t_number=False) merged_variables, owner_file = Merge.merge_entities(variable_dict) merged_variables = Entities.sorted_entities(merged_variables) merged_sections, _ = Merge.merge_entities(section_dict) merged_variables_hash = Merge.merge_hash(variable_hash_dict) ctakes_dir = input_dir.replace("input", "ctakes_output") ctakes_variables, ctakes_variables_hash, ctakes_sections = Entities.get_ctakes_entities(bunch, ctakes_dir, t_number=False) merged_variables, merged_variables_hash, merged_sections = Merge.merge_ctakes_annotators(merged_variables, merged_variables_hash, merged_sections, ctakes_variables, ctakes_variables_hash, ctakes_sections) merged_variables = Entities.sorted_entities(merged_variables) section_variable = Merge.merge_variables_sections(merged_variables, merged_sections) # section_variable = Merge.diagnostic_filterring(section_variable) section_variable = Merge.diagnostic_filterring_new(section_variable) Write.accepted_variables_reannote(owner_file, section_variable, merged_variables_hash, bunch, input_dir, output_dir) print("Done")