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Tutorial: NEON → Corrected ENVI (BRDF + Topographic)

This tutorial walks through converting NEON hyperspectral HDF5 files into physically corrected ENVI reflectance cubes. The output is the foundational product used in all downstream harmonization workflows (e.g., Landsat-style reflectance).

Overview

You will learn how to:

  1. download NEON directional reflectance tiles
  2. export them to ENVI format
  3. apply topographic correction
  4. apply BRDF correction
  5. inspect corrected outputs and QA artifacts

This tutorial assumes you have installed cross-sensor-cal and have run through the Quickstart.

1. Set up a working directory

```bash BASE=output_neon_to_envi mkdir -p "$BASE" 2. Run the pipeline for one flight line Here we process a single NEON hyperspectral flight line at NIWO. cscal-pipeline \ --base-folder "$BASE" \ --site-code NIWO \ --year-month 2023-08 \ --product-code DP1.30006.001 \ --flight-lines NEON_D13_NIWO_DP1_L020-1_20230815_directional_reflectance \ --engine thread \ --max-workers 2 The command will: fetch the necessary HDF5 files export directional reflectance to ENVI (_envi.img/.hdr) apply topographic correction apply BRDF correction write corrected ENVI reflectance (_brdfandtopo_corrected_envi.img) generate QA PNG, PDF, and JSON files Re-running the command will skip completed stages. 3. What the corrected ENVI product contains A corrected flight line directory contains files such as: _directional_reflectance_envi.img _topocorrected_envi.img _brdfandtopo_corrected_envi.img _qa.png _qa.pdf _qa.json The key output is: *_brdfandtopo_corrected_envi.img This file contains physically corrected reflectance values suitable for sensor harmonization or modeling. 4. Inspect the corrected ENVI cube You can view the ENVI product using: ENVI/IDL QGIS (with raster bands exposed) Python libraries such as rioxarray or spectral Example in Python: import rioxarray as rxr

cube = rxr.open_rasterio("path/to/..._brdfandtopo_corrected_envi.img") cube This loads the corrected reflectance cube into an xarray DataArray. 5. Inspect QA outputs Open the QA PNG: open "$BASE/..._qa.png" The QA panel includes: reflectance range checks brightness differences across correction stages mask summary statistics wavelength and band metadata BRDF / topographic coefficient summaries The PDF version includes multi-page diagnostics and expanded panels. 6. Next steps Proceed to: NEON → Landsat reflectance Pipeline stages for in-depth explanations Working with Parquet to extract and analyze pixel spectra