papylio.File
============

.. currentmodule:: papylio

.. autoclass:: File

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~File.__init__
      ~File.add_extensions
      ~File.analyze_dwells
      ~File.apply_classifications
      ~File.apply_selections
      ~File.apply_trace_corrections
      ~File.autoThreshold
      ~File.average_image
      ~File.calculate_FRET
      ~File.classification_binary
      ~File.classification_configurations
      ~File.classify_hmm
      ~File.clear_selections
      ~File.coordinates_from_channel
      ~File.copy_coordinates_to_selected_files
      ~File.copy_selections_to_selected_files
      ~File.create_classification
      ~File.create_selection
      ~File.determine_dwells_from_classification
      ~File.determine_psf_size
      ~File.determine_sequences_at_current_coordinates
      ~File.determine_trace_correction
      ~File.export_coeff_file
      ~File.export_map_file
      ~File.export_mapping
      ~File.export_pks_file
      ~File.export_sequencing_match
      ~File.export_traces_file
      ~File.extract_background
      ~File.extract_traces
      ~File.find_and_add_extensions
      ~File.find_coordinates
      ~File.find_extensions
      ~File.find_sequences_using_stage_coordinates
      ~File.generate_sequencing_match
      ~File.get_data
      ~File.get_projection_image
      ~File.get_sequencing_data
      ~File.get_traces
      ~File.get_variable
      ~File.histogram_2D_FRET_intensity_total
      ~File.histogram_2D_intensity_per_channel
      ~File.import_coeff_file
      ~File.import_excel_file
      ~File.import_map_file
      ~File.import_mapping_file
      ~File.import_movie
      ~File.import_pks_file
      ~File.import_sequencing_match
      ~File.import_traces_file
      ~File.insert_sequencing_data_into_file_dataset
      ~File.maximum_projection_image
      ~File.noneFunction
      ~File.perform_mapping
      ~File.plot_dwell_analysis
      ~File.plot_hmm_rates
      ~File.plot_sequencing_match
      ~File.projection_image
      ~File.save_dataset_selected
      ~File.savetoExcel
      ~File.selection_configurations
      ~File.set_coordinates_of_channel
      ~File.set_variable
      ~File.show_average_image
      ~File.show_coordinates
      ~File.show_coordinates_in_image
      ~File.show_histogram
      ~File.show_image
      ~File.show_mapping_in_image
      ~File.show_traces
      ~File.state_count
      ~File.state_fraction
      ~File.use_for_darkfield_correction
      ~File.use_mapping_for_all_files
      ~File.use_sequences_as_molecules
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~File.absoluteFilePath
      ~File.classification
      ~File.classification_names
      ~File.classifications
      ~File.configuration
      ~File.coordinates
      ~File.coordinates_metric
      ~File.coordinates_stage
      ~File.cycle_time
      ~File.data_vars
      ~File.dataset
      ~File.dataset_attributes
      ~File.dataset_selected
      ~File.dwell_analysis
      ~File.dwells
      ~File.frame_rate
      ~File.has_sequencing_match
      ~File.intensity_total
      ~File.number_of_channels
      ~File.number_of_molecules
      ~File.number_of_selected_molecules
      ~File.number_of_states_from_classification
      ~File.relativeFilePath
      ~File.sampling_interval
      ~File.selected_molecules
      ~File.selection_names
      ~File.selection_names_active
      ~File.selections
      ~File.sequencing_data
      ~File.sequencing_match