Mercurial > hg > GlobalNeighbors
view globalneighbors/distance.py @ 2:50ee13cddf58
remove this test; the datafile was too large
author | Jeff Hammel <k0scist@gmail.com> |
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date | Sat, 24 Jun 2017 14:04:00 -0700 |
parents | 1b94f3bf97e5 |
children | 49aae0c0293b |
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""" distance functionality """ import argparse import json import sys import time from math import asin, sin, cos, sqrt, pi, fabs from .cli import CitiesParser from .constants import Rearth from .locations import locations from .read import read_cities from .schema import fields DEGREESTORADIANS = pi/180. def haversine(lat1, lon1, lat2, lon2, r=1): """ see https://en.wikipedia.org/wiki/Haversine_formula Coordinates in radians """ return 2*r*asin( sqrt(sin(0.5*(lat2-lat1))**2 +cos(lat1)*cos(lat2)*(sin(0.5*(lon2-lon1))**2) )) def deg_to_rad(degrees): return degrees*DEGREESTORADIANS def calculate_distances(locations, r=Rearth): """ WARNING! This is an N-squared approach """ # convert to rad rad_locations = [(location, tuple([deg_to_rad(i) for i in latlon])) for location, latlon in locations.items()] # use haversince function on N-body problem for index, loc1 in enumerate(rad_locations): id1, (lat1, lon1) = loc1 for loc2 in rad_locations[index+1:]: id2, (lat2, lon2) = loc2 key = (id1, id2) if id2 > id1 else (id2, id1) yield (key, haversine(lat1, lon1, lat2, lon2, r=r)) def calculate_neighbors(locations, k=10, lat_tol=1., lon_tol=1., output=1000, neighbors=None): """ calculate `k` nearest neighbors for each location """ neighbors = neighbors or {} items = locations.items() index = 0 n_items = len(items) start = int(time.time()) while items: index += 1 if not index % output: # output status counter now = int(time.time()) duration = now - start start = now print ('{},{},{},{}'.format(index, len(items), n_items, duration)) id1, (lat1, lon1) = items.pop() for loc2 in items: id2, (lat2, lon2) = loc2 # filter out locations based on latlon boxing if fabs(lat2 - lat1) > lat_tol: continue if fabs(lon2 - lon1) > lon_tol: continue # determine distance args = [deg_to_rad(i) for i in (lat1, lon1, lat2, lon2)] new_distance = haversine(*args, r=Rearth) # insert in order for i in (id1, id2): distances = neighbors.setdefault(i, []) if len(distances) == k and new_distance >= distances[-1][-1]: continue # TODO: Binary Search Tree for _index, (geoid, old_distance) in enumerate(distances): if new_distance < old_distance: distances.insert(_index, (i, new_distance)) if len(distances) == k+1: distances.pop() break else: distances.append((i, new_distance)) return neighbors def main(args=sys.argv[1:]): """CLI""" # parse command line arguments description = """write nearest neighborfiles""" parser = CitiesParser(description=description) parser.add_argument('output', type=argparse.FileType('w'), help="output file to dump JSON to") parser.add_argument('--counter', '--output-counter', dest='output_counter', type=int, default=100, help="how often to output progress updates [DEFAULT: %(default)s]") parser.add_argument('-k', dest='k', type=int, default=50, help="number of neighbors to determine [DEFAULT: %(default)s]") options = parser.parse_args(args) # parse cities cities = list(read_cities(options.cities, fields=fields)) # get locations city_locations = locations(cities) # calculate neighbors neighbors = calculate_neighbors(city_locations, k=options.k, output=options.output_counter) # output options.output.write(json.dumps(neighbors, indent=2)) if __name__ == '__main__': main()