I wish to do some basic preprocessing on 3D maps (EMDB .map files), in python.
The steps I wish to carry out are -

1. open a file, and read as numpy array,
2. apply c_value contour (to get the surface of the enclosed structure),
3. remove dust (and apply filters),
4. reshape, e.g. initial volume (560,560,600) to (100,100,100) without distorting (padding with zeros if necessary)

I can load the map as numpy array as -

input_map = gemmi.read_ccp4_map(fname)
map_3d_array = np.array(input_map.grid, copy=False)

However, is it also possible to do the step 2, 3, and 4?
I am aware of chimera, but I wish to do it within my own python script.
Any help is highly appreciated.