I have recently switched to using the "zonal statistics as table- 2" supplemental tool instead of the regular "zonal statistics" because I have overlapping polygons which zonal statistics does not deal with. However, I have attempted running zonal statistics 2 a couple of times now and after running for many hours through the night it ends up encountering a fatal error and will not finish. I am not sure how to ameliorate this issue. I am trying to calculate mean elevation within over 100,000 buffer polygons, and will need to do this multiple times with other raster layers. Is there an alternative or a way to get the tool to complete the command?

2 Answers 2


To solve this you'll need to split your polygons into groups without overlap. It is called graph coloring.

To make script below work a)install networkx package and b)run:

PolygonNeighbors("POLYGONS", "neighbours", area_overlap="AREA_OVERLAP")


creates non-adjacent groups of polygons
import arcpy
import networkx as nx
infc = arcpy.GetParameterAsText(0)
table = arcpy.GetParameterAsText(1)

sourceList=[f.name for f in arcpy.ListFields(table)]
try:arcpy.AddField_management(infc, "COLOR","Short")

allGroups=sorted(nx.connected_components(G), key = len, reverse=True)

arcpy.AddMessage("%i connected groups found" %len(allGroups))
for item in allGroups:
    d = nx.coloring.greedy_color(subG, strategy=nx.coloring.strategy_largest_first)
    with arcpy.da.UpdateCursor(infc,("OID@","COLOR")) as cursor:
        for row in cursor:
            if row[0] not in item:continue

will add and populate field "COLOR" with numbers in range (1..4). This is theoretical range, expect something bigger, depending on extent of overlaps. I'd say the worst case scenario is 7 colors. You might hard code input feature class (infc) and adjacency table (table) if you don't want to assign script to tool with 2 parameters.

Note that script skips island polygons, this will result in None or 0 value in field COLOR depending on the source of feature class:

enter image description here

You have a couple of options on how to proceed:

  1. manually define n layers from POLYGONS using definition queries,e.g. "COLOR" = 1, run zonal statistics on each. Merge results.
  2. Write script or develop model to automate above tasks.

I suspect that this is exactly what zonal statistics 2 does behind the scenes, not sure why it's failing, unless you messed up processing extent and cell size environment settings or use different projections on raster and buffers.


Whenever I run into problems similar to yours I immediately suspect that the vector data has corrupt geometry. Use the Repair Geometry tool and see if that solves your problem.

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