def test_pixelated_detector():
gpts = (512, 512)
extent = (12, 12)
probe = Probe(energy=60e3, extent=extent, gpts=gpts, semiangle_cutoff=80, rolloff=0.2)
detector = PixelatedDetector(max_angle=30, resample='uniform')
wave = probe.build().downsample(max_angle=30)
measurement = detector.detect(wave)
assert measurement.shape == wave.array.shape
detector = PixelatedDetector(max_angle='valid', resample='uniform')
measurement = detector.detect(wave)
assert measurement.shape == wave.array.shape
detector = PixelatedDetector(max_angle='limit', resample='uniform')
measurement = detector.detect(wave)
assert measurement.shape == wave.array.shape
gpts = (512, 512)
extent = (10, 12)
probe = Probe(energy=60e3, extent=extent, gpts=gpts, semiangle_cutoff=80, rolloff=0.2)
detector = PixelatedDetector(max_angle='valid', resample='uniform')
wave = probe.build()
measurement = detector.allocate_measurement(wave)
assert measurement.array.shape[0] == measurement.array.shape[1]
def test_gridscan_to_file(tmp_path):
d = tmp_path / 'sub'
d.mkdir()
path = d / 'measurement2.hdf5'
atoms = read(_set_path('orthogonal_graphene.cif'))
potential = Potential(atoms=atoms, sampling=.05)
probe = Probe(energy=200e3, semiangle_cutoff=30)
probe.grid.match(potential)
scan = GridScan(start=[0, 0], end=[0, potential.extent[1]], gpts=(10, 9))
detector = PixelatedDetector()
export_detector = PixelatedDetector(save_file=path)
measurements = probe.scan(scan, [detector, export_detector],
potential,
pbar=False)
measurement = measurements[0]
imported_measurement = Measurement.read(measurements[1])
assert np.allclose(measurement.array, imported_measurement.array)
assert measurement.calibrations[0] == imported_measurement.calibrations[0]
assert measurement.calibrations[1] == imported_measurement.calibrations[1]
def test_interpolate():
detector = PixelatedDetector()
array = np.random.rand(2, 32, 32)
gpts = array.shape[-2:]
new_gpts = (16, 9)
v, u, vw, uw = detector._bilinear_nodes_and_weight(gpts, new_gpts,
(1 / 32, 1 / 32),
(1 / 16, 1 / 9), np)
interpolated = interpolate_bilinear_cpu(array, v, u, vw, uw)
kx, ky = spatial_frequencies(gpts, (1, 1))
kx = np.fft.fftshift(kx)
ky = np.fft.fftshift(ky)
kx_new, ky_new = spatial_frequencies(new_gpts, (1, 1))
kx_new = np.fft.fftshift(kx_new)
ky_new = np.fft.fftshift(ky_new)
px, py = np.meshgrid(kx_new, ky_new, indexing='ij')
p = np.array([px.ravel(), py.ravel()]).T
interpolated2 = interpn((kx, ky), array[0], p)
interpolated2 = interpolated2.reshape(new_gpts)
assert np.allclose(interpolated[0], interpolated2)
def test_resample_diffraction_patterns():
for extent in [(5, 10), (5, 8)]:
for gpts in [(256, 256), (256, 296)]:
probe = Probe(energy=60e3,
extent=extent,
gpts=gpts,
semiangle_cutoff=80,
rolloff=0.2)
detector = PixelatedDetector(max_angle='valid', resample='uniform')
wave = probe.build()
measurement = detector.detect(wave)
measurement /= measurement.max()
probe = Probe(energy=60e3,
extent=(5, 5),
gpts=(256, 256),
semiangle_cutoff=80,
rolloff=0.2)
wave = probe.build()
measurement2 = detector.detect(wave)
measurement2 /= measurement2.max()
s1 = (measurement2.shape[-2] - measurement.shape[-2]) // 2
s2 = (measurement2.shape[-1] - measurement.shape[-1]) // 2
measurement2 = measurement2[..., s1:s1 + measurement.shape[-2],
s2:s2 + measurement.shape[-1]]
assert np.all(np.abs(measurement2[0] - measurement[0]) < .5)
def test_detector_consistency():
atoms = read('data/srtio3_100.cif')
atoms *= (4, 4, 1)
potential = Potential(
atoms,
gpts=256,
projection='infinite',
slice_thickness=.5,
parametrization='kirkland',
).build(pbar=False)
probe = Probe(energy=300e3, semiangle_cutoff=9.4, rolloff=0.05)
flexible_detector = FlexibleAnnularDetector()
annular_detector = AnnularDetector(inner=20, outer=40)
pixelated_detector = PixelatedDetector()
end = (potential.extent[0] / 4, potential.extent[1] / 4)
gridscan = GridScan(start=[0, 0], end=end, sampling=.5)
measurements = probe.scan(
gridscan, [flexible_detector, pixelated_detector, annular_detector],
potential,
pbar=False)
assert np.allclose(measurements[0].integrate(20, 40).array,
measurements[2].array)
assert np.allclose(
annular_detector.integrate(measurements[1]).array,
measurements[2].array)
def test_preallocated_measurement():
atoms = read(
os.path.join(os.path.dirname(os.path.abspath(__file__)),
'data/amorphous_carbon.cif'))
potential = Potential(atoms,
gpts=256,
slice_thickness=1,
projection='infinite',
parametrization='kirkland').build(pbar=False)
scan = GridScan(start=[0, 0], end=potential.extent, gpts=4)
detector1 = AnnularDetector(inner=70, outer=100)
probe = Probe(semiangle_cutoff=15,
energy=300e3,
extent=potential.extent,
gpts=512)
measurement = detector1.allocate_measurement(probe, scan)
probe.scan(scan, detector1, potential, measurement, pbar=False)
assert np.any(measurement.array > 0)
detector2 = PixelatedDetector()
measurement1 = detector1.allocate_measurement(probe, scan)
measurement2 = detector2.allocate_measurement(probe, scan)
with pytest.raises(ValueError) as e:
probe.scan(scan, [detector1, detector2],
potential,
measurement1,
pbar=False)
probe.scan(scan, [detector1, detector2],
potential, {
detector1: measurement1,
detector2: measurement2
},
pbar=False)