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netcdf_read_write.py
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netcdf_read_write.py
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# Netcdf reading and writing functions
# Bring a netcdf3 file into python!
# Written by Kathryn Materna
# Modified by Ellis Vavra
# Last update: 09/10/2019
import numpy as np
import scipy.io.netcdf as netcdf
import matplotlib.pyplot as plt
import subprocess
# --------------- READING ------------------- #
def read_grd(filename):
data0 = netcdf.netcdf_file(filename, 'r').variables['z'][::-1];
data = data0.copy()
return data
def read_grd_xy(filename):
xdata0 = netcdf.netcdf_file(filename, 'r').variables['x'][::-1];
ydata0 = netcdf.netcdf_file(filename, 'r').variables['y'][::-1];
xdata = xdata0.copy()
ydata = ydata0.copy()
return [xdata, ydata]
def read_grd_xyz(filename):
xdata0 = netcdf.netcdf_file(filename, 'r').variables['x'][::-1];
ydata0 = netcdf.netcdf_file(filename, 'r').variables['y'][::-1];
zdata0 = netcdf.netcdf_file(filename, 'r').variables['z'][::-1];
xdata = xdata0.copy()
ydata = ydata0.copy()
zdata = zdata0.copy()
return [xdata, ydata, zdata]
def read_grd_lonlatz(filename):
xdata0 = netcdf.netcdf_file(filename, 'r').variables['lon'][::-1];
ydata0 = netcdf.netcdf_file(filename, 'r').variables['lat'][::-1];
zdata0 = netcdf.netcdf_file(filename, 'r').variables['z'][::-1];
xdata = xdata0.copy()
ydata = ydata0.copy()
zdata = zdata0.copy()
return [xdata, ydata, zdata]
def read_grd_variables(filename, var1, var2, var3):
xdata0 = netcdf.netcdf_file(filename, 'r').variables[var1][::-1];
xdata = xdata0.copy()
ydata0 = netcdf.netcdf_file(filename, 'r').variables[var2][::-1];
ydata = ydata0.copy()
zdata0 = netcdf.netcdf_file(filename, 'r').variables[var3][::-1];
zdata = zdata0.copy()
return [xdata, ydata, zdata]
def read_netcdf4_xy(filename):
netcdf4file = filename
netcdf3file = filename + 'nc3'
subprocess.call('nccopy -k classic ' + netcdf4file + ' ' + netcdf3file, shell=True)
[xdata, ydata] = read_grd_xy(netcdf3file)
return [xdata, ydata]
def read_netcdf4(filename):
netcdf4file = filename
netcdf3file = filename + 'nc3'
subprocess.call('nccopy -k classic ' + netcdf4file + ' ' + netcdf3file, shell=True)
data = read_grd(netcdf3file)
return data
def read_netcdf4_xyz(filename):
netcdf4file = filename
netcdf3file = filename + 'nc3'
subprocess.call('nccopy -k classic ' + netcdf4file + ' ' + netcdf3file, shell=True)
zdata = read_grd(netcdf3file)
[xdata, ydata] = read_grd_xy(netcdf3file)
return [xdata, ydata, zdata]
def read_netcdf4_variables(filename, var1, var2, var3):
netcdf4file = filename
netcdf3file = filename + 'nc3'
subprocess.call('nccopy -k classic ' + netcdf4file + ' ' + netcdf3file, shell=True)
[xdata, ydata, zdata] = read_grd_variables(filename + 'nc3', var1, var2, var3)
return [xdata, ydata, zdata]
def read_any_grd_xyz(filename):
# Switch between netcdf4 and netcdf3 automatically.
try:
[xdata, ydata, zdata] = read_grd_xyz(filename)
except TypeError:
[xdata, ydata, zdata] = read_netcdf4_xyz(filename)
return [xdata, ydata, zdata]
def read_any_grd_variables(filename, var1, var2, var3):
# Switch between netcdf4 and netcdf3 automatically.
try:
[xdata, ydata, zdata] = read_grd_variables(filename, var1, var2, var3)
except TypeError:
[xdata, ydata, zdata] = read_netcdf4_variables(filename, var1, var2, var3)
return [xdata, ydata, zdata]
# --------------- WRITING ------------------- #
def produce_output_netcdf(xdata, ydata, zdata, zunits, netcdfname):
# # Write the netcdf velocity grid file.
f = netcdf.netcdf_file(netcdfname, 'w')
f.history = 'Created for a test'
f.createDimension('x', len(xdata))
f.createDimension('y', len(ydata))
print(np.shape(zdata))
x = f.createVariable('x', float, ('x',))
x[:] = xdata;
x.units = 'range'
y = f.createVariable('y', float, ('y',))
y[:] = ydata;
y.units = 'azimuth'
z = f.createVariable('z', float, ('y', 'x',))
z[:, :] = zdata;
z.units = zunits
f.close()
return
def flip_if_necessary(filename):
# IF WE NEED TO FLIP DATA:
xinc = subprocess.check_output('gmt grdinfo -M -C ' + filename + ' | awk \'{print $8}\'', shell=True) # the x-increment
yinc = subprocess.check_output('gmt grdinfo -M -C ' + filename + ' | awk \'{print $9}\'', shell=True) # the x-increment
xinc = float(xinc.split()[0])
yinc = float(yinc.split()[0])
if xinc < 0: # FLIP THE X-AXIS
print("flipping the x-axis")
[xdata, ydata] = read_grd_xy(filename)
data = read_grd(filename)
# This is the key! Flip the x-axis when necessary.
# xdata=np.flip(xdata,0); # This is sometimes necessary and sometimes not! Not sure why.
produce_output_netcdf(xdata, ydata, data, 'mm/yr', filename)
xinc = subprocess.check_output('gmt grdinfo -M -C ' + filename + ' | awk \'{print $8}\'', shell=True) # the x-increment
xinc = float(xinc.split()[0])
print("New xinc is: %f " % (xinc));
if yinc < 0:
print("flipping the y-axis")
[xdata, ydata] = read_grd_xy(filename)
data = read_grd(filename)
# Flip the y-axis when necessary.
# ydata=np.flip(ydata,0);
produce_output_netcdf(xdata, ydata, data, 'mm/yr', filename)
yinc = subprocess.check_output('gmt grdinfo -M -C ' + filename + ' | awk \'{print $9}\'', shell=True) # the x-increment
yinc = float(yinc.split()[0])
print("New yinc is: %f" % (yinc));
return
def produce_output_plot(netcdfname, plottitle, filename, cblabel):
# Read in the dataset
fr = netcdf.netcdf_file(netcdfname, 'r')
xread = fr.variables['x']
yread = fr.variables['y']
zread = fr.variables['z']
zread_copy = zread[:][:].copy();
# Make a plot
fig = plt.figure(figsize=(7, 10))
ax1 = fig.add_axes([0.0, 0.1, 0.9, 0.8])
plt.imshow(zread_copy, aspect=1.2)
plt.gca().invert_yaxis()
plt.gca().invert_xaxis()
plt.gca().get_xaxis().set_ticks([])
plt.gca().get_yaxis().set_ticks([])
plt.title(plottitle)
plt.gca().set_xlabel("Range", fontsize=16)
plt.gca().set_ylabel("Azimuth", fontsize=16)
cb = plt.colorbar()
cb.set_label(cblabel, size=16)
plt.savefig(filename)
plt.close()
return