I am using the zonal_stats function in the rasterstats package to calculate summary statistics from GeoTiffs containing vegetative index values. The summary statistics come out fine, however with each iteration of the zonal_stats function I run, I encounter the warning UserWarning: Setting nodata to -999; specify nodata explicitly warnings.warn("Setting nodata to -999; specify nodata explicitly")

When I created each GeoTIFF file, I set the nodata value as outband.SetNoDataValue(np.nan). Each geotiff is opened and VI statistics calculated with:

    raster = [FILE PATH]
    raster = rasterio.open(raster, mode='r')

    # Assign raster values to numpy nd array
    vi_array = raster.read(1)
    affine = raster.transform

    # Calculate VI stats
    zonal_stats = rasterstats.zonal_stats(shapefile, vi_array, affine=affine,
                                       stats="mean count std median",

How does one get rid of this warning message?

  • Maybe see here for an answer: github.com/perrygeo/python-rasterstats/issues/115
    – GBG
    Apr 19 at 14:59
  • @GBG The numpy version I am using in this environment is 1.21.5
    – nburner
    Apr 19 at 15:11
  • Post an issue on the rasterstats github page. Get around the error and use a Python try/except block to catch the exception. Then use pass to ignore and move on?
    – GBG
    Apr 19 at 18:48
  • @GBG it's not an exception, it's a warning.
    – user2856
    Jun 18 at 9:42

1 Answer 1


You may have set nodata on your raster, but you are not passing that raster to rasterstats.zonal_stats, you are passing a numpy array. And numpy arrays don't have a nodata property.

Just like you specify the affine transform when passing an array to rasterstats.zonal_stats instead of a raster, you can also specify the nodata value:

# Calculate VI stats
zonal_stats = zonal_stats(shapefile, vi_array,
                          affine=affine, nodata=np.nan,
                          stats="mean count std median",

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