Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | R | S | T | U | W | X A absolute_time_calculation() (ctdam.parser.cnvfile.CnvFile method) add_cast_number() (ctdam.parser.cnvfile.CnvFile method) add_default_metadata() (ctdam.parser.parameter.Parameters method) add_info() (ctdam.parser.processing_steps.CnvProcessingSteps method) add_parameter() (ctdam.parser.parameter.Parameters method) add_position_columns() (ctdam.parser.bottlefile.BottleFile method) (ctdam.parser.cnvfile.CnvFile method) add_processing_metadata() (ctdam.parser.cnvfile.CnvFile method) (ctdam.proc.module.Module method) add_start_time() (ctdam.parser.cnvfile.CnvFile method) add_station_and_event_column() (ctdam.parser.bottlefile.BottleFile method) (ctdam.parser.cnvfile.CnvFile method) add_whitespace() (in module ctdam.proc.modules.create_bottlefile) adding_timestamp_column() (ctdam.parser.bottlefile.BottleFile method) AirPressureCorrection (class in ctdam.proc.modules.air_pressure_correction) AlignCTD (class in ctdam.proc.modules.seabird_functions) array2cnv() (ctdam.parser.cnvfile.CnvFile method) (ctdam.parser.ctddata.CTDData method) ArrayModule (class in ctdam.proc.module) available_modules() (ctdam.proc.modules.external_functions.ExternalFunctions method) B basic_bokeh_plot (class in ctdam.vis.visualize) basic_bokeh_plot() (in module ctdam.vis.visualize) BinAvg (class in ctdam.proc.modules.seabird_functions) BinnedDataError BottleFile (class in ctdam.parser.bottlefile) BottleLogFile (class in ctdam.parser.bottlelogfile) build_new_name() (ctdam.proc.seabird.step.ProcessingStep method) C cancel() (ctdam.proc.seabird.routine.ProcessingRoutine method) Casts (class in ctdam.parser.casts) CellTM (class in ctdam.proc.modules.seabird_functions) check_and_create_path() (in module ctdam.vis.visualize) check_config_entry() (ctdam.proc.procedure.Procedure method) check_converted_data() (ctdam.parser.casts.Casts method) check_correlation_result() (ctdam.proc.modules.seabird_functions.AlignCTD method) check_input_path() (ctdam.proc.seabird.module.ProcessingModule method) check_whether_working_on_binned_data() (ctdam.proc.module.ArrayModule method) CnvCollection (class in ctdam.parser.file_collection) CnvFile (class in ctdam.parser.cnvfile) CnvProcessingSteps (class in ctdam.parser.processing_steps) collect_files() (ctdam.parser.file_collection.FileCollection method) Configuration (class in ctdam.proc.settings) convert() (ctdam.parser.casts.Casts method) (ctdam.proc.procedure.Procedure method) convert_conductivity() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_date() (ctdam.parser.bottlelogfile.BottleLogFile method) convert_freq_temperature() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_oxygen() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_oxygen_pyro_science() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_pressure() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_salinity() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_sbe43_oxygen() (ctdam.conv.parameter_mapping.ParameterMapping method) convert_temperature() (ctdam.conv.parameter_mapping.ParameterMapping method) create_bottle_file() (in module ctdam.proc.modules.create_bottlefile) create_btl() (ctdam.proc.modules.create_bottlefile.OwnBtlFile method) create_cnv_metadata() (ctdam.proc.modules.external_functions.ExternalFunctionInfo method) create_dataframe() (ctdam.parser.bottlefile.BottleFile method) (ctdam.parser.bottlelogfile.BottleLogFile method) (ctdam.parser.cnvfile.CnvFile method) (ctdam.parser.geomar_ctd_file_parser.GEOMARCTDFile method) create_event_string() (in module ctdam.utils) create_flag_array_if_missing() (ctdam.proc.module.ArrayModule method) create_full_ndarray() (ctdam.parser.parameter.Parameters method) create_header() (ctdam.parser.ctddata.CTDData method) create_list() (ctdam.parser.bottlelogfile.BottleLogFile method) create_main_html() (in module ctdam.vis.visualize) create_modules() (ctdam.proc.seabird.routine.ProcessingRoutine method) create_parameter() (ctdam.conv.parameter_mapping.ParameterMapping method) (ctdam.parser.parameter.Parameters method) create_parameter_instances() (ctdam.parser.parameter.Parameters method) create_seabird_module() (ctdam.proc.procedure.Procedure method) create_seabird_step() (ctdam.proc.procedure.Procedure method) create_step_instance() (ctdam.parser.processing_steps.CnvProcessingSteps method) create_steps() (ctdam.proc.seabird.routine.ProcessingRoutine method) cruise_plots() (in module ctdam.vis.visualize) ctdam module ctdam.conv module ctdam.conv.cast_borders module ctdam.conv.hexdecoder module ctdam.conv.parameter_mapping module ctdam.parser module ctdam.parser.bottlefile module ctdam.parser.bottlelogfile module ctdam.parser.casts module ctdam.parser.cnvfile module ctdam.parser.ctddata module ctdam.parser.datafiles module ctdam.parser.file_collection module ctdam.parser.geomar_ctd_file_parser module ctdam.parser.hexfile module ctdam.parser.parameter module ctdam.parser.processing_steps module ctdam.parser.xmlfiles module ctdam.proc module ctdam.proc.module module ctdam.proc.modules module 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 ctdam.proc.procedure module ctdam.proc.seabird module ctdam.proc.seabird.module module ctdam.proc.seabird.routine module ctdam.proc.seabird.step module ctdam.proc.settings module ctdam.proc.utils module ctdam.utils module ctdam.vis module ctdam.vis.visualize module CTDData (class in ctdam.parser.ctddata) D data_whitespace_removal() (ctdam.parser.bottlelogfile.BottleLogFile method) DataFile (class in ctdam.parser.datafiles) DataFrameModule (class in ctdam.proc.module) decode_hex() (in module ctdam.conv.hexdecoder) default_seabird_exe_path() (in module ctdam.proc.utils) define_output_path() (ctdam.parser.datafiles.DataFile method) df2cnv() (ctdam.parser.cnvfile.CnvFile method) drop_flagged_rows() (ctdam.parser.ctddata.CTDData method) E estimate_sensor_delay() (ctdam.proc.modules.seabird_functions.AlignCTD method) execute_funtion() (ctdam.proc.modules.external_functions.ExternalFunctionInfo method) ExternalFunctionCaller (class in ctdam.proc.modules.external_functions) ExternalFunctionInfo (class in ctdam.proc.modules.external_functions) ExternalFunctions (class in ctdam.proc.modules.external_functions) extra_data_table_desc() (ctdam.parser.ctddata.CTDData method) extract_coefficients() (ctdam.conv.parameter_mapping.ParameterMapping method) extract_file_type() (ctdam.parser.file_collection.FileCollection method) extract_individual_modules() (ctdam.parser.processing_steps.CnvProcessingSteps method) extract_sensor_name() (in module ctdam.utils) F FileCollection (class in ctdam.parser.file_collection) fill_file_type_dir() (in module ctdam.proc.utils) find_corresponding_temperature() (ctdam.proc.modules.seabird_functions.AlignCTD method) find_file() (ctdam.proc.seabird.module.ProcessingModule method) find_xmlcon() (ctdam.proc.seabird.routine.ProcessingRoutine method) functions_of_certain_module() (ctdam.proc.modules.external_functions.ExternalFunctions method) G GEOMARCTDFile (class in ctdam.parser.geomar_ctd_file_parser) get_alignment_delay_and_correlation_values() (in module ctdam.proc.utils) get_all_functions() (ctdam.proc.modules.external_functions.ExternalFunctions method) get_array() (ctdam.parser.file_collection.CnvCollection method) (ctdam.proc.module.ArrayModule method) get_cast_borders() (in module ctdam.conv.cast_borders) get_cast_borders_dict() (ctdam.parser.ctddata.CTDData method) get_collection() (in module ctdam.parser.file_collection) get_collection_dataframe() (ctdam.parser.file_collection.FileCollection method) get_correlation() (ctdam.proc.modules.seabird_functions.AlignCTD method) get_corresponding_xmlcon() (ctdam.parser.hexfile.HexFile method) get_data_length() (ctdam.parser.parameter.Parameters method) get_data_size() (ctdam.proc.module.ArrayModule method) get_data_table_meta_info() (ctdam.parser.file_collection.CnvCollection method) get_dataframes() (ctdam.parser.file_collection.CnvCollection method) (ctdam.parser.file_collection.FileCollection method) get_dict_of_available_processing_modules() (in module ctdam.proc.modules.available_modules) get_downcast_end() (in module ctdam.conv.cast_borders) get_downcast_start() (in module ctdam.conv.cast_borders) get_full_data_array() (ctdam.parser.parameter.Parameters method) get_list_of_custom_exes() (in module ctdam.proc.modules.available_modules) get_list_of_installed_seabird_modules() (in module ctdam.proc.modules.available_modules) get_metadata() (ctdam.parser.parameter.Parameters method) get_module_functions() (ctdam.proc.modules.external_functions.ExternalFunctions method) get_names() (ctdam.parser.parameter.Parameters method) (ctdam.parser.processing_steps.CnvProcessingSteps method) get_pandas_dataframe() (ctdam.parser.parameter.Parameters method) get_pandas_series() (ctdam.parser.parameter.Parameter method) get_param_types() (ctdam.parser.parameter.Parameters method) get_parameter_list() (ctdam.parser.parameter.Parameters method) get_processing_info() (ctdam.parser.ctddata.CTDData method) get_processing_step_infos() (ctdam.parser.cnvfile.CnvFile method) get_processing_steps() (ctdam.parser.file_collection.CnvCollection method) get_sample_rate() (ctdam.parser.parameter.Parameters method) get_sensor_info() (ctdam.parser.xmlfiles.XMLCONFile method) get_spans() (ctdam.parser.parameter.Parameters method) get_step() (ctdam.parser.processing_steps.CnvProcessingSteps method) get_time_gaps() (in module ctdam.conv.hexdecoder) get_unique_sensor_data() (in module ctdam.utils) get_upcast_end() (in module ctdam.conv.cast_borders) get_upcast_start() (in module ctdam.conv.cast_borders) get_xmlcons() (ctdam.parser.file_collection.HexCollection method) go() (ctdam.proc.procedure.Procedure method) H handle_fill_type_dir_creation() (ctdam.proc.procedure.Procedure method) handle_new_flags() (ctdam.proc.module.ArrayModule method) handle_parameter_input() (ctdam.proc.modules.seabird_functions.AlignCTD method) handle_time() (in module ctdam.conv.hexdecoder) hex_reading() (in module ctdam.conv.hexdecoder) HexCollection (class in ctdam.parser.file_collection) HexFile (class in ctdam.parser.hexfile) I IncompleteProcedureConfig InvalidArgumentCombination is_directly_measured_value() (in module ctdam.proc.utils) is_seabird_module() (ctdam.proc.procedure.Procedure method) J jens_loop_removal() (ctdam.proc.modules.seabird_functions.LoopRemoval method) L list_of_function_names() (ctdam.proc.modules.external_functions.ExternalFunctions method) load_config() (ctdam.proc.procedure.Procedure method) load_file() (ctdam.proc.module.Module method) load_files() (ctdam.parser.file_collection.FileCollection method) locate_sensor_data() (ctdam.conv.parameter_mapping.ParameterMapping method) LoopRemoval (class in ctdam.proc.modules.seabird_functions) M map_metadata() (ctdam.conv.parameter_mapping.ParameterMapping method) map_parameter() (ctdam.proc.modules.external_functions.ExternalFunctionInfo method) map_proc_name_to_class() (in module ctdam.proc.modules.available_modules) MissingParameterError modify() (ctdam.proc.settings.Configuration method) module ctdam ctdam.conv ctdam.conv.cast_borders ctdam.conv.hexdecoder ctdam.conv.parameter_mapping ctdam.parser ctdam.parser.bottlefile ctdam.parser.bottlelogfile ctdam.parser.casts ctdam.parser.cnvfile ctdam.parser.ctddata ctdam.parser.datafiles ctdam.parser.file_collection ctdam.parser.geomar_ctd_file_parser ctdam.parser.hexfile ctdam.parser.parameter ctdam.parser.processing_steps ctdam.parser.xmlfiles ctdam.proc ctdam.proc.module ctdam.proc.modules ctdam.proc.modules.air_pressure_correction ctdam.proc.modules.available_modules ctdam.proc.modules.create_bottlefile ctdam.proc.modules.external_functions ctdam.proc.modules.geomar_wildedit ctdam.proc.modules.seabird_functions ctdam.proc.procedure ctdam.proc.seabird ctdam.proc.seabird.module ctdam.proc.seabird.routine ctdam.proc.seabird.step ctdam.proc.settings ctdam.proc.utils ctdam.utils ctdam.vis ctdam.vis.visualize Module (class in ctdam.proc.module) N new_file_path() (ctdam.proc.procedure.Procedure method) O obtaining_reset_time() (ctdam.parser.bottlelogfile.BottleLogFile method) own_bin_average() (ctdam.proc.modules.seabird_functions.BinAvg method) OwnBtlFile (class in ctdam.proc.modules.create_bottlefile) P Parameter (class in ctdam.parser.parameter) ParameterMapping (class in ctdam.conv.parameter_mapping) Parameters (class in ctdam.parser.parameter) parse_docstring() (ctdam.proc.modules.external_functions.ExternalFunctionInfo method) parse_output_sensor_info() (ctdam.parser.ctddata.CTDData method) parse_to_float() (ctdam.parser.parameter.Parameter method) parse_xmlcon_sensor_data() (in module ctdam.utils) pick_output_columns() (ctdam.parser.ctddata.CTDData method) plot() (ctdam.parser.casts.Casts method) Procedure (class in ctdam.proc.procedure), [1] procedure_fingerprint() (ctdam.proc.procedure.Procedure method) process() (ctdam.parser.casts.Casts method) ProcessingModule (class in ctdam.proc.seabird.module) ProcessingRoutine (class in ctdam.proc.seabird.routine) ProcessingStep (class in ctdam.parser.processing_steps) (class in ctdam.proc.seabird.step) PsaFile (class in ctdam.parser.xmlfiles) R read_event_information() (ctdam.parser.datafiles.DataFile method) read_event_name() (in module ctdam.utils) read_file() (ctdam.parser.datafiles.DataFile method) (ctdam.parser.geomar_ctd_file_parser.GEOMARCTDFile method) read_sensor_info() (ctdam.parser.casts.Casts method) reading_data_header() (ctdam.parser.bottlefile.BottleFile method) (ctdam.parser.parameter.Parameters method) reading_start_time() (ctdam.parser.datafiles.DataFile method) run() (ctdam.proc.modules.external_functions.ExternalFunctionInfo method) (ctdam.proc.procedure.Procedure method) (ctdam.proc.seabird.routine.ProcessingRoutine method) (ctdam.proc.seabird.step.ProcessingStep method) run_process() (ctdam.proc.seabird.step.ProcessingStep method) run_string() (ctdam.proc.seabird.step.ProcessingStep method) S sbe_to_decimal() (in module ctdam.utils) select_real_scan_data() (ctdam.parser.file_collection.FileCollection method) selecting_columns() (ctdam.parser.datafiles.DataFile method) selecting_rows() (ctdam.parser.bottlefile.BottleFile method) sensor_xml_to_flattened_dict() (ctdam.parser.datafiles.DataFile method) set_dtype_to_float() (ctdam.parser.file_collection.FileCollection method) set_output_format() (ctdam.parser.parameter.Parameter method) set_sample_rate() (ctdam.parser.parameter.Parameters method) setting_dataframe_dtypes() (ctdam.parser.bottlefile.BottleFile method) smoothing() (in module ctdam.conv.cast_borders) sort_parameters() (ctdam.parser.parameter.Parameters method) sorting_parameters() (in module ctdam.conv.hexdecoder) start_thread() (ctdam.proc.seabird.routine.ProcessingRoutine method) structure_metadata() (ctdam.parser.datafiles.DataFile method) T tidy_collection_dataframe() (ctdam.parser.file_collection.FileCollection method) to_cnv() (ctdam.parser.cnvfile.CnvFile method) (ctdam.parser.ctddata.CTDData method) (ctdam.proc.module.ArrayModule method) (ctdam.proc.module.DataFrameModule method) (ctdam.proc.module.Module method) to_csv() (ctdam.parser.datafiles.DataFile method) (ctdam.parser.file_collection.FileCollection method) (ctdam.proc.module.DataFrameModule method) to_ctd_data() (ctdam.parser.cnvfile.CnvFile method) to_json() (ctdam.parser.xmlfiles.XMLFile method) to_netCDF() (ctdam.parser.ctddata.CTDData method) to_tsv() (ctdam.parser.casts.Casts method) to_xml() (ctdam.parser.xmlfiles.XMLFile method) transformation() (ctdam.proc.module.ArrayModule method) (ctdam.proc.module.DataFrameModule method) (ctdam.proc.modules.air_pressure_correction.AirPressureCorrection method) (ctdam.proc.modules.external_functions.ExternalFunctionCaller method) (ctdam.proc.modules.geomar_wildedit.WildeditGEOMAR method) (ctdam.proc.modules.seabird_functions.AlignCTD method) (ctdam.proc.modules.seabird_functions.BinAvg method) (ctdam.proc.modules.seabird_functions.CellTM method) (ctdam.proc.modules.seabird_functions.LoopRemoval method) (ctdam.proc.modules.seabird_functions.WFilter method) U UnexpectedFileFormat update_salinity() (ctdam.parser.ctddata.CTDData method) update_span() (ctdam.parser.parameter.Parameter method) update_spans() (ctdam.parser.parameter.Parameters method) use_bad_flag_for_nan() (ctdam.parser.file_collection.FileCollection method) use_name() (ctdam.parser.parameter.Parameter method) W WFilter (class in ctdam.proc.modules.seabird_functions) wildedit_geomar() (in module ctdam.proc.modules.geomar_wildedit) WildeditGEOMAR (class in ctdam.proc.modules.geomar_wildedit) window_filter() (ctdam.proc.modules.seabird_functions.WFilter method) with_name_type() (ctdam.parser.parameter.Parameters method) write() (ctdam.proc.settings.Configuration method) X XMLCONFile (class in ctdam.parser.xmlfiles) XMLFile (class in ctdam.parser.xmlfiles)