def setup_method(self, method):
# Set the stack
self.ref_holo = hs.stack([reference_hologram()] * 2)
self.ref_holo = hs.stack([self.ref_holo] * 3)
# Parameters measured using Gatan HoloWorks:
self.REF_FRINGE_SPACING = 3.48604
self.REF_FRINGE_SAMPLING = 3.7902
# Measured using the definition of fringe contrast from the centre of image
self.REF_FRINGE_CONTRAST = 0.0736
# Prepare test data and derived statistical parameters
self.ref_carrier_freq = 1.0 / self.REF_FRINGE_SAMPLING
self.ref_carrier_freq_nm = 1.0 / self.REF_FRINGE_SPACING
ht = self.ref_holo.metadata.Acquisition_instrument.TEM.beam_energy
momentum = (
2
* constants.m_e
* constants.elementary_charge
* ht
* 1000
* (
1
+ constants.elementary_charge
* ht
* 1000
/ (2 * constants.m_e * constants.c ** 2)
)
)
wavelength = constants.h / np.sqrt(momentum) * 1e9 # in nm
self.ref_carrier_freq_mrad = self.ref_carrier_freq_nm * 1000 * wavelength
def test_statistics(parallel, lazy, single_values, fringe_contrast_algorithm):
# Parameters measured using Gatan HoloWorks:
REF_FRINGE_SPACING = 3.48604
REF_FRINGE_SAMPLING = 3.7902
# Measured using the definition of fringe contrast from the centre of image
REF_FRINGE_CONTRAST = 0.0736
RTOL = 1e-5
# 0. Prepare test data and derived statistical parameters
ref_carrier_freq = 1. / REF_FRINGE_SAMPLING
ref_carrier_freq_nm = 1. / REF_FRINGE_SPACING
ref_holo = hs.stack([reference_hologram(), reference_hologram()])
ref_holo = hs.stack([ref_holo, ref_holo, ref_holo])
ht = ref_holo.metadata.Acquisition_instrument.TEM.beam_energy
momentum = 2 * constants.m_e * constants.elementary_charge * ht * \
1000 * (1 + constants.elementary_charge * ht *
1000 / (2 * constants.m_e * constants.c ** 2))
wavelength = constants.h / np.sqrt(momentum) * 1e9 # in nm
ref_carrier_freq_mrad = ref_carrier_freq_nm * 1000 * wavelength
if lazy:
ref_holo.as_lazy()
# 1. Test core functionality
stats = ref_holo.statistics(high_cf=True,
parallel=parallel,
single_values=single_values,
fringe_contrast_algorithm=fringe_contrast_algorithm)
if single_values:
# Fringe contrast in experimental conditions can be only an estimate
# therefore tolerance is 10%:
assert_allclose(
stats['Fringe contrast'],
REF_FRINGE_CONTRAST,
rtol=0.1)
assert_allclose(
stats['Fringe sampling (px)'],
REF_FRINGE_SAMPLING,
rtol=RTOL)
assert_allclose(
stats['Fringe spacing (nm)'],
REF_FRINGE_SPACING,
rtol=RTOL)
assert_allclose(
stats['Carrier frequency (1 / nm)'],
ref_carrier_freq_nm,
rtol=RTOL)
assert_allclose(
stats['Carrier frequency (1/px)'],
ref_carrier_freq,
rtol=RTOL)
assert_allclose(
stats['Carrier frequency (mrad)'],
ref_carrier_freq_mrad,
rtol=RTOL)
else:
ref_fringe_contrast_stack = np.repeat(
REF_FRINGE_CONTRAST, 6).reshape((3, 2))
ref_fringe_sampling_stack = np.repeat(
REF_FRINGE_SAMPLING, 6).reshape((3, 2))
ref_fringe_spacing_stack = np.repeat(
REF_FRINGE_SPACING, 6).reshape((3, 2))
ref_carrier_freq_nm_stack = np.repeat(
ref_carrier_freq_nm, 6).reshape((3, 2))
ref_carrier_freq_stack = np.repeat(ref_carrier_freq, 6).reshape((3, 2))
ref_carrier_freq_mrad_stack = np.repeat(
ref_carrier_freq_mrad, 6).reshape((3, 2))
# Fringe contrast in experimental conditions can be only an estimate
# therefore tolerance is 10%:
assert_allclose(
stats['Fringe contrast'].data,
ref_fringe_contrast_stack,
rtol=0.1)
assert_allclose(
stats['Fringe sampling (px)'].data,
ref_fringe_sampling_stack,
rtol=RTOL)
assert_allclose(
stats['Fringe spacing (nm)'].data,
ref_fringe_spacing_stack,
rtol=RTOL)
assert_allclose(
stats['Carrier frequency (1 / nm)'].data,
ref_carrier_freq_nm_stack,
rtol=RTOL)
assert_allclose(
stats['Carrier frequency (1/px)'].data,
ref_carrier_freq_stack,
rtol=RTOL)
assert_allclose(
stats['Carrier frequency (mrad)'].data,
ref_carrier_freq_mrad_stack,
rtol=RTOL)
# 2. Test raises:
holo_raise = hs.signals.HologramImage(np.random.random(20).reshape((5, 4)))
# 2a. Test raise for absent units:
with pytest.raises(ValueError):
holo_raise.statistics(sb_position=(1, 1))
holo_raise.axes_manager.signal_axes[0].units = 'nm'
holo_raise.axes_manager.signal_axes[1].units = 'nm'
# 2b. Test raise for absent beam_energy:
with pytest.raises(AttributeError):
holo_raise.statistics(sb_position=(1, 1))
holo_raise.set_microscope_parameters(beam_energy=300.)
# 2c. Test raise for wrong value of `fringe_contrast_algorithm`
with pytest.raises(ValueError):
holo_raise.statistics(
sb_position=(
1,
1),
fringe_contrast_algorithm='pure_guess')
def test_statistics(parallel, lazy, single_values, fringe_contrast_algorithm):
# Parameters measured using Gatan HoloWorks:
REF_FRINGE_SPACING = 3.48604
REF_FRINGE_SAMPLING = 3.7902
# Measured using the definition of fringe contrast from the centre of image
REF_FRINGE_CONTRAST = 0.0736
RTOL = 1e-5
# 0. Prepare test data and derived statistical parameters
ref_carrier_freq = 1. / REF_FRINGE_SAMPLING
ref_carrier_freq_nm = 1. / REF_FRINGE_SPACING
ref_holo = hs.stack([reference_hologram(), reference_hologram()])
ref_holo = hs.stack([ref_holo, ref_holo, ref_holo])
ht = ref_holo.metadata.Acquisition_instrument.TEM.beam_energy
momentum = 2 * constants.m_e * constants.elementary_charge * ht * \
1000 * (1 + constants.elementary_charge * ht *
1000 / (2 * constants.m_e * constants.c ** 2))
wavelength = constants.h / np.sqrt(momentum) * 1e9 # in nm
ref_carrier_freq_mrad = ref_carrier_freq_nm * 1000 * wavelength
if lazy:
ref_holo.as_lazy()
# 1. Test core functionality
stats = ref_holo.statistics(
high_cf=True,
parallel=parallel,
single_values=single_values,
fringe_contrast_algorithm=fringe_contrast_algorithm)
if single_values:
# Fringe contrast in experimental conditions can be only an estimate
# therefore tolerance is 10%:
assert_allclose(stats['Fringe contrast'],
REF_FRINGE_CONTRAST,
rtol=0.1)
assert_allclose(stats['Fringe sampling (px)'],
REF_FRINGE_SAMPLING,
rtol=RTOL)
assert_allclose(stats['Fringe spacing (nm)'],
REF_FRINGE_SPACING,
rtol=RTOL)
assert_allclose(stats['Carrier frequency (1 / nm)'],
ref_carrier_freq_nm,
rtol=RTOL)
assert_allclose(stats['Carrier frequency (1/px)'],
ref_carrier_freq,
rtol=RTOL)
assert_allclose(stats['Carrier frequency (mrad)'],
ref_carrier_freq_mrad,
rtol=RTOL)
else:
ref_fringe_contrast_stack = np.repeat(REF_FRINGE_CONTRAST, 6).reshape(
(3, 2))
ref_fringe_sampling_stack = np.repeat(REF_FRINGE_SAMPLING, 6).reshape(
(3, 2))
ref_fringe_spacing_stack = np.repeat(REF_FRINGE_SPACING, 6).reshape(
(3, 2))
ref_carrier_freq_nm_stack = np.repeat(ref_carrier_freq_nm, 6).reshape(
(3, 2))
ref_carrier_freq_stack = np.repeat(ref_carrier_freq, 6).reshape((3, 2))
ref_carrier_freq_mrad_stack = np.repeat(ref_carrier_freq_mrad,
6).reshape((3, 2))
# Fringe contrast in experimental conditions can be only an estimate
# therefore tolerance is 10%:
assert_allclose(stats['Fringe contrast'].data,
ref_fringe_contrast_stack,
rtol=0.1)
assert_allclose(stats['Fringe sampling (px)'].data,
ref_fringe_sampling_stack,
rtol=RTOL)
assert_allclose(stats['Fringe spacing (nm)'].data,
ref_fringe_spacing_stack,
rtol=RTOL)
assert_allclose(stats['Carrier frequency (1 / nm)'].data,
ref_carrier_freq_nm_stack,
rtol=RTOL)
assert_allclose(stats['Carrier frequency (1/px)'].data,
ref_carrier_freq_stack,
rtol=RTOL)
assert_allclose(stats['Carrier frequency (mrad)'].data,
ref_carrier_freq_mrad_stack,
rtol=RTOL)
# 2. Test raises:
holo_raise = hs.signals.HologramImage(np.random.random(20).reshape((5, 4)))
# 2a. Test raise for absent units:
with pytest.raises(ValueError):
holo_raise.statistics(sb_position=(1, 1))
holo_raise.axes_manager.signal_axes[0].units = 'nm'
holo_raise.axes_manager.signal_axes[1].units = 'nm'
# 2b. Test raise for absent beam_energy:
with pytest.raises(AttributeError):
holo_raise.statistics(sb_position=(1, 1))
holo_raise.set_microscope_parameters(beam_energy=300.)
# 2c. Test raise for wrong value of `fringe_contrast_algorithm`
with pytest.raises(ValueError):
holo_raise.statistics(sb_position=(1, 1),
fringe_contrast_algorithm='pure_guess')