papylio.Experiment

class papylio.Experiment(*args, **kwargs)

__init__(*args, **kwargs)

Init method for the Experiment class

Loads config file if it locates one in the main directory, otherwise it exports the default config file to the main directory. Scans all directory in the main directory recursively and imports all found files (if import_all is set to True).

Parameters:

• main_path (str) – Absolute path to the main experiment folder

• channels (list of str) – Channels used in the experiment

• import_all (bool) – If true, then all files in the main folder are automatically imported.

  If false, then files are detected, but not imported.

Methods

__init__(*args, **kwargs)	Init method for the Experiment class
add_common_image_corrections_to_movies()
add_files(paths[, test_duplicates])	Find unique files in all subfolders and add them to the experiment
boxplot_number_of_molecules()	Boxplot of the number of molecules in each file
determine_flatfield_and_darkfield_corrections(files)
export_number_of_molecules_per_file()
files_with_sequencing_match([files])
find_file_paths_and_extensions(paths)	Find unique files in all subfolders and add them to the experiment
generate_tile_mappings(files_for_mapping[, ...])
histogram([axis, bins, parameter, ...])	FRET histogram of all molecules in the experiment or a specified selection
import_sequencing_data(file_path[, ...])
import_sequencing_data_for_mapping(file_path)
import_sequencing_data_old()
load_darkfield_correction()
load_flatfield_correction()
plot_trace([files, query])
print_files()
select()	Simple method to look through all molecules in the experiment
sequencing_match_info_mean([distance_threshold])
sequencing_match_info_per_file()
sequencing_matches([files])
show_sequencing_matches([show_file_coordinates])
transform_sequencing_to_single_molecule_coordinates()

Attributes

analysis_path
channels	Channels used in the experiment.
file_paths
mapping_file
nc_file_paths
number_of_channels	Number of channels used in the experiment (read-only)
pairs	List of channel pairs
selectedFiles	List of selected files
tile_mappings
tile_mappings_dict