How to plot a polygon with holes/voids in bokeh

Question

System - Python 3.6.5, Bokeh 1.1.0, Shapely 1.6.4

I'm trying to plot a polygon with voids/holes in Bokeh. Here's my code:

from shapely.geometry import LineString
import numpy as np
from bokeh.plotting import figure
from bokeh.io import output_file, show

coords = np.array([
    [0, 0, 0],
    [0.000796326711, 0.999999683, 0],
    [-0.999202405, 1.00159234, 0],
    [-1.98359251, 1.1775927, 0],
    [-2.92219092, 1.52260431, 0],
    [-3.78621865, 2.02604854, 0],
    [-4.75089683, 2.28947977, 0],
    [-5.75088129, 2.29505403, 0],
    [-6.71843634, 2.04239373, 0],
    [-7.58802294, 1.54861327, 0],
    [-7.93751519, 0.611674017, 0],
    [-7.60373939, -0.330978472, 0],
    [-6.74253141, -0.839231188, 0],
    [-5.75597881, -0.675787108, 0],
    [-5.48640738, 0.287193288, 0],
    [-6.24471932, 0.939085149, 0],
    [-6.49121061, 1.90823016, 0],
    [-6.13650105, 2.8432067, 0],
    [-5.30921186, 3.40498298, 0],
    [-4.39661375, 3.81384077, 0],
    [-3.42668851, 4.05724379, 0],
    [-2.42917568, 4.12772889, 0],
    [-1.43466068, 4.02313489, 0],
    [-0.44683782, 4.17871769, 0],
    [0.467380974, 4.58393862, 0],
    [1.2460695, 5.21134931, 0],
    [1.83648192, 6.01845103, 0],
    [1.77076367, 7.01628925, 0],
    [1.07959782, 7.73898542, 0],
    [1.36065246, 8.69867719, 0],
    [2.33248521, 8.9343488, 0],
    [3.02192258, 8.21000351, 0],
    [3.17042178, 7.22109098, 0],
    [2.72413551, 6.32620072, 0],
    [2.40767989, 7.27480804, 0],
    [3.30185823, 6.82709709, 0],
    [2.35274811, 6.51215267, 0],
    [2.38220794, 7.51171864, 0],
    [3.31112226, 7.14142393, 0],
    [2.69243164, 7.92705865, 0],
    [2.83462789, 6.93722016, 0],
    [3.2071407, 7.86524721, 0],
    [2.75445232, 6.97357842, 0],
    [3.28380791, 7.82197848, 0],
    [2.68188764, 7.02342229, 0],
    [3.35170769, 7.76594576, 0],
    [2.97550277, 6.83940927, 0],
    [3.01292139, 7.83870895, 0],
    [3.31878194, 6.88663263, 0],
    [2.70636709, 7.67716919, 0],
    [3.69830293, 7.55042818, 0],
    [2.90679201, 6.93927315, 0],
    [3.86117545, 6.64068939, 0],
    [3.55910813, 7.59397599, 0],
    [2.95084789, 6.80023832, 0],
    [3.87479046, 7.18276954, 0],
    [2.8834715, 7.31424852, 0],
    [3.67575378, 6.7040938, 0],
    [3.29543092, 7.62894759, 0],
    [3.59294004, 6.67422861, 0],
    [3.38055037, 7.65141366, 0],
    [3.50617457, 6.65933576, 0],
    [3.46828944, 7.65861786, 0],
    [3.84492686, 6.7322571, 0],
    [3.17476024, 7.47446779, 0],
    [2.55957061, 6.68608863, 0],
    [1.94375336, 5.8981996, 0],
    [1.32730889, 5.11080121, 0],
    [0.710237596, 4.32389397, 0],
    [0.482766922, 3.35010904, 0],
    [0.687368358, 2.37126367, 0],
    [1.28584038, 1.57011996, 0],
    [2.16644112, 1.09626099, 0],
    [3.09577174, 1.46550968, 0],
    [3.41102886, 2.41451598, 0],
    [2.88736947, 3.26644371, 0],
    [1.89827015, 3.41369362, 0],
    [1.49930958, 2.49672554, 0],
    [2.28127802, 1.87340752, 0],
    [3.08621808, 2.46676365, 0],
    [2.72215545, 3.39813812, 0],
    [1.86773544, 2.87855517, 0],
    [2.52719481, 2.12681496, 0],
    [3.15362139, 2.90629539, 0],
    [2.27758894, 3.38854755, 0],
    [2.38423092, 2.39425007, 0],
    [3.13806789, 3.05131157, 0],
    [2.16764342, 3.29271652, 0],
    [2.52576528, 2.35904167, 0],
    [2.68324652, 3.34656364, 0],
    [2.05248464, 2.57058719, 0],
    [2.24068913, 1.58845733, 0],
    [1.6086922, 0.813486444, 0],
    [1.7693182, 1.80050179, 0],
    [2.12297492, 0.865126504, 0],
    [1.34951607, 1.49897303, 0],
    [2.31258524, 1.76822716, 0],
    [1.98000043, 0.825153807, 0],
    [2.88237044, 1.25611595, 0],
    [1.93982797, 1.59020233, 0],
    [2.36935241, 0.687147091, 0],
    [2.27538732, 1.68272258, 0],
    [2.02240825, 0.715250833, 0],
    [2.73321392, 0.0118623958, 0],
    [2.82480034, -0.983934737, 0],
    [2.25421938, -1.8051761, 0],
    [1.28903664, -2.0667526, 0],
    [0.289038757, -2.06881209, 0],
    [-0.677213231, -1.81121338, 0],
    [-0.034783313, -1.04486894, 0],
    [-1.00079436, -1.30336971, 0],
    [-1.50176903, -2.16883166, 0],
    [-1.2448071, -3.13525319, 0],
    [-0.38014413, -3.6376056, 0],
    [0.388154841, -2.99751444, 0],
    [0.0501889901, -2.05635607, 0],
    [-0.949797967, -2.05124865, 0],
    [-1.29735985, -2.98890569, 0],
    [-0.333189804, -3.25419068, 0],
    [-0.152164036, -2.27071233, 0],
    [-1.14760173, -2.17529848, 0],
    [-1.15669068, -3.17525717, 0],
    [-0.28576497, -2.68384248, 0],
    [-1.1464002, -2.17462052, 0],
    [-1.15787801, -3.17455465, 0],
    [-0.285780804, -2.68522198, 0],
    [-1.28075125, -2.58505308, 0],
    [-0.523693737, -3.23840132, 0],
    [-0.76832174, -2.26878431, 0],
    [-1.12482779, -3.20307732, 0],
    [-0.61081635, -2.34529399, 0],
    [-1.26657273, -3.10026656, 0],
    [-0.489178007, -2.47125349, 0],
    [-1.36437484, -2.95502047, 0],
    [-0.643655461, -2.26179354, 0],
    [-1.1610782, -3.11752347, 0],
    [-0.88200064, -2.15725491, 0],
    [-0.903829214, -3.15701664, 0],
    [-1.52912076, -2.3766254, 0],
    [-0.548650127, -2.57329095, 0],
    [-1.42653001, -3.05217184, 0],
    [-1.06111234, -2.12132818, 0],
    [-0.372490874, -2.84644919, 0],
    [-1.32095035, -3.16334762, 0],
    [-0.362479159, -3.44853698, 0],
    [-0.983410887, -2.66467233, 0],
    [-0.925174642, -3.66297516, 0],
    [-0.808381766, -2.66981886, 0],
    [-1.0966227, -3.62737678, 0],
    [-0.295873537, -4.2263766, 0],
    [0.0973636203, -5.14581368, 0],
    [-0.022592165, -6.13859291, 0],
    [-0.623503247, -6.93790879, 0],
    [-1.29238483, -7.68127777, 0],
    [-2.02405304, -8.36293869, 0],
    [-2.81283743, -8.97760868, 0],
    [-3.65262488, -9.52052399, 0],
    [-4.25671377, -10.3174409, 0],
    [-4.55257078, -11.2726732, 0],
    [-4.50467215, -12.2715254, 0],
    [-4.1187691, -13.1940647, 0],
    [-3.19386309, -13.5742605, 0],
    [-2.2707103, -13.1898273, 0],
    [-1.88904191, -12.2655279, 0],
    [-2.27200443, -11.3417641, 0],
    [-3.27107409, -11.3848897, 0],
    [-3.57301046, -12.3382178, 0],
    [-2.78092926, -12.9486335, 0],
    [-1.93599218, -12.4137678, 0],
    [-2.54183032, -11.6181799, 0],
    [-3.28212411, -12.2904634, 0],
    [-4.07867591, -12.8950337, 0],
    [-4.92531242, -13.4272053, 0],
    [-5.81547216, -13.8828539, 0],
    [-6.49669089, -14.6149338, 0],
    [-6.88717425, -15.5355438, 0],
    [-6.94003665, -16.5341456, 0],
    [-6.64893087, -17.4908365, 0],
    [-5.76698046, -17.9621787, 0],
    [-4.80982717, -17.6725969, 0],
    [-4.02410748, -18.2911796, 0],
    [-4.08094552, -19.289563, 0],
    [-4.93179296, -19.8149759, 0],
    [-5.93137812, -19.843777, 0],
    [-6.81106642, -19.3682263, 0],
    [-5.88102777, -19.0007646, 0],
    [-6.75995757, -18.5238134, 0],
    [-7.7596294, -18.5494304, 0],
    [-8.61297752, -19.0707719, 0],
    [-9.09202707, -19.9485598, 0],
    [-8.64847045, -20.8448061, 0],
    [-7.66001513, -20.9963188, 0],
    [-6.96837319, -20.2740782, 0],
    [-7.16250739, -19.2931032, 0],
    [-8.16230648, -19.3131474, 0],
    [-8.3169669, -20.3011151, 0],
    [-8.80090203, -21.176219, 0],
    [-9.55547824, -21.8324314, 0],
    [-10.489271, -22.1902456, 0],
    [-11.3886733, -22.6273676, 0],
    [-12.2469643, -23.1405309, 0],
    [-12.6826532, -22.2404336, 0],
    [-12.4955545, -23.2227747, 0],
    [-11.5263757, -23.4691329, 0],
    [-10.8928903, -22.6953782, 0],
    [-11.32571, -21.7938977, 0],
    [-12.2275349, -22.2259993, 0],
    [-11.7961515, -23.128168, 0],
    [-11.528749, -24.091753, 0],
    [-11.4335264, -25.087209, 0],
    [-11.5134034, -26.0840137, 0],
    [-11.3333499, -27.0676705, 0],
    [-10.905562, -27.9715497, 0],
    [-11.7691193, -28.4758004, 0],
    [-10.86456, -28.0494527, 0],
    [-11.803111, -28.3945932, 0],
    [-10.8378421, -28.1333347, 0],
    [-11.6560006, -28.7083275, 0],
    [-11.0831893, -27.8886402, 0],
    [-11.9895551, -27.4661465, 0],
    [-12.2490106, -28.4319015, 0],
    [-11.2529438, -28.5205069, 0],
    [-11.7509926, -27.6533579, 0],
    [-12.1763713, -28.5583734, 0],
    [-12.1802155, -29.558366, 0],
    [-11.7618076, -30.4666252, 0],
    [-10.9992693, -31.1135682, 0],
    [-10.0133983, -30.9460619, 0],
    [-9.50732286, -30.0835727, 0],
    [-8.52118632, -29.9176368, 0],
    [-7.76071255, -30.5670054, 0],
    [-7.77013098, -31.5669611, 0],
    [-8.20198486, -32.4689047, 0],
    [-8.9750606, -33.1032184, 0],
    [-9.05044793, -32.1060641, 0],
    [-8.19079308, -32.6169393, 0],
    [-9.10268249, -33.0273753, 0],
    [-9.34776313, -32.0578726, 0],
    [-8.35037373, -31.9856619, 0],
    [-8.45324705, -32.9803564, 0],
    [-9.41474758, -32.7055533, 0],
    [-9.39736662, -31.7057043, 0],
    [-8.42689579, -31.4644858, 0],
    [-7.9434172, -32.339842, 0],
    [-8.66436495, -33.0328314, 0],
    [-9.65855654, -32.9252067, 0],
    [-10.2145035, -32.0939889, 0],
    [-9.93434503, -31.1340352, 0],
    [-9.01857521, -30.7323317, 0],
    [-8.01885729, -30.756082, 0],
    [-7.12319629, -31.2008194, 0],
    [-8.00161475, -31.6787117, 0],
    [-7.8884498, -30.6851354, 0],
    [-7.13999644, -31.3483229, 0],
    [-7.92357113, -31.9696205, 0],
    [-8.39866294, -31.0896842, 0],
    [-7.44934549, -30.7753653, 0],
    [-7.30543703, -31.7649563, 0],
    [-8.22437664, -32.1593546, 0],
    [-8.84254942, -31.3733123, 0],
    [-8.15880176, -32.1030309, 0],
    [-7.37177597, -31.4861108, 0],
    [-7.91708735, -30.6478772, 0],
    [-8.80003233, -31.1173537, 0],
    [-8.05741687, -31.7870717, 0],
    [-7.68133922, -30.8604836, 0],
    [-7.47109679, -29.8828343, 0],
    [-7.43301967, -28.8835595, 0],
    [-7.5682543, -27.8927459, 0],
    [-8.2467546, -27.1581458, 0],
    [-9.22372923, -26.9447903, 0],
    [-9.44247386, -25.9690081, 0],
    [-8.9793374, -26.8552951, 0],
    [-9.65549433, -26.1185375, 0],
    [-8.8121176, -26.6558602, 0],
    [-9.80366964, -26.7855697, 0],
])

creature_morphology = LineString(coords[:, 0:2])
creature_patch = creature_morphology.buffer(0.5)
patch_x, patch_y = creature_patch.exterior.coords.xy

p3 = figure(plot_width=500, plot_height=500,
            title="Best Creature", output_backend="webgl")
p3.line(x=coords[:, 0], y=coords[:, 1], line_color='red')
p3.patch(x=patch_x, y=patch_y)

output_file('p3.html')
show(p3)

which works fine and produces a plot like so (zoomed in):

However, there should be a void in the middle of the circle. I've tested this with other examples as well and each time the voids are missing. Suspected solutions:

1. Plot patch using Descartes. Unsure if Bokeh has Descartes compatibility.
2. Coordinates from creature_patch.exterior.coords.xy are wrong, use others. Which though?

Any help is appreciated thanks!

Answer 1

There is a user guide section on Polygons With Holes As well as a nice example in the reference guide.

multi_polygon data is 4-level list:

1. list of multi-polygons
2. each multi-polygon is a list of polygons
3. each polygon is a list with one exterior and zero or more holes
4. each exterior/hole is a list of coordinates

Here is an example:

from bokeh.plotting import figure, show, output_file

output_file('multipolygon_with_holes.html')

p = figure(plot_width=400, plot_height=400)
p.multi_polygons(xs=[[[ [1, 2, 2, 1], [1.2, 1.6, 1.6], [1.8, 1.8, 1.6] ]]],
                 ys=[[[ [3, 3, 4, 4], [3.2, 3.6, 3.2], [3.4, 3.8, 3.8] ]]])

show(p)

Answer 2

To anyone else who might want to do this. Shapely does provide the coordinates for the voids. However, you need to iterate over the voids list to plot them separately like so:

# creature_patch.interiors is the list of all the interior voids that may exist
for i, _ in enumerate(creature_patch.interiors):
    # iterate over the list and add a patch of white for each void
    inside_x, inside_y = creature_patch.interiors[i].coords.xy
    p3.patch(x=inside_x, y=inside_y, fill_color='white')