Question

I try to find the nearest point in geoida database for every point stored in second database.
Here’s may approach, which is extremely slow. geoida.db stores +55000 coordinates

import sqlite3
from kdtree import KDTree

database = sqlite3.connect('geoida.db')
cursor = database.cursor()
cursor.execute("select lat, lon  from coords")
geoid = cursor.fetchall()

database = sqlite3.connect('F.tsj')
cursor = database.cursor()
cursor.execute("select C1, C2 from tblSoPoints") 
results = cursor.fetchall()
for line in results:
    tree = KDTree.construct_from_data(geoid)
    nearest = tree.query(query_point=line, t=2)
    print nearest[0]

both databases contain latitudes and longitudes

Answer 1

Simply create the tree outside the loop:

tree = KDTree.construct_from_data(geoid)
for line in results:
  nearest = tree.query(query_point=line, t=2)