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scipy_regridder.py
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scipy_regridder.py
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import sys
import numpy as np
import matplotlib.pyplot as plt
from netCDF4 import Dataset
from mpl_toolkits.basemap import Basemap
from scipy.interpolate import griddata as regridder
class RegridFV3():
def __init__(self, debug=0, datafiles=[], gridspecfiles=[]):
self.debug = debug
if(self.debug):
print('debug = ', debug)
self.setDataFiles(datafiles=datafiles)
self.setGridSpecFiles(gridspecfiles=gridspecfiles)
self.has_snd_file = 0
self.snd_files = []
def setDataFiles(self, datafiles=[]):
self.datafiles = datafiles
def setSecondFiles(self, files):
self.has_snd_file = 1
self.snd_files = files
def setGridSpecFiles(self, gridspecfiles=[]):
self.gridspecfiles = gridspecfiles
#if(len(self.gridspecfiles)):
# self.readGridSpecFiles()
#else:
# print('No gridspecfiles specified. exit.')
# sys.exit(-1)
def interp_to_latlon(self, lon_1d, lat_1d, var_1d, nlon=360, nlat=181, method='linear'):
'''
Interpolate a variable on cube-sphere grid (such as FV3) to LatLon grid
'''
dlon = 360.0/nlon
dlat = 180.0/(nlat - 1)
#Create a lat-lon uniform grid
out_lon = np.arange(0.0, 360.0, dlon)
out_lat = np.arange(-90.0, 91.0, dlat)
lon, lat = np.meshgrid(out_lon, out_lat)
#print('out_lon.size = ', out_lon.size)
#print('lon.size = ', lon.size)
#print('lon_1d.ndim = ', lon_1d.ndim)
#print('lon_1d.size = ', lon_1d.size)
#print('lon_1d.shape = ', lon_1d.shape)
#print('var_1d.ndim = ', var_1d.ndim)
#print('var_1d.size = ', var_1d.size)
#print('var_1d.shape = ', var_1d.shape)
# Interpolate from cube to lat-lon grid
out_var = regridder((lon_1d,lat_1d), var_1d,
(lon,lat), method=method)
nlen = int(nlon*nlat)
#print('nlen = ', nlen)
#print('lon.size = ', lon.size)
olon = np.reshape(lon, (nlen, ))
olat = np.reshape(lat, (nlen, ))
ovar = np.reshape(out_var, (nlen, ))
olat = olat[~np.isnan(ovar)]
olon = olon[~np.isnan(ovar)]
ovar = ovar[~np.isnan(ovar)]
#Fill in extrapolated values with nearest neighbor
out_var = regridder((olon,olat), ovar,
(lon,lat), method='nearest')
#print('out_var.ndim=', out_var.ndim)
#print('out_var.shape=', out_var.shape)
#print('out_var.size=', out_var.size)
return lon, lat, out_var
def readGridSpecFiles(self):
'''
gridspecfiles : list of grid_spec filenames for each tile.
'''
nc = 0
nt = len(self.gridspecfiles)
lon1d = []
lat1d = []
for gridspecfile in self.gridspecfiles:
print('reading ',gridspecfile)
nc = Dataset(gridspecfile)
lons = nc.variables['x'][:]
lats = nc.variables['y'][:]
#print('lons.ndim=', lons.ndim)
#print('lons.shape=', lons.shape)
#print('lons.size=', lons.size)
ny, nx = lons.shape
latc = np.zeros(((ny-1),(nx-1)))
lonc = np.zeros(((ny-1),(nx-1)))
latc[0:ny-1,0:nx-1] = 0.25*(lats[0:ny-1,0:nx-1] + lats[0:ny-1,1:nx] + lats[1:ny,0:nx-1] + lats[1:ny,1:nx])
lonc[0:ny-1,0:nx-1] = 0.25*(lons[0:ny-1,0:nx-1] + lons[0:ny-1,1:nx] + lons[1:ny,0:nx-1] + lons[1:ny,1:nx])
#print('lonc.ndim=', lonc.ndim)
#print('lonc.shape=', lonc.shape)
#print('lonc.size=', lonc.size)
lonc1d = np.reshape(lonc, ((nx-1)*(ny-1),))
latc1d = np.reshape(latc, ((nx-1)*(ny-1),))
#print('len(lonc1d) = ', len(lonc1d))
lon1d.extend(lonc1d)
lat1d.extend(latc1d)
#print('len(lon1d) = ', len(lon1d))
nc.close()
#print('len(lon1d) = ', len(lon1d))
return lat1d, lon1d
def get_GridSpec_latlon(self):
'''
gridspecfiles : list of grid_spec filenames for each tile.
'''
nc = 0
nt = len(self.gridspecfiles)
lon1d = []
lat1d = []
for gridspecfile in self.gridspecfiles:
print('reading ',gridspecfile)
nc = Dataset(gridspecfile)
lons = nc.variables['x'][:]
lats = nc.variables['y'][:]
#print('lons.ndim=', lons.ndim)
#print('lons.shape=', lons.shape)
#print('lons.size=', lons.size)
ny, nx = lons.shape
latc = np.zeros(((ny-1),(nx-1)))
lonc = np.zeros(((ny-1),(nx-1)))
latc[0:ny-1,0:nx-1] = 0.25*(lats[0:ny-1,0:nx-1] + lats[0:ny-1,1:nx] + lats[1:ny,0:nx-1] + lats[1:ny,1:nx])
lonc[0:ny-1,0:nx-1] = 0.25*(lons[0:ny-1,0:nx-1] + lons[0:ny-1,1:nx] + lons[1:ny,0:nx-1] + lons[1:ny,1:nx])
print('lonc.ndim=', lonc.ndim)
print('lonc.shape=', lonc.shape)
print('lonc.size=', lonc.size)
#lonc1d = np.reshape(lonc, ((nx-1)*(ny-1),))
#latc1d = np.reshape(latc, ((nx-1)*(ny-1),))
lon1d.append(lonc)
lat1d.append(latc)
nc.close()
return lat1d, lon1d
def read3Dvar(self,datafiles,varname,ntime=0):
"""
read FV3 cubed sphere 3D data.
datafiles : list of data filenames for each tile
varname : var name to read from data files
returns data array"""
data = None
nt = len(self.datafiles)
for it in range(nt):
datafile = datafiles[it]
print('reading ',datafile)
nc = Dataset(datafile)
arr = nc.variables[varname][ntime,:,:,:]
nz, ny, nx = arr.shape
print('arr.ndim=', arr.ndim)
print('arr.shape=', arr.shape)
print('arr.size=', arr.size)
if(data is None):
data = np.zeros((nt, nz, ny, nx))
arr[np.isnan(arr)] = 0
data[it,:,:,:] = arr[:,:,:]
nc.close()
return data
def readTileInfo(self,datafiles,varname):
var1d = []
nt = len(self.datafiles)
for it in range(nt):
datafile = datafiles[it]
nc = Dataset(datafile)
arr = nc.variables[varname][:,:]
ny, nx = arr.shape
#print('arr.ndim=', arr.ndim)
#print('arr.shape=', arr.shape)
#print('arr.size=', arr.size)
varc = np.zeros(((ny-1),(nx-1)))
varc[0:ny-1,0:nx-1] = 0.25*(arr[0:ny-1,0:nx-1] + arr[0:ny-1,1:nx] + arr[1:ny,0:nx-1] + arr[1:ny,1:nx])
varc1d = np.reshape(varc, ((nx-1)*(ny-1),))
var1d.extend(varc1d)
nc.close()
return var1d
def get_level(self, data, level=0):
if(3 == data.ndim):
nz, ny, nx = data.shape
var2d = data[level,:,:]
var1d = np.reshape(var2d, (ny*nx, ))
else:
var1d = []
nt, nz, ny, nx = data.shape
for it in range(nt):
var = data[it,level,:,:]
var = var.reshape((ny*nx))
var1d.extend(var)
#print('len(var1d) = ', len(var1d))
return var1d
def get_latlon_data(self, varname, nlon=360, nlat=181, method='linear'):
lat1d, lon1d = self.readGridSpecFiles()
print('len(lon1d) = ', len(lon1d))
print('len(lat1d) = ', len(lat1d))
#varname = 'T'
if(self.has_snd_file):
var1 = self.read3Dvar(self.datafiles, varname)
var2 = self.read3Dvar(self.snd_files, varname)
var = var2 - var1
else:
var = self.read3Dvar(self.datafiles, varname)
print('var.ndim=', var.ndim)
print('var.shape=', var.shape)
print('var.size=', var.size)
latlon_var = self.interp2latlon_data(lon1d, lat1d, var, nlon=nlon, nlat=nlat, method=method)
return latlon_var
def get_original_data(self, varname):
lat1d, lon1d = self.get_GridSpec_latlon()
print('len(lon1d) = ', len(lon1d))
print('len(lat1d) = ', len(lat1d))
#varname = 'T'
if(self.has_snd_file):
var1 = self.read3Dvar(self.datafiles, varname)
var2 = self.read3Dvar(self.snd_files, varname)
var = var2 - var1
else:
var = self.read3Dvar(self.datafiles, varname)
print('var.ndim=', var.ndim)
print('var.shape=', var.shape)
print('var.size=', var.size)
return lat1d, lon1d, var
def get_latlon_tile(self, varname, nlon=360, nlat=181, method='linear'):
lat1d, lon1d = self.readGridSpecFiles()
var1d = self.readTileInfo(self.datafiles, varname)
olons,olats,latlon_var = self.interp_to_latlon(lon1d, lat1d, var1d, nlon=nlon, nlat=nlat, method=method)
return latlon_var
def interp2latlon_data(self, lon1d, lat1d, var, nlon=360, nlat=181, method='linear'):
print('var.ndim = ', var.ndim)
if(2 == var.ndim):
ny, nx = var.shape
var1d = np.reshape(var, (ny*nx, ))
olons,olats,latlon_var = self.interp_to_latlon(lon1d, lat1d, var1d, nlon=nlon, nlat=nlat, method=method)
else:
if(3 == var.ndim):
nz, ny, nx = var.shape
else:
nt, nz, ny, nx = var.shape
latlon_var = np.zeros((nz, int(nlat), int(nlon)), dtype=float)
for level in range(nz):
var1d = self.get_level(var, level=level)
if(self.debug):
print('processing level ', level)
olons,olats,ovar = self.interp_to_latlon(lon1d, lat1d, var1d, nlon=nlon, nlat=nlat, method=method)
latlon_var[level,:,:] = ovar[:,:]
return latlon_var
#----------------------------------------------------------------------------------------------------------
if __name__ == '__main__':
debug = 1
datadir = '/work/noaa/gsienkf/weihuang/jedi/case_study/sondes/analysis.getkf.80members.36procs/increment/'
#griddir = '/work/noaa/gsienkf/weihuang/tools/UFS-RNR-tools/JEDI.FV3-increments/grid/C96/'
griddir = '/work/noaa/gsienkf/weihuang/tools/UFS-RNR-tools/JEDI.FV3-increments/grid/C48/'
datafiles = []
gridspecfiles = []
for ntile in range(1,7,1):
#datafiles.append('fv3_history.tile%s.nc'%ntile)
datafile = '%s20210109.000000.fv_core.res.tile%s.nc' %(datadir, ntile)
datafiles.append(datafile)
#gridspecfiles.append('grid_spec.tile%s.nc'%ntile)
#gridfile = '%sC96_grid.tile%s.nc' %(griddir, ntile)
gridfile = '%sC48_grid.tile%s.nc' %(griddir, ntile)
gridspecfiles.append(gridfile)
rf = RegridFV3(debug=debug, datafiles=datafiles, gridspecfiles=gridspecfiles)
lat1d, lon1d = rf.readGridSpecFiles()
varname = 'T'
var = rf.read3Dvar(varname)
#print('var.ndim=', var.ndim)
#print('var.shape=', var.shape)
#print('var.size=', var.size)
var1d = rf.get_level(var, level=30)
print('len(lon1d) = ', len(lon1d))
print('len(lat1d) = ', len(lat1d))
print('len(var1d) = ', len(var1d))
olons,olats,pvar = rf.interp_to_latlon(lon1d, lat1d, var1d, nlon=360, nlat=181, method='linear')
#make plot on output mesh
m = Basemap(lon_0=180)
m.drawcoastlines()
m.drawmapboundary()
#m.contourf(olons,olats,pvar,15)
m.contourf(olons,olats,pvar,5)
m.colorbar()
plt.show()