├── .gitignore ├── .gitmodules ├── .readthedocs.yml ├── .travis.yml ├── CONTRIBUTING.md ├── LICENSE.md ├── MANIFEST.in ├── README.md ├── binder ├── apt.txt ├── postBuild └── requirements.txt ├── docs ├── Makefile ├── make.bat └── source │ ├── CONTRIBUTING.md │ ├── README.md │ ├── UsingAzure.md │ ├── UsingZenodo.md │ ├── conf.py │ ├── index.rst │ ├── paper │ └── pveg_flow.png │ ├── pyveg.scripts.rst │ └── pyveg.src.rst ├── notebooks └── tutorials │ ├── results_summary_TigerBush_Niger.json │ ├── tutorial_analyse_gee_data.ipynb │ ├── tutorial_download_and_process_gee_images.ipynb │ └── tutorial_simulate_patterned_vegetation.ipynb ├── pyveg ├── README.md ├── UsingAzure.md ├── UsingZenodo.md ├── __init__.py ├── azure_config_template.py ├── configs │ ├── __init__.py │ ├── collections.py │ ├── config_all.py │ ├── config_coords-17_Sentinel2.py │ ├── config_coords-17_Sentinel2_batch.py │ ├── config_coords-18_Sentinel2_batch.py │ ├── config_template.py │ ├── test_Sentinel2_azure.py │ ├── test_Sentinel2_batch.py │ └── test_Sentinel2_local.py ├── coordinates.py ├── gee_editor │ ├── analyse_gee_editor_output.py │ ├── map_declines.js │ └── time_series.js ├── paper │ ├── Makefile │ ├── paper.bib │ ├── paper.md │ └── pveg_flow.png ├── requirements.txt ├── scripts │ ├── analyse_gee_data.py │ ├── analyse_pyveg_summary_data.py │ ├── batch_commands.sh │ ├── calc_euler_characteristic.py │ ├── create_analysis_report.py │ ├── crop_and_convert_images.py │ ├── download_from_azure.py │ ├── generate_config_file.py │ ├── generate_pattern.py │ ├── plot_feature_vectors.py │ ├── run_pyveg_module.py │ ├── run_pyveg_pipeline.py │ └── upload_to_zenodo.py ├── src │ ├── __init__.py │ ├── analysis_preprocessing.py │ ├── azure_utils.py │ ├── batch_utils.py │ ├── combiner_modules.py │ ├── coordinate_utils.py │ ├── data_analysis_utils.py │ ├── date_utils.py │ ├── download_modules.py │ ├── file_utils.py │ ├── gee_interface.py │ ├── image_utils.py │ ├── pattern_generation.py │ ├── plotting.py │ ├── processor_modules.py │ ├── pyveg_pipeline.py │ ├── subgraph_centrality.py │ └── zenodo_utils.py ├── testdata │ ├── ERA5 │ │ ├── test_json │ │ │ └── 2018-03-01 │ │ │ │ └── JSON │ │ │ │ └── WEATHER │ │ │ │ └── weather_data.json │ │ └── test_tif │ │ │ └── 2016-01-16 │ │ │ └── RAW │ │ │ ├── ad52b5b29f06e8bec6e68ffb1a4b8968.total_precipitation.tif │ │ │ └── c56d3a39a21f3ee3b53a0e7dd48141d8.mean_2m_air_temperature.tif │ ├── PG-1mm-100iterations.csv │ ├── Sentinel2 │ │ ├── test_json │ │ │ └── 2018-03-01 │ │ │ │ └── JSON │ │ │ │ └── NC │ │ │ │ └── network_centralities.json │ │ ├── test_png │ │ │ └── 2018-03-01 │ │ │ │ └── SPLIT │ │ │ │ ├── sub100_11.550_27.943_BWNDVI.png │ │ │ │ ├── sub100_11.550_27.943_NDVI.png │ │ │ │ ├── sub100_11.550_27.943_RGB.png │ │ │ │ ├── sub101_11.550_27.939_BWNDVI.png │ │ │ │ ├── sub101_11.550_27.939_NDVI.png │ │ │ │ ├── sub101_11.550_27.939_RGB.png │ │ │ │ ├── sub102_11.550_27.934_BWNDVI.png │ │ │ │ ├── sub102_11.550_27.934_NDVI.png │ │ │ │ ├── sub102_11.550_27.934_RGB.png │ │ │ │ ├── sub103_11.550_27.930_BWNDVI.png │ │ │ │ ├── sub103_11.550_27.930_NDVI.png │ │ │ │ ├── sub103_11.550_27.930_RGB.png │ │ │ │ ├── sub104_11.550_27.925_BWNDVI.png │ │ │ │ ├── sub104_11.550_27.925_NDVI.png │ │ │ │ ├── sub104_11.550_27.925_RGB.png │ │ │ │ ├── sub105_11.550_27.920_BWNDVI.png │ │ │ │ ├── sub105_11.550_27.920_NDVI.png │ │ │ │ ├── sub105_11.550_27.920_RGB.png │ │ │ │ ├── sub106_11.550_27.916_BWNDVI.png │ │ │ │ ├── sub106_11.550_27.916_NDVI.png │ │ │ │ ├── sub106_11.550_27.916_RGB.png │ │ │ │ ├── sub107_11.550_27.911_BWNDVI.png │ │ │ │ ├── sub107_11.550_27.911_NDVI.png │ │ │ │ ├── sub107_11.550_27.911_RGB.png │ │ │ │ ├── sub108_11.550_27.907_BWNDVI.png │ │ │ │ ├── sub108_11.550_27.907_NDVI.png │ │ │ │ ├── sub108_11.550_27.907_RGB.png │ │ │ │ ├── sub109_11.550_27.902_BWNDVI.png │ │ │ │ ├── sub109_11.550_27.902_NDVI.png │ │ │ │ ├── sub109_11.550_27.902_RGB.png │ │ │ │ ├── sub10_11.532_27.952_BWNDVI.png │ │ │ │ ├── sub10_11.532_27.952_NDVI.png │ │ │ │ └── sub10_11.532_27.952_RGB.png │ │ └── test_tif │ │ │ └── 2018-03-01 │ │ │ └── RAW │ │ │ ├── download.B2.tif │ │ │ ├── download.B3.tif │ │ │ ├── download.B4.tif │ │ │ └── download.NDVI.tif │ ├── binary_image.png │ ├── binary_image.txt │ ├── binary_labyrinths_50.csv │ ├── binary_labyrinths_50T.csv │ ├── black.png │ ├── black_and_white_diagonal.png │ ├── black_and_white_diagonal_2.png │ ├── gee_labyrinths_summary.json │ ├── network_json_data │ │ ├── image-labeller-output.json │ │ ├── results_summary.json │ │ └── test-results-summary.json │ ├── patternGenConfig.json │ ├── random-initialisation_m=200.csv │ ├── random-initialisation_m=50.csv │ ├── test.gif │ ├── test_float_pattern_50x50_1.csv │ └── white.png ├── tests │ ├── test_analyse_gee_data.py │ ├── test_analysis_preprocessing.py │ ├── test_azure_utils.py │ ├── test_combiner_modules.py │ ├── test_data_analysis_utils.py │ ├── test_date_utils.py │ ├── test_download_modules.py │ ├── test_image_utils.py │ ├── test_pattern_gen.py │ ├── test_pipeline_core.py │ ├── test_processor_modules.py │ └── test_sc.py └── zenodo_config_template.py ├── rveg ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── EC_calc.R │ ├── README.md │ ├── crystal_ball_function.R │ ├── decay_rate_functions.R │ └── generatePattern.R ├── README.md ├── inst │ └── extdata │ │ ├── PG-1mm-100iterations.csv │ │ ├── binary_image.png │ │ ├── binary_image.txt │ │ ├── binary_labyrinths_50.csv │ │ ├── binary_labyrinths_50T.csv │ │ ├── black.png │ │ ├── black_and_white_diagonal.png │ │ ├── black_and_white_diagonal_2.png │ │ ├── network_json_data │ │ └── test-results-summary.json │ │ ├── patternGenConfig.json │ │ ├── random-initialisation_m=200.csv │ │ ├── random-initialisation_m=50.csv │ │ ├── test.gif │ │ ├── test_float_pattern_50x50_1.csv │ │ └── white.png └── tests │ ├── testthat.R │ └── testthat │ ├── test_EC_calculation.R │ └── test_pattern_generation.R └── setup.py /.gitignore: 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