def test_freq2(shape):
x = [np.linspace(0, 1, s) if s > 1 else np.array([0]) for s in shape]
y = to_recip(from_recip(x))
z = from_recip(to_recip(x))
for i in range(len(shape)):
assert abs(x[i] - y[i] + y[i].min()).max() < 1e-6
assert abs(x[i] - z[i] + z[i].min()).max() < 1e-6
def FT(self, y, out=None):
"""
Parameters
----------
y : `numpy.ndarray`, (nx, ny, nz, 3) or list of arrays of shape [(nx,), (ny,), (nz,)]
Mesh of Fourier coordinates at which to evaluate the probe density
out : `numpy.ndarray`, (nx, ny, nz), optional
If provided then computation is performed inplace
Returns
-------
out : `numpy.ndarray`, (nx, ny, nz)
An array equal to `FourierTransform(probe)(y)`
"""
if hasattr(y, "shape"):
y_start = y[(0, ) * (y.ndim - 1)]
y_end = y[(-1, ) * (y.ndim - 1)]
y = [
linspace(y_start[i], y_end[i], y.shape[i], endpoint=True)
for i in range(3)
]
x = from_recip(y)
ft = get_DFT(x, y)[0]
tmp = ft(self(x, out=out))
if out is None:
out = tmp
else:
out[...] = tmp
return out
def __init__(self,
accelerating_voltage,
detector,
reciprocal_mesh=False,
debye_waller_factors=None):
self.wavelength = get_electron_wavelength(accelerating_voltage)
# Always store a 'real' mesh
self.detector = detector if not reciprocal_mesh else from_recip(
detector)
if debye_waller_factors:
raise NotImplementedError('Not implemented for this simulator')
self.debye_waller_factors = debye_waller_factors or {}
def test_freq(shape, dX, rX, dY, rY):
x, y = get_recip_points(len(shape), shape, dX, rX, dY, rY)
X, Y = from_recip(y), to_recip(x)
assert len(x) == len(shape)
assert len(y) == len(shape)
assert len(X) == len(shape)
assert len(Y) == len(shape)
for i in range(len(shape)):
assert y[i].size == x[i].size
if shape[i] is None:
if dX[i] is not None:
assert abs(x[i].item(1) - x[i].item(0)) <= dX[i] + 1e-8
if rY[i] is not None:
assert y[i].ptp() >= rY[i] - 1e-8
if rX[i] is not None:
assert x[i].ptp() >= rX[i] - 1e-8
if dY[i] is not None:
assert abs(y[i].item(1) - y[i].item(0)) <= dY[i] + 1e-8
np.testing.assert_allclose(x[i], X[i], 1e-5)
np.testing.assert_allclose(y[i], Y[i], 1e-5)
def FT(self, y, out=None):
"""Returns the Fourier transform of func on the mesh `y`. Again,
if `out` is provided then computation is `inplace`. If `y` is a
list of arrays then it is converted into a mesh first. If this
function is not overridden then an approximation is made using
`func` and the `fft`.
Parameters
----------
y : numpy.ndarray, (nx, ny, nz, 3) or list of arrays of shape
[(nx,), (ny,), (nz,)]
Mesh of Fourier coordinates at which to evaluate the probe
density.
out : numpy.ndarray, (nx, ny, nz), optional
If provided then computation is performed inplace.
Returns
-------
out : numpy.ndarray, (nx, ny, nz)
An array equal to `FourierTransform(probe)(y)`.
"""
if hasattr(y, "shape"):
y_start = y[(0, ) * (y.ndim - 1)]
y_end = y[(-1, ) * (y.ndim - 1)]
y = [
linspace(y_start[i], y_end[i], y.shape[i], endpoint=True)
for i in range(3)
]
x = from_recip(y)
ft = get_DFT(x, y)[0]
tmp = ft(self(x, out=out))
if out is None:
out = tmp
else:
out[...] = tmp
return out
def __init__(self, accelerating_voltage, detector, reciprocal_mesh=False):
self.wavelength = get_electron_wavelength(accelerating_voltage)
# Always store a 'real' mesh
self.detector = detector if not reciprocal_mesh else from_recip(detector)