Index

_

__post_init__() (palmwtc.config.DataPaths method) __version__ (in module palmwtc) _add_trendline() (in module palmwtc.viz.interactive) _anomaly_score() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) _apply_tree_volume_correction() (in module palmwtc.pipeline) _choose_h2o_column() (in module palmwtc.flux.chamber) _closure_score() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) _COLOR_HEX (in module palmwtc.qc.reporting) _convert_to_html() (in module palmwtc.notebooks_runner) _CUML_AVAILABLE (in module palmwtc.hardware.gpu), [1] _CUML_IF_UNSUPPORTED (in module palmwtc.hardware.gpu) _DEFAULT_CHAMBER_TREE_MAP (in module palmwtc.pipeline) _DEFAULT_THREADS (in module palmwtc.notebooks_runner) _downsample_uniform() (in module palmwtc.viz.interactive) _drift_score_lookup() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) _evaluate_cycle_wrapper() (in module palmwtc.flux) (in module palmwtc.flux.cycles) _extract_relayout_payload() (in module palmwtc.viz.interactive) _extract_xrange_from_relayout() (in module palmwtc.viz.interactive) _find_qc_parquet() (in module palmwtc.pipeline)

_group_mean() (in module palmwtc.windows.selector) _light_response() (in module palmwtc.validation.science) _load_sensor_exclusions() (in module palmwtc.qc.rules) _load_yaml() (in module palmwtc.config) _main() (in module palmwtc.cli) _ML_FEATURE_ALIASES (in module palmwtc.flux.cycles) _nan() (in module palmwtc.windows.selector) _natural_key() (in module palmwtc.viz.interactive) _path_or_default() (in module palmwtc.config) _prettify_chemical() (in module palmwtc.qc.reporting) _regression_score() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) _robustness_score() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) _run_with_papermill() (in module palmwtc.notebooks_runner) _SENSOR_PATTERNS (in module palmwtc.io.cloud) _sensor_qc_score() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) _SKLEARN_AVAILABLE (in module palmwtc.flux.cycles) _status_atleast() (in module palmwtc.validation.science) _status_inrange() (in module palmwtc.validation.science) _STEP_FUNCTIONS (in module palmwtc.pipeline) _version_callback() (in module palmwtc.cli)

A

add_cycle_id() (in module palmwtc.qc) (in module palmwtc.qc.rules) add_par_estimates() (in module palmwtc.flux) (in module palmwtc.flux.scaling) app (in module palmwtc.cli) apply_battery_proxy_flags() (in module palmwtc.qc) (in module palmwtc.qc.rules) apply_drift_correction() (in module palmwtc.qc) (in module palmwtc.qc.drift) apply_iqr_flags() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.rules) apply_persistence_flags() (in module palmwtc.qc) (in module palmwtc.qc.rules)

apply_physical_bounds_flags() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.rules) apply_rate_of_change_flags() (in module palmwtc.qc) (in module palmwtc.qc.rules) apply_sensor_exclusion_flags() (in module palmwtc.qc) (in module palmwtc.qc.rules) apply_wpl_correction() (in module palmwtc.flux) (in module palmwtc.flux.chamber) apply_wpl_qc_overrides() (in module palmwtc.flux) (in module palmwtc.flux.chamber) approved_windows (palmwtc.windows.selector.WindowSelector attribute) (palmwtc.windows.WindowSelector attribute) (palmwtc.WindowSelector attribute) artefacts (palmwtc.pipeline.StepResult attribute)

B

build_cycle_wpl_metrics() (in module palmwtc.flux) (in module palmwtc.flux.chamber)

build_field_alert_context() (in module palmwtc.qc) (in module palmwtc.qc.reporting)

C

calc_aicc() (in module palmwtc.flux.cycles) calculate_absolute_flux() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.absolute) calculate_flux_cycles() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.chamber) calculate_flux_for_chamber() (in module palmwtc.flux) (in module palmwtc.flux.absolute) calculate_h2o_absolute_flux() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.absolute) calculate_h2o_flux_cycles() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.chamber) calculate_h2o_flux_for_cycle() (in module palmwtc.flux) (in module palmwtc.flux.chamber) calculate_lai_effective() (in module palmwtc.flux) (in module palmwtc.flux.scaling) check_baseline_drift() (in module palmwtc.qc) (in module palmwtc.qc.breakpoints) check_cross_variable_consistency() (in module palmwtc.qc) (in module palmwtc.qc.breakpoints) combine_qc_flags() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.rules)

compute_closure_confidence() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.chamber) compute_day_scores() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.cycles) compute_ensemble_score() (in module palmwtc.flux) (in module palmwtc.flux.advanced_outlier) compute_ml_anomaly_flags() (in module palmwtc.flux) (in module palmwtc.flux.cycles) compute_rolling_zscore() (in module palmwtc.flux) (in module palmwtc.flux.advanced_outlier) compute_stl_residual_scores() (in module palmwtc.flux) (in module palmwtc.flux.advanced_outlier) compute_temporal_coherence() (in module palmwtc.flux) (in module palmwtc.flux.cycles) config (palmwtc.windows.selector.WindowSelector attribute) (palmwtc.windows.WindowSelector attribute) (palmwtc.WindowSelector attribute) config_dir (palmwtc.config.DataPaths attribute) CYCLE_GAP_SEC (in module palmwtc.flux.cycles) cycles_df (palmwtc.windows.selector.WindowSelector attribute) (palmwtc.windows.WindowSelector attribute) (palmwtc.WindowSelector attribute)

D

data_integrity_report() (in module palmwtc.io) (in module palmwtc.io.paths) DataPaths (class in palmwtc.config) DEFAULT_ADVANCED_OUTLIER_CONFIG (in module palmwtc.flux) (in module palmwtc.flux.advanced_outlier) DEFAULT_CO2_QC_THRESHOLDS (in module palmwtc.flux) (in module palmwtc.flux.chamber) DEFAULT_CONFIG (in module palmwtc.flux) (in module palmwtc.flux.chamber) (in module palmwtc.validation) (in module palmwtc.validation.science) (in module palmwtc.windows) (in module palmwtc.windows.selector) DEFAULT_H2O_QC_THRESHOLDS (in module palmwtc.flux) (in module palmwtc.flux.chamber) DEFAULT_ML_FEATURES (in module palmwtc.flux.cycles) DEFAULT_PROJECT_CONFIG (in module palmwtc.config) DEFAULT_USER_CONFIG (in module palmwtc.config) DEFAULT_WPL_QC_THRESHOLDS (in module palmwtc.flux) (in module palmwtc.flux.chamber) derive_is_daytime() (in module palmwtc) (in module palmwtc.validation) (in module palmwtc.validation.science) describe() (palmwtc.config.DataPaths method)

detect_bimodal_cycle() (in module palmwtc.flux) (in module palmwtc.flux.cycles) detect_breakpoints_ruptures() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.breakpoints) detect_device() (in module palmwtc.hardware) (in module palmwtc.hardware.gpu) detect_drift() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) detect_drift_windstats() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.drift) DEVICE (in module palmwtc.hardware) (in module palmwtc.hardware.gpu) (in module palmwtc.qc) (in module palmwtc.qc.ml) df (palmwtc.qc.processor.QCProcessor attribute) (palmwtc.qc.QCProcessor attribute) (palmwtc.QCProcessor attribute) discover_notebooks() (in module palmwtc.notebooks_runner) drift_df (palmwtc.windows.selector.WindowSelector attribute) (palmwtc.windows.WindowSelector attribute) (palmwtc.WindowSelector attribute)

E

elapsed_seconds (palmwtc.notebooks_runner.NotebookResult attribute) (palmwtc.pipeline.StepResult attribute) ENV_CONFIG_FILE (in module palmwtc.config) ENV_DATA_DIR (in module palmwtc.config) error (palmwtc.notebooks_runner.NotebookResult attribute) (palmwtc.pipeline.StepResult attribute) estimate_leaf_area() (in module palmwtc.flux) (in module palmwtc.flux.scaling) estimate_par_from_radiation() (in module palmwtc.flux) (in module palmwtc.flux.scaling)

evaluate_cycle() (in module palmwtc.flux.cycles) export() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) export_monthly() (in module palmwtc.io) (in module palmwtc.io.loaders) export_qc_data() (in module palmwtc.qc) (in module palmwtc.qc.reporting) exports_dir (palmwtc.config.DataPaths attribute) extras (palmwtc.config.DataPaths attribute)

F

filter_major_breakpoints() (in module palmwtc.qc) (in module palmwtc.qc.breakpoints) filter_plot() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots)

find_latest_qc_file() (in module palmwtc) (in module palmwtc.io) (in module palmwtc.io.paths) fit_linear_optimized() (in module palmwtc.flux.cycles) fit_quadratic_fast() (in module palmwtc.flux.cycles)

G

generate_exclusion_recommendations() (in module palmwtc.qc) (in module palmwtc.qc.rules) generate_qc_summary() (in module palmwtc.qc) (in module palmwtc.qc.rules) generate_qc_summary_from_results() (in module palmwtc.qc) (in module palmwtc.qc.reporting) get_cloud_sensor_dirs() (in module palmwtc) (in module palmwtc.io) (in module palmwtc.io.cloud) get_isolation_forest() (in module palmwtc.hardware) (in module palmwtc.hardware.gpu) (in module palmwtc.qc) (in module palmwtc.qc.ml)

get_processed_dataframe() (palmwtc.qc.processor.QCProcessor method) (palmwtc.qc.QCProcessor method) (palmwtc.QCProcessor method) get_tree_volume_at_date() (in module palmwtc.flux) (in module palmwtc.flux.chamber) get_usecols() (in module palmwtc) (in module palmwtc.io) (in module palmwtc.io.paths) get_variable_config() (in module palmwtc.qc) (in module palmwtc.qc.rules)

H

HARD_LIMITS (in module palmwtc.flux.cycles)

I

identify_cycles() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.cycles) identify_windows() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method)

info() (in module palmwtc.cli) integrate_temp_humidity_c2() (in module palmwtc.io) (in module palmwtc.io.loaders) interactive_flux_dashboard() (in module palmwtc) (in module palmwtc.viz) (in module palmwtc.viz.interactive)

L

load_biophysical_data() (in module palmwtc.flux) (in module palmwtc.flux.scaling) load_data_in_range() (in module palmwtc.io) (in module palmwtc.io.loaders) load_from_multiple_dirs() (in module palmwtc) (in module palmwtc.io) (in module palmwtc.io.loaders) load_monthly_data() (in module palmwtc) (in module palmwtc.io) (in module palmwtc.io.loaders)

load_radiation_data() (in module palmwtc) (in module palmwtc.io) (in module palmwtc.io.loaders) load_regime_diagnostics() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) load_tree_biophysics() (in module palmwtc.flux) (in module palmwtc.flux.chamber)

M

mad_outlier_mask() (in module palmwtc.flux.cycles) MAX_OUTLIER_REFIT_FRAC (in module palmwtc.flux.cycles) merge_sensor_qc_onto_cycles() (in module palmwtc) (in module palmwtc.windows) (in module palmwtc.windows.selector) metrics (palmwtc.pipeline.StepResult attribute) MIN_DURATION_SEC (in module palmwtc.flux.cycles) MIN_POINTS (in module palmwtc.flux.cycles) module palmwtc palmwtc.cli palmwtc.config palmwtc.data palmwtc.flux palmwtc.flux.absolute palmwtc.flux.advanced_outlier palmwtc.flux.chamber palmwtc.flux.cycles palmwtc.flux.scaling palmwtc.hardware palmwtc.hardware.gpu palmwtc.io palmwtc.io.cloud palmwtc.io.loaders palmwtc.io.paths palmwtc.notebooks_runner palmwtc.pipeline palmwtc.qc palmwtc.qc.breakpoints palmwtc.qc.drift palmwtc.qc.ml palmwtc.qc.processor palmwtc.qc.reporting palmwtc.qc.rules palmwtc.validation palmwtc.validation.science palmwtc.viz palmwtc.viz.diagnostics palmwtc.viz.interactive palmwtc.viz.qc_plots palmwtc.viz.style palmwtc.viz.timeseries palmwtc.windows palmwtc.windows.selector

monotonic_fraction() (in module palmwtc.flux.cycles)

N

name (palmwtc.notebooks_runner.NotebookResult attribute) (palmwtc.pipeline.StepResult attribute) NIGHTTIME_CO2_QC_THRESHOLDS (in module palmwtc.flux) (in module palmwtc.flux.chamber) NIGHTTIME_H2O_QC_THRESHOLDS (in module palmwtc.flux) (in module palmwtc.flux.chamber)

NIGHTTIME_QC_THRESHOLDS (in module palmwtc.flux) (in module palmwtc.flux.cycles) NOISE_EPS_PPM (in module palmwtc.flux.cycles) NotebookResult (class in palmwtc.notebooks_runner)

O

ok (palmwtc.notebooks_runner.NotebookResult attribute) (palmwtc.pipeline.PipelineResult property) (palmwtc.pipeline.StepResult attribute)

OUTLIER_Z (in module palmwtc.flux.cycles)

P

palmwtc module palmwtc.cli module palmwtc.config module palmwtc.data module palmwtc.flux module palmwtc.flux.absolute module palmwtc.flux.advanced_outlier module palmwtc.flux.chamber module palmwtc.flux.cycles module palmwtc.flux.scaling module palmwtc.hardware module palmwtc.hardware.gpu module palmwtc.io module palmwtc.io.cloud module palmwtc.io.loaders module palmwtc.io.paths module palmwtc.notebooks_runner module palmwtc.pipeline module palmwtc.qc module palmwtc.qc.breakpoints module palmwtc.qc.drift module palmwtc.qc.ml module palmwtc.qc.processor module palmwtc.qc.reporting module palmwtc.qc.rules module palmwtc.validation module palmwtc.validation.science module palmwtc.viz module palmwtc.viz.diagnostics module palmwtc.viz.interactive module palmwtc.viz.qc_plots module palmwtc.viz.style module

palmwtc.viz.timeseries module palmwtc.windows module palmwtc.windows.selector module paths (palmwtc.pipeline.PipelineResult attribute) PipelineResult (class in palmwtc.pipeline) plot_baseline_drift() (in module palmwtc.viz.qc_plots) plot_breakpoints_analysis() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots) plot_chamber_resizing_validation() (in module palmwtc.viz) (in module palmwtc.viz.diagnostics) plot_chamber_resizing_validation_interactive() (in module palmwtc.viz.interactive) plot_concentration_slope_boxplot_vs_tree_age() (in module palmwtc.viz.timeseries) plot_concentration_slope_boxplot_vs_tree_age_interactive() (in module palmwtc.viz.interactive) plot_concentration_slope_vs_tree_age() (in module palmwtc.viz) (in module palmwtc.viz.timeseries) plot_concentration_slope_vs_tree_age_interactive() (in module palmwtc.viz.interactive) plot_cumulative_flux_by_date() (in module palmwtc.viz.timeseries) plot_cumulative_flux_with_gaps() (in module palmwtc.viz.timeseries) plot_cumulative_flux_with_gaps_interactive() (in module palmwtc.viz.interactive) plot_cycle_by_id() (in module palmwtc.viz) (in module palmwtc.viz.diagnostics) plot_cycle_diagnostics() (in module palmwtc.viz) (in module palmwtc.viz.diagnostics) plot_drift_and_hq_timeseries() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots) plot_flux_boxplot_vs_tree_age() (in module palmwtc.viz.timeseries) plot_flux_boxplot_vs_tree_age_interactive() (in module palmwtc.viz.interactive) plot_flux_heatmap() (in module palmwtc) (in module palmwtc.viz) (in module palmwtc.viz.timeseries) plot_flux_heatmap_interactive() (in module palmwtc.viz.interactive) plot_flux_monthly_boxplot() (in module palmwtc.viz.timeseries) plot_flux_monthly_boxplot_interactive() (in module palmwtc.viz.interactive) plot_flux_timeseries_tiers() (in module palmwtc.viz.timeseries) plot_flux_timeseries_tiers_interactive() (in module palmwtc.viz.interactive) plot_flux_vs_tree_age() (in module palmwtc.viz) (in module palmwtc.viz.timeseries) plot_flux_vs_tree_age_interactive() (in module palmwtc.viz.interactive) plot_high_quality_timeseries() (in module palmwtc.viz.qc_plots) plot_qc_comparison() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots) plot_qc_summary_heatmap() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots) plot_soil_var() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots) plot_specific_cycle() (in module palmwtc.viz) (in module palmwtc.viz.diagnostics) plot_tropical_seasonal_diurnal() (in module palmwtc) (in module palmwtc.viz) (in module palmwtc.viz.timeseries) plot_tropical_seasonal_diurnal_interactive() (in module palmwtc.viz.interactive) prepare_chamber_data() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.chamber) process_variable() (palmwtc.qc.processor.QCProcessor method) (palmwtc.qc.QCProcessor method) (palmwtc.QCProcessor method) process_variable_qc() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.rules) processed_dir (palmwtc.config.DataPaths attribute)

Q

QC_THRESHOLDS (in module palmwtc.flux.cycles) QCProcessor (class in palmwtc) (class in palmwtc.qc) (class in palmwtc.qc.processor)

R

raw_dir (palmwtc.config.DataPaths attribute) read_toa5_file() (in module palmwtc.io) (in module palmwtc.io.loaders) regime_agreement (palmwtc.windows.selector.WindowSelector attribute) (palmwtc.windows.WindowSelector attribute) (palmwtc.WindowSelector attribute) render_field_alert_html() (in module palmwtc) (in module palmwtc.qc) (in module palmwtc.qc.reporting)

resolve() (palmwtc.config.DataPaths class method) rows_in (palmwtc.pipeline.StepResult attribute) rows_out (palmwtc.pipeline.StepResult attribute) run() (in module palmwtc.cli) run_notebooks() (in module palmwtc.notebooks_runner) run_pipeline() (in module palmwtc.pipeline) run_science_validation() (in module palmwtc) (in module palmwtc.validation) (in module palmwtc.validation.science) run_step() (in module palmwtc.pipeline)

S

sample_app (in module palmwtc.cli) sample_dir() (in module palmwtc.data) sample_path() (in module palmwtc.cli) scale_to_leaf_basis() (in module palmwtc.flux) (in module palmwtc.flux.scaling) score_cycle() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.cycles) score_cycles() (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method) score_day_quality() (in module palmwtc) (in module palmwtc.flux) (in module palmwtc.flux.cycles) score_h2o_flux_qc() (in module palmwtc.flux) (in module palmwtc.flux.chamber) select_best_window_fast() (in module palmwtc.flux.cycles) set_style() (in module palmwtc) (in module palmwtc.viz) (in module palmwtc.viz.style)

show_sample_cycles() (in module palmwtc.viz) (in module palmwtc.viz.diagnostics) Site (in module palmwtc.config) site (palmwtc.config.DataPaths attribute) source (palmwtc.config.DataPaths attribute) SPINE_PREFIXES (in module palmwtc.notebooks_runner) START_CUTOFF_SEC (in module palmwtc.flux.cycles) START_SEARCH_SEC (in module palmwtc.flux.cycles) step_flux() (in module palmwtc.pipeline) step_qc() (in module palmwtc.pipeline) step_validation() (in module palmwtc.pipeline) step_windows() (in module palmwtc.pipeline) StepResult (class in palmwtc.pipeline) steps (palmwtc.pipeline.PipelineResult attribute) STEPS_IN_ORDER (in module palmwtc.pipeline) summarize_wpl_correction() (in module palmwtc.flux) (in module palmwtc.flux.chamber) summary() (palmwtc.pipeline.PipelineResult method) (palmwtc.windows.selector.WindowSelector method) (palmwtc.windows.WindowSelector method) (palmwtc.WindowSelector method)

T

test_inter_chamber() (in module palmwtc.validation.science) test_light_response() (in module palmwtc.validation.science)

test_q10() (in module palmwtc.validation.science) test_wue() (in module palmwtc.validation.science) total_seconds (palmwtc.pipeline.PipelineResult attribute)

U

USE_MULTIPROCESSING (in module palmwtc.flux.cycles)

V

var_config_dict (palmwtc.qc.processor.QCProcessor attribute) (palmwtc.qc.QCProcessor attribute) (palmwtc.QCProcessor attribute) visualize_breakpoints() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots)

visualize_drift() (in module palmwtc.viz.qc_plots) visualize_missing_data() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots) visualize_qc_flags() (in module palmwtc.viz) (in module palmwtc.viz.qc_plots)

W

windows_df (palmwtc.windows.selector.WindowSelector attribute) (palmwtc.windows.WindowSelector attribute) (palmwtc.WindowSelector attribute)

WindowSelector (class in palmwtc) (class in palmwtc.windows) (class in palmwtc.windows.selector) with_overrides() (palmwtc.config.DataPaths method)