PRTF-evaluation

Scripts to evaluate the correctness of the phase-retrieval transfer function

Example

Create particle

To change detector settings and photon count, edit the file particle_class.py. Class is imported by create_elser_particle.py and used to create test particles and save the data.

python create_elser_particle.py {output directory} {particle id} {particle size in m} {feature size as decimal}

python create_elser_particle.py /home/elsin/scratch/particles/ 001 450e-9 0.2

Creates a test particle in the folder /home/elsin/scrath/particles/particle_001/

The outputs are in the form of hdf5 files containing the relevant particle data:

particle_diffracted_wave.h5 Fourier transform of the binary contrast matrix particle_detected_intensity.h5 Poisson distribution using fourier amplitudes squared as lambda particle_support.h5 A circular mask showing location of the particle particle_shape.hdf5 Contains the binary contrast matrix, parameters

Iterative phase retrieval

Edit the file multi_phase_particle.py to set the number of independant retrievals, target particle, input and output directories.

sbatch multi_phase_particle.py

Phase retrieval transfer function

Edit the file prtf.py to change input and output directories.

sbatch prtf.py

Plots of the PRTF were done using Tomas Ekeberg's Python Tools library. While in the output directory of the prtf.py file:

eke_plot_prtf.py prtf -w 1.127 -d 400000 -p 75

True vs reconstructed PRTF

Uses the prtf function from Hawk.

prtf {output name} {target files}

example from a subdirectory in the particle folder:

prtf prtf_true_vs_rec prtf-avg_image.h5 ../particle_real_space.h5

Plotting

To create the images used in the report, run the script master_plotter.py on a target test partcicle directory.

example:

python master_plotter.py /home/elsin/scratch/particles/particle_001/