I have shapefile that intersects with a raster but do not fully overlap :

enter image description here

I would like to clip the raster with this shapefile but every time I try I get this error message:

ValueError: Input shapes do not overlap raster.

I have tried two methods to clip the raster: once with rasterio:

#get coordinates of shapefile
def getFeatures(gdf):
      """Function to parse features from GeoDataFrame in such a manner that rasterio wants them"""
       import json
       return [json.loads(gdf.to_json())['features'][0]['geometry']]

coords = getFeatures(plots)

out_img, out_transform = mask(img,coords, crop=True)

and once with earthpy:


both give me the same errors.

This is how I read the shape and the image:

#load shapefile
poly = geopandas.read_file(r'very\nice\path\and\polygon.shp')

#determine projection for shape and change it into the image projection
poly.crs = {'init' :'epsg:4326'}
poly=poly.to_crs({'init': 'epsg:32721'})

#Load image

after this I used the methods that demonstrated.

How can I clip the raster with the polygon even if they are not the overlap 100%?


I have tried this:

out_image, out_meta = es.crop_image(img, plots.geometry)

and also the same with rasterio as was suggested here but for some reason it clips only for the extent of the shape but not to the actual shape:

enter image description here


You can simplify the solution (without a function like def getFeatures(gdf))

import rasterio 
out_image, out_transform = rasterio.mask.mask(img, poly.geometry, crop=True)

enter image description hereenter image description here

Same with EarthPy

  out_image, out_meta = es.crop_image(img, poly.geometry)
  • thank you for your answer, I have tried it but the results I get is clip to the polygon extent and not to the actual shape like in your image , do you have any idea why would it occur? – Reut Jun 18 '20 at 10:36
  • The result is a clip of the original raster (coloured) to the polygon extent (grey raster) – gene Jun 18 '20 at 13:37

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