I'm trying to clip a shapefile with another .shp using pure python.

Original shp I need to clip:

enter image description here

Area of Interest for clipping (shown overlapped to the original .shp for convenience):

enter image description here

If I invoke clipvectorbypolygon from QGIS toolbox via processing.run, I get the desired result:

params = {'INPUT': original_shape,
          'MASK': area_of_interest,
          'OUTPUT': result_shape

processing.run("gdal:clipvectorbypolygon", parameters = params)

enter image description here

But, when trying to replicate it using pure python, I always obtain a clipped polygon with the inner areas filled:

I've tried by using geopandas.clip

input = gpd.read_file(original_shape)

clipped = gpd.clip(input, area_of_interest)


and geopandas.GeoSeries.intersection:

input = gpd.read_file(original_shape)

clipped = gpd.GeoSeries.intersection(input, area_of_interest)


Both produce the same result:

enter image description here

exploding the original .shp gives a slightly different output, but same problem:

input = gpd.read_file(original_shape).explode()

for index, row in input['geometry'].iteritems():
    clipped = gpd.clip(area_of_interest, row)
    clipped.to_file(os.path.join(output_path, f'{index}.shp'))

enter image description here

The only way of not getting filled polygons is passing as mask just the extent of the Area of Interest with total_bounds, but (predictably) the output is a shape with more geometry as needed:

input = gpd.read_file(original_shape)

clipped = gpd.clip(input, area_of_interest.total_bounds)


enter image description here

EDIT: Additional info

The problem seems to be when the result is written to a file. Plotting clipped apparently gives the expected outcome:


enter image description here


1 Answer 1


In case of invalid geometry, you might get a result like this.

Try make_valid function of shapely

from shapely.validation import make_valid

Before clipping:

input_df["geometry"] = input_df.geometry.apply(make_valid)

or after clipping:

clipped["geometry"] = clipped.geometry.apply(make_valid)

  • Thanks for the input. For better or worse, the geometry seems to be already valid and it doesn't have an impact on the outcome...
    – Jucjon
    Commented Apr 5, 2023 at 11:53
  • Could you share your data, if you don't mind? Commented Apr 5, 2023 at 11:55

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