Faster way of polygon intersection with shapely

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Consider using Rtree to help identify which grid cells that a polygon may intersect. This way, you can remove the for loop used with the array of lat/lons, which is probably the slow part.

Structure your code something like this:

from shapely.ops import cascaded_union
from rtree import index
idx = index.Index()

# Populate R-tree index with bounds of grid cells
for pos, cell in enumerate(grid_cells):
    # assuming cell is a shapely object
    idx.insert(pos, cell.bounds)

# Loop through each Shapely polygon
for poly in polygons:
    # Merge cells that have overlapping bounding boxes
    merged_cells = cascaded_union([grid_cells[pos] for pos in idx.intersection(poly.bounds)])
    # Now do actual intersection
    print(poly.intersection(merged_cells).area)

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