Compute Canopy-Only NDVI per Plot in QGIS (Ignoring Bare Soil)

Standard zonal statistics for NDVI averages every pixel inside a polygon — including bare soil, paths, and shadows. In a plantation or orchard where open ground is common within plot boundaries, this gives a misleading health reading. This script uses a canopy mask to fix that.

What it does

The canopy_ndvi_median_calc.py script samples NDVI values from the NDVI raster within each polygon in the active layer, but only where the canopy mask pixel is greater than zero (indicating actual vegetation). The median of those canopy-only NDVI values is written as a new NDVI_median field on each polygon feature.

What you need

QGIS 3.28 or newer
numpy, rasterio (bundled with QGIS)
A polygon layer (plots or zones) set as the active layer
A raster layer named exactly canopy_mask checked in the Layers panel
An NDVI raster with “ndvi” in the layer name, checked in the Layers panel
The canopy_ndvi_median_calc.py script from the Vegetation & Field Analysis Pack

Steps

Run generate_canopy_mask.py first to create the canopy_mask layer (see the tutorial on generating a canopy mask).
Load your polygon plot layer and click it to make it the active layer.
Check (tick) the canopy_mask and NDVI rasters in the Layers panel.
Open Plugins → Python Console → Show Editor.
Paste the script and click Run.

The output file {input_name}_with_ndvi.geojson is saved alongside the original and added to your QGIS project, with a new NDVI_median field on each polygon.

Why median, not mean?

Median is more robust to outliers. A few very low-NDVI pixels (dry spots, exposed rock) or very high pixels (specular reflection) within the canopy won’t skew the median the way they would a mean. For health comparisons across plots, median NDVI is generally the more stable metric.

Typical NDVI values to expect

Range	Interpretation
< 0.2	Bare soil or stressed/absent vegetation
0.2–0.4	Sparse or stressed canopy
0.4–0.6	Moderate healthy canopy
> 0.6	Dense healthy canopy

Exact thresholds vary by crop, sensor, and atmospheric conditions.

Get the script

canopy_ndvi_median_calc.py is part of the Vegetation & Field Analysis Pack — six vegetation analysis scripts for QGIS at $40 USD.

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