from netCDF4 import Dataset
import numpy as np
from mpl_toolkits.basemap import Basemap, cm
import matplotlib.pyplot as plt
import numpy as np
#import h5py as h5py

#nc_file = './3B-DAY-L.MS.MRG.3IMERG.20181112-S000000-E235959.V05.nc4.nc'
nc_file= '3B-DAY-L.MS.MRG.3IMERG.20181113-S000000-E235959.V05.nc4.nc'
dataset = Dataset(nc_file, mode='r')

precip1 = dataset.variables['precipitationCal'][:]
precip1 = np.transpose(precip1)

precip = precip1

theLats= dataset['lat'][:]
theLons = dataset['lon'][:]

# Plot the figure, define the geographic bounds
fig = plt.figure(dpi=300)
latcorners = ([38,46])
loncorners = ([34,45])



m = Basemap(projection='cyl',llcrnrlat=latcorners[0],urcrnrlat=latcorners[1],llcrnrlon=loncorners[0],urcrnrlon=loncorners[1],resolution="h")



# Draw coastlines, state and country boundaries, edge of map.

m.drawcoastlines(linewidth=1.2, linestyle='solid', color='k', antialiased=3, ax=None, zorder=None)
m.drawcountries(linewidth=0.8, linestyle='solid', color='k', antialiased=3, ax=None, zorder=None)

m.bluemarble(scale=3)
#m.shadedrelief(scale=2)
#m.etopo(scale=3)

#m.drawstates()
#m.drawcountries()

# Draw filled contours.
clevs = np.arange(0,60,5)
  #color scale changing
#clevs = [2,5,10,20,30,40,50,60,70,100]

# Define the latitude and longitude data
x, y = np.float32(np.meshgrid(theLons, theLats))

# Mask the values less than 0 because there is no data to plot.
masked_array = np.ma.masked_where(precip < 0,precip)
# Plot every masked value as white

#cmap = cm.GMT_drywet
cmap = cm.GMT_drywet
cmap.set_bad('w',1.)

# Plot the data
cs = m.contourf(x,y,precip,clevs,cmap=cmap,latlon=True)
parallels = np.arange(-60.,61,20.)
m.drawparallels(parallels,labels=[True,False,True,False])
meridians = np.arange(-180.,180.,60.)
m.drawmeridians(meridians,labels=[False,False,False,True])
# Set the title and fonts
plt.title('Black Sea Total Rain Rate')
font = {'weight' : 'bold', 'size' : 6}
plt.rc('font', **font)
# Add colorbar
cbar = m.colorbar(cs,location='right',pad="5%")
cbar.set_label('mm/h')
plt.savefig('a.png',dpi=200)   #change to your directory

https://github.com/onurhdogan/GPM-data-Visualization/blob/master/BlackSea.py