Reconstruction Module

The reconstruction module performs the main EMC reconstruction.

Usage

The reconstruction is typically run via the command line:

mpirun -n 4 dragonfly.emc -c config.ini -t 8 100

Or programmatically:

from dragonfly.recon import EMCRecon
from dragonfly.iterate import Iterate

recon = EMCRecon(num_threads=8)
itr = Iterate('config.ini')
itr.params.num_iter = 100
recon.set_iterate(itr)

for itr.params.iteration in range(1, itr.params.num_iter+1):
    recon.run_iteration()

In each case, 100 iterations are run from a random start using 4 MPI ranks and 8 threads per rank.

Output Files

Each iteration produces an output_XXX.h5 HDF5 file containing:

  • intens - Current model intensities

  • orientations - Most likely orientations

  • mutual_info - Mutual information per frame

  • likelihood - Log-likelihood per frame

  • quaternions - Orientation quaternions

  • params/* - Reconstruction parameters