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I'm trying to determine the number of points within a set of polygons for a large number of points. There are 2GB of lat-long coordinates in a CSV file, and I want to see how many are contained in each polygon.

The number of points seems too large to import as a layer of points and then do a spatial join.

Is there any alternative that works well with large datasets?

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    On the contrary, the file is too large to not load into a spatial dataset (FGDB or Enterprise GDB), spatially index, and query with the polygons. – Vince Jul 24 at 13:54
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    What happens when you load your points into a file geodatabase and try this? – PolyGeo Jul 24 at 20:34
  • I tried this and at the stage where I do the spatial join, it stops in the middle without completing it and does not give an error message. There are roughly 16 million observations. – user68479 Jul 26 at 4:02
  • I was able to solve the problem, and the size of the data size was not an issue. I think the problem was that I imported the GPS data in the wrong coordinate system. I also did some data cleaning before I imported the data again. A few observations had missing data. – user68479 Jul 30 at 15:31
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A CSV file is not a spatial dataset, it is nothing more than a comma separated text file. The only structure it has is the comma.

As the other commentators indicate you need to import it into a geodatabase. 2GB is well within their limits and once in as a spatial dataset with spatial indexing you could easily answer this question with a spatial Join.

Also EXCEL is not a spatial format either!

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