Input Format to pcolormesh - matplotlib

Question

I'm attempting to make heat/intensity map using Basemap. My inputs are a set of lats, lons, and intensity at that point. The dataset looks like this:
lat[0], lon[0] = intensity[0]
lat[1], lon[1] = intensity[1]
...
lat[n], lon[n] = intensity[n]
At each index the lat and lon correspond to the correct sensor reading. My code looks something like this:
fig = plt.figure(figsize=(10, 8))
# Set title
fig.suptitle("Intensities {} {}".format(start_time, stop_time))
# US Centered Map
map_axis = fig.add_subplot(111)
map = Basemap(
ax = map_axis,
lat_0 = 40, lon_0 = -95,
width = 6500e3, height = 6500e3,
projection = 'stere',
resolution = 'l'
)
map.drawcoastlines()
lats = ...
lons = ...
intn = ...
# Convert coordinates
lons, lats = map(lons, lats)
LONS, LATS = np.meshgrid(lons, lats)
map.pcolormesh(
LONS, LATS,
intn,
vmin = 0, vmax = 100
)
fig.savefig(file_name)
plt.close(fig)
This code never completes. I've successfully plotted the Basemap by itself. The pcolormesh is what is failing. The program crashes with this error.
$ ./plot_intensities.py
Running 2013-04-10 00:02:30 2013-04-10 00:02:45
Traceback (most recent call last):
File "./plot_intensities.py", line 151, in <module>
make_maps(samples)
File "./plot_intensities.py", line 144, in make_maps
make_map(bin_samples, start, walk)
File "./plot_intensities.py", line 117, in make_map
vmin = 0, vmax = 100
File "/usr/lib/python3/dist-packages/mpl_toolkits/basemap/__init__.py", line 521, in with_transform
return plotfunc(self,x,y,data,*args,**kwargs)
File "/usr/lib/python3/dist-packages/mpl_toolkits/basemap/__init__.py", line 3418, in pcolormesh
ret = ax.pcolormesh(x,y,data,**kwargs)
File "/usr/lib/python3/dist-packages/matplotlib/__init__.py", line 1814, in inner
return func(ax, *args, **kwargs)
File "/usr/lib/python3/dist-packages/matplotlib/axes/_axes.py", line 5395, in pcolormesh
X, Y, C = self._pcolorargs('pcolormesh', *args, allmatch=allmatch)
File "/usr/lib/python3/dist-packages/matplotlib/axes/_axes.py", line 4995, in _pcolorargs
numRows, numCols = C.shape
ValueError: not enough values to unpack (expected 2, got 1)
I understand that my data, the third argument intn is not formatted correctly. I cannot find any documentation as to how I should shape that list. How do I format it to the correct shape?
Thanks.

Answer 1

As you know, pcolormesh is used to plot a quadrilateral mesh by creating a pseudocolor plot of a 2-D array. The error details indeed indicated that: at line numRows, numCols = C.shape, it expect C to be a 2-D array, while the C you provided seems to be a 1-D array, judging from ValueError: not enough values to unpack (expected 2, got 1). The dataset you introduced seems to me having only intensity values on the diagonal (where lat == lon). To get a colormesh, you need to at least extend intensity data into 2-D array and somehow fill in missing values. For example:
import matplotlib.pyplot as plt
from mpl_toolkits.basemap import Basemap
import numpy as np
fig = plt.figure(figsize=(10, 8))
# Set title
fig.suptitle("Intensities {} {}".format('start_time', 'stop_time'))
# US Centered Map
map_axis = fig.add_subplot(111)
map = Basemap(
ax = map_axis,
lat_0 = 40, lon_0 = -95,
width = 6500e3, height = 6500e3,
projection = 'stere',
resolution = 'l'
)
map.drawcoastlines()
# Tried my best to simulate your data example. Don't be surprise if the result is ugly ...
nstep = 1
lats = np.arange(map.latmin, map.latmax, nstep)
lons = np.arange(map.lonmin, map.lonmax, nstep)
l = min(len(lats), len(lons))
lats = lats[:l]
lons = lons[:l]
intn = np.random.randint(0, 100, size=l)
# Convert coordinates
lons, lats = map(lons, lats)
LONS, LATS = np.meshgrid(lons, lats)
# The following 3 lines are just an example of the minimum you got to do before it works.
intn_array = np.zeros(LONS.shape)
for i in range(l):
intn_array[i, i] = intn[i]
intn = intn_array
map.pcolormesh(
LONS, LATS,
intn_array,
vmin = 0, vmax = 100
)
plt.show()