log.log_to_list() as log_list:
l.append('foo')
except TypeError as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0].startswith(
"homogeneous list must contain only objects of type ")
else:
assert False
assert len(log_list) == 1
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message.startswith(
"TypeError: homogeneous list must contain only objects of type ")
assert log_list[0].origin == 'astropy.utils.collections'
def test_exception_logging_origin():
# The point here is to get an exception raised from another location
# and make sure the error's origin is reported correctly
from astropy.utils.collections import HomogeneousList
l = HomogeneousList(int) # noqa
try:
log.enable_exception_logging()
with log.log_to_list() as log_list:
l.append('foo')
except TypeError as exc:
sys.excepthook(*sys.exc_info())
assert exc.args[0].startswith(
"homogeneous list must contain only objects of type ")
else:
assert False
assert len(log_list) == 1
assert log_list[0].levelname == 'ERROR'
assert log_list[0].message.startswith(
"TypeError: homogeneous list must contain only objects of type ")
assert log_list[0].origin == 'astropy.utils.collections'
def line_fitter(self, linecat, line_idx, niter,\
input_resid_level, max_contorder, max_ladjust, adjust_preference,\
input_continuum_deviation, llimits, max_exclusion_level, blends,\
autoadjust, fwhm_block):
'''
This is module fits the spectral lines using pyspeckit. It automatically
determines the goodness of fit and decides the best solution for the line
and continuum fit. It handles blended lines in a way a maximum lines ratio
can not be exceeded to not make the weaker blend the dominant lines.
Additionally, the limits in wavelength range in iteration :math:`n` can be
adjusted automatically based on iteration :math:`n` to accomodate for
larger wavelength shifts.
In this way it is possible to fit spectral lines using a line catalog as
only input.
Args:
linecat : :func:`numpy.array`
Array with the spectral lines and their wavelengths
line_idx : :obj:`str`
Name of the primary line
niter : :obj:`int`
Number of iterations
input_resid_level : :obj:`float`
The maximum MAD for the fit residuals for a succesfull fit
max_contorder : :obj:`int`
The maximum polynominal order of the continuum to have
max_ladjust : :obj:`str`
The maximum number of wavelength range adjustments in steps of 5
Angstrom
adjust_preference : :obj:`str`
contorder: continuum order is adjusted first
wavelength: wavelength range is adjusted first
input_continuum_deviation : :obj:`float`
by how much the continuum is allowed to deviate from a running
median estimate. This is set to prevent lines mimicking a continuum
llimits : :obj:`list`
the limits for the wavelength fit as set in ``ppxf``
max_exclusion_level : :obj:`float`
The exclusion level for lines to be excluded from the next baseline
estimate as set in ``pyspeckit``
blends : :obj:`ascii`-file or :obj:`None`
A file with primary lines that contain blends to provide a maximum
amplitude ratio of the primary and the blend to prevent that the
blend becomes the dominant line in the fit.
autoadjust : :obj:`bool`
:obj:`True`: the wavelength limits ``llimit`` will be adjusted to
the fit of the previous iteration. All other wavelength range are
adjusted accordingly taking into account the proper velocity
corrected shift :math:`\Delta \lambda/\lambda`. This is especially
important to detect hyper-velocity stars.
:obj:`False`: no adjustment to the limits done
fwhm_block : :obj:`bool:obj:`
:obj:`True`: The minimum fwhm of the voigt profiles of the fitted
lines is the instrument's dispersion
:obj:`False`: The minimum fwhm of the voigt profiles of the fitted
lines is zero
Returns:
line_idx : :obj:`str`
Name of the primary line
temp_l : :obj:`float`
fitted wavelength of the primary line
temp_a : :obj:`float`
fitted amplitude of the primary line
temp_sl : :obj:`float`
fitted Lorentzian gamma of the primary line
temp_sg : :obj:`float`
fitted Gaussian sigma of the primary line
spec_select_idx : :func:`numpy.array`
indices of the used part of the spectrum
template_f : :func:`numpy.array`
template spectrum shifted to the rest-frame
continuum : :func:`numpy.array`
the fitted continuum
lstart : :obj:`float`
first used wavelength bin (might differ from input if it was
adjusted during fitting)
lend : :obj:`float`
last used wavelength bin (might differ from input if it was
adjusted during fitting)
contorder : :obj:`int`
The order of the polynominal used for the continuum
fit_f : array
the fitted spectrum
significance : :obj:`float`
the line strength over the continuum
fit_failed : :obj:`bool`
:obj:`True`: if the fit failed for some reason. This line will be
excluded from further analyses
fit_f_highres : :obj:`float`
the fitted spectrum and the oversampling resolution
spec_select_idx_highres : :func:`numpy.array`
indices of the used part of the over sampled spectrum
template_f_highres : :func:`numpy.array`
over sampled template spectrum shifted to the rest-frame
continuum_highres : :func:`numpy.array`
the fitted over sampled continuum
'''
self.logger.info('Started line ' + line_idx)
resid_level = 5.
std_resid = resid_level + 1.
continuum_dev = input_continuum_deviation[line_idx] + 1.
lstart = float(self.cat.loc[line_idx, 'l_start'])
lend = float(self.cat.loc[line_idx, 'l_end'])
contorder = self.cat.loc[line_idx, 'cont_order']
n_ladjust = 0
max_cont_reached = False
max_n_ladjust_reached = False
significant = True
fit_failed = False
niter += 1 # Iteration 1 are setting the intial guesses
while (std_resid > resid_level or np.isnan(std_resid)\
or continuum_dev > input_continuum_deviation[line_idx]\
or np.isnan(continuum_dev)) and not fit_failed:
lines_select = linecat[np.where((linecat >= lstart)\
& (linecat < lend))]
spec_select_idx\
= np.where((self.spec_lambda >= lstart) & (self.spec_lambda < lend))
spec_select_idx_highres\
= np.where((self.spec_lambda_highres >= lstart) &\
(self.spec_lambda_highres < lend))
linefit_guess, linefit_limits, linefit_limited =\
initial_guesses(self, lines_select, blends, llimits=llimits)
exponent\
= int(np.log10(np.nanmedian(self.spec_f[spec_select_idx])) - 4.)
factor = float(10**(exponent * (-1)))
template_f = np.zeros_like(self.spec_lambda, dtype=float)
fit_f = np.zeros_like(self.spec_lambda, dtype=float)
temp_f = np.array(self.spec_f[spec_select_idx] * factor, dtype=float)
temp_err = np.array(self.spec_err[spec_select_idx] * factor,\
dtype=float)
temp_lambda = np.array(self.spec_lambda[spec_select_idx], dtype=float)
continuum = np.zeros_like(self.spec_lambda, dtype=float)
template_f_highres\
= np.zeros_like(self.spec_lambda_highres, dtype=float)
fit_f_highres = np.zeros_like(self.spec_lambda_highres, dtype=float)
temp_lambda_highres\
= np.array(self.spec_lambda_highres[spec_select_idx_highres],\
dtype=float)
continuum_highres\
= np.zeros_like(self.spec_lambda_highres, dtype=float)
if input_resid_level == None:
resid_level = np.std(temp_err / np.max(temp_err))
else:
resid_level = input_resid_level
sp = pyspeckit.Spectrum(data=temp_f, error=temp_err, xarr=temp_lambda,\
unit=r'flux [$10^{' + str(exponent)\
+ '}$ erg$^{-1}$ s$^{-1}$ cm$^{-2}$ '\
+ '$\AA^{-1}$]', header={})
sp.xarr.set_unit(u.AA)
sp.xarr.xtype = 'wavelength'
if self.loglevel == "DEBUG":
plt.ion()
sp.plotter(linewidth=2, title=line_idx)
exclusion_level = 0.01
iterations = 0
pat = []
while iterations < niter:
if iterations == 1:
newparinfo = update_parinfo(self, linefit_guess, \
llimits, line_idx, blends, sp.specfit.parinfo, False, False)
if iterations > 1:
newparinfo = update_parinfo(self, linefit_guess,\
llimits, line_idx, blends, sp.specfit.parinfo,\
autoadjust, fwhm_block)
with log.log_to_list() as log_list:
sp.baseline(order=int(contorder), plot_baseline=False,\
subtract=False, annotate=False, highlight_fitregion=False,\
excludefit=True, save=True, exclude=None,\
fit_plotted_area=False, exclusionlevel=float(exclusion_level))
if iterations == 0:
sp.specfit.multifit(fittype='voigt', renormalize='auto',\
annotate=False, show_components=False, verbose=False,\
color=None, guesses=list(linefit_guess), parinfo=None,\
reset_fitspec=True, plot=False, limits=linefit_limits,\
limited=linefit_limited)
if iterations > 0:
sp.specfit.multifit(fittype='voigt', renormalize='auto',\
annotate=False, show_components=False, verbose=False,\
color=None, parinfo=newparinfo,\
reset_fitspec=True, plot=False)
if exclusion_level >= max_exclusion_level:
self.logger.error(line_idx + ': LINE FIT FAILED !!!!!: \
Exclusion level reached max of '\
+ str(max_exclusion_level))
fit_failed = True
break
if len(log_list) > 0 and log_list[0].message[:8] == 'gnorm=0.'\
and exclusion_level < max_exclusion_level:
exclusion_level += 0.01
self.logger.info(line_idx + ': Adjusting exclusion level'\
+ ' to: ' + str('{:2.2f}'.format(exclusion_level)))
iterations = 0
sp = pyspeckit.Spectrum(data=temp_f, error=temp_err,\
xarr=temp_lambda, unit=r'flux [$10^{' + str(exponent)\
+ '}$ erg$^{-1}$ s$^{-1}$ cm$^{-2}$ $\AA^{-1}$]',\
header={})
sp.xarr.set_unit(u.AA)
sp.xarr.xtype = 'wavelength'
if self.loglevel == "DEBUG":
sp.plotter()
if len(log_list) == 0 or log_list[0].message[:8] != 'gnorm=0.':
if iterations > 0:
chi2_change =\
(chi2 - sp.specfit.optimal_chi2(reduced=True,\
threshold='auto'))\
/ sp.specfit.optimal_chi2(reduced=True,\
threshold='auto')
if sp.specfit.optimal_chi2(reduced=True,\
threshold='auto') == chi2\
or np.abs(chi2_change) < 0.05:
break
self.logger.debug(line_idx + ': Iteration: '\
+ str(iterations) + ' delta Chi2: '\
+ str('{:2.3f}'.format(chi2_change)))
chi2 = sp.specfit.optimal_chi2(reduced=True,\
threshold='auto')
self.logger.debug(line_idx + ': Iteration: '\
+ str(iterations) + ' Chi2: '\
+ str('{:3.3f}'.format(chi2)))
if self.loglevel == "DEBUG":
sp.specfit.plot_components(axis=sp.plotter.axis,\
add_baseline=True,\
component_fit_color=plotcolor(iterations))
ax = sp.plotter.axis
pat.append(mlines.Line2D([], [],\
color=plotcolor(iterations),\
label='# iter: ' + str(iterations)))
ax.legend(handles=pat)
iterations += 1
if self.loglevel == "DEBUG":
input("Press ENTER to continue")
if self.loglevel == "DEBUG":
sp.specfit.plotresiduals(axis=sp.plotter.axis, clear=False,\
yoffset=0.9 * np.min(temp_f), label=False, linewidth=2, color='g')
sp.specfit.plot_fit(annotate=False, lw=2, composite_fit_color='r')
sp.baseline.plot_baseline(annotate=False,\
baseline_fit_color='orange', linewidth=2)
print('Parinfo:')
print(sp.specfit.parinfo)
print(' ')
input("Press ENTER to close the plot window")
if not fit_failed:
if iterations < niter:
self.logger.info(line_idx + ': Converged after '\
+ str(iterations) + ' iterations; Chi2: '\
+ str('{:3.3f}'.format(chi2)) + ' delta Chi2 [%]: '\
+ str('{:2.3f}'.format(chi2_change)))
if iterations == niter:
self.logger.info(line_idx\
+ ': Maximum number of iterations (' + str(iterations)\
+ ') reached; Chi2: ' + str(chi2))
par_extract_idx = []
for lab_line_idx, lab_lines\
in enumerate(np.array([self.cat.loc[line_idx, 'l_lab']])):
par_extract_idx = np.concatenate((par_extract_idx,\
np.where(lines_select == lab_lines)[0]))
for i in range(len(lines_select)):
xcen = lines_select[i]
gamma = sp.specfit.parinfo[int(4 * i + 3)]['value']
sigma = sp.specfit.parinfo[int(4 * i + 2)]['value']
amp = sp.specfit.parinfo[int(4 * i + 0)]['value']
highres_f = voigt_funct(self.spec_lambda_highres, xcen, 1,\
sigma, gamma)
lowres_f = spec_res_downgrade(self.spec_lambda_highres,\
highres_f, self.spec_lambda)
lineflux = amp * lowres_f
lineflux_highres = amp * highres_f
template_f += lineflux / factor
template_f_highres += lineflux_highres / factor
highres_f = voigt_funct(self.spec_lambda_highres,\
sp.specfit.parinfo[int(4 * i + 1)]['value'], 1, sigma, gamma)
lowres_f = spec_res_downgrade(self.spec_lambda_highres,\
highres_f, self.spec_lambda)
lineflux_fit = amp * lowres_f
lineflux_fit_highres = amp * highres_f
fit_f += lineflux_fit / factor
fit_f_highres += lineflux_fit_highres / factor
if (i == par_extract_idx).any():
temp_a = sp.specfit.parinfo[int(4 * i + 0)]['value']\
/ factor
temp_l = sp.specfit.parinfo[int(4 * i + 1)]['value']
temp_sg = sp.specfit.parinfo[int(4 * i + 2)]['value']
temp_sl = sp.specfit.parinfo[int(4 * i + 3)]['value']
baseline_temp = baseline_extract(self, sp, contorder)
baseline_sub_spec =\
sp.data / baseline_temp(temp_lambda - temp_lambda[0])
continuum = baseline_temp(temp_lambda - temp_lambda[0]) / factor
continuum_highres = baseline_temp(temp_lambda_highres\
- temp_lambda_highres[0]) / factor
resid = \
(self.spec_f[spec_select_idx] - fit_f[spec_select_idx]) / continuum
std_resid = np.std(resid)
continuum_dev = continuum_deviation(self, temp_lambda,\
temp_f, continuum, contorder)
if std_resid > resid_level or np.isnan(std_resid)\
or continuum_dev > input_continuum_deviation[line_idx]\
or np.isnan(continuum_dev):
if std_resid > resid_level or np.isnan(std_resid):
self.logger.info(line_idx\
+ ': STD of residuals: '\
+ str('{:2.4f}'.format(std_resid))\
+ ' targeted: ' + str('{:2.4f}'.format(resid_level)))
if continuum_dev > input_continuum_deviation[line_idx]:
self.logger.info(line_idx + ': Continuum deviation: '\
+ str('{:2.4f}'.format(continuum_dev)) + ' targeted: '\
+ str('{:2.4f}'.format(input_continuum_deviation[line_idx])))
if contorder == max_contorder:
max_cont_reached = True
if n_ladjust == max_ladjust:
max_n_ladjust_reached = True
if max_cont_reached and max_n_ladjust_reached:
self.logger.warning(line_idx\
+ ": Maximum adjustments reached: Check the output")
break
if adjust_preference == 'contorder':
if not max_cont_reached:
contorder += 1
self.logger.info(line_idx\
+ ': Adjusting continuum order to: ' + str(contorder))
if max_cont_reached and not max_n_ladjust_reached:
lstart -= 5.
lend += 5.
self.logger.info(line_idx\
+ ': maximum continuum order reached => Adjusting'\
+ ' wavelength range to: [' + str(lstart)\
+ ',' + str(lend) + ']')
n_ladjust += 1
max_cont_reached = False
contorder = self.cat.loc[line_idx, 'cont_order']
if adjust_preference != 'contorder':
contorder = self.cat.loc[line_idx, 'cont_order']
if not max_n_ladjust_reached:
if adjust_preference == 'min_lambda'\
or adjust_preference == 'minmax_lambda':
lstart -= 5.
self.logger.info(line_idx\
+ ': Adjusting lower wavelength range to: '\
+ str(lstart))
if adjust_preference == 'max_lambda'\
or adjust_preference == 'minmax_lambda':
lend += 5.
self.logger.info(line_idx + ': Adjusting upper \
wavelength range to: ' + str(lend))
n_ladjust += 1
if max_n_ladjust_reached and not max_cont_reached:
contorder += 1
self.logger.info(line_idx\
+ ': maximum wavelength adjustment reached =>'\
+ ' Adjusting continuum order to: ' + str(contorder))
lstart = self.cat.loc[line_idx, 'l_start']
lend = self.cat.loc[line_idx, 'l_end']
if fit_failed:
temp_l = 0.
temp_a = 0.
temp_sl = 0.
temp_sg = 0.
significance = np.abs(temp_a) / np.median(temp_err / factor)
if not fit_failed:
self.logger.info(line_idx + ': STD of residuals: '\
+ str('{:2.4f}'.format(std_resid)) + ' targeted: '\
+ str('{:2.4f}'.format(resid_level)))
self.logger.info(line_idx + ': Continuum deviation: '\
+ str('{:2.4f}'.format(continuum_dev)) + ' targeted: '\
+ str('{:2.4f}'.format(input_continuum_deviation[line_idx])))
self.logger.info(line_idx + ' Line significance: '\
+ str('{:3.2f}'.format(significance)))
if (temp_l - self.cat.loc[line_idx, 'l_lab'] < 0.8 * llimits[0]\
or temp_l - self.cat.loc[line_idx, 'l_lab'] > 0.8 * llimits[1])\
and not autoadjust:
self.logger.warning(line_idx\
+ ' exceeds 0.8 of lambda limits; lfit: ' + str(temp_l)\
+ ' llab: ' + str(self.cat.loc[line_idx, 'l_lab'])\
+ ' llimits = [' + str(llimits[0]) + ' ' + str(llimits[1]) + ']')
self.logger.info('Finished line ' + line_idx)
return line_idx, temp_l, temp_a, temp_sl, temp_sg, spec_select_idx,\
template_f, continuum, lstart, lend, contorder, fit_f, significance,\
fit_failed, fit_f_highres, spec_select_idx_highres, template_f_highres,\
continuum_highres
def _hducut(img_hdu, center_coord, cutout_size, correct_wcs=False, verbose=False):
"""
Takes an ImageHDU (image and associated metatdata in the fits format), as well as a center
coordinate and size and make a cutout of that image, which is returned as another ImageHDU,
including updated WCS information.
Parameters
----------
img_hdu : `~astropy.io.fits.hdu.image.ImageHDU`
The image and assciated metadata that is being cut out.
center_coord : `~astropy.coordinates.sky_coordinate.SkyCoord`
The coordinate to cut out around.
cutout_size : array
The size of the cutout as [nx,ny], where nx/ny can be integers (assumed to be pixels)
or `~astropy.Quantity` values, either pixels or angular quantities.
correct_wcs : bool
Default False. If true a new WCS will be created for the cutout that is tangent projected
and does not include distortions.
verbose : bool
Default False. If true intermediate information is printed.
Returns
-------
response : `~astropy.io.fits.hdu.image.ImageHDU`
The cutout image and associated metadata.
"""
hdu_header = fits.Header(img_hdu.header, copy=True)
# We are going to reroute the logging to a string stream temporarily so we can
# intercept any message from astropy, chiefly the "Inconsistent SIP distortion information"
# INFO message which will indicate that we need to remove existing SIP keywords
# from a WCS whose CTYPE does not include SIP. In this we are taking the CTYPE to be
# correct and adjusting the header keywords to match.
hdlrs = log.handlers
log.handlers = []
with log.log_to_list() as log_list:
img_wcs = wcs.WCS(hdu_header, relax=True)
for hd in hdlrs:
log.addHandler(hd)
no_sip = False
if (len(log_list) > 0):
if ("Inconsistent SIP distortion information" in log_list[0].msg):
# Remove sip coefficients
img_wcs.sip = None
no_sip = True
else: # Message(s) we didn't prepare for we want to go ahead and display
for log_rec in log_list:
log.log(log_rec.levelno, log_rec.msg, extra={"origin": log_rec.name})
img_data = img_hdu.data
if verbose:
print("Original image shape: {}".format(img_data.shape))
# Get cutout limits
cutout_lims = get_cutout_limits(img_wcs, center_coord, cutout_size)
if verbose:
print("xmin,xmax: {}".format(cutout_lims[0]))
print("ymin,ymax: {}".format(cutout_lims[1]))
# These limits are not guarenteed to be within the image footprint
xmin, xmax = cutout_lims[0]
ymin, ymax = cutout_lims[1]
ymax_img, xmax_img = img_data.shape
# Check the cutout is on the image
if (xmax <= 0) or (xmin >= xmax_img) or (ymax <= 0) or (ymin >= ymax_img):
raise InvalidQueryError("Cutout location is not in image footprint!")
# Adjust limits and figuring out the` padding
padding = np.zeros((2, 2), dtype=int)
if xmin < 0:
padding[1, 0] = -xmin
xmin = 0
if ymin < 0:
padding[0, 0] = -ymin
ymin = 0
if xmax > xmax_img:
padding[1, 1] = xmax - xmax_img
xmax = xmax_img
if ymax > ymax_img:
padding[0, 1] = ymax - ymax_img
ymax = ymax_img
img_cutout = img_hdu.data[ymin:ymax, xmin:xmax]
# Adding padding to the cutout so that it's the expected size
if padding.any(): # only do if we need to pad
img_cutout = np.pad(img_cutout, padding, 'constant', constant_values=np.nan)
if verbose:
print("Image cutout shape: {}".format(img_cutout.shape))
# Getting the cutout wcs
cutout_wcs = get_cutout_wcs(img_wcs, cutout_lims)
# Updating the header with the new wcs info
if no_sip:
hdu_header.update(cutout_wcs.to_header(relax=False))
else:
hdu_header.update(cutout_wcs.to_header(relax=True)) # relax arg is for sip distortions if they exist
# Naming the extension and preserving the original name
hdu_header["O_EXT_NM"] = (hdu_header.get("EXTNAME"), "Original extension name.")
hdu_header["EXTNAME"] = "CUTOUT"
# Moving the filename, if present, into the ORIG_FLE keyword
hdu_header["ORIG_FLE"] = (hdu_header.get("FILENAME"), "Original image filename.")
hdu_header.remove("FILENAME", ignore_missing=True)
hdu = fits.ImageHDU(header=hdu_header, data=img_cutout)
return hdu
