def read_data(path):
CMIP_label = dt(path + '/enso_round1_train_20210201/CMIP_label.nc',
'r')
CMIP_train = dt(path + '/enso_round1_train_20210201/CMIP_train.nc',
'r')
SODA_label = dt(path + '/enso_round1_train_20210201/SODA_label.nc',
'r')
SODA_train = dt(path + '/enso_round1_train_20210201/SODA_train.nc',
'r')
return CMIP_label.variables, CMIP_train.variables, SODA_label.variables, SODA_train.variables
def ROMS_CV_Load(RomsFile, VarName, IndBounds):
"""Loads ROMS variables in control volume defined by lat and lon bounds
lat_rho/psi, lon_rho/psi, time, u, ubar, v, vbar, w, and a defined variable
at defined latitude and longitude. Stores in dictionary"""
#load nc file
RomsNC = dt(RomsFile, 'r')
#subset variables in control volume and store in dictionary
ROMS_CV = {'lat_rho' : np.array(RomsNC.variables['lat_rho'][IndBounds['Rho']['lat_li']:IndBounds['Rho']['lat_ui'], \
IndBounds['Rho']['lon_li']:IndBounds['Rho']['lon_ui']], dtype = np.float64), \
'lon_rho' : np.array(RomsNC.variables['lon_rho'][IndBounds['Rho']['lat_li']:IndBounds['Rho']['lat_ui'],\
IndBounds['Rho']['lon_li']:IndBounds['Rho']['lon_ui']], dtype = np.float64), \
'time' : np.array(RomsNC.variables['ocean_time'][:], dtype = np.float64), \
#'w' : np.array(RomsNC.variables['w'][:, :, IndBounds['Rho']['lat_li']:IndBounds['Rho']['lat_ui'],IndBounds['Rho']['lon_li']:IndBounds['Rho']['lon_ui']], dtype = np.float64), \
VarName : np.array(RomsNC.variables[VarName][:, :, IndBounds['Rho']['lat_li']:IndBounds['Rho']['lat_ui'], \
IndBounds['Rho']['lon_li']:IndBounds['Rho']['lon_ui']], dtype = np.float64), \
# psi variables (on edges)
'lat_psi': np.array(RomsNC.variables['lat_psi'][IndBounds['Psi']['lat_li']:IndBounds['Psi']['lat_ui'], \
IndBounds['Psi']['lon_li']:IndBounds['Psi']['lon_ui']], dtype = np.float64), \
'lon_psi': np.array(RomsNC.variables['lon_psi'][IndBounds['Psi']['lat_li']:IndBounds['Psi']['lat_ui'], \
IndBounds['Psi']['lon_li']:IndBounds['Psi']['lon_ui']], dtype = np.float64), \
'u' : np.array(RomsNC.variables['u'][:, :, IndBounds['Psi']['lat_li']:IndBounds['Psi']['lat_ui'], \
IndBounds['Psi']['lon_li']:IndBounds['Psi']['lon_ui']], dtype = np.float64), \
#'ubar' : np.array(RomsNC.variable['ubar'][:, IndBounds['Psi']['lat_li']:IndBounds['Psi']['lat_ui'], IndBounds['Psi']['lon_li']:IndBounds['Psi']['lon_ui']], dtype = np.float64), \
'v' : np.array(RomsNC.variables['v'][:, :, IndBounds['Psi']['lat_li']:IndBounds['Psi']['lat_ui'], \
IndBounds['Psi']['lon_li']:IndBounds['Psi']['lon_ui']], dtype = np.float64), \
#'vbar' : np.array(RomsNC.variables['vbar'][:, IndBounds['Psi']['lat_li']:IndBounds['Psi']['lat_ui'], IndBounds['Psi']['lon_li']:IndBounds['Psi']['lon_ui']], dtype = np.float64)
}
return ROMS_CV
def ROMS_CV_AddVar(RomsFile, ROMS_CV, VarName, IndBounds):
"""Add variable to ROMS control volume dictionary """
RomsNC = dt(RomsFile, 'r')
#update dictionary with new variable
ROMS_CV[VarName] = np.array(RomsNC.variables[VarName][:, :, \
IndBounds['Rho']['lat_li']:IndBounds['Rho']['lat_ui'], \
IndBounds['Rho']['lon_li']:IndBounds['Rho']['lon_ui']], dtype = np.float64)
return ROMS_CV
def RhoPsiIndex(RomsFile, latbounds, lonbounds):
"""locates indices of lat and lon within ROMS Output File assuming regular spacing"""
#load nc file
RomsNC = dt(RomsFile, 'r')
#check if lat bounds are increasing
if latbounds[0] < latbounds[1]:
#locate lat rho points within bounds
RhoInd = {'lat_li' : np.argmin(np.array(np.abs(RomsNC.variables['lat_rho'][:, 0] - latbounds[0]))), \
'lat_ui' : np.argmin(np.array(np.abs(RomsNC.variables['lat_rho'][:, 0] - latbounds[1]))), \
}
#locate lat psi points within bounds; add one to psi upper bound
PsiInd = {'lat_li' : np.argmin(np.array(np.abs(RomsNC.variables['lat_psi'][:, 0] - latbounds[0]))), \
'lat_ui' : np.argmin(np.array(np.abs(RomsNC.variables['lat_psi'][:, 0] - latbounds[1])))+1, \
}
else:
RhoInd = {'lat_li' : np.argmin(np.array(np.abs(RomsNC.variables['lat_rho'][:, 0] - latbounds[1]))), \
'lat_ui' : np.argmin(np.array(np.abs(RomsNC.variables['lat_rho'][:, 0] - latbounds[0]))), \
}
PsiInd = {'lat_li' : np.argmin(np.array(np.abs(RomsNC.variables['lat_psi'][:, 0] - latbounds[1]))), \
'lat_ui' : np.argmin(np.array(np.abs(RomsNC.variables['lat_psi'][:, 0] - latbounds[0])))+1, \
}
#check if lon bounds are increasing
if lonbounds[0] < lonbounds[1]:
#locate lon rho & psi points; add 1 to psi points to get last grid cell
RhoInd['lon_li'] = np.argmin(
np.array(np.abs(RomsNC.variables['lon_rho'][0, :] - lonbounds[0])))
RhoInd['lon_ui'] = np.argmin(
np.array(np.abs(RomsNC.variables['lon_rho'][0, :] - latbounds[1])))
PsiInd['lon_li'] = np.argmin(
np.array(np.abs(RomsNC.variables['lon_psi'][0, :] - lonbounds[0])))
PsiInd['lon_ui'] = np.argmin(
np.array(
np.abs(RomsNC.variables['lon_psi'][0, :] - latbounds[1]))) + 1
else:
RhoInd['lon_li'] = np.argmin(
np.array(np.abs(RomsNC.variables['lon_rho'][0, :] - lonbounds[1])))
RhoInd['lon_ui'] = np.argmin(
np.array(np.abs(RomsNC.variables['lon_rho'][0, :] - lonbounds[0])))
PsiInd['lon_li'] = np.argmin(
np.array(np.abs(RomsNC.variables['lon_psi'][0, :] - lonbounds[1])))
PsiInd['lon_ui'] = np.argmin(
np.array(
np.abs(RomsNC.variables['lon_psi'][0, :] - lonbounds[0]))) + 1
IndBounds = {'Rho': RhoInd, 'Psi': PsiInd}
return IndBounds
def write_CAETE_output(nc_filename, arr, var):
t, la, lo, = arr.shape
# create netcdf file
rootgrp = dt(nc_filename, mode='w', format='NETCDF4')
#dimensions
rootgrp.createDimension("time", None)
rootgrp.createDimension("latitude", la)
rootgrp.createDimension("longitude", lo)
#variables
time = rootgrp.createVariable(varname="time", datatype=np.float32, dimensions=("time",))
latitude = rootgrp.createVariable(varname="latitude", datatype=np.float32,dimensions=("latitude",))
longitude = rootgrp.createVariable(varname="longitude", datatype=np.float32, dimensions=("longitude",))
var_ = rootgrp.createVariable(varname = 'annual_cycle_mean_of_'+str(flt_attrs()[var][2]), datatype=np.float32,
dimensions=("time","latitude","longitude",),
fill_value=NO_DATA[0])
#attributes
## rootgrp
rootgrp.description = flt_attrs()[var][0] + " from CAETE_1981-2010--> annual cycle"
rootgrp.source = "CAETE model outputs"
## time
time.units = "days since 1850-01-01 00:00:00.0"
time.calendar = "noleap"
time.axis='T'
## lat
latitude.units = u"degrees_north"
latitude.long_name=u"latitude"
latitude.standart_name =u"latitude"
latitude.axis = u'Y'
## lon
longitude.units = "degrees_east"
longitude.long_name = "longitude"
longitude.standart_name = "longitude"
longitude.axis = 'X'
## var
var_.long_name=flt_attrs()[var][0]
var_.units = flt_attrs()[var][1]
var_.standard_name=flt_attrs()[var][2]
var_.missing_value=NO_DATA[0]
## WRITING DATA
times_fill = np.array([15.5, 45., 74.5, 105., 135.5, 166.,
196.5, 227.5, 258., 288.5, 319., 349.5])
time[:] = times_fill
longitude[:] = np.arange(-179.75, 180, 0.5)
latitude[:] = np.arange(-89.75, 90, 0.5)
var_[:,:,:] = np.fliplr(np.ma.masked_array(arr, lsmk))
rootgrp.close()
def x_grad_GridCor00(RomsFile, RomsGrd, varname) :
"""
compute gradient in x (lon) direction
"""
#load roms file
RomsNC = dt(RomsFile, 'r')
#load variable and compute differential
var = RomsNC.variables[varname][:]
dvar_x = np.diff(var, n = 1, axis = 3)
dvar_z = np.diff(var, n = 1, axis = 1)
#compute depth at rho points
depth = dep._set_depth_T(RomsFile, None, 'rho', RomsNC.variables['h'],RomsNC.variables['zeta'])
#distance between rho points in x and y directions
x_dist = dist(RomsGrd)[0]
#repeat over depth and time space
_DX = np.repeat(np.array(x_dist)[np.newaxis, :, :], depth.shape[1], axis = 0)
dx = np.repeat(np.array(_DX)[np.newaxis, :, :, :], depth.shape[0], axis = 0)
#depth difference between adjacent rho points
dz_x = np.diff(depth, n = 1, axis = 3)
#vertical derivative
dz_z = np.diff(depth, n = 1, axis = 1)
dp_dz0 = dvar_z/dz_z
dp_dz = 0.5*(dp_dz0[:,:,:,0:_dp_dz.shape[3]-1] + dp_dz0[:,:,:, 1:dp_dz0.shape[3]])
#distance between adjacent rho points
dl = np.sqrt(dx*dx + dz*dz)
#correction for roms grid
dp_dl = dvar/dl*dl/dx
#gradient
dp_dx = dvar/dx
rat = np.abs(dp_dl[0,:,:,:])/np.abs(dp_dx[0,:,:,:])
grat = dl[0,:,:,:]/dx[0,:,:,:]
stat = np.array(rat).flatten()
def ModelDepth(RomsFile, point_type, IndBounds):
"""Computes ROMS depth within control volume defined by lat and lon bounds
uses obs_depth, converted from set_depth.m"""
#load nc file
RomsNC = dt(RomsFile, 'r')
#ROMS variables
romsvars = {'h' : RomsNC.variables['h'], \
'zeta' : RomsNC.variables['zeta'],\
'N' : RomsNC.variables['Cs_r'].size}
#compute depth
depth_domain = dep._set_depth(RomsFile, None, point_type, romsvars['h'],
romsvars['zeta'])
#subset at control volume
depth = np.array(depth_domain[:,IndBounds['Rho']['lat_li']:IndBounds['Rho']['lat_ui'],\
IndBounds['Rho']['lon_li']:IndBounds['Rho']['lon_ui']])
return depth
def GetMonthArray(file_name, min_lat, max_lat,
min_lon, max_lon, var='V_GRD_L100'):
"""
This function takes the month and the data and stacks up
all the arrays
SIDENOTE: anyone hiring will really like a docstring like
this for any functions on your github.
SIDENOTE2: Notice there are no numbers hard coded into this
function. That way you can call it from anywhere
with any changes you want to make, like increasing
the latitude
SIDENOTE3: This is a good way to open a dataset like this
because after this function runs, the dataset
is not left in memory
Parameters
----------
file_name : str
A three letter string for the month
lat and long variables: integer
These are the min and max latitude and longitude of
interest in grid format
var : str
The NETCDF 4 variable name that you want to extract
* Optional, it will use 'V_GRD_L100' if nothing is given
Returns
-------
arr : numpy array
3 dimensional numpy array of form:
[4 * days in month, max_lat - min_lat, max_lon - min_lon]
example for June is [120, 17, 11]
"""
full_data = dt(file_name, 'r')
chopped_data = np.array(full_data.variables[var][:,
min_lat:max_lat,
min_lon:max_lon])
return chopped_data
def get_var(self, var):
if (type(var) == type('str')) and (self.files is not None) and (len(self.files) > 0):
fname = [filename for filename in self.files if var == filename.split('_')[0]]
else:
self.NotWork = True
return None
try:
fname_comp = self.files_dir + os.sep + fname[0]
except:
print('variável --> %s não está no diretório --> %s' % (var, self.files_dir))
self.NotWork = True
return None
try:
dataset = dt(fname_comp, 'r')
except IOError:
print('Cannot open %s file' % var)
self.NotWork = True
return None
else:
# data, time, units & etc.
calendar = dataset.variables['time'].calendar
time_units = dataset.variables['time'].units
time_arr = dataset.variables['time'][:]
data_units = dataset.variables[var].units
var_longname = dataset.variables[var].long_name
self.metadata[var] = (calendar, time_units, time_arr, data_units, var_longname)
dados = dataset.variables[var][:,:,:]
dataset.close()
return np.fliplr(np.array(dados))
def rho_dist(RomsFile):
"""
Use seawater package to compute distance between rho points
"""
RomsNC = dt(RomsFile, 'r')
lat = RomsNC.variables['lat_rho'][:]
lon = RomsNC.variables['lon_rho'][:]
x_dist = np.empty((lon.shape[0], lon.shape[1] - 1))
x_dist.fill(np.nan)
for i in range(lon.shape[0]):
for j in range(lon.shape[1] - 1):
x_dist[i, j] = sw.dist([lat[i, j], lat[i, j + 1]],
[lon[i, j], lon[i, j + 1]])[0]
y_dist = np.empty((lat.shape[0] - 1, lat.shape[1]))
y_dist.fill(np.nan)
for i in range(y_dist.shape[0]):
for j in range(y_dist.shape[1]):
y_dist[i, j] = sw.dist([lat[i, j], lat[i + 1, j]],
[lon[i, j], lon[i + 1, j]])
return x_dist, y_dist
import matplotlib
import os
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from matplotlib import colors as c
from netCDF4 import Dataset as dt, num2date
from mpl_toolkits.basemap import Basemap, cm, shiftgrid
import statsmodels.tsa.api as sm
import scipy
############################################################
# import variable data (SH lats only) from /LENSoutput directory
# data begins December of year 1 for easier data management
# time dimension may be restricted to 10-years
# to speed up analysis processes at first
ICEFRAC_file = dt(
'b.e11.B1850C5CN.f09_g16.005.cam.h1.ICEFRAC.04020101-04991231.nc')
FSNS_file = dt('b.e11.B1850C5CN.f09_g16.005.cam.h1.FSNS.04020101-04991231.nc')
ICEFRAC = ICEFRAC_file.variables['ICEFRAC'][333:3983, 0:60, :]
FSNS = FSNS_file.variables['FSNS'][333:3983, 0:60, :]
# convert ICEFRAC from decimal to %
ICEFRAC = ICEFRAC * 100
# import time data to aid in seasonal selection
time = ICEFRAC_file.variables['time'][333:3983]
# set day 1 to 0 instead of "days since year 256 (see header file)"
time = time - 42674
# import LAT and LON data from one variable for map generation
lons = ICEFRAC_file.variables['lon'][:]
lats = ICEFRAC_file.variables['lat'][0:60]
import numpy as np
from matplotlib import pyplot as plt
from netCDF4 import Dataset as dt
# LOAD DATA FROM NETCDF AS PARENT DATASET
dataset = dt('your_netcdf_file.nc', 'r')
lon = np.array(dataset['longitude'])
lat = np.array(dataset['latitude'])
zvar = np.array(dataset['skt'])
# DEFINE YOUR DOMAIN
lat1 = 14
lat2 = 15
lon1 = 75
lon2 = 76
if lat1 > lat2 or lat1 < lat.min() or lat2 > lat.max():
print "INVALID DOMAIN: PLEASE"
a1 = np.where(lat >= lat1)[0][-1]+1
a2 = np.where(lat >= lat2)[0][-1]-1
lat_new = lat[a2:a1+1]
a1 = np.where(lon >= lon1)[0][0]-1
a2 = np.where(lon >= lon2)[0][0]+1
lon_new = lon[a1:a2+1]
zvar_new = zvar[:, a2:a1+1, a1:a2+1]
import matplotlib
import numpy as np
import time
import scipy.io as sio
from subprocess import call
# lat1 = np.linspace(-90,90,37)
# lat2 = np.linspace(-87.5,87.5,36)
# lon1 = np.linspace(-180,180,73)
# lon2 = np.linspace(-177.5,177.5,72)
# top1 = np.linspace(1,53,53)
# top2 = np.linspace(1.5,52.5,52)
filestr = "ncfile2.nc"
ncfile = dt(filestr, "r")
# ZNU = np.array(ncfile.variables['ZNU'][:],order='F')
lat = np.array(ncfile.variables["latitude"][:], dtype=np.float32)
lon = np.array(ncfile.variables["longitude"][:], dtype=np.float32)
t = np.array(ncfile.variables["time"][:], dtype=np.int32)
u = np.array(ncfile.variables["u10"][:], dtype=np.float32)
v = np.array(ncfile.variables["v10"][:], dtype=np.float32)
T = np.array(ncfile.variables["t2m"][:], dtype=np.float32)
al = np.array(ncfile.variables["al"][:], dtype=np.float32)
# us = np.linspace(-20, 20, 11, endpoint=True)
# plt.contourf(lon,lat,u[5][:][:],us,cmap='seismic')
# plt.contourf(lat2,top2,x.T,40,linewidth=3,cmap='gist_heat_r',vmin=0,vmax=0.0035)
# Use seismic colour map as well
# plt.xlabel('Longitude', fontsize=10)
# plt.ylabel('Latitude', fontsize=10)
def write_CAETE_output(nc_filename, arr, var, pls_mode=False):
if var in flt_attrs().keys():
ldim = flt_attrs()[var][3]
else:
ldim = 1
if ldim > 1:
t, la, lo, = arr.shape
one_layer = False
else:
la, lo = arr.shape
one_layer = True
lsmk_internal = mask_gen(ldim)
# create netcdf file
rootgrp = dt(nc_filename, mode='w', format='NETCDF3_CLASSIC')
#dimensions & variables
rootgrp.createDimension("latitude", la)
rootgrp.createDimension("longitude", lo)
if var in monthly_out:
rootgrp.createDimension("time", None)
time = rootgrp.createVariable(varname="time",
datatype=np.float32,
dimensions=("time", ))
elif var in npls_out:
rootgrp.createDimension("pls", npls)
pls = rootgrp.createVariable(varname="pls",
datatype=np.int32,
dimensions=("pls", ))
latitude = rootgrp.createVariable(varname="latitude",
datatype=np.float32,
dimensions=("latitude", ))
longitude = rootgrp.createVariable(varname="longitude",
datatype=np.float32,
dimensions=("longitude", ))
if var in monthly_out:
var_ = rootgrp.createVariable(varname='annual_cycle_mean_of_' +
str(flt_attrs()[var][2]),
datatype=np.float32,
dimensions=(
"time",
"latitude",
"longitude",
),
fill_value=NO_DATA[0])
elif var in npls_out:
var_ = rootgrp.createVariable(varname=str(flt_attrs()[var][2]),
datatype=np.float32,
dimensions=(
"pls",
"latitude",
"longitude",
),
fill_value=NO_DATA[0])
elif one_layer:
var_ = rootgrp.createVariable(varname=str(flt_attrs()[var][2]),
datatype=np.float32,
dimensions=(
"latitude",
"longitude",
),
fill_value=NO_DATA[0])
#attributes
## rootgrp
rootgrp.description = flt_attrs()[var][0] + " caete-v1.0 OUTPUT"
rootgrp.source = "CAETE model outputs"
## time
if var in monthly_out:
time.units = "days since 1850-01-01 00:00:00.0"
time.calendar = "noleap"
time.axis = 'T'
if var in npls_out:
pls.units = '1'
pls.axis = u'T'
## lat
latitude.units = u"degrees_north"
latitude.long_name = u"latitude"
latitude.standart_name = u"latitude"
latitude.axis = u'Y'
## lon
longitude.units = "degrees_east"
longitude.long_name = "longitude"
longitude.standart_name = "longitude"
longitude.axis = u'X'
## var
var_.long_name = flt_attrs()[var][0]
var_.units = flt_attrs()[var][1]
var_.standard_name = flt_attrs()[var][2]
var_.missing_value = NO_DATA[0]
## WRITING DATA
if var in monthly_out:
time[:] = np.array([
15.5, 45., 74.5, 105., 135.5, 166., 196.5, 227.5, 258., 288.5,
319., 349.5
])
if var in npls_out:
pls[:] = np.arange(1, npls + 1)
longitude[:] = np.arange(-179.75, 180, 0.5)
latitude[:] = np.arange(-89.75, 90, 0.5)
if not one_layer:
var_[:, :, :] = np.fliplr(np.ma.masked_array(arr, lsmk_internal))
else:
var_[:, :] = np.flipud(np.ma.masked_array(arr, lsmk_internal))
rootgrp.close()
import numpy as np
import matplotlib.pyplot as plt
from glob import glob
#%%
June = glob('*06.grb2.nc')
July = glob('*07.grb2.nc')
Aug = glob('*08.grb2.nc')
Sep = glob('*09.grb2.nc')
JUNE_ALL = np.zeros([120, 17, 11, 27])
JULY_ALL = np.zeros([124, 17, 11, 27])
AUG_ALL = np.zeros([124, 17, 11, 27])
SEP_ALL = np.zeros([120, 17, 11, 27])
#%%
for i in range(len(June)):
dummy = June[i]
dummy = dt(dummy, 'r')
dummy = np.array(dummy.variables['V_GRD_L100'][:, 150:167, 670:681])
JUNE_ALL[:, :, :, i] = dummy
for i in range(len(July)):
dummy = July[i]
dummy = dt(dummy, 'r')
dummy = np.array(dummy.variables['V_GRD_L100'][:, 150:167, 670:681])
JULY_ALL[:, :, :, i] = dummy
for i in range(len(Aug)):
dummy = Aug[i]
dummy = dt(dummy, 'r')
dummy = np.array(dummy.variables['V_GRD_L100'][:, 150:167, 670:681])
AUG_ALL[:, :, :, i] = dummy
for i in range(len(Sep)):
dummy = Sep[i]
dummy = dt(dummy, 'r')
#print 'Argument List:', str(sys.argv)
Args = sys.argv
#print Args
p1 = [0.20943952, 6.96069e+06, 1.25266] #lon rad lat
p2 = [3.66519, 8.01733e+06, 0.338019]
file = '../ModelRunGeo-2019-019-221500.nc'
#file = Args[1];
p1 = [float(Args[2]), float(Args[3]),
float(Args[4])]
#p2 = [float(Args[5]), float(Args[6]), float(Args[7])];
#print p1, p2
ncfile = dt(file, 'r')
#ED = np.array(ncfile.variables['Electron_Density'][:], dtype=np.float32);
ED = ncfile.variables['Electron_Density'][:][0]
Geo_Lon = ncfile.variables['Geo_Lon'][:][0]
Geo_Radius = ncfile.variables['Geo_Radius'][:][0]
Geo_Lat = ncfile.variables['Geo_Lat'][:][0]
P1 = []
P2 = []
def appendCoord(array, len): # вычисление в координатах массива
for i in range(0, len(Geo_Lon) - 1):
if Geo_Lon[i][0][0] <= p1[0] and p1[0] <= Geo_Lon[i + 1][0][0]:
break
# -*- coding: utf-8 -*- """ Created on Thu Jun 16 22:49:45 2016 @author: kushal """ from netCDF4 import Dataset as dt # note the change of case in netCDF4 import numpy as np # Dataset is a netcdf object, similar to a dictionary filestr = 'data/ncfile2.nc' # This is the file name ncfile = dt(filestr, 'r') # Create a netcdf object in read mode #print ncfile.variables # To print all the variables lat = np.array(ncfile.variables['latitude'][:],dtype=np.float32) ''' Extract a variable named 'latitude' from the netcdf object as a numpy array, having all it's entries as real numbers of type float32 (32 bit real numbers). The numpy array's name is lat ''' lon = np.array(ncfile.variables['longitude'][:],dtype=np.float32) t = np.array(ncfile.variables['time'][:],dtype=np.int32) u = np.array(ncfile.variables['u10'][:],dtype=np.float32) v = np.array(ncfile.variables['v10'][:],dtype=np.float32)
def write_snap_output(arr,
var,
flt_attrs,
time_index,
experiment="TEST RUN HISTORICAL ISIMIP"):
NO_DATA = [-9999.0, -9999.0]
time_units = TIME_UNITS
calendar = CALENDAR
nc_out = Path("../nc_outputs")
time_dim = time_index
longitude_0 = np.arange(-179.75, 180, 0.5)[201:272]
latitude_0 = np.arange(89.75, -90, -0.5)[160:221]
print("\nSaving netCDF4 files")
print_progress(0, len(var), prefix='Progress:', suffix='Complete')
for i, v in enumerate(var):
nc_filename = os.path.join(nc_out, Path(f'{v}.nc4'))
with dt(nc_filename, mode='w', format='NETCDF4') as rootgrp:
# dimensions & variables
rootgrp.createDimension("latitude", latitude_0.size)
rootgrp.createDimension("longitude", longitude_0.size)
rootgrp.createDimension("time", None)
time = rootgrp.createVariable(varname="time",
datatype=np.int32,
dimensions=("time", ))
latitude = rootgrp.createVariable(varname="latitude",
datatype=np.float32,
dimensions=("latitude", ))
longitude = rootgrp.createVariable(varname="longitude",
datatype=np.float32,
dimensions=("longitude", ))
var_ = rootgrp.createVariable(varname=flt_attrs[v][2],
datatype=np.float32,
dimensions=(
"time",
"latitude",
"longitude",
),
zlib=True,
fill_value=NO_DATA[0],
fletcher32=True)
# attributes
# rootgrp
rootgrp.description = flt_attrs[v][0] + " from CAETÊ-CNP OUTPUT"
rootgrp.source = "CAETE model outputs - [email protected]"
rootgrp.experiment = experiment
# time
time.units = time_units
time.calendar = calendar
time.axis = 'T'
# lat
latitude.units = u"degrees_north"
latitude.long_name = u"latitude"
latitude.standart_name = u"latitude"
latitude.axis = u'Y'
# lon
longitude.units = "degrees_east"
longitude.long_name = "longitude"
longitude.standart_name = "longitude"
longitude.axis = u'X'
# var
var_.long_name = flt_attrs[v][0]
var_.units = flt_attrs[v][1]
var_.standard_name = flt_attrs[v][2]
var_.missing_value = NO_DATA[0]
# WRITING DATA
longitude[:] = longitude_0
latitude[:] = latitude_0
time[:] = time_dim
var_[:, :, :] = np.ma.masked_array(arr[i],
mask=arr[i] == NO_DATA[0])
print_progress(i + 1,
len(var),
prefix='Progress:',
suffix='Complete')
from netCDF4 import Dataset as dt
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
test_file = 'data/atmPrf_C001.2010.001.00.00.G20_2013.3520.nc'
test_ncfile = dt(test_file, 'r')
test_lat = np.array(test_ncfile.variables['Lat'][:])
test_lon = np.array(test_ncfile.variables['Lon'][:])
test_pres = np.array(test_ncfile.variables['Pres'][:])
test_temp = np.array(test_ncfile.variables['Temp'][:])
test_s = (len(test_lat), 4)
test_data = np.zeros(test_s)
for i in range(len(test_lat)):
test_data[i][0] = test_pres[i]
test_data[i][1] = test_lat[i]
test_data[i][2] = test_lon[i]
test_data[i][3] = test_temp[i]
train_file = 'ta_6hrPlev_CMAM-Ext_CMAM30-SD_r1i1p1_2010010100-2010063018.nc'
train_ncfile = dt(train_file, 'r')
train_time = np.array(train_ncfile.variables['time'][:]) #len 724
train_plev = np.array(train_ncfile.variables['plev'][:]) #len 87
train_lat = np.array(train_ncfile.variables['lat'][:]) #len 32
train_lon = np.array(train_ncfile.variables['lon'][:]) #len 64
train_temp = np.array(train_ncfile.variables['ta'])
def write_area_output(arr,
time_index,
experiment="TEST RUN HISTORICAL ISIMIP"):
NO_DATA = [-9999.0, -9999.0]
time_units = TIME_UNITS
calendar = CALENDAR
nc_out = Path("../nc_outputs")
time_dim = time_index
longitude_0 = np.arange(-179.75, 180, 0.5)[201:272]
latitude_0 = np.arange(89.75, -90, -0.5)[160:221]
nc_filename = os.path.join(nc_out, Path(f'ocp_area.nc4'))
with dt(nc_filename, mode='w', format='NETCDF4') as rootgrp:
# dimensions & variables
rootgrp.createDimension("latitude", latitude_0.size)
rootgrp.createDimension("longitude", longitude_0.size)
rootgrp.createDimension("pls", arr.shape[1])
rootgrp.createDimension("time", None)
time = rootgrp.createVariable(varname="time",
datatype=np.int32,
dimensions=("time", ))
pls = rootgrp.createVariable(varname="PLS",
datatype=np.int16,
dimensions=("pls", ))
latitude = rootgrp.createVariable(varname="latitude",
datatype=np.float32,
dimensions=("latitude", ))
longitude = rootgrp.createVariable(varname="longitude",
datatype=np.float32,
dimensions=("longitude", ))
var_ = rootgrp.createVariable(varname='ocp_area',
datatype=np.float32,
dimensions=(
"time",
"pls",
"latitude",
"longitude",
),
fill_value=NO_DATA[0])
# attributes
# rootgrp
rootgrp.description = "Ocupation coefficients of Plant Life Strategies" + \
" from CAETÊ-CNP OUTPUT"
rootgrp.source = "CAETE model outputs"
rootgrp.experiment = experiment
# time
time.units = time_units
time.calendar = calendar
time.axis = u'T'
# time
pls.units = u'unitless'
pls.axis = u'P'
# lat
latitude.units = u"degrees_north"
latitude.long_name = u"latitude"
latitude.standart_name = u"latitude"
latitude.axis = u'Y'
# lon
longitude.units = "degrees_east"
longitude.long_name = "longitude"
longitude.standart_name = "longitude"
longitude.axis = u'X'
# var
var_.long_name = "Occupation coefficients of Plant Life Strategies (Abundance data)"
var_.units = "unitless"
var_.standard_name = 'ocp_area'
var_.missing_value = NO_DATA[0]
# WRITING DATA
pls[:] = np.arange(100, dtype=np.int16)
longitude[:] = longitude_0
latitude[:] = latitude_0
time[:] = time_dim
var_[:, :, :, :] = np.ma.masked_array(arr, mask=arr == NO_DATA[0])
# Program to visualize the data import numpy as np from netCDF4 import Dataset as dt import matplotlib.pyplot as plt import matplotlib from mpl_toolkits.mplot3d import Axes3D from scipy.interpolate import griddata fname = 'datas_small_rotation.nc' fp = dt(fname, 'r') # print(fp.variables) x = np.array(fp.variables['X Distance'][:]) y = np.array(fp.variables['Y Distance'][:]) t = np.array(fp.variables['T Time'][:]) h = np.array(fp.variables['H_Level'][:]) u = np.array(fp.variables['U_Velocity'][:]) v = np.array(fp.variables['V_Velocity'][:]) uv = (u**2.0 + v**2.0)**0.5 # regridding data for smoother values X, Y = np.meshgrid(x, y) # X, Y = np.mgrid[0:10:1001j, 0:10:1001j] # H = np.zeros((10001,1001,1001)) ''' for i in range(0, 10001):
Created on Tue May 12 17:06:07 2020 @author: Jasen Load World Ocean Atlas Data """ import numpy as np from netCDF4 import Dataset as dt #WOA data location TempFile = '/Users/Jasen/Documents/Data/WOA_Data/AnalyzedMean/woa18_decav_t00_01.nc' SaltFile = '/Users/Jasen/Documents/Data/WOA_Data/AnalyzedMean/woa18_decav_s00_01.nc' NO3_File = '/Users/Jasen/Documents/Data/WOA_Data/AnalyzedMean/woa18_all_n00_01.nc' #WOA data load TempNC = dt(TempFile, 'r') SaltNC = dt(SaltFile, 'r') NO3_NC = dt(NO3_File, 'r') #Extract location [NOTE: _NC.variables == ncdisp(), _NC.variables.keys == simple list] #ROMS reference file RomsFile = '/Users/Jasen/Documents/Data/ROMS_ICBC/wc12_hycom_20090101_dnref99_ini_Darwin_NuteMap.nc' RomsNC = dt(RomsFile, 'r') ROMSlat = np.array(RomsNC.variables[latitude][:], dtype=np.float64) #Select every point at 1 degree intervals on 0.5 degree locaitons #Expand domain to include points outside of ROMS wc12 domain for interpolation #locate indices of WOA lat within ROMS wc12 domain
import matplotlib
import numpy as np
import time
import scipy.io as sio
from subprocess import call
#lat1 = np.linspace(-90,90,37)
#lat2 = np.linspace(-87.5,87.5,36)
#lon1 = np.linspace(-180,180,73)
#lon2 = np.linspace(-177.5,177.5,72)
#top1 = np.linspace(1,53,53)
#top2 = np.linspace(1.5,52.5,52)
filestr = 'ncfile2.nc'
ncfile = dt(filestr, 'r')
#ZNU = np.array(ncfile.variables['ZNU'][:],order='F')
lat = np.array(ncfile.variables['latitude'][:],dtype=np.float32)
lon = np.array(ncfile.variables['longitude'][:],dtype=np.float32)
t = np.array(ncfile.variables['time'][:],dtype=np.int32)
u = np.array(ncfile.variables['u10'][:],dtype=np.float32)
v = np.array(ncfile.variables['v10'][:],dtype=np.float32)
T = np.array(ncfile.variables['t2m'][:],dtype=np.float32)
al = np.array(ncfile.variables['al'][:],dtype=np.float32)
#us = np.linspace(-20, 20, 11, endpoint=True)
#plt.contourf(lon,lat,u[5][:][:],us,cmap='seismic')
# plt.contourf(lat2,top2,x.T,40,linewidth=3,cmap='gist_heat_r',vmin=0,vmax=0.0035)
# Use seismic colour map as well
#plt.xlabel('Longitude', fontsize=10)
#plt.ylabel('Latitude', fontsize=10)
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 17 08:23:36 2015
@author: arun
"""
import numpy as np
# import matplotlib.pyplot as plt
import scipy.io as sio
from netCDF4 import Dataset as dt
filestr = 'ncfile2.nc'
ncfile = dt(filestr, 'r')
#ZNU = np.array(ncfile.variables['ZNU'][:],order='F')
lat = np.array(ncfile.variables['latitude'][:],dtype=np.float32)
lon = np.array(ncfile.variables['longitude'][:],dtype=np.float32)
u = np.array(ncfile.variables['u10'][:],dtype=np.float32)
v = np.array(ncfile.variables['v10'][:],dtype=np.float32)
T = np.array(ncfile.variables['t2m'][:],dtype=np.float32)
'''
To save in mat files, first you need a dictionary having all the values as keys
Second, you need to specify a proper key values to them.
Finally, you need the sio.savemat() option to save them!
'''
mat = {}
mat['lat'] = lat
mat['lon'] = lon
# lat_ts is the latitude of true scale.
# resolution = 'c' means use crude resolution coastlines.
m = Basemap(projection='merc',llcrnrlat=-80,urcrnrlat=80,\
llcrnrlon=-180,urcrnrlon=180,lat_ts=20,resolution='c')
m.drawcoastlines()
m.fillcontinents(color='coral',lake_color='aqua')
# draw parallels and meridians.
m.drawparallels(np.arange(-90.,91.,30.))
m.drawmeridians(np.arange(-180.,181.,60.))
m.drawmapboundary(fill_color='aqua')
plt.title("Mercator Projection")
plt.show()
#%%
JUNE_79 = 'wnd700.gdas.197906.grb2.nc'
JUNE_79 = dt(JUNE_79,'r')
# JUNE_79=np.array(JUNE_79.variables['V_GRD_L100'][:])
JUNE_80 = 'wnd700.gdas.198006.grb2.nc'
JUNE_80 = dt(JUNE_80,'r')
# JUNE_80=np.array(JUNE_80.variables['V_GRD_L100'][:])
JUNE_81 = 'wnd700.gdas.198106.grb2.nc'
JUNE_81 = dt(JUNE_81,'r')
# JUNE_81=np.array(JUNE_81.variables['V_GRD_L100'][:])
JUNE_82 = 'wnd700.gdas.198206.grb2.nc'
JUNE_82 = dt(JUNE_82,'r')
# JUNE_82=np.array(JUNE_82.variables['V_GRD_L100'][:])
JUNE_83 = 'wnd700.gdas.198306.grb2.nc'
from netCDF4 import Dataset as dt, num2date
from mpl_toolkits.basemap import Basemap, cm, shiftgrid
import statsmodels.tsa.api as sm
import scipy
############################################################
# import VAR model variables of interest:
# FSNS (net surface shortwave radiation)
# FSNSC (net surface shortwave radiation: clear sky)
# FLNS (net surface longwave radiation)
# FLNSC (not surface longwave radiation: clear sky)
# ICEFRAC (ice fraction)
# TGCLDLWP (total grid cloud liquid water path)
# CLDTOT (vertically integrated cloud fraction)
FSNS_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h1.FSNS.15000101-15991231.nc')
FSNSC_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h1.FSNSC.15000101-15991231.nc')
FLNS_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h1.FLNS.15000101-15991231.nc')
FLNSC_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h1.FLNSC.15000101-15991231.nc')
ICEFRAC_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h1.ICEFRAC.15000101-15991231.nc')
TGCLDLWP_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h2.TGCLDLWP.1500010100Z-1510123118Z.nc')
CLDTOT_file =\
dt('b.e11.B1850C5CN.f09_g16.005.cam.h2.CLDTOT.1500010100Z-1510123118Z.nc')
###########################################################
# for monthly climatologies, we trim time dimension to start at march 1st