Plot only on continent in matplotlib

Question

I am drawing a map using basemap from matplotlib. The data are spreaded all over the world, but I just want to retain all the data on the continent and drop those on the ocean. Is there a way that I can filter the data, or is there a way to draw the ocean again to cover the data?

Pool

Answer 1

There's method in matplotlib.basemap: is_land(xpt, ypt)

It returns True if the given x,y point (in projection coordinates) is over land, False otherwise. The definition of land is based upon the GSHHS coastline polygons associated with the class instance. Points over lakes inside land regions are not counted as land points.

For more information, see here.

Natalia

Thanks that's what I was looking for. But, when I use is_land I run into a problem. It's here. – Pool

Answer 2

is_land() will loop all the polygons to check whether it's land or not. For large data size, it's very slow. You can use points_inside_poly() from matplotlib to check an array of points quickly. Here is the code. It doesn't check lakepolygons, if you want remove points in lakes, you can add your self.

It took 2.7 seconds to check 100000 points on my PC. If you want more speed, you can convert the polygons into a bitmap, but it's a little difficult to do this. Please tell me if the following code is not fast enought for your dataset.

from mpl_toolkits.basemap import Basemap
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.nxutils as nx

def points_in_polys(points, polys):
    result = []
    for poly in polys:
        mask = nx.points_inside_poly(points, poly)
        result.extend(points[mask])
        points = points[~mask]
    return np.array(result)

points = np.random.randint(0, 90, size=(100000, 2))
m = Basemap(projection='moll',lon_0=0,resolution='c')
m.drawcoastlines()
m.fillcontinents(color='coral',lake_color='aqua')
x, y = m(points[:,0], points[:,1])
loc = np.c_[x, y]
polys = [p.boundary for p in m.landpolygons]
land_loc = points_in_polys(loc, polys)
m.plot(land_loc[:, 0], land_loc[:, 1],'ro')
plt.show()

Bulrush

I think points_inside_poly (and if I remember the whole nxutils) is depreciated in mpl 1.2, but it works with the new method too (can't remember what the new method is at the moment, but the depreciation warning will tell it) – Seamstress

matplotlib.org/1.2.1/api/… – Olive

Answer 3

The HYRY's answer won't work on new versions of matplotlib (nxutils is deprecated). I've made a new version that works:

from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
from matplotlib.path import Path
import numpy as np

map = Basemap(projection='cyl', resolution='c')

lons = [0., 0., 16., 76.]
lats = [0., 41., 19., 51.]

x, y = map(lons, lats)

locations = np.c_[x, y]

polygons = [Path(p.boundary) for p in map.landpolygons]

result = np.zeros(len(locations), dtype=bool) 

for polygon in polygons:

    result += np.array(polygon.contains_points(locations))

print result

Bazooka

Answer 4

The simplest way is to use basemap's maskoceans.

If for each lat, lon you have a data and you want to use contours: After meshgrid and interpolation:

from scipy.interpolate import griddata as gd
from mpl_toolkits.basemap import Basemap, cm, maskoceans
xi, yi = np.meshgrid(xi, yi)
zi = gd((mlon, mlat),
            scores,
            (xi, yi),
            method=grid_interpolation_method)
#mask points on ocean
data = maskoceans(xi, yi, zi)
con = m.contourf(xi, yi, data, cmap=cm.GMT_red2green)
#note instead of zi we have data now.

Update (much faster than in_land or in_polygon solutions):

If for each lat, lon you don't have any data, and you just want to scatter the points only over land:

x, y = m(lons, lats)
samples = len(lons)
ocean = maskoceans(lons, lats, datain=np.arange(samples),
                   resolution='i')
ocean_samples = np.ma.count_masked(ocean)
print('{0} of {1} points in ocean'.format(ocean_samples, samples))
m.scatter(x[~ocean.mask], y[~ocean.mask], marker='.', color=colors[~ocean.mask], s=1)
m.drawcountries()
m.drawcoastlines(linewidth=0.7)
plt.savefig('a.png')

Maxon

Answer 5

I was answering this question, when I was told that it would be better to post my answer over here. Basically, my solution extracts the polygons that are used to draw the coastlines of the Basemap instance and combines these polygons with the outline of the map to produce a matplotlib.PathPatch that overlays the ocean areas of the map.

This especially useful if the data is coarse and interpolation of the data is not wanted. In this case using maskoceans produces a very grainy outline of the coastlines, which does not look very good.

Here is the same example I posted as answer for the other question:

from matplotlib import pyplot as plt
from mpl_toolkits import basemap as bm
from matplotlib import colors
import numpy as np
import numpy.ma as ma
from matplotlib.patches import Path, PathPatch

fig, ax = plt.subplots()

lon_0 = 319
lat_0 = 72

##some fake data
lons = np.linspace(lon_0-60,lon_0+60,10)
lats = np.linspace(lat_0-15,lat_0+15,5)
lon, lat = np.meshgrid(lons,lats)
TOPO = np.sin(np.pi*lon/180)*np.exp(lat/90)

m = bm.Basemap(resolution='i',projection='laea', width=1500000, height=2900000, lat_ts=60, lat_0=lat_0, lon_0=lon_0, ax = ax)
m.drawcoastlines(linewidth=0.5)

x,y = m(lon,lat)
pcol = ax.pcolormesh(x,y,TOPO)

##getting the limits of the map:
x0,x1 = ax.get_xlim()
y0,y1 = ax.get_ylim()
map_edges = np.array([[x0,y0],[x1,y0],[x1,y1],[x0,y1]])

##getting all polygons used to draw the coastlines of the map
polys = [p.boundary for p in m.landpolygons]

##combining with map edges
polys = [map_edges]+polys[:]

##creating a PathPatch
codes = [
    [Path.MOVETO] + [Path.LINETO for p in p[1:]]
    for p in polys
]
polys_lin = [v for p in polys for v in p]
codes_lin = [c for cs in codes for c in cs]
path = Path(polys_lin, codes_lin)
patch = PathPatch(path,facecolor='white', lw=0)

##masking the data:
ax.add_patch(patch)

plt.show()

This produces the following plot:

Hope this is helpful to someone :)

Engvall

+1 for comprehensive answer. In my case its completely inverse, I want to mask the land and show data in the ocean. What can be changed to bring that to effect? – Subatomic

hope you can assist – Subatomic