autoemx.core.em_runtime package

Runtime modules for electron microscopy acquisition and control.

Subpackages

• autoemx.core.em_runtime.particle_segmentation_models package
  • load_models()
  • is_model_available()
  • available_models()
  • install_hint()
  • require_model()
  • Submodules
    • autoemx.core.em_runtime.particle_segmentation_models.SAM2 module
      • GENERATOR_DEFAULTS
      • is_available()
      • get_mask_generator()
      • generate_masks()
      • segment_particles()
    • autoemx.core.em_runtime.particle_segmentation_models.microSAM module
      • is_available()
      • get_predictor_and_segmenter()
      • instance_labels()
      • segment_particles()
    • autoemx.core.em_runtime.particle_segmentation_models._instance_filters module
      • FILTER_DEFAULTS
      • filter_options()
      • particle_labels()
    • autoemx.core.em_runtime.particle_segmentation_models.segmentation_model_template module
      • segment_particles()

Submodules

• autoemx.core.em_runtime.controller module
  • Main Classes
  • Example Usage
  • EM_Controller
    • EM_Controller.from_configs()
    • EM_Controller.initialise_SEM()
    • EM_Controller.initialise_sample_navigator()
    • EM_Controller.initialise_XS_analyzer()
    • EM_Controller.get_XSp_coords()
    • EM_Controller.acquire_XS_spot_spectrum()
    • EM_Controller.adjust_BCF()
    • EM_Controller.set_frame_width()
    • EM_Controller.update_pixel_size_from_frame_width()
    • EM_Controller.get_current_image()
    • EM_Controller.get_image_drift_pixels()
    • EM_Controller.move_to_pos()
    • EM_Controller.convert_pixel_pos_to_mm()
    • EM_Controller.convert_XS_coords_to_pixels()
    • EM_Controller.standby()
    • EM_Controller.go_to_next_frame()
    • EM_Controller.save_frame_image()
    • EM_Controller.frame_pos_mm
    • EM_Controller.frame_labels
    • EM_Controller.num_frames
    • EM_Controller.current_frame_label
    • EM_Controller.particle_finder
• autoemx.core.em_runtime.drift_correction module
  • preprocess_image()
  • shift_image()
  • estimate_drift_of()
• autoemx.core.em_runtime.frame_navigator module
  • Classes
  • FrameNavigator
    • FrameNavigator.initialise_sample_navigator()
    • FrameNavigator.reset_frame_cursor()
    • FrameNavigator.skip_frames()
    • FrameNavigator.skip_frames_overlapping()
    • FrameNavigator.get_visited_band_frames()
    • FrameNavigator.configure_top_level_particle_frames()
    • FrameNavigator.configure_particle_subframes()
    • FrameNavigator.update_current_pos_from_stage()
    • FrameNavigator.go_to_next_frame()
• autoemx.core.em_runtime.image_utilities module
  • Functions
  • convert_pixel_pos_to_mm()
  • convert_XS_coords_to_pixels()
  • draw_annotations()
  • RAW_IMAGE_SUFFIX
  • load_raw_saved_image()
  • particle_mark_annotations()
  • xsp_spot_annotation()
  • save_frame_image()
  • normalise_img()
• autoemx.core.em_runtime.microscope_controller module
  • Classes
  • MicroscopeController
    • MicroscopeController.initialise_SEM()
    • MicroscopeController.adjust_BCF()
    • MicroscopeController.set_frame_width()
    • MicroscopeController.move_to_pos()
    • MicroscopeController.standby()
• autoemx.core.em_runtime.particle_finder module
  • Main Class
  • Example Usage
  • FRAME_EDGE_MARGIN_PX
  • STATS_SAVE_EVERY_N_FRAMES
  • min_valid_diameter_um()
  • plan_size_bands_um()
  • diameter_um_to_area_um2()
  • FRAME_WIDTH_PER_MAX_DIAMETER
  • frame_width_um_from_max_area()
  • is_binary_mask()
  • label_image_stats()
  • StatsProgress
    • StatsProgress.n_par_target
    • StatsProgress.powder_meas_cfg
    • StatsProgress.bands
    • StatsProgress.measurement
    • StatsProgress.segmentation_id
  • EM_Particle_Finder
    • EM_Particle_Finder.current_par_area_um2
    • EM_Particle_Finder.current_par_coordinates_mm
    • EM_Particle_Finder.analyzed_pars
    • EM_Particle_Finder.pending_eds_frames
    • EM_Particle_Finder.is_manual_particle_selection
    • EM_Particle_Finder.is_list_particle_selection
    • EM_Particle_Finder.uses_absolute_particle_ids
    • EM_Particle_Finder.par_selection_mode
    • EM_Particle_Finder.set_particle_targets()
    • EM_Particle_Finder.go_to_next_particle()
    • EM_Particle_Finder.segment_frame()
    • EM_Particle_Finder.is_particle_at_frame_edge()
    • EM_Particle_Finder.prepare_mask_for_visualization()
    • EM_Particle_Finder.get_XS_acquisition_spots_coord_list()
    • EM_Particle_Finder.attach_stats_ledger()
    • EM_Particle_Finder.get_particle_stats()
    • EM_Particle_Finder.save_particle_statistics()
• autoemx.core.em_runtime.sample_finder module
  • Classes
  • EM_Sample_Finder
    • EM_Sample_Finder.detect_Ctape()
• autoemx.core.em_runtime.spectrum_acquisition module
  • Classes
  • SpectrumAcquisition
    • SpectrumAcquisition.initialise_XS_analyzer()
    • SpectrumAcquisition.get_XSp_coords()
    • SpectrumAcquisition.acquire_XS_spot_spectrum()
• autoemx.core.em_runtime.xsp_spot_selection module
  • XSpSpotSelectionContext
    • XSpSpotSelectionContext.particle_id
    • XSpSpotSelectionContext.n_tot_sp_collected
    • XSpSpotSelectionContext.ref_image
    • XSpSpotSelectionContext.pixel_size_um
    • XSpSpotSelectionContext.frame_label
    • XSpSpotSelectionContext.im_width
    • XSpSpotSelectionContext.im_height
    • XSpSpotSelectionContext.particle_finder
  • validate_xsp_spot_pixels()