Artifacts in a filled contour plot on 3D axes

Question

I have a frustrating problem that only manifests itself when plotting filled contour plots on 3D axes and only in certain situations.

Here is an example of the issue I am experiencing:

and

These are the same data at different contouring intervals. You'll notice on the left side of the domain there is mis-filling occurring. This is a plot with the Z points squished into the Z=0 plane, via a plotting command like

ax3d.contourf(X, Y, dbz[z25,:,:], zdir='z', offset=0, levels=levels, cmap='pymeteo_radar', alpha=0.50)

The miscontouring happens regardless of alpha level or colormap used, but is sensitive to the number of levels. The use of zdir and offset do not effect the mis-contouring (the artifact just occurs on the Z surface. If I do not fill the contour, there is no mis-contouring. I can also alter the domain to sometimes make the issue better (or worse), but I have many plots to make within the same domain so that is not a fix.

This issue does not occur when the same data is plotted on 2D axes, e.g.:

This plot has some extra data on it, but you can see that the filled contouring does not have the same artifact from mis-filling the contour that occurs on the 3d axes.

Below is a script you can run to reproduce the issue.

#!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d.axes3d as p3

data=np.array([[53.9751,  51.5681,  50.7119,  51.1049,  51.5339,  51.4977,  51.2387,50.761,  50.1732,  49.8218,  49.5442,  48.936,  47.4498,  46.6484, 45.8542,  45.136,  44.5268,  44.071,  43.7665,  43.5928,  43.5269, 43.5385,  43.6053,  45.565,  47.0071,  46.8664,  47.372,  47.8324, 48.295,  48.731,  49.0522,  49.4001,  49.7111,  49.9919,  50.2527, 50.4928,  50.7135,  50.8831,  51.0806,  51.2683 ],
               [55.6671,  52.53,  50.7764,  50.5632,  51.2095,  51.5659,  51.521,  51.2143,  50.653,  50.2371,  49.989,  49.8089,  49.6058,  47.8355, 47.3124,  46.7346,  46.1616,  45.6498,  45.2462,  44.967,  44.8005, 44.7284,  44.7295,  44.7869,  46.959,  45.0194,  46.73,  48.0766, 48.9395,  49.5325,  49.8498,  50.1887,  50.4798,  50.7406,  50.9808, 51.2003,  51.4074,  51.555,  51.7429,  51.9218 ],
               [56.6513,  53.5919,  51.2774,  50.3133,  50.7705,  51.533,  51.8287, 51.7083,  51.2816,  50.7933,  50.4806,  50.2671,  50.1009,  50.0096, 49.9052,  49.4698,  47.4655,  47.0717,  46.6849,  46.3583,  46.1122, 45.952,  45.8678,  45.8485,  45.8811,  45.956,  46.0634,  47.2225, 49.4363,  50.2482,  50.527,  50.8558,  51.1358,  51.3809,  51.607, 51.8179,  52.0161,  52.1454,  52.3263,  52.497 ],
               [57.078,  54.3224,  52.0759,  50.4679,  50.4677,  51.297,  52.0284, 52.1594,  51.9395,  51.5518,  51.1419,  50.8765,  50.6686,  50.5101, 50.4078,  50.3473,  50.3592,  50.3813,  49.7504,  47.55,  47.324, 47.1365,  46.9978,  46.9119,  46.8743,  46.8811,  46.9257,  47.0013, 50.0148,  50.9106,  51.1133,  51.4282,  51.7064,  51.943,  52.1587, 52.3597,  52.4789,  52.6631,  52.8359,  52.9966 ],
               [57.3835,  54.9025,  52.8571,  50.9842,  50.5197,  51.1494,  52.0599, 52.4732,  52.4716,  52.2656,  51.9535,  51.6068,  51.3466,  51.1513, 50.9708,  50.8321,  50.7639,  50.7944,  50.8817,  49.8122,  48.2038, 48.086,  47.9704,  47.8735,  47.8035,  47.7644,  47.7574,  47.7803, 50.8194,  51.5486,  51.6645,  51.9745,  52.2349,  52.4508,  52.6481, 52.8317,  52.9412,  53.1097,  53.2699,  53.4171 ],
               [57.9157,  55.6092,  53.6306,  51.8011,  50.9372,  51.2615,  52.1406, 52.7436,  52.8528,  52.7829,  52.6322,  52.403,  52.1149,  51.866, 51.6624,  51.4773,  51.317,  51.2183,  51.2153,  51.1367,  48.5913, 48.6216,  48.6218,  48.5951,  48.5589,  48.527,  48.5081,  50.5185, 51.6998,  51.905,  52.2258,  52.4891,  52.7062,  52.8926,  53.0655, 53.2251,  53.3262,  53.4755,  53.6169,  53.7471 ],
               [58.6093,  56.432,  54.307,  52.6277,  51.584,  51.6482,  52.3762, 53.0685,  53.2545,  53.217,  53.1356,  53.0351,  52.8481,  52.6154, 52.39,  52.177,  51.9977,  51.843,  51.7172,  51.4587,  48.7481,  48.7984, 48.864,  48.9291,  48.9843,  49.0228,  50.496,  51.8667,  52.3404, 52.4759,  52.6889,  52.8851,  53.0525,  53.2072,  53.354,  53.4576, 53.5925,  53.7217,  53.8432,  53.956 ],
               [58.9719,  56.9885,  54.8768,  53.3526,  52.3025,  52.2089,  52.7762, 53.4444,  53.6768,  53.6706,  53.5692,  53.5162,  53.4373,  53.2886, 53.1113,  52.9065,  52.6988,  52.5193,  52.3544,  52.0384,  48.9624, 48.9653,  49.0005,  49.0574,  49.1258,  50.692,  51.9726,  52.4309, 52.699,  52.8194,  52.9845,  53.1336,  53.2669,  53.393,  53.5118, 53.6086,  53.7213,  53.8293,  53.9308,  54.026 ],
              [58.5754,  56.945,  55.068,  53.7798,  52.9469,  52.854,  53.3136,53.8929,  54.1205,  54.1178,  54.0128,  53.9289,  53.8906,  53.8239,53.717,  53.5724,  53.3818,  53.1892,  53.009,  49.3078,  49.2524,49.2165,  49.2032,  49.2187,  50.463,  51.9497,  52.4487,  52.7041,52.8358,  52.9776,  53.1101,  53.2293,  53.3419,  53.4487,  53.5401,53.6365,  53.7301,  53.8205,  53.9062,  53.9869 ],
              [57.623,  56.547,  55.0117,  54.0512,  53.5372,  53.5246,  53.927,54.3868,  54.5828,  54.5811,  54.4501,  54.3235,  54.2626,  54.2334,54.1802,  54.1137,  53.9897,  53.8202,  49.796,  49.6864,  49.5946,49.5216,  49.4703,  49.4432,  51.8479,  52.5574,  52.8359,  52.9722,53.0827,  53.1826,  53.2747,  53.3597,  53.4405,  53.5138,  53.5944,53.6751,  53.7536,  53.829,  53.9019,  53.9721 ],
              [56.902,  56.0005,  54.9159,  54.3352,  54.123,  54.2014,  54.5659,54.8917,  55.0307,  55.0139,  54.8838,  54.7044,  54.5863,  54.5548,54.5258,  54.4957,  54.4633,  51.4821,  50.1897,  50.0758,  49.9683,49.8704,  49.7842,  51.5064,  52.7625,  53.0724,  53.1926,  53.2682,53.3404,  53.4119,  53.4831,  53.5517,  53.6169,  53.6763,  53.7383,53.8009,  53.8644,  53.9281,  53.9905,  54.0517 ],
              [56.3455,  55.5524,  54.9336,  54.6836,  54.703,  54.8657,  55.1749,55.3844,  55.4521,  55.4019,  55.2622,  55.0281,  54.8981,  54.6591,54.7866,  54.7678,  54.7654,  54.0436,  54.2302,  52.2533,  50.3305,50.2276,  50.1268,  52.9617,  53.4395,  53.5504,  53.5481,  53.5524,53.5699,  53.6014,  53.644,  53.6931,  53.7445,  53.7996,  53.8548,53.9097,  53.9655,  54.0229,  54.0813,  54.1393 ],
              [55.7493,  55.3019,  55.1012,  55.0906,  55.234,  55.4751,  55.7134,55.8462,  55.8461,  55.7425,  55.5725,  55.3535,  55.1612,  54.958,55.0193,  54.9584,  54.9531,  54.8886,  54.8256,  54.2211,  50.6477,50.5564,  53.0546,  53.8592,  54.08,  54.0288,  53.9509,  53.8796,53.8307,  53.8073,  53.8034,  53.8142,  53.8383,  53.8725,  53.9128,53.9558,  54.0013,  54.0497,  54.103,  54.1597 ],
              [55.2575,  55.1664,  55.3165,  55.5004,  55.7345,  55.9901,  56.1852,56.2599,  56.2027,  56.0454,  55.818,  55.5754,  55.302,  55.2083,55.0224,  55.1415,  55.0656,  55.0446,  55.0263,  54.7728,  50.8924,53.4671,  54.2587,  54.5146,  54.6171,  54.519,  54.3857,  54.2497,54.1355,  54.0509,  53.9932,  53.9584,  53.941,  53.939,  53.9527,53.9798,  54.0111,  54.0465,  54.0868,  54.1339 ],
              [54.8665,  55.1533,  55.5095,  55.8512,  56.1541,  56.3995,  56.5593,56.6009,  56.5079,  56.3001,  56.0178,  55.7187,  55.448,  55.063,55.2016,  55.2116,  55.1817,  55.112,  55.1099,  55.0299,  54.3358,54.6966,  54.9199,  55.0156,  55.0728,  54.975,  54.8299,  54.6609,54.493,  54.3475,  54.2349,  54.1517,  54.0928,  54.0516,  54.0245,54.013,  54.0206,  54.0404,  54.0667,  54.0989 ],
              [54.2676,  55.1132,  55.6112,  56.09,  56.428,  56.6661,  56.8056,56.8374,  56.7339,  56.4923,  56.1474,  55.7977,  55.4805,  55.2341,54.8999,  55.2662,  55.2927,  55.185,  55.1237,  55.1268,  54.9772,55.1418,  55.2612,  55.3333,  55.379,  55.3244,  55.2153,  55.0629,54.881,  54.6926,  54.523,  54.3866,  54.2855,  54.2118,  54.1583,54.1191,  54.0935,  54.0834,  54.0885,  54.1057 ],
              [54.1771,  55.0795,  55.7075,  56.1772,  56.5183,  56.7522,  56.8898,56.9315,  56.8427,  56.6056,  56.2317,  55.8095,  55.4436,  55.183,55.0284,  54.9504,  55.2833,  55.2563,  55.1498,  55.1342,  55.1331,55.259,  55.3705,  55.4452,  55.4955,  55.5087,  55.4697,  55.3766,55.2324,  55.049,  54.8485,  54.6578,  54.4995,  54.3822,  54.3002,54.2427,  54.2022,  54.1749,  54.1598,  54.1561 ],
              [53.9112,  54.85,  55.6641,  56.0844,  56.4062,  56.6232,  56.757,56.8149,  56.7669,  56.5754,  56.2311,  55.785,  55.366,  55.0104,54.812,  54.8845,  55.1273,  55.2339,  55.1976,  55.1049,  55.0913,55.1843,  55.3048,  55.4076,  55.4709,  55.518,  55.5455,  55.5329,55.4636,  55.3349,  55.1595,  54.9529,  54.7462,  54.5681,  54.4342,54.3439,  54.2848,  54.2446,  54.2222,  54.2135 ],
              [53.9368,  54.9196,  55.4408,  55.7999,  56.0652,  56.2423,  56.348,56.4106,  56.4114,  56.3028,  56.0519,  55.6779,  55.2493,  54.8836,54.6592,  54.6347,  54.8341,  55.0606,  55.1396,  55.0967,  55.0325,55.0501,  55.1451,  55.2627,  55.3559,  55.4216,  55.4789,  55.5183,55.5245,  55.4779,  55.3701,  55.2072,  55.0029,  54.7876,  54.5915,54.4378,  54.3368,  54.2787,  54.2415,  54.2271 ],
              [53.9325,  54.6506,  55.0421,  55.2926,  55.4603,  55.5679,  55.6285,55.6792,  55.7234,  55.731,  55.639,  55.3923,  55.043,  54.6845,54.4188,  54.3242,  54.4606,  54.7449,  54.9548,  55.0171,  55.0047,54.9454,  54.9666,  55.0651,  55.1828,  55.2677,  55.3308,  55.3914,55.438,  55.4544,  55.4277,  55.3385,  55.1907,  54.9981,  54.7786,54.5691,  54.4013,  54.2898,  54.233,  54.1994 ] ])

fig = plt.figure()
ax = fig.add_subplot(111,projection='3d')
X,Y = np.meshgrid(np.arange(-30.0,-20.0,0.25), np.arange(20.0,25,0.25))
ax.contourf(X,Y,data,zdir='z',offset=0, levels=np.arange(0,75,1))
ax.set_zlim(0.0,2.0)
plt.savefig('testfig.png')
plt.close()

This code will produce the plot:

In all of the cases I have observed this mis-contouring the bad triangle always has a vertex near the bottom left of the domain. My data is regularly gridded and for the domain in question is uniform in X and Y. In this case the mis-filling will go away if the number of contour levels is reduced. In some other cases this does not always help or just changes the visual appearance of the error. In any case, even at very coarse contouring I still get errors in a subset of my plots.

Has anyone seen this before and found a fix for it? Am I overlooking something? I'm open to workarounds that don't involve lowering my contouring level (which does reduce the errors overall). If others are in agreement that this could be a bug in the mplot3d, I will file a bug report with them (Issue opened here). I have a feeling the problem lies with contouring very strong gradients when the levels option causes dense contours, but oddly only on 3d axes.

Relevant version information:

• Python 3.4.1
• matplotlib 1.4.3
• numpy 1.9.0

Answer 1

This turned out to be a longstanding bug in matplotlib.mplot3d that ignores path information when taking 2D contourf sets and extending them into 3D. This causes, under certain circumstances, paths with holes to render improperly when a path segment intended as a "move" is instead "drawn".

I contributed a fix for this issue to matplotlib and this bug is fixed in the matplotlib 1.5.0 stable release.

The same test code as in the question produces a correct plot with matplotlib 1.5, as seen below: