def to_data(self, obj):
coords = SpectralCoordinates(obj.spectral_axis)
data = Data(coords=coords)
data['flux'] = obj.flux
data.get_component('flux').units = str(obj.unit)
data.meta.update(obj.meta)
return data
def test_to_spectrum1d_with_spectral_coordinates():
coords = SpectralCoordinates([1, 4, 10] * u.micron)
data = Data(label='spectrum1d', coords=coords)
data.add_component(Component(np.array([3, 4, 5]), units='Jy'), 'x')
assert_allclose(data.coords.pixel2world([0, 0.5, 1, 1.5, 2]),
[[1, 2.5, 4, 7, 10]])
spec = data.get_object(Spectrum1D, attribute=data.id['x'])
assert_quantity_allclose(spec.spectral_axis, [1, 4, 10] * u.micron)
assert_quantity_allclose(spec.flux, [3, 4, 5] * u.Jy)
def to_data(self, obj):
coords = SpectralCoordinates(obj.spectral_axis)
data = Data(coords=coords)
data['flux'] = obj.flux
data[
'uncertainty'] = obj.uncertainty.array if obj.uncertainty is not None else np.ones(
obj.flux.shape)
data['mask'] = obj.mask if hasattr(
obj, 'mask') and obj.mask is not None else np.zeros(
obj.flux.shape).astype(bool)
data.get_component('flux').units = str(obj.unit)
data.get_component('uncertainty').units = str(obj.unit)
data.meta.update(obj.meta)
return data
def to_data(self, obj):
coords = SpectralCoordinates(obj.spectral_axis)
data = Data(coords=coords)
data['flux'] = obj.flux
data.get_component('flux').units = str(obj.unit)
# Include uncertainties if they exist
if obj.uncertainty is not None:
data['uncertainty'] = obj.uncertainty.quantity
data.get_component('uncertainty').units = str(obj.uncertainty.unit)
data.meta.update(
{'uncertainty_type': obj.uncertainty.uncertainty_type})
# Include mask if it exists
if obj.mask is not None:
data['mask'] = obj.mask
data.meta.update(obj.meta)
return data
def to_data(self, obj):
# Glue expects spectral axis first for cubes (opposite of specutils).
# Swap the spectral axis to first here. to_object doesn't need this because
# Spectrum1D does it automatically on initialization.
if len(obj.flux.shape) == 3:
data = Data(coords=obj.wcs.swapaxes(-1, 0))
data['flux'] = np.swapaxes(obj.flux, -1, 0)
data.get_component('flux').units = str(obj.unit)
else:
if obj.flux.ndim == 1 and obj.wcs.world_n_dim == 1 and isinstance(
obj.wcs, GWCS):
data = Data(coords=SpectralCoordinates(obj.spectral_axis))
elif obj.flux.ndim == 2 and obj.wcs.world_n_dim == 1:
data = Data(coords=PaddedSpectrumWCS(obj.wcs))
else:
data = Data(coords=obj.wcs)
data['flux'] = obj.flux
data.get_component('flux').units = str(obj.unit)
# Include uncertainties if they exist
if obj.uncertainty is not None:
if len(obj.flux.shape) == 3:
data['uncertainty'] = np.swapaxes(obj.uncertainty.quantity, -1,
0)
else:
data['uncertainty'] = obj.uncertainty.quantity
data.get_component('uncertainty').units = str(obj.uncertainty.unit)
data.meta.update(
{'uncertainty_type': obj.uncertainty.uncertainty_type})
# Include mask if it exists
if obj.mask is not None:
if len(obj.flux.shape) == 3:
data['mask'] = np.swapaxes(obj.mask, -1, 0)
else:
data['mask'] = obj.mask
data.meta.update(obj.meta)
return data
def test_to_spectrum1d_default_attribute():
coords = SpectralCoordinates([1, 4, 10] * u.micron)
data = Data(label='spectrum1d', coords=coords)
with pytest.raises(ValueError) as exc:
data.get_object(Spectrum1D)
assert exc.value.args[0] == 'Data object has no attributes.'
data.add_component(Component(np.array([3, 4, 5]), units='Jy'), 'x')
spec = data.get_object(Spectrum1D)
assert_quantity_allclose(spec.flux, [3, 4, 5] * u.Jy)
data.add_component(Component(np.array([3, 4, 5]), units='Jy'), 'y')
with pytest.raises(ValueError) as exc:
data.get_object(Spectrum1D)
assert exc.value.args[0] == ('Data object has more than one attribute, so '
'you will need to specify which one to use as '
'the flux for the spectrum using the attribute= '
'keyword argument.')