Dragonfly
User Guides
Installation
Quick Start with Simulations
Data Stream Simulator
Configuration Guide
Quick Start with Experimental Data
Progress Viewer (autoplot)
Frame Viewer
Frequently Asked Questions
Background
Background
API Reference
API Reference
Dragonfly
Index
Index
A
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
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)