I have a source raster data set (tif file) and a number of polygon features. For each one of those polygons I need to:

a) 'clip' the raster.
b) change values of those clipped raster cells (with the average value).
c) write new values back to the source raster.

I've managed to do a and b, which means I now have a numpy.ndarray variable where all cells have been populated with the average value. How can I write this back to the source raster?

I believe I'd be able to write a script which could do such a thing. I have arrays dimensions (width and height) and top left cell's position, so I guess it'd just be a matter of operating with these arrays. However, I was wondering whether there's any existing function that does that already.

My code:

import os, sys, datetime, time
import geopandas as gpd
import gdal
import rasterio
from rasterio.mask import mask
from fiona.crs import from_epsg
import numpy as np
import pycrs

alr_path = r'Z:\GRAU_Team_Admin\Alfonso Jimenez\Flood Modelling\Building Footprint\OUTPUT\NI_RIVER_ALR_1000.tif'

gdb_vml_polygs = r'\\lwukwvdi11\data\Data\UK\UK_Mapping\VML\data\Europa20190403\RSA_VML_BUILDINGS_NI.gdb'
fc_vml_polygs = r'VML_Buildings_NI'

alr = rasterio.open(alr_path)

vml_polygs = gpd.read_file(gdb_vml_polygs, driver='FileGDB', layer=fc_vml_polygs)

for index, row in vml_polygs.iterrows():
    #row[3] contains the geometry
    window, out_transform = mask(alr, row[3], all_touched=True, crop=True)
    if np.all([window < 0]):
        avg = -1
        avg = window[window != -1].mean().item()
        window_avg = (np.where(window!=-1, int(round(avg,0)), window))

In the script window_avg is a numpy array containing the new values. How can I write these values back into the source raster?

  • 1
  • I can see WriteArray (to be used with gdal.band type of data) does what I'm looking for. Any idea whether there's anything similar for raster data opened with 'rasterio'? The reason I'm asking is because the processing done so far is with rasterio (like the use of 'mask' for example). If I open the raster with gdal instead I guess I would need to find a 'gdal' way to do the mask... Jul 18, 2019 at 14:42
  • I haven't used rasterio but as far as I know, it runs on top of gdal. That means that there is a chance their .write() method accepts an offset as well. You could take a look at the documentation or tweak around with the .write() method to see if its possible. Jul 18, 2019 at 14:53

2 Answers 2


I would recommend using rioxarray.

import numpy
import rioxarray
from shapely.geometry import mapping

xds = rioxarray.open_rasterio("NI_RIVER_ALR_1000.tif").sel(band=1).squeeze()
gdb_vml_polygs = 'RSA_VML_BUILDINGS_NI.gdb'
fc_vml_polygs = 'VML_Buildings_NI'
vml_polygs = gpd.read_file(gdb_vml_polygs, driver='FileGDB', layer=fc_vml_polygs)
out_xds = xds.copy()
for geom in vml_polygs.geometry.apply(mapping):
    clipped = xds.rio.clip([geom], vml_polygs.crs, drop=False)
    out_xds = out_xds.where(numpy.isnan(clipped), clipped.mean())

I tested it on this input raster:

enter image description here

And with four regions to average over, this was the result:

enter image description here


With rasterio

filled=False gives back masked array which can be utilised to replace with mean value.

Make sure to set crop=False and set the indexes to the band you want to replace it with.

import geopandas as gpd
import rasterio.mask
import rasterio as rio

gdf = gpd.read_file('input_shp.shp')

with rio.open("input.tif", "r") as src:
    band_num = 1
    src_image = src.read(band_num, out_dtype=rio.float64)

    # for each feature geom, replace with mean
    for geom in gdf.geometry:
        out_image, out_transform = rio.mask.mask(
            src, [geom], crop=False, filled=False, indexes=band_num
        src_image[~out_image.mask] = src_image[~out_image.mask].mean()
    # save tif
    profile = src.profile
    profile.update(dtype=rio.float64, count=1, compress="lzw")

    with rasterio.open("output.tif", "w", **profile) as dst:
        dst.write(src_image, 1)

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