Plotting oceans in maps using basemap and python

Question

I am plotting the netCDF file available here: https://goo.gl/QyUI4J

Using the code below, the map looks like this:

However, I want the oceans to be in white color. Better still, I want to be able to specify what color the oceans show up in. How do I change the code below to do that? Right now, the issue is that the oceans are getting plotted on the data scale. (please note that the netCDF file is huge ~3.5 GB).

import pdb, os, glob, netCDF4, numpy
from matplotlib import pyplot as plt
from mpl_toolkits.basemap import Basemap

def plot_map(path_nc, var_name):
    """
    Plot var_name variable from netCDF file
    :param path_nc: Name of netCDF file
    :param var_name: Name of variable in netCDF file to plot on map
    :return: Nothing, side-effect: plot an image
    """

    nc = netCDF4.Dataset(path_nc, 'r', format='NETCDF4')
    tmax  = nc.variables['time'][:]

    m = Basemap(projection='robin',resolution='c',lat_0=0,lon_0=0)

    m.drawcoastlines()
    m.drawcountries()

    # find x,y of map projection grid.
    lons, lats = get_latlon_data(path_nc)
    lons, lats = numpy.meshgrid(lons, lats)
    x, y = m(lons, lats)
    nc_vars = numpy.array(nc.variables[var_name])

    # Plot!
    m.drawlsmask(land_color='white',ocean_color='white')
    cs = m.contourf(x,y,nc_vars[len(tmax)-1,:,:],numpy.arange(0.0,1.0,0.1),cmap=plt.cm.RdBu)

    # add colorbar
    cb = m.colorbar(cs,"bottom", size="5%", pad='2%')
    cb.set_label('Land cover percentage '+var_name+' in '+os.path.basename(path_nc))

    plt.show()


plot_map('perc_crops.nc','LU_Corn.nc')

Answer 1

You need to use maskoceans on your nc_vars dataset

Before contourf, insert this

nc_new = maskoceans(lons,lats,nc_vars[len(tmax)-1,:,:])

and then call contourf with the newly masked dataset i.e.

cs = m.contourf(x,y,nc_new,numpy.arange(0.0,1.0,0.1),cmap=plt.cm.RdBu)

To dictate the ocean colour, you can either drop the call to drawslmask if you want white oceans or specify an ocean colour in that call - e.g. insert m.drawlsmask(land_color='white',ocean_color='cyan').

I've given the working code with as few alterations to yours as possible below. Uncomment the call to drawslmask to see cyan coloured oceans.

Output

Full working version of code

import pdb, os, glob, netCDF4, numpy
from matplotlib import pyplot as plt
from mpl_toolkits.basemap import Basemap, maskoceans

def plot_map(path_nc, var_name):
    """
    Plot var_name variable from netCDF file
    :param path_nc: Name of netCDF file
    :param var_name: Name of variable in netCDF file to plot on map
    :return: Nothing, side-effect: plot an image
    """

    nc = netCDF4.Dataset(path_nc, 'r', format='NETCDF4')
    tmax  = nc.variables['time'][:]

    m = Basemap(projection='robin',resolution='c',lat_0=0,lon_0=0)

    m.drawcoastlines()
    m.drawcountries()    

    # find x,y of map projection grid.
    lons, lats = nc.variables['lon'][:],nc.variables['lat'][:]
    # N.B. I had to substitute the above for unknown function get_latlon_data(path_nc)
    # I guess it does the same job

    lons, lats = numpy.meshgrid(lons, lats)
    x, y = m(lons, lats)
    nc_vars = numpy.array(nc.variables[var_name])
    
    #mask the oceans in your dataset
    nc_new = maskoceans(lons,lats,nc_vars[len(tmax)-1,:,:])
    
    #plot!
    #optionally give the oceans a colour with the line below
    #Note - if land_color is omitted it will default to grey
    #m.drawlsmask(land_color='white',ocean_color='cyan')
    cs = m.contourf(x,y,nc_new,numpy.arange(0.0,1.0,0.1),cmap=plt.cm.RdBu)

    # add colorbar
    cb = m.colorbar(cs,"bottom", size="5%", pad='2%')
    cb.set_label('Land cover percentage '+var_name+' in '+os.path.basename(path_nc))

    plt.show()


plot_map('perc_crops.nc','LU_Corn.nc')

---

P.S. That's a big file to test!!

Answer 2

The colors that youbsee in the map are related to the colormap cm.plt.RdBu which is passed to the contourcf function. You need to change this color map to achieve the results that you want. Here you can find a tutorial for the basemap colormap.

Answer 3

The lawful good solution is to use the utility function maskoceans, which takes in a data array and masks all the points in oceans and lakes.

Instead, you could take the easy way out. Draw your contour plot first, then use drawlsmask, which allows transparent colors:

# Colors can be RGBA tuples
m.drawlsmask(land_color=(0, 0, 0, 0), ocean_color='deeppink', lakes=True)

Land is transparent, which lets the contour plot shows through.