Index

A

add_stack() (diffractem.dataset.Dataset method) Adxv (class in diffractem.adxv) agg_file_suffix (diffractem.pre_proc_opts.PreProcOpts attribute) agg_query (diffractem.pre_proc_opts.PreProcOpts attribute) aggregate (diffractem.pre_proc_opts.PreProcOpts attribute) aggregate() (diffractem.dataset.Dataset method)

analyze_and_correct() (in module diffractem.proc2d) analyze_hkl() (in module diffractem.tools) apply_flatfield() (in module diffractem.proc2d) apply_saturation_correction() (in module diffractem.proc2d) apply_virtual_detector() (in module diffractem.proc2d) augment_stream() (in module diffractem.stream_parser)

C

call_indexamajig() (in module diffractem.tools) call_indexamajig_slurm() (in module diffractem.tools) call_partialator() (in module diffractem.tools) call_partialator_simple() (in module diffractem.tools) cam_length (diffractem.pre_proc_opts.PreProcOpts attribute) Cell (class in diffractem.proc_peaks) cell (diffractem.stream_parser.StreamParser property) center_friedel() (in module diffractem.proc_peaks) center_image() (in module diffractem.proc2d) center_of_mass() (in module diffractem.proc2d) center_of_mass2() (in module diffractem.proc2d) centering (diffractem.proc_peaks.Cell property) change_filenames() (diffractem.dataset.Dataset method) change_path() (diffractem.stream_parser.StreamParser method) chop_stream() (in module diffractem.stream_parser) (in module diffractem.tools) close_files() (diffractem.dataset.Dataset method)

close_stacks() (diffractem.dataset.Dataset method) com_threshold (diffractem.pre_proc_opts.PreProcOpts attribute) com_xrng (diffractem.pre_proc_opts.PreProcOpts attribute) com_yrng (diffractem.pre_proc_opts.PreProcOpts attribute) compression (diffractem.pre_proc_opts.PreProcOpts attribute) compute_and_save() (diffractem.dataset.Dataset method) compute_pattern_info() (diffractem.dataset.Dataset method) contrast_max() (diffractem.adxv.Adxv method) contrast_min() (diffractem.adxv.Adxv method) copy() (diffractem.dataset.Dataset method) copy_h5() (in module diffractem.nexus) correct_dead_pixels() (in module diffractem.proc2d) correct_image() (in module diffractem.proc2d) correct_saturation (diffractem.pre_proc_opts.PreProcOpts attribute) ctr_types (diffractem.proc_peaks.Cell attribute) cubic() (diffractem.proc_peaks.Cell class method) cut_peaks() (in module diffractem.proc2d)

D

d() (diffractem.proc_peaks.Cell method) d_spacing() (diffractem.proc_peaks.Cell method) data_pattern (diffractem.dataset.Dataset attribute) dataframe_hash() (in module diffractem.tools) Dataset (class in diffractem.dataset) dead_time (diffractem.pre_proc_opts.PreProcOpts attribute) dead_time_gap_factor (diffractem.pre_proc_opts.PreProcOpts attribute) define_spot() (diffractem.adxv.Adxv method) delete_stack() (diffractem.dataset.Dataset method) det_shift_x_path (diffractem.pre_proc_opts.PreProcOpts attribute) det_shift_y_path (diffractem.pre_proc_opts.PreProcOpts attribute) diamond() (diffractem.proc_peaks.Cell class method) dict2file() (in module diffractem.tools) dict_to_h5() (in module diffractem.io) diff_data (diffractem.dataset.Dataset property) diff_stack_label (diffractem.dataset.Dataset property) diffractem module diffractem.adxv module

diffractem.compute module diffractem.dataset module diffractem.io module diffractem.nexus module diffractem.pre_proc_opts module diffractem.proc2d module diffractem.proc_peaks module diffractem.stream_parser module diffractem.tools module

E

ellipse_angle (diffractem.pre_proc_opts.PreProcOpts attribute) ellipse_ratio (diffractem.pre_proc_opts.PreProcOpts attribute)

exit() (diffractem.adxv.Adxv method) expand_files() (in module diffractem.io) export() (diffractem.proc_peaks.Cell method)

F

features (diffractem.dataset.Dataset property) file_handles (diffractem.dataset.Dataset property) files (diffractem.dataset.Dataset property) (diffractem.stream_parser.StreamParser property) find_peaks (diffractem.pre_proc_opts.PreProcOpts attribute)

float (diffractem.pre_proc_opts.PreProcOpts attribute) friedel_max_radius (diffractem.pre_proc_opts.PreProcOpts attribute) friedel_refine (diffractem.pre_proc_opts.PreProcOpts attribute) from_files() (diffractem.dataset.Dataset class method) from_list() (diffractem.dataset.Dataset class method) func_lorentz() (in module diffractem.proc2d)

G

geometry (diffractem.stream_parser.StreamParser property) get_acf() (in module diffractem.proc_peaks) get_cxi_format() (diffractem.stream_parser.StreamParser method) get_hkl_settings() (in module diffractem.tools) get_indexing_solution() (diffractem.dataset.Dataset method) get_map() (diffractem.dataset.Dataset method) get_meta() (diffractem.dataset.Dataset method)

get_meta_fields() (in module diffractem.nexus) get_pattern_info() (in module diffractem.proc2d) get_peaks() (in module diffractem.proc2d) get_pk_data() (in module diffractem.proc_peaks) get_random_subset() (diffractem.dataset.Dataset method) get_selection() (diffractem.dataset.Dataset method) get_table() (in module diffractem.nexus)

H

h5_to_dict() (in module diffractem.io)

hexagonal() (diffractem.proc_peaks.Cell class method)

I

im_exc (diffractem.pre_proc_opts.PreProcOpts attribute) increment_files() (diffractem.adxv.Adxv method) increment_slabs() (diffractem.adxv.Adxv method) indexed (diffractem.stream_parser.StreamParser property) indexing_params (diffractem.pre_proc_opts.PreProcOpts attribute) init_files() (diffractem.dataset.Dataset method) init_hkl() (diffractem.proc_peaks.Cell method) init_shot_table() (diffractem.dataset.Dataset method)

init_stacks() (diffractem.dataset.Dataset method) input_file (diffractem.stream_parser.StreamParser property) insert_init() (in module diffractem.tools) instrument_pattern (diffractem.dataset.Dataset attribute) int_factor (diffractem.pre_proc_opts.PreProcOpts attribute) integration_params (diffractem.pre_proc_opts.PreProcOpts attribute) interpolate_dead (diffractem.pre_proc_opts.PreProcOpts attribute) is_alive() (diffractem.adxv.Adxv method)

L

lattices (diffractem.proc_peaks.Cell attribute) load() (diffractem.pre_proc_opts.PreProcOpts method) load_image() (diffractem.adxv.Adxv method) load_spots() (diffractem.adxv.Adxv method) load_tables() (diffractem.dataset.Dataset method)

loop_over_stack() (in module diffractem.proc2d) lorentz_fast() (in module diffractem.proc2d) lorentz_fit() (in module diffractem.proc2d) lorentz_maxshift (diffractem.pre_proc_opts.PreProcOpts attribute) lorentz_radius (diffractem.pre_proc_opts.PreProcOpts attribute)

M

make_command() (in module diffractem.tools) make_geometry() (in module diffractem.tools) make_master_h5() (in module diffractem.io) make_reference() (in module diffractem.tools) make_substream() (in module diffractem.stream_parser) map_pattern (diffractem.dataset.Dataset attribute) map_reduction_func() (in module diffractem.compute) mask_gaps (diffractem.pre_proc_opts.PreProcOpts attribute) max_peaks (diffractem.pre_proc_opts.PreProcOpts attribute) mean_clip() (in module diffractem.proc2d) merge_meta() (diffractem.dataset.Dataset method) merge_pattern_info() (diffractem.dataset.Dataset method) merge_stream() (diffractem.dataset.Dataset method) meta_to_nxs() (in module diffractem.nexus)

min_peaks (diffractem.pre_proc_opts.PreProcOpts attribute) module diffractem diffractem.adxv diffractem.compute diffractem.dataset diffractem.io diffractem.nexus diffractem.pre_proc_opts diffractem.proc2d diffractem.proc_peaks diffractem.stream_parser diffractem.tools monoclinic() (diffractem.proc_peaks.Cell class method)

N

num_crystals (diffractem.stream_parser.StreamParser property)

num_shots (diffractem.stream_parser.StreamParser property)

O

open_stacks() (diffractem.dataset.Dataset method)

options (diffractem.stream_parser.StreamParser property) orthorhombic() (diffractem.proc_peaks.Cell class method)

P

parallel_io (diffractem.dataset.Dataset attribute) parse() (diffractem.stream_parser.StreamParser method) parse_str_val() (in module diffractem.stream_parser) peak_data (diffractem.dataset.Dataset property) peak_data_path (diffractem.pre_proc_opts.PreProcOpts attribute) peak_search_params (diffractem.pre_proc_opts.PreProcOpts attribute) peak_sigma (diffractem.pre_proc_opts.PreProcOpts attribute)

peaks (diffractem.dataset.Dataset property) (diffractem.stream_parser.StreamParser property) persist_stacks() (diffractem.dataset.Dataset method) pixel_size (diffractem.pre_proc_opts.PreProcOpts attribute) predict (diffractem.dataset.Dataset property) PreProcOpts (class in diffractem.pre_proc_opts) proc_dir (diffractem.pre_proc_opts.PreProcOpts attribute) pxmask (diffractem.pre_proc_opts.PreProcOpts attribute)

Q

quantize_y_scan() (in module diffractem.tools)

R

r_adf1 (diffractem.pre_proc_opts.PreProcOpts attribute) r_adf2 (diffractem.pre_proc_opts.PreProcOpts attribute) radial_proj() (in module diffractem.proc2d) raise_image() (diffractem.adxv.Adxv method) raise_window() (diffractem.adxv.Adxv method) rechunk_stacks() (diffractem.dataset.Dataset method)

reference (diffractem.pre_proc_opts.PreProcOpts attribute) refine_powder() (diffractem.proc_peaks.Cell method) remove_background (diffractem.pre_proc_opts.PreProcOpts attribute) remove_background() (in module diffractem.proc2d) reset_id() (diffractem.dataset.Dataset method) result_pattern (diffractem.dataset.Dataset attribute) rhombohedral() (diffractem.proc_peaks.Cell class method)

S

save() (diffractem.pre_proc_opts.PreProcOpts method) save_image() (diffractem.adxv.Adxv method) scratch_dir (diffractem.pre_proc_opts.PreProcOpts attribute) select() (diffractem.dataset.Dataset method) select_query (diffractem.pre_proc_opts.PreProcOpts attribute) selection_rules (diffractem.proc_peaks.Cell attribute) send() (diffractem.adxv.Adxv method) set_frames() (in module diffractem.tools) set_slab() (diffractem.adxv.Adxv method) set_slabs() (diffractem.adxv.Adxv method) shots (diffractem.dataset.Dataset property) (diffractem.stream_parser.StreamParser property) shots_pattern (diffractem.dataset.Dataset attribute) shutter_time (diffractem.pre_proc_opts.PreProcOpts attribute)

slab() (diffractem.adxv.Adxv method) slabs() (diffractem.adxv.Adxv method) stack_nested() (in module diffractem.proc2d) stacks (diffractem.dataset.Dataset property) Stacks() (diffractem.dataset.Dataset method) stacks_to_shots() (diffractem.dataset.Dataset method) start() (diffractem.adxv.Adxv method) store_stack_fast() (diffractem.dataset.Dataset method) store_stacks() (diffractem.dataset.Dataset method) store_table() (in module diffractem.nexus) store_tables() (diffractem.dataset.Dataset method) StreamParser (class in diffractem.stream_parser) stride() (diffractem.adxv.Adxv method) strip_file_path() (in module diffractem.tools) strip_img() (in module diffractem.proc2d)

T

tetragonal() (diffractem.proc_peaks.Cell class method)

transform_stack_groups() (diffractem.dataset.Dataset method) triclinic() (diffractem.proc_peaks.Cell class method)

U

update_det_shift() (diffractem.dataset.Dataset method) (in module diffractem.tools)

V

view() (diffractem.dataset.Dataset method)

volume (diffractem.proc_peaks.Cell property)

W

wavelength (diffractem.pre_proc_opts.PreProcOpts attribute) write() (diffractem.stream_parser.StreamParser method)

write_list() (diffractem.dataset.Dataset method) write_virtual_file() (diffractem.dataset.Dataset method)

X

xsize (diffractem.pre_proc_opts.PreProcOpts attribute)

Y

y_scale (diffractem.pre_proc_opts.PreProcOpts attribute)

ysize (diffractem.pre_proc_opts.PreProcOpts attribute)

Z

zchunks (diffractem.dataset.Dataset property)