Configuration Guide

Dragonfly uses configuration files (typically config.ini) that organize parameters by workflow section. The first few sections correspond to the data stream simulator workflow.

If processing experimental data with a known detector file, only the [emc] section is needed.

Geometry Parameters

The [parameters] section defines the experimental geometry:

Parameter	Description
`detd`	Detector distance (millimeters)
`lambda`	Photon wavelength (Angstrom)
`detsize`	Linear detector size (pixels, integer)
`pixsize`	Pixel size (millimeters)
`stoprad`	Beamstop radius (pixels, float)
`polarization`	Polarization correction (‘x’, ‘y’, or ‘none’)

make_densities Section

Creates electron density map from PDB file.

Parameter	Description
`pdb_code`	PDB code to fetch (alternative to `in_pdb_file`)
`in_pdb_file`	Path to custom PDB file
`scatt_dir`	Directory with atomic scattering factors (Henke table)
`out_density_file`	Output electron density file

make_intensities Section

Creates 3D intensity map from electron density with low-pass filtering.

Parameter	Description
`in_density_file`	Input density file (e.g., `make_densities:::out_density_file`)
`out_intensity_file`	Output 3D intensity file

make_detector Section

Generates detector geometry file.

Parameter	Description
`out_detector_file`	Output detector geometry file

make_data Section

Simulates photon diffraction patterns.

Parameter	Description
`num_data`	Number of data frames to simulate
`fluence`	Incident photon fluence (photons/um^2)
`in_detector_file`	Detector geometry file
`in_intensity_file`	Input 3D intensity volume
`out_photons_file`	Output photon data file

EMC Section

Parameters for the EMC reconstruction.

Parameter	Description
`in_photons_file`	Input photon data file
`in_detector_file`	Detector geometry file
`num_div`	Quaternion sampling refinement (`10(5n^3 + n)` rotations)
`beta`	Initial annealing value. Use `auto` to estimate per-frame starting values automatically.
`beta_factor`	Additional multiplicative factor applied to the starting `beta` values
`beta_schedule`	Increase the effective `beta` by multiplying by <first> every <second> iterations
`output_folder`	Directory for output files
`log_file`	Reconstruction log file
`need_scaling`	Fluence scaling (0=off, 1=on)

Configuration Chaining

Use ::: syntax to link outputs between sections:

in_detector_file = make_detector:::out_detector_file
in_photons_file = make_data:::out_photons_file

This chains the output of one module as input to another.