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# Copyright (c) 2008-2016 MetPy Developers. |
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# Distributed under the terms of the BSD 3-Clause License. |
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# SPDX-License-Identifier: BSD-3-Clause |
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""" |
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Natural Neighbor Verification |
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============================= |
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Walks through the steps of Natural Neighbor interpolation to validate that the algorithmic |
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approach taken in MetPy is correct. |
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""" |
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########################################### |
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# Find natural neighbors visual test |
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# |
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# A triangle is a natural neighbor for a point if the |
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# `circumscribed circle <https://en.wikipedia.org/wiki/Circumscribed_circle>`_ of the |
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# triangle contains that point. It is important that we correctly grab the correct triangles |
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# for each point before proceeding with the interpolation. |
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# |
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# Algorithmically: |
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# |
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# 1. We place all of the grid points in a KDTree. These provide worst-case O(n) time |
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# complexity for spatial searches. |
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# |
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# 2. We generate a `Delaunay Triangulation <https://docs.scipy.org/doc/scipy/ |
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# reference/tutorial/spatial.html#delaunay-triangulations>`_ |
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# using the locations of the provided observations. |
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# |
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# 3. For each triangle, we calculate its circumcenter and circumradius. Using |
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# KDTree, we then assign each grid a triangle that has a circumcenter within a |
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# circumradius of the grid's location. |
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# |
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# 4. The resulting dictionary uses the grid index as a key and a set of natural |
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# neighbor triangles in the form of triangle codes from the Delaunay triangulation. |
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# This dictionary is then iterated through to calculate interpolation values. |
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# |
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# 5. We then traverse the ordered natural neighbor edge vertices for a particular |
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# grid cell in groups of 3 (n - 1, n, n + 1), and perform calculations to generate |
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# proportional polygon areas. |
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# |
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# Circumcenter of (n - 1), n, grid_location |
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# Circumcenter of (n + 1), n, grid_location |
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# |
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# Determine what existing circumcenters (ie, Delaunay circumcenters) are associated |
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# with vertex n, and add those as polygon vertices. Calculate the area of this polygon. |
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# |
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# 6. Increment the current edges to be checked, i.e.: |
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# n - 1 = n, n = n + 1, n + 1 = n + 2 |
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# |
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# 7. Repeat steps 5 & 6 until all of the edge combinations of 3 have been visited. |
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# |
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# 8. Repeat steps 4 through 7 for each grid cell. |
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import matplotlib.pyplot as plt |
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import numpy as np |
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from scipy.spatial import ConvexHull, Delaunay, delaunay_plot_2d, Voronoi, voronoi_plot_2d |
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from scipy.spatial.distance import euclidean |
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from metpy.gridding import polygons, triangles |
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from metpy.gridding.interpolation import nn_point |
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plt.rcParams['figure.figsize'] = (15, 10) |
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########################################### |
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# For a test case, we generate 10 random points and observations, where the |
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# observation values are just the x coordinate value times the y coordinate |
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# value divided by 1000. |
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# |
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# We then create two test points (grid 0 & grid 1) at which we want to |
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# estimate a value using natural neighbor interpolation. |
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# |
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# The locations of these observations are then used to generate a Delaunay triangulation. |
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np.random.seed(100) |
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pts = np.random.randint(0, 100, (10, 2)) |
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xp = pts[:, 0] |
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yp = pts[:, 1] |
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zp = (pts[:, 0] * pts[:, 0]) / 1000 |
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tri = Delaunay(pts) |
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delaunay_plot_2d(tri) |
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for i, zval in enumerate(zp): |
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plt.annotate('{} F'.format(zval), xy=(pts[i, 0] + 2, pts[i, 1])) |
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sim_gridx = [30., 60.] |
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sim_gridy = [30., 60.] |
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plt.plot(sim_gridx, sim_gridy, '+', markersize=10) |
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plt.axes().set_aspect('equal', 'datalim') |
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plt.title('Triangulation of observations and test grid cell ' |
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'natural neighbor interpolation values') |
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members, tri_info = triangles.find_natural_neighbors(tri, list(zip(sim_gridx, sim_gridy))) |
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val = nn_point(xp, yp, zp, (sim_gridx[0], sim_gridy[0]), tri, members[0], tri_info) |
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plt.annotate('grid 0: {:.3f}'.format(val), xy=(sim_gridx[0] + 2, sim_gridy[0])) |
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val = nn_point(xp, yp, zp, (sim_gridx[1], sim_gridy[1]), tri, members[1], tri_info) |
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plt.annotate('grid 1: {:.3f}'.format(val), xy=(sim_gridx[1] + 2, sim_gridy[1])) |
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########################################### |
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# Using the circumcenter and circumcircle radius information from |
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# :func:`metpy.gridding.triangles.find_natural_neighbors`, we can visually |
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# examine the results to see if they are correct. |
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def draw_circle(x, y, r, m, label): |
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nx = x + r * np.cos(np.deg2rad(list(range(360)))) |
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ny = y + r * np.sin(np.deg2rad(list(range(360)))) |
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plt.plot(nx, ny, m, label=label) |
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members, tri_info = triangles.find_natural_neighbors(tri, list(zip(sim_gridx, sim_gridy))) |
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delaunay_plot_2d(tri) |
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plt.plot(sim_gridx, sim_gridy, 'ks', markersize=10) |
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for i, info in tri_info.items(): |
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x_t = info['cc'][0] |
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y_t = info['cc'][1] |
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if i in members[1] and i in members[0]: |
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draw_circle(x_t, y_t, info['r'], 'm-', str(i) + ': grid 1 & 2') |
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plt.annotate(str(i), xy=(x_t, y_t), fontsize=15) |
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elif i in members[0]: |
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draw_circle(x_t, y_t, info['r'], 'r-', str(i) + ': grid 0') |
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plt.annotate(str(i), xy=(x_t, y_t), fontsize=15) |
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elif i in members[1]: |
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draw_circle(x_t, y_t, info['r'], 'b-', str(i) + ': grid 1') |
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plt.annotate(str(i), xy=(x_t, y_t), fontsize=15) |
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else: |
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draw_circle(x_t, y_t, info['r'], 'k:', str(i) + ': no match') |
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plt.annotate(str(i), xy=(x_t, y_t), fontsize=9) |
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plt.axes().set_aspect('equal', 'datalim') |
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plt.legend() |
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########################################### |
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# What?....the circle from triangle 8 looks pretty darn close. Why isn't |
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# grid 0 included in that circle? |
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x_t, y_t = tri_info[8]['cc'] |
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r = tri_info[8]['r'] |
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print('Distance between grid0 and Triangle 8 circumcenter:', |
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euclidean([x_t, y_t], [sim_gridx[0], sim_gridy[0]])) |
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print('Triangle 8 circumradius:', r) |
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########################################### |
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# Lets do a manual check of the above interpolation value for grid 0 (southernmost grid) |
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# Grab the circumcenters and radii for natural neighbors |
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cc = np.array([tri_info[m]['cc'] for m in members[0]]) |
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r = np.array([tri_info[m]['r'] for m in members[0]]) |
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print('circumcenters:\n', cc) |
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print('radii\n', r) |
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########################################### |
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# Draw the natural neighbor triangles and their circumcenters. Also plot a `Voronoi diagram |
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# <https://docs.scipy.org/doc/scipy/reference/tutorial/spatial.html#voronoi-diagrams>`_ |
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# which serves as a complementary (but not necessary) |
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# spatial data structure that we use here simply to show areal ratios. |
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# Notice that the two natural neighbor triangle circumcenters are also vertices |
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# in the Voronoi plot (green dots), and the observations are in the the polygons (blue dots). |
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vor = Voronoi(list(zip(xp, yp))) |
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voronoi_plot_2d(vor) |
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nn_ind = np.array([0, 5, 7, 8]) |
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z_0 = zp[nn_ind] |
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x_0 = xp[nn_ind] |
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y_0 = yp[nn_ind] |
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for x, y, z in zip(x_0, y_0, z_0): |
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plt.annotate('{}, {}: {:.3f} F'.format(x, y, z), xy=(x, y)) |
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plt.plot(sim_gridx[0], sim_gridy[0], 'k+', markersize=10) |
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plt.annotate('{}, {}'.format(sim_gridx[0], sim_gridy[0]), xy=(sim_gridx[0] + 2, sim_gridy[0])) |
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plt.plot(cc[:, 0], cc[:, 1], 'ks', markersize=15, fillstyle='none', |
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label='natural neighbor\ncircumcenters') |
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for center in cc: |
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plt.annotate('{:.3f}, {:.3f}'.format(center[0], center[1]), |
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xy=(center[0] + 1, center[1] + 1)) |
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tris = tri.points[tri.simplices[members[0]]] |
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for triangle in tris: |
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x = [triangle[0, 0], triangle[1, 0], triangle[2, 0], triangle[0, 0]] |
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y = [triangle[0, 1], triangle[1, 1], triangle[2, 1], triangle[0, 1]] |
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plt.plot(x, y, ':', linewidth=2) |
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plt.legend() |
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plt.axes().set_aspect('equal', 'datalim') |
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def draw_polygon_with_info(polygon, off_x=0, off_y=0): |
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"""Draw one of the natural neighbor polygons with some information.""" |
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pts = np.array(polygon)[ConvexHull(polygon).vertices] |
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for i, pt in enumerate(pts): |
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plt.plot([pt[0], pts[(i + 1) % len(pts)][0]], |
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[pt[1], pts[(i + 1) % len(pts)][1]], 'k-') |
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avex, avey = np.mean(pts, axis=0) |
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plt.annotate('area: {:.3f}'.format(polygons.area(pts)), xy=(avex + off_x, avey + off_y), |
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fontsize=12) |
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cc1 = triangles.circumcenter((53, 66), (15, 60), (30, 30)) |
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cc2 = triangles.circumcenter((34, 24), (53, 66), (30, 30)) |
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draw_polygon_with_info([cc[0], cc1, cc2]) |
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cc1 = triangles.circumcenter((53, 66), (15, 60), (30, 30)) |
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cc2 = triangles.circumcenter((15, 60), (8, 24), (30, 30)) |
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draw_polygon_with_info([cc[0], cc[1], cc1, cc2], off_x=-9, off_y=3) |
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cc1 = triangles.circumcenter((8, 24), (34, 24), (30, 30)) |
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cc2 = triangles.circumcenter((15, 60), (8, 24), (30, 30)) |
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draw_polygon_with_info([cc[1], cc1, cc2], off_x=-15) |
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cc1 = triangles.circumcenter((8, 24), (34, 24), (30, 30)) |
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cc2 = triangles.circumcenter((34, 24), (53, 66), (30, 30)) |
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draw_polygon_with_info([cc[0], cc[1], cc1, cc2]) |
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########################################### |
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# Put all of the generated polygon areas and their affiliated values in arrays. |
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# Calculate the total area of all of the generated polygons. |
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areas = np.array([60.434, 448.296, 25.916, 70.647]) |
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values = np.array([0.064, 1.156, 2.809, 0.225]) |
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total_area = np.sum(areas) |
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print(total_area) |
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########################################### |
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# For each polygon area, calculate its percent of total area. |
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proportions = areas / total_area |
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print(proportions) |
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########################################### |
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# Multiply the percent of total area by the respective values. |
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contributions = proportions * values |
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print(contributions) |
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########################################### |
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# The sum of this array is the interpolation value! |
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interpolation_value = np.sum(contributions) |
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function_output = nn_point(xp, yp, zp, (sim_gridx[0], sim_gridy[0]), tri, members[0], tri_info) |
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print(interpolation_value, function_output) |
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########################################### |
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# The values are slightly different due to truncating the area values in |
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# the above visual example to the 3rd decimal place. |
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Unidata /
MetPy
