Restored usage of numpy in `_mask_with_shp` (#2209) #1334

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Run time

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Job	Run time
Linux Python 3.9	4m 35s
Linux Python 3.10	4m 56s
Linux Python 3.11	4m 55s
OSX Python 3.9	12m 57s
OSX Python 3.10	12m 50s
OSX Python 3.11	13m 21s
	53m 34s