- Implemented `run_spectral_extraction.py` to batch extract spectral indices (NDVI, BSI, NDWI) from 4-band TIFF files, saving results in a structured CSV format.
- Created `spectral_features.py` for calculating various spectral indices, including NDVI, BSI, NDWI, CI_green, CI_red, GNDVI, SAVI, and EVI2.
- Added Jupyter notebook `02_season_normalization_analysis.ipynb` for analyzing season-length normalization, comparing ESA and Angata spectral indices, and visualizing growth patterns.
- Included functions for computing season age, plotting trajectories, and performing peak and amplitude analysis.
- Consolidate 80_kpi_utils.R, 80_weekly_stats_utils.R, 80_report_building_utils.R into three client-aware files:
- 80_utils_common.R (50+ functions): Shared utilities, constants, and helpers
- 80_utils_agronomic_support.R: AURA-specific KPI calculations (6 KPIs)
- 80_utils_cane_supply.R: ANGATA placeholder for future expansion
- Move all internal helpers (calculate_cv, calculate_change_percentages, calculate_spatial_autocorrelation, extract_ci_values, etc.) to common
- Add MORAN_THRESHOLD_* constants to common
- Fix parameters_project.R field boundaries path (removed extra 'Data' directory)
- Update 80_calculate_kpis.R with conditional client-type sourcing logic
- Validate both ANGATA (cane_supply) and AURA (agronomic_support) workflows with comprehensive testing
- All 96+ functions accounted for; ready for production use
- Updated `detect_mosaic_mode` function to check for grid-size subdirectories in addition to tile-named files.
- Added comprehensive tests for DOY reset logic in `test_doy_logic.py`.
- Implemented feature extraction tests in `test_feature_extraction.py`.
- Created tests for growing window method in `test_growing_window_only.py`.
- Developed a complete model inference test in `test_model_inference.py`.
- Added a debug script for testing two-step refinement logic in `test_script22_debug.py`.
Major Changes:
- NEW: Scripts 09 & 10 for KPI calculation and enhanced reporting
- NEW: Shell script wrappers (01-10) for easier execution
- NEW: R packages flextable and officer for enhanced Word reports
- NEW: DEPLOYMENT_README.md with complete deployment guide
- RENAMED: Numbered R scripts (02, 03, 04) for clarity
- REMOVED: Old package management scripts (using renv only)
- UPDATED: Workflow now uses scripts 09->10 instead of 05
Files Changed: 90+ files
New Packages: flextable, officer
New Scripts: 09_run_calculate_kpis.sh, 10_run_kpi_report.sh
Documentation: DEPLOYMENT_README.md, EMAIL_TO_ADMIN.txt
See DEPLOYMENT_README.md for full deployment instructions.
- Replace raster package with terra throughout the codebase
- Update map visualizations with better layout and legends
- Add descriptive headers to report sections
- Improve map legend positioning and sizing
- Enhance error handling for missing data
- Remove redundant legends in field-specific visualizations
- Optimize figure dimensions to prevent page overflow
- Expand documentation of CI index and report components
- Update package dependencies in packages.
Timon
