papylio.File#

class papylio.File(*args, **kwargs)#

__init__(*args, **kwargs)#

Methods

`__init__`(args, *kwargs)
`add_extensions`(extensions[, load])
`add_selection`(variable, channel, aggregator, ...)
`analyze_dwells`([plot, axes, name, ...])
`apply_classifications`(**kwargs)
`apply_selections`([selection_names])
`apply_trace_corrections`([...])
`autoThreshold`(trace_name[, threshold, ...])
`average_image`()
`calculate_FRET`()
`classification_binary`([...])
`classify_hmm`(variable[, seed, n_states, ...])
`clear_selections`()
`coordinates_from_channel`(channel)
`copy_coordinates_to_selected_files`()
`copy_selections_to_selected_files`()
`determine_dwells_from_classification`([...])
`determine_psf_size`([method, ...])
`determine_sequences_at_current_coordinates`([...])
`determine_trace_correction`()
`export_coeff_file`()
`export_map_file`()
`export_mapping`([filetype])
`export_pks_file`()
`export_sequencing_match`()
`export_traces_file`()
`extract_background`([configuration])
`extract_traces`([mask_size, ...])
`find_and_add_extensions`()
`find_coordinates`(**configuration)	This function finds and sets the locations of all molecules within the movie's images.
`find_extensions`()
`find_sequences_using_stage_coordinates`([...])
`generate_sequencing_match`([...])
`get_data`(key)
`get_projection_image`([load])
`get_sequencing_data`([margin, mapping_name])
`get_traces`([selected])
`get_variable`(variable[, selected, ...])	Get a variable.
`histogram_2D_FRET_intensity_total`([...])	Generates a 2D histogram plot of FRET vs.
`histogram_2D_intensity_per_channel`([...])	Generates a 2D histogram plot of intensity between two specified channels, with optional marginal histograms.
`import_coeff_file`(extension)
`import_excel_file`([filename])
`import_map_file`(extension)
`import_mapping_file`(extension)
`import_movie`(extension)
`import_pks_file`(extension)
`import_sequencing_match`()
`import_traces_file`(extension)
`insert_sequencing_data_into_file_dataset`([...])
`maximum_projection_image`()
`noneFunction`(args, *kwargs)
`perform_mapping`(**configuration)
`plot_hmm_rates`([name])
`plot_sequencing_match`()
`projection_image`()
`save_dataset_selected`()
`savetoExcel`([filename, save])
`set_coordinates_of_channel`(coordinates, channel)
`set_variable`(data, **kwargs)
`show_average_image`([figure])
`show_coordinates`([figure, annotate, unit])
`show_coordinates_in_image`([figure])
`show_histogram`(variable[, selected, ...])
`show_image`([projection_type, figure, unit])
`show_mapping_in_image`([axis, save])
`show_traces`([plot_variables, ylims, ...])
`state_count`([selected, states])
`state_fraction`(**state_count_kwargs)
`use_for_darkfield_correction`()
`use_mapping_for_all_files`()
`use_sequences_as_molecules`()

Attributes

`absoluteFilePath`
`configuration`
`coordinates`
`coordinates_metric`
`coordinates_stage`
`cycle_time`
`data_vars`
`dataset`
`dataset_selected`
`dwell_analysis`
`dwells`
`frame_rate`
`has_sequencing_match`
`intensity_total`
`number_of_channels`
`number_of_molecules`
`number_of_selected_molecules`
`number_of_states_from_classification`
`relativeFilePath`
`selected_molecules`
`selection_names`
`selections`
`selections_dataset`
`sequencing_data`
`sequencing_match`