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I have a Uniform Grid of 1KMx1KM squares as a shapefile with population data in each grid in a specific column as an integer. I would like to extrude each polygon based on the population and export the whole dataset using a python library. ArcScene can do this, but ArcPy can't hook into that program.

Can someone recommend a python package to do this?

It doesn't have to be dependent on ArcGIS Desktop.

I was looking at matplotlib, but I can't figure out how to create 3D bar graphs.

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It is only necessary to learn matplotlib using the examples provided.

enter image description here

or on StackOverFlow:

You only must adapt the script to your grid (look at Visualize shapefile in Python)

As Kelsey says, you can also use Mayavi or visvis

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