Index

A

add_cc() (in module pelagos_py.steps.input_output.write_report) add_log() (in module pelagos_py.steps.input_output.write_report) add_step() (pelagos_py.pipeline.Pipeline method)

AdjustSalinity (class in pelagos_py.steps.processing.salinity) apply_dark_correction() (pelagos_py.steps.processing.chla.chla_deep_correction method) apply_xing2012_quenching_correction() (pelagos_py.steps.processing.chla.chla_quenching_correction method) ApplyQC (class in pelagos_py.steps.quality_control.apply_qc)

B

BaseQC (class in pelagos_py.steps.base_qc) BaseStep (class in pelagos_py.steps.base_step) basic_geo() (in module pelagos_py.steps.input_output.write_report) BBPFromBeta (class in pelagos_py.steps.processing.bbp)

blank_qc (class in pelagos_py.steps.templates.blank_qc) BlankStep (class in pelagos_py.steps.templates.blank_step) build_qc_dict() (in module pelagos_py.steps.input_output.write_report) build_steps() (pelagos_py.pipeline.Pipeline method)

C

calculate_solar_elevation() (in module pelagos_py.steps.quality_control.par_irregularity_qc) capture_figures() (in module pelagos_py.utils.diagnostic_capture) check_config() (in module pelagos_py.steps.processing.oxygen) check_data() (pelagos_py.steps.base_step.BaseStep method) check_missing_values() (in module pelagos_py.utils.diagnostics) chla_deep_correction (class in pelagos_py.steps.processing.chla) chla_quenching_correction (class in pelagos_py.steps.processing.chla) coerce() (in module pelagos_py.utils.parameter_spec)

ColorFormatter (class in pelagos_py.utils.log_levels) compute_dark_value() (pelagos_py.steps.processing.chla.chla_deep_correction method) console_summary() (in module pelagos_py.steps.input_output.format_check) correct_ct_lag() (pelagos_py.steps.processing.salinity.AdjustSalinity method) correct_thermal_lag() (pelagos_py.steps.processing.salinity.AdjustSalinity method) CorrectValues (class in pelagos_py.steps.input_output.correct_values) create_step() (in module pelagos_py.steps) current_info() (in module pelagos_py.steps.input_output.write_report)

D

DeriveCalibratedPhase (class in pelagos_py.steps.processing.oxygen) DeriveCTDVariables (class in pelagos_py.steps.processing.derive_ctd) DeriveOptodeTemperature (class in pelagos_py.steps.processing.oxygen) DeriveOxygenConcentration (class in pelagos_py.steps.processing.oxygen)

DeriveUncalibratedPhase (class in pelagos_py.steps.processing.oxygen) describe() (in module pelagos_py.utils.parameter_spec) describe_parameters() (pelagos_py.steps.base_qc.BaseQC class method) (pelagos_py.steps.base_step.BaseStep class method) discover_steps() (in module pelagos_py.steps)

E

execute_step() (pelagos_py.pipeline.Pipeline method)

export_config() (pelagos_py.pipeline.Pipeline method) ExportStep (class in pelagos_py.steps.input_output.export)

F

find_candidate_glider_pairs() (in module pelagos_py.utils.diagnostics) find_closest_prof() (in module pelagos_py.utils.diagnostics) FindProfilesStep (class in pelagos_py.steps.processing.find_profiles) flag_cols (in module pelagos_py.steps.base_qc)

flag_full_profile (class in pelagos_py.steps.quality_control.flag_full_profile) flatten_qc_dict() (in module pelagos_py.steps.input_output.write_report) force_headless_backend() (in module pelagos_py.utils.diagnostic_capture) format() (pelagos_py.utils.log_levels.ColorFormatter method) FormatCheck (class in pelagos_py.steps.input_output.format_check)

G

generate_config() (pelagos_py.pipeline.Pipeline method) (pelagos_py.steps.base_step.BaseStep method) generate_diagnostics() (pelagos_py.steps.input_output.export.ExportStep method) (pelagos_py.steps.input_output.load_data.LoadOG1 method) (pelagos_py.steps.processing.find_profiles.FindProfilesStep method) (pelagos_py.steps.processing.interpolate_data.InterpolateVariables method) (pelagos_py.steps.processing.salinity.AdjustSalinity method)

generate_info() (in module pelagos_py.utils.diagnostics) GenerateData (class in pelagos_py.steps.input_output.gen_data) get_data() (pelagos_py.pipeline.Pipeline method)

H

halt() (pelagos_py.steps.base_step.BaseStep method)

I

img_rst() (in module pelagos_py.steps.input_output.write_report) impossible_date_qc (class in pelagos_py.steps.quality_control.impossible_date_qc) impossible_location_qc (class in pelagos_py.steps.quality_control.impossible_location_qc) impossible_speed_qc (class in pelagos_py.steps.quality_control.impossible_speed_qc)

inset_geo() (in module pelagos_py.steps.input_output.write_report) InterpolateVariables (class in pelagos_py.steps.processing.interpolate_data) is_required() (in module pelagos_py.utils.parameter_spec) IsolateBBPSpikes (class in pelagos_py.steps.processing.bbp)

L

LoadOG1 (class in pelagos_py.steps.input_output.load_data) log() (pelagos_py.steps.base_qc.BaseQC method) (pelagos_py.steps.base_step.BaseStep method)

log_warn() (pelagos_py.steps.base_qc.BaseQC method) (pelagos_py.steps.base_step.BaseStep method)

M

make_diagnostics_safe() (in module pelagos_py.utils.diagnostic_capture) make_plots() (in module pelagos_py.steps.input_output.write_report) matches_type() (in module pelagos_py.utils.parameter_spec) module pelagos_py pelagos_py.pipeline pelagos_py.steps pelagos_py.steps.base_qc pelagos_py.steps.base_step pelagos_py.steps.input_output pelagos_py.steps.input_output.correct_values pelagos_py.steps.input_output.export pelagos_py.steps.input_output.format_check pelagos_py.steps.input_output.gen_data pelagos_py.steps.input_output.load_data pelagos_py.steps.input_output.write_report pelagos_py.steps.input_output.write_report_python pelagos_py.steps.processing pelagos_py.steps.processing.bbp pelagos_py.steps.processing.chla pelagos_py.steps.processing.derive_ctd pelagos_py.steps.processing.find_profiles pelagos_py.steps.processing.interpolate_data pelagos_py.steps.processing.oxygen pelagos_py.steps.processing.salinity pelagos_py.steps.quality_control pelagos_py.steps.quality_control.apply_qc pelagos_py.steps.quality_control.flag_full_profile pelagos_py.steps.quality_control.impossible_date_qc pelagos_py.steps.quality_control.impossible_location_qc pelagos_py.steps.quality_control.impossible_speed_qc pelagos_py.steps.quality_control.par_irregularity_qc pelagos_py.steps.quality_control.position_on_land_qc pelagos_py.steps.quality_control.range_qc pelagos_py.steps.quality_control.spike_qc pelagos_py.steps.quality_control.stuck_value_qc pelagos_py.steps.quality_control.valid_profile_qc pelagos_py.steps.templates pelagos_py.steps.templates.blank_qc pelagos_py.steps.templates.blank_step pelagos_py.utils pelagos_py.utils.diagnostic_capture pelagos_py.utils.diagnostics pelagos_py.utils.log_levels pelagos_py.utils.parameter_spec pelagos_py.utils.qc_handling pelagos_py.utils.yaml_loading

MolarDOXYPressureCorrection (class in pelagos_py.steps.processing.oxygen) MolarDOXYSalinityCorrection (class in pelagos_py.steps.processing.oxygen)

N

normalise_qc_flags() (pelagos_py.steps.input_output.load_data.LoadOG1 method)

O

organise_flags() (pelagos_py.steps.quality_control.apply_qc.ApplyQC method)

P

par_irregularity_qc (class in pelagos_py.steps.quality_control.par_irregularity_qc) pelagos_py module pelagos_py.pipeline module pelagos_py.steps module pelagos_py.steps.base_qc module pelagos_py.steps.base_step module pelagos_py.steps.input_output module pelagos_py.steps.input_output.correct_values module pelagos_py.steps.input_output.export module pelagos_py.steps.input_output.format_check module pelagos_py.steps.input_output.gen_data module pelagos_py.steps.input_output.load_data module pelagos_py.steps.input_output.write_report module pelagos_py.steps.input_output.write_report_python module pelagos_py.steps.processing module pelagos_py.steps.processing.bbp module pelagos_py.steps.processing.chla module pelagos_py.steps.processing.derive_ctd module pelagos_py.steps.processing.find_profiles module pelagos_py.steps.processing.interpolate_data module pelagos_py.steps.processing.oxygen module pelagos_py.steps.processing.salinity module pelagos_py.steps.quality_control module pelagos_py.steps.quality_control.apply_qc module pelagos_py.steps.quality_control.flag_full_profile module pelagos_py.steps.quality_control.impossible_date_qc module pelagos_py.steps.quality_control.impossible_location_qc module pelagos_py.steps.quality_control.impossible_speed_qc module

pelagos_py.steps.quality_control.par_irregularity_qc module pelagos_py.steps.quality_control.position_on_land_qc module pelagos_py.steps.quality_control.range_qc module pelagos_py.steps.quality_control.spike_qc module pelagos_py.steps.quality_control.stuck_value_qc module pelagos_py.steps.quality_control.valid_profile_qc module pelagos_py.steps.templates module pelagos_py.steps.templates.blank_qc module pelagos_py.steps.templates.blank_step module pelagos_py.utils module pelagos_py.utils.diagnostic_capture module pelagos_py.utils.diagnostics module pelagos_py.utils.log_levels module pelagos_py.utils.parameter_spec module pelagos_py.utils.qc_handling module pelagos_py.utils.yaml_loading module PelagosSafeLoader (class in pelagos_py.utils.yaml_loading) PhasePressureCorrection (class in pelagos_py.steps.processing.oxygen) Pipeline (class in pelagos_py.pipeline) plot_boxplot() (in module pelagos_py.utils.diagnostics) plot_correlation_matrix() (in module pelagos_py.utils.diagnostics) plot_diagnostics() (pelagos_py.steps.base_qc.BaseQC method) (pelagos_py.steps.quality_control.flag_full_profile.flag_full_profile method) (pelagos_py.steps.quality_control.impossible_date_qc.impossible_date_qc method) (pelagos_py.steps.quality_control.impossible_location_qc.impossible_location_qc method) (pelagos_py.steps.quality_control.impossible_speed_qc.impossible_speed_qc method) (pelagos_py.steps.quality_control.par_irregularity_qc.par_irregularity_qc method) (pelagos_py.steps.quality_control.position_on_land_qc.position_on_land_qc method) (pelagos_py.steps.quality_control.range_qc.range_qc method) (pelagos_py.steps.quality_control.spike_qc.spike_qc method) (pelagos_py.steps.quality_control.stuck_value_qc.stuck_value_qc method) (pelagos_py.steps.quality_control.valid_profile_qc.valid_profile_qc method) (pelagos_py.steps.templates.blank_qc.blank_qc method) plot_distance_time_grid() (in module pelagos_py.utils.diagnostics) plot_glider_pair_heatmap_grid() (in module pelagos_py.utils.diagnostics) plot_heatmap_glider_df() (in module pelagos_py.utils.diagnostics) plot_histogram() (in module pelagos_py.utils.diagnostics) plot_time_series() (in module pelagos_py.utils.diagnostics) position_on_land_qc (class in pelagos_py.steps.quality_control.position_on_land_qc)

Q

QC_CLASSES (in module pelagos_py.steps) qc_hist() (in module pelagos_py.steps.input_output.write_report)

qc_par_flagging() (in module pelagos_py.steps.quality_control.par_irregularity_qc) qc_section() (in module pelagos_py.steps.input_output.write_report)

R

range_qc (class in pelagos_py.steps.quality_control.range_qc) register_qc() (in module pelagos_py.steps.base_qc) register_step() (in module pelagos_py.steps.base_step) REGISTERED_QC (in module pelagos_py.steps.base_qc) REGISTERED_STEPS (in module pelagos_py.steps.base_step) REPORT_STEP_NAME (in module pelagos_py.pipeline) resolve() (in module pelagos_py.utils.parameter_spec) return_qc() (pelagos_py.steps.base_qc.BaseQC method) (pelagos_py.steps.quality_control.flag_full_profile.flag_full_profile method) (pelagos_py.steps.quality_control.impossible_date_qc.impossible_date_qc method) (pelagos_py.steps.quality_control.impossible_location_qc.impossible_location_qc method) (pelagos_py.steps.quality_control.impossible_speed_qc.impossible_speed_qc method) (pelagos_py.steps.quality_control.par_irregularity_qc.par_irregularity_qc method) (pelagos_py.steps.quality_control.position_on_land_qc.position_on_land_qc method) (pelagos_py.steps.quality_control.range_qc.range_qc method) (pelagos_py.steps.quality_control.spike_qc.spike_qc method) (pelagos_py.steps.quality_control.stuck_value_qc.stuck_value_qc method) (pelagos_py.steps.quality_control.valid_profile_qc.valid_profile_qc method) (pelagos_py.steps.templates.blank_qc.blank_qc method)

run() (pelagos_py.pipeline.Pipeline method) (pelagos_py.steps.processing.bbp.BBPFromBeta method) (pelagos_py.steps.processing.bbp.IsolateBBPSpikes method) (pelagos_py.steps.processing.chla.chla_deep_correction method) (pelagos_py.steps.processing.chla.chla_quenching_correction method) (pelagos_py.steps.processing.interpolate_data.InterpolateVariables method) (pelagos_py.steps.processing.oxygen.DeriveCalibratedPhase method) (pelagos_py.steps.processing.oxygen.DeriveOptodeTemperature method) (pelagos_py.steps.processing.oxygen.DeriveOxygenConcentration method) (pelagos_py.steps.processing.oxygen.DeriveUncalibratedPhase method) (pelagos_py.steps.processing.oxygen.MolarDOXYPressureCorrection method) (pelagos_py.steps.processing.oxygen.MolarDOXYSalinityCorrection method) (pelagos_py.steps.processing.oxygen.PhasePressureCorrection method) (pelagos_py.steps.quality_control.apply_qc.ApplyQC method) run_info_page() (in module pelagos_py.steps.input_output.write_report) run_last_step() (pelagos_py.pipeline.Pipeline method) run_sphinx() (in module pelagos_py.steps.input_output.write_report)

S

safe_load() (in module pelagos_py.utils.yaml_loading) save_config() (pelagos_py.pipeline.Pipeline method) (pelagos_py.steps.base_step.BaseStep method) spike_qc (class in pelagos_py.steps.quality_control.spike_qc)

STEP_CLASSES (in module pelagos_py.steps) step_name (pelagos_py.steps.processing.interpolate_data.InterpolateVariables attribute) STOP (in module pelagos_py.utils.log_levels) stuck_value_qc (class in pelagos_py.steps.quality_control.stuck_value_qc) summarising_profiles() (in module pelagos_py.utils.diagnostics)

T

type_errors() (in module pelagos_py.utils.parameter_spec)

U

update_parameters() (pelagos_py.steps.base_step.BaseStep method)

V

valid_profile_qc (class in pelagos_py.steps.quality_control.valid_profile_qc)

W

write_conf_py() (in module pelagos_py.steps.input_output.write_report)

WriteDataReport (class in pelagos_py.steps.input_output.write_report) WriteDataReportPython (class in pelagos_py.steps.input_output.write_report_python)