Code

• pypet2bids
  • pypet2bids.ecat_cli module
    • cli()
    • main()
    • update_json_with_ecat_value_cli()
  • pypet2bids.dcm2niix4pet module
    • Dcm2niix4PET
      • Dcm2niix4PET.check_for_dcm2niix()
      • Dcm2niix4PET.check_posix()
      • Dcm2niix4PET.convert()
      • Dcm2niix4PET.extract_dicom_headers()
      • Dcm2niix4PET.extract_metadata()
      • Dcm2niix4PET.load_spread_sheet_data()
      • Dcm2niix4PET.match_dicom_header_to_file()
      • Dcm2niix4PET.open_meta_data()
      • Dcm2niix4PET.post_dcm2niix()
      • Dcm2niix4PET.run_dcm2niix()
    • cli()
    • collect_date_time_from_file_name()
    • dicom_datetime_to_dcm2niix_time()
    • main()
  • pypet2bids.ecat module
    • Ecat
      • Ecat.convert()
      • Ecat.extract_affine()
      • Ecat.json_out()
      • Ecat.make_nifti()
      • Ecat.populate_sidecar()
      • Ecat.prune_sidecar()
      • Ecat.show_affine()
      • Ecat.show_directory_table()
      • Ecat.show_header()
      • Ecat.show_sidecar()
      • Ecat.show_subheaders()
      • Ecat.update_pet_json()
      • Ecat.write_out_blood_files()
    • parse_this_date()
  • pypet2bids.ecat2nii module
    • ecat2nii()
  • pypet2bids.helper_functions module
    • CustomFormatter
      • CustomFormatter.FORMATS
      • CustomFormatter.bold_red
      • CustomFormatter.format()
      • CustomFormatter.grey
      • CustomFormatter.red
      • CustomFormatter.reset
      • CustomFormatter.yellow
    • ParseKwargs
    • ad_hoc_checks()
    • check_pet2bids_config()
    • check_units()
    • collect_bids_part()
    • collect_spreadsheets()
    • compress()
    • decompress()
    • drop_row()
    • expand_path()
    • first_middle_last_frames_to_text()
    • flatten_series()
    • get_coordinates_containing()
    • get_recon_method()
    • get_version()
    • hash_fields()
    • import_and_write_out_module()
    • is_numeric()
    • load_vars_from_config()
    • logger()
    • modify_config_file()
    • open_meta_data()
    • reorder_isotope()
    • replace_nones()
    • sanitize_bad_path()
    • single_spreadsheet_reader()
    • transform_row_to_dict()
    • translate_metadata()
    • very_tolerant_literal_eval()
    • write_out_module()
  • pypet2bids.read_ecat module
    • collect_specific_bytes()
    • filter_bytes()
    • get_buffer_size()
    • get_directory_data()
    • get_ecat_bytes()
    • get_header_data()
    • read_bytes()
    • read_ecat()
  • pypet2bids.sidecar module
  • pypet2bids.convert_pmod_to_blood module
    • PmodToBlood
      • PmodToBlood.ask_recording_type()
      • PmodToBlood.check_for_interpolated_data()
      • PmodToBlood.check_fraction_is_fraction()
      • PmodToBlood.check_time_info()
      • PmodToBlood.load_pmod_file()
      • PmodToBlood.scale_time_rename_columns()
      • PmodToBlood.write_out_jsons()
      • PmodToBlood.write_out_tsvs()
    • cli()
    • main()
    • type_cast_cli_input()
  • pypet2bids.multiple_spreadsheets module
    • cli()
    • read_multi_subject_spreadsheets()
    • write_multi_subject_spreadsheets()
  • pypet2bids.update_pet_json module
    • check_json()
    • check_meta_radio_inputs()
    • get_metadata_from_spreadsheet()
    • get_radionuclide()
    • update_json_cli()
    • update_json_with_dicom_value()
    • update_json_with_dicom_value_cli()
  • Module contents
• matlab