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I run my script from the command prompt. I also just tried running through your steps in the Python command window within ArcGIS. Same result as before - the array contains one more row than the raster does.

spalka
– spalka

2017-04-05 20:33:37 +00:00
Commented Apr 5, 2017 at 20:33
Snap raster and cell size in environment settings?

FelixIP
– FelixIP

2017-04-05 20:55:22 +00:00
Commented Apr 5, 2017 at 20:55
Snap raster and cell size are both set to the input raster values. I am still seeing the row difference.

spalka
– spalka

2017-04-05 20:59:00 +00:00
Commented Apr 5, 2017 at 20:59

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