fold_slice structure

(Top)

Part of a series on Phase retrieval

prepare_data_PSO_science.m

• reads cbed dataset, initializes basic parameters

ptycho_electron_PSO_science.m

• main reconstruction file, assigns parameters in the p object
• engines are configured separately in the eng object, and appended to p via +core/append_engine.m
• 336~338: +core/ptycho_recons
  • 172: +core/initialize_ptycho.m
    • 81~103: calculates proper dx (object pixel pitch)
    • 107: +scans/read_positions.m
      • 19~20: +scans/positions/{function_name}.m
        • use the 'matlab_pos' function
        • grid mode 'raster'
        • +core/ptycho_adjust_positions.m does a primitive refinement of the positions (Affine transform etc/)
    • 141: +core/ptycho_prepare_scans.m
      • 132: +core/prepare_initial_guess.m
        • Object
        • 73: +core/update_object_size.m
        • 75: +core/prepare_initial_object.m
          • use rand option
          • 27: generate random phase object
          • 30~: if using other initial guess
        • Probe
        • 78: +core/prepare_initial_probes.m
          • 7: +core/ptycho_model_probe.m
            • 23~73: theoretical electron probe
          • 15~81: split into modes mode energies assigned by p.mode_start_pow mode splitting algorithm assigned by p.mode_start (default "herm")
          • 84~154: orthogonalization
    • 147: custom prepare data function
    • 156~232: preprocessing for abnormal cbed detections
    • 238~273: plotting initial guesses
  • 193: enumerate over engines in p
  • 202: +core/run_engine.m (with engine id as argument)
    • 79: +core/engine_status (set status to 0)
    • 80~81: +engines/{engine_name}.m (assigned to engine_fnct)
      • use 'GPU_MS' engine
      • 22: +engines/+GPU_MS/+initialize/get_defaults.m: generate default parameters as param
      • 29: +engines/+GPU_MS/+initialize/load_from_p.m: get the presupplied parameters from p and param; returns self, param, p
      • 58~71: initialize GPU and solver
      • 78~123: GPU safety
      • 127: +engines/+GPU_MS/ptycho_solver.m
        • 280~289: +engines/+GPU_MS/{method}.m
        1. LSQML
        2. DM
        3. PIE