benchcdist.py

import numpy as np
import trimesh

import timeit
import time

from collections import deque

import matplotlib.pyplot as plt
from scipy.spatial import cKDTree as KDTree
from shapely.geometry import Polygon, Point, LineString
from trimesh import util, grouping
from trimesh.constants import tol

from scipy.sparse import coo_matrix
from scipy.sparse import csgraph
from scipy import spatial
import trimesh.transformations as tr
import networkx as nx
import numpy as np
import os

import subprocess


def tile(a, b):
    dim = a.shape[1]
    v_tile = np.tile(b, len(a)).reshape((-1, dim))
    # tile a per voronoi vertex
    p_tile = np.tile(a, (len(b), 1)).reshape((-1, dim))
    r2 = ((p_tile - v_tile)**2).sum(axis=1).reshape((len(b), -1)).max(axis=1)

    return r2

def cdist(a, b):
    radii_c = spatial.distance.cdist(
        b, a, metric='sqeuclidean').max(axis=1)
    return radii_c

def loop(a, b):
    radii_b = np.array([((a - v)**2).sum(axis=1).max()
                        for v in b])
    return radii_b

    
if __name__ == '__main__':

    trimesh.util.attach_to_log()

    m = trimesh.load('models/fuze.obj')
    b = trimesh.load('models/fuze.zip')

    globs = {'cdist': cdist,
             'loop': loop,
             'tile': tile,
             'np': np}

    for s in [(10, 10), (10, 100), (100, 10),
              (1000, 1000), (10000, 1000), (10000, 10000)]:
    
        a = np.random.random((s[0], 3))
        b = np.random.random((s[1], 3))

        setup = 'a=np.random.random(({},3));'
        setup += 'b=np.random.random(({},3))'
        setup = setup.format(*s)

        
        r = []; tic=[]; label = []

        for func in [tile, cdist, loop]:
            label.append(func.__name__)
            stmt = '{}(a,b)'.format(func.__name__)
            try:
                tic.append(min(timeit.repeat(stmt,
                                             setup=setup,
                                             number=3,
                                             globals=globs)))
            except MemoryError:
                tic.append(np.inf)
                continue
            r.append(func(a,b))
            
        # results should be the same
        assert np.array(r).ptp(axis=0).max() < 1e-10
        
        print('\na.shape: {}   b.shape: {}'.format(a.shape, b.shape))
        print('\n'.join('{}: {}'.format(l, t) for t,l in zip(tic, label)))