I have a feature class of points, a few thousands I have now, but I expect to deal with hundreds of thousands of points.  I would like find pair of points that is within a specific distance.  The points I have is typically spread apart spatially so I don't expect to find many pairs.  How I can find those pairs.

Right now the points are originally from ESRI shape file, and read into geopandas geodataframe.  I tried to `tbl = df['geometry'].distance(df['geometry'])` see if I can get distance of all pairs.  <del>But I got the error "python: GeometryComponentFilter.cpp:34: virtual void geos::geom::GeometryComponentFilter::filter_ro(const geos::geom::Geometry*): Assertion `0' failed.".  Beside</del> But, I don't want to get full set of distance as I am only interested in points that are close to each other. 

I have a version of code which uses ArcGIS, and [GenerateNearTable_analysis][1] is what I used for the purpose.  

I want to run code with open source code now.  

My solution has to be python and should run on Linux.

  


  [1]: http://resources.arcgis.com/EN/HELP/MAIN/10.2/index.html#//00080000001n000000