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from __future__ import print_function, absolute_import, division
import operator
import itertools
import warnings
import mmap
from distutils.version import LooseVersion
import pytest
import astropy
from astropy.io import fits
from astropy import units as u
from astropy.wcs import WCS
from astropy.wcs import _wcs
from astropy.tests.helper import assert_quantity_allclose
from astropy.extern import six
from astropy.convolution import Gaussian2DKernel, Tophat2DKernel
import numpy as np
from .. import (SpectralCube, VaryingResolutionSpectralCube, BooleanArrayMask,
FunctionMask, LazyMask, CompositeMask)
from ..spectral_cube import OneDSpectrum, Projection, VaryingResolutionOneDSpectrum
from ..np_compat import allbadtonan
from .. import spectral_axis
from .. import base_class
from .. import utils
from . import path
from .helpers import assert_allclose, assert_array_equal
# needed to test for warnings later
warnings.simplefilter('always', UserWarning)
warnings.simplefilter('error', utils.UnsupportedIterationStrategyWarning)
warnings.simplefilter('error', utils.NotImplementedWarning)
warnings.simplefilter('error', utils.WCSMismatchWarning)
try:
import joblib
JOBLIB_INSTALLED = True
except ImportError:
JOBLIB_INSTALLED = False
try:
import scipy.ndimage
SCIPYOK = True
except ImportError:
SCIPYOK = False
try:
import yt
YT_INSTALLED = True
YT_LT_301 = LooseVersion(yt.__version__) < LooseVersion('3.0.1')
except ImportError:
YT_INSTALLED = False
YT_LT_301 = False
try:
import bottleneck
BOTTLENECK_INSTALLED = True
except ImportError:
BOTTLENECK_INSTALLED = False
from radio_beam import Beam
NUMPY_LT_19 = LooseVersion(np.__version__) < LooseVersion('1.9.0')
def cube_and_raw(filename):
p = path(filename)
d = fits.getdata(p)
c = SpectralCube.read(p, format='fits', mode='readonly')
return c, d
def test_arithmetic_warning(recwarn):
cube, data = cube_and_raw('vda_Jybeam_lower.fits')
assert not cube._is_huge
# make sure the small cube raises a warning about loading into memory
cube + 5*cube.unit
w = recwarn.list[-1]
assert 'requires loading the entire cube into' in str(w.message)
def test_huge_disallowed():
cube, data = cube_and_raw('vda_Jybeam_lower.fits')
cube = SpectralCube(data=data, wcs=cube.wcs)
assert not cube._is_huge
# We need to reduce the memory threshold rather than use a large cube to
# make sure we don't use too much memory during testing.
from .. import cube_utils
OLD_MEMORY_THRESHOLD = cube_utils.MEMORY_THRESHOLD
try:
cube_utils.MEMORY_THRESHOLD = 10
assert cube._is_huge
with pytest.raises(ValueError) as exc:
cube + 5*cube.unit
assert 'entire cube into memory' in exc.value.args[0]
with pytest.raises(ValueError) as exc:
cube.max(how='cube')
assert 'entire cube into memory' in exc.value.args[0]
cube.allow_huge_operations = True
# just make sure it doesn't fail
cube + 5*cube.unit
finally:
cube_utils.MEMORY_THRESHOLD = OLD_MEMORY_THRESHOLD
class BaseTest(object):
def setup_method(self, method):
c, d = cube_and_raw('adv.fits')
mask = BooleanArrayMask(d > 0.5, c._wcs)
c._mask = mask
self.c = c
self.mask = mask
self.d = d
class BaseTestMultiBeams(object):
def setup_method(self, method):
c, d = cube_and_raw('adv_beams.fits')
mask = BooleanArrayMask(d > 0.5, c._wcs)
c._mask = mask
self.c = c
self.mask = mask
self.d = d
translist = [('advs', [0, 1, 2, 3]),
('dvsa', [2, 3, 0, 1]),
('sdav', [0, 2, 1, 3]),
('sadv', [0, 1, 2, 3]),
('vsad', [3, 0, 1, 2]),
('vad', [2, 0, 1]),
('vda', [0, 2, 1]),
('adv', [0, 1, 2]),
]
translist_vrsc = [('vda_beams', [0, 2, 1])]
class TestSpectralCube(object):
@pytest.mark.parametrize(('name', 'trans'), translist + translist_vrsc)
def test_consistent_transposition(self, name, trans):
"""data() should return velocity axis first, then world 1, then world 0"""
c, d = cube_and_raw(name + '.fits')
expected = np.squeeze(d.transpose(trans))
assert_allclose(c._get_filled_data(), expected)
@pytest.mark.parametrize(('file', 'view'), (
('adv.fits', np.s_[:, :,:]),
('adv.fits', np.s_[::2, :, :2]),
('adv.fits', np.s_[0]),
))
def test_world(self, file, view):
p = path(file)
d = fits.getdata(p)
wcs = WCS(p)
c = SpectralCube(d, wcs)
shp = d.shape
inds = np.indices(d.shape)
pix = np.column_stack([i.ravel() for i in inds[::-1]])
world = wcs.all_pix2world(pix, 0).T
world = [w.reshape(shp) for w in world]
world = [w[view] * u.Unit(wcs.wcs.cunit[i])
for i, w in enumerate(world)][::-1]
w2 = c.world[view]
for result, expected in zip(w2, world):
assert_allclose(result, expected)
@pytest.mark.parametrize('view', (np.s_[:, :,:],
np.s_[:2, :3, ::2]))
def test_world_transposes_3d(self, view):
c1, d1 = cube_and_raw('adv.fits')
c2, d2 = cube_and_raw('vad.fits')
for w1, w2 in zip(c1.world[view], c2.world[view]):
assert_allclose(w1, w2)
@pytest.mark.parametrize('view',
(np.s_[:, :,:],
np.s_[:2, :3, ::2],
np.s_[::3, ::2, :1],
np.s_[:], ))
def test_world_transposes_4d(self, view):
c1, d1 = cube_and_raw('advs.fits')
c2, d2 = cube_and_raw('sadv.fits')
for w1, w2 in zip(c1.world[view], c2.world[view]):
assert_allclose(w1, w2)
@pytest.mark.parametrize(('name','masktype','unit'),
itertools.product(('advs', 'dvsa', 'sdav', 'sadv', 'vsad', 'vad', 'adv',),
(BooleanArrayMask, LazyMask, FunctionMask, CompositeMask),
('Hz', u.Hz),
)
)
def test_with_spectral_unit(self, name, masktype, unit):
cube, data = cube_and_raw(name + '.fits')
cube_freq = cube.with_spectral_unit(unit)
if masktype == BooleanArrayMask:
# don't use data here:
# data haven't necessarily been rearranged to the correct shape by
# cube_utils.orient
mask = BooleanArrayMask(cube.filled_data[:].value>0,
wcs=cube._wcs)
elif masktype == LazyMask:
mask = LazyMask(lambda x: x>0, cube=cube)
elif masktype == FunctionMask:
mask = FunctionMask(lambda x: x>0)
elif masktype == CompositeMask:
mask1 = FunctionMask(lambda x: x>0)
mask2 = LazyMask(lambda x: x>0, cube)
mask = CompositeMask(mask1, mask2)
cube2 = cube.with_mask(mask)
cube_masked_freq = cube2.with_spectral_unit(unit)
assert cube_freq._wcs.wcs.ctype[cube_freq._wcs.wcs.spec] == 'FREQ-W2F'
assert cube_masked_freq._wcs.wcs.ctype[cube_masked_freq._wcs.wcs.spec] == 'FREQ-W2F'
assert cube_masked_freq._mask._wcs.wcs.ctype[cube_masked_freq._mask._wcs.wcs.spec] == 'FREQ-W2F'
# values taken from header
rest = 1.42040571841E+09*u.Hz
crval = -3.21214698632E+05*u.m/u.s
outcv = crval.to(u.m, u.doppler_optical(rest)).to(u.Hz, u.spectral())
assert_allclose(cube_freq._wcs.wcs.crval[cube_freq._wcs.wcs.spec],
outcv.to(u.Hz).value)
assert_allclose(cube_masked_freq._wcs.wcs.crval[cube_masked_freq._wcs.wcs.spec],
outcv.to(u.Hz).value)
assert_allclose(cube_masked_freq._mask._wcs.wcs.crval[cube_masked_freq._mask._wcs.wcs.spec],
outcv.to(u.Hz).value)
@pytest.mark.parametrize(('operation', 'value'),
((operator.add, 0.5*u.K),
(operator.sub, 0.5*u.K),
(operator.mul, 0.5*u.K),
(operator.truediv, 0.5*u.K),
(operator.div if hasattr(operator,'div') else operator.floordiv, 0.5*u.K),
))
def test_apply_everywhere(self, operation, value):
c1, d1 = cube_and_raw('advs.fits')
# append 'o' to indicate that it has been operated on
c1o = c1._apply_everywhere(operation, value)
d1o = operation(u.Quantity(d1, u.K), value)
assert np.all(d1o == c1o.filled_data[:])
# allclose fails on identical data?
#assert_allclose(d1o, c1o.filled_data[:])
@pytest.mark.parametrize(('name', 'trans'), translist)
def test_getitem(self, name, trans):
c, d = cube_and_raw(name + '.fits')
expected = np.squeeze(d.transpose(trans))
assert_allclose(c[0,:,:].value, expected[0,:,:])
assert_allclose(c[:,:,0].value, expected[:,:,0])
assert_allclose(c[:,0,:].value, expected[:,0,:])
# Not implemented:
#assert_allclose(c[0,0,:].value, expected[0,0,:])
#assert_allclose(c[0,:,0].value, expected[0,:,0])
assert_allclose(c[:,0,0].value, expected[:,0,0])
assert_allclose(c[1,:,:].value, expected[1,:,:])
assert_allclose(c[:,:,1].value, expected[:,:,1])
assert_allclose(c[:,1,:].value, expected[:,1,:])
# Not implemented:
#assert_allclose(c[1,1,:].value, expected[1,1,:])
#assert_allclose(c[1,:,1].value, expected[1,:,1])
assert_allclose(c[:,1,1].value, expected[:,1,1])
c2 = c.with_spectral_unit(u.km/u.s, velocity_convention='radio')
assert_allclose(c2[0,:,:].value, expected[0,:,:])
assert_allclose(c2[:,:,0].value, expected[:,:,0])
assert_allclose(c2[:,0,:].value, expected[:,0,:])
# Not implemented:
#assert_allclose(c2[0,0,:].value, expected[0,0,:])
#assert_allclose(c2[0,:,0].value, expected[0,:,0])
assert_allclose(c2[:,0,0].value, expected[:,0,0])
assert_allclose(c2[1,:,:].value, expected[1,:,:])
assert_allclose(c2[:,:,1].value, expected[:,:,1])
assert_allclose(c2[:,1,:].value, expected[:,1,:])
# Not implemented:
#assert_allclose(c2[1,1,:].value, expected[1,1,:])
#assert_allclose(c2[1,:,1].value, expected[1,:,1])
assert_allclose(c2[:,1,1].value, expected[:,1,1])
@pytest.mark.parametrize(('name', 'trans'), translist_vrsc)
def test_getitem_vrsc(self, name, trans):
c, d = cube_and_raw(name + '.fits')
expected = np.squeeze(d.transpose(trans))
# No pv slices for VRSC.
assert_allclose(c[0,:,:].value, expected[0,:,:])
# Not implemented:
#assert_allclose(c[0,0,:].value, expected[0,0,:])
#assert_allclose(c[0,:,0].value, expected[0,:,0])
assert_allclose(c[:,0,0].value, expected[:,0,0])
assert_allclose(c[1,:,:].value, expected[1,:,:])
# Not implemented:
#assert_allclose(c[1,1,:].value, expected[1,1,:])
#assert_allclose(c[1,:,1].value, expected[1,:,1])
assert_allclose(c[:,1,1].value, expected[:,1,1])
c2 = c.with_spectral_unit(u.km/u.s, velocity_convention='radio')
assert_allclose(c2[0,:,:].value, expected[0,:,:])
# Not implemented:
#assert_allclose(c2[0,0,:].value, expected[0,0,:])
#assert_allclose(c2[0,:,0].value, expected[0,:,0])
assert_allclose(c2[:,0,0].value, expected[:,0,0])
assert_allclose(c2[1,:,:].value, expected[1,:,:])
# Not implemented:
#assert_allclose(c2[1,1,:].value, expected[1,1,:])
#assert_allclose(c2[1,:,1].value, expected[1,:,1])
assert_allclose(c2[:,1,1].value, expected[:,1,1])
# @pytest.mark.xfail(raises=AttributeError)
@pytest.mark.parametrize(('name', 'trans'), translist_vrsc)
def test_getitem_vrsc(self, name, trans):
c, d = cube_and_raw(name + '.fits')
expected = np.squeeze(d.transpose(trans))
assert_allclose(c[:,:,0].value, expected[:,:,0])
class TestArithmetic(object):
def setup_method(self, method):
self.c1, self.d1 = cube_and_raw('adv.fits')
# make nice easy-to-test numbers
self.d1.flat[:] = np.arange(self.d1.size)
self.c1._data.flat[:] = np.arange(self.d1.size)
@pytest.mark.parametrize(('value'),(1,1.0,2,2.0))
def test_add(self,value):
d2 = self.d1 + value
c2 = self.c1 + value*u.K
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K
def test_add_cubes(self):
d2 = self.d1 + self.d1
c2 = self.c1 + self.c1
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K
@pytest.mark.parametrize(('value'),(1,1.0,2,2.0))
def test_subtract(self, value):
d2 = self.d1 - value
c2 = self.c1 - value*u.K
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K
# regression test #251: the _data attribute must not be a quantity
assert not hasattr(c2._data, 'unit')
def test_subtract_cubes(self):
d2 = self.d1 - self.d1
c2 = self.c1 - self.c1
assert np.all(d2 == c2.filled_data[:].value)
assert np.all(c2.filled_data[:].value == 0)
assert c2.unit == u.K
# regression test #251: the _data attribute must not be a quantity
assert not hasattr(c2._data, 'unit')
@pytest.mark.parametrize(('value'),(1,1.0,2,2.0))
def test_mul(self, value):
d2 = self.d1 * value
c2 = self.c1 * value
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K
def test_mul_cubes(self):
d2 = self.d1 * self.d1
c2 = self.c1 * self.c1
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K**2
@pytest.mark.parametrize(('value'),(1,1.0,2,2.0))
def test_div(self, value):
d2 = self.d1 / value
c2 = self.c1 / value
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K
def test_div_cubes(self):
d2 = self.d1 / self.d1
c2 = self.c1 / self.c1
assert np.all((d2 == c2.filled_data[:].value) | (np.isnan(c2.filled_data[:])))
assert np.all((c2.filled_data[:] == 1) | (np.isnan(c2.filled_data[:])))
assert c2.unit == u.dimensionless_unscaled
@pytest.mark.parametrize(('value'),
(1,1.0,2,2.0))
def test_pow(self, value):
d2 = self.d1 ** value
c2 = self.c1 ** value
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K**value
def test_cube_add(self):
c2 = self.c1 + self.c1
d2 = self.d1 + self.d1
assert np.all(d2 == c2.filled_data[:].value)
assert c2.unit == u.K
class TestFilters(BaseTest):
def test_mask_data(self):
c, d = self.c, self.d
expected = np.where(d > .5, d, np.nan)
assert_allclose(c._get_filled_data(), expected)
expected = np.where(d > .5, d, 0)
assert_allclose(c._get_filled_data(fill=0), expected)
@pytest.mark.parametrize('operation', (operator.lt, operator.gt, operator.le, operator.ge))
def test_mask_comparison(self, operation):
c, d = self.c, self.d
dmask = operation(d, 0.6) & self.c.mask.include()
cmask = operation(c, 0.6*u.K)
assert (self.c.mask.include() & cmask.include()).sum() == dmask.sum()
np.testing.assert_almost_equal(c.with_mask(cmask).sum().value,
d[dmask].sum())
def test_flatten(self):
c, d = self.c, self.d
expected = d[d > 0.5]
assert_allclose(c.flattened(), expected)
def test_flatten_weights(self):
c, d = self.c, self.d
expected = d[d > 0.5] ** 2
assert_allclose(c.flattened(weights=d), expected)
def test_slice(self):
c, d = self.c, self.d
expected = d[:3, :2, ::2]
expected = expected[expected > 0.5]
assert_allclose(c[0:3, 0:2, 0::2].flattened(), expected)
class TestNumpyMethods(BaseTest):
def _check_numpy(self, cubemethod, array, func):
for axis in [None, 0, 1, 2]:
for how in ['auto', 'slice', 'cube', 'ray']:
expected = func(array, axis=axis)
actual = cubemethod(axis=axis)
assert_allclose(actual, expected)
def test_sum(self):
d = np.where(self.d > 0.5, self.d, np.nan)
self._check_numpy(self.c.sum, d, allbadtonan(np.nansum))
# Need a secondary check to make sure it works with no
# axis keyword being passed (regression test for issue introduced in
# 150)
assert np.all(self.c.sum().value == np.nansum(d))
def test_max(self):
d = np.where(self.d > 0.5, self.d, np.nan)
self._check_numpy(self.c.max, d, np.nanmax)
def test_min(self):
d = np.where(self.d > 0.5, self.d, np.nan)
self._check_numpy(self.c.min, d, np.nanmin)
def test_argmax(self):
d = np.where(self.d > 0.5, self.d, -10)
self._check_numpy(self.c.argmax, d, np.nanargmax)
def test_argmin(self):
d = np.where(self.d > 0.5, self.d, 10)
self._check_numpy(self.c.argmin, d, np.nanargmin)
@pytest.mark.parametrize('iterate_rays', (True,False))
def test_median(self, iterate_rays):
# Make sure that medians ignore empty/bad/NaN values
m = np.empty(self.d.shape[1:])
for y in range(m.shape[0]):
for x in range(m.shape[1]):
ray = self.d[:, y, x]
# the cube mask is for values >0.5
ray = ray[ray > 0.5]
m[y, x] = np.median(ray)
scmed = self.c.median(axis=0, iterate_rays=iterate_rays)
assert_allclose(scmed, m)
assert not np.any(np.isnan(scmed.value))
assert scmed.unit == self.c.unit
@pytest.mark.skipif('NUMPY_LT_19')
def test_bad_median_apply(self):
# this is a test for manually-applied numpy medians, which are different
# from the cube.median method that does "the right thing"
#
# for regular median, we expect a failure, which is why we don't use
# regular median.
scmed = self.c.apply_numpy_function(np.median, axis=0)
# this checks whether numpy <=1.9.3 has a bug?
# as far as I can tell, np==1.9.3 no longer has this bug/feature
#if LooseVersion(np.__version__) <= LooseVersion('1.9.3'):
# # print statements added so we get more info in the travis builds
# print("Numpy version is: {0}".format(LooseVersion(np.__version__)))
# assert np.count_nonzero(np.isnan(scmed)) == 5
#else:
# print("Numpy version is: {0}".format(LooseVersion(np.__version__)))
assert np.count_nonzero(np.isnan(scmed)) == 6
scmed = self.c.apply_numpy_function(np.nanmedian, axis=0)
assert np.count_nonzero(np.isnan(scmed)) == 0
# use a more aggressive mask to force there to be some all-nan axes
m2 = self.c>0.65*self.c.unit
scmed = self.c.with_mask(m2).apply_numpy_function(np.nanmedian, axis=0)
assert np.count_nonzero(np.isnan(scmed)) == 1
@pytest.mark.parametrize('iterate_rays', (True,False))
def test_bad_median(self, iterate_rays):
# This should have the same result as np.nanmedian, though it might be
# faster if bottleneck loads
scmed = self.c.median(axis=0, iterate_rays=iterate_rays)
assert np.count_nonzero(np.isnan(scmed)) == 0
m2 = self.c>0.65*self.c.unit
scmed = self.c.with_mask(m2).median(axis=0, iterate_rays=iterate_rays)
assert np.count_nonzero(np.isnan(scmed)) == 1
@pytest.mark.parametrize(('pct', 'iterate_rays'),
(zip((3,25,50,75,97)*2,(True,)*5 + (False,)*5)))
def test_percentile(self, pct, iterate_rays):
m = np.empty(self.d.sum(axis=0).shape)
for y in range(m.shape[0]):
for x in range(m.shape[1]):
ray = self.d[:, y, x]
ray = ray[ray > 0.5]
m[y, x] = np.percentile(ray, pct)
scpct = self.c.percentile(pct, axis=0, iterate_rays=iterate_rays)
assert_allclose(scpct, m)
assert not np.any(np.isnan(scpct.value))
assert scpct.unit == self.c.unit
@pytest.mark.parametrize('method', ('sum', 'min', 'max', 'std', 'mad_std',
'median', 'argmin', 'argmax'))
def test_transpose(self, method):
c1, d1 = cube_and_raw('adv.fits')
c2, d2 = cube_and_raw('vad.fits')
for axis in [None, 0, 1, 2]:
assert_allclose(getattr(c1, method)(axis=axis),
getattr(c2, method)(axis=axis))
# check that all these accept progressbar kwargs
assert_allclose(getattr(c1, method)(axis=axis, progressbar=True),
getattr(c2, method)(axis=axis, progressbar=True))
class TestSlab(BaseTest):
def test_closest_spectral_channel(self):
c = self.c
ms = u.m / u.s
assert c.closest_spectral_channel(-321214.698632 * ms) == 0
assert c.closest_spectral_channel(-319926.48366321 * ms) == 1
assert c.closest_spectral_channel(-318638.26869442 * ms) == 2
assert c.closest_spectral_channel(-320000 * ms) == 1
assert c.closest_spectral_channel(-340000 * ms) == 0
assert c.closest_spectral_channel(0 * ms) == 3
def test_spectral_channel_bad_units(self):
with pytest.raises(u.UnitsError) as exc:
self.c.closest_spectral_channel(1 * u.s)
assert exc.value.args[0] == "'value' should be in frequency equivalent or velocity units (got s)"
with pytest.raises(u.UnitsError) as exc:
self.c.closest_spectral_channel(1. * u.Hz)
assert exc.value.args[0] == "Spectral axis is in velocity units and 'value' is in frequency-equivalent units - use SpectralCube.with_spectral_unit first to convert the cube to frequency-equivalent units, or search for a velocity instead"
def test_slab(self):
ms = u.m / u.s
c2 = self.c.spectral_slab(-320000 * ms, -318600 * ms)
assert_allclose(c2._data, self.d[1:3])
assert c2._mask is not None
def test_slab_reverse_limits(self):
ms = u.m / u.s
c2 = self.c.spectral_slab(-318600 * ms, -320000 * ms)
assert_allclose(c2._data, self.d[1:3])
assert c2._mask is not None
def test_slab_preserves_wcs(self):
# regression test
ms = u.m / u.s
crpix = list(self.c._wcs.wcs.crpix)
self.c.spectral_slab(-318600 * ms, -320000 * ms)
assert list(self.c._wcs.wcs.crpix) == crpix
class TestSlabMultiBeams(BaseTestMultiBeams, TestSlab):
""" same tests with multibeams """
pass
class TestRepr(BaseTest):
def test_repr(self):
assert repr(self.c) == """
SpectralCube with shape=(4, 3, 2) and unit=K:
n_x: 2 type_x: RA---SIN unit_x: deg range: 24.062698 deg: 24.063349 deg
n_y: 3 type_y: DEC--SIN unit_y: deg range: 29.934094 deg: 29.935209 deg
n_s: 4 type_s: VOPT unit_s: km / s range: -321.215 km / s: -317.350 km / s
""".strip()
def test_repr_withunit(self):
self.c._unit = u.Jy
assert repr(self.c) == """
SpectralCube with shape=(4, 3, 2) and unit=Jy:
n_x: 2 type_x: RA---SIN unit_x: deg range: 24.062698 deg: 24.063349 deg
n_y: 3 type_y: DEC--SIN unit_y: deg range: 29.934094 deg: 29.935209 deg
n_s: 4 type_s: VOPT unit_s: km / s range: -321.215 km / s: -317.350 km / s
""".strip()
@pytest.mark.xfail
@pytest.mark.skipif('not YT_INSTALLED')
class TestYt():
def setup_method(self, method):
self.cube = SpectralCube.read(path('adv.fits'))
# Without any special arguments
self.ytc1 = self.cube.to_yt()
# With spectral factor = 0.5
self.spectral_factor = 0.5
self.ytc2 = self.cube.to_yt(spectral_factor=self.spectral_factor)
# With nprocs = 4
self.nprocs = 4
self.ytc3 = self.cube.to_yt(nprocs=self.nprocs)
def test_yt(self):
# The following assertions just make sure everything is
# kosher with the datasets generated in different ways
ytc1,ytc2,ytc3 = self.ytc1,self.ytc2,self.ytc3
ds1,ds2,ds3 = ytc1.dataset, ytc2.dataset, ytc3.dataset
assert_array_equal(ds1.domain_dimensions, ds2.domain_dimensions)
assert_array_equal(ds2.domain_dimensions, ds3.domain_dimensions)
assert_allclose(ds1.domain_left_edge.value, ds2.domain_left_edge.value)
assert_allclose(ds2.domain_left_edge.value, ds3.domain_left_edge.value)
assert_allclose(ds1.domain_width.value,
ds2.domain_width.value*np.array([1,1,1.0/self.spectral_factor]))
assert_allclose(ds1.domain_width.value, ds3.domain_width.value)
assert self.nprocs == len(ds3.index.grids)
assert ds1.spec_cube
assert ds2.spec_cube
assert ds3.spec_cube
ds1.index
ds2.index
ds3.index
unit1 = ds1.field_info["fits","flux"].units
unit2 = ds2.field_info["fits","flux"].units
unit3 = ds3.field_info["fits","flux"].units
ds1.quan(1.0,unit1)
ds2.quan(1.0,unit2)
ds3.quan(1.0,unit3)
@pytest.mark.skipif('YT_LT_301', reason='yt 3.0 has a FITS-related bug')
def test_yt_fluxcompare(self):
# Now check that we can compute quantities of the flux
# and that they are equal
ytc1,ytc2,ytc3 = self.ytc1,self.ytc2,self.ytc3
ds1,ds2,ds3 = ytc1.dataset, ytc2.dataset, ytc3.dataset
dd1 = ds1.all_data()
dd2 = ds2.all_data()
dd3 = ds3.all_data()
flux1_tot = dd1.quantities.total_quantity("flux")
flux2_tot = dd2.quantities.total_quantity("flux")
flux3_tot = dd3.quantities.total_quantity("flux")
flux1_min, flux1_max = dd1.quantities.extrema("flux")
flux2_min, flux2_max = dd2.quantities.extrema("flux")
flux3_min, flux3_max = dd3.quantities.extrema("flux")
assert flux1_tot == flux2_tot
assert flux1_tot == flux3_tot
assert flux1_min == flux2_min
assert flux1_min == flux3_min
assert flux1_max == flux2_max
assert flux1_max == flux3_max
def test_yt_roundtrip_wcs(self):
# Now test round-trip conversions between yt and world coordinates
ytc1,ytc2,ytc3 = self.ytc1,self.ytc2,self.ytc3
ds1,ds2,ds3 = ytc1.dataset, ytc2.dataset, ytc3.dataset
yt_coord1 = ds1.domain_left_edge + np.random.random(size=3)*ds1.domain_width
world_coord1 = ytc1.yt2world(yt_coord1)
assert_allclose(ytc1.world2yt(world_coord1), yt_coord1.value)
yt_coord2 = ds2.domain_left_edge + np.random.random(size=3)*ds2.domain_width
world_coord2 = ytc2.yt2world(yt_coord2)
assert_allclose(ytc2.world2yt(world_coord2), yt_coord2.value)
yt_coord3 = ds3.domain_left_edge + np.random.random(size=3)*ds3.domain_width
world_coord3 = ytc3.yt2world(yt_coord3)
assert_allclose(ytc3.world2yt(world_coord3), yt_coord3.value)
def test_read_write_rountrip(tmpdir):
cube = SpectralCube.read(path('adv.fits'))
tmp_file = str(tmpdir.join('test.fits'))
cube.write(tmp_file)
cube2 = SpectralCube.read(tmp_file)
assert cube.shape == cube.shape
assert_allclose(cube._data, cube2._data)
if (((hasattr(_wcs, '__version__')
and LooseVersion(_wcs.__version__) < LooseVersion('5.9'))
or not hasattr(_wcs, '__version__'))):
# see https://github.com/astropy/astropy/pull/3992 for reasons:
# we should upgrade this for 5.10 when the absolute accuracy is
# maximized
assert cube._wcs.to_header_string() == cube2._wcs.to_header_string()
# in 5.11 and maybe even 5.12, the round trip fails. Maybe
# https://github.com/astropy/astropy/issues/4292 will solve it?
@pytest.mark.parametrize(('memmap', 'base'),
((True, mmap.mmap),
(False, None)))
def test_read_memmap(memmap, base):
cube = SpectralCube.read(path('adv.fits'), memmap=memmap)
bb = cube.base
while hasattr(bb, 'base'):
bb = bb.base
if base is None:
assert bb is None
else:
assert isinstance(bb, base)
def _dummy_cube():
data = np.array([[[0, 1, 2, 3, 4]]])
wcs = WCS(naxis=3)
wcs.wcs.ctype = ['RA---TAN', 'DEC--TAN', 'VELO-HEL']
def lower_threshold(data, wcs, view=()):
return data[view] > 0
m1 = FunctionMask(lower_threshold)
cube = SpectralCube(data, wcs=wcs, mask=m1)
return cube
def test_with_mask():
def upper_threshold(data, wcs, view=()):
return data[view] < 3
m2 = FunctionMask(upper_threshold)
cube = _dummy_cube()
cube2 = cube.with_mask(m2)
assert_allclose(cube._get_filled_data(), [[[np.nan, 1, 2, 3, 4]]])
assert_allclose(cube2._get_filled_data(), [[[np.nan, 1, 2, np.nan, np.nan]]])
def test_with_mask_with_boolean_array():
cube = _dummy_cube()
mask = cube._data > 2
cube2 = cube.with_mask(mask, inherit_mask=False)
assert isinstance(cube2._mask, BooleanArrayMask)
assert cube2._mask._wcs is cube._wcs
assert cube2._mask._mask is mask
def test_with_mask_with_good_array_shape():
cube = _dummy_cube()
mask = np.zeros((1, 5), dtype=np.bool)
cube2 = cube.with_mask(mask, inherit_mask=False)
assert isinstance(cube2._mask, BooleanArrayMask)
np.testing.assert_equal(cube2._mask._mask, mask.reshape((1, 1, 5)))
def test_with_mask_with_bad_array_shape():
cube = _dummy_cube()
mask = np.zeros((5, 5), dtype=np.bool)
with pytest.raises(ValueError) as exc:
cube.with_mask(mask)
assert exc.value.args[0] == ("Mask shape is not broadcastable to data shape: "
"(5, 5) vs (1, 1, 5)")
class TestMasks(BaseTest):
@pytest.mark.parametrize('op', (operator.gt, operator.lt,
operator.le, operator.ge))
def test_operator_threshold(self, op):
# choose thresh to exercise proper equality tests
thresh = self.d.ravel()[0]
m = op(self.c, thresh*u.K)
self.c._mask = m
expected = self.d[op(self.d, thresh)]
actual = self.c.flattened()
assert_allclose(actual, expected)
def test_preserve_spectral_unit():
# astropy.wcs has a tendancy to change spectral units from e.g. km/s to
# m/s, so we have a workaround - check that it works.
cube, data = cube_and_raw('advs.fits')
cube_freq = cube.with_spectral_unit(u.GHz)
assert cube_freq.wcs.wcs.cunit[2] == 'Hz' # check internal
assert cube_freq.spectral_axis.unit is u.GHz
# Check that this preferred unit is propagated
new_cube = cube_freq.with_fill_value(fill_value=3.4)
assert new_cube.spectral_axis.unit is u.GHz
@pytest.mark.skipif('not BOTTLENECK_INSTALLED')
def test_endians():
"""
Test that the endianness checking returns something in Native form
(this is only needed for non-numpy functions that worry about the
endianness of their data)
WARNING: Because the endianness is machine-dependent, this may fail on
different architectures! This is because numpy automatically converts
little-endian to native in the dtype parameter; I need a workaround for
this.
"""
big = np.array([[[1],[2]]], dtype='>f4')
lil = np.array([[[1],[2]]], dtype='<f4')
mywcs = WCS(naxis=3)
mywcs.wcs.ctype[0] = 'RA'
mywcs.wcs.ctype[1] = 'DEC'
mywcs.wcs.ctype[2] = 'VELO'
bigcube = SpectralCube(data=big, wcs=mywcs)
xbig = bigcube._get_filled_data(check_endian=True)
lilcube = SpectralCube(data=lil, wcs=mywcs)
xlil = lilcube._get_filled_data(check_endian=True)
assert xbig.dtype.byteorder == '='
assert xlil.dtype.byteorder == '='
xbig = bigcube._get_filled_data(check_endian=False)
xlil = lilcube._get_filled_data(check_endian=False)
assert xbig.dtype.byteorder == '>'
assert xlil.dtype.byteorder == '='
def test_header_naxis():
cube, data = cube_and_raw('advs.fits')
assert cube.header['NAXIS'] == 3 # NOT data.ndim == 4
assert cube.header['NAXIS1'] == data.shape[3]
assert cube.header['NAXIS2'] == data.shape[2]
assert cube.header['NAXIS3'] == data.shape[1]
assert 'NAXIS4' not in cube.header
def test_slicing():
cube, data = cube_and_raw('advs.fits')
# just to check that we're starting in the right place
assert cube.shape == (2,3,4)
sl = cube[:,1,:]
assert sl.shape == (2,4)
v = cube[1:2,:,:]
assert v.shape == (1,3,4)
# make sure this works. Not sure what keys to test for...
v.header
assert cube[:,:,:].shape == (2,3,4)
assert cube[:,:].shape == (2,3,4)
assert cube[:].shape == (2,3,4)
assert cube[:1,:1,:1].shape == (1,1,1)
@pytest.mark.parametrize(('view','naxis'),
[((slice(None), 1, slice(None)), 2),
((1, slice(None), slice(None)), 2),
((slice(None), slice(None), 1), 2),
((slice(None), slice(None), slice(1)), 3),
((slice(1), slice(1), slice(1)), 3),
((slice(None, None, -1), slice(None), slice(None)), 3),
])
def test_slice_wcs(view, naxis):
cube, data = cube_and_raw('advs.fits')
sl = cube[view]
assert sl.wcs.naxis == naxis
def test_slice_wcs_reversal():
cube, data = cube_and_raw('advs.fits')
view = (slice(None,None,-1), slice(None), slice(None))
rcube = cube[view]
rrcube = rcube[view]
np.testing.assert_array_equal(np.diff(cube.spectral_axis),
-np.diff(rcube.spectral_axis))
np.testing.assert_array_equal(rrcube.spectral_axis.value,
cube.spectral_axis.value)
np.testing.assert_array_equal(rcube.spectral_axis.value,
cube.spectral_axis.value[::-1])
np.testing.assert_array_equal(rrcube.world_extrema.value,
cube.world_extrema.value)
# check that the lon, lat arrays are *entirely* unchanged
np.testing.assert_array_equal(rrcube.spatial_coordinate_map[0].value,
cube.spatial_coordinate_map[0].value)
np.testing.assert_array_equal(rrcube.spatial_coordinate_map[1].value,
cube.spatial_coordinate_map[1].value)
def test_spectral_slice_preserve_units():
cube, data = cube_and_raw('advs.fits')
cube = cube.with_spectral_unit(u.km/u.s)
sl = cube[:,0,0]
assert cube._spectral_unit == u.km/u.s
assert sl._spectral_unit == u.km/u.s
assert cube.spectral_axis.unit == u.km/u.s
assert sl.spectral_axis.unit == u.km/u.s
def test_header_units_consistent():
cube, data = cube_and_raw('advs.fits')
cube_ms = cube.with_spectral_unit(u.m/u.s)
cube_kms = cube.with_spectral_unit(u.km/u.s)
cube_Mms = cube.with_spectral_unit(u.Mm/u.s)
assert cube.header['CUNIT3'] == 'km s-1'
assert cube_ms.header['CUNIT3'] == 'm s-1'
assert cube_kms.header['CUNIT3'] == 'km s-1'
assert cube_Mms.header['CUNIT3'] == 'Mm s-1'
# Wow, the tolerance here is really terrible...
assert_allclose(cube_Mms.header['CDELT3'], cube.header['CDELT3']/1e3,rtol=1e-3,atol=1e-5)
assert_allclose(cube.header['CDELT3'], cube_kms.header['CDELT3'],rtol=1e-2,atol=1e-5)
assert_allclose(cube.header['CDELT3']*1e3, cube_ms.header['CDELT3'],rtol=1e-2,atol=1e-5)
cube_freq = cube.with_spectral_unit(u.Hz)
assert cube_freq.header['CUNIT3'] == 'Hz'
cube_freq_GHz = cube.with_spectral_unit(u.GHz)
assert cube_freq_GHz.header['CUNIT3'] == 'GHz'
def test_spectral_unit_conventions():
cube, data = cube_and_raw('advs.fits')
cube_frq = cube.with_spectral_unit(u.Hz)
cube_opt = cube.with_spectral_unit(u.km/u.s,
rest_value=cube_frq.spectral_axis[0],
velocity_convention='optical')
cube_rad = cube.with_spectral_unit(u.km/u.s,
rest_value=cube_frq.spectral_axis[0],
velocity_convention='radio')
cube_rel = cube.with_spectral_unit(u.km/u.s,
rest_value=cube_frq.spectral_axis[0],
velocity_convention='relativistic')
# should all be exactly 0 km/s
for x in (cube_rel.spectral_axis[0], cube_rad.spectral_axis[0],
cube_opt.spectral_axis[0]):
np.testing.assert_almost_equal(0,x.value)
assert cube_rel.spectral_axis[1] != cube_rad.spectral_axis[1]
assert cube_opt.spectral_axis[1] != cube_rad.spectral_axis[1]
assert cube_rel.spectral_axis[1] != cube_opt.spectral_axis[1]
assert cube_rel.velocity_convention == u.doppler_relativistic
assert cube_rad.velocity_convention == u.doppler_radio
assert cube_opt.velocity_convention == u.doppler_optical
def test_invalid_spectral_unit_conventions():
cube, data = cube_and_raw('advs.fits')
with pytest.raises(ValueError) as exc:
cube.with_spectral_unit(u.km/u.s,
velocity_convention='invalid velocity convention')
assert exc.value.args[0] == ("Velocity convention must be radio, optical, "
"or relativistic.")
@pytest.mark.parametrize('rest', (50, 50*u.K))
def test_invalid_rest(rest):
cube, data = cube_and_raw('advs.fits')
with pytest.raises(ValueError) as exc:
cube.with_spectral_unit(u.km/u.s,
velocity_convention='radio',
rest_value=rest)
assert exc.value.args[0] == ("Rest value must be specified as an astropy "
"quantity with spectral equivalence.")
def test_airwave_to_wave():
cube, data = cube_and_raw('advs.fits')
cube._wcs.wcs.ctype[2] = 'AWAV'
cube._wcs.wcs.cunit[2] = 'm'
cube._spectral_unit = u.m
cube._wcs.wcs.cdelt[2] = 1e-7
cube._wcs.wcs.crval[2] = 5e-7
ax1 = cube.spectral_axis
ax2 = cube.with_spectral_unit(u.m).spectral_axis
np.testing.assert_almost_equal(spectral_axis.air_to_vac(ax1).value,
ax2.value)
@pytest.mark.parametrize(('func','how','axis'),
itertools.product(('sum','std','max','min','mean'),
('slice','cube','auto'),
(0,1,2)
))
def test_twod_numpy(func, how, axis):
# Check that a numpy function returns the correct result when applied along
# one axis
# This is partly a regression test for #211
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
proj = getattr(cube,func)(axis=axis, how=how)
# data has a redundant 1st axis
dproj = getattr(data,func)(axis=(0,axis+1)).squeeze()
assert isinstance(proj, Projection)
np.testing.assert_almost_equal(proj.value, dproj)
assert cube.unit == proj.unit
@pytest.mark.parametrize(('func','how','axis'),
itertools.product(('sum','std','max','min','mean'),
('slice','cube','auto'),
((0,1),(1,2),(0,2))
))
def test_twod_numpy_twoaxes(func, how, axis):
# Check that a numpy function returns the correct result when applied along
# one axis
# This is partly a regression test for #211
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
if func == 'mean' and axis != (1,2):
with warnings.catch_warnings(record=True) as wrn:
spec = getattr(cube,func)(axis=axis, how=how)
assert 'Averaging over a spatial and a spectral' in str(wrn[-1].message)
spec = getattr(cube,func)(axis=axis, how=how)
# data has a redundant 1st axis
dspec = getattr(data.squeeze(),func)(axis=axis)
if axis == (1,2):
assert isinstance(spec, OneDSpectrum)
assert cube.unit == spec.unit
np.testing.assert_almost_equal(spec.value, dspec)
else:
np.testing.assert_almost_equal(spec, dspec)
def test_preserves_header_values():
# Check that the non-WCS header parameters are preserved during projection
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
cube._header['OBJECT'] = 'TestName'
proj = cube.sum(axis=0, how='auto')
assert isinstance(proj, Projection)
assert proj.header['OBJECT'] == 'TestName'
assert proj.hdu.header['OBJECT'] == 'TestName'
@pytest.mark.parametrize('func',('sum','std','max','min','mean'))
def test_oned_numpy(func):
# Check that a numpy function returns an appropriate spectrum
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
spec = getattr(cube,func)(axis=(1,2))
dspec = getattr(data,func)(axis=(2,3)).squeeze()
assert isinstance(spec, OneDSpectrum)
# data has a redundant 1st axis
np.testing.assert_equal(spec.value, dspec)
assert cube.unit == spec.unit
def test_oned_slice():
# Check that a slice returns an appropriate spectrum
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
spec = cube[:,0,0]
assert isinstance(spec, OneDSpectrum)
# data has a redundant 1st axis
np.testing.assert_equal(spec.value, data[0,:,0,0])
assert cube.unit == spec.unit
assert spec.header['BUNIT'] == cube.header['BUNIT']
def test_oned_slice_beams():
# Check that a slice returns an appropriate spectrum
cube, data = cube_and_raw('sdav_beams.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
spec = cube[:,0,0]
assert isinstance(spec, OneDSpectrum)
# data has a redundant 1st axis
np.testing.assert_equal(spec.value, data[:,0,0,0])
assert cube.unit == spec.unit
assert spec.header['BUNIT'] == cube.header['BUNIT']
assert hasattr(spec, 'beams')
assert 'BMAJ' in spec.hdulist[1].data.names
def test_subcube_slab_beams():
cube, data = cube_and_raw('sdav_beams.fits')
slcube = cube[1:]
assert all(slcube.hdulist[1].data['CHAN'] == np.arange(slcube.shape[0]))
# collapsing to one dimension raywise doesn't make sense and is therefore
# not supported.
@pytest.mark.parametrize('how', ('auto', 'cube', 'slice'))
def test_oned_collapse(how):
# Check that an operation along the spatial dims returns an appropriate
# spectrum
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
spec = cube.mean(axis=(1,2), how=how)
assert isinstance(spec, OneDSpectrum)
# data has a redundant 1st axis
np.testing.assert_equal(spec.value, data.mean(axis=(0,2,3)))
assert cube.unit == spec.unit
assert spec.header['BUNIT'] == cube.header['BUNIT']
def test_oned_collapse_beams():
# Check that an operation along the spatial dims returns an appropriate
# spectrum
cube, data = cube_and_raw('sdav_beams.fits')
cube._meta['BUNIT'] = 'K'
cube._unit = u.K
spec = cube.mean(axis=(1,2))
assert isinstance(spec, OneDSpectrum)
# data has a redundant 1st axis
np.testing.assert_equal(spec.value, data.mean(axis=(1,2,3)))
assert cube.unit == spec.unit
assert spec.header['BUNIT'] == cube.header['BUNIT']
assert hasattr(spec, 'beams')
assert 'BMAJ' in spec.hdulist[1].data.names
def test_preserve_bunit():
cube, data = cube_and_raw('advs.fits')
assert cube.header['BUNIT'] == 'K'
hdu = fits.open(path('advs.fits'))[0]
hdu.header['BUNIT'] = 'Jy'
cube = SpectralCube.read(hdu)
assert cube.unit == u.Jy
assert cube.header['BUNIT'] == 'Jy'
def test_preserve_beam():
cube, data = cube_and_raw('advs.fits')
beam = Beam.from_fits_header(path("advs.fits"))
assert cube.beam == beam
def test_beam_attach_to_header():
cube, data = cube_and_raw('adv.fits')
header = cube._header.copy()
del header["BMAJ"], header["BMIN"], header["BPA"]
newcube = SpectralCube(data=data, wcs=cube.wcs, header=header,
beam=cube.beam)
assert cube.header["BMAJ"] == newcube.header["BMAJ"]
assert cube.header["BMIN"] == newcube.header["BMIN"]
assert cube.header["BPA"] == newcube.header["BPA"]
# Should be in meta too
assert newcube.meta['beam'] == cube.beam
def test_beam_custom():
cube, data = cube_and_raw('adv.fits')
header = cube._header.copy()
beam = Beam.from_fits_header(header)
del header["BMAJ"], header["BMIN"], header["BPA"]
newcube = SpectralCube(data=data, wcs=cube.wcs, header=header)
# newcube should now not have a beam
assert not hasattr(newcube, "beam")
# Attach the beam
newcube = newcube.with_beam(beam=beam)
assert newcube.beam == cube.beam
# Header should be updated
assert cube.header["BMAJ"] == newcube.header["BMAJ"]
assert cube.header["BMIN"] == newcube.header["BMIN"]
assert cube.header["BPA"] == newcube.header["BPA"]
# Should be in meta too
assert newcube.meta['beam'] == cube.beam
# Try changing the beam properties
newbeam = Beam(beam.major * 2)
newcube2 = newcube.with_beam(beam=newbeam)
assert newcube2.beam == newbeam
# Header should be updated
assert newcube2.header["BMAJ"] == newbeam.major.value
assert newcube2.header["BMIN"] == newbeam.minor.value
assert newcube2.header["BPA"] == newbeam.pa.value
# Should be in meta too
assert newcube2.meta['beam'] == newbeam
def test_multibeam_slice():
cube, data = cube_and_raw('vda_beams.fits')
assert isinstance(cube, VaryingResolutionSpectralCube)
np.testing.assert_almost_equal(cube.beams[0].major.value, 0.1)
np.testing.assert_almost_equal(cube.beams[3].major.value, 0.4)
scube = cube[:2,:,:]
np.testing.assert_almost_equal(scube.beams[0].major.value, 0.1)
np.testing.assert_almost_equal(scube.beams[1].major.value, 0.2)
flatslice = cube[0,:,:]
np.testing.assert_almost_equal(flatslice.header['BMAJ'],
(0.1/3600.))
def test_basic_unit_conversion():
cube, data = cube_and_raw('advs.fits')
assert cube.unit == u.K
mKcube = cube.to(u.mK)
np.testing.assert_almost_equal(mKcube.filled_data[:].value,
(cube.filled_data[:].value *
1e3))
def test_basic_unit_conversion_beams():
cube, data = cube_and_raw('vda_beams.fits')
cube._unit = u.K # want beams, but we want to force the unit to be something non-beamy
cube._meta['BUNIT'] = 'K'
assert cube.unit == u.K
mKcube = cube.to(u.mK)
np.testing.assert_almost_equal(mKcube.filled_data[:].value,
(cube.filled_data[:].value *
1e3))
def test_beam_jtok_array():
cube, data = cube_and_raw('advs.fits')
cube._meta['BUNIT'] = 'Jy / beam'
cube._unit = u.Jy/u.beam
equiv = cube.beam.jtok_equiv(cube.with_spectral_unit(u.GHz).spectral_axis)
jtok = cube.beam.jtok(cube.with_spectral_unit(u.GHz).spectral_axis)
Kcube = cube.to(u.K, equivalencies=equiv)
np.testing.assert_almost_equal(Kcube.filled_data[:].value,
(cube.filled_data[:].value *
jtok[:,None,None]).value)
# test that the beam equivalencies are correctly automatically defined
Kcube = cube.to(u.K)
np.testing.assert_almost_equal(Kcube.filled_data[:].value,
(cube.filled_data[:].value *
jtok[:,None,None]).value)
def test_multibeam_jtok_array():
cube, data = cube_and_raw('vda_beams.fits')
assert cube.meta['BUNIT'].strip() == 'Jy / beam'
assert cube.unit.is_equivalent(u.Jy/u.beam)
#equiv = [bm.jtok_equiv(frq) for bm, frq in zip(cube.beams, cube.with_spectral_unit(u.GHz).spectral_axis)]
jtok = u.Quantity([bm.jtok(frq) for bm, frq in zip(cube.beams, cube.with_spectral_unit(u.GHz).spectral_axis)])
# don't try this, it's nonsense for the multibeam case
# Kcube = cube.to(u.K, equivalencies=equiv)
# np.testing.assert_almost_equal(Kcube.filled_data[:].value,
# (cube.filled_data[:].value *
# jtok[:,None,None]).value)
# test that the beam equivalencies are correctly automatically defined
Kcube = cube.to(u.K)
np.testing.assert_almost_equal(Kcube.filled_data[:].value,
(cube.filled_data[:].value *
jtok[:,None,None]).value)
def test_beam_jtok():
# regression test for an error introduced when the previous test was solved
# (the "is this an array?" test used len(x) where x could be scalar)
cube, data = cube_and_raw('advs.fits')
# technically this should be jy/beam, but astropy's equivalency doesn't
# handle this yet
cube._meta['BUNIT'] = 'Jy'
cube._unit = u.Jy
equiv = cube.beam.jtok_equiv(np.median(cube.with_spectral_unit(u.GHz).spectral_axis))
jtok = cube.beam.jtok(np.median(cube.with_spectral_unit(u.GHz).spectral_axis))
Kcube = cube.to(u.K, equivalencies=equiv)
np.testing.assert_almost_equal(Kcube.filled_data[:].value,
(cube.filled_data[:].value *
jtok).value)
def test_varyres_moment():
cube, data = cube_and_raw('vda_beams.fits')
assert isinstance(cube, VaryingResolutionSpectralCube)
# the beams are very different, but for this test we don't care
cube.beam_threshold = 1.0
with warnings.catch_warnings(record=True) as wrn:
warnings.simplefilter('default')
m0 = cube.moment0()
assert "Arithmetic beam averaging is being performed" in str(wrn[-1].message)
assert_quantity_allclose(m0.meta['beam'].major, 0.25*u.arcsec)
def test_append_beam_to_hdr():
cube, data = cube_and_raw('advs.fits')
orig_hdr = fits.getheader(path('advs.fits'))
assert cube.header['BMAJ'] == orig_hdr['BMAJ']
assert cube.header['BMIN'] == orig_hdr['BMIN']
assert cube.header['BPA'] == orig_hdr['BPA']
def test_cube_with_swapped_axes():
"""
Regression test for #208
"""
cube, data = cube_and_raw('vda.fits')
# Check that masking works (this should apply a lazy mask)
cube.filled_data[:]
def test_jybeam_upper():
cube, data = cube_and_raw('vda_JYBEAM_upper.fits')
assert cube.unit == u.Jy/u.beam
assert hasattr(cube, 'beam')
np.testing.assert_almost_equal(cube.beam.sr.value,
(((1*u.arcsec/np.sqrt(8*np.log(2)))**2).to(u.sr)*2*np.pi).value)
def test_jybeam_lower():
cube, data = cube_and_raw('vda_Jybeam_lower.fits')
assert cube.unit == u.Jy/u.beam
assert hasattr(cube, 'beam')
np.testing.assert_almost_equal(cube.beam.sr.value,
(((1*u.arcsec/np.sqrt(8*np.log(2)))**2).to(u.sr)*2*np.pi).value)
# Regression test for #257 (https://github.com/radio-astro-tools/spectral-cube/pull/257)
def test_jybeam_whitespace():
cube, data = cube_and_raw('vda_Jybeam_whitespace.fits')
assert cube.unit == u.Jy/u.beam
assert hasattr(cube, 'beam')
np.testing.assert_almost_equal(cube.beam.sr.value,
(((1*u.arcsec/np.sqrt(8*np.log(2)))**2).to(u.sr)*2*np.pi).value)
def test_beam_proj_meta():
cube, data = cube_and_raw('advs.fits')
moment = cube.moment0(axis=0)
# regression test for #250
assert 'beam' in moment.meta
assert 'BMAJ' in moment.hdu.header
slc = cube[0,:,:]
assert 'beam' in slc.meta
proj = cube.max(axis=0)
assert 'beam' in proj.meta
def test_proj_meta():
cube, data = cube_and_raw('advs.fits')
moment = cube.moment0(axis=0)
assert 'BUNIT' in moment.meta
assert moment.meta['BUNIT'] == 'K'
slc = cube[0,:,:]
assert 'BUNIT' in slc.meta
assert slc.meta['BUNIT'] == 'K'
proj = cube.max(axis=0)
assert 'BUNIT' in proj.meta
assert proj.meta['BUNIT'] == 'K'
def test_pix_sign():
cube, data = cube_and_raw('advs.fits')
s,y,x = (cube._pix_size_slice(ii) for ii in range(3))
assert s>0
assert y>0
assert x>0
cube.wcs.wcs.cdelt *= -1
s,y,x = (cube._pix_size_slice(ii) for ii in range(3))
assert s>0
assert y>0
assert x>0
cube.wcs.wcs.pc *= -1
s,y,x = (cube._pix_size_slice(ii) for ii in range(3))
assert s>0
assert y>0
assert x>0
def test_varyres_moment_logic_issue364():
""" regression test for issue364 """
cube, data = cube_and_raw('vda_beams.fits')
assert isinstance(cube, VaryingResolutionSpectralCube)
# the beams are very different, but for this test we don't care
cube.beam_threshold = 1.0
with warnings.catch_warnings(record=True) as wrn:
warnings.simplefilter('default')
# note that cube.moment(order=0) is different from cube.moment0()
# because cube.moment0() calls cube.moment(order=0, axis=(whatever)),
# but cube.moment doesn't necessarily have to receive the axis kwarg
m0 = cube.moment(order=0)
if six.PY2:
# sad face, tests do not work
pass
else:
assert "Arithmetic beam averaging is being performed" in str(wrn[-1].message)
assert_quantity_allclose(m0.meta['beam'].major, 0.25*u.arcsec)
def test_mask_bad_beams():
cube, data = cube_and_raw('vda_beams.fits')
# make sure all of the beams are initially good (finite)
assert np.all(cube._goodbeams_mask)
# make sure cropping the cube maintains the mask
assert np.all(cube[:3]._goodbeams_mask)
# middle two beams have same area
masked_cube = cube.mask_out_bad_beams(0.01,
reference_beam=Beam(0.3*u.arcsec,
0.2*u.arcsec,
60*u.deg))
assert np.all(masked_cube.mask.include()[:,0,0] == [False,False,True,False])
assert np.all(masked_cube._goodbeams_mask == [False,False,True,False])
mean = masked_cube.mean(axis=0)
assert np.all(mean == cube[2,:,:])
masked_cube2 = cube.mask_out_bad_beams(0.5,)
mean2 = masked_cube2.mean(axis=0)
assert np.all(mean2 == (cube[2,:,:]+cube[1,:,:])/2)
assert np.all(masked_cube2._goodbeams_mask == [False,True,True,False])
def test_convolve_to_with_bad_beams():
cube, data = cube_and_raw('vda_beams.fits')
convolved = cube.convolve_to(Beam(0.5*u.arcsec))
with pytest.raises(ValueError) as exc:
# should not work: biggest beam is 0.4"
convolved = cube.convolve_to(Beam(0.35*u.arcsec))
assert exc.value.args[0] == "Beam could not be deconvolved"
# middle two beams are smaller than 0.4
masked_cube = cube.mask_channels([False, True, True, False])
# should work: biggest beam is 0.3 arcsec (major)
convolved = masked_cube.convolve_to(Beam(0.35*u.arcsec))
# this is a copout test; should really check for correctness...
assert np.all(np.isfinite(convolved.filled_data[1:3]))
def test_jybeam_factors():
cube, data = cube_and_raw('vda_beams.fits')
assert_allclose(cube.jtok_factors(),
[15111171.12641629, 10074201.06746361, 10074287.73828087,
15111561.14508185])
def test_channelmask_singlebeam():
cube, data = cube_and_raw('adv.fits')
masked_cube = cube.mask_channels([False, True, True, False])
assert np.all(masked_cube.mask.include()[:,0,0] == [False, True, True, False])
def test_mad_std():
cube, data = cube_and_raw('adv.fits')
if int(astropy.__version__[0]) < 2:
with pytest.raises(NotImplementedError) as exc:
cube.mad_std()
else:
# mad_std run manually on data
result = np.array([[0.15509701, 0.45763670],
[0.55907956, 0.42932451],
[0.48819454, 0.25499305]])
np.testing.assert_almost_equal(cube.mad_std(axis=0).value, result)
mcube = cube.with_mask(cube < 0.98*u.K)
result2 = np.array([[0.15509701, 0.45763670],
[0.55907956, 0.23835865],
[0.48819454, 0.25499305]])
np.testing.assert_almost_equal(mcube.mad_std(axis=0).value, result2)
def test_caching():
cube, data = cube_and_raw('adv.fits')
assert len(cube._cache) == 0
worldextrema = cube.world_extrema
assert len(cube._cache) == 1
# see https://stackoverflow.com/questions/46181936/access-a-parent-class-property-getter-from-the-child-class
world_extrema_function = base_class.SpatialCoordMixinClass.world_extrema.fget.wrapped_function
assert cube.world_extrema is cube._cache[(world_extrema_function, ())]
np.testing.assert_almost_equal(worldextrema.value,
cube.world_extrema.value)
def test_spatial_smooth_g2d():
cube, data = cube_and_raw('adv.fits')
#
# Guassian 2D smoothing test
#
g2d = Gaussian2DKernel(3)
cube_g2d = cube.spatial_smooth(g2d)
# Check first slice
result0 = np.array([[ 0.06653894, 0.06598313],
[ 0.07206352, 0.07151016],
[ 0.0702898 , 0.0697944 ]])
np.testing.assert_almost_equal(cube_g2d[0].value, result0)
# Check third slice
result2 = np.array([[ 0.04217102, 0.04183251],
[ 0.04470876, 0.04438826],
[ 0.04269588, 0.04242956]])
np.testing.assert_almost_equal(cube_g2d[2].value, result2)
def test_spatial_smooth_t2d():
cube, data = cube_and_raw('adv.fits')
#
# Tophat 2D smoothing test
#
t2d = Tophat2DKernel(3)
cube_t2d = cube.spatial_smooth(t2d)
# Check first slice
result0 = np.array([[ 0.14864167, 0.14864167],
[ 0.14864167, 0.14864167],
[ 0.14864167, 0.14864167]])
np.testing.assert_almost_equal(cube_t2d[0].value, result0)
# Check third slice
result2 = np.array([[ 0.09203958, 0.09203958],
[ 0.09203958, 0.09203958],
[ 0.09203958, 0.09203958]])
np.testing.assert_almost_equal(cube_t2d[2].value, result2)
@pytest.mark.skipif('not SCIPYOK')
def test_spatial_smooth_median():
cube, data = cube_and_raw('adv.fits')
cube_median = cube.spatial_smooth_median(3)
# Check first slice
result0 = np.array([[ 0.54671028, 0.54671028],
[ 0.89482735, 0.77513282],
[ 0.93949894, 0.89482735]])
np.testing.assert_almost_equal(cube_median[0].value, result0)
# Check third slice
result2 = np.array([[ 0.38867729, 0.35675333],
[ 0.38867729, 0.35675333],
[ 0.35675333, 0.54269608]])
np.testing.assert_almost_equal(cube_median[2].value, result2)
@pytest.mark.skipif('not SCIPYOK')
def test_spectral_smooth_median():
cube, data = cube_and_raw('adv.fits')
cube_spectral_median = cube.spectral_smooth_median(3)
# Check first slice
result = np.array([0.77513282, 0.35675333, 0.35675333, 0.98688694])
np.testing.assert_almost_equal(cube_spectral_median[:,1,1].value, result)
@pytest.mark.skipif('not SCIPYOK')
@pytest.mark.skipif('not JOBLIB_INSTALLED')
def test_spectral_smooth_median_4cores():
cube, data = cube_and_raw('adv.fits')
cube_spectral_median = cube.spectral_smooth_median(3, num_cores=4)
# Check first slice
result = np.array([0.77513282, 0.35675333, 0.35675333, 0.98688694])
np.testing.assert_almost_equal(cube_spectral_median[:,1,1].value, result)
def test_initialization_from_units():
"""
Regression test for issue 447
"""
cube, data = cube_and_raw('adv.fits')
newcube = SpectralCube(data=cube.filled_data[:], wcs=cube.wcs)
assert newcube.unit == cube.unit
def test_varyres_spectra():
cube, data = cube_and_raw('vda_beams.fits')
assert isinstance(cube, VaryingResolutionSpectralCube)
sp = cube[:,0,0]
assert isinstance(sp, VaryingResolutionOneDSpectrum)
assert hasattr(sp, 'beams')
sp = cube.mean(axis=(1,2))
assert isinstance(sp, VaryingResolutionOneDSpectrum)
assert hasattr(sp, 'beams')
def test_median_2axis():
"""
As of this writing the bottleneck.nanmedian did not accept an axis that is a tuple/list so this test
is to make sure that is properly taken into account.
:return:
"""
cube, data = cube_and_raw('adv.fits')
cube_median = cube.median(axis=(1, 2))
# Check first slice
result0 = np.array([0.83498009, 0.2606566 , 0.37271531, 0.48548023])
np.testing.assert_almost_equal(cube_median.value, result0)
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