def _observe_through_filter(bp, B, unit):
if not synphot:
raise AstropyWarning('synphot is required for bandpass filtering.')
obs = Observation(B, bp)
wave = obs.effective_wavelength()
fluxd = obs.effstim(unit)
return wave, fluxd
class CommCase(object):
"""Base class for commissioning tests."""
obsmode = None # Observation mode string
spectrum = None # SYNPHOT-like string to construct spectrum
force = None
# Default tables are the latest available as of 2016-07-25.
tables = {
'graphtable': os.path.join('mtab$OLD_FILES', '07r1502mm_tmg.fits'),
'comptable': os.path.join('mtab$OLD_FILES', '07r1502nm_tmc.fits'),
'thermtable': 'mtab$tae17277m_tmt.fits'
}
def setup_class(self):
"""Subclass needs to define ``obsmode`` and ``spectrum``
class variables for this to work.
"""
if not HAS_PYSYNPHOT:
raise ImportError(
'ASTROLIB PYSYNPHOT must be installed to run these tests')
# Make sure both software use the same graph and component tables.
conf.graphtable = self.tables['graphtable']
conf.comptable = self.tables['comptable']
conf.thermtable = self.tables['thermtable']
S.setref(graphtable=self.tables['graphtable'],
comptable=self.tables['comptable'],
thermtable=self.tables['thermtable'])
# Construct spectra for both software.
self.sp = parse_spec(self.spectrum)
self.bp = band(self.obsmode)
# Astropy version has no prior knowledge of instrument-specific
# binset, so it has to be set explicitly.
if hasattr(self.bp, 'binset'):
self.obs = Observation(self.sp,
self.bp,
force=self.force,
binset=self.bp.binset)
else:
self.obs = Observation(self.sp, self.bp, force=self.force)
# Astropy version does not assume a default waveset
# (you either have it or you don't). If there is no
# waveset, no point comparing obs waveset against ASTROLIB.
if self.sp.waveset is None or self.bp.waveset is None:
self._has_obswave = False
else:
self._has_obswave = True
self.spref = old_parse_spec(self.spectrum)
self.bpref = S.ObsBandpass(self.obsmode)
self.obsref = S.Observation(self.spref, self.bpref, force=self.force)
# Ensure we are comparing in the same units
self.bpref.convert(self.bp._internal_wave_unit.name)
self.spref.convert(self.sp._internal_wave_unit.name)
self.spref.convert(self.sp._internal_flux_unit.name)
self.obsref.convert(self.obs._internal_wave_unit.name)
self.obsref.convert(self.obs._internal_flux_unit.name)
@staticmethod
def _get_new_wave(sp):
"""Astropy version does not assume a default waveset
(you either have it or you don't). This is a convenience
method to duck-type ASTROLIB waveset behavior.
"""
wave = sp.waveset
if wave is None:
wave = conf.waveset_array
else:
wave = wave.value
return wave
def _assert_allclose(self,
actual,
desired,
rtol=1e-07,
atol=sys.float_info.min):
"""``assert_allclose`` only report percentage but we
also want to know some extra info conveniently."""
if isinstance(actual, Iterable):
ntot = len(actual)
else:
ntot = 1
n = np.count_nonzero(
abs(actual - desired) > atol + rtol * abs(desired))
msg = 'obsmode: {0}\nspectrum: {1}\n(mismatch {2}/{3})'.format(
self.obsmode, self.spectrum, n, ntot)
assert_allclose(actual, desired, rtol=rtol, atol=atol, err_msg=msg)
# TODO: Confirm whether non-default atol is acceptable.
# Have to use this value to avoid AssertionError for very
# small non-zero flux values like 1.8e-26 to 2e-311.
def _compare_nonzero(self, new, old, thresh=0.01, atol=1e-29):
"""Compare normally when results from both are non-zero."""
i = (new != 0) & (old != 0)
# Make sure non-zero atol is not too high, otherwise just let it fail.
if atol > (thresh * min(new.max(), old.max())):
atol = sys.float_info.min
self._assert_allclose(new[i], old[i], rtol=thresh, atol=atol)
def _compare_zero(self, new, old, thresh=0.01):
"""Special handling for comparison when one of the results
is zero. This is because ``rtol`` will not work."""
i = ((new == 0) | (old == 0)) & (new != old)
try:
self._assert_allclose(new[i], old[i], rtol=thresh)
except AssertionError as e:
pytest.xfail(str(e)) # TODO: Will revisit later
def test_band_wave(self, thresh=0.01):
"""Test bandpass waveset."""
wave = self._get_new_wave(self.bp)
self._assert_allclose(wave, self.bpref.wave, rtol=thresh)
def test_spec_wave(self, thresh=0.01):
"""Test source spectrum waveset."""
wave = self._get_new_wave(self.sp)
# TODO: Failure due to different wavesets for blackbody; Ignore?
try:
self._assert_allclose(wave, self.spref.wave, rtol=thresh)
except (AssertionError, ValueError) as e:
self._has_obswave = False # Skip obs waveset tests
if 'bb(' in self.spectrum:
pytest.xfail('Blackbody waveset implementations are different')
elif 'unit(' in self.spectrum:
pytest.xfail('Flat does not use default waveset anymore')
else:
raise
def test_obs_wave(self, thresh=0.01):
"""Test observation waveset."""
if not self._has_obswave: # Nothing to test
return
# Native
wave = self.obs.waveset.value
# TODO: Failure due to different wavesets for blackbody; Ignore?
try:
self._assert_allclose(wave, self.obsref.wave, rtol=thresh)
except (AssertionError, ValueError) as e:
if 'bb(' in self.spectrum:
pytest.xfail('Blackbody waveset implementations are different')
elif 'unit(' in self.spectrum:
self._has_obswave = False # Skip binned flux test
pytest.xfail('Flat does not use default waveset anymore')
else:
raise
# Binned
binset = self.obs.binset.value
self._assert_allclose(binset, self.obsref.binwave, rtol=thresh)
@pytest.mark.parametrize('thrutype', ['zero', 'nonzero'])
def test_band_thru(self, thrutype, thresh=0.01):
"""Test bandpass throughput, which is always between 0 and 1."""
wave = self.bpref.wave
thru = self.bp(wave).value
if thrutype == 'zero':
self._compare_zero(thru, self.bpref.throughput, thresh=thresh)
else: # nonzero
self._compare_nonzero(thru, self.bpref.throughput, thresh=thresh)
@pytest.mark.parametrize('fluxtype', ['zero', 'nonzero'])
def test_spec_flux(self, fluxtype, thresh=0.01):
"""Test flux for source spectrum in PHOTLAM."""
wave = self.spref.wave
flux = self.sp(wave).value
if fluxtype == 'zero':
self._compare_zero(flux, self.spref.flux, thresh=thresh)
else: # nonzero
self._compare_nonzero(flux, self.spref.flux, thresh=thresh)
@pytest.mark.parametrize('fluxtype', ['zero', 'nonzero'])
def test_obs_flux(self, fluxtype, thresh=0.01):
"""Test flux for observation in PHOTLAM."""
wave = self.obsref.wave
flux = self.obs(wave).value
# Native
if fluxtype == 'zero':
self._compare_zero(flux, self.obsref.flux, thresh=thresh)
else: # nonzero
self._compare_nonzero(flux, self.obsref.flux, thresh=thresh)
if not self._has_obswave: # Do not compare binned flux
return
# Binned (cannot be resampled)
binflux = self.obs.binflux.value
if fluxtype == 'zero':
self._compare_zero(binflux, self.obsref.binflux, thresh=thresh)
else: # nonzero
try:
self._compare_nonzero(binflux,
self.obsref.binflux,
thresh=thresh)
except AssertionError as e:
if 'unit(' in self.spectrum:
pytest.xfail('Flat does not use default waveset anymore:\n'
'{0}'.format(str(e)))
else:
raise
def test_countrate(self, thresh=0.01):
"""Test observation countrate calculations."""
ans = self.obsref.countrate()
# Astropy version does not assume a default area.
val = self.obs.countrate(conf.area).value
self._assert_allclose(val, ans, rtol=thresh)
def test_efflam(self, thresh=0.01):
"""Test observation effective wavelength."""
ans = self.obsref.efflam()
val = self.obs.effective_wavelength().value
self._assert_allclose(val, ans, rtol=thresh)
def teardown_class(self):
"""Reset config for both software."""
for cfgname in self.tables:
conf.reset(cfgname)
S.setref()
class CommCase(object):
"""Base class for commissioning tests."""
obsmode = None # Observation mode string
spectrum = None # SYNPHOT-like string to construct spectrum
force = None
# Default tables are the latest available as of 2016-07-25.
tables = {
'graphtable': os.path.join('mtab$OLD_FILES', '07r1502mm_tmg.fits'),
'comptable': os.path.join('mtab$OLD_FILES', '07r1502nm_tmc.fits'),
'thermtable': 'mtab$tae17277m_tmt.fits'}
def setup_class(self):
"""Subclass needs to define ``obsmode`` and ``spectrum``
class variables for this to work.
"""
if not HAS_PYSYNPHOT:
raise ImportError(
'ASTROLIB PYSYNPHOT must be installed to run these tests')
# Make sure both software use the same graph and component tables.
conf.graphtable = self.tables['graphtable']
conf.comptable = self.tables['comptable']
conf.thermtable = self.tables['thermtable']
S.setref(graphtable=self.tables['graphtable'],
comptable=self.tables['comptable'],
thermtable=self.tables['thermtable'])
# Construct spectra for both software.
self.sp = parse_spec(self.spectrum)
self.bp = band(self.obsmode)
# Astropy version has no prior knowledge of instrument-specific
# binset, so it has to be set explicitly.
if hasattr(self.bp, 'binset'):
self.obs = Observation(self.sp, self.bp, force=self.force,
binset=self.bp.binset)
else:
self.obs = Observation(self.sp, self.bp, force=self.force)
# Astropy version does not assume a default waveset
# (you either have it or you don't). If there is no
# waveset, no point comparing obs waveset against ASTROLIB.
if self.sp.waveset is None or self.bp.waveset is None:
self._has_obswave = False
else:
self._has_obswave = True
self.spref = old_parse_spec(self.spectrum)
self.bpref = S.ObsBandpass(self.obsmode)
self.obsref = S.Observation(self.spref, self.bpref, force=self.force)
# Ensure we are comparing in the same units
self.bpref.convert(self.bp._internal_wave_unit.name)
self.spref.convert(self.sp._internal_wave_unit.name)
self.spref.convert(self.sp._internal_flux_unit.name)
self.obsref.convert(self.obs._internal_wave_unit.name)
self.obsref.convert(self.obs._internal_flux_unit.name)
@staticmethod
def _get_new_wave(sp):
"""Astropy version does not assume a default waveset
(you either have it or you don't). This is a convenience
method to duck-type ASTROLIB waveset behavior.
"""
wave = sp.waveset
if wave is None:
wave = conf.waveset_array
else:
wave = wave.value
return wave
def _assert_allclose(self, actual, desired, rtol=1e-07,
atol=sys.float_info.min):
"""``assert_allclose`` only report percentage but we
also want to know some extra info conveniently."""
if isinstance(actual, Iterable):
ntot = len(actual)
else:
ntot = 1
n = np.count_nonzero(
abs(actual - desired) > atol + rtol * abs(desired))
msg = 'obsmode: {0}\nspectrum: {1}\n(mismatch {2}/{3})'.format(
self.obsmode, self.spectrum, n, ntot)
assert_allclose(actual, desired, rtol=rtol, atol=atol, err_msg=msg)
# TODO: Confirm whether non-default atol is acceptable.
# Have to use this value to avoid AssertionError for very
# small non-zero flux values like 1.8e-26 to 2e-311.
def _compare_nonzero(self, new, old, thresh=0.01, atol=1e-29):
"""Compare normally when results from both are non-zero."""
i = (new != 0) & (old != 0)
# Make sure non-zero atol is not too high, otherwise just let it fail.
if atol > (thresh * min(new.max(), old.max())):
atol = sys.float_info.min
self._assert_allclose(new[i], old[i], rtol=thresh, atol=atol)
def _compare_zero(self, new, old, thresh=0.01):
"""Special handling for comparison when one of the results
is zero. This is because ``rtol`` will not work."""
i = ((new == 0) | (old == 0)) & (new != old)
try:
self._assert_allclose(new[i], old[i], rtol=thresh)
except AssertionError as e:
pytest.xfail(str(e)) # TODO: Will revisit later
def test_band_wave(self, thresh=0.01):
"""Test bandpass waveset."""
wave = self._get_new_wave(self.bp)
self._assert_allclose(wave, self.bpref.wave, rtol=thresh)
def test_spec_wave(self, thresh=0.01):
"""Test source spectrum waveset."""
wave = self._get_new_wave(self.sp)
# TODO: Failure due to different wavesets for blackbody; Ignore?
try:
self._assert_allclose(wave, self.spref.wave, rtol=thresh)
except (AssertionError, ValueError):
self._has_obswave = False # Skip obs waveset tests
if 'bb(' in self.spectrum:
pytest.xfail('Blackbody waveset implementations are different')
elif 'unit(' in self.spectrum:
pytest.xfail('Flat does not use default waveset anymore')
else:
raise
def test_obs_wave(self, thresh=0.01):
"""Test observation waveset."""
if not self._has_obswave: # Nothing to test
return
# Native
wave = self.obs.waveset.value
# TODO: Failure due to different wavesets for blackbody; Ignore?
try:
self._assert_allclose(wave, self.obsref.wave, rtol=thresh)
except (AssertionError, ValueError):
if 'bb(' in self.spectrum:
pytest.xfail('Blackbody waveset implementations are different')
elif 'unit(' in self.spectrum:
self._has_obswave = False # Skip binned flux test
pytest.xfail('Flat does not use default waveset anymore')
else:
raise
# Binned
binset = self.obs.binset.value
self._assert_allclose(binset, self.obsref.binwave, rtol=thresh)
@pytest.mark.parametrize('thrutype', ['zero', 'nonzero'])
def test_band_thru(self, thrutype, thresh=0.01):
"""Test bandpass throughput, which is always between 0 and 1."""
wave = self.bpref.wave
thru = self.bp(wave).value
if thrutype == 'zero':
self._compare_zero(thru, self.bpref.throughput, thresh=thresh)
else: # nonzero
self._compare_nonzero(thru, self.bpref.throughput, thresh=thresh)
@pytest.mark.parametrize('fluxtype', ['zero', 'nonzero'])
def test_spec_flux(self, fluxtype, thresh=0.01):
"""Test flux for source spectrum in PHOTLAM."""
wave = self.spref.wave
flux = self.sp(wave).value
if fluxtype == 'zero':
self._compare_zero(flux, self.spref.flux, thresh=thresh)
else: # nonzero
self._compare_nonzero(flux, self.spref.flux, thresh=thresh)
@pytest.mark.parametrize('fluxtype', ['zero', 'nonzero'])
def test_obs_flux(self, fluxtype, thresh=0.01):
"""Test flux for observation in PHOTLAM."""
wave = self.obsref.wave
flux = self.obs(wave).value
# Native
if fluxtype == 'zero':
self._compare_zero(flux, self.obsref.flux, thresh=thresh)
else: # nonzero
self._compare_nonzero(flux, self.obsref.flux, thresh=thresh)
if not self._has_obswave: # Do not compare binned flux
return
# Binned (cannot be resampled)
binflux = self.obs.binflux.value
if fluxtype == 'zero':
self._compare_zero(binflux, self.obsref.binflux, thresh=thresh)
else: # nonzero
try:
self._compare_nonzero(binflux, self.obsref.binflux,
thresh=thresh)
except AssertionError as e:
if 'unit(' in self.spectrum:
pytest.xfail('Flat does not use default waveset anymore:\n'
'{0}'.format(str(e)))
else:
raise
def test_countrate(self, thresh=0.01):
"""Test observation countrate calculations."""
ans = self.obsref.countrate()
# Astropy version does not assume a default area.
val = self.obs.countrate(conf.area).value
self._assert_allclose(val, ans, rtol=thresh)
def test_efflam(self, thresh=0.01):
"""Test observation effective wavelength."""
ans = self.obsref.efflam()
val = self.obs.effective_wavelength().value
self._assert_allclose(val, ans, rtol=thresh)
def teardown_class(self):
"""Reset config for both software."""
for cfgname in self.tables:
conf.reset(cfgname)
S.setref()
