def test_redshift(self):
"""Test SourceSpectrum apply_redshift() method."""
# Zero redshift should return the same spectrum.
sp_z0 = self.sp.apply_redshift(0)
np.testing.assert_array_equal(sp_z0.wave.value, self.sp.wave.value)
np.testing.assert_array_equal(sp_z0.flux.value, self.sp.flux.value)
assert sp_z0.wave.unit == self.sp.wave.unit
assert sp_z0.flux.unit == self.sp.flux.unit
assert sp_z0.metadata['expr'] != self.sp.metadata['expr']
assert sp_z0.metadata['FILENAME'] == self.sp.metadata['FILENAME']
# Non-zero redshift (length)
sp_zlen = sp_z0.apply_redshift(1.65)
np.testing.assert_array_equal(
sp_zlen.wave.value, sp_z0.wave.value * 2.65)
np.testing.assert_array_equal(sp_zlen.flux.value, sp_z0.flux.value)
# Non-zero redshift (frequency).
# Should give same result as length after conversion.
sp_z0.convert_wave(u.Hz)
sp_zfrq = sp_z0.apply_redshift(1.65)
np.testing.assert_array_equal(sp_zfrq.flux.value, sp_z0.flux.value)
sp_zfrq.convert_wave(sp_zlen.wave.unit)
np.testing.assert_allclose(
sp_zfrq.wave.value, sp_zlen.wave.value, rtol=1e-6)
assert sp_zfrq.metadata['expr'] == sp_zlen.metadata['expr']
# Exceptions
with pytest.raises(exceptions.SynphotError):
sp_zlen = sp_z0.apply_redshift([1, 2, 3])
with pytest.raises(exceptions.SynphotError):
sp_zlen = sp_z0.apply_redshift(u.Quantity(2))
def test_load_bad(tmpdir):
meta = dict(group_name='g', band_name='b')
# Missing wavelength column.
table = astropy.table.QTable(meta=meta)
table['response'] = [1, 1]
name = str(tmpdir.join('bad.ecsv'))
table.write(name, format='ascii.ecsv', overwrite=True)
with pytest.raises(RuntimeError):
load_filter(name)
# Missing response column.
table = astropy.table.QTable(meta=meta)
table['wavelength'] = [1, 2] * u.Angstrom
name = str(tmpdir.join('bad.ecsv'))
table.write(name, format='ascii.ecsv', overwrite=True)
with pytest.raises(RuntimeError):
load_filter(name)
# Missing wavelength units.
table = astropy.table.QTable(meta=meta)
table['wavelength'] = [1, 2]
table['response'] = [1, 1]
name = str(tmpdir.join('bad.ecsv'))
table.write(name, format='ascii.ecsv', overwrite=True)
with pytest.raises(RuntimeError):
load_filter(name)
# Unexpected response units.
table = astropy.table.QTable(meta=meta)
table['wavelength'] = [1, 2] * u.Angstrom
table['response'] = [1, 1] * u.erg
name = str(tmpdir.join('bad.ecsv'))
table.write(name, format='ascii.ecsv', overwrite=True)
with pytest.raises(RuntimeError):
load_filter(name)
def test_payload_invalid_item2(self):
with pytest.raises(TypeError):
self.payload['l']
payload = self.Payload(self.payload.words.copy(), bps=8,
sample_shape=(2,), complex_data=False)
with pytest.raises(TypeError):
payload['l'] = 1
def test_set_We(particle_dists):
"""
test sync calculation
"""
from ..models import Synchrotron, PionDecay
ECPL, PL, BPL = particle_dists
sy = Synchrotron(ECPL, B=1 * u.G, **electron_properties)
pp = PionDecay(ECPL)
W = 1e49 * u.erg
Eemax = 100 * u.TeV
for Eemin in [1 * u.GeV, 10 * u.GeV, None]:
for Eemax in [100 * u.TeV, None]:
sy.set_We(W, Eemin, Eemax)
assert_allclose(W, sy.compute_We(Eemin, Eemax))
sy.set_We(W, Eemin, Eemax, amplitude_name='amplitude')
assert_allclose(W, sy.compute_We(Eemin, Eemax))
pp.set_Wp(W, Eemin, Eemax)
assert_allclose(W, pp.compute_Wp(Eemin, Eemax))
pp.set_Wp(W, Eemin, Eemax, amplitude_name='amplitude')
assert_allclose(W, pp.compute_Wp(Eemin, Eemax))
with pytest.raises(AttributeError):
sy.set_We(W, amplitude_name='norm')
with pytest.raises(AttributeError):
pp.set_Wp(W, amplitude_name='norm')
def test_load_filter():
load_filter('sdss2010-r', load_from_cache=False, verbose=True)
load_filter('sdss2010-r', load_from_cache=True, verbose=True)
with pytest.raises(ValueError):
load_filter('none')
with pytest.raises(ValueError):
load_filter('none.dat')
def test_create_deviation(ccd_data, u_image, u_gain, u_readnoise,
expect_succes):
ccd_data.unit = u_image
if u_gain:
gain = 2.0 * u_gain
else:
gain = None
readnoise = 5 * u_readnoise
if expect_succes:
ccd_var = create_deviation(ccd_data, gain=gain, readnoise=readnoise)
assert ccd_var.uncertainty.array.shape == (10, 10)
assert ccd_var.uncertainty.array.size == 100
assert ccd_var.uncertainty.array.dtype == np.dtype(float)
if gain:
expected_var = np.sqrt(2 * ccd_data.data + 5 ** 2) / 2
else:
expected_var = np.sqrt(ccd_data.data + 5 ** 2)
np.testing.assert_array_equal(ccd_var.uncertainty.array,
expected_var)
assert ccd_var.unit == ccd_data.unit
# uncertainty should *not* have any units -- does it?
with pytest.raises(AttributeError):
ccd_var.uncertainty.array.unit
else:
with pytest.raises(u.UnitsError):
ccd_var = create_deviation(ccd_data, gain=gain, readnoise=readnoise)
def test_large_scale_density_spherical_annulus_exception_handling():
"""
"""
npts1, npts2 = 100, 200
sample = generate_locus_of_3d_points(npts1, xc=0.1, yc=0.1, zc=0.1, seed=fixed_seed)
tracers = generate_locus_of_3d_points(npts2, xc=0.15, yc=0.1, zc=0.1, seed=fixed_seed)
inner_radius, outer_radius = 0.1, 0.2
with pytest.raises(HalotoolsError) as err:
result = large_scale_density_spherical_annulus(
sample, tracers, inner_radius, outer_radius)
substr = "If period is None, you must pass in ``sample_volume``."
assert substr in err.value.args[0]
with pytest.raises(HalotoolsError) as err:
result = large_scale_density_spherical_annulus(
sample, tracers, inner_radius, outer_radius, period=[1, 1])
substr = "Input ``period`` must either be a float or length-3 sequence"
assert substr in err.value.args[0]
with pytest.raises(HalotoolsError) as err:
result = large_scale_density_spherical_annulus(
sample, tracers, inner_radius, outer_radius, period=1, sample_volume=0.4)
substr = "If period is not None, do not pass in sample_volume"
assert substr in err.value.args[0]
with pytest.raises(HalotoolsError) as err:
result = large_scale_density_spherical_annulus(
sample, tracers, 0.5, outer_radius, period=1, sample_volume=0.4)
substr = "Input ``outer_radius`` must be larger than input ``inner_radius``"
assert substr in err.value.args[0]
def test_add_ptclcat_to_cache1(self):
""" Verify the overwrite requirement is enforced
"""
ptclcat = UserSuppliedPtclCatalog(Lbox=200,
particle_mass=100, redshift=self.redshift,
**self.good_ptclcat_args)
basename = 'abc'
fname = os.path.join(self.dummy_cache_baseloc, basename)
_t = Table({'x': [0]})
_t.write(fname, format='ascii')
assert os.path.isfile(fname)
dummy_string = ' '
with pytest.raises(HalotoolsError) as err:
ptclcat.add_ptclcat_to_cache(
fname, dummy_string, dummy_string, dummy_string)
substr = "Either choose a different fname or set ``overwrite`` to True"
assert substr in err.value.args[0]
with pytest.raises(HalotoolsError) as err:
ptclcat.add_ptclcat_to_cache(
fname, dummy_string, dummy_string, dummy_string,
overwrite=True)
assert substr not in err.value.args[0]
def test_payload(self):
with open(SAMPLE_FILE, 'rb') as fh:
fh.seek(16) # skip header
payload = mark5b.Mark5BPayload.fromfile(fh, nchan=8, bps=2)
assert payload._size == 10000
assert payload.size == 10000
assert payload.shape == (5000, 8)
assert payload.dtype == np.float32
assert np.all(payload[:3].astype(int) ==
np.array([[-3, -1, +1, -1, +3, -3, -3, +3],
[-3, +3, -1, +3, -1, -1, -1, +1],
[+3, -1, +3, +3, +1, -1, +3, -1]]))
with io.BytesIO() as s:
payload.tofile(s)
s.seek(0)
payload2 = mark5b.Mark5BPayload.fromfile(s, payload.nchan,
payload.bps)
assert payload2 == payload
with pytest.raises(EOFError):
# Too few bytes.
s.seek(100)
mark5b.Mark5BPayload.fromfile(s, payload.nchan, payload.bps)
payload3 = mark5b.Mark5BPayload.fromdata(payload.data, bps=payload.bps)
assert payload3 == payload
with pytest.raises(ValueError):
mark5b.Mark5BPayload.fromdata(np.zeros((5000, 8), np.complex64),
bps=2)
def test_behroozi10_redshift_safety():
"""
"""
model = Behroozi10SmHm()
result0 = model.mean_log_halo_mass(11)
result1 = model.mean_log_halo_mass(11, redshift=4)
result2 = model.mean_log_halo_mass(11, redshift=sim_defaults.default_redshift)
assert result0 == result2
assert result0 != result1
result0 = model.mean_stellar_mass(prim_haloprop=1e12)
result1 = model.mean_stellar_mass(prim_haloprop=1e12, redshift=4)
result2 = model.mean_stellar_mass(prim_haloprop=1e12, redshift=sim_defaults.default_redshift)
assert result0 == result2
assert result0 != result1
model = Behroozi10SmHm(redshift=sim_defaults.default_redshift)
result0 = model.mean_log_halo_mass(11)
with pytest.raises(HalotoolsError):
result1 = model.mean_log_halo_mass(11, redshift=4)
result2 = model.mean_log_halo_mass(11, redshift=model.redshift)
assert result0 == result2
result0 = model.mean_stellar_mass(prim_haloprop=1e12)
with pytest.raises(HalotoolsError):
result1 = model.mean_stellar_mass(prim_haloprop=1e12, redshift=4)
result2 = model.mean_stellar_mass(prim_haloprop=1e12, redshift=model.redshift)
assert result0 == result2
def test_should_not_create_dir():
""" Require that attempting to create a cache subdirectory
for an unsupported simulation and/or halo-finder raises an IOError.
"""
with pytest.raises(IOError) as exc:
parent_dir = cache_config.get_catalogs_dir('raw_halos')
nonsense_dirname = 'JoseCanseco'
func = cache_config.cache_subdir_for_simulation
s1 = func(parent_dir, nonsense_dirname)
exception_string = ("It is not permissible to create a subdirectory of " +
"Halotools cache \nfor simulations which have no class defined in " +
"the halotools/sim_manager/supported_sims module. \n")
assert exc.value.args[0] == exception_string
with pytest.raises(IOError) as exc:
parent_dir = cache_config.get_catalogs_dir('raw_halos')
nonsense_dirname = 'JoseCanseco'
func = cache_config.cache_subdir_for_halo_finder
s1 = func(parent_dir, 'bolshoi', nonsense_dirname)
exception_string = ("It is not permissible to create a subdirectory of "
"Halotools cache \nfor a combination of "
"simulation + halo-finder which has no corresponding class defined in "
"the halotools/sim_manager/supported_sims module. \n")
assert exc.value.args[0] == exception_string
def test_add_entry_to_cache_log(self):
cache = HaloTableCache(read_log_from_standard_loc=False)
assert len(cache.log) == 0
with pytest.raises(TypeError) as err:
cache.add_entry_to_cache_log('abc', update_ascii=False)
substr = "You can only add instances of HaloTableCacheLogEntry to the cache log"
assert substr in err.value.args[0]
cache.add_entry_to_cache_log(self.good_log_entry, update_ascii=False)
assert len(cache.log) == 1
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
cache.add_entry_to_cache_log(self.good_log_entry, update_ascii=False)
substr = "cache log already contains the entry"
assert substr in str(w[-1].message)
assert len(cache.log) == 1
cache.add_entry_to_cache_log(self.good_log_entry2, update_ascii=False)
assert len(cache.log) == 2
with pytest.raises(InvalidCacheLogEntry) as err:
cache.add_entry_to_cache_log(self.bad_log_entry, update_ascii=False)
substr = "The input filename does not exist."
assert substr in err.value.args[0]
def test_payload(self):
with open(SAMPLE_FILE, 'rb') as fh:
fh.seek(0xa88)
header = mark4.Mark4Header.fromfile(fh, ntrack=64, decade=2010)
payload = mark4.Mark4Payload.fromfile(fh, header)
assert payload.size == (20000 - 160) * 64 // 8
assert payload.shape == ((20000 - 160) * 4, 8)
assert payload.dtype == np.float32
assert np.all(payload.data[0].astype(int) ==
np.array([-1, +1, +1, -3, -3, -3, +1, -1]))
assert np.all(payload.data[1].astype(int) ==
np.array([+1, +1, -3, +1, +1, -3, -1, -1]))
with io.BytesIO() as s:
payload.tofile(s)
s.seek(0)
payload2 = mark4.Mark4Payload.fromfile(s, header)
assert payload2 == payload
with pytest.raises(EOFError):
# Too few bytes.
s.seek(100)
mark4.Mark4Payload.fromfile(s, header)
payload3 = mark4.Mark4Payload.fromdata(payload.data, header)
assert payload3 == payload
with pytest.raises(ValueError):
# Wrong number of channels.
mark4.Mark4Payload.fromdata(np.empty((payload.shape[0], 2)),
header)
with pytest.raises(ValueError):
# Too few data.
mark4.Mark4Payload.fromdata(payload.data[:100], header)
def test_run_advanced(self, tmpdir):
temp_path = os.path.join(str(tmpdir), "temp")
log_path = os.path.join(str(tmpdir), "log")
paths = {"temp": temp_path, "log": log_path}
pipe = pipeline.Pipeline(paths=paths, create_paths=True)
pipe.add_step(test_func1, ["func1"], var1=3, var2=4)
pipe.add_step(test_func2, ["func2"], var1=25, var2=10)
pipe.add_step(test_func2, ["func2"], var1=1, var2=0)
pipe.add_step(test_func3, var1=1, var2=0)
with pytest.raises(pipeline.PipelineError):
pipe.run()
pipe = dill.load(open(os.path.join(paths["log"], "pipeline.p"), "rb"))
assert pipe.run_step_idx == 2
assert pipe.steps[0].results == {"next_id": 4, "status": "success", "step_id": 0, "sum": 7}
with pytest.raises(ZeroDivisionError):
for step in pipe.steps:
step.results = None
pipe.run(resume=True, ignore_errors=True)
new_pipe = dill.load(open(os.path.join(paths["log"], "pipeline.p"), "rb"))
result = new_pipe.run(start_idx=1, ignore_errors=True, ignore_exceptions=True)
assert result["status"] == "success"
assert new_pipe.steps[0].results == None
assert new_pipe.steps[1].results == {"diff": 2.5, "status": "success"}
assert new_pipe.steps[2].results == {"error": "Division by 0", "status": "error"}
assert new_pipe.steps[3].results["status"] == "error"
def test_DataStore_filenames(data_manager):
"""Check if filenames are constructed correctly"""
data_store = data_manager['hess-hap-hd-prod01-std_zeta_fullEnclosure']
filename = data_store.filename(obs_id=23037, filetype='aeff')
assert filename == '/Users/deil/work/_Data/hess/fits/hap-hd/fits_prod01/std_zeta_fullEnclosure/run023000-023199/run023037/hess_aeff_023037.fits.gz'
filename = data_store.filename(obs_id=23037, filetype='aeff', abspath=False)
assert filename == 'run023000-023199/run023037/hess_aeff_023037.fits.gz'
with pytest.raises(IndexError) as exc:
data_store.filename(obs_id=89565, filetype='aeff')
msg = 'File not in table: OBS_ID = 89565, TYPE = aeff'
assert exc.value.args[0] == msg
with pytest.raises(ValueError):
data_store.filename(obs_id=89565, filetype='effective area')
data_store = data_manager['hess-paris-prod02']
filename = data_store.filename(obs_id=23037, filetype='aeff')
assert filename == '/Users/deil/work/_Data/hess/fits/parisanalysis/fits_prod02/pa/Model_Deconvoluted_Prod26/Mpp_Std/run023000-023199/run023037/hess_aeff_2d_023037.fits.gz'
filename = data_store.filename(obs_id=23037, filetype='aeff', abspath=False)
assert filename == 'run023000-023199/run023037/hess_aeff_2d_023037.fits.gz'
def test_seek(self):
with sf.open(self.files) as fh:
fh.seek(self.offsets[1])
assert fh.file_nr == 1
assert fh.tell() == self.offsets[1]
fh.seek(self.offsets[1] + 1)
assert fh.file_nr == 1
fh.seek(self.offsets[2])
assert fh.file_nr == 2
fh.seek(self.offsets[3])
assert fh.tell() == self.size
assert fh.file_nr == 2
fh.seek(self.size)
assert fh.file_nr == 2
fh.seek(10, 2)
assert fh.file_nr == 2
assert fh.tell() == self.size + 10
with pytest.raises(OSError):
fh.seek(-3)
fh.seek(-3, 2)
assert fh.tell() == self.size - 3
assert fh.file_nr == 2
fh.seek(-5, 1)
assert fh.tell() == self.size - 3 - 5
assert fh.file_nr == 1
with pytest.raises(ValueError):
fh.seek(-5, -1)
with pytest.raises(ValueError):
fh.seek(-5, 3)
# cannot seek closed file
with pytest.raises(ValueError):
fh.seek(10)
def test_parse_output_projection(tmpdir):
header = fits.Header.fromtextfile(get_pkg_data_filename('data/gc_ga.hdr'))
wcs = WCS(header)
# As header
with pytest.raises(ValueError) as exc:
parse_output_projection(header)
assert exc.value.args[0] == "Need to specify shape since output header does not contain complete shape information"
parse_output_projection(header, shape_out=(200, 200))
header['NAXIS'] = 2
header['NAXIS1'] = 200
header['NAXIS2'] = 300
parse_output_projection(header)
# As WCS
with pytest.raises(ValueError) as exc:
parse_output_projection(wcs)
assert exc.value.args[0] == "Need to specify shape when specifying output_projection as WCS object"
parse_output_projection(wcs, shape_out=(200, 200))
def test_write(self, tmpdir):
self._setup(tmpdir)
with sf.open(self.files, 'wb', file_size=10) as fh:
fh.write(self.data[:5])
assert fh.tell() == 5
assert fh.file_nr == 0
assert self.files_exist() == [True, False, False]
fh.write(self.data[5:20])
assert fh.tell() == 20
assert fh.file_nr == 1
assert self.files_exist() == [True, True, False]
fh.write(self.data[20:])
assert fh.tell() == len(self.data)
assert fh.file_nr == 2
# Cannot write to closed file.
with pytest.raises(ValueError):
fh.write(b' ')
assert self.files_exist() == [True, True, True]
with sf.open(self.files, 'rb') as fh:
assert fh.read() == self.data
with pytest.raises(OSError):
with sf.open(self.files, 'wb', file_size=10) as fh:
fh.write(b' ' * (len(self.files) * 10 + 1))
def test_memmap(self, tmpdir):
self._setup(tmpdir)
data = self.uint8_data
with sf.open(self.files, 'w+b', file_size=10) as fh:
mm = fh.memmap(shape=(5,))
assert fh.tell() == 5
mm[:] = data[:5]
mm2 = fh.memmap(offset=5, shape=(5,))
mm2[:4] = data[5:9]
mm2[-1] = data[-1]
mm3 = fh.memmap(shape=(5,))
mm3[:] = data[10:15]
with pytest.raises(ValueError):
fh.memmap(shape=(6,)) # beyond file.
with pytest.raises(ValueError):
fh.memmap() # Need to pass in shape
with pytest.raises(ValueError):
fh.memmap(offset=4) # Cannot seek
mm4 = fh.memmap(dtype=np.uint16, shape=(2,))
mm4[:] = data[15:19].view(np.uint16)
assert self.files_exist() == [True, True, False]
with sf.open(self.files[:2], 'rb') as fh:
check = fh.read()
assert len(check) == 19
assert check[:9] == self.data[:9]
assert check[9] == self.data[-1]
assert check[10:] == self.data[10:19]
def test_build_data_table():
ene = np.logspace(-2,2,20) * u.TeV
flux = (ene/(1*u.TeV))**-2 * u.Unit('1/(cm2 s TeV)')
flux_error_hi = 0.2 * flux
flux_error_lo = 0.1 * flux
ul = np.zeros(len(ene))
ul[0] = 1
dene = generate_energy_edges(ene)
table = build_data_table(ene, flux, flux_error_hi=flux_error_hi, flux_error_lo=flux_error_lo, ul=ul)
table = build_data_table(ene, flux, flux_error_hi=flux_error_hi, flux_error_lo=flux_error_lo, ul=ul, cl=0.99)
table = build_data_table(ene, flux, flux_error=flux_error_hi, energy_width=dene[0])
table = build_data_table(ene, flux, flux_error=flux_error_hi, energy_lo=(ene-dene[0]), energy_hi=(ene+dene[1]))
# no flux_error
with pytest.raises(TypeError):
table = build_data_table(ene, flux)
# errors in energy physical type validation
with pytest.raises(TypeError):
table = build_data_table(ene.value, flux, flux_error=flux_error_hi)
with pytest.raises(TypeError):
table = build_data_table(ene.value*u.Unit('erg/(cm2 s)'), flux, flux_error=flux_error_hi)
def test_memmap(self):
with sf.open(self.files) as fh:
mm = fh.memmap(offset=0, shape=(5,))
assert fh.tell() == 5
assert (mm == self.uint8_data[:5]).all()
mm = fh.memmap(shape=(5,))
assert fh.tell() == 10
assert (mm == self.uint8_data[5:10]).all()
with pytest.raises(ValueError):
fh.memmap(offset=7, shape=(5,))
offset = self.offsets[1]
fh.seek(offset)
mm = fh.memmap(shape=5)
assert (mm == self.uint8_data[offset:offset+5]).all()
fh.seek(-2, 2)
mm = fh.memmap()
assert (mm == self.uint8_data[-2:]).all()
fh.seek(-4, 2)
mm = fh.memmap(mode='r', dtype=np.uint16)
assert (mm == self.uint8_data[-4:].view(np.uint16)).all()
fh.seek(-3, 2)
with pytest.raises(ValueError):
fh.memmap(dtype=np.uint16)
with pytest.raises(ValueError): # file closed.
fh.memmap(offset=0, shape=(5,))
def test_celestial_mismatch_3d():
"""
Make sure an error is raised if the input image has celestial WCS
information and the output does not (and vice-versa). This example will
use the _reproject_full route.
"""
hdu_in = fits.open(os.path.join(DATA, 'equatorial_3d.fits'))[0]
header_out = hdu_in.header.copy()
header_out['CTYPE1'] = 'APPLES'
header_out['CTYPE2'] = 'ORANGES'
header_out['CTYPE3'] = 'BANANAS'
data = hdu_in.data
wcs1 = WCS(hdu_in.header)
wcs2 = WCS(header_out)
with pytest.raises(ValueError) as exc:
array_out, footprint_out = reproject_interp((data, wcs1), wcs2, shape_out=(1, 2, 3))
assert exc.value.args[0] == "Input WCS has celestial components but output WCS does not"
with pytest.raises(ValueError) as exc:
array_out, footprint_out = reproject_interp((data, wcs2), wcs1, shape_out=(1, 2, 3))
assert exc.value.args[0] == "Output WCS has celestial components but input WCS does not"
def test_time_inputs():
"""
Test validation and conversion of inputs for equinox and obstime attributes.
"""
from astropy.time import Time
from astropy.coordinates.builtin_frames import FK4
c = FK4(1 * u.deg, 2 * u.deg, equinox='J2001.5', obstime='2000-01-01 12:00:00')
assert c.equinox == Time('J2001.5')
assert c.obstime == Time('2000-01-01 12:00:00')
with pytest.raises(ValueError) as err:
c = FK4(1 * u.deg, 2 * u.deg, equinox=1.5)
assert 'Invalid time input' in str(err)
with pytest.raises(ValueError) as err:
c = FK4(1 * u.deg, 2 * u.deg, obstime='hello')
assert 'Invalid time input' in str(err)
# A vector time should work if the shapes match, but we don't automatically
# broadcast the basic data (just like time).
FK4([1, 2] * u.deg, [2, 3] * u.deg, obstime=['J2000', 'J2001'])
with pytest.raises(ValueError) as err:
FK4(1 * u.deg, 2 * u.deg, obstime=['J2000', 'J2001'])
assert 'shape' in str(err)
def test_different_wcs_types():
inp_cube = np.arange(3, dtype='float').repeat(4*5).reshape(3,4,5)
header_in = fits.Header.fromtextfile(get_pkg_data_filename('../../tests/data/cube.hdr'))
header_out = header_in.copy()
header_out['CTYPE3'] = 'VRAD'
header_out['CUNIT3'] = 'm/s'
header_in['CTYPE3'] = 'VELO'
header_in['CUNIT3'] = 'm/s'
wcs_in = WCS(header_in)
wcs_out = WCS(header_out)
with pytest.raises(ValueError) as ex:
out_cube, out_cube_valid = _reproject_celestial(inp_cube, wcs_in, wcs_out, (2, 4, 5))
assert str(ex.value) == ("The input and output spectral coordinate types "
"are not equivalent.")
header_in['CTYPE3'] = 'FREQ'
header_in['CUNIT3'] = 'Hz'
wcs_in = WCS(header_in)
with pytest.raises(ValueError) as ex:
out_cube, out_cube_valid = _reproject_celestial(inp_cube, wcs_in, wcs_out, (2, 4, 5))
assert str(ex.value) == ("The input and output WCS are not equivalent")
def test_invalid_source():
buff = io.BytesIO()
ff = asdf.AsdfFile(_get_small_tree())
ff.write_to(buff)
buff.seek(0)
ff2 = asdf.AsdfFile.read(buff)
ff2.blocks.get_block(0)
with pytest.raises(ValueError):
ff2.blocks.get_block(2)
with pytest.raises(IOError):
ff2.blocks.get_block("http://127.0.0.1/")
with pytest.raises(TypeError):
ff2.blocks.get_block(42.0)
with pytest.raises(ValueError):
ff2.blocks.get_source(42.0)
block = ff2.blocks.get_block(0)
assert ff2.blocks.get_source(block) == 0
def test_query_region_radius_error(patch_post, coordinates, radius, equinox, epoch):
with pytest.raises(u.UnitsError):
result1 = simbad.core.Simbad.query_region(coordinates, radius=radius,
equinox=equinox, epoch=epoch)
with pytest.raises(u.UnitsError):
result2 = simbad.core.Simbad().query_region(coordinates, radius=radius,
equinox=equinox, epoch=epoch)
def test_initializing_from_table_file_that_does_not_exist(self,
triage_setup,
tmpdir):
log = tmpdir.join('tmp.log')
self._setup_logger(log.strpath)
# Do we get a warning if we try reading a file that doesn't exist,
# but where we can initialize from a directory?
ic = image_collection.ImageFileCollection(
location=triage_setup.test_dir,
info_file='iufadsdhfasdifre')
with open(log.strpath) as f:
warnings = f.readlines()
assert (len(warnings) == 1)
is_in = ['unable to open table file' in w for w in warnings]
assert all(is_in)
# Do we raise an error if the table name is bad AND the location
# is None?
with pytest.raises(IOError):
ic = image_collection.ImageFileCollection(location=None,
info_file='iufadsdhfasdifre')
# Do we raise an error if the table name is bad AND
# the location is given but is bad?
with pytest.raises(OSError):
ic = image_collection.ImageFileCollection(location='dasifjoaurun',
info_file='iufadsdhfasdifre')
def test_equivalent_frames():
from astropy.coordinates import SkyCoord
from astropy.coordinates.builtin_frames import ICRS, FK4, FK5, AltAz
i = ICRS()
i2 = ICRS(1*u.deg, 2*u.deg)
assert i.is_equivalent_frame(i)
assert i.is_equivalent_frame(i2)
with pytest.raises(TypeError):
assert i.is_equivalent_frame(10)
with pytest.raises(TypeError):
assert i2.is_equivalent_frame(SkyCoord(i2))
f0 = FK5() # this J2000 is TT
f1 = FK5(equinox='J2000')
f2 = FK5(1*u.deg, 2*u.deg, equinox='J2000')
f3 = FK5(equinox='J2010')
f4 = FK4(equinox='J2010')
assert f1.is_equivalent_frame(f1)
assert not i.is_equivalent_frame(f1)
assert f0.is_equivalent_frame(f1)
assert f1.is_equivalent_frame(f2)
assert not f1.is_equivalent_frame(f3)
assert not f3.is_equivalent_frame(f4)
aa1 = AltAz()
aa2 = AltAz(obstime='J2010')
assert aa2.is_equivalent_frame(aa2)
assert not aa1.is_equivalent_frame(i)
assert not aa1.is_equivalent_frame(aa2)
def test_ic_seed_fluxes(particle_dists):
"""
test per seed flux computation
"""
from ..models import InverseCompton
_, PL, _ = particle_dists
ic = InverseCompton(
PL,
seed_photon_fields=['CMB',
['test', 5000 * u.K, 0],
['test2', 5000 * u.K, 10 * u.eV / u.cm**3],
['test3', 5000 * u.K, 10 * u.eV / u.cm**3, 90 *
u.deg],],)
ene = np.logspace(-3, 0, 5) * u.TeV
for idx, name in enumerate(['CMB', 'test', 'test2', 'test3',]):
icname = ic.sed(ene, seed=name)
icnumber = ic.sed(ene, seed=idx)
assert_allclose(icname, icnumber)
with pytest.raises(ValueError):
_ = ic.sed(ene, seed='FIR')
with pytest.raises(ValueError):
_ = ic.sed(ene, seed=10)
def test_spectral_mismatch_3d():
"""
Make sure an error is raised if there are mismatches between the presence
or type of spectral axis.
"""
hdu_in = fits.open(os.path.join(DATA, 'equatorial_3d.fits'))[0]
header_out = hdu_in.header.copy()
header_out['CTYPE3'] = 'FREQ'
header_out['CUNIT3'] = 'Hz'
data = hdu_in.data
wcs1 = WCS(hdu_in.header)
wcs2 = WCS(header_out)
with pytest.raises(ValueError) as exc:
array_out, footprint_out = reproject_interp((data, wcs1), wcs2, shape_out=(1, 2, 3))
assert exc.value.args[0] == "The input (VOPT) and output (FREQ) spectral coordinate types are not equivalent."
header_out['CTYPE3'] = 'BANANAS'
wcs2 = WCS(header_out)
with pytest.raises(ValueError) as exc:
array_out, footprint_out = reproject_interp((data, wcs1), wcs2, shape_out=(1, 2, 3))
assert exc.value.args[0] == "Input WCS has a spectral component but output WCS does not"
with pytest.raises(ValueError) as exc:
array_out, footprint_out = reproject_interp((data, wcs2), wcs1, shape_out=(1, 2, 3))
assert exc.value.args[0] == "Output WCS has a spectral component but input WCS does not"
def test_representation():
"""
Test the getter and setter properties for `representation`
"""
from astropy.coordinates.builtin_frames import ICRS
# Create the frame object.
icrs = ICRS(ra=1*u.deg, dec=1*u.deg)
data = icrs.data
# Create some representation objects.
icrs_cart = icrs.cartesian
icrs_spher = icrs.spherical
# Testing when `_representation` set to `CartesianRepresentation`.
icrs.representation_type = r.CartesianRepresentation
assert icrs.representation_type == r.CartesianRepresentation
assert icrs_cart.x == icrs.x
assert icrs_cart.y == icrs.y
assert icrs_cart.z == icrs.z
assert icrs.data == data
# Testing that an ICRS object in CartesianRepresentation must not have spherical attributes.
for attr in ('ra', 'dec', 'distance'):
with pytest.raises(AttributeError) as err:
getattr(icrs, attr)
assert 'object has no attribute' in str(err.value)
# Testing when `_representation` set to `CylindricalRepresentation`.
icrs.representation_type = r.CylindricalRepresentation
assert icrs.representation_type == r.CylindricalRepresentation
assert icrs.data == data
# Testing setter input using text argument for spherical.
icrs.representation_type = 'spherical'
assert icrs.representation_type is r.SphericalRepresentation
assert icrs_spher.lat == icrs.dec
assert icrs_spher.lon == icrs.ra
assert icrs_spher.distance == icrs.distance
assert icrs.data == data
# Testing that an ICRS object in SphericalRepresentation must not have cartesian attributes.
for attr in ('x', 'y', 'z'):
with pytest.raises(AttributeError) as err:
getattr(icrs, attr)
assert 'object has no attribute' in str(err.value)
# Testing setter input using text argument for cylindrical.
icrs.representation_type = 'cylindrical'
assert icrs.representation_type is r.CylindricalRepresentation
assert icrs.data == data
with pytest.raises(ValueError) as err:
icrs.representation_type = 'WRONG'
assert 'but must be a BaseRepresentation class' in str(err.value)
with pytest.raises(ValueError) as err:
icrs.representation_type = ICRS
assert 'but must be a BaseRepresentation class' in str(err.value)
def test_init_with_inf_segment(self):
segment_size = np.inf
with pytest.raises(ValueError):
assert AveragedPowerspectrum(self.lc, segment_size)
def test_init_with_none_segment(self):
segment_size = None
with pytest.raises(TypeError):
assert AveragedPowerspectrum(self.lc, segment_size)
def test_init_without_segment(self):
with pytest.raises(TypeError):
assert AveragedPowerspectrum(self.lc)
def test_classical_significances_fails_in_rms(self):
ps = Powerspectrum(lc=self.lc, norm="frac")
with pytest.raises(ValueError):
ps.classical_significances()
def test_fractional_rms_fails_when_rms_not_leahy(self):
with pytest.raises(Exception):
ps = Powerspectrum(lc=self.lc, norm="rms")
rms_ps, rms_err = ps.compute_rms(min_freq=ps.freq[0],
max_freq=ps.freq[-1])
def test_EffectiveAreaTable2D_generic():
# This tests NDData subclassing. Not needed for other IRF classes
# Exercise __init__ method
energy = np.logspace(0, 1, 4) * u.TeV
offset = [0.2, 0.3] * u.deg
effective_area = np.arange(6).reshape(3, 2) * u.cm * u.cm
meta = dict(name='example')
aeff = EffectiveAreaTable2D(offset=offset,
energy=energy,
data=effective_area,
meta=meta)
assert (aeff.axes[0].data == energy).all()
assert (aeff.axes[1].data == offset).all()
assert (aeff.data == effective_area).all()
assert aeff.meta.name == 'example'
wrong_data = np.arange(8).reshape(4, 2) * u.cm * u.cm
with pytest.raises(ValueError):
aeff.data = wrong_data
aeff = EffectiveAreaTable(offset=offset,
energy=energy,
data=wrong_data)
# Test evaluate function
# Check that nodes are evaluated correctly
e_node = 1
off_node = 0
offset = aeff.offset.nodes[off_node]
energy = aeff.energy.nodes[e_node]
actual = aeff.evaluate(offset=offset, energy=energy, method='nearest')
desired = aeff.data[e_node, off_node]
assert_allclose(actual, desired)
actual = aeff.evaluate(offset=offset, energy=energy, method='linear')
desired = aeff.data[e_node, off_node]
assert_allclose(actual, desired)
# Check that values between node make sense
energy2 = aeff.energy.nodes[e_node + 1]
upper = aeff.evaluate(offset=offset, energy=energy)
lower = aeff.evaluate(offset=offset, energy=energy2)
e_val = (energy + energy2) / 2
actual = aeff.evaluate(offset=offset, energy=e_val)
assert_equal(lower > actual and actual > upper, True)
# Test return shape
# Case 0; offset = scalar, energy = scalar, done
# Case 1: offset = scalar, energy = None
offset = 0.234 * u.deg
actual = aeff.evaluate(offset=offset).shape
desired = aeff.energy.nodes.shape
assert_equal(actual, desired)
# Case 2: offset = scalar, energy = 1Darray
offset = 0.564 * u.deg
nbins = 10
energy = np.logspace(3, 4, nbins) * u.GeV
actual = aeff.evaluate(offset=offset, energy=energy).shape
desired = np.zeros(nbins).shape
assert_equal(actual, desired)
# Case 3: offset = None, energy = scalar
energy = 1.1 * u.TeV
actual = aeff.evaluate(energy=energy).shape
desired = tuple([aeff.offset.nbins])
assert_equal(actual, desired)
# Case 4: offset = 1Darray, energy = scalar
energy = 1.5 * u.TeV
nbins = 4
offset = np.linspace(0, 1, nbins) * u.deg
actual = aeff.evaluate(offset=offset, energy=energy).shape
desired = np.zeros(nbins).shape
assert_equal(actual, desired)
# case 5: offset = 1Darray, energy = 1Darray
nbinse = 5
nbinso = 3
offset = np.linspace(0.2, 0.3, nbinso) * u.deg
energy = np.logspace(0, 1, nbinse) * u.TeV
actual = aeff.evaluate(offset=offset, energy=energy).shape
desired = np.zeros([nbinse, nbinso]).shape
assert_equal(actual, desired)
# case 6: offset = 2Darray, energy = 1Darray
nbinse = 4
nx, ny = (12, 3)
offset = np.linspace(0.2, 0.3, nx * ny).reshape(nx, ny) * u.deg
energy = np.logspace(0, 1, nbinse) * u.TeV
actual = aeff.evaluate(offset=offset, energy=energy).shape
desired = np.zeros([nbinse, nx, ny]).shape
assert_equal(actual, desired)
# Misc functions
assert 'EffectiveAreaTable2D' in str(aeff)
def test_set_vector_invalid_order(attribute):
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
setattr(o, attribute, [0.3, 0.1, 0.2])
assert exc.value.args[
0] == attribute + ' should be monotonically increasing'
def test_set_vector_invalid_type2(attribute):
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
setattr(o, attribute, 0.5)
assert exc.value.args[0] == attribute + ' should be a 1-D sequence'
def test_range_nu_invalid2():
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
o.nu = [-1., 0.5, 0.8]
assert exc.value.args[0] == 'nu should be strictly positive'
def test_range_mu_invalid2():
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
o.mu = [-1., 0., 1.3]
assert exc.value.args[0] == 'mu should be in the range [-1:1]'
def test_set_vector_invalid_shape2(attribute):
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
setattr(o, attribute, np.array([[0., 1.], [0.5, 1.]]))
assert exc.value.args[0] == attribute + ' should be a 1-D sequence'
def test_range_chi_invalid1():
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
o.chi = [-1., 0.5, 0.8]
assert exc.value.args[0] == 'chi should be positive'
def test_set_array_invalid_order2(attribute):
o = OpticalProperties()
o.mu = [-0.5, 0.5]
with pytest.raises(ValueError) as exc:
setattr(o, attribute, np.ones((3, 2)))
assert exc.value.args[0] == 'nu needs to be set before ' + attribute
def test_spectra_timeout(patch_get, patch_get_readable_fileobj_slow):
with pytest.raises(TimeoutError):
sdss.SDSS.get_spectra(plate=2345, fiberID=572)
def test_range_albedo_invalid2():
o = OpticalProperties()
with pytest.raises(ValueError) as exc:
o.albedo = [0., 0.5, 1.1]
assert exc.value.args[0] == 'albedo should be in the range [0:1]'
def test_raises_correct_exception():
default_model = Zheng07Cens()
with pytest.raises(HalotoolsError) as err:
_ = default_model.mean_occupation(x=4)
substr = "You must pass either a ``table`` or ``prim_haloprop`` argument"
assert substr in err.value.args[0]
def test_images_timeout(patch_get, patch_get_readable_fileobj_slow):
with pytest.raises(TimeoutError):
sdss.SDSS.get_images(run=1904, camcol=3, field=164)
def test_simulate_with_incorrect_arguments(self):
with pytest.raises(ValueError):
self.simulator.simulate(1, 2, 3, 4)
def test_query_timeout(patch_get_slow, coord=coords):
with pytest.raises(TimeoutError):
sdss.SDSS.query_region(coords, timeout=1)
def test_open_invalid_filename(tmpdir):
fname = tmpdir.join('test.fits')
with pytest.raises(IOError):
d = Donuts(str(fname))
def test_incorrect_simulate_channel(self):
"""Test simulating a channel that already exists."""
self.simulator.simulate_channel('3.5-4.5', 2)
with pytest.raises(KeyError):
self.simulator.simulate_channel('3.5-4.5', 2)
self.simulator.delete_channel('3.5-4.5')
def test_process_radial_bins2():
input_rbins = np.arange(5)[::-1]
period = None
PBCs = False
with pytest.raises(ValueError) as err:
rbins = _process_radial_bins(input_rbins, period, PBCs)
def test_simulate_wrong_model(self):
"""
Simulate with a model that does not exist.
"""
with pytest.raises(ValueError):
self.simulator.simulate('unsupported', [0.6, 0.2, 0.6, 0.5])
def test_missing_properties(tmpdir):
d = SphericalDust()
with pytest.raises(Exception) as e:
d.write(tmpdir.join(random_id()).strpath)
assert e.value.args[
0] == "The following attributes of the optical properties have not been set: nu, chi, albedo, mu, P1, P2, P3, P4"
def test_process_radial_bins3():
input_rbins = np.linspace(0.1, 2, 5)
period = 1
PBCs = True
with pytest.raises(ValueError) as err:
rbins = _process_radial_bins(input_rbins, period, PBCs)
def test_fit_fails_when_object_is_not_posterior_or_likelihood(self):
x = np.ones(10)
y = np.ones(10)
pe = ParameterEstimation()
with pytest.raises(TypeError):
res = pe.fit(x, y)
def test_sample1_cell_size():
period, search_length, approx_cell_size = 1, 0.5, 0.1
with pytest.raises(ValueError) as err:
_ = sample1_cell_size(period, search_length, approx_cell_size)
substr = "Input ``search_length`` cannot exceed period/3"
assert substr in err.value.args[0]
def test_fit_fails_with_incorrect_number_of_parameters(self):
pe = PSDParEst(self.ps)
t0 = [1, 2]
with pytest.raises(ValueError):
res = pe.fit(self.lpost, t0)
def test_fit_fails_without_lpost_or_t0(self):
pe = ParameterEstimation()
with pytest.raises(TypeError):
res = pe.fit()