Index

A

adaptive_threshold() (in module pyveg.src.image_utils) add_rgb_images() (in module pyveg.scripts.create_analysis_report) add_task() (in module pyveg.src.batch_utils) add_time_series_plots() (in module pyveg.scripts.create_analysis_report)

analyse_gee_data() (in module pyveg.scripts.analyse_gee_data) analyse_pyveg_summary_data() (in module pyveg.scripts.analyse_pyveg_summary_data) ar1_moving_average_time_series() (in module pyveg.src.data_analysis_utils) assign_dates_to_tasks() (in module pyveg.src.date_utils)

B

barplot_plots() (in module pyveg.scripts.analyse_pyveg_summary_data) BaseModule (class in pyveg.src.pyveg_pipeline)

boxplot_plots() (in module pyveg.scripts.analyse_pyveg_summary_data) build_module() (in module pyveg.scripts.run_pyveg_module) build_pipeline() (in module pyveg.scripts.run_pyveg_pipeline)

C

calc_adjacency_matrix() (in module pyveg.src.subgraph_centrality) calc_and_sort_sc_indices() (in module pyveg.src.subgraph_centrality) calc_distance_matrix() (in module pyveg.src.subgraph_centrality) calc_euler_characteristic() (in module pyveg.src.subgraph_centrality) calc_plant_change() (pyveg.src.pattern_generation.PatternGenerator static method) calc_soil_water_change() (pyveg.src.pattern_generation.PatternGenerator static method) calc_surface_water_change() (pyveg.src.pattern_generation.PatternGenerator static method) calculate_ci() (in module pyveg.src.data_analysis_utils) cball() (in module pyveg.src.data_analysis_utils) cball_parfit() (in module pyveg.src.data_analysis_utils) check_blob_exists() (in module pyveg.src.azure_utils) check_config() (pyveg.src.pyveg_pipeline.BaseModule method) check_container_exists() (in module pyveg.src.azure_utils) check_for_existing_files() (pyveg.src.pyveg_pipeline.BaseModule method) check_if_finished() (pyveg.src.processor_modules.ProcessorModule method) (pyveg.src.pyveg_pipeline.BaseModule method) (pyveg.src.pyveg_pipeline.Sequence method) check_image_ok() (in module pyveg.src.image_utils) check_input_data_exists() (pyveg.src.processor_modules.ProcessorModule method) check_output_data_exists() (pyveg.src.processor_modules.ProcessorModule method) check_output_dict() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method) check_sub_image() (pyveg.src.processor_modules.NDVICalculator method) (pyveg.src.processor_modules.NetworkCentralityCalculator method) check_task_failed_dependencies() (in module pyveg.src.batch_utils) check_tasks_status() (in module pyveg.src.batch_utils) check_timeout() (pyveg.src.processor_modules.ProcessorModule method) cleanup() (pyveg.src.pyveg_pipeline.Pipeline method) (pyveg.src.pyveg_pipeline.Sequence method) coarse_dataframe() (in module pyveg.src.data_analysis_utils) combine_json_lists() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method) combine_tif() (in module pyveg.src.image_utils) CombinerModule (class in pyveg.src.combiner_modules) compare_binary_image_files() (in module pyveg.src.image_utils)

compare_binary_images() (in module pyveg.src.image_utils) configure() (pyveg.src.pattern_generation.PatternGenerator method) (pyveg.src.pyveg_pipeline.BaseModule method) (pyveg.src.pyveg_pipeline.Pipeline method) (pyveg.src.pyveg_pipeline.Sequence method) configure_and_run_module() (in module pyveg.scripts.run_pyveg_module) configure_and_run_pipeline() (in module pyveg.scripts.run_pyveg_pipeline) consolidate_json_to_list() (in module pyveg.src.file_utils) construct_filename_from_metadata() (in module pyveg.src.file_utils) construct_image_savepath() (in module pyveg.src.file_utils) (pyveg.src.processor_modules.VegetationImageProcessor method) convert_to_bw() (in module pyveg.src.image_utils) convert_to_geopandas() (in module pyveg.src.data_analysis_utils) convert_to_rgb() (in module pyveg.src.image_utils) coords_dict_to_coords_string() (in module pyveg.src.coordinate_utils) coords_list_to_coords_string() (in module pyveg.src.coordinate_utils) copy_to_output_location() (pyveg.src.pyveg_pipeline.BaseModule method) correlation_plots() (in module pyveg.scripts.analyse_pyveg_summary_data) create_batch_client() (in module pyveg.src.batch_utils) create_batch_job_if_needed() (pyveg.src.pyveg_pipeline.Sequence method) create_container() (in module pyveg.src.azure_utils) create_deposition() (in module pyveg.src.zenodo_utils) create_gif_from_images() (in module pyveg.src.image_utils) create_job() (in module pyveg.src.batch_utils) create_lat_long_metric_figures() (in module pyveg.src.data_analysis_utils) create_markdown_pdf_report() (in module pyveg.scripts.create_analysis_report) create_new_deposition() (in module pyveg.scripts.upload_to_zenodo) create_pool() (in module pyveg.src.batch_utils) create_task_dict() (pyveg.src.processor_modules.ProcessorModule method) crop_and_convert_all() (in module pyveg.src.image_utils) crop_and_convert_to_bw() (in module pyveg.src.image_utils) crop_image_array() (in module pyveg.src.subgraph_centrality) crop_image_nparts() (in module pyveg.src.image_utils) crop_image_npix() (in module pyveg.src.image_utils)

D

decay_rate() (in module pyveg.src.data_analysis_utils) delete_blob() (in module pyveg.src.azure_utils) delete_file() (in module pyveg.src.zenodo_utils) delete_job() (in module pyveg.src.batch_utils) delete_pool() (in module pyveg.src.batch_utils) detrend_data() (in module pyveg.src.analysis_preprocessing)

detrend_df() (in module pyveg.src.analysis_preprocessing) download_and_unzip() (in module pyveg.src.file_utils) download_file() (in module pyveg.src.zenodo_utils) download_results_by_coord_id() (in module pyveg.src.zenodo_utils) download_rgb() (in module pyveg.src.azure_utils) download_summary_json() (in module pyveg.src.azure_utils) drop_veg_outliers() (in module pyveg.src.analysis_preprocessing)

E

early_warnings_null_hypothesis() (in module pyveg.src.data_analysis_utils) early_warnings_sensitivity_analysis() (in module pyveg.src.data_analysis_utils)

err_func() (in module pyveg.src.data_analysis_utils) evolve_pattern() (pyveg.src.pattern_generation.PatternGenerator method) exp_model_fit() (in module pyveg.src.data_analysis_utils)

F

feature_vector_metrics() (in module pyveg.src.subgraph_centrality) fft_series() (in module pyveg.src.data_analysis_utils) fill_feature_vector() (in module pyveg.src.subgraph_centrality)

fill_sc_pixels() (in module pyveg.src.subgraph_centrality) fill_veg_gaps() (in module pyveg.src.analysis_preprocessing) find_coords_string() (in module pyveg.src.coordinate_utils) find_mid_period() (in module pyveg.src.date_utils)

G

generate_sc_images() (in module pyveg.src.subgraph_centrality) get() (pyveg.src.pyveg_pipeline.Pipeline method) (pyveg.src.pyveg_pipeline.Sequence method) get_AR1_parameter_estimate() (in module pyveg.src.data_analysis_utils) get_ar1_var_timeseries_df() (in module pyveg.src.data_analysis_utils) get_base_url_and_token() (in module pyveg.src.zenodo_utils) get_blob_to_tempfile() (in module pyveg.src.azure_utils) get_bucket_url() (in module pyveg.src.zenodo_utils) get_collection_and_suffix() (in module pyveg.scripts.create_analysis_report) get_confidence_intervals() (in module pyveg.src.data_analysis_utils) get_config() (pyveg.src.pyveg_pipeline.BaseModule method) get_correlation_lag_ts() (in module pyveg.src.data_analysis_utils) get_corrs_by_lag() (in module pyveg.src.data_analysis_utils) get_date_range_for_collection() (in module pyveg.src.date_utils) get_date_strings_for_time_period() (in module pyveg.src.date_utils) get_datetime_xs() (in module pyveg.src.data_analysis_utils) get_dependent_batch_tasks() (pyveg.src.processor_modules.ProcessorModule method) get_deposition_id() (in module pyveg.src.zenodo_utils) get_deposition_info() (in module pyveg.src.zenodo_utils)

get_file() (pyveg.src.pyveg_pipeline.BaseModule method) get_filepath_after_directory() (in module pyveg.src.file_utils) get_image() (pyveg.src.processor_modules.ProcessorModule method) get_json() (pyveg.src.pyveg_pipeline.BaseModule method) get_kendell_tau() (in module pyveg.src.data_analysis_utils) get_max_lagged_cor() (in module pyveg.src.data_analysis_utils) get_metadata() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method) get_missing_time_points() (in module pyveg.src.analysis_preprocessing) get_num_n_day_slices() (in module pyveg.src.date_utils) get_region_string() (in module pyveg.src.coordinate_utils) get_results_summary_json() (in module pyveg.src.zenodo_utils) get_sas_token() (in module pyveg.src.azure_utils) get_signal_pixels() (in module pyveg.src.subgraph_centrality) get_sub_image_coords() (in module pyveg.src.coordinate_utils) get_tag() (in module pyveg.src.file_utils) get_template_text() (in module pyveg.scripts.generate_config_file) get_time_diff() (in module pyveg.src.date_utils) get_veg_time_series() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method) get_weather_time_series() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method)

H

has_batch_job() (pyveg.src.pyveg_pipeline.Sequence method)

hist_eq() (in module pyveg.src.image_utils)

I

image_all_same_colour() (in module pyveg.src.image_utils) image_file_all_same_colour() (in module pyveg.src.image_utils) image_file_to_array() (in module pyveg.src.image_utils) image_from_array() (in module pyveg.src.image_utils)

initial_conditions() (pyveg.src.pattern_generation.PatternGenerator method) initialize() (pyveg.src.pattern_generation.PatternGenerator method) invert_binary_image() (in module pyveg.src.image_utils) invert_y_coord() (in module pyveg.src.subgraph_centrality)

J

join_path() (pyveg.src.pyveg_pipeline.BaseModule method) (pyveg.src.pyveg_pipeline.Sequence method)

K

kendall_tau_histograms() (in module pyveg.src.plotting)

L

list_depositions() (in module pyveg.src.zenodo_utils) list_directory() (in module pyveg.src.azure_utils) (pyveg.src.pyveg_pipeline.BaseModule method)

list_files() (in module pyveg.src.zenodo_utils) load_config() (pyveg.src.pattern_generation.PatternGenerator method) lookup_country() (in module pyveg.src.coordinate_utils)

M

main() (in module pyveg.scripts.analyse_gee_data) (in module pyveg.scripts.analyse_pyveg_summary_data) (in module pyveg.scripts.calc_euler_characteristic) (in module pyveg.scripts.create_analysis_report) (in module pyveg.scripts.crop_and_convert_images) (in module pyveg.scripts.generate_config_file) (in module pyveg.scripts.generate_pattern) (in module pyveg.scripts.run_pyveg_module) (in module pyveg.scripts.run_pyveg_pipeline) (in module pyveg.scripts.upload_to_zenodo) make_binary() (pyveg.src.pattern_generation.PatternGenerator method) make_filename() (in module pyveg.scripts.generate_config_file) make_graph() (in module pyveg.src.subgraph_centrality) make_output_location() (in module pyveg.scripts.generate_config_file) make_time_series() (in module pyveg.src.analysis_preprocessing) mean_annual_ts() (in module pyveg.src.data_analysis_utils) median_filter() (in module pyveg.src.image_utils) module pyveg.scripts pyveg.scripts.analyse_gee_data pyveg.scripts.analyse_pyveg_summary_data pyveg.scripts.calc_euler_characteristic pyveg.scripts.create_analysis_report pyveg.scripts.crop_and_convert_images pyveg.scripts.generate_config_file pyveg.scripts.generate_pattern pyveg.scripts.run_pyveg_module pyveg.scripts.run_pyveg_pipeline pyveg.scripts.upload_to_zenodo pyveg.src pyveg.src.analysis_preprocessing pyveg.src.azure_utils pyveg.src.batch_utils pyveg.src.combiner_modules pyveg.src.coordinate_utils pyveg.src.data_analysis_utils pyveg.src.date_utils pyveg.src.file_utils pyveg.src.image_utils pyveg.src.pattern_generation pyveg.src.plotting pyveg.src.processor_modules pyveg.src.pyveg_pipeline pyveg.src.subgraph_centrality pyveg.src.zenodo_utils

moving_window_analysis() (in module pyveg.src.data_analysis_utils)

N

NDVICalculator (class in pyveg.src.processor_modules) network_figure() (in module pyveg.src.data_analysis_utils)

NetworkCentralityCalculator (class in pyveg.src.processor_modules) numpy_to_pillow() (in module pyveg.src.image_utils)

P

PatternGenerator (class in pyveg.src.pattern_generation) pillow_to_numpy() (in module pyveg.src.image_utils) Pipeline (class in pyveg.src.pyveg_pipeline) plot_autocorrelation_function() (in module pyveg.src.plotting) plot_band_values() (in module pyveg.src.image_utils) plot_correlation_mwa() (in module pyveg.src.plotting) plot_cross_correlations() (in module pyveg.src.plotting) plot_ews_resiliance() (in module pyveg.src.plotting) plot_feature_vector() (in module pyveg.src.plotting) plot_image() (pyveg.src.pattern_generation.PatternGenerator method) plot_moving_window_analysis() (in module pyveg.src.plotting) plot_ndvi_time_series() (in module pyveg.src.plotting) plot_sensitivity_heatmap() (in module pyveg.src.plotting) plot_stl_decomposition() (in module pyveg.src.plotting) plot_time_series() (in module pyveg.src.plotting) prepare_for_run() (pyveg.src.pyveg_pipeline.BaseModule method) prepare_for_task_submission() (in module pyveg.src.batch_utils) prepare_results_zipfile() (in module pyveg.src.zenodo_utils) preprocess_data() (in module pyveg.src.analysis_preprocessing) print_config() (pyveg.src.pattern_generation.PatternGenerator method) print_run_status() (pyveg.src.pyveg_pipeline.BaseModule method) (pyveg.src.pyveg_pipeline.Pipeline method) (pyveg.src.pyveg_pipeline.Sequence method) print_task_output() (in module pyveg.src.batch_utils) process_and_threshold() (in module pyveg.src.image_utils) process_input_data() (in module pyveg.scripts.analyse_pyveg_summary_data) process_single_date() (pyveg.src.processor_modules.NDVICalculator method) (pyveg.src.processor_modules.NetworkCentralityCalculator method) (pyveg.src.processor_modules.VegetationImageProcessor method) (pyveg.src.processor_modules.WeatherImageToJSON method) process_sub_image() (in module pyveg.src.processor_modules) (pyveg.src.processor_modules.NDVICalculator method) ProcessorModule (class in pyveg.src.processor_modules) publish_deposition() (in module pyveg.src.zenodo_utils) pyveg.scripts module pyveg.scripts.analyse_gee_data module pyveg.scripts.analyse_pyveg_summary_data module pyveg.scripts.calc_euler_characteristic module pyveg.scripts.create_analysis_report module

pyveg.scripts.crop_and_convert_images module pyveg.scripts.generate_config_file module pyveg.scripts.generate_pattern module pyveg.scripts.run_pyveg_module module pyveg.scripts.run_pyveg_pipeline module pyveg.scripts.upload_to_zenodo module pyveg.src module pyveg.src.analysis_preprocessing module pyveg.src.azure_utils module pyveg.src.batch_utils module pyveg.src.combiner_modules module pyveg.src.coordinate_utils module pyveg.src.data_analysis_utils module pyveg.src.date_utils module pyveg.src.file_utils module pyveg.src.image_utils module pyveg.src.pattern_generation module pyveg.src.plotting module pyveg.src.processor_modules module pyveg.src.pyveg_pipeline module pyveg.src.subgraph_centrality module pyveg.src.zenodo_utils module

R

read_image() (in module pyveg.src.azure_utils) read_json() (in module pyveg.src.azure_utils) read_json_to_dataframes() (in module pyveg.src.analysis_preprocessing) read_results_summary() (in module pyveg.src.analysis_preprocessing) remove_container_name_from_blob_path() (in module pyveg.src.azure_utils) resample_data() (in module pyveg.src.analysis_preprocessing) resample_dataframe() (in module pyveg.src.analysis_preprocessing) resample_time_series() (in module pyveg.src.analysis_preprocessing) retrieve_blob() (in module pyveg.src.azure_utils)

reverse_normalise_ts() (in module pyveg.src.data_analysis_utils) run() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method) (pyveg.src.processor_modules.ProcessorModule method) (pyveg.src.pyveg_pipeline.Pipeline method) (pyveg.src.pyveg_pipeline.Sequence method) run_batch() (pyveg.src.processor_modules.ProcessorModule method) run_early_warnings_resilience_analysis() (in module pyveg.scripts.analyse_gee_data) run_local() (pyveg.src.processor_modules.ProcessorModule method) run_time_series_analysis() (in module pyveg.scripts.analyse_gee_data)

S

sanitize_container_name() (in module pyveg.src.azure_utils) save_as_csv() (pyveg.src.pattern_generation.PatternGenerator method) save_as_matlab() (pyveg.src.pattern_generation.PatternGenerator method) save_as_png() (pyveg.src.pattern_generation.PatternGenerator method) save_config() (pyveg.src.pyveg_pipeline.BaseModule method) save_image() (in module pyveg.src.azure_utils) (in module pyveg.src.file_utils) (pyveg.src.processor_modules.ProcessorModule method) save_json() (in module pyveg.src.azure_utils) (in module pyveg.src.file_utils) (pyveg.src.pyveg_pipeline.BaseModule method) save_rgb_image() (pyveg.src.processor_modules.VegetationImageProcessor method) save_sc_images() (in module pyveg.src.subgraph_centrality) save_ts_summary_stats() (in module pyveg.src.analysis_preprocessing) scale_tif() (in module pyveg.src.image_utils) scatter_plots() (in module pyveg.scripts.analyse_pyveg_summary_data) Sequence (class in pyveg.src.pyveg_pipeline) set_config() (pyveg.src.pyveg_pipeline.Sequence method) set_default_parameters() (pyveg.src.combiner_modules.VegAndWeatherJsonCombiner method) (pyveg.src.processor_modules.NDVICalculator method) (pyveg.src.processor_modules.NetworkCentralityCalculator method) (pyveg.src.processor_modules.ProcessorModule method) (pyveg.src.processor_modules.VegetationImageProcessor method) (pyveg.src.processor_modules.WeatherImageToJSON method) (pyveg.src.pyveg_pipeline.BaseModule method)

set_output_location() (pyveg.src.pyveg_pipeline.Sequence method) set_parameters() (pyveg.src.pyveg_pipeline.BaseModule method) set_rainfall() (pyveg.src.pattern_generation.PatternGenerator method) set_random_starting_pattern() (pyveg.src.pattern_generation.PatternGenerator method) set_starting_pattern_from_file() (pyveg.src.pattern_generation.PatternGenerator method) slice_time_period() (in module pyveg.src.date_utils) slice_time_period_into_n() (in module pyveg.src.date_utils) smooth_all_sub_images() (in module pyveg.src.analysis_preprocessing) smooth_subimage() (in module pyveg.src.analysis_preprocessing) smooth_veg_data() (in module pyveg.src.analysis_preprocessing) split_and_save_sub_images() (pyveg.src.processor_modules.VegetationImageProcessor method) split_filepath() (in module pyveg.src.file_utils) stl_decomposition() (in module pyveg.src.data_analysis_utils) store_feature_vectors() (in module pyveg.src.analysis_preprocessing) subgraph_centrality() (in module pyveg.src.subgraph_centrality) submit_tasks() (in module pyveg.src.batch_utils)

T

text_file_to_array() (in module pyveg.src.subgraph_centrality)

U

unlock_deposition() (in module pyveg.src.zenodo_utils) upload_custom_metadata() (in module pyveg.src.zenodo_utils) upload_file() (in module pyveg.src.zenodo_utils)

upload_file_to_container() (in module pyveg.src.batch_utils) upload_results_summary() (in module pyveg.scripts.upload_to_zenodo) upload_standard_metadata() (in module pyveg.src.zenodo_utils) upload_summary_stats() (in module pyveg.scripts.upload_to_zenodo)

V

variance_moving_average_time_series() (in module pyveg.src.data_analysis_utils)

VegAndWeatherJsonCombiner (class in pyveg.src.combiner_modules) VegetationImageProcessor (class in pyveg.src.processor_modules)

W

wait_for_tasks_to_complete() (in module pyveg.src.batch_utils) WeatherImageToJSON (class in pyveg.src.processor_modules) write_csv() (in module pyveg.src.subgraph_centrality) write_dict_to_csv() (in module pyveg.src.subgraph_centrality)

write_file() (in module pyveg.scripts.generate_config_file) write_file_to_blob() (in module pyveg.src.azure_utils) write_files_to_blob() (in module pyveg.src.azure_utils) write_slimmed_csv() (in module pyveg.src.data_analysis_utils) write_to_json() (in module pyveg.src.data_analysis_utils)