Index A | B | C | D | E | F | G | H | I | J | L | M | N | O | P | Q | R | S | T | U | W | X A absolute_time_calculation() (ctdam.CnvFile method) (ctdam.parser.CnvFile method) (ctdam.parser.seabird_data_files.CnvFile method) add_processing_metadata() (ctdam.proc.module.Module method) adding_timestamp_column() (ctdam.BottleFile method) (ctdam.parser.BottleFile method) (ctdam.parser.seabird_data_files.BottleFile method) AirPressureCorrection (class in ctdam.proc.modules.air_pressure_correction) AlignCTD (class in ctdam.proc.modules.seabird_functions) altimeter() (in module ctdam.conv.raw_conversion) anomalous_data (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) apply_default_range_checks() (in module ctdam.qc.range_checks) apply_default_spike_checks() (in module ctdam.qc.spike_checks) apply_range_check() (in module ctdam.qc.range_checks) apply_range_check_to_parameter() (in module ctdam.qc.range_checks) apply_spike_check() (in module ctdam.qc.spike_checks) apply_spike_check_to_parameter() (in module ctdam.qc.spike_checks) B BAD (ctdam.qc.quality_flags.SeaDataNetFlag attribute) bad_flag (ctdam.proc.module.Module attribute) basic_bokeh_plot (class in ctdam.vis.visualize) basic_bokeh_plot() (in module ctdam) (in module ctdam.vis) (in module ctdam.vis.visualize) BELOW_DETECTION (ctdam.qc.quality_flags.SeaDataNetFlag attribute) best_estimate() (ctdam.parser.custom_xarray_accessors.QCAccessor method) bin_unit (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor property) BinAvg (class in ctdam.proc.modules.seabird_functions) binned (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor property) BinnedDataError BottleFile (class in ctdam) (class in ctdam.parser) (class in ctdam.parser.seabird_data_files) (class in ctdam.proc.modules.bottle_file) BottleLogFile (class in ctdam) (class in ctdam.parser) (class in ctdam.parser.seabird_data_files) bottles() (ctdam.parser.custom_xarray_accessors.InputAccessor method) btl_info (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor property) build_sensor_pairs() (in module ctdam.parser.read_ctd_data) C calculate_dvdt_window() (in module ctdam.conv.raw_conversion) calculate_oxsol() (in module ctdam.conv.raw_conversion) calculate_tau() (in module ctdam.conv.raw_conversion) Casts (class in ctdam) (class in ctdam.parser) (class in ctdam.parser.casts) CellTM (class in ctdam.proc.modules.seabird_functions) CHANGED (ctdam.qc.quality_flags.SeaDataNetFlag attribute) check_and_create_path() (in module ctdam.vis.visualize) check_config_entry() (ctdam.proc.Workflow method) (ctdam.proc.workflow.Workflow method) (ctdam.Workflow method) check_converted_data() (ctdam.Casts method) (ctdam.parser.Casts method) (ctdam.parser.casts.Casts method) check_sensor_agreement() (ctdam.parser.custom_xarray_accessors.QCAccessor method) check_whether_working_on_binned_data() (ctdam.proc.module.Module method) CnvFile (class in ctdam) (class in ctdam.parser) (class in ctdam.parser.seabird_data_files) combine_downcast_start() (in module ctdam.conv.cast_borders) conductivity() (in module ctdam.conv.raw_conversion) Configuration (class in ctdam.proc.settings) convert() (ctdam.Casts method) (ctdam.parser.Casts method) (ctdam.parser.casts.Casts method) convert_sbe43_oxygen() (in module ctdam.conv.raw_conversion) coordinates_to_float() (in module ctdam.utils) create_array_attrs() (in module ctdam.parser.read_ctd_data) create_array_coords() (in module ctdam.parser.read_ctd_data) create_dataframe() (ctdam.BottleFile method) (ctdam.BottleLogFile method) (ctdam.parser.BottleFile method) (ctdam.parser.BottleLogFile method) (ctdam.parser.geomar_ctd_file_parser.GEOMARCTDFile method) (ctdam.parser.seabird_data_files.BottleFile method) (ctdam.parser.seabird_data_files.BottleLogFile method) create_event_string() (in module ctdam.utils) create_flag_array_if_missing() (ctdam.proc.module.Module method) create_main_html() (in module ctdam) (in module ctdam.vis) (in module ctdam.vis.visualize) cruise (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) cruise_plots() (in module ctdam) (in module ctdam.vis) (in module ctdam.vis.visualize) ctdam module ctdam.conv module ctdam.conv.cast_borders module ctdam.conv.raw_conversion module ctdam.conv.unit_conversion module ctdam.exceptions module ctdam.parser module ctdam.parser.casts module ctdam.parser.custom_xarray_accessors module ctdam.parser.geomar_ctd_file_parser module ctdam.parser.read_ctd_data module ctdam.parser.seabird_data_files module ctdam.parser.sst_ctd_file_parser module ctdam.parser.xmlfiles module ctdam.proc module ctdam.proc.entry 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.bottle_file module ctdam.proc.modules.geomar_wildedit module ctdam.proc.modules.gsw_functions module ctdam.proc.modules.seabird_functions module ctdam.proc.settings module ctdam.proc.utils module ctdam.proc.workflow module ctdam.qc module ctdam.qc.quality_flags module ctdam.qc.range_checks module ctdam.qc.spike_checks module ctdam.utils module ctdam.vis module ctdam.vis.visualize module custom (ctdam.parser.custom_xarray_accessors.MetadataAccessor property) D data (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) data_whitespace_removal() (ctdam.BottleLogFile method) (ctdam.parser.BottleLogFile method) (ctdam.parser.seabird_data_files.BottleLogFile method) DataRetrievalAccessor (class in ctdam.parser.custom_xarray_accessors) default_seabird_exe_path() (in module ctdam.proc.utils) E edit_value() (ctdam.parser.custom_xarray_accessors.QCAccessor method) event_name (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) ExportAccessor (class in ctdam.parser.custom_xarray_accessors) extract_sensor_name() (in module ctdam.utils) F file_dir (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) file_name (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) fill_file_type_dir() (in module ctdam) (in module ctdam.proc) (in module ctdam.proc.utils) flagged() (ctdam.parser.custom_xarray_accessors.PlotAccessor method) flattened_ds() (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor method) fluorescence() (in module ctdam.conv.raw_conversion) fluorowetlabcdom() (in module ctdam.conv.raw_conversion) G GEOMARCTDFile (class in ctdam.parser.geomar_ctd_file_parser) get_cast_borders() (in module ctdam) (in module ctdam.conv) (in module ctdam.conv.cast_borders) get_corresponding_xmlcon() (ctdam.HexFile method) (ctdam.parser.HexFile method) (ctdam.parser.seabird_data_files.HexFile 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_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_potential_density() (in module ctdam) (in module ctdam.conv) (in module ctdam.conv.unit_conversion) get_sensor_info() (ctdam.parser.XMLCONFile method) (ctdam.parser.xmlfiles.XMLCONFile method) (ctdam.XMLCONFile method) 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) GOOD (ctdam.qc.quality_flags.SeaDataNetFlag attribute) GSWFunction (class in ctdam.proc.modules.gsw_functions) H handle_new_flags() (ctdam.proc.module.Module method) HexFile (class in ctdam) (class in ctdam.parser) (class in ctdam.parser.seabird_data_files) I IN_EXCESS (ctdam.qc.quality_flags.SeaDataNetFlag attribute) IncompleteProcedureConfig InputAccessor (class in ctdam.parser.custom_xarray_accessors) INTERPOLATED (ctdam.qc.quality_flags.SeaDataNetFlag attribute) InvalidArgumentCombination is_directly_measured_value() (in module ctdam) (in module ctdam.proc) (in module ctdam.proc.utils) J jens_loop_removal() (ctdam.proc.modules.seabird_functions.LoopRemoval method) L last (ctdam.parser.custom_xarray_accessors.ProcessingAccessor property) load_config() (ctdam.proc.Workflow method) (ctdam.proc.workflow.Workflow method) (ctdam.Workflow method) LoopRemoval (class in ctdam.proc.modules.seabird_functions) M map_metadata() (in module ctdam.utils) map_proc_name_to_class() (in module ctdam.proc.modules.available_modules) masked() (ctdam.parser.custom_xarray_accessors.QCAccessor method) maximum (ctdam.qc.range_checks.RangeLimit attribute) metadata (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) MetadataAccessor (class in ctdam.parser.custom_xarray_accessors) minimum (ctdam.qc.range_checks.RangeLimit attribute) MISSING (ctdam.qc.quality_flags.SeaDataNetFlag attribute) MissingParameterError modify() (ctdam.proc.settings.Configuration method) module ctdam ctdam.conv ctdam.conv.cast_borders ctdam.conv.raw_conversion ctdam.conv.unit_conversion ctdam.exceptions ctdam.parser ctdam.parser.casts ctdam.parser.custom_xarray_accessors ctdam.parser.geomar_ctd_file_parser ctdam.parser.read_ctd_data ctdam.parser.seabird_data_files ctdam.parser.sst_ctd_file_parser ctdam.parser.xmlfiles ctdam.proc ctdam.proc.entry ctdam.proc.module ctdam.proc.modules ctdam.proc.modules.air_pressure_correction ctdam.proc.modules.available_modules ctdam.proc.modules.bottle_file ctdam.proc.modules.geomar_wildedit ctdam.proc.modules.gsw_functions ctdam.proc.modules.seabird_functions ctdam.proc.settings ctdam.proc.utils ctdam.proc.workflow ctdam.qc ctdam.qc.quality_flags ctdam.qc.range_checks ctdam.qc.spike_checks ctdam.utils ctdam.vis ctdam.vis.visualize Module (class in ctdam.proc.module) module() (ctdam.parser.custom_xarray_accessors.ProcessingAccessor method) N new_file_path() (ctdam.proc.Workflow method) (ctdam.proc.workflow.Workflow method) (ctdam.Workflow method) NO_QC (ctdam.qc.quality_flags.SeaDataNetFlag attribute) NoDataError numpy_array() (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor method) O obtaining_reset_time() (ctdam.BottleLogFile method) (ctdam.parser.BottleLogFile method) (ctdam.parser.seabird_data_files.BottleLogFile method) oxygen() (in module ctdam.conv.raw_conversion) oxygen_mlperl_to_umolperkg() (in module ctdam) (in module ctdam.conv) (in module ctdam.conv.unit_conversion) oxygen_mlperl_to_umolperl() (in module ctdam) (in module ctdam.conv) (in module ctdam.conv.unit_conversion) oxygen_umolperkg_to_umolperl() (in module ctdam) (in module ctdam.conv) (in module ctdam.conv.unit_conversion) oxygen_umolperl_to_umolperkg() (in module ctdam) (in module ctdam.conv) (in module ctdam.conv.unit_conversion) P pandas_dataframe (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor property) par_biosphericallicorchelsea() (in module ctdam.conv.raw_conversion) parameter() (ctdam.parser.custom_xarray_accessors.InputAccessor method) parameter_name (ctdam.qc.range_checks.RangeLimit attribute) (ctdam.qc.spike_checks.SpikeLimit attribute) parse_cnv_data_format() (ctdam.CnvFile method) (ctdam.parser.CnvFile method) (ctdam.parser.seabird_data_files.CnvFile method) parse_hex() (ctdam.HexFile method) (ctdam.parser.HexFile method) (ctdam.parser.seabird_data_files.HexFile method) parse_oxygen_data() (in module ctdam.parser.read_ctd_data) parse_xmlcon_sensor_data() (in module ctdam.utils) path_to_data (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) path_to_file (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) plot() (ctdam.Casts method) (ctdam.parser.Casts method) (ctdam.parser.casts.Casts method) plot_dir (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) PlotAccessor (class in ctdam.parser.custom_xarray_accessors) pressure() (in module ctdam.conv.raw_conversion) PROBABLY_BAD (ctdam.qc.quality_flags.SeaDataNetFlag attribute) PROBABLY_GOOD (ctdam.qc.quality_flags.SeaDataNetFlag attribute) process() (ctdam.Casts method) (ctdam.parser.Casts method) (ctdam.parser.casts.Casts method) (in module ctdam) (in module ctdam.proc) (in module ctdam.proc.entry) processing_info (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) processing_metadata() (ctdam.parser.custom_xarray_accessors.InputAccessor method) ProcessingAccessor (class in ctdam.parser.custom_xarray_accessors) profile() (ctdam.parser.custom_xarray_accessors.PlotAccessor method) provenance (ctdam.parser.custom_xarray_accessors.MetadataAccessor property) PsaFile (class in ctdam.parser.xmlfiles) Q QCAccessor (class in ctdam.parser.custom_xarray_accessors) R RangeLimit (class in ctdam.qc.range_checks) read_cnv() (in module ctdam) (in module ctdam.parser) (in module ctdam.parser.read_ctd_data) read_ctd_data() (in module ctdam) (in module ctdam.parser) (in module ctdam.parser.read_ctd_data) read_event_information() (ctdam.parser.seabird_data_files.SeabirdDataFile method) read_event_name() (in module ctdam.utils) read_file() (ctdam.parser.geomar_ctd_file_parser.GEOMARCTDFile method) (ctdam.parser.seabird_data_files.SeabirdDataFile method) read_hex() (in module ctdam) (in module ctdam.parser) (in module ctdam.parser.read_ctd_data) read_sensor_info() (ctdam.Casts method) (ctdam.parser.Casts method) (ctdam.parser.casts.Casts method) read_xml_config() (ctdam.parser.XMLCONFile method) (ctdam.parser.xmlfiles.XMLCONFile method) (ctdam.XMLCONFile method) reading_data_header() (ctdam.BottleFile method) (ctdam.parser.BottleFile method) (ctdam.parser.seabird_data_files.BottleFile method) reading_start_position() (ctdam.parser.seabird_data_files.SeabirdDataFile method) reading_start_time() (ctdam.parser.seabird_data_files.SeabirdDataFile method) run() (ctdam.proc.Workflow method) (ctdam.proc.workflow.Workflow method) (ctdam.Workflow method) S salinity() (in module ctdam.conv.raw_conversion) sample_rate (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor property) sbe_to_decimal() (in module ctdam.utils) SeabirdDataFile (class in ctdam.parser.seabird_data_files) SeaDataNetFlag (class in ctdam.qc.quality_flags) selecting_rows() (ctdam.BottleFile method) (ctdam.parser.BottleFile method) (ctdam.parser.seabird_data_files.BottleFile method) sensor_info (ctdam.Casts attribute) (ctdam.parser.Casts attribute) (ctdam.parser.casts.Casts attribute) sensor_strand() (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor method) sensor_xml_to_flattened_dict() (ctdam.parser.seabird_data_files.SeabirdDataFile method) set_flag() (ctdam.parser.custom_xarray_accessors.QCAccessor method) size (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor property) smoothing() (in module ctdam.conv.cast_borders) soaking_detection() (in module ctdam.conv.cast_borders) soaking_removal() (in module ctdam.conv.cast_borders) sorting_parameters() (in module ctdam.parser.read_ctd_data) spans() (ctdam.parser.custom_xarray_accessors.DataRetrievalAccessor method) spar() (in module ctdam.conv.raw_conversion) SpikeLimit (class in ctdam.qc.spike_checks) sst2xarray() (in module ctdam.parser.sst_ctd_file_parser) start_position (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) start_time (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) station (ctdam.parser.seabird_data_files.SeabirdDataFile attribute) structure_metadata() (ctdam.parser.seabird_data_files.SeabirdDataFile method) T temperature() (in module ctdam.conv.raw_conversion) teos10_vars() (ctdam.parser.custom_xarray_accessors.InputAccessor method) test_name (ctdam.qc.range_checks.RangeLimit attribute) (ctdam.qc.spike_checks.SpikeLimit attribute) threshold (ctdam.qc.spike_checks.SpikeLimit attribute) time_dependent_loop_removal() (ctdam.proc.modules.seabird_functions.LoopRemoval method) to_btl() (ctdam.parser.custom_xarray_accessors.ExportAccessor method) to_cnv() (ctdam.parser.custom_xarray_accessors.ExportAccessor method) to_json() (ctdam.parser.xmlfiles.XMLFile method) to_tsv() (ctdam.Casts method) (ctdam.parser.Casts method) (ctdam.parser.casts.Casts method) to_xml() (ctdam.parser.xmlfiles.XMLFile method) transformation() (ctdam.proc.module.Module method) (ctdam.proc.modules.air_pressure_correction.AirPressureCorrection method) (ctdam.proc.modules.bottle_file.BottleFile method) (ctdam.proc.modules.geomar_wildedit.WildeditGEOMAR method) (ctdam.proc.modules.gsw_functions.GSWFunction 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) turbidity() (in module ctdam.conv.raw_conversion) U UnexpectedFileFormat 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) Workflow (class in ctdam) (class in ctdam.proc) (class in ctdam.proc.workflow) workflow() (ctdam.parser.custom_xarray_accessors.ProcessingAccessor method) write() (ctdam.proc.settings.Configuration method) X xml_coeffs_to_float() (ctdam.parser.XMLCONFile method) (ctdam.parser.xmlfiles.XMLCONFile method) (ctdam.XMLCONFile method) XMLCONFile (class in ctdam) (class in ctdam.parser) (class in ctdam.parser.xmlfiles) XMLFile (class in ctdam.parser.xmlfiles)