Parameters Module

The parameters module stores reconstruction parameters.

Configuration

Load parameters from a configuration file, which should be the most common way to set the various parameters:

from dragonfly.params import EMCParams

param = EMCParams()
param.from_config('config.ini', section_name='emc')

class dragonfly.params.EMCParams

Bases: object

Class storing reconstruction parameters.

Holds all configuration parameters for EMC reconstruction including iteration settings, algorithm parameters, and symmetry options.

alpha: Model smoothing factor.

axial_sym: N-fold axial symmetry order.

beta_config: Configured beta parameter (-1 means auto).

beta_factor: Beta scaling factor.

beta_jump: Beta value jump per period.

beta_period: Iterations per beta period.

coarse_div: Coarse division for refinement.

coverage_bias: Bias stochastic sampling toward long-unused frames.

data_fraction: Fraction of non-blacklisted frames to use per iteration.

data_fraction_period: Iterations to keep each stochastic data subset.

fine_div: Fine division for refinement.

fixed_seed: Fixed seed for testing.

free(self): Free allocated parameter memory.

friedel_sym: Whether Friedel symmetry is applied.

from_config(self, config_fname, section_name='emc')

Load parameters from configuration file.

Parameters:

config_fname (str) – Path to configuration file.
section_name (str) – Section name. Default ‘emc’.

iteration: Current iteration number.

known_scale: Whether scale factors are known.

lazy_data: Whether to load active sparse frames on demand.

log_fname: Path to log file.

need_scaling: Whether frame scaling is enabled.

nonrot_modes: Number of non-rotating modes.

num_iter: Number of iterations.

num_modes: Number of modes.

num_proc: Number of MPI processes.

output_folder: Path to output folder.

oversampling: Pixel oversampling factor.

radius: Reconstruction radius.

radius_jump: Radius jump per period.

radius_period: Iterations per radius period.

rank: MPI rank.

refine: Whether refinement mode is enabled.

rot_per_mode: Rotations per mode.

rtype: Returns the reconstruction type (RECON3D, RECON2D, or RECONRZ).

save_prob: Whether to save probabilities.

sigmasq: Squared Gaussian sigma.

start_iter: Starting iteration number.

update_scale: Whether to update scale factors during iteration.

verbosity: Verbosity level.

Reconstruction Types

RECON3D - 3D volume reconstruction
RECON2D - 2D slice reconstruction
RECONRZ - Cylindrical (R-Z) reconstruction