correlation_threshold=avg_threshold, aligning_option='dft',
method=avg_method, debugging=debug)
avg_counter = avg_counter + flag_avg
avg_obj = avg_obj / avg_counter
print('\nAverage performed over ', avg_counter, 'reconstructions\n')
del obj, ref_obj
gc.collect()
################
# unwrap phase #
################
phase, extent_phase = pu.unwrap(avg_obj, support_threshold=threshold_unwrap_refraction, debugging=debug)
print('Extent of the phase over an extended support (ceil(phase range))~ ', int(extent_phase), '(rad)')
phase = pru.wrap(phase, start_angle=-extent_phase/2, range_angle=extent_phase)
if debug:
gu.multislices_plot(phase, width_z=2*zrange, width_y=2*yrange, width_x=2*xrange,
plot_colorbar=True, title='Phase after unwrap + wrap')
#############################################
# phase ramp removal before phase filtering #
#############################################
amp, phase, rampz, rampy, rampx = pu.remove_ramp(amp=abs(avg_obj), phase=phase, initial_shape=original_size,
method='gradient', amplitude_threshold=isosurface_strain,
gradient_threshold=threshold_gradient)
del avg_obj
gc.collect()
if debug:
gu.multislices_plot(phase, width_z=2*zrange, width_y=2*yrange, width_x=2*xrange,
indexing='ij')
phase = z + y + x
if debug and not flat_phase:
gu.multislices_plot(phase,
sum_frames=False,
plot_colorbar=True,
width_z=200,
width_y=200,
width_x=200,
vmin=-phase_range,
vmax=phase_range,
cmap=my_cmap,
title='Phase before wrapping\n')
phase = pru.wrap(phase, start_angle=-np.pi, range_angle=2 * np.pi)
support[abs(amp) < support_threshold * abs(amp).max()] = 0
del amp
volume = support.sum() * voxel_size**3 # in nm3
print('estimated volume', volume, ' nm3')
phase[support == 0] = 0
if ref_axis_outplane == "x":
_, _, strain = np.gradient(
planar_dist / (2 * np.pi) * phase,
voxel_size) # q is along x after rotating the crystal
elif ref_axis_outplane == "y":
_, strain, _ = np.gradient(
phase, (numz // 2 - zcom, numy // 2 - ycom, numx // 2 - xcom),
axis=(0, 1, 2))
support = np.zeros(amp.shape)
support[amp > isosurface * amp.max()] = 1
zcom, ycom, xcom = center_of_mass(support)
zcom, ycom, xcom = [
int(np.rint(zcom)),
int(np.rint(ycom)),
int(np.rint(xcom))
] # used for the reference phase
phase, extent_phase = pu.unwrap(amp * np.exp(1j * phase),
support_threshold=0.05,
debugging=debug)
phase = pru.wrap(phase,
start_angle=-extent_phase / 2,
range_angle=extent_phase)
phase = phase - phase[zcom, ycom, xcom]
phase, extent_phase = pu.unwrap(amp * np.exp(1j * phase),
support_threshold=0.05,
debugging=debug)
phase = pru.wrap(
phase, start_angle=-extent_phase / 2,
range_angle=extent_phase) # rewrap after modifying phase
ref_amp = np.copy(amp)
else: # align it with the reference object
# TODO: interpolate object if the shape is different from ref_amp (different voxel sizes between datasets)
shiftz, shifty, shiftx = reg.getimageregistration(ref_amp,
amp,
precision=1000)
print('Shift of array', index, 'with the reference array:', shiftz,