Data Stream Simulator

The data stream simulator generates synthetic single-particle diffraction data from PDB files, including realistic noise and photon statistics.

sim_setup

Convenience utility that runs the simulator pipeline sequentially:

dragonfly.utils.sim_setup.main()

Runs through simulation utilities to generate data.

This is a convenience wrapper that sequentially executes: * make_densities * make_intensities * make_detector * make_data

Usage:
dragonfly.utils.sim_setup
dragonfly.utils.sim_setup -c config.ini
dragonfly.utils.sim_setup -y

make_densities

Creates electron density map from PDB file using atomic scattering factors.

dragonfly.utils.make_densities.make_dens(config_fname, yes=False, verbose=False)

Generate density map from parameters in config file.

param config_fname:

Path to configuration file.

type config_fname:

str

param yes:

Skip confirmation prompts.

type yes:

bool

param verbose:

Enable verbose logging.

type verbose:

bool

returns:

Outputs binary density file specified in config.

rtype:

None

Usage:
dragonfly.utils.make_densities
dragonfly.utils.make_densities -c config.ini
Output: Binary file containing 3D cubic electron density distribution at the appropriate voxel size.

A low-pass filter eliminates artifacts from electron density discretization on a cubic grid.

make_intensities

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

dragonfly.utils.make_intensities.make_intens(config_fname, yes=False, verbose=False)

Generate intensity volume from config file parameters.

param config_fname:

Path to configuration file.

type config_fname:

str

param yes:

Skip confirmation prompts.

type yes:

bool

param verbose:

Enable verbose logging.

type verbose:

bool

returns:

Outputs binary intensity file specified in config.

rtype:

None

Usage:
dragonfly.utils.make_intensities
dragonfly.utils.make_intensities -c config.ini
Output: Binary file containing 3D intensity distribution in reciprocal space.

make_detector

Generates detector geometry file with pixel information.

dragonfly.utils.make_detector.make_detector(config_fname, yes=False, verbose=False)

Generate detector file from parameters in config file.

param config_fname:

Path to configuration file.

type config_fname:

str

param yes:

Skip confirmation prompts.

type yes:

bool

param verbose:

Enable verbose logging.

type verbose:

bool

returns:

Outputs detector file specified in config.

rtype:

None

Usage:
dragonfly.utils.make_detector
dragonfly.utils.make_detector -c config.ini
Output: Detector geometry file (.h5 or .dat) containing:

Detector distance

Pixel size

Beam center coordinates

Mask information

Ewald sphere radius

make_data

Simulates photon diffraction patterns from 3D intensity volume.

dragonfly.utils.make_data.make_data_cdef(config_fname, yes=False, verbose=False)

Generate simulated photon data from configuration file.

Parameters:

config_fname (str) – Path to configuration file.
yes (bool) – Skip confirmation prompts.
verbose (bool) – Enable verbose logging.

Returns:

Outputs photon data file specified in config.

Return type:

None

Usage:

dragonfly.utils.make_data
dragonfly.utils.make_data -c config.ini

Output: Binary file (.emc or .h5) containing sparse photon data.

Data Format

The simulator outputs photon data in sparse format with three arrays:

Single-photon locations (variable): - Pixel indices where exactly one photon was detected
Multi-photon locations (variable): - Pixel indices for multi-photon events
Multi-photon counts (variable): - Photon count at each multi-photon pixel

This sparse format is efficient for high-resolution SPI where most pixels receive zero or one photon.

Pipeline Flow

PDB file
   |
   v
make_densities --> densityMap.bin
   |
   v
make_intensities --> intensities.bin
   |
   v
make_detector --> det_geom.dat
   |
   v
make_data --> photons.emc