Filter a Raster by Threshold in QGIS (NDVI Masking and More)

Sometimes you want to isolate only the pixels in a raster that meet a condition — for example, keeping only healthy vegetation (NDVI > 0.4) and masking out everything else. This script does that in one step for any single-band raster.

What it does

The raster_mask_generator.py script creates a filtered copy of a raster where only pixels that pass a threshold test are kept. All other pixels are set to NoData, making them transparent in QGIS.

Two comparison modes:

• greater_than — keeps pixels above the threshold (e.g. NDVI > 0.4 → healthy vegetation only)
• less_than — keeps pixels below the threshold (e.g. elevation < 850 m → low-lying areas only)

Output: {input_name}_mask_{gt|lt}{threshold}_nodata_{value|none}.tif saved in the same directory as the input, loaded into the QGIS project.

Before — the raw NDVI raster, every pixel coloured regardless of value:

After — the same raster with threshold=0.4, comparison='greater_than' applied. Everything at or below 0.4 becomes transparent NoData, leaving only healthy vegetation:

What you need

• QGIS 3.28 or newer
• QGIS processing framework (bundled)
• The first checked raster layer in the Layers panel (any single-band raster)
• The raster_mask_generator.py script from the Vegetation & Field Analysis Pack

Before you start

The raw NDVI raster above didn’t need to be built by hand — it was generated automatically the moment the multispectral orthomosaic was loaded into QGIS, by an auto-running startup script (auto_generate_ndvi.py). See the startup scripts guide for how to set that automation up. If you’re masking a CHM instead of NDVI, generate it first with generate_chm.py.

Steps

1. Load your raster (NDVI, elevation, CHM, or any single-band raster) into QGIS and check (tick) it in the Layers panel.
2. Open Plugins → Python Console → Show Editor.
3. Paste the script. At the bottom, set:
   • threshold — the cutoff value (e.g. 0.4 for NDVI)
   • comparison — 'greater_than' or 'less_than'
   • nodata — value for masked pixels (default: None for NaN / transparent)
4. Click Run.

Common use cases

Use case	Raster	Threshold	Comparison
Isolate healthy vegetation	NDVI	0.4	greater_than
Show stressed or bare areas	NDVI	0.2	less_than
Map low-elevation zones	DTM/DEM	850	less_than
Show tall canopy only	CHM	5	greater_than

Combining with other scripts

The output of this script can be used as an additional visual layer on top of your main analysis, or as a filtered input to further processing:

• Run raster_mask_generator.py on NDVI with threshold 0.4 to get a “healthy canopy” highlight layer
• Overlay it on your classified CHM from style_chm.py to see where healthy vegetation and tall trees overlap
• Or feed the masked raster straight into zonal_statistics.py against a sampling grid — this is a common real-world pairing: mask out bare soil/noise first, then average only the pixels that matter per grid cell

Get the script

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