def test_pix_to_shapely(region):
try:
from shapely.geometry.base import BaseGeometry
shape = region.to_shapely()
assert isinstance(shape, BaseGeometry)
except NotImplementedError:
pytest.xfail()
def test_pix_to_mask(region, mode):
try:
mask = region.to_mask(mode=mode)
assert isinstance(mask, np.ndarray)
assert mask.ndim == 2
except NotImplementedError:
pytest.xfail()
def test_searches(self):
tab_2 = conesearch.conesearch(SCS_CENTER,
SCS_RADIUS,
catalog_db=self.url,
pedantic=self.pedantic,
verbose=self.verbose)
tab_3 = conesearch.conesearch(SCS_CENTER,
SCS_RADIUS,
catalog_db=[self.catname, self.url],
pedantic=self.pedantic,
verbose=self.verbose)
tab_4 = conesearch.conesearch(
SCS_CENTER,
SCS_RADIUS,
catalog_db=vos_catalog.get_remote_catalog_db(
conf.conesearch_dbname),
pedantic=self.pedantic,
verbose=self.verbose)
assert tab_2.url == tab_3.url
np.testing.assert_array_equal(tab_2.array, tab_3.array)
# If this fails, it is because of dict hashing, no big deal.
if tab_2.url == tab_4.url:
np.testing.assert_array_equal(tab_2.array, tab_4.array)
else:
pytest.xfail('conesearch_simple.json used a different URL')
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_pix_to_shapely(region):
try:
from shapely.geometry.base import BaseGeometry
shape = region.to_shapely()
assert isinstance(shape, BaseGeometry)
except NotImplementedError:
pytest.xfail()
def test_pix_to_mask(region, mode):
try:
mask = region.to_mask(mode=mode)
assert isinstance(mask, np.ndarray)
assert mask.ndim == 2
except NotImplementedError:
pytest.xfail()
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 compare_xid_data(xid, data):
if six.PY3:
pytest.xfail('xid/data comparison fails in PY3 because the instrument '
'column is bytes in xid and str in data')
else:
for col in xid.colnames:
if xid[col].dtype.type is np.string_:
assert xid[col] == data[col]
else:
assert_allclose(xid[col], data[col])
def compare_xid_data(xid, data):
if six.PY3:
pytest.xfail('xid/data comparison fails in PY3 because the instrument '
'column is bytes in xid and str in data')
else:
for col in xid.colnames:
if xid[col].dtype.type is np.string_:
assert xid[col] == data[col]
else:
assert_allclose(xid[col], data[col])
def test_extrap_mjd(self, interpval, ans):
"""Test extrapolation without using default column."""
try:
sp = spectrum.interpolate_spectral_element(self.fname_cos,
interpval)
except RuntimeError:
if _IS_PY32:
pytest.xfail('python3.2 urllib bug')
else:
raise
w = sp.waveset[400:3000:500]
np.testing.assert_allclose(sp(w).value, ans, rtol=1e-5)
def test_uresp(self, obsmode, ans):
"""Unit response for different detector settings."""
try:
obs = spectrum.band(obsmode, graphtable=GT_FILE, comptable=CP_FILE)
except RuntimeError:
if _IS_PY32:
pytest.xfail('python3.2 urllib bug')
else:
raise
np.testing.assert_allclose(obs.unit_response(obs.area).value,
ans,
rtol=1e-4)
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_write_eps(tmpdir, format):
filename = os.path.join(str(tmpdir), 'test_output.eps')
data = np.zeros((16, 16))
f = FITSFigure(data)
f.show_grayscale()
try:
f.save(filename, format=format)
except TypeError:
pytest.xfail()
finally:
f.close()
if format is None:
assert is_format(filename, 'eps')
else:
assert is_format(filename, format)
def conesearch_compare(self, xmlfile, msg):
"""
Bypassing Cone Search query and just imitating the reply,
then check if appropriate error message is caught.
"""
# conesearch_error4.xml is a wont-fix for now
if xmlfile == 'conesearch_error4.xml':
pytest.xfail('Currently not supported, '
'see astropy.io.votable.exceptions.W22')
url = get_pkg_data_filename(os.path.join(self.datadir, xmlfile))
try:
vos_catalog._vo_service_request(url, self.pedantic, {})
except VOSError as e:
assert msg in str(e)
def test_async(self):
async_search = conesearch.AsyncConeSearch(SCS_CENTER,
SCS_RADIUS,
pedantic=self.pedantic)
# Wait a little for the instance to set up properly
time.sleep(1)
tab = async_search.get(timeout=data.conf.remote_timeout)
try:
assert async_search.done()
except AssertionError as exc:
pytest.xfail(str(exc))
else:
assert tab.array.size > 0
def test_to_yt(self, tmpdir, grid_type):
from yt.mods import ProjectionPlot
g = self.grid[grid_type]
g['density'] = []
g['density'].append(self.density[grid_type])
pf = g.to_yt()
# TEMP: xfail due to bug in yt
# https://bitbucket.org/yt_analysis/yt/pull-requests/2362/fix-type-issue-in-octree-construction/diff
if grid_type == 'oct':
pytest.xfail()
p = ProjectionPlot(pf, 'x', ["density"], center='c', origin='native')
p.save(tmpdir.join('test.png').strpath)
def test_write_stringio(tmpdir, format):
s = StringIO()
data = np.zeros((16, 16))
f = FITSFigure(data)
f.show_grayscale()
try:
f.save(s, format=format)
except TypeError:
pytest.xfail()
finally:
f.close()
s.seek(0)
if format is None:
assert is_format(s, 'png')
else:
assert is_format(s, format)
def test_write_stringio(tmpdir, format):
s = StringIO()
data = np.zeros((16, 16))
f = FITSFigure(data)
f.show_grayscale()
try:
f.save(s, format=format)
except TypeError:
pytest.xfail()
finally:
f.close()
s.seek(0)
if format is None:
assert is_format(s, 'png')
else:
assert is_format(s, format)
def test_arithmetic_ops(op2):
if not MIN_VERSIONS['NUMPY_1_10'] and isinstance(op2, np.ma.MaskedArray):
pytest.xfail("masked arrays didn't respect numpy priority yet...")
ndd = create_ndd()
compare_ndd_identical(ndd.add(op2), ndd + op2)
compare_ndd_identical(ndd.subtract(op2), ndd - op2)
compare_ndd_identical(ndd.multiply(op2), ndd * op2)
compare_ndd_identical(ndd.divide(op2), ndd / op2)
compare_ndd_identical(ndd.power(op2), ndd ** op2)
# and reverse
compare_ndd_identical(ndd.add(op2, ndd), op2 + ndd)
compare_ndd_identical(ndd.subtract(op2, ndd), op2 - ndd)
compare_ndd_identical(ndd.multiply(op2, ndd), op2 * ndd)
compare_ndd_identical(ndd.divide(op2, ndd), op2 / ndd)
compare_ndd_identical(ndd.power(op2, ndd), op2 ** ndd)
def test_async_all(self):
async_search_all = conesearch.AsyncSearchAll(SCS_CENTER,
SCS_RADIUS,
pedantic=self.pedantic)
# Wait a little for the instance to set up properly
time.sleep(1)
all_results = async_search_all.get(timeout=data.conf.remote_timeout *
3)
try:
assert async_search_all.done()
except AssertionError as exc:
pytest.xfail(str(exc))
else:
for tab in all_results.values():
assert tab.array.size > 0
def test_gtanalysis_sed(create_diffuse_dir, create_draco_analysis):
gta = create_draco_analysis
gta.load_roi('fit1')
np.random.seed(1)
gta.simulate_roi()
params = gta.roi['draco'].params
prefactor = 3E-12
index = 1.9
scale = params['Scale']['value']
emin = gta.energies[:-1]
emax = gta.energies[1:]
flux_true = spectrum.PowerLaw.eval_flux(emin, emax, [prefactor, -index],
scale)
gta.simulate_source({
'SpatialModel': 'PointSource',
'Index': index,
'Scale': scale,
'Prefactor': prefactor
})
gta.free_source('draco')
gta.fit()
o = gta.sed('draco', make_plots=True)
flux_resid = (flux_true - o['flux']) / o['flux_err']
assert_allclose(flux_resid, 0, atol=3.0)
params = gta.roi['draco'].params
index_resid = (-params['Index']['value'] - index) / \
params['Index']['error']
assert_allclose(index_resid, 0, atol=3.0)
prefactor_resid = (params['Prefactor']['value'] -
prefactor) / params['Prefactor']['error']
try:
assert_allclose(prefactor_resid, 0, atol=3.0)
gta.simulate_roi(restore=True)
except AssertionError:
pytest.xfail("Known issue with fit stability in macos")
def test_therm_spec(self, fluxtype, thresh=0.01):
"""Test bandpass thermal spectrum."""
thspref = self.bpref.obsmode.ThermalSpectrum()
thsp = self.bp.obsmode.thermal_spectrum()
# Make sure comparing same units
thspref.convert(thsp._internal_wave_unit.name)
thspref.convert(thsp._internal_flux_unit.name)
# waveset not expected to be same here, so just compare flux
flux = thsp(thspref.wave).value
if fluxtype == 'zero':
self._compare_zero(flux, thspref.flux, thresh=thresh)
else: # nonzero
# TODO: Is the refactored version really better?
try:
self._compare_nonzero(flux, thspref.flux, thresh=thresh)
except AssertionError:
pytest.xfail('New thermal spectrum samples better')
def test_reference_file(filename):
basename = os.path.basename(filename)
known_fail = False
if sys.version_info[:2] == (2, 6):
known_fail = (basename in ('complex.asdf', 'unicode_spp.asdf'))
elif sys.version_info[:2] == (2, 7):
known_fail = (basename in ('complex.asdf'))
try:
with open(filename) as asdf:
asdf.resolve_and_inline()
with open(filename[:-4] + "yaml") as ref:
assert_tree_match(asdf.tree, ref.tree, 'assert_allclose')
except:
if known_fail:
pytest.xfail()
else:
raise
def test_reference_file(filename):
basename = os.path.basename(filename)
known_fail = False
if sys.version_info[:2] == (2, 6):
known_fail = (basename in ('complex.asdf', 'unicode_spp.asdf'))
elif sys.version_info[:2] == (2, 7):
known_fail = (basename in ('complex.asdf'))
try:
with open(filename) as asdf:
asdf.resolve_and_inline()
with open(filename[:-4] + "yaml") as ref:
assert_tree_match(asdf.tree, ref.tree, 'assert_allclose')
except:
if known_fail:
pytest.xfail()
else:
raise
def test_interp_mjd(self):
"""Test whether the algorithm gets the correct throughput table
when input value does not correspond to a column and interpolation
is required.
"""
try:
sp = spectrum.interpolate_spectral_element(self.fname_stis, 51000)
except RuntimeError:
if _IS_PY32:
pytest.xfail('python3.2 urllib bug')
else:
raise
np.testing.assert_array_equal(sp.waveset[::25].value, self.wave_stis)
np.testing.assert_allclose(
sp(sp.waveset[:10]).value, [
0, 0.97830353, 0.97830353, 0.97830353, 0.97722476, 0.98524689,
0.98975077, 0.99019109, 0.98536552, 0.97710241
])
assert sp(sp.waveset[0]) == sp(sp.waveset[-1])
def test_write_stringio(tmpdir, format):
s = StringIO()
data = np.zeros((16, 16))
f = FITSFigure(data)
f.show_grayscale()
try:
f.save(s, format=format)
except TypeError:
pytest.xfail()
finally:
f.close()
try:
s.seek(0)
except ValueError:
if format == 'svg' and sys.version_info[:2] >= (3, 3):
pytest.xfail()
else:
raise
if format is None:
assert is_format(s, 'png')
else:
assert is_format(s, format)
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)
def test_arithmetic_ops_optional_kwargs(op2):
if not MIN_VERSIONS['NUMPY_1_10'] and isinstance(op2, np.ma.MaskedArray):
pytest.xfail("masked arrays didn't respect numpy priority yet...")
ndd = create_ndd()
# Let us test the context manager ... to change the defaults.
with ContextArithmeticDefaults() as d:
d['handle_mask'] = None
d['propagate_uncertainties'] = None
opkwargs = {'handle_mask': None, 'propagate_uncertainties': None}
compare_ndd_identical(ndd.add(op2, **opkwargs), ndd + op2)
compare_ndd_identical(ndd.subtract(op2, **opkwargs), ndd - op2)
compare_ndd_identical(ndd.multiply(op2, **opkwargs), ndd * op2)
compare_ndd_identical(ndd.divide(op2, **opkwargs), ndd / op2)
compare_ndd_identical(ndd.power(op2, **opkwargs), ndd ** op2)
# and reverse
compare_ndd_identical(ndd.add(op2, ndd, **opkwargs), op2 + ndd)
compare_ndd_identical(ndd.subtract(op2, ndd, **opkwargs), op2 - ndd)
compare_ndd_identical(ndd.multiply(op2, ndd, **opkwargs), op2 * ndd)
compare_ndd_identical(ndd.divide(op2, ndd, **opkwargs), op2 / ndd)
compare_ndd_identical(ndd.power(op2, ndd, **opkwargs), op2 ** ndd)
def test_castro_test_spectra_yaml(yamlfile):
# There is a bug in numpy that won't let it read back the yaml file we are using for
# this test in python 3.
# Catch this for now
try:
c = castro.CastroData.create_from_yamlfile(yamlfile)
except Exception:
pytest.xfail("Known issue with numpy/pyyaml")
test_dict = c.test_spectra()
assert_allclose(test_dict['PowerLaw']['TS'][0], 0.0, atol=0.01)
assert_allclose(test_dict['LogParabola']['TS'][0], 0.01304611, atol=0.01)
assert_allclose(test_dict['PLExpCutoff']['TS'][0], 0.33051415, atol=0.01)
assert_allclose(test_dict['PowerLaw']['Result'],
np.array([0.0, -3.44375000e+00]),
atol=0.01)
assert_allclose(test_dict['LogParabola']['Result'],
np.array([0.0, -2.70092870e+00, 1.73633042e-03]),
atol=0.01)
assert_allclose(test_dict['PLExpCutoff']['Result'],
np.array([0.0, -1.00927917e+00, 7.18812858e+02]),
atol=0.01)
def test_pix_area(region):
try:
area = region.area
assert not isinstance(area, u.Quantity)
except NotImplementedError:
pytest.xfail()
def test_pix_to_sky(region, mode):
try:
sky_region = region.to_sky(COMMON_WCS, mode=mode)
assert isinstance(sky_region, SkyRegion)
except NotImplementedError:
pytest.xfail()
def test_sky_to_pix(region, mode):
try:
pix_region = region.to_pixel(mode=mode, wcs=COMMON_WCS)
assert isinstance(pix_region, PixelRegion)
except NotImplementedError:
pytest.xfail()
def _compare_xid_data(xid ,data):
if six.PY3:
pytest.xfail('xid/data comparison fails in PY3 because the instrument column is bytes in xid and str in data')
else:
return all(xid == data)
def test_pix_to_sky(region, mode):
try:
sky_region = region.to_sky(COMMON_WCS, mode=mode)
assert isinstance(sky_region, SkyRegion)
except NotImplementedError:
pytest.xfail()
def test_pix_area(region):
try:
area = region.area
assert not isinstance(area, u.Quantity)
except NotImplementedError:
pytest.xfail()
def test_pix_in(region):
try:
PixCoord(1, 1) in region
except NotImplementedError:
pytest.xfail()
def test_sky_to_pix(region, mode):
try:
pix_region = region.to_pixel(mode=mode, wcs=COMMON_WCS)
assert isinstance(pix_region, PixelRegion)
except NotImplementedError:
pytest.xfail()
def test_sky_in(region):
try:
ICRS(1 * u.deg, 1 * u.deg) in region
except NotImplementedError:
pytest.xfail()
def test_pix_in(region):
try:
PixCoord(1, 1) in region
except NotImplementedError:
pytest.xfail()
def _url_tester(dr):
if dr < 11:
pytest.xfail('DR<12 not yet supported')
assert sdss.core.SDSS._last_url == 'http://skyserver.sdss.org/dr' + str(dr) + '/en/tools/search/sql.asp'
if dr == 12:
assert sdss.core.SDSS._last_url == 'http://skyserver.sdss.org/dr12/en/tools/search/x_sql.aspx'
def test_isfile(self):
if self.vegafile.startswith('ftp'):
# This is the case on Travis CI
pytest.xfail('Cannot test this over FTP')
else:
assert os.path.isfile(self.vegafile)
def test_pix_to_mask(region, mode):
try:
mask = region.to_mask(mode=mode)
assert isinstance(mask, Mask)
except NotImplementedError:
pytest.xfail()
def test_pix_area(region):
try:
area = region.area
assert not isinstance(area, u.Quantity)
except AttributeError:
pytest.xfail()
def test_sky_in(region):
try:
ICRS(1 * u.deg, 1 * u.deg) in region
except NotImplementedError:
pytest.xfail()
