Index A | B | C | D | F | G | H | I | L | M | O | P | R | S | U A add_circle_mask() (derotation.analysis.full_derotation_pipeline.FullPipeline static method) adjust_rotation_increment() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) apply_homography() (in module derotation.derotate_by_line) B BlobDetection (class in derotation.analysis.blob_detection) BO_for_derotation (class in derotation.analysis.bayesian_optimization) C calculate_angles_by_line_and_frame() (derotation.analysis.full_derotation_pipeline.FullPipeline method) calculate_mean_images() (in module derotation.analysis.mean_images) calculate_pixel_shift() (derotation.simulate.line_scanning_microscope.Rotator method) calculate_velocity() (derotation.analysis.full_derotation_pipeline.FullPipeline method) check_number_of_frame_angles() (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) check_number_of_rotations() (derotation.analysis.full_derotation_pipeline.FullPipeline method) check_rotation_number() (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) check_rotation_number_after_interpolation() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) clock_to_latest_frame_start() (derotation.analysis.full_derotation_pipeline.FullPipeline method) clock_to_latest_line_start() (derotation.analysis.full_derotation_pipeline.FullPipeline method) clock_to_latest_rotation_start() (derotation.analysis.full_derotation_pipeline.FullPipeline method) convert_to_volts() (in module derotation.load_data.custom_data_loaders) correct_start_and_end_rotation_signal() (derotation.analysis.full_derotation_pipeline.FullPipeline method) create_homography_matrices() (derotation.simulate.line_scanning_microscope.Rotator method) create_image_stack() (derotation.simulate.synthetic_data.SyntheticData method) create_rotation_angles() (derotation.simulate.synthetic_data.SyntheticData static method) create_sample_image_with_cells() (derotation.simulate.synthetic_data.SyntheticData method) create_signed_rotation_array() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) D derive_angles_from_ellipse_fits() (in module derotation.analysis.fit_ellipse) derotate() (in module derotation.derotate_batch) derotate_an_image_array_line_by_line() (in module derotation.derotate_by_line) derotate_frames_line_by_line() (derotation.analysis.full_derotation_pipeline.FullPipeline method) derotation.analysis.bayesian_optimization module derotation.analysis.blob_detection module derotation.analysis.fit_ellipse module derotation.analysis.full_derotation_pipeline module derotation.analysis.incremental_derotation_pipeline module derotation.analysis.mean_images module derotation.analysis.metrics module derotation.config.load_config module derotation.derotate_batch module derotation.derotate_by_line module derotation.load_data.custom_data_loaders module derotation.plotting_hooks.for_derotation module derotation.sample_data module derotation.simulate.line_scanning_microscope module derotation.simulate.synthetic_data module drop_ticks_outside_of_rotation() (derotation.analysis.full_derotation_pipeline.FullPipeline method) F fetch_data() (in module derotation.sample_data) find_center_of_rotation() (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) find_image_offset() (derotation.analysis.full_derotation_pipeline.FullPipeline static method) find_missing_rotation_on_periods() (derotation.analysis.full_derotation_pipeline.FullPipeline method) find_optimal_parameters() (derotation.analysis.full_derotation_pipeline.FullPipeline method) find_rotation_peaks() (derotation.analysis.full_derotation_pipeline.FullPipeline method) fit_ellipse_to_points() (in module derotation.analysis.fit_ellipse) FullPipeline (class in derotation.analysis.full_derotation_pipeline) G get_analog_signals() (in module derotation.load_data.custom_data_loaders) get_blank_pixels_value() (derotation.simulate.line_scanning_microscope.Rotator method) get_center_of_rotation() (derotation.simulate.synthetic_data.SyntheticData method) get_config() (derotation.analysis.full_derotation_pipeline.FullPipeline method) get_coords_of_largest_blob() (derotation.analysis.blob_detection.BlobDetection method) get_interpolated_angles() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) get_peaks_in_rotation() (derotation.analysis.full_derotation_pipeline.FullPipeline method) get_start_end_times_with_threshold() (derotation.analysis.full_derotation_pipeline.FullPipeline static method) H homography_rotation_to_scanning_plane() (derotation.simulate.line_scanning_microscope.Rotator method) I image_completed() (in module derotation.plotting_hooks.for_derotation) IncrementalPipeline (class in derotation.analysis.incremental_derotation_pipeline) integration_pipeline() (derotation.simulate.synthetic_data.SyntheticData method) is_number_of_ticks_correct() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) L line_addition() (in module derotation.plotting_hooks.for_derotation) load_config() (in module derotation.config.load_config) load_data() (derotation.analysis.full_derotation_pipeline.FullPipeline method) M mean_image_for_each_rotation() (derotation.analysis.full_derotation_pipeline.FullPipeline method) module derotation.analysis.bayesian_optimization derotation.analysis.blob_detection derotation.analysis.fit_ellipse derotation.analysis.full_derotation_pipeline derotation.analysis.incremental_derotation_pipeline derotation.analysis.mean_images derotation.analysis.metrics derotation.config.load_config derotation.derotate_batch derotation.derotate_by_line derotation.load_data.custom_data_loaders derotation.plotting_hooks.for_derotation derotation.sample_data derotation.simulate.line_scanning_microscope derotation.simulate.synthetic_data O optimize() (derotation.analysis.bayesian_optimization.BO_for_derotation method) P plot_a_few_rotated_frames() (derotation.simulate.synthetic_data.SyntheticData method) plot_angles() (derotation.simulate.synthetic_data.SyntheticData method) plot_blob_detection() (derotation.analysis.blob_detection.BlobDetection method) plot_derotated_frames() (derotation.simulate.synthetic_data.SyntheticData method) plot_each_frame() (derotation.simulate.synthetic_data.SyntheticData method) plot_ellipse_fit_and_centers() (in module derotation.analysis.fit_ellipse) plot_max_projection_with_center() (derotation.analysis.full_derotation_pipeline.FullPipeline method) plot_mean_projection() (derotation.simulate.synthetic_data.SyntheticData method) plot_original_image() (derotation.simulate.synthetic_data.SyntheticData method) plot_rotation_angles_and_velocity() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) plot_rotation_on_and_ticks() (derotation.analysis.full_derotation_pipeline.FullPipeline method) plot_rotation_speeds() (derotation.analysis.full_derotation_pipeline.FullPipeline method) (derotation.analysis.incremental_derotation_pipeline.IncrementalPipeline method) process_analog_signals() (derotation.analysis.full_derotation_pipeline.FullPipeline method) ptd_of_most_detected_blob() (in module derotation.analysis.metrics) R read_randomized_stim_table() (in module derotation.load_data.custom_data_loaders) remove_artifacts_from_interpolated_angles() (derotation.analysis.full_derotation_pipeline.FullPipeline method) rotate_by_line() (derotation.simulate.line_scanning_microscope.Rotator method) rotate_sample() (derotation.simulate.line_scanning_microscope.Rotator method) Rotator (class in derotation.simulate.line_scanning_microscope) S save() (derotation.analysis.full_derotation_pipeline.FullPipeline method) save_csv_with_derotation_data() (derotation.analysis.full_derotation_pipeline.FullPipeline method) set_optimal_center() (derotation.analysis.full_derotation_pipeline.FullPipeline method) start_logging() (derotation.analysis.full_derotation_pipeline.FullPipeline method) SyntheticData (class in derotation.simulate.synthetic_data) U update_config_paths() (in module derotation.config.load_config)