Animation of pcolormesh() with mpl_toolkit.basemap giving attribute error

Question

I am trying to animate some density data on a basemap map. Following an approach as was done in [this SO question][1], I get the following error:

/usr/local/lib/python2.7/dist-packages/matplotlib/collections.pyc in update_scalarmappable(self)
    627         if self._A is None:
    628             return
--> 629         if self._A.ndim > 1:
    630             raise ValueError('Collections can only map rank 1 arrays')
    631         if not self.check_update("array"):

AttributeError: 'list' object has no attribute 'ndim'

If I instead set the data in init() with null values by self.quad.set_array(self.z.ravel()), I end up with two plotted maps with no data being animated.

Any light that anybody could shed on what I'm doing wrong would be greatly appreciated. Thanks!

example code:

def plot_pcolor(lons,lats):

    class UpdateQuad(object):

        def __init__(self,ax, map_object, lons, lats):
                self.ax = ax
                self.m  = map_object
                self.lons = lons
                self.lats = lats

                self.ydim, self.xdim = lons.shape

                self.z = np.zeros((self.ydim-1,self.xdim-1))

                x, y = self.m(lons, lats)
                self.quad = ax.pcolormesh(x, y, self.z, cmap=plt.cm.Reds)

        def init(self):
            print 'update init'
            self.quad.set_array([])
            return self.quad

        def __call__(self,i):

            data = np.zeros((self.ydim-1,self.xdim-1))

            for i in range(self.ydim-1):
                for j in range(self.xdim-1):
                    data[i,j]=random.random()+4

            self.quad.set_array(data.ravel())
            return self.quad

    fig = plt.figure()
    ax = fig.add_axes([0.1,0.1,0.8,0.8])

    m = Basemap(width=2000000,height=2000000,
                resolution='l', projection='laea',\
                lat_ts=10.,\
                lat_0=64.,lon_0=10., ax=ax)

    m.fillcontinents()

    ud = UpdateQuad(ax, m, lons, lats)

    anim = animation.FuncAnimation(fig, ud, init_func=ud.init,
                                   frames=20,  blit=False)

    plt.show()

if __name__ == '__main__':
    import matplotlib.pyplot as plt
    import matplotlib.animation as animation
    from mpl_toolkits.basemap import Basemap
    import numpy as np
    import random

    lons = np.linspace(-5.,25., num = 25)[:50]
    lats = np.linspace(56., 71., num = 25)[:50]
    lons,lats =  np.meshgrid(lons,lats)

    plot_pcolor(lons,lats)

Stomatology

Answer 1

It looks like the set_data method should require an ndarray (not sure why the example I had followed was working correctly).

So in the init() function, you should use quad.set_array(np.array([])) rather than quad.set_array([]).

Other problems to be aware of:

• As mentioned before, you also want set blit=False in your FuncAnimation() call.

• I was also experiencing problems when I set the quad artist attribute animated to True. Leave that be (i.e. quad.set_animated(False), which is the default anyway).

• If you do not specify the bounds via norm in your first pcolormesh() call, it will set them according to the data you pass (in my case null), which resulting in my getting blank animations. Setting them according to the data you will animate later in the initial call prevented this problem in my case.

• pcolormesh() takes the bounding positions to the data field, which should be +1 in the y and x dimension of the data array. If the data array is equal (or greater than) the dimensions of the position data, pcolormesh() will omit any data outside of this boundary requirement. I thought that my data would just appear offset by one grid cell, but everything was all whacky before I passed the correct boundary positions. See another question of mine for calculating these HERE.

• Older versions of matplotlib do not have very good error reporting. I recommend upgrading to the latest version if that is an option for you.

Some random trouble-shooting:

After updating matplotlib and basemap and attempting to implement this in my existing plotting routine, I received the following error:

ValueError: All values in the dash list must be positive

I first thought it had to do with my pcolormesh() objects, but it took me way too long to discover that it was due to my previous setting of the dash attribute in my m.drawmeridians() call to dashes=[1,0] for a solid meridian. In the new version of matplotlib the handling of dashes was changed to give this error. The new prefered method for setting a solid line for the dash attribute is dashes=(None,None), which I don't like.

Resulting animation:

Code example for above output:

def plot_pcolor(lons,lats):

    class UpdateQuad(object):

        def __init__(self,ax, map_object, lons, lats):
            self.ax = ax
            self.m  = map_object
            self.lons = lons
            self.lats = lats
            vmin = 0
            vmax = 1
            self.ydim, self.xdim = lons.shape

            self.z = np.zeros((self.ydim-1,self.xdim-1))

            levels = MaxNLocator(nbins=15).tick_values(vmin,vmax)
            cmap = plt.cm.cool
            norm = BoundaryNorm(levels, ncolors=cmap.N, clip=True)
            x, y = self.m(lons, lats)

            self.quad = self.ax.pcolormesh(x, y, self.z, alpha=0.9,
                                           norm=norm, cmap=cmap,
                                           vmin=vmin, vmax=vmax)
        def init(self):
            print 'update init'
            self.quad.set_array(np.asarray([]))
            return self.quad

        def __call__(self,i):

            for i in range(self.ydim-1):
                for j in range(self.xdim-1):
                    self.z[i,j]=random.random()

            self.quad.set_array(self.z.ravel())

            return self.quad


    fig, ax = plt.subplots()

    m = Basemap(width=2000000,height=2000000,
                resolution='l', projection='laea',\
                lat_ts=10.,\
                lat_0=64.,lon_0=10., ax=ax)

    m.fillcontinents()

    ud = UpdateQuad(ax, m, lons, lats)

    anim = animation.FuncAnimation(fig, ud, init_func=ud.init,
                                   frames=20,  blit=False)

    fig.tight_layout()

    plt.show()

    return ud.quad

if __name__ == '__main__':
    import matplotlib.pyplot as plt
    import matplotlib.animation as animation
    from mpl_toolkits.basemap import Basemap
    import numpy as np
    import random
    from matplotlib.colors import BoundaryNorm
    from matplotlib.ticker import MaxNLocator

    lons = np.linspace(-5.,25., num = 25)[:50]
    lats = np.linspace(56., 71., num = 25)[:50]
    lons,lats =  np.meshgrid(lons,lats)

    quad = plot_pcolor(lons,lats)

Stomatology