This collection of scripts assembles and phases the spontaneous rocking data collected at NanoMAX during

• Experiment 20180278 Jun 2019 (data1) and
• Follow-up in-house time 20200322 (data2).

The analysis is described in

A. Björling et al, "Three-dimensional coherent Bragg imaging of spontaneously rotating nanoparticles", in preparation (2020).

The data are deposited separately in a root folder referred to as DPATH (supplied to the first script as the only command-line argument). There are nine particle hits analyzed in total four in DPATH/data1 and five in DPATH/data2.

Each particle hit is analyzed in its own folder, where the following scripts are run in sequence.

• 1_pick_frames.py $DPATH picks a specific CDI hit and crops the data.
• 2_assemble.py does the diffraction volume assembly.
• 3_prepare_pynx.py crops and scales the model volume for phasing.
• 4_reconstructr.sbatch does the phasing with PyNX as SLURM jobs, but its pynx commands can be run in a normal terminal with the correct environment.
• 5_validate and rectify.py resamples the particle on an orthogonal grid and does the FSV analysis.

In addition, the folder fig2 contains the scripts for creating the figure based on the body_strain example from bcdi-assemble, while fig3 contains the scripts for creating the experimental data figure.

These scripts depend on the bcdi-assemble library for assembly, and on PyNX for phasing.