def test_energy():
energy = Accelerator(energy=300e3)
assert energy.energy == 300e3
assert np.isclose(energy.wavelength, energy2wavelength(300e3))
energy.energy = 200e3
assert np.isclose(energy.wavelength, energy2wavelength(200e3))
def __init__(self,
expansion_cutoff: float,
interpolation: int = 1,
ctf: CTF = None,
extent: Union[float, Sequence[float]] = None,
gpts: Union[int, Sequence[int]] = None,
sampling: Union[float, Sequence[float]] = None,
energy: float = None,
device: str = 'cpu',
storage: str = None):
if not isinstance(interpolation, int):
raise ValueError('Interpolation factor must be int')
self._interpolation = interpolation
self._expansion_cutoff = expansion_cutoff
self._ctf = ctf
self._grid = Grid(extent=extent, gpts=gpts, sampling=sampling)
self._accelerator = Accelerator(energy=energy)
self._device = device
if storage is None:
storage = device
self._storage = storage
def __init__(self,
array: np.ndarray,
expansion_cutoff: float,
interpolation: int,
k: Tuple[np.ndarray, np.ndarray],
ctf: CTF = None,
extent: Union[float, Sequence[float]] = None,
sampling: Union[float, Sequence[float]] = None,
energy: float = None,
device='cpu'):
self._array = array
self._interpolation = interpolation
self._expansion_cutoff = expansion_cutoff
self._k = k
self._grid = Grid(extent=extent,
gpts=array.shape[1:],
sampling=sampling,
lock_gpts=True)
self._accelerator = Accelerator(energy=energy)
if ctf is None:
ctf = CTF(semiangle_cutoff=expansion_cutoff, rolloff=.1)
self.set_ctf(ctf)
self._device = device
def __init__(self,
array: np.ndarray,
slice_thicknesses: Union[float, Sequence],
extent: np.ndarray = None,
sampling: np.ndarray = None,
energy: float = None):
self._accelerator = Accelerator(energy=energy)
super().__init__(array, slice_thicknesses, extent, sampling)
def __init__(self,
extent: Union[float, Sequence[float]] = None,
gpts: Union[int, Sequence[int]] = None,
sampling: Union[float, Sequence[float]] = None,
energy: float = None,
device: str = 'cpu'):
self._grid = Grid(extent=extent, gpts=gpts, sampling=sampling)
self._accelerator = Accelerator(energy=energy)
self._device = device
def __init__(self,
semiangle_cutoff: float = np.inf,
rolloff: float = 0.,
focal_spread: float = 0.,
angular_spread: float = 0.,
gaussian_spread: float = 0.,
energy: float = None,
parameters: Mapping[str, float] = None,
**kwargs):
for key in kwargs.keys():
if ((key not in polar_symbols)
and (key not in polar_aliases.keys())):
raise ValueError('{} not a recognized parameter'.format(key))
self.changed = Event()
self._accelerator = Accelerator(energy=energy)
self._semiangle_cutoff = semiangle_cutoff
self._rolloff = rolloff
self._focal_spread = focal_spread
self._angular_spread = angular_spread
self._gaussian_spread = gaussian_spread
self._parameters = dict(zip(polar_symbols, [0.] * len(polar_symbols)))
if parameters is None:
parameters = {}
parameters.update(kwargs)
self.set_parameters(parameters)
def parametrization_property(key):
def getter(self):
return self._parameters[key]
def setter(self, value):
old = getattr(self, key)
self._parameters[key] = value
self.changed.notify(**{
'notifier': self,
'property_name': key,
'change': old != value
})
return property(getter, setter)
for symbol in polar_symbols:
setattr(self.__class__, symbol, parametrization_property(symbol))
for key, value in polar_aliases.items():
if key != 'defocus':
setattr(self.__class__, key, parametrization_property(value))
def __init__(self,
array: np.ndarray,
extent: Union[float, Sequence[float]] = None,
sampling: Union[float, Sequence[float]] = None,
energy: float = None):
if len(array.shape) < 2:
raise RuntimeError(
'Wave function array should be have 2 dimensions or more')
self._array = array
self._grid = Grid(extent=extent,
gpts=array.shape[-2:],
sampling=sampling,
lock_gpts=True)
self._accelerator = Accelerator(energy=energy)
def test_accelerator_event():
accelerator = Accelerator(300e3)
accelerator.energy = 200e3
assert accelerator.changed._notify_count == 1
def test_energy_raises():
accelerator1 = Accelerator(300e3)
accelerator2 = Accelerator()
with pytest.raises(RuntimeError):
accelerator2.check_is_defined()
accelerator2.energy = 200e3
with pytest.raises(RuntimeError):
accelerator1.check_match(accelerator2)
accelerator2.energy = accelerator1.energy
accelerator1.check_match(accelerator2)