def generate_pattern(self,
pattern_size_pixels=1024,
detector_distance=740e-3,
detector_pixel_size=75e-6,
wavelength=conversions.ev_to_m(1100),
number_of_scattered_photons=1e9):
#Method for simulating a diffraction pattern, based on generate_single.py by Tomas Ekeberg. Wavelength in meters.
# Small angle approximation
max_scattering_angle = pattern_size_pixels * detector_pixel_size / (
2 * detector_distance)
real_space_pixel_size = wavelength / (max_scattering_angle * 2)
# Sample is self
real_space = np.zeros((pattern_size_pixels, ) * 2)
support = tools.circular_mask(pattern_size_pixels,
self.particle_size / 2)
# Use FFT to simulate diffraction pattern
tools.insert_array_at_center(real_space, self.particle.sum(axis=0))
diffracted_wave = np.fft.fftshift(
np.fft.fft2(np.fft.fftshift(real_space)))
rescale_factor = np.sqrt(number_of_scattered_photons /
(abs(diffracted_wave)**2).sum())
diffracted_wave *= rescale_factor
real_space *= rescale_factor
detected_intensity = np.random.poisson(abs(diffracted_wave)**2)
#Utput
return detected_intensity, diffracted_wave, support
import numpy as np import spimage import matplotlib.pyplot as plt """ 1. Create the particle 2. Generate the diffraction pattern 3. Multiple phase retrieveal (PRTF) 4. Output relevant data (What data is relevant?) This should happen for each particle, with parameters size and photon intensity (logrange)( Feature size?). """ #Setup values pattern_size_pixels = 1024 detector_distance = 740e-3 detector_pixel_size = 75e-6 wavelength = conversions.ev_to_m(1100) #Iteration process f_len = int(3) p_len = int(3) np_len = int(3) index = int(os.environ["SLURM_ARRAY_TASK_ID"]) ps1 = np.linspace(20, 200, p_len) a = np.zeros((f_len, p_len, np_len)) ps3 = ps1[np.newaxis, :, np.newaxis] + a particle_size = int(ps3.flatten()[index]) fs1 = np.linspace(particle_size / 10, particle_size / 5, f_len) fs3 = fs1[:, np.newaxis, np.newaxis] + a feature_size = int(fs3.flatten()[index])
# Class for generating an Elser Particle for testing diffraction patterns
# Takes inputs for particle and detector in SI units
# By Vidar Elsin, based on generate_single by Tomas Ekeberg and classes.py by August Wolter
from eke import elser_particles
from eke import conversions
from eke import tools
import numpy as np
# SETUP AND DETECTOR SETTINGS
pattern_size_pixels = 1024
detector_distance = 400.e-3
detector_pixel_size = 75e-6
wavelength = conversions.ev_to_m(1100) # ca 1.127 nm
#number_of_photons = 2.5e6
number_of_photons = 1e9 #high
#number_of_photons = 2.5e4 #low
# Small angle approximation
max_scattering_angle = (pattern_size_pixels *
detector_pixel_size) / (2 * detector_distance)
real_space_pixel_size = wavelength / max_scattering_angle
settings = {
'pattern_size_pixels': pattern_size_pixels,
'detector_distance': detector_distance,
'detector_pixel_size': detector_pixel_size,
'wavelength': wavelength,
'number_of_photons': number_of_photons,
'real_space_pixel_size': real_space_pixel_size,