#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 22 10:29:13 2021
@author: rodierq
"""
import netCDF4 as nc
import numpy as np
def read_netcdf(LnameFiles, Dvar_input, path='.', removeHALO=True):
Dvar = {}
for i,nameFiles in enumerate(LnameFiles):
f_nb = 'f' + str(i+1)
print('Reading file ' + f_nb)
print(path + nameFiles)
if '000' in nameFiles[-6:-3]: #time series file (diachronic)
theFile = nc.Dataset(path + nameFiles,'r')
if theFile['MASDEV'][0] <= 54:
read_TIMESfiles_54(theFile, f_nb, Dvar_input, Dvar)
else : # 55 groups variables
read_TIMESfiles_55(theFile, f_nb, Dvar_input, Dvar, removeHALO)
theFile.close()
else:
read_BACKUPfile(nameFiles, f_nb, Dvar_input, Dvar, path=path, removeHALO=removeHALO)
return Dvar #Return the dic of [files][variables]
def read_BACKUPfile(nameF, ifile, Dvar_input, Dvar_output, path='.', removeHALO=True):
theFile = nc.Dataset(path + nameF,'r')
Dvar_output[ifile] = {} #initialize dic for each files
# Reading date since beginning of the model run
Dvar_output[ifile]['date'] = theFile.variables['time'].units
Dvar_output[ifile]['time'] = theFile.variables['time'][0]
for var in Dvar_input[ifile]: #For each files
# Read variables
n_dim = theFile.variables[var].ndim
name_dim = theFile.variables[var].dimensions
# print(var + " n_dim = " + str(n_dim))
if (n_dim ==0) or (n_dim == 1 and 'time' in name_dim): #Scalaires or Variable time
Dvar_output[ifile][var] = theFile.variables[var][0].data
else:
if removeHALO:
if n_dim == 1:
Dvar_output[ifile][var] = theFile.variables[var][1:-1] #Variables 1D
elif n_dim == 2:
if theFile.variables[var].shape[0] == 1 and 'size' in name_dim[1]: #Variables 2D with the second dimension not a coordinate (--> list of strings : chemicals)
Dvar_output[ifile][var] = theFile.variables[var][0,:] #Variables 2D
elif theFile.variables[var].shape[0] == 1: #Variables 2D with first dim = 0
Dvar_output[ifile][var] = theFile.variables[var][0,1:-1] #Variables 2D
else:
Dvar_output[ifile][var] = theFile.variables[var][1:-1,1:-1] #Variables 2D
elif n_dim == 5: #Variables time, sizeXX, level, nj, ni (ex: chemical budgets in 3D)
Dvar_output[ifile][var] = theFile.variables[var][0, :, 1:-1,:1:-1,1:-1]
elif n_dim == 4 and 'time' in name_dim and ('level' in name_dim or 'level_w' in name_dim): # time,z,y,x
if theFile.variables[var].shape[1] == 1: #Variables 4D time,z,y,x with time=0 z=0
Dvar_output[ifile][var] = theFile.variables[var][0,0,1:-1,1:-1] #Variables 2D y/x
elif theFile.variables[var].shape[2] == 1: #Variable 2D (0,zz,0,xx)
Dvar_output[ifile][var] = theFile.variables[var][0,1:-1,0,1:-1] #Variables 2D z/y
elif theFile.variables[var].shape[3] == 1: #Variable 2D (0,zz,yy,0)
Dvar_output[ifile][var] = theFile.variables[var][0,1:-1,1:-1,0] #Variables 2D z/x
## ATTENTION VARIABLE 1D codé en 4D non faite
else: #Variable 3D simple
Dvar_output[ifile][var] = theFile.variables[var][0,1:-1,1:-1,1:-1] #Variables time + 3D
elif n_dim == 4 and 'time' in name_dim and 'level' not in name_dim and 'level_w' not in name_dim: # time,nb_something,y,x
Dvar_output[ifile][var] = theFile.variables[var][0,:,1:-1,1:-1] #Variables 2D y/x
elif n_dim == 3 and 'time' in name_dim: # time, y, x
Dvar_output[ifile][var] = theFile.variables[var][0,1:-1,1:-1]
else :
Dvar_output[ifile][var] = theFile.variables[var][1:-1,1:-1,1:-1] #Variables 3D
else:
if n_dim == 1:
Dvar_output[ifile][var] = theFile.variables[var][:] #Variables 1D
elif n_dim == 2:
if theFile.variables[var].shape[0] == 1 and 'size' in name_dim[1]: #Variables 2D with the second dimension not a coordinate (--> list of strings : chemicals)
Dvar_output[ifile][var] = theFile.variables[var][0,:] #Variables 2D
elif theFile.variables[var].shape[0] == 1: #Variables 2D with first dim = 0
Dvar_output[ifile][var] = theFile.variables[var][0,:] #Variables 2D
else:
Dvar_output[ifile][var] = theFile.variables[var][:,:] #Variables 2D
elif n_dim == 5: #Variables time, sizeXX, level, nj, ni (ex: chemical budgets in 3D)
Dvar_output[ifile][var] = theFile.variables[var][0,:,:,:,:]
elif n_dim == 4: # time,z,y,x
if theFile.variables[var].shape[1] == 1: #Variables 4D time,z,y,x with time=0 z=0
Dvar_output[ifile][var] = theFile.variables[var][0,0,:,:] #Variables 2D y/x
elif theFile.variables[var].shape[2] == 1: #Variable 2D (0,zz,0,xx)
Dvar_output[ifile][var] = theFile.variables[var][0,:,0,:] #Variables 2D z/y
elif theFile.variables[var].shape[3] == 1: #Variable 2D (0,zz,yy,0)
Dvar_output[ifile][var] = theFile.variables[var][0,:,:,0] #Variables 2D z/x
## ATTENTION VARIABLE 1D codé en 4D non faite
else: #Variable 3D simple
Dvar_output[ifile][var] = theFile.variables[var][0,:,:,:] #Variables time + 3D
elif n_dim ==3 and name_dim in var.dimensions: # time, y, x
Dvar_output[ifile][var] = theFile.variables[var][0,:,:]
else:
Dvar_output[ifile][var] = theFile.variables[var][:,:,:] #Variables 3D
# For all variables except scalars, change Fill_Value to NaN
Dvar_output[ifile][var]= np.where(Dvar_output[ifile][var] != -99999.0, Dvar_output[ifile][var], np.nan)
Dvar_output[ifile][var]= np.where(Dvar_output[ifile][var] != 999.0, Dvar_output[ifile][var], np.nan)
theFile.close()
return Dvar_output #Return the dic of [files][variables]
def read_TIMESfiles_54(theFile, ifile, Dvar_input, Dvar_output):
Dvar_output[ifile] = {} #initialize dic for each files
# Level variable is automatically read without the Halo
Dvar_output[ifile]['level'] = theFile.variables['level'][1:-1]
# Time variable is automatically read (time since begging of the run) from the 1st variable of the asked variable to read
suffix, name_first_var = remove_PROC(Dvar_input[ifile][0])
try: # It is possible that there is only one value (one time) in the .000 file, as such time series are not suitable and the following line can't be executed. The time variable is then not written
increment = theFile.variables[name_first_var+'___DATIM'][1,-1] - theFile.variables[name_first_var+'___DATIM'][0,-1] #-1 is the last entry of the date (current UTC time in seconds)
length_time = theFile.variables[name_first_var+'___DATIM'].shape[0]
Dvar_output[ifile]['time'] = np.arange(increment,increment*(length_time+1),increment)
except:
pass
for var in Dvar_input[ifile]: #For each files
suffix, var_name = remove_PROC(var)
n_dim = theFile.variables[var].ndim
name_dim = theFile.variables[var].dimensions
# First, test if the variable is a dimension/coordinate variable
if (n_dim ==0): # Scalaires variable
Dvar_output[ifile][var] = theFile.variables[var][0].data
pass
elif n_dim == 1:
Dvar_output[ifile][var_name] = theFile.variables[var][1:-1] # By default, the Halo is always removed because is not in the other variables in any .000 variable
pass
elif n_dim == 2:
Lsize1 = list_size1(n_dim, name_dim)
if Lsize1 == [True, False]: Dvar_output[ifile][var_name] = theFile.variables[var][0,1:-1]
pass
Lsize1 = list_size1(n_dim, name_dim)
if Lsize1 == [True, False, False, True, True]: Dvar_output[ifile][var_name] = theFile.variables[var][0,:,:,0,0].T # Need to be transposed here
if Lsize1 == [True, True, False, True, False]: Dvar_output[ifile][var_name] = theFile.variables[var][0,0,:,0,:]
return Dvar_output #Return the dic of [files][variables]
def read_TIMESfiles_55(theFile, ifile, Dvar_input, Dvar_output, removeHALO=False):
"""
Read variables from MNH MASDEV >= 5.5.0
Parameters :
- Dvar_input : dictionnary of {file : var}. var can be either
- a string = the variable name
- or a tuple of ('group_name','var_name')
If the variable desired is in a group_name and the group_name is not specified, it is assumed group_name = variable_name
except for specific variable as (cart, neb, clear, cs1, cs2, cs3) type
Return :
Dvar_output : dictionnary of Dvar_output[ifile][variables or tuple (group,variables) if the user specified a tuple]
"""
Dvar_output[ifile] = {} #initialize dic for each files
def read_var(theFile, Dvar_output, var):
suffix, var_name = remove_PROC(var)
try: # NetCDF4 Variables
n_dim = theFile.variables[var_name].ndim
# First, test if the variable is a dimension/coordinate variable
if (n_dim ==0): # Scalaires variable
Dvar_output[var_name] = theFile.variables[var_name][0].data
else:
if(removeHALO):
if n_dim == 1:
Dvar_output[var_name] = theFile.variables[var_name][1:-1]
elif n_dim == 2:
Dvar_output[var_name] = theFile.variables[var_name][1:-1,1:-1]
else:
raise NameError("Lecture des variables de dimension sup a 2 pas encore implementees pour fichiers .000")
else:
if n_dim == 1:
Dvar_output[var_name] = theFile.variables[var_name][:]
elif n_dim == 2:
Dvar_output[var_name] = theFile.variables[var_name][:,:]
else:
raise NameError("Lecture des variables de dimension sup a 2 pas encore implementees pour fichiers .000")
except KeyError: # NetCDF4 Group not specified by the user
if '(cart)' in var_name or '(neb)' in var_name or '(clear)' in var_name or '(cs1)' in var_name or '(cs2)' in var_name or '(cs3)' in var_name:
# If users specify the complete variable name with averaging type
group_name = get_group_from_varname(var_name)
else:
group_name = var_name
read_from_group(theFile, Dvar_output, var, var)
return Dvar_output
def read_from_group(theFile, Dvar_output, group_name, var):
suffix, var_name = remove_PROC(var)
if group_name == 'TSERIES': #always 1D
Dvar_output[(group_name,var)] = theFile.groups['TSERIES'].variables[var][:]
elif group_name == 'ZTSERIES': #always 2D
Dvar_output[(group_name,var)] = theFile.groups['ZTSERIES'].variables[var][:,:].T
elif 'XTSERIES' in group_name: #always 2D
Dvar_output[(group_name,var)] = theFile.groups[group_name].variables[var][:,:].T
elif theFile.groups[group_name].type == 'TLES' : # LES type
try: #By default, most variables read are 2D cart and user does not specify it in the variable name
whites = ' '*(17 - len('(cart)') - len(var_name))
Dvar_output[var] = theFile.groups[var].variables[var + whites + '(cart)'][:,:].T
except:
try: #Variable 3D sv,time_les, level_les
Dvar_output[var] = theFile.groups[group_name].variables[var][:,:,:]
except:
try: #Variable 2D with type of variable specified (cart, neb, clear, cs1, cs2, cs3)
Dvar_output[var] = theFile.groups[group_name].variables[var][:,:].T
except ValueError: # Variable 1D
Dvar_output[var] = theFile.groups[group_name].variables[var][:]
elif theFile.groups[group_name].type == 'CART': # Budget CART type
shapeVar = theFile.groups[group_name].variables[suffix].shape
Ltosqueeze=[] # Build a tuple with the number of the axis which are 0 dimensions to be removed by np.squeeze
if shapeVar[0]==1: Ltosqueeze.append(0)
if shapeVar[1]==1: Ltosqueeze.append(1)
if shapeVar[2]==1: Ltosqueeze.append(2)
if shapeVar[3]==1: Ltosqueeze.append(3)
Ltosqueeze=tuple(Ltosqueeze)
Dvar_output[group_name] = np.squeeze(theFile.groups[group_name].variables[suffix][:,:,:,:], axis=Ltosqueeze)
else:
raise NameError("Type de groups variables not implemented in read_MNHfile.py")
return Dvar_output
for var in Dvar_input[ifile]: #For each var
if type(var) == tuple:
Dvar_output[ifile] = read_from_group(theFile, Dvar_output, var[0], var[1])
else:
Dvar_output[ifile] = read_var(theFile, Dvar_output, var)
return Dvar_output #Return the dic of [files][variables]
def list_size1(n_dim, named_dim):
Lsize1 = []
for i in range(n_dim):
if 'size1' == named_dim[i]:
Lsize1.append(True)
else:
Lsize1.append(False)
return Lsize1
def remove_PROC(var):
if '___PROC' in var:
var_name = var[:-8]
suffix = "" # No need of suffix for MNHVERSION < 550 (suffix is for NetCDF4 group)
elif '___ENDF' in var or '___INIF' in var or '___AVEF' in var:
var_name = var[:-7]
suffix = var[-4:]
else:
var_name = var
suffix = ''
return suffix, var_name
def get_group_from_varname(var):
group_name=''
for i in range(len(var)):
if var[i] is not ' ':
group_name+=var[i]
else: # As soon as the caracter is a blank, the group variable is set
break
return group_name