#!/usr/bin/env python
# -*- coding: utf-8 -*-
#*******************************************************************************
# @Author: Anne Fouilloux (University of Oslo)
#
# @Date: October 2014
#
# @Change History:
#
# November 2015 - Leopold Haimberger (University of Vienna):
# - extended with class Control
# - removed functions mkdir_p, daterange, years_between, months_between
# - added functions darain, dapoly, to_param_id, init128, normal_exit,
# my_error, clean_up, install_args_and_control,
# interpret_args_and_control,
# - removed function __del__ in class EIFLexpart
# - added the following functions in EIFlexpart:
# - create_namelist
# - process_output
# - deacc_fluxes
# - modified existing EIFlexpart - functions for the use in
# flex_extract
# - retrieve also longer term forecasts, not only analyses and
# short term forecast data
# - added conversion into GRIB2
# - added conversion into .fp format for faster execution of FLEXPART
# (see https://www.flexpart.eu/wiki/FpCtbtoWo4FpFormat)
#
# February 2018 - Anne Philipp (University of Vienna):
# - applied PEP8 style guide
# - added documentation
# - removed function getFlexpartTime in class EcFlexpart
# - outsourced class ControlFile
# - outsourced class MarsRetrieval
# - changed class name from EIFlexpart to EcFlexpart
# - applied minor code changes (style)
# - removed "dead code" , e.g. retrieval of Q since it is not needed
# - removed "times" parameter from retrieve-method since it is not used
#
# @License:
# (C) Copyright 2014-2018.
#
# This software is licensed under the terms of the Apache Licence Version 2.0
# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
#
# @Class Description:
# FLEXPART needs grib files in a specifc format. All necessary data fields
# for one time step are stored in a single file. The class represents an
# instance with all the parameter and settings necessary for retrieving
# MARS data and modifing them so they are fitting FLEXPART need. The class
# is able to disaggregate the fluxes and convert grid types to the one needed
# by FLEXPART, therefore using the FORTRAN program.
#
# @Class Content:
# - __init__
# - write_namelist
# - retrieve
# - process_output
# - create
# - deacc_fluxes
#
# @Class Attributes:
# - dtime
# - basetime
# - server
# - marsclass
# - stream
# - resol
# - accuracy
# - number
# - expver
# - glevelist
# - area
# - grid
# - level
# - levelist
# - types
# - dates
# - area
# - gaussian
# - params
# - inputdir
# - outputfilelist
#
#*******************************************************************************
#pylint: disable=unsupported-assignment-operation
# this is disabled because its an error in pylint for this specific case
#pylint: disable=consider-using-enumerate
# this is not useful in this case
# ------------------------------------------------------------------------------
# MODULES
# ------------------------------------------------------------------------------
import subprocess
import shutil
import os
import glob
from datetime import datetime, timedelta
import numpy as np
from gribapi import grib_set, grib_index_select, grib_new_from_index, grib_get,\
grib_write, grib_get_values, grib_set_values, grib_release,\
grib_index_release, grib_index_get
# software specific classes and modules from flex_extract
import _config
from GribTools import GribTools
from tools import init128, to_param_id, silent_remove, product, my_error
from MarsRetrieval import MarsRetrieval
import disaggregation
# ------------------------------------------------------------------------------
# CLASS
# ------------------------------------------------------------------------------
class EcFlexpart(object):
'''
Class to retrieve FLEXPART specific ECMWF data.
'''
# --------------------------------------------------------------------------
# CLASS FUNCTIONS
# --------------------------------------------------------------------------
def __init__(self, c, fluxes=False):
'''
@Description:
Creates an object/instance of EcFlexpart with the
associated settings of its attributes for the retrieval.
@Input:
self: instance of EcFlexpart
The current object of the class.
c: instance of class ControlFile
Contains all the parameters of CONTROL file, which are e.g.:
DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
For more information about format and content of the parameter
see documentation.
fluxes: boolean, optional
Decides if the flux parameter settings are stored or
the rest of the parameter list.
Default value is False.
@Return:
<nothing>
'''
# different mars types for retrieving data for flexpart
self.types = dict()
if c.maxstep > len(c.type): # Pure forecast mode
c.type = [c.type[1]]
c.step = ['{:0>3}'.format(int(c.step[0]))]
c.time = [c.time[0]]
for i in range(1, c.maxstep + 1):
c.type.append(c.type[0])
c.step.append('{:0>3}'.format(i))
c.time.append(c.time[0])
self.inputdir = c.inputdir
self.basetime = c.basetime
self.dtime = c.dtime
i = 0
if fluxes and c.maxstep <= 24:
# no forecast beyond one day is needed!
# Thus, prepare flux data manually as usual
# with only forecast fields with start times at 00/12
# (but without 00/12 fields since these are
# the initialisation times of the flux fields
# and therefore are zero all the time)
self.types[c.type[1]] = {'times': '00/12', 'steps':
'{}/to/12/by/{}'.format(c.dtime, c.dtime)}
else:
for ty, st, ti in zip(c.type, c.step, c.time):
btlist = range(24)
if c.basetime == '12':
btlist = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
if c.basetime == '00':
btlist = [13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 0]
if i % int(c.dtime) == 0 and (i in btlist or c.maxstep > 24):
if ty not in self.types.keys():
self.types[ty] = {'times': '', 'steps': ''}
if ti not in self.types[ty]['times']:
if self.types[ty]['times']:
self.types[ty]['times'] += '/'
self.types[ty]['times'] += ti
if st not in self.types[ty]['steps']:
if self.types[ty]['steps']:
self.types[ty]['steps'] += '/'
self.types[ty]['steps'] += st
i += 1
self.marsclass = c.marsclass
self.stream = c.stream
self.number = c.number
self.resol = c.resol
self.accuracy = c.accuracy
self.level = c.level
self.expver = c.expver
self.levelist = c.levelist
# for gaussian grid retrieval
self.glevelist = '1/to/' + c.level
if hasattr(c, 'gaussian') and c.gaussian:
self.gaussian = c.gaussian
else:
self.gaussian = ''
if 'N' in c.grid: # Gaussian output grid
self.grid = c.grid
self.area = 'G'
else:
self.grid = '{}/{}'.format(int(c.grid) / 1000., int(c.grid) / 1000.)
self.area = '{}/{}/{}/{}'.format(int(c.upper) / 1000.,
int(c.left) / 1000.,
int(c.lower) / 1000.,
int(c.right) / 1000.)
self.outputfilelist = []
# Now comes the nasty part that deals with the different
# scenarios we have:
# 1) Calculation of etadot on
# a) Gaussian grid
# b) Output grid
# c) Output grid using parameter 77 retrieved from MARS
# 3) Calculation/Retrieval of omega
# 4) Download also data for WRF
# Different grids need different retrievals
# SH = Spherical Harmonics, GG = Gaussian Grid,
# OG = Output Grid, ML = MultiLevel, SL = SingleLevel
self.params = {'SH__ML': '', 'SH__SL': '',
'GG__ML': '', 'GG__SL': '',
'OG__ML': '', 'OG__SL': '',
'OG_OROLSM_SL': '', 'OG_acc_SL': ''}
if fluxes is False:
self.params['SH__SL'] = ['LNSP', 'ML', '1', 'OFF']
# "SD/MSL/TCC/10U/10V/2T/2D/129/172"
self.params['OG__SL'] = ["141/151/164/165/166/167/168/129/172", \
'SFC', '1', self.grid]
if c.addpar:
if c.addpar[0] == '/':
c.addpar = c.addpar[1:]
self.params['OG__SL'][0] += '/' + '/'.join(c.addpar)
self.params['OG_OROLSM__SL'] = ["160/27/28/173", \
'SFC', '1', self.grid]
self.params['OG__ML'] = ['T/Q', 'ML', self.levelist, self.grid]
#if c.gauss == '0' and c.eta == '1':
if not c.gauss and c.eta:
# the simplest case
self.params['OG__ML'][0] += '/U/V/77'
#elif c.gauss == '0' and c.eta == '0':
elif not c.gauss and not c.eta:
# this is not recommended (inaccurate)
self.params['OG__ML'][0] += '/U/V'
#elif c.gauss == '1' and c.eta == '0':
elif c.gauss and not c.eta:
# this is needed for data before 2008, or for reanalysis data
self.params['GG__SL'] = ['Q', 'ML', '1', \
'{}'.format((int(self.resol) + 1) / 2)]
self.params['SH__ML'] = ['U/V/D', 'ML', self.glevelist, 'OFF']
else:
print('Warning: This is a very costly parameter combination, \
use only for debugging!')
self.params['GG__SL'] = ['Q', 'ML', '1', \
'{}'.format((int(self.resol) + 1) / 2)]
self.params['GG__ML'] = ['U/V/D/77', 'ML', self.glevelist, \
'{}'.format((int(self.resol) + 1) / 2)]
if c.omega:
self.params['OG__ML'][0] += '/W'
# add cloud water content if necessary
if c.cwc:
self.params['OG__ML'][0] += '/CLWC/CIWC'
# add vorticity and geopotential height for WRF if necessary
if c.wrf:
self.params['OG__ML'][0] += '/Z/VO'
if '/D' not in self.params['OG__ML'][0]:
self.params['OG__ML'][0] += '/D'
#wrf_sfc = 'sp/msl/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/stl1/ /
# stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4'.upper()
wrf_sfc = '134/235/167/165/166/168/129/172/34/31/141/ \
139/170/183/236/39/40/41/42'.upper()
lwrt_sfc = wrf_sfc.split('/')
for par in lwrt_sfc:
if par not in self.params['OG__SL'][0]:
self.params['OG__SL'][0] += '/' + par
else:
self.params['OG_acc_SL'] = ["LSP/CP/SSHF/EWSS/NSSS/SSR", \
'SFC', '1', self.grid]
# if needed, add additional WRF specific parameters here
return
def write_namelist(self, c, filename):
'''
@Description:
Creates a namelist file in the temporary directory and writes
the following values to it: maxl, maxb, mlevel,
mlevelist, mnauf, metapar, rlo0, rlo1, rla0, rla1,
momega, momegadiff, mgauss, msmooth, meta, metadiff, mdpdeta
@Input:
self: instance of EcFlexpart
The current object of the class.
c: instance of class ControlFile
Contains all the parameters of CONTROL files, which are e.g.:
DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
For more information about format and content of the parameter
see documentation.
filename: string
Name of the namelist file.
@Return:
<nothing>
'''
self.inputdir = c.inputdir
area = np.asarray(self.area.split('/')).astype(float)
grid = np.asarray(self.grid.split('/')).astype(float)
if area[1] > area[3]:
area[1] -= 360
maxl = int((area[3] - area[1]) / grid[1]) + 1
maxb = int((area[0] - area[2]) / grid[0]) + 1
with open(self.inputdir + '/' + filename, 'w') as f:
f.write('&NAMGEN\n')
f.write(',\n '.join(['maxl = ' + str(maxl), 'maxb = ' + str(maxb),
'mlevel = ' + str(self.level),
'mlevelist = ' + '"' + str(self.levelist)
+ '"',
'mnauf = ' + str(self.resol),
'metapar = ' + '77',
'rlo0 = ' + str(area[1]),
'rlo1 = ' + str(area[3]),
'rla0 = ' + str(area[2]),
'rla1 = ' + str(area[0]),
'momega = ' + str(c.omega),
'momegadiff = ' + str(c.omegadiff),
'mgauss = ' + str(c.gauss),
'msmooth = ' + str(c.smooth),
'meta = ' + str(c.eta),
'metadiff = ' + str(c.etadiff),
'mdpdeta = ' + str(c.dpdeta)]))
f.write('\n/\n')
return
def retrieve(self, server, dates, request, inputdir='.'):
'''
@Description:
Finalizing the retrieval information by setting final details
depending on grid type.
Prepares MARS retrievals per grid type and submits them.
@Input:
self: instance of EcFlexpart
The current object of the class.
server: instance of ECMWFService or ECMWFDataServer
The connection to the ECMWF server. This is different
for member state users which have full access and non
member state users which have only access to the public
data sets. The decision is made from command line argument
"public"; for public access its True (ECMWFDataServer)
for member state users its False (ECMWFService)
dates: string
Contains start and end date of the retrieval in the format
"YYYYMMDD/to/YYYYMMDD"
inputdir: string, optional
Path to the directory where the retrieved data is about
to be stored. The default is the current directory ('.').
@Return:
<nothing>
'''
self.dates = dates
self.server = server
self.inputdir = inputdir
oro = False
for ftype in self.types:
for pk, pv in self.params.iteritems():
if isinstance(pv, str):
continue
mftype = '' + ftype
mftime = self.types[ftype]['times']
mfstep = self.types[ftype]['steps']
mfdate = self.dates
mfstream = self.stream
mftarget = self.inputdir + "/" + ftype + pk + '.' + \
self.dates.split('/')[0] + '.' + str(os.getppid()) +\
'.' + str(os.getpid()) + ".grb"
if pk == 'OG__SL':
pass
if pk == 'OG_OROLSM__SL':
if not oro:
mfstream = 'OPER'
mftype = 'AN'
mftime = '00'
mfstep = '000'
mfdate = self.dates.split('/')[0]
mftarget = self.inputdir + "/" + pk + '.' + mfdate + \
'.' + str(os.getppid()) + '.' + \
str(os.getpid()) + ".grb"
oro = True
else:
continue
if pk == 'GG__SL' and pv[0] == 'Q':
area = ""
gaussian = 'reduced'
else:
area = self.area
gaussian = self.gaussian
# ------ on demand path --------------------------------------------------
if not self.basetime:
MR = MarsRetrieval(self.server,
marsclass=self.marsclass,
stream=mfstream,
type=mftype,
levtype=pv[1],
levelist=pv[2],
resol=self.resol,
gaussian=gaussian,
accuracy=self.accuracy,
grid=pv[3],
target=mftarget,
area=area,
date=mfdate,
time=mftime,
number=self.number,
step=mfstep,
expver=self.expver,
param=pv[0])
if request == 0:
MR.display_info()
MR.data_retrieve()
elif request == 1:
MR.print_info()
elif request == 2:
MR.print_info()
MR.display_info()
MR.data_retrieve()
else:
print('Failure')
# ------ operational path ------------------------------------------------
else:
# check if mars job requests fields beyond basetime.
# If yes eliminate those fields since they may not
# be accessible with user's credentials
if 'by' in mfstep:
sm1 = 2
else:
sm1 = -1
if 'by' in mftime:
tm1 = 2
else:
tm1 = -1
maxdate = datetime.strptime(mfdate.split('/')[-1] +
mftime.split('/')[tm1],
'%Y%m%d%H')
istep = int(mfstep.split('/')[sm1])
maxtime = maxdate + timedelta(hours=istep)
elimit = datetime.strptime(mfdate.split('/')[-1] +
self.basetime, '%Y%m%d%H')
if self.basetime == '12':
# -------------- flux data ----------------------------
if 'acc' in pk:
# Strategy:
# if maxtime-elimit >= 24h reduce date by 1,
# if 12h <= maxtime-elimit<12h reduce time for last date
# if maxtime-elimit<12h reduce step for last time
# A split of the MARS job into 2 is likely necessary.
maxtime = elimit - timedelta(hours=24)
mfdate = '/'.join(['/'.join(mfdate.split('/')[:-1]),
datetime.strftime(maxtime,
'%Y%m%d')])
MR = MarsRetrieval(self.server,
marsclass=self.marsclass,
stream=self.stream,
type=mftype,
levtype=pv[1],
levelist=pv[2],
resol=self.resol,
gaussian=gaussian,
accuracy=self.accuracy,
grid=pv[3],
target=mftarget,
area=area,
date=mfdate,
time=mftime,
number=self.number,
step=mfstep,
expver=self.expver,
param=pv[0])
MR.display_info()
MR.data_retrieve()
maxtime = elimit - timedelta(hours=12)
mfdate = datetime.strftime(maxtime, '%Y%m%d')
mftime = '00'
mftarget = self.inputdir + "/" + ftype + pk + \
'.' + mfdate + '.' + str(os.getppid()) +\
'.' + str(os.getpid()) + ".grb"
MR = MarsRetrieval(self.server,
marsclass=self.marsclass,
stream=self.stream,
type=mftype,
levtype=pv[1],
levelist=pv[2],
resol=self.resol,
gaussian=gaussian,
accuracy=self.accuracy,
grid=pv[3],
target=mftarget,
area=area,
date=mfdate,
time=mftime,
number=self.number,
step=mfstep,
expver=self.expver,
param=pv[0])
MR.display_info()
MR.data_retrieve()
# -------------- non flux data ------------------------
else:
MR = MarsRetrieval(self.server,
marsclass=self.marsclass,
stream=self.stream,
type=mftype,
levtype=pv[1],
levelist=pv[2],
resol=self.resol,
gaussian=gaussian,
accuracy=self.accuracy,
grid=pv[3],
target=mftarget,
area=area,
date=mfdate,
time=mftime,
number=self.number,
step=mfstep,
expver=self.expver,
param=pv[0])
MR.display_info()
MR.data_retrieve()
else: # basetime == 0 ??? #AP
maxtime = elimit - timedelta(hours=24)
mfdate = datetime.strftime(maxtime, '%Y%m%d')
mftimesave = ''.join(mftime)
if '/' in mftime:
times = mftime.split('/')
while ((int(times[0]) +
int(mfstep.split('/')[0]) <= 12) and
(pk != 'OG_OROLSM__SL') and 'acc' not in pk):
times = times[1:]
if len(times) > 1:
mftime = '/'.join(times)
else:
mftime = times[0]
MR = MarsRetrieval(self.server,
marsclass=self.marsclass,
stream=self.stream,
type=mftype,
levtype=pv[1],
levelist=pv[2],
resol=self.resol,
gaussian=gaussian,
accuracy=self.accuracy,
grid=pv[3],
target=mftarget,
area=area,
date=mfdate,
time=mftime,
number=self.number,
step=mfstep,
expver=self.expver,
param=pv[0])
MR.display_info()
MR.data_retrieve()
if (int(mftimesave.split('/')[0]) == 0 and
int(mfstep.split('/')[0]) == 0 and
pk != 'OG_OROLSM__SL'):
mfdate = datetime.strftime(elimit, '%Y%m%d')
mftime = '00'
mfstep = '000'
mftarget = self.inputdir + "/" + ftype + pk + \
'.' + mfdate + '.' + str(os.getppid()) +\
'.' + str(os.getpid()) + ".grb"
MR = MarsRetrieval(self.server,
marsclass=self.marsclass,
stream=self.stream,
type=mftype,
levtype=pv[1],
levelist=pv[2],
resol=self.resol,
gaussian=gaussian,
accuracy=self.accuracy,
grid=pv[3],
target=mftarget,
area=area,
date=mfdate,
time=mftime,
number=self.number,
step=mfstep,
expver=self.expver,
param=pv[0])
MR.display_info()
MR.data_retrieve()
if request == 0 or request == 2:
print('MARS retrieve done ... ')
elif request == 1:
print('MARS request printed ...')
return
def process_output(self, c):
'''
@Description:
The grib files are postprocessed depending on the selection in
CONTROL file. The resulting files are moved to the output
directory if its not equla to the input directory.
The following modifications might be done if
properly switched in CONTROL file:
GRIB2 - Conversion to GRIB2
ECTRANS - Transfer of files to gateway server
ECSTORAGE - Storage at ECMWF server
GRIB2FLEXPART - Conversion of GRIB files to FLEXPART binary format
@Input:
self: instance of EcFlexpart
The current object of the class.
c: instance of class ControlFile
Contains all the parameters of CONTROL file, which are e.g.:
DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
For more information about format and content of the parameter
see documentation.
@Return:
<nothing>
'''
print('\n\nPostprocessing:\n Format: {}\n'.format(c.format))
if not c.ecapi:
print('ecstorage: {}\n ecfsdir: {}\n'.
format(c.ecstorage, c.ecfsdir))
#if not hasattr(c, 'gateway'):
# c.gateway = os.getenv('GATEWAY')
#if not hasattr(c, 'destination'):
# c.destination = os.getenv('DESTINATION')
print('ectrans: {}\n gateway: {}\n destination: {}\n '
.format(c.ectrans, c.gateway, c.destination))
print('Output filelist: \n')
print(self.outputfilelist)
if c.format.lower() == 'grib2':
for ofile in self.outputfilelist:
p = subprocess.check_call(['grib_set', '-s', 'edition=2, \
productDefinitionTemplateNumber=8',
ofile, ofile + '_2'])
p = subprocess.check_call(['mv', ofile + '_2', ofile])
if c.ectrans and not c.ecapi:
for ofile in self.outputfilelist:
p = subprocess.check_call(['ectrans', '-overwrite', '-gateway',
c.gateway, '-remote', c.destination,
'-source', ofile])
#print('ectrans:', p)
if c.ecstorage and not c.ecapi:
for ofile in self.outputfilelist:
p = subprocess.check_call(['ecp', '-o', ofile,
os.path.expandvars(c.ecfsdir)])
if c.outputdir != c.inputdir:
for ofile in self.outputfilelist:
p = subprocess.check_call(['mv', ofile, c.outputdir])
# prepare environment for the grib2flexpart run
# to convert grib to flexpart binary
if c.grib2flexpart:
# generate AVAILABLE file
# Example of AVAILABLE file data:
# 20131107 000000 EN13110700 ON DISC
clist = []
for ofile in self.outputfilelist:
fname = ofile.split('/')
if '.' in fname[-1]:
l = fname[-1].split('.')
timestamp = datetime.strptime(l[0][-6:] + l[1],
'%y%m%d%H')
timestamp += timedelta(hours=int(l[2]))
cdate = datetime.strftime(timestamp, '%Y%m%d')
chms = datetime.strftime(timestamp, '%H%M%S')
else:
cdate = '20' + fname[-1][-8:-2]
chms = fname[-1][-2:] + '0000'
clist.append(cdate + ' ' + chms + ' '*6 +
fname[-1] + ' '*14 + 'ON DISC')
clist.sort()
with open(c.outputdir + '/' + 'AVAILABLE', 'w') as f:
f.write('\n'.join(clist) + '\n')
# generate pathnames file
pwd = os.path.abspath(c.outputdir)
with open(pwd + '/pathnames', 'w') as f:
f.write(pwd + '/Options/\n')
f.write(pwd + '/\n')
f.write(pwd + '/\n')
f.write(pwd + '/AVAILABLE\n')
f.write(' = == = == = == = == = == == = \n')
# create Options dir if necessary
if not os.path.exists(pwd + '/Options'):
os.makedirs(pwd+'/Options')
# read template COMMAND file
with open(os.path.expandvars(os.path.expanduser(
c.flexpart_root_scripts)) + '/../Options/COMMAND', 'r') as f:
lflist = f.read().split('\n')
# find index of list where to put in the
# date and time information
# usually after the LDIRECT parameter
i = 0
for l in lflist:
if 'LDIRECT' in l.upper():
break
i += 1
# insert the date and time information of run start and end
# into the list of lines of COMMAND file
lflist = lflist[:i+1] + \
[clist[0][:16], clist[-1][:16]] + \
lflist[i+3:]
# write the new COMMAND file
with open(pwd + '/Options/COMMAND', 'w') as g:
g.write('\n'.join(lflist) + '\n')
# change to outputdir and start the grib2flexpart run
# afterwards switch back to the working dir
os.chdir(c.outputdir)
p = subprocess.check_call([
os.path.expandvars(os.path.expanduser(c.flexpart_root_scripts))
+ '/../FLEXPART_PROGRAM/grib2flexpart', 'useAvailable', '.'])
os.chdir(pwd)
return
def create(self, inputfiles, c):
'''
@Description:
This method is based on the ECMWF example index.py
https://software.ecmwf.int/wiki/display/GRIB/index.py
An index file will be created which depends on the combination
of "date", "time" and "stepRange" values. This is used to iterate
over all messages in each grib file which were passed through the
parameter "inputfiles" to seperate specific parameters into fort.*
files. Afterwards the FORTRAN program Convert2 is called to convert
the data fields all to the same grid and put them in one file
per unique time step (combination of "date", "time" and
"stepRange").
@Input:
self: instance of EcFlexpart
The current object of the class.
inputfiles: instance of UioFiles
Contains a list of files.
c: instance of class ControlFile
Contains all the parameters of CONTROL files, which are e.g.:
DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
For more information about format and content of the parameter
see documentation.
@Return:
<nothing>
'''
table128 = init128(_config.PATH_GRIBTABLE)
wrfpars = to_param_id('sp/mslp/skt/2t/10u/10v/2d/z/lsm/sst/ci/sd/\
stl1/stl2/stl3/stl4/swvl1/swvl2/swvl3/swvl4',
table128)
index_keys = ["date", "time", "step"]
indexfile = os.path.join(c.inputdir, _config.FILE_GRIB_INDEX)
silent_remove(indexfile)
grib = GribTools(inputfiles.files)
# creates new index file
iid = grib.index(index_keys=index_keys, index_file=indexfile)
# read values of index keys
index_vals = []
for key in index_keys:
index_vals.append(grib_index_get(iid, key))
print(index_vals[-1])
# index_vals looks for example like:
# index_vals[0]: ('20171106', '20171107', '20171108') ; date
# index_vals[1]: ('0', '1200', '1800', '600') ; time
# index_vals[2]: ('0', '12', '3', '6', '9') ; stepRange
fdict = {'10':None, '11':None, '12':None, '13':None, '16':None,
'17':None, '19':None, '21':None, '22':None, '20':None}
for prod in product(*index_vals):
# e.g. prod = ('20170505', '0', '12')
# ( date ,time, step)
# per date e.g. time = 0, 1200
# per time e.g. step = 3, 6, 9, 12
# flag for Fortran program CONVERT2 and file merging
convertFlag = False
print('current prod: ', prod)
# e.g. prod = ('20170505', '0', '12')
# ( date ,time, step)
# per date e.g. time = 0, 600, 1200, 1800
# per time e.g. step = 0, 3, 6, 9, 12
for i in range(len(index_keys)):
grib_index_select(iid, index_keys[i], prod[i])
# get first id from current product
gid = grib_new_from_index(iid)
# if there is data for this product combination
# prepare some date and time parameter before reading the data
if gid is not None:
# Combine all temporary data files into final grib file if
# gid is at least one time not None. Therefore set convertFlag
# to save information. The fortran program CONVERT2 is also
# only done if convertFlag is True
convertFlag = True
# remove old fort.* files and open new ones
# they are just valid for a single product
for k, f in fdict.iteritems():
fortfile = os.path.join(c.inputdir, 'fort.' + k)
silent_remove(fortfile)
fdict[k] = open(fortfile, 'w')
cdate = str(grib_get(gid, 'date'))
time = grib_get(gid, 'time')
step = grib_get(gid, 'step')
# create correct timestamp from the three time informations
# date, time, step
timestamp = datetime.strptime(cdate + '{:0>2}'.format(time/100),
'%Y%m%d%H')
timestamp += timedelta(hours=int(step))
cdateH = datetime.strftime(timestamp, '%Y%m%d%H')
if c.basetime is not None:
slimit = datetime.strptime(c.start_date + '00', '%Y%m%d%H')
bt = '23'
if c.basetime == '00':
bt = '00'
slimit = datetime.strptime(c.end_date + bt, '%Y%m%d%H')\
- timedelta(hours=12-int(c.dtime))
if c.basetime == '12':
bt = '12'
slimit = datetime.strptime(c.end_date + bt, '%Y%m%d%H')\
- timedelta(hours=12-int(c.dtime))
elimit = datetime.strptime(c.end_date + bt, '%Y%m%d%H')
if timestamp < slimit or timestamp > elimit:
continue
else:
pass
try:
if c.wrf:
if 'olddate' not in locals() or cdate != olddate:
fwrf = open(os.path.join(c.outputdir,
'WRF' + cdate + '.{:0>2}'.format(time) +
'.000.grb2'), 'w')
olddate = cdate[:]
except AttributeError:
pass
# helper variable to remember which fields were already used.
savedfields = []
while 1:
if gid is None:
break
paramId = grib_get(gid, 'paramId')
gridtype = grib_get(gid, 'gridType')
levtype = grib_get(gid, 'typeOfLevel')
if paramId == 133 and gridtype == 'reduced_gg':
# Specific humidity (Q.grb) is used as a template only
# so we need the first we "meet"
with open(os.path.join(c.inputdir, 'fort.18'), 'w') as fout:
grib_write(gid, fout)
elif paramId == 131 or paramId == 132:
grib_write(gid, fdict['10'])
elif paramId == 130:
grib_write(gid, fdict['11'])
elif paramId == 133 and gridtype != 'reduced_gg':
grib_write(gid, fdict['17'])
elif paramId == 152:
grib_write(gid, fdict['12'])
elif paramId == 155 and gridtype == 'sh':
grib_write(gid, fdict['13'])
elif paramId in [129, 138, 155] and levtype == 'hybrid' \
and c.wrf:
pass
elif paramId == 246 or paramId == 247:
# cloud liquid water and ice
if paramId == 246:
clwc = grib_get_values(gid)
else:
clwc += grib_get_values(gid)
grib_set_values(gid, clwc)
grib_set(gid, 'paramId', 201031)
grib_write(gid, fdict['22'])
elif paramId == 135:
grib_write(gid, fdict['19'])
elif paramId == 77:
grib_write(gid, fdict['21'])
else:
if paramId not in savedfields:
grib_write(gid, fdict['16'])
savedfields.append(paramId)
else:
print('duplicate ' + str(paramId) + ' not written')
try:
if c.wrf:
# model layer
if levtype == 'hybrid' and \
paramId in [129, 130, 131, 132, 133, 138, 155]:
grib_write(gid, fwrf)
# sfc layer
elif paramId in wrfpars:
grib_write(gid, fwrf)
except AttributeError:
pass
grib_release(gid)
gid = grib_new_from_index(iid)
for f in fdict.values():
f.close()
# call for CONVERT2 if flag is True
if convertFlag:
pwd = os.getcwd()
os.chdir(c.inputdir)
if os.stat('fort.21').st_size == 0 and c.eta:
print('Parameter 77 (etadot) is missing, most likely it is \
not available for this type or date/time\n')
print('Check parameters CLASS, TYPE, STREAM, START_DATE\n')
my_error(c.mailfail, 'fort.21 is empty while parameter eta \
is set to 1 in CONTROL file')
# create the corresponding output file fort.15
# (generated by CONVERT2) + fort.16 (paramId 167 and 168)
p = subprocess.check_call([os.path.join(c.exedir, 'CONVERT2')],
shell=True)
os.chdir(pwd)
# create final output filename, e.g. EN13040500 (ENYYMMDDHH)
fnout = os.path.join(c.inputdir, c.prefix)
if c.maxstep > 12:
suffix = cdate[2:8] + '.{:0>2}'.format(time/100) + \
'.{:0>3}'.format(step)
else:
suffix = cdateH[2:10]
fnout += suffix
print("outputfile = " + fnout)
self.outputfilelist.append(fnout) # needed for final processing
# create outputfile and copy all data from intermediate files
# to the outputfile (final GRIB files)
orolsm = os.path.basename(glob.glob(
c.inputdir + '/OG_OROLSM__SL.*.' + c.ppid + '*')[0])
fluxfile = 'flux' + cdate[0:2] + suffix
if not c.cwc:
flist = ['fort.15', fluxfile, 'fort.16', orolsm]
else:
flist = ['fort.15', 'fort.22', fluxfile, 'fort.16', orolsm]
with open(fnout, 'wb') as fout:
for f in flist:
shutil.copyfileobj(open(os.path.join(c.inputdir, f),
'rb'), fout)
if c.omega:
with open(os.path.join(c.outputdir, 'OMEGA'), 'wb') as fout:
shutil.copyfileobj(
open(os.path.join(c.inputdir, 'fort.25'),
'rb'), fout)
else:
pass
if c.wrf:
fwrf.close()
grib_index_release(iid)
return
def deacc_fluxes(self, inputfiles, c):
'''
@Description:
Goes through all flux fields in ordered time and de-accumulate
the fields. Afterwards the fields are disaggregated in time.
Different versions of disaggregation is provided for rainfall
data (darain, modified linear) and the surface fluxes and
stress data (dapoly, cubic polynomial).
@Input:
self: instance of EcFlexpart
The current object of the class.
inputfiles: instance of UioFiles
Contains a list of files.
c: instance of class ControlFile
Contains all the parameters of CONTROL file, which are e.g.:
DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
For more information about format and content of the parameter
see documentation.
@Return:
<nothing>
'''
table128 = init128(_config.PATH_GRIBTABLE)
pars = to_param_id(self.params['OG_acc_SL'][0], table128)
index_keys = ["date", "time", "step"]
indexfile = os.path.join(c.inputdir, _config.FILE_GRIB_INDEX)
silent_remove(indexfile)
grib = GribTools(inputfiles.files)
# creates new index file
iid = grib.index(index_keys=index_keys, index_file=indexfile)
# read values of index keys
index_vals = []
for key in index_keys:
key_vals = grib_index_get(iid, key)
print(key_vals)
# have to sort the steps for disaggregation,
# therefore convert to int first
if key == 'step':
key_vals = [int(k) for k in key_vals]
key_vals.sort()
key_vals = [str(k) for k in key_vals]
index_vals.append(key_vals)
# index_vals looks for example like:
# index_vals[0]: ('20171106', '20171107', '20171108') ; date
# index_vals[1]: ('0', '1200') ; time
# index_vals[2]: (3', '6', '9', '12') ; stepRange
valsdict = {}
svalsdict = {}
stepsdict = {}
for p in pars:
valsdict[str(p)] = []
svalsdict[str(p)] = []
stepsdict[str(p)] = []
print('maxstep: ', c.maxstep)
for prod in product(*index_vals):
# e.g. prod = ('20170505', '0', '12')
# ( date ,time, step)
# per date e.g. time = 0, 1200
# per time e.g. step = 3, 6, 9, 12
print('current prod: ', prod)
for i in range(len(index_keys)):
grib_index_select(iid, index_keys[i], prod[i])
# get first id from current product
gid = grib_new_from_index(iid)
# if there is data for this product combination
# prepare some date and time parameter before reading the data
if gid is not None:
cdate = grib_get(gid, 'date')
time = grib_get(gid, 'time')
step = grib_get(gid, 'step')
# date+time+step-2*dtime
# (since interpolated value valid for step-2*dtime)
sdate = datetime(year=cdate/10000,
month=(cdate % 10000)/100,
day=(cdate % 100),
hour=time/100)
fdate = sdate + timedelta(hours=step-2*int(c.dtime))
sdates = sdate + timedelta(hours=step)
elimit = None
else:
break
if c.maxstep > 12:
fnout = os.path.join(c.inputdir, 'flux' +
sdate.strftime('%Y%m%d') +
'.{:0>2}'.format(time/100) +
'.{:0>3}'.format(step-2*int(c.dtime)))
gnout = os.path.join(c.inputdir, 'flux' +
sdate.strftime('%Y%m%d') +
'.{:0>2}'.format(time/100) +
'.{:0>3}'.format(step-int(c.dtime)))
hnout = os.path.join(c.inputdir, 'flux' +
sdate.strftime('%Y%m%d') +
'.{:0>2}'.format(time/100) +
'.{:0>3}'.format(step))
else:
fnout = os.path.join(c.inputdir, 'flux' +
fdate.strftime('%Y%m%d%H'))
gnout = os.path.join(c.inputdir, 'flux' +
(fdate + timedelta(hours=int(c.dtime))).
strftime('%Y%m%d%H'))
hnout = os.path.join(c.inputdir, 'flux' +
sdates.strftime('%Y%m%d%H'))
print("outputfile = " + fnout)
f_handle = open(fnout, 'w')
g_handle = open(gnout, 'w')
h_handle = open(hnout, 'w')
# read message for message and store relevant data fields
# data keywords are stored in pars
while 1:
if gid is None:
break
cparamId = str(grib_get(gid, 'paramId'))
step = grib_get(gid, 'step')
atime = grib_get(gid, 'time')
ni = grib_get(gid, 'Ni')
nj = grib_get(gid, 'Nj')
if cparamId in valsdict.keys():
values = grib_get_values(gid)
vdp = valsdict[cparamId]
svdp = svalsdict[cparamId]
sd = stepsdict[cparamId]
if cparamId == '142' or cparamId == '143':
fak = 1. / 1000.
else:
fak = 3600.
values = (np.reshape(values, (nj, ni))).flatten() / fak
vdp.append(values[:]) # save the accumulated values
if step <= int(c.dtime):
svdp.append(values[:] / int(c.dtime))
else: # deaccumulate values
svdp.append((vdp[-1] - vdp[-2]) / int(c.dtime))
print(cparamId, atime, step, len(values),
values[0], np.std(values))
# save the 1/3-hourly or specific values
# svdp.append(values[:])
sd.append(step)
# len(svdp) correspond to the time
if len(svdp) >= 3:
if len(svdp) > 3:
if cparamId == '142' or cparamId == '143':
values = disaggregation.darain(svdp)
else:
values = disaggregation.dapoly(svdp)
if not (step == c.maxstep and c.maxstep > 12 \
or sdates == elimit):
vdp.pop(0)
svdp.pop(0)
else:
if c.maxstep > 12:
values = svdp[1]
else:
values = svdp[0]
grib_set_values(gid, values)
if c.maxstep > 12:
grib_set(gid, 'step', max(0, step-2*int(c.dtime)))
else:
grib_set(gid, 'step', 0)
grib_set(gid, 'time', fdate.hour*100)
grib_set(gid, 'date', fdate.year*10000 +
fdate.month*100+fdate.day)
grib_write(gid, f_handle)
if c.basetime is not None:
elimit = datetime.strptime(c.end_date +
c.basetime, '%Y%m%d%H')
else:
elimit = sdate + timedelta(2*int(c.dtime))
# squeeze out information of last two steps contained
# in svdp
# if step+int(c.dtime) == c.maxstep and c.maxstep>12
# or sdates+timedelta(hours = int(c.dtime))
# >= elimit:
# Note that svdp[0] has not been popped in this case
if step == c.maxstep and c.maxstep > 12 or \
sdates == elimit:
values = svdp[3]
grib_set_values(gid, values)
grib_set(gid, 'step', 0)
truedatetime = fdate + timedelta(hours=
2*int(c.dtime))
grib_set(gid, 'time', truedatetime.hour * 100)
grib_set(gid, 'date', truedatetime.year * 10000 +
truedatetime.month * 100 +
truedatetime.day)
grib_write(gid, h_handle)
#values = (svdp[1]+svdp[2])/2.
if cparamId == '142' or cparamId == '143':
values = disaggregation.darain(list(reversed(svdp)))
else:
values = disaggregation.dapoly(list(reversed(svdp)))
grib_set(gid, 'step', 0)
truedatetime = fdate + timedelta(hours=int(c.dtime))
grib_set(gid, 'time', truedatetime.hour * 100)
grib_set(gid, 'date', truedatetime.year * 10000 +
truedatetime.month * 100 +
truedatetime.day)
grib_set_values(gid, values)
grib_write(gid, g_handle)
grib_release(gid)
gid = grib_new_from_index(iid)
f_handle.close()
g_handle.close()
h_handle.close()
grib_index_release(iid)
return