smc_anom_1D-2D_1979-2012_6levels_Africa_v2.py

# smc_anom_1D-2D_1979-2012_6levels_Africa_v2.py

# This Python2.7 code was used on CEDA JASMIN to produce monthly

# animation frames for an animated gif that was then made into an MP4

# for showing the seasonal anomaly of soil moisture

# over Africa from 1979-2012

# using (as input) monthly-averaged JULES land-only 1D data.

# This Python2.7 code was adapted from the code given in Emma Robinson’s

# data visualization tutorial for plotting JULES data at http://jules.jchmr.org/content/training .

# The adaptation was done in November-December 2017 by Patrick McGuire and Pier Luigi Vidale

# at the University of Reading (email: p.mcguire@reading.ac.uk )

from netCDF4 import Dataset, num2date, date2num

# Import libraries useful for times

import datetime as dt

import calendar as cal

# widget library

#from ipywidgets.widgets import *

import numpy as np

import matplotlib.pyplot as plt

from mpl_toolkits.basemap import Basemap

# Import locators for fancying up plots

from matplotlib.dates import YearLocator, MonthLocator

from matplotlib.ticker import MultipleLocator

from matplotlib.colors import LinearSegmentedColormap

from matplotlib.colors import ListedColormap

def ReadData(fname, vname, rescale):

# Open the file

f = Dataset(fname,’r’)

# Print file headers

#print f

# Print variable information

#print f.variables[‘fqw_gb’]

#print f.variables[‘ftl_gb’]

# Read the evaporation variable

data = f.variables[vname][:]

# Get the shape

nt, ny, nx = data.shape

# Since we know that the y dimension is degenerate, we select y=0 and collapse

# the data to 2d (nt*nx)

data = data[:,0,:]

# Get the fill value for later use

fill_value = f.variables[vname]._FillValue

# Get latitude and longitude variables

# latitude and longitude are ny*nx, so we select y=0 and collapse to a vector

lat = f.variables[‘latitude’][0,:]

lon = f.variables[‘longitude’][0,:]

# Find information about times

startyr, startmn, startdy = [int(t) \

for t in f.variables[‘time’].units.split()[2].split(‘-‘)]

# Read the time and convert to datetime data structures

# Since we’re looking at monthly averages, we use the time at the start of the

# month. So we read the time_bounds array and use the lower value

# time_bounds = f.variables[‘time_bounds’][:]

time_bounds = f.variables[‘time_bnds’][:]

time = [dt.datetime(startyr,startmn,startdy)+dt.timedelta(seconds=int(t)) \

for t in time_bounds[:,0] ]

# We want to rescale the precip from kg/m2/s to mm/month, so we need to

# know how long the month is

days_in_month = np.array([ [cal.monthrange(t.year,t.month)[1],] for t in time ])

secs_in_day = 86400

if(rescale):

# Rescale precip

data *= (days_in_month * secs_in_day)

# Close the file

f.close()

return data, lon, lat, nt, nx, fill_value

def VectorToGrid(data,lon,lat,nt,nx,fill_value):

# Define the grid we want to end up on

lon_min = -180.0

lon_max = 180.0

dlon = 0.5

lat_min = -90.0

lat_max = 90.0

dlat = 0.5

# Create the grid

grid_lon, grid_lat = np.meshgrid( np.arange( lon_min+dlon/2., lon_max, dlon ), \

np.arange( lat_min+dlat/2., lat_max, dlat ) )

# Grid shape

ny_grid, nx_grid = grid_lon.shape

# Map the vector to the grid

# If it’s not a regular lat/lon grid, then use the np.where function to find

# the right point in the grid

# indx = [np.where( np.logical_and( grid_lon == lon[i], grid_lat == lat[i] )) \

# for i in range(nx) ]

# But, since this is regular lat/lon, we can save time and calculate where

# each point will be relative to the minimum values

# This is quicker than the np.where function call

indx = zip(* [ [ int((lat[i] – lat_min)/dlat), int((lon[i] – lon_min)/dlon) ] \

for i in range(nx)] )

# Create a new masked array with no data in it

data_grid = np.ma.masked_equal( np.ones([nt,ny_grid,nx_grid])*fill_value, \

fill_value )

# Put the vector data into the grid

data_grid[:,indx[0],indx[1]] = data[:]

return data_grid, grid_lon, grid_lat, lon_min, lon_max, lat_min, lat_max

def custom_div_cmap(numcolors=13, name=’custom_div_cmap’,

mincol=’darkred’, midcol=’white’, maxcol=’darkblue’):

“”” Create a custom diverging colormap with three colors

Default is red to white to blue with 11 colors. Colors can be specified

in any way understandable by matplotlib.colors.ColorConverter.to_rgb()

“””

cmap2 = LinearSegmentedColormap.from_list(name=name,

colors =[mincol, midcol, maxcol],

N=numcolors)

return cmap2

#Make sure to pick subset LAT/LON’s to be a half a pixel off of where you want (0.25- or 0.75-degree offsets from a degree)

lon_min_Africa = -30.25

lon_max_Africa = 60.25

lat_min_Africa = -40.25

lat_max_Africa = 40.25

bwr_custom = custom_div_cmap()

for year in range(1979,2013):

#fname = ‘/work/scratch/pmcguire/config/outputs/wfdei_WRR2_4.9positiverain_16proc45min_U-aq934.monthly.2011.nc’

# print ‘Year=’+str(year)

fname = ‘Euro44_bvv_nancil_CTL-BCJ-GL_jules-vn4.9p_u-as052globeE_monmean_’+str(year)+’__1979_2012_ymonstd1anom.nc’

#vname = ‘precip’

#vnamelong = ‘Precipitation’

#vnamedir = ‘precip’

#cmap0 = ‘gist_rainbow’

##units = ‘mm/s’

##vmin0 = 0

##vmax0 = 1e-4

##tickformat = ‘%.0e’

#units = ‘mm/month’

#vmin0 = 0

#vmax0 = 300

#tickformat = ‘%.0f’

#rescale = 1

vname = ‘smc_avail_tot’

vnamelong = ‘Soil_moisture_avail_tot’

vnamedir = ‘smc_anom_6levels_Africa’

#cmap0 = custom_div_cmap(numcolors=5)

cmap0=ListedColormap([‘DarkRed’, ‘LightSalmon’, ‘White’,’White’,’LightBlue’, ‘DarkBlue’])

units = ‘Std. Devs.’

vmin0 = -3

vmax0 = 3

tickformat = ‘%.1f’

tickspacing = np.arange(-3,4,1.0)

rescale = 0

# vname = ‘npp_gb’

# vnamelong = ‘Net_primary_production(NPP)’

# vnamedir = ‘npp’

# cmap0 = ‘PRGn’

# units = ‘kg m-2 s-1’

# vmin0 = -5e-8

# vmax0 = 5e-8

# tickformat = ‘%.0e’

# rescale = 0

data, lon, lat, nt, nx, fill_value = ReadData(fname,vname,rescale)

data_grid,grid_lon,grid_lat,lon_min,lon_max,lat_min,lat_max = VectorToGrid(data,lon,lat,nt,nx,fill_value)

#print data_grid.shape

for month in range(0,12):

if(month<9):

month2=’0’+str(month+1)

else:

month2=str(month+1)

# print ‘Year=’+str(year)+’ Month=’+month2

#figname2=’test_JULES1D2D.pdf’

#fig = plt.figure(figsize=(48.,32.))

fig = plt.figure(figsize=(12.,8.))

# Create a new plot

fig,ax = plt.subplots(1,1)

# Make a world map

m = Basemap(projection=’cyl’, resolution=’c’, ax = ax , \

llcrnrlat = lat_min_Africa, \

llcrnrlon = lon_min_Africa, \

urcrnrlat = lat_max_Africa, \

urcrnrlon = lon_max_Africa )

m.drawcoastlines(zorder=2)

m.fillcontinents([0.8,0.8,0.8],zorder=0)

# latitude lower and upper index

latli = np.argmin( np.abs( grid_lat[:,0] – lat_min_Africa ) )

latui = np.argmin( np.abs( grid_lat[:,0] – lat_max_Africa ) )

# print ‘Lat index min/max=’+str(latli)+’ ‘+str(latui)

# print ‘Lat min/max=’+str(grid_lat[latli,0])+’ ‘+str(grid_lat[latui,0])

# longitude lower and upper index

lonli = np.argmin( np.abs( grid_lon[0,:] – lon_min_Africa) )

lonui = np.argmin( np.abs( grid_lon[0,:] – lon_max_Africa) )

# print ‘Lon index min/max=’+str(lonli)+’ ‘+str(lonui)

# print ‘Lon min/max=’+str(grid_lon[0,lonli])+’ ‘+str(grid_lon[0,lonui])

# Plot array as a colormap

#im = ax.imshow(data_grid[7,:,:], cmap = ‘gist_ncar’, \

im = ax.imshow(data_grid[month,latli:latui,lonli:lonui], cmap = cmap0, \

interpolation = ‘nearest’, origin = ‘lower’, \

vmin = vmin0, vmax = vmax0, zorder=1, \

extent = [lon_min_Africa, lon_max_Africa, lat_min_Africa, lat_max_Africa])

# Set grid

ax.xaxis.set_major_locator(MultipleLocator(30))

ax.yaxis.set_major_locator(MultipleLocator(30))

ax.grid(True)

# Create a colorbar

cb=plt.colorbar(im, ax = ax, orientation=’horizontal’, \

label=’Monthly anomaly ‘+vnamelong+’ (‘+units+’): ‘+str(month2)+’-‘+str(year), format = tickformat, ticks = tickspacing, extend=’both’ )

# Save the figure

#fig.savefig(‘python_sensible_map.png’,dpi=600)

fig.savefig(vnamedir+’_pngs/’+str(vname)+’_’+str(year)+’-‘+str(month2)+’.png’,dpi=150)

# Show the figures on screen

#plt.show()

plt.close(fig)

#air = f.variables[‘esoil_gb’]

#print air

#lat = f.variables[‘latitude’]

#lon = f.variables[‘longitude’]

#print lat

#print lon

#m = Basemap(projection=’npstere’,boundinglat=60,lon_0=0,resolution=’l’)

#nlon, nlat = np.meshgrid(lon[0,:], lat[0,:])

#print nlon,nlat

#x, y = m(lon, lat)

#print x,y

#m.fillcontinents(color=’gray’,lake_color=’gray’)

#m.drawparallels(np.arange(-80.,81.,20.))

#m.drawmeridians(np.arange(-180.,181.,20.))

#m.drawmapboundary(fill_color=’white’)

#cs = m.contourf(x,y,air[0,0,:])

##imshow(vv[time,:,:])

#m.colorbar()

#fig.savefig(figname2)

#plt.close

#plt.show()