Mask rasterio raster with geopandas shapefile

Question

I am loading a shapefile using geopandas as follows:

import geopandas as gpd
StudyA = gpd.read_file('.../Study_Area_Polygon.shp')

Next, I am using folium to plot it interactively:

m = folium.Map([36.43, 43.06], zoom_start=12)
folium.GeoJson(StudyA).add_to(m)
m

My objective is now to use rasterio to mask a raster using the shapefile I have loaded before with the following code:

img, out_transform = rasterio.mask.mask(img, StudyA, crop=True, all_touched=True)

However, I am facing an issue as the information of the mask should be provided as a list of GeoJSON-like dicts according to rasterio documentation. How can I produce that GeoJSON-like dicts when reading the shapefile with geopandas.

Previously, I was reading the shp using the following code and it worked well. The issue is that I want/need to use geopandas for interactive plotting with folium

with fiona.open(".../Study_Area_Polygon.shp", "r") as StudyArea:
    shape = [feature["geometry"] for feature in StudyArea]

Answer 1

If your geodataframe has a column named "geometry" and geometry consists of Shapely Polygons, the following works for me

from rasterio.mask import mask

out, _ = mask(data, gdf.geometry, invert=False)

Answer 2

Assuming you have a geodataframe (gdf), you can just pass the geometry values flattened to rasterio:

masked_raster, masked_raster_transform = rasterio.mask.mask(raster, gdf[['geometry']].values.flatten())

Answer 3

In case someone is interested in the future, I managed to make it work with the following code.

First, open an empty list. Then import the shp with geopandas. Next, we access the geometric information and extract it. The output of that is a dict containing the information required by rasterio.mask.mask

geom = []

StudyA = gpd.read_file('.../Study_Area_Polygon.shp')
coord = shapely.geometry.mapping(StudyA)["features"][0]["geometry"]
geom.append(coord)