Index

A

allocate() (dragonfly.model.Model method) alpha (dragonfly.params.EMCParams attribute)

append() (dragonfly.emcfile.CDataset method) assemble_frame() (dragonfly.detector.Detector method) axial_sym (dragonfly.params.EMCParams attribute)

B

background (dragonfly.detector.CDetector attribute) beta (dragonfly.iterate.Iterate attribute) beta_config (dragonfly.params.EMCParams attribute) beta_factor (dragonfly.params.EMCParams attribute) beta_jump (dragonfly.params.EMCParams attribute) beta_period (dragonfly.params.EMCParams attribute)

beta_start (dragonfly.iterate.Iterate attribute) bgscale (dragonfly.iterate.Iterate attribute) blacklist (dragonfly.emcfile.EMCReader attribute) (dragonfly.iterate.Iterate attribute) built-in function dragonfly.utils.make_data.make_data_cdef()

C

calc_beta() (dragonfly.iterate.Iterate method) calc_from_coords() (dragonfly.detector.Detector method) calculate_size() (dragonfly.iterate.Iterate static method) CCCalculator (class in dragonfly.utils.py_src.calc_cc) CDataset (class in dragonfly.emcfile) CDetector (class in dragonfly.detector) center (dragonfly.model.Model attribute) check_to_overwrite() (in module dragonfly.utils.py_src.py_utils)

coarse_div (dragonfly.params.EMCParams attribute) compare() (dragonfly.utils.py_src.calc_cc.CCCalculator method) compute_q_params() (in module dragonfly.utils.py_src.read_config) confirm_oversampling() (in module dragonfly.utils.py_src.py_utils) coords_xy (dragonfly.detector.Detector property) corr (dragonfly.detector.CDetector attribute) count_multi (dragonfly.emcfile.CDataset attribute) coverage_bias (dragonfly.params.EMCParams attribute)

D

data (dragonfly.iterate.Iterate attribute) data_fraction (dragonfly.params.EMCParams attribute) data_fraction_period (dragonfly.params.EMCParams attribute) det (dragonfly.emcfile.CDataset attribute) det_mapping (dragonfly.iterate.Iterate attribute) detd (dragonfly.detector.CDetector attribute) Detector (class in dragonfly.detector) dets (dragonfly.iterate.Iterate attribute) divide() (dragonfly.quaternion.Quaternion method) dragonfly.detector module dragonfly.emcfile module dragonfly.iterate module dragonfly.model module dragonfly.params module dragonfly.quaternion module

dragonfly.utils.make_data module dragonfly.utils.make_data.make_data_cdef() built-in function dragonfly.utils.make_densities module dragonfly.utils.make_detector module dragonfly.utils.make_intensities module dragonfly.utils.py_src.calc_cc module dragonfly.utils.py_src.py_utils module dragonfly.utils.py_src.read_config module dragonfly.utils.py_src.slices module dragonfly.utils.sim_setup module

E

EMCParams (class in dragonfly.params) EMCReader (class in dragonfly.emcfile)

EMCWriter (class in dragonfly.emcfile) ewald_rad (dragonfly.detector.CDetector attribute)

F

fcounts (dragonfly.iterate.Iterate attribute) finalize_blacklist() (dragonfly.iterate.Iterate method) fine_div (dragonfly.params.EMCParams attribute) finish_write() (dragonfly.emcfile.EMCWriter method) fixed_seed (dragonfly.params.EMCParams attribute) fname (dragonfly.detector.CDetector attribute) (dragonfly.emcfile.CDataset attribute) frame_shape (dragonfly.detector.Detector attribute) free() (dragonfly.detector.CDetector method) (dragonfly.emcfile.CDataset method) (dragonfly.iterate.Iterate method) (dragonfly.model.Model method) (dragonfly.params.EMCParams method) (dragonfly.quaternion.Quaternion method)

friedel_sym (dragonfly.params.EMCParams attribute) from_config() (dragonfly.iterate.Iterate method) (dragonfly.params.EMCParams method) (dragonfly.quaternion.Quaternion method) ftype (dragonfly.emcfile.CDataset attribute)

G

gen_det_and_emc() (in module dragonfly.utils.py_src.py_utils) generate_2d() (dragonfly.quaternion.Quaternion method) generate_3d() (dragonfly.quaternion.Quaternion method) get_assembled_cen() (dragonfly.detector.Detector method) get_detector_config() (dragonfly.utils.py_src.read_config.MyConfigParser method)

get_filename() (dragonfly.utils.py_src.read_config.MyConfigParser method) get_frame() (dragonfly.emcfile.EMCReader method) get_powder() (dragonfly.emcfile.EMCReader method) get_quat() (dragonfly.utils.py_src.slices.SliceGenerator method) get_samples() (dragonfly.utils.py_src.calc_cc.CCCalculator method) get_slice() (dragonfly.utils.py_src.slices.SliceGenerator method)

I

icosahedral_flag (dragonfly.quaternion.Quaternion attribute) indices_xy (dragonfly.detector.Detector property) initialize_last_selected() (dragonfly.iterate.Iterate method)

initialize_stochastic_scale() (dragonfly.iterate.Iterate method) inter_weight (dragonfly.model.Model attribute) Iterate (class in dragonfly.iterate) iteration (dragonfly.params.EMCParams attribute)

K

known_scale (dragonfly.params.EMCParams attribute)

L

last_selected (dragonfly.iterate.Iterate attribute) lazy (dragonfly.emcfile.CDataset attribute) lazy_data (dragonfly.params.EMCParams attribute) likelihood (dragonfly.iterate.Iterate attribute)

load_active_data() (dragonfly.iterate.Iterate method) load_active_frames() (dragonfly.emcfile.CDataset method) load_previous_blacklist() (dragonfly.iterate.Iterate method) log_fname (dragonfly.params.EMCParams attribute)

M

main() (in module dragonfly.utils.make_data) (in module dragonfly.utils.make_densities) (in module dragonfly.utils.make_detector) (in module dragonfly.utils.make_intensities) (in module dragonfly.utils.py_src.calc_cc) (in module dragonfly.utils.sim_setup) make_data() (in module dragonfly.utils.make_data) make_dens() (in module dragonfly.utils.make_densities) make_detector() (in module dragonfly.utils.make_detector) make_intens() (in module dragonfly.utils.make_intensities) make_rot_quat() (dragonfly.model.Model static method) mask (dragonfly.detector.Detector attribute) mask_assem (dragonfly.detector.Detector attribute) mean_count (dragonfly.emcfile.EMCWriter attribute) (dragonfly.iterate.Iterate attribute) Model (class in dragonfly.model) model (dragonfly.iterate.Iterate attribute) model1 (dragonfly.model.Model attribute) model2 (dragonfly.model.Model attribute) module dragonfly.detector dragonfly.emcfile dragonfly.iterate dragonfly.model dragonfly.params dragonfly.quaternion dragonfly.utils.make_data dragonfly.utils.make_densities dragonfly.utils.make_detector dragonfly.utils.make_intensities dragonfly.utils.py_src.calc_cc dragonfly.utils.py_src.py_utils dragonfly.utils.py_src.read_config dragonfly.utils.py_src.slices dragonfly.utils.sim_setup

mtype (dragonfly.model.Model attribute) multi (dragonfly.emcfile.CDataset attribute) multi_accum (dragonfly.emcfile.CDataset attribute) multi_total (dragonfly.emcfile.CDataset attribute) mutual_info (dragonfly.iterate.Iterate attribute) MyConfigParser (class in dragonfly.utils.py_src.read_config) MyTimer (class in dragonfly.utils.py_src.py_utils)

N

ndim (dragonfly.model.Model attribute) need_scaling (dragonfly.params.EMCParams attribute) next (dragonfly.emcfile.CDataset attribute) nonrot_modes (dragonfly.params.EMCParams attribute) normalize_scale() (dragonfly.iterate.Iterate method) num_blacklist (dragonfly.emcfile.EMCReader attribute) num_data (dragonfly.emcfile.CDataset attribute) (dragonfly.emcfile.EMCWriter attribute) num_det (dragonfly.iterate.Iterate attribute) num_dfiles (dragonfly.iterate.Iterate attribute)

num_div (dragonfly.quaternion.Quaternion attribute) num_frames (dragonfly.emcfile.EMCReader attribute) num_iter (dragonfly.params.EMCParams attribute) num_modes (dragonfly.model.Model attribute) (dragonfly.params.EMCParams attribute) num_pix (dragonfly.detector.CDetector attribute) (dragonfly.emcfile.CDataset attribute) (dragonfly.emcfile.EMCWriter attribute) num_proc (dragonfly.params.EMCParams attribute) num_rot (dragonfly.quaternion.Quaternion attribute) num_rot_p (dragonfly.quaternion.Quaternion attribute)

O

octahedral_flag (dragonfly.quaternion.Quaternion attribute) ones (dragonfly.emcfile.CDataset attribute) ones_accum (dragonfly.emcfile.CDataset attribute)

ones_total (dragonfly.emcfile.CDataset attribute) output_folder (dragonfly.params.EMCParams attribute) oversampling (dragonfly.params.EMCParams attribute)

P

params (dragonfly.iterate.Iterate attribute) parse() (dragonfly.detector.CDetector method) (dragonfly.detector.Detector method) (dragonfly.emcfile.CDataset method) (dragonfly.quaternion.Quaternion method)

parse_background() (dragonfly.detector.CDetector method) parse_blacklist() (dragonfly.iterate.Iterate method) parse_scale() (dragonfly.iterate.Iterate method) place_multi (dragonfly.emcfile.CDataset attribute) place_ones (dragonfly.emcfile.CDataset attribute)

Q

qmax() (dragonfly.detector.CDetector method) quat (dragonfly.iterate.Iterate attribute)

Quaternion (class in dragonfly.quaternion) quats (dragonfly.quaternion.Quaternion attribute) qvals (dragonfly.detector.CDetector attribute)

R

radius (dragonfly.params.EMCParams attribute) radius_jump (dragonfly.params.EMCParams attribute) radius_period (dragonfly.params.EMCParams attribute) rand_quat() (in module dragonfly.utils.make_data) rank (dragonfly.params.EMCParams attribute) raw_mask (dragonfly.detector.CDetector attribute) read() (dragonfly.utils.py_src.read_config.MyConfigParser method) read_density() (in module dragonfly.utils.py_src.py_utils) read_gui_config() (in module dragonfly.utils.py_src.read_config) reduce_icosahedral() (dragonfly.quaternion.Quaternion method) reduce_octahedral() (dragonfly.quaternion.Quaternion method) reduced (dragonfly.quaternion.Quaternion attribute)

refine (dragonfly.params.EMCParams attribute) refresh_data_stats() (dragonfly.iterate.Iterate method) remask() (dragonfly.detector.Detector method) report_time_since_beginning() (dragonfly.utils.py_src.py_utils.MyTimer method) rescale (dragonfly.iterate.Iterate attribute) reset() (dragonfly.utils.py_src.py_utils.MyTimer method) reset_global() (dragonfly.utils.py_src.py_utils.MyTimer method) rms_change (dragonfly.iterate.Iterate attribute) rot_per_mode (dragonfly.params.EMCParams attribute) rotate_model() (dragonfly.model.Model static method) rtype (dragonfly.params.EMCParams attribute) run() (dragonfly.utils.py_src.calc_cc.CCCalculator method)

S

save() (dragonfly.quaternion.Quaternion method) save_cc() (dragonfly.utils.py_src.calc_cc.CCCalculator method) save_prob (dragonfly.params.EMCParams attribute) scale (dragonfly.iterate.Iterate attribute) set_data() (dragonfly.iterate.Iterate method) set_model() (dragonfly.iterate.Iterate method) set_params() (dragonfly.iterate.Iterate method) set_quat() (dragonfly.iterate.Iterate method) sigmasq (dragonfly.params.EMCParams attribute) size (dragonfly.model.Model attribute)

slice_gen() (dragonfly.model.Model method) slice_merge() (dragonfly.model.Model method) SliceGenerator (class in dragonfly.utils.py_src.slices) start_iter (dragonfly.params.EMCParams attribute) static_blacklist (dragonfly.iterate.Iterate attribute) symmetrize_axial() (dragonfly.model.Model static method) symmetrize_friedel() (dragonfly.model.Model static method) symmetrize_friedel2d() (dragonfly.model.Model static method) symmetrize_icosahedral() (dragonfly.model.Model static method) symmetrize_octahedral() (dragonfly.model.Model static method)

T

tot_num_data (dragonfly.iterate.Iterate attribute)

U

update_blacklist() (dragonfly.iterate.Iterate method)

update_data() (dragonfly.iterate.Iterate method) update_scale (dragonfly.params.EMCParams attribute)

V

verbosity (dragonfly.params.EMCParams attribute)

vol (dragonfly.model.Model attribute) voronoi_subset() (dragonfly.quaternion.Quaternion method)

W

write() (dragonfly.detector.Detector method) write_density() (in module dragonfly.utils.py_src.py_utils)

write_frame() (dragonfly.emcfile.EMCWriter method) write_sparse_frame() (dragonfly.emcfile.EMCWriter method)

Z

zoom_bounds (dragonfly.detector.Detector attribute)