Closed
Description
Bug report
Bug summary
I am using Matplotlib with Basemap to create heatmaps of data.
A change introduced between version 2.0.0 and 2.0.1 caused my code to:
- Produce a different result
- Run significantly slower
The problem still seems to exist in 2.0.2.
I also ran some profiling to have a look at the differences, and the increase in time seems to be in the resample function (from 0.473s total time to 19.042s total time)
Code for reproduction
import csv
import time
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from mpl_toolkits.basemap import Basemap
def create_basemap():
m = Basemap(projection='cyl', llcrnrlat=-90, urcrnrlat=90,
llcrnrlon=-180, urcrnrlon=180, resolution='c')
m.drawmapboundary(fill_color='#b4d0d0')
m.drawcoastlines(linewidth=0.25, color="#ffffff")
m.fillcontinents(color="grey", lake_color='#b4d0d0')
m.drawparallels(np.arange(-90., 91., 30.), linewidth="0.25", color="#333333")
m.drawmeridians(np.arange(-180., 181., 60.), linewidth="0.25", color="#555555")
return m
def create_heatmap(positions):
heatmap = np.zeros((180, 360))
extents = [[-90, 90], [-180, 180]]
lats, lons = map(list, zip(*positions))
subheatmap, xedges, yedges = np.histogram2d(lats, lons, bins=[180, 360], range=extents)
extent = [xedges[0], xedges[-1], yedges[0], yedges[-1]]
heatmap = np.add(heatmap, subheatmap)
fig = plt.figure()
m = create_basemap()
cmap = cm.jet
cmap.set_bad(alpha=0.0)
im = m.imshow(heatmap, cmap=cmap, interpolation='bicubic', extent=extent, origin='lower', alpha=1.0, norm=matplotlib.colors.LogNorm(), vmin=1, vmax=2, zorder=100)
cb = fig.colorbar(im, shrink=0.5, format="%d")
plt.title("Test")
plt.savefig("test.png", dpi=500, bbox_inches='tight', pad_inches=0.1)
plt.close()
positions = [(50, i) for i in range(50)]
start = time.time()
create_heatmap(positions)
print "Runtime: {0}".format(time.time() - start)Version 2.0.0 outcome
Runtime: 2.31200003624
python -m cProfile --sort=tottime script.py:
667764 function calls (659117 primitive calls) in 3.555 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
2 0.702 0.351 0.702 0.351 {matplotlib._png.write_png}
2 0.473 0.237 0.473 0.237 {matplotlib._image.resample}
1 0.138 0.138 0.138 0.138 {_tkinter.create}
890 0.117 0.000 0.117 0.000 {method 'is_valid' of '_geoslib.BaseGeometry' objects}
15 0.106 0.007 0.632 0.042 __init__.py:1(<module>)
1 0.090 0.090 0.135 0.135 __init__.py:14(<module>)
296 0.083 0.000 0.083 0.000 {method 'intersection' of '_geoslib.BaseGeometry' objects}
2 0.068 0.034 0.681 0.340 image.py:275(_make_image)
11413 0.055 0.000 0.058 0.000 {numpy.core.multiarray.array}
300 0.050 0.000 0.072 0.000 {method 'draw_path' of 'matplotlib.backends._backend_agg.RendererAgg' objects}
...
Version 2.0.1 outcome
Runtime: 21.0169999599
python -m cProfile --sort=tottime script.py:
1763720 function calls (1754827 primitive calls) in 23.725 seconds
Ordered by: internal time
ncalls tottime percall cumtime percall filename:lineno(function)
4 19.042 4.761 19.043 4.761 {matplotlib._image.resample}
2 0.735 0.367 0.735 0.367 {matplotlib._png.write_png}
2 0.609 0.304 1.377 0.688 font_manager.py:558(createFontList)
60 0.138 0.002 0.336 0.006 afm.py:181(_parse_char_metrics)
1 0.135 0.135 0.135 0.135 {_tkinter.create}
2 0.133 0.067 19.309 9.655 image.py:275(_make_image)
890 0.115 0.000 0.115 0.000 {method 'is_valid' of '_geoslib.BaseGeometry' objects}
1 0.107 0.107 0.159 0.159 __init__.py:14(<module>)
15 0.106 0.007 0.637 0.042 __init__.py:1(<module>)
559 0.104 0.000 0.104 0.000 {method 'get_sfnt' of 'matplotlib.ft2font.FT2Font' objects}
Matplotlib version
- Operating System: Windows 10
- Matplotlib Version: 2.0.0/2.0.1 (from pip)
- Python Version: 2.7.13
- Jupyter Version (if applicable): N/A
- Other Libraries: basemap 1.1.0, numpy 1.13.1