|
|
import numpy as np |
|
|
|
|
|
from pykdtree.kdtree import KDTree |
|
|
|
|
|
|
|
|
data_pts_real = np.array([[ 790535.062, -369324.656, 6310963.5 ], |
|
|
[ 790024.312, -365155.688, 6311270. ], |
|
|
[ 789515.75 , -361009.469, 6311572. ], |
|
|
[ 789011. , -356886.562, 6311869.5 ], |
|
|
[ 788508.438, -352785.969, 6312163. ], |
|
|
[ 788007.25 , -348707.219, 6312452. ], |
|
|
[ 787509.188, -344650.875, 6312737. ], |
|
|
[ 787014.438, -340616.906, 6313018. ], |
|
|
[ 786520.312, -336604.156, 6313294.5 ], |
|
|
[ 786030.312, -332613.844, 6313567. ], |
|
|
[ 785541.562, -328644.375, 6313835.5 ], |
|
|
[ 785054.75 , -324696.031, 6314100.5 ], |
|
|
[ 784571.188, -320769.5 , 6314361.5 ], |
|
|
[ 784089.312, -316863.562, 6314618.5 ], |
|
|
[ 783610.562, -312978.719, 6314871.5 ], |
|
|
[ 783133. , -309114.312, 6315121. ], |
|
|
[ 782658.25 , -305270.531, 6315367. ], |
|
|
[ 782184.312, -301446.719, 6315609. ], |
|
|
[ 781715.062, -297643.844, 6315847.5 ], |
|
|
[ 781246.188, -293860.281, 6316083. ], |
|
|
[ 780780.125, -290096.938, 6316314.5 ], |
|
|
[ 780316.312, -286353.469, 6316542.5 ], |
|
|
[ 779855.625, -282629.75 , 6316767.5 ], |
|
|
[ 779394.75 , -278924.781, 6316988.5 ], |
|
|
[ 778937.312, -275239.625, 6317206.5 ], |
|
|
[ 778489.812, -271638.094, 6317418. ], |
|
|
[ 778044.688, -268050.562, 6317626. ], |
|
|
[ 777599.688, -264476.75 , 6317831.5 ], |
|
|
[ 777157.625, -260916.859, 6318034. ], |
|
|
[ 776716.688, -257371.125, 6318233.5 ], |
|
|
[ 776276.812, -253838.891, 6318430.5 ], |
|
|
[ 775838.125, -250320.266, 6318624.5 ], |
|
|
[ 775400.75 , -246815.516, 6318816.5 ], |
|
|
[ 774965.312, -243324.953, 6319005. ], |
|
|
[ 774532.062, -239848.25 , 6319191. ], |
|
|
[ 774100.25 , -236385.516, 6319374.5 ], |
|
|
[ 773667.875, -232936.016, 6319555.5 ], |
|
|
[ 773238.562, -229500.812, 6319734. ], |
|
|
[ 772810.938, -226079.562, 6319909.5 ], |
|
|
[ 772385.25 , -222672.219, 6320082.5 ], |
|
|
[ 771960. , -219278.5 , 6320253. ], |
|
|
[ 771535.938, -215898.609, 6320421. ], |
|
|
[ 771114. , -212532.625, 6320587. ], |
|
|
[ 770695. , -209180.859, 6320749.5 ], |
|
|
[ 770275.25 , -205842.562, 6320910.5 ], |
|
|
[ 769857.188, -202518.125, 6321068.5 ], |
|
|
[ 769442.312, -199207.844, 6321224.5 ], |
|
|
[ 769027.812, -195911.203, 6321378. ], |
|
|
[ 768615.938, -192628.859, 6321529. ], |
|
|
[ 768204.688, -189359.969, 6321677.5 ], |
|
|
[ 767794.062, -186104.844, 6321824. ], |
|
|
[ 767386.25 , -182864.016, 6321968.5 ], |
|
|
[ 766980.062, -179636.969, 6322110. ], |
|
|
[ 766575.625, -176423.75 , 6322249.5 ], |
|
|
[ 766170.688, -173224.172, 6322387. ], |
|
|
[ 765769.812, -170038.984, 6322522.5 ], |
|
|
[ 765369.5 , -166867.312, 6322655. ], |
|
|
[ 764970.562, -163709.594, 6322786. ], |
|
|
[ 764573. , -160565.781, 6322914.5 ], |
|
|
[ 764177.75 , -157435.938, 6323041. ], |
|
|
[ 763784.188, -154320.062, 6323165.5 ], |
|
|
[ 763392.375, -151218.047, 6323288. ], |
|
|
[ 763000.938, -148129.734, 6323408. ], |
|
|
[ 762610.812, -145055.344, 6323526.5 ], |
|
|
[ 762224.188, -141995.141, 6323642.5 ], |
|
|
[ 761847.188, -139025.734, 6323754. ], |
|
|
[ 761472.375, -136066.312, 6323863.5 ], |
|
|
[ 761098.125, -133116.859, 6323971.5 ], |
|
|
[ 760725.25 , -130177.484, 6324077.5 ], |
|
|
[ 760354. , -127247.984, 6324181.5 ], |
|
|
[ 759982.812, -124328.336, 6324284.5 ], |
|
|
[ 759614. , -121418.844, 6324385. ], |
|
|
[ 759244.688, -118519.102, 6324484.5 ], |
|
|
[ 758877.125, -115629.305, 6324582. ], |
|
|
[ 758511.562, -112749.648, 6324677.5 ], |
|
|
[ 758145.625, -109879.82 , 6324772.5 ], |
|
|
[ 757781.688, -107019.953, 6324865. ], |
|
|
[ 757418.438, -104170.047, 6324956. ], |
|
|
[ 757056.562, -101330.125, 6325045.5 ], |
|
|
[ 756697. , -98500.266, 6325133.5 ], |
|
|
[ 756337.375, -95680.289, 6325219.5 ], |
|
|
[ 755978.062, -92870.148, 6325304.5 ], |
|
|
[ 755621.188, -90070.109, 6325387.5 ], |
|
|
[ 755264.625, -87280.008, 6325469. ], |
|
|
[ 754909.188, -84499.828, 6325549. ], |
|
|
[ 754555.062, -81729.609, 6325628. ], |
|
|
[ 754202.938, -78969.43 , 6325705. ], |
|
|
[ 753850.688, -76219.133, 6325781. ], |
|
|
[ 753499.875, -73478.836, 6325855. ], |
|
|
[ 753151.375, -70748.578, 6325927.5 ], |
|
|
[ 752802.312, -68028.188, 6325999. ], |
|
|
[ 752455.75 , -65317.871, 6326068.5 ], |
|
|
[ 752108.625, -62617.344, 6326137.5 ], |
|
|
[ 751764.125, -59926.969, 6326204.5 ], |
|
|
[ 751420.125, -57246.434, 6326270. ], |
|
|
[ 751077.438, -54575.902, 6326334.5 ], |
|
|
[ 750735.312, -51915.363, 6326397.5 ], |
|
|
[ 750396.188, -49264.852, 6326458.5 ], |
|
|
[ 750056.375, -46624.227, 6326519. ], |
|
|
[ 749718.875, -43993.633, 6326578. ]]) |
|
|
|
|
|
def test1d(): |
|
|
|
|
|
data_pts = np.arange(1000) |
|
|
kdtree = KDTree(data_pts, leafsize=15) |
|
|
query_pts = np.arange(400, 300, -10) |
|
|
dist, idx = kdtree.query(query_pts) |
|
|
assert idx[0] == 400 |
|
|
assert dist[0] == 0 |
|
|
assert idx[1] == 390 |
|
|
|
|
|
def test3d(): |
|
|
|
|
|
|
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
dist, idx = kdtree.query(query_pts, sqr_dists=True) |
|
|
|
|
|
epsilon = 1e-5 |
|
|
assert idx[0] == 7 |
|
|
assert idx[1] == 93 |
|
|
assert idx[2] == 45 |
|
|
assert dist[0] == 0 |
|
|
assert abs(dist[1] - 3.) < epsilon * dist[1] |
|
|
assert abs(dist[2] - 20001.) < epsilon * dist[2] |
|
|
|
|
|
def test3d_float32(): |
|
|
|
|
|
|
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]], dtype=np.float32) |
|
|
|
|
|
|
|
|
kdtree = KDTree(data_pts_real.astype(np.float32)) |
|
|
dist, idx = kdtree.query(query_pts, sqr_dists=True) |
|
|
epsilon = 1e-5 |
|
|
assert idx[0] == 7 |
|
|
assert idx[1] == 93 |
|
|
assert idx[2] == 45 |
|
|
assert dist[0] == 0 |
|
|
assert abs(dist[1] - 3.) < epsilon * dist[1] |
|
|
assert abs(dist[2] - 20001.) < epsilon * dist[2] |
|
|
assert kdtree.data_pts.dtype == np.float32 |
|
|
|
|
|
def test3d_float32_mismatch(): |
|
|
|
|
|
|
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]], dtype=np.float32) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
dist, idx = kdtree.query(query_pts, sqr_dists=True) |
|
|
|
|
|
def test3d_float32_mismatch2(): |
|
|
|
|
|
|
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real.astype(np.float32)) |
|
|
try: |
|
|
dist, idx = kdtree.query(query_pts, sqr_dists=True) |
|
|
assert False |
|
|
except TypeError: |
|
|
assert True |
|
|
|
|
|
|
|
|
def test3d_8n(): |
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
dist, idx = kdtree.query(query_pts, k=8) |
|
|
|
|
|
exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, |
|
|
8.17063009e+03, 1.20904577e+04, 1.22902057e+04, 1.60775136e+04], |
|
|
[ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, |
|
|
5.43793210e+03, 8.07855631e+03, 8.17119970e+03, 1.07513693e+04], |
|
|
[ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, |
|
|
6.81038455e+03, 9.89140135e+03, 1.01918659e+04, 1.31892516e+04]]) |
|
|
|
|
|
exp_idx = np.array([[ 7, 8, 6, 9, 5, 10, 4, 11], |
|
|
[93, 94, 92, 95, 91, 96, 90, 97], |
|
|
[45, 46, 44, 47, 43, 48, 42, 49]]) |
|
|
|
|
|
assert np.array_equal(idx, exp_idx) |
|
|
assert np.allclose(dist, exp_dist) |
|
|
|
|
|
def test3d_8n_ub(): |
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
dist, idx = kdtree.query(query_pts, k=8, distance_upper_bound=10e3, sqr_dists=False) |
|
|
|
|
|
exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, |
|
|
8.17063009e+03, np.Inf, np.Inf, np.Inf], |
|
|
[ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, |
|
|
5.43793210e+03, 8.07855631e+03, 8.17119970e+03, np.Inf], |
|
|
[ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, |
|
|
6.81038455e+03, 9.89140135e+03, np.Inf, np.Inf]]) |
|
|
n = 100 |
|
|
exp_idx = np.array([[ 7, 8, 6, 9, 5, n, n, n], |
|
|
[93, 94, 92, 95, 91, 96, 90, n], |
|
|
[45, 46, 44, 47, 43, 48, n, n]]) |
|
|
|
|
|
assert np.array_equal(idx, exp_idx) |
|
|
assert np.allclose(dist, exp_dist) |
|
|
|
|
|
def test3d_8n_ub_leaf20(): |
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real, leafsize=20) |
|
|
dist, idx = kdtree.query(query_pts, k=8, distance_upper_bound=10e3, sqr_dists=False) |
|
|
|
|
|
exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, |
|
|
8.17063009e+03, np.Inf, np.Inf, np.Inf], |
|
|
[ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, |
|
|
5.43793210e+03, 8.07855631e+03, 8.17119970e+03, np.Inf], |
|
|
[ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, |
|
|
6.81038455e+03, 9.89140135e+03, np.Inf, np.Inf]]) |
|
|
n = 100 |
|
|
exp_idx = np.array([[ 7, 8, 6, 9, 5, n, n, n], |
|
|
[93, 94, 92, 95, 91, 96, 90, n], |
|
|
[45, 46, 44, 47, 43, 48, n, n]]) |
|
|
|
|
|
assert np.array_equal(idx, exp_idx) |
|
|
assert np.allclose(dist, exp_dist) |
|
|
|
|
|
def test3d_8n_ub_eps(): |
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
dist, idx = kdtree.query(query_pts, k=8, eps=0.1, distance_upper_bound=10e3, sqr_dists=False) |
|
|
|
|
|
exp_dist = np.array([[ 0.00000000e+00, 4.05250235e+03, 4.07389794e+03, 8.08201128e+03, |
|
|
8.17063009e+03, np.Inf, np.Inf, np.Inf], |
|
|
[ 1.73205081e+00, 2.70216896e+03, 2.71431274e+03, 5.39537066e+03, |
|
|
5.43793210e+03, 8.07855631e+03, 8.17119970e+03, np.Inf], |
|
|
[ 1.41424892e+02, 3.25500021e+03, 3.44284958e+03, 6.58019346e+03, |
|
|
6.81038455e+03, 9.89140135e+03, np.Inf, np.Inf]]) |
|
|
n = 100 |
|
|
exp_idx = np.array([[ 7, 8, 6, 9, 5, n, n, n], |
|
|
[93, 94, 92, 95, 91, 96, 90, n], |
|
|
[45, 46, 44, 47, 43, 48, n, n]]) |
|
|
|
|
|
assert np.array_equal(idx, exp_idx) |
|
|
assert np.allclose(dist, exp_dist) |
|
|
|
|
|
def test3d_large_query(): |
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
|
|
|
n = 20000 |
|
|
query_pts = np.repeat(query_pts, n, axis=0) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
dist, idx = kdtree.query(query_pts, sqr_dists=True) |
|
|
|
|
|
epsilon = 1e-5 |
|
|
assert np.all(idx[:n] == 7) |
|
|
assert np.all(idx[n:2*n] == 93) |
|
|
assert np.all(idx[2*n:] == 45) |
|
|
assert np.all(dist[:n] == 0) |
|
|
assert np.all(abs(dist[n:2*n] - 3.) < epsilon * dist[n:2*n]) |
|
|
assert np.all(abs(dist[2*n:] - 20001.) < epsilon * dist[2*n:]) |
|
|
|
|
|
def test_scipy_comp(): |
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
assert id(kdtree.data) == id(kdtree.data_pts) |
|
|
|
|
|
|
|
|
def test1d_mask(): |
|
|
data_pts = np.arange(1000) |
|
|
|
|
|
np.random.shuffle(data_pts) |
|
|
bad_idx = np.nonzero(data_pts == 400) |
|
|
nearest_idx_1 = np.nonzero(data_pts == 399) |
|
|
nearest_idx_2 = np.nonzero(data_pts == 390) |
|
|
kdtree = KDTree(data_pts, leafsize=15) |
|
|
|
|
|
|
|
|
query_pts = np.arange(399.9, 299.9, -10) |
|
|
query_mask = np.zeros(data_pts.shape[0]).astype(bool) |
|
|
query_mask[bad_idx] = True |
|
|
dist, idx = kdtree.query(query_pts, mask=query_mask) |
|
|
assert idx[0] == nearest_idx_1 |
|
|
assert np.isclose(dist[0], 0.9) |
|
|
assert idx[1] == nearest_idx_2 |
|
|
assert np.isclose(dist[1], 0.1) |
|
|
|
|
|
|
|
|
def test1d_all_masked(): |
|
|
data_pts = np.arange(1000) |
|
|
np.random.shuffle(data_pts) |
|
|
kdtree = KDTree(data_pts, leafsize=15) |
|
|
query_pts = np.arange(400, 300, -10) |
|
|
query_mask = np.ones(data_pts.shape[0]).astype(bool) |
|
|
dist, idx = kdtree.query(query_pts, mask=query_mask) |
|
|
|
|
|
assert np.all(i >= 1000 for i in idx) |
|
|
assert np.all(d >= 1001 for d in dist) |
|
|
|
|
|
|
|
|
def test3d_mask(): |
|
|
|
|
|
query_pts = np.array([[ 787014.438, -340616.906, 6313018.], |
|
|
[751763.125, -59925.969, 6326205.5], |
|
|
[769957.188, -202418.125, 6321069.5]]) |
|
|
|
|
|
kdtree = KDTree(data_pts_real) |
|
|
query_mask = np.zeros(data_pts_real.shape[0]) |
|
|
query_mask[6:10] = True |
|
|
dist, idx = kdtree.query(query_pts, sqr_dists=True, mask=query_mask) |
|
|
|
|
|
epsilon = 1e-5 |
|
|
assert idx[0] == 5 |
|
|
assert idx[1] == 93 |
|
|
assert idx[2] == 45 |
|
|
|
|
|
assert abs(dist[0] - 66759196.1053) < epsilon * dist[0] |
|
|
assert abs(dist[1] - 3.) < epsilon * dist[1] |
|
|
assert abs(dist[2] - 20001.) < epsilon * dist[2] |
|
|
|
