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Incorrect polygon filling of mplot3d filled contouring #4784
Description
I have a dataset with large gradients in a quantity I am plotting. In many cases, this results in mis-filled contours when I use many contouring levels. For example:
This does not occur on 2D axes, even with 2 orders of magnitude more contouring levels. I can reduce some of the fill errors by reducing the number of contouring levels or zooming in on the domain so the strong gradients aren't as relatively strong in figure space. If I don't fill the contours, e.g. calling contour rather than contourf there are no errors. This is restricted to the filling,
Here is a script that should reproduce the problem for you. Tested with matplotlib 1.4.3 and python 3.4.1.
#!/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()
which produces the image:
In this case, reducing the contouring level will fix the mis-fill but for the plots I want to produce this isn't a feasible option.
Activity
cwebster2 commented on Jul 24, 2015
To supplement the first image I posted, here is the same data at a much lower contouring interval which still produces miss-fill.
WeatherGod commented on Jul 24, 2015
This looks a lot like #186 and #178, which I had forgotten about. But I thought we fixed some of those issues in the 1.4 release...? In any case, I can reproduce the image on the master branch...
cwebster2 commented on Jul 24, 2015
Thanks. I had a feeling it was related to those issues, but wasn't sure. I'm happy to test any potential fixes. I'm trying to put together animations like this and the mis-fill is quite problematic.
cwebster2 commented on Jul 25, 2015
I've narrowed down the issue with this particular data a bit. If you do an axes3d.contour() for the 55 and 56 levels, you'll get:
but if you do an axes3d.contourf() for the 55 and 56 levels you get:
You can see similar results if you narrow the two contours to be 55.0 and 55.2.
I'm going to be taking a look at the contourset returned by contourf and trying to pinpoint where it is going wrong. I'm assuming the return from Axes.contourf() is proper (since 2d plots are fine) and the issue is either in the transform to 3d or in the projection for drawing.
cwebster2 commented on Jul 25, 2015
Some more investigation! Using the same test data above and plotting except that levels=[55.0,55.2] in the contourf call. All of these are running against the master branch as of around 18Z 25 July 2015.
This produces this miss-filled contour
The dumped contents of self._vec in Poly3DCollection::do_3d_projection (art3d.py:564) contain this data:
This represented 2 distinct polygons with the larger one containing two holes. After the 3d projection (art3d.py:576), the txs,tys and tzs have two elements each and render to these shapes:
In the second image you can see the lines that are causing the mis-fill. I'm still not familiar enough with the code to know how paths are determined to be lines or moves and the nuances of rendering but I'm continuing to dig and posting these updates in case anyone else can shed some light.
ianthomas23 commented on Jul 25, 2015
@cwebster2: if you want some light shed, this is a well-known problem that has been hanging around since 2010. I wrote the following in PR #1928:
That PR contains a (poor quality) candidate fix that needs reworking by someone who knows something about the mplot3d codebase and cares about fixing such problems. No such person has come forward in the last couple of years.
cwebster2 commented on Jul 25, 2015
@ianthomas23 perfect! I think I skimmed across that earlier but forgot about it as a dove into the code. Thanks for pointing it out. I have a local branch that is probably 90% of your code but slightly reorganized. Once I regenerate my plots and make sure nothing blows up I'll see if I can clean it up any better and submit a PR. You saved a ton of time for me, thank you very much! (and this has been a longstanding problem with my 3d plots that I had chalked up to me doing something wrong before I looked more into it)
Added code information to Poly3DCollection
Added code information to Poly3DCollection
Added code information to Poly3DCollection
Add path code information to Poly3DCollection