How to solve rasterstats nodata warning

Question

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",
                                       geojson_out=True)

How does one get rid of this warning message?

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:

shapefile = [FILE PATH]
raster = [FILE PATH]

with rasterio.open(raster) as src:

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

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