Index

A

add_measurement_channel() (bacteria_density.bd_worker.BacteriaDensityWorker method) add_region() (bacteria_density.bd_worker.BacteriaDensityWorker method) are_measures_generated() (bacteria_density.bd_worker.BacteriaDensityWorker method) are_medial_paths_generated() (bacteria_density.bd_worker.BacteriaDensityWorker method)

are_regions_exported() (bacteria_density.bd_worker.BacteriaDensityWorker method) are_skeletons_generated() (bacteria_density.bd_worker.BacteriaDensityWorker method) as_polygon() (in module bacteria_density.utils) avg_in_bins() (in module bacteria_density.utils)

B

bacteria_density module bacteria_density.bd_worker module bacteria_density.graph module bacteria_density.measure module bacteria_density.plots module

bacteria_density.process module bacteria_density.qt_workers module bacteria_density.utils module BacteriaDensityWorker (class in bacteria_density.bd_worker) bbox_to_polygon() (in module bacteria_density.utils) bbox_to_str() (in module bacteria_density.utils)

C

chunks_as_json() (bacteria_density.bd_worker.BacteriaDensityWorker method) chunks_from_json() (bacteria_density.bd_worker.BacteriaDensityWorker method)

clr_to_str() (in module bacteria_density.utils) control_affectations() (in module bacteria_density.process) cumulative_distance() (in module bacteria_density.measure)

E

error() (bacteria_density.bd_worker.BacteriaDensityWorker method)

export_processed_set() (bacteria_density.bd_worker.BacteriaDensityWorker method) export_regions() (bacteria_density.bd_worker.BacteriaDensityWorker method)

F

find_next_bbox() (in module bacteria_density.graph) find_root() (in module bacteria_density.graph) finished (bacteria_density.qt_workers.QtExportCrops attribute) (bacteria_density.qt_workers.QtMakeMasks attribute) (bacteria_density.qt_workers.QtMeasure attribute) (bacteria_density.qt_workers.QtMedialAxis attribute) (bacteria_density.qt_workers.QtPlot attribute)

from_polygon() (in module bacteria_density.utils)

G

get_binned_distances() (in module bacteria_density.utils) get_execution_order() (in module bacteria_density.measure) get_functions() (in module bacteria_density.measure) get_leaves() (in module bacteria_density.graph)

get_measurement_channels() (bacteria_density.bd_worker.BacteriaDensityWorker method) get_metrics_by_order() (in module bacteria_density.measure) get_processed_metrics() (bacteria_density.bd_worker.BacteriaDensityWorker method) get_rank() (bacteria_density.bd_worker.BacteriaDensityWorker method) get_segmentation_channel() (bacteria_density.bd_worker.BacteriaDensityWorker method)

I

info() (bacteria_density.bd_worker.BacteriaDensityWorker method)

integrated_intensity() (in module bacteria_density.measure) integrated_volume() (in module bacteria_density.measure)

K

keep_largest() (in module bacteria_density.process)

L

launch_analysis_workflow() (in module bacteria_density.bd_worker) launch_recover_workflow() (in module bacteria_density.bd_worker) launch_synthetic_workflow() (in module bacteria_density.bd_worker)

local_density() (in module bacteria_density.measure) local_width() (in module bacteria_density.measure) longest_path_from() (in module bacteria_density.graph)

M

main() (in module bacteria_density.plots) make_affectations() (in module bacteria_density.process) make_crop() (in module bacteria_density.utils) make_mask_and_skeleton() (bacteria_density.bd_worker.BacteriaDensityWorker method) make_measures() (bacteria_density.bd_worker.BacteriaDensityWorker method) make_medial_path() (bacteria_density.bd_worker.BacteriaDensityWorker method) make_metric_control() (in module bacteria_density.process) make_plots() (bacteria_density.bd_worker.BacteriaDensityWorker method) merge_measures() (bacteria_density.bd_worker.BacteriaDensityWorker method)

module bacteria_density bacteria_density.bd_worker bacteria_density.graph bacteria_density.measure bacteria_density.plots bacteria_density.process bacteria_density.qt_workers bacteria_density.utils

P

path_as_img() (in module bacteria_density.graph)

polygon_to_bbox() (in module bacteria_density.utils) polygon_to_mask() (in module bacteria_density.utils)

Q

QtExportCrops (class in bacteria_density.qt_workers) QtMakeMasks (class in bacteria_density.qt_workers)

QtMeasure (class in bacteria_density.qt_workers) QtMedialAxis (class in bacteria_density.qt_workers) QtPlot (class in bacteria_density.qt_workers)

R

random_id() (in module bacteria_density.utils) recover() (bacteria_density.bd_worker.BacteriaDensityWorker method) recover_calibration() (bacteria_density.bd_worker.BacteriaDensityWorker method) recover_images() (bacteria_density.bd_worker.BacteriaDensityWorker method) recover_metrics() (bacteria_density.bd_worker.BacteriaDensityWorker method) recover_regions() (bacteria_density.bd_worker.BacteriaDensityWorker method)

reset_folder() (in module bacteria_density.utils) run() (bacteria_density.qt_workers.QtExportCrops method) (bacteria_density.qt_workers.QtMakeMasks method) (bacteria_density.qt_workers.QtMeasure method) (bacteria_density.qt_workers.QtMedialAxis method) (bacteria_density.qt_workers.QtPlot method) run1() (in module bacteria_density.graph)

S

save_measurement_channels() (bacteria_density.bd_worker.BacteriaDensityWorker method) save_metrics() (bacteria_density.bd_worker.BacteriaDensityWorker method) save_original() (bacteria_density.bd_worker.BacteriaDensityWorker method) save_plot() (in module bacteria_density.plots) save_regions() (bacteria_density.bd_worker.BacteriaDensityWorker method) save_segmentation_ch() (bacteria_density.bd_worker.BacteriaDensityWorker method) set_binning_distance() (bacteria_density.bd_worker.BacteriaDensityWorker method) set_calibration() (bacteria_density.bd_worker.BacteriaDensityWorker method)

set_merge_measures() (bacteria_density.bd_worker.BacteriaDensityWorker method) set_segmentation_channel() (bacteria_density.bd_worker.BacteriaDensityWorker method) set_starting_hint() (bacteria_density.bd_worker.BacteriaDensityWorker method) set_threshold_factor() (bacteria_density.bd_worker.BacteriaDensityWorker method) set_working_dir() (bacteria_density.bd_worker.BacteriaDensityWorker method) skeleton_to_undirected_graph() (in module bacteria_density.graph) state_as_json() (bacteria_density.bd_worker.BacteriaDensityWorker method) str_to_clr() (in module bacteria_density.utils) sum_in_bins() (in module bacteria_density.utils)

U

use_metric() (bacteria_density.bd_worker.BacteriaDensityWorker method)

W

warning() (bacteria_density.bd_worker.BacteriaDensityWorker method)