ctdam package

Subpackages

• ctdam.conv package
  • Submodules
  • ctdam.conv.cast_borders module
    • smoothing()
    • get_cast_borders()
    • get_downcast_end()
    • get_downcast_start()
    • get_upcast_start()
    • get_upcast_end()
  • ctdam.conv.hexdecoder module
    • hex_reading()
    • sorting_parameters()
    • get_time_gaps()
    • handle_time()
    • decode_hex()
  • ctdam.conv.parameter_mapping module
    • ParameterMapping
      • ParameterMapping.extract_coefficients()
      • ParameterMapping.locate_sensor_data()
      • ParameterMapping.create_parameter()
      • ParameterMapping.convert_freq_temperature()
      • ParameterMapping.convert_temperature()
      • ParameterMapping.convert_pressure()
      • ParameterMapping.convert_conductivity()
      • ParameterMapping.convert_salinity()
      • ParameterMapping.convert_sbe43_oxygen()
      • ParameterMapping.convert_oxygen()
      • ParameterMapping.convert_oxygen_pyro_science()
      • ParameterMapping.map_metadata()
  • Module contents
• ctdam.parser package
  • Submodules
  • ctdam.parser.bottlefile module
    • BottleFile
      • BottleFile.create_dataframe()
      • BottleFile.adding_timestamp_column()
      • BottleFile.setting_dataframe_dtypes()
      • BottleFile.selecting_rows()
      • BottleFile.reading_data_header()
      • BottleFile.add_station_and_event_column()
      • BottleFile.add_position_columns()
  • ctdam.parser.bottlelogfile module
    • BottleLogFile
      • BottleLogFile.data_whitespace_removal()
      • BottleLogFile.obtaining_reset_time()
      • BottleLogFile.create_list()
      • BottleLogFile.convert_date()
      • BottleLogFile.create_dataframe()
  • ctdam.parser.cnvfile module
    • CnvFile
      • CnvFile.create_dataframe()
      • CnvFile.absolute_time_calculation()
      • CnvFile.add_start_time()
      • CnvFile.get_processing_step_infos()
      • CnvFile.df2cnv()
      • CnvFile.array2cnv()
      • CnvFile.to_cnv()
      • CnvFile.to_ctd_data()
      • CnvFile.add_processing_metadata()
      • CnvFile.add_station_and_event_column()
      • CnvFile.add_position_columns()
      • CnvFile.add_cast_number()
  • ctdam.parser.ctddata module
    • CTDData
      • CTDData.get_cast_borders_dict()
      • CTDData.update_salinity()
      • CTDData.array2cnv()
      • CTDData.parse_output_sensor_info()
      • CTDData.get_processing_info()
      • CTDData.create_header()
      • CTDData.extra_data_table_desc()
      • CTDData.drop_flagged_rows()
      • CTDData.pick_output_columns()
      • CTDData.to_cnv()
  • ctdam.parser.datafiles module
    • DataFile
      • DataFile.read_event_information()
      • DataFile.read_file()
      • DataFile.reading_start_time()
      • DataFile.sensor_xml_to_flattened_dict()
      • DataFile.structure_metadata()
      • DataFile.define_output_path()
      • DataFile.to_csv()
      • DataFile.selecting_columns()
  • ctdam.parser.file_collection module
    • get_collection()
    • FileCollection
      • FileCollection.extract_file_type()
      • FileCollection.collect_files()
      • FileCollection.load_files()
      • FileCollection.get_dataframes()
      • FileCollection.get_collection_dataframe()
      • FileCollection.tidy_collection_dataframe()
      • FileCollection.use_bad_flag_for_nan()
      • FileCollection.set_dtype_to_float()
      • FileCollection.select_real_scan_data()
      • FileCollection.to_csv()
    • CnvCollection
      • CnvCollection.get_dataframes()
      • CnvCollection.get_data_table_meta_info()
      • CnvCollection.get_array()
      • CnvCollection.get_processing_steps()
    • HexCollection
      • HexCollection.get_xmlcons()
  • ctdam.parser.geomar_ctd_file_parser module
    • GEOMARCTDFile
      • GEOMARCTDFile.read_file()
      • GEOMARCTDFile.create_dataframe()
  • ctdam.parser.hexfile module
    • HexFile
      • HexFile.get_corresponding_xmlcon()
  • ctdam.parser.parameter module
    • Parameters
      • Parameters.get_param_types()
      • Parameters.get_data_length()
      • Parameters.get_full_data_array()
      • Parameters.get_names()
      • Parameters.get_metadata()
      • Parameters.get_parameter_list()
      • Parameters.set_sample_rate()
      • Parameters.get_sample_rate()
      • Parameters.create_full_ndarray()
      • Parameters.sort_parameters()
      • Parameters.create_parameter_instances()
      • Parameters.add_parameter()
      • Parameters.create_parameter()
      • Parameters.add_default_metadata()
      • Parameters.update_spans()
      • Parameters.get_spans()
      • Parameters.get_pandas_dataframe()
      • Parameters.with_name_type()
      • Parameters.reading_data_header()
    • Parameter
      • Parameter.get_pandas_series()
      • Parameter.use_name()
      • Parameter.parse_to_float()
      • Parameter.update_span()
      • Parameter.set_output_format()
  • ctdam.parser.processing_steps module
    • CnvProcessingSteps
      • CnvProcessingSteps.get_names()
      • CnvProcessingSteps.extract_individual_modules()
      • CnvProcessingSteps.create_step_instance()
      • CnvProcessingSteps.get_step()
      • CnvProcessingSteps.add_info()
    • ProcessingStep
  • ctdam.parser.xmlfiles module
    • XMLFile
      • XMLFile.to_xml()
      • XMLFile.to_json()
    • XMLCONFile
      • XMLCONFile.get_sensor_info()
    • PsaFile
  • Module contents
• ctdam.proc package
  • Subpackages
    • ctdam.proc.modules package
      • Submodules
      • ctdam.proc.modules.air_pressure_correction module
      • ctdam.proc.modules.available_modules module
      • ctdam.proc.modules.create_bottlefile module
      • ctdam.proc.modules.external_functions module
      • ctdam.proc.modules.geomar_wildedit module
      • ctdam.proc.modules.seabird_functions module
      • Module contents
    • ctdam.proc.seabird package
      • Submodules
      • ctdam.proc.seabird.module module
      • ctdam.proc.seabird.routine module
      • ctdam.proc.seabird.step module
      • Module contents
  • Submodules
  • ctdam.proc.module module
    • Module
      • Module.add_processing_metadata()
      • Module.load_file()
      • Module.to_cnv()
    • ArrayModule
      • ArrayModule.transformation()
      • ArrayModule.get_array()
      • ArrayModule.get_data_size()
      • ArrayModule.create_flag_array_if_missing()
      • ArrayModule.handle_new_flags()
      • ArrayModule.check_whether_working_on_binned_data()
      • ArrayModule.to_cnv()
    • DataFrameModule
      • DataFrameModule.transformation()
      • DataFrameModule.to_cnv()
      • DataFrameModule.to_csv()
    • MissingParameterError
  • ctdam.proc.procedure module
    • Procedure
      • Procedure.run()
      • Procedure.load_config()
      • Procedure.check_config_entry()
      • Procedure.is_seabird_module()
      • Procedure.create_seabird_module()
      • Procedure.create_seabird_step()
      • Procedure.convert()
      • Procedure.new_file_path()
      • Procedure.go()
      • Procedure.procedure_fingerprint()
      • Procedure.handle_fill_type_dir_creation()
  • ctdam.proc.settings module
    • Configuration
      • Configuration.write()
      • Configuration.modify()
    • IncompleteConfigFile
  • ctdam.proc.utils module
    • default_seabird_exe_path()
    • is_directly_measured_value()
    • get_alignment_delay_and_correlation_values()
    • fill_file_type_dir()
    • BinnedDataError
  • Module contents
• ctdam.vis package
  • Submodules
  • ctdam.vis.visualize module
  • Module contents

Submodules

ctdam.utils module

ctdam.utils.read_event_name(station_string, regex_string='(?P<c>[a-z]{1,3}\\\\d{1,3})(-|_|\\\\/)?(?P<cn>1|2)?(-|_)(?P<s>\\\\d{1,4})(-|_)(?P<e>\\\\d{1,2})')

Return type:

Tuple[str, str]

ctdam.utils.create_event_string(cruise, station_event, leading_zeroes=True)

Return type:

str

ctdam.utils.parse_xmlcon_sensor_data(sensor_info)

Return type:

dict

ctdam.utils.extract_sensor_name(sensors)

Return type:

list

ctdam.utils.get_unique_sensor_data(sensor_data)

Returns all the unique sensors and their configuration used in the given collection of sensor data. These will typically be parsed from xml inside .cnv or .xmlcon files. If for example, the first oxygen sensor has been replaced after the 8 cast, then we will see that in the output structure by a seconde tuple, with the number 8 and the individual sensor information for that new oxygen sensor.

Parameters:

sensor_data (list[list[dict]]) – The structure of xml-parsed dicts inside two organizing lists.

Return type:

list[tuple[list[dict]]]

Returns:

• The input structure stripped down to unique sensor data and appended by

• the index, at which this new sensor appeared the first time.

exception ctdam.utils.UnexpectedFileFormat(file_type, error)

Bases: Exception

Module contents