bacteria_density package

Submodules

• bacteria_density.bd_worker module
  • BacteriaDensityWorker
    • BacteriaDensityWorker.add_measurement_channel()
    • BacteriaDensityWorker.add_region()
    • BacteriaDensityWorker.are_measures_generated()
    • BacteriaDensityWorker.are_medial_paths_generated()
    • BacteriaDensityWorker.are_regions_exported()
    • BacteriaDensityWorker.are_skeletons_generated()
    • BacteriaDensityWorker.chunks_as_json()
    • BacteriaDensityWorker.chunks_from_json()
    • BacteriaDensityWorker.error()
    • BacteriaDensityWorker.export_processed_set()
    • BacteriaDensityWorker.export_regions()
    • BacteriaDensityWorker.get_measurement_channels()
    • BacteriaDensityWorker.get_processed_metrics()
    • BacteriaDensityWorker.get_rank()
    • BacteriaDensityWorker.get_segmentation_channel()
    • BacteriaDensityWorker.info()
    • BacteriaDensityWorker.make_mask_and_skeleton()
    • BacteriaDensityWorker.make_measures()
    • BacteriaDensityWorker.make_medial_path()
    • BacteriaDensityWorker.make_plots()
    • BacteriaDensityWorker.merge_measures()
    • BacteriaDensityWorker.recover()
    • BacteriaDensityWorker.recover_calibration()
    • BacteriaDensityWorker.recover_images()
    • BacteriaDensityWorker.recover_metrics()
    • BacteriaDensityWorker.recover_regions()
    • BacteriaDensityWorker.save_measurement_channels()
    • BacteriaDensityWorker.save_metrics()
    • BacteriaDensityWorker.save_original()
    • BacteriaDensityWorker.save_regions()
    • BacteriaDensityWorker.save_segmentation_ch()
    • BacteriaDensityWorker.set_binning_distance()
    • BacteriaDensityWorker.set_calibration()
    • BacteriaDensityWorker.set_merge_measures()
    • BacteriaDensityWorker.set_segmentation_channel()
    • BacteriaDensityWorker.set_starting_hint()
    • BacteriaDensityWorker.set_threshold_factor()
    • BacteriaDensityWorker.set_working_dir()
    • BacteriaDensityWorker.state_as_json()
    • BacteriaDensityWorker.use_metric()
    • BacteriaDensityWorker.warning()
  • launch_analysis_workflow()
  • launch_recover_workflow()
  • launch_synthetic_workflow()
• bacteria_density.graph module
  • find_next_bbox()
  • find_root()
  • get_leaves()
  • longest_path_from()
  • path_as_img()
  • run1()
  • skeleton_to_undirected_graph()
• bacteria_density.measure module
  • cumulative_distance()
  • get_execution_order()
  • get_functions()
  • get_metrics_by_order()
  • integrated_intensity()
  • integrated_volume()
  • local_density()
  • local_width()
• bacteria_density.plots module
  • main()
  • save_plot()
• bacteria_density.process module
  • control_affectations()
  • keep_largest()
  • make_affectations()
  • make_metric_control()
• bacteria_density.qt_workers module
  • QtExportCrops
    • QtExportCrops.finished
    • QtExportCrops.run()
  • QtMakeMasks
    • QtMakeMasks.finished
    • QtMakeMasks.run()
  • QtMeasure
    • QtMeasure.finished
    • QtMeasure.run()
  • QtMedialAxis
    • QtMedialAxis.finished
    • QtMedialAxis.run()
  • QtPlot
    • QtPlot.finished
    • QtPlot.run()
• bacteria_density.utils module
  • as_polygon()
  • avg_in_bins()
  • bbox_to_polygon()
  • bbox_to_str()
  • clr_to_str()
  • from_polygon()
  • get_binned_distances()
  • make_crop()
  • polygon_to_bbox()
  • polygon_to_mask()
  • random_id()
  • reset_folder()
  • str_to_clr()
  • sum_in_bins()

Module contents