observationoperator.py 13.5 KB
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#!/usr/bin/env python
# model.py

import logging
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import os
import sys
import subprocess
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import da.cosmo.io4 as io
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import numpy as np
from netCDF4 import Dataset
from datetime import datetime, timedelta
from dateutil import rrule
from cdo import *
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from . import site_height
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from da.cosmo.icbc4ctdas import ct
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from itertools import repeat
from multiprocessing import Pool
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from da.tools.general import to_datetime
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identifier = 'ObservationOperator'
version = '10'
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cdo = Cdo()

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################### Begin Class ObservationOperator ###################
class ObservationOperator(object):
    def __init__(self, dacycle=None):
        self.ID = identifier
        self.version = version
        self.restart_filelist = []
        self.output_filelist = []
        self.outputdir = None # Needed for opening the samples.nc files created 

        logging.info('Observation Operator object initialized: %s' % self.ID)

        if dacycle != None:
            self.dacycle = dacycle
        else:
            self.dacycle = {}

    
    def get_initial_data(self):
        """ This method places all initial data needed by an ObservationOperator in the proper folder for the model """

    def setup(self,dacycle):
        """ Perform all steps necessary to start the observation operator through a simple Run() call """

        self.dacycle = dacycle
        self.outputdir = dacycle['dir.output']

    def prepare_run(self):
        """ Prepare the running of the actual forecast model, for example compile code """

	# Define the name of the file that will contain the modeled output of each observation

        self.simulated_file = os.path.join(self.outputdir, 'samples_simulated.%s.nc' % self.dacycle['time.sample.stamp'])
        self.forecast_nmembers = int(self.dacycle['da.optimizer.nmembers'])

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    def run(self,lag,dacycle,statevector):
        members = statevector.ensemble_members[lag]
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        absolute_start_time = str((to_datetime(dacycle['abs.time.start'])).strftime('%Y%m%d%H'))
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        absolute_start_time_ch = str((to_datetime(dacycle['abs.time.start'])).strftime('%Y-%m-%d'))
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        starth = abs((to_datetime(dacycle['abs.time.start'])-dacycle['time.start']).days)*24
        endh = abs((to_datetime(dacycle['abs.time.start'])-dacycle['time.finish']).days)*24

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        f = io.CT_CDF(self.simulated_file, method='create')
        logging.debug('Creating new simulated observation file in ObservationOperator (%s)' % self.simulated_file)
	
        dimid = f.createDimension('obs_num', size=None)
        dimid = ('obs_num',)
        savedict = io.std_savedict.copy() 
        savedict['name'] = "obs_num"
        savedict['dtype'] = "int"
        savedict['long_name'] = "Unique_Dataset_observation_index_number"
        savedict['units'] = ""
        savedict['dims'] = dimid
        savedict['comment'] = "Unique index number within this dataset ranging from 0 to UNLIMITED."
        f.add_data(savedict,nsets=0)

        dimmember = f.createDimension('nmembers', size=self.forecast_nmembers)
        dimmember = ('nmembers',)
        savedict = io.std_savedict.copy() 
        savedict['name'] = "flask"
        savedict['dtype'] = "float"
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        savedict['long_name'] = "mole_fraction_of_trace_gas_in_dry_air"
        savedict['units'] = "ppm"
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        savedict['dims'] = dimid + dimmember
        savedict['comment'] = "Simulated model value created by COSMO"
        f.add_data(savedict,nsets=0)

	# Open file with x,y,z,t of model samples that need to be sampled

        f_in = io.ct_read(self.dacycle['ObsOperator.inputfile'],method='read') 

	# Get simulated values and ID

        ids = f_in.get_variable('obs_num')
        obs = f_in.get_variable('observed')
        mdm = f_in.get_variable('modeldatamismatch')

        f_in.close()

        shape = (self.forecast_nmembers,mdm.size)
        model_data=np.empty(shape=shape)   # 3x7

#        self.obspack_dir = dacycle.dasystem['obspack.input.dir']

#        infile = os.path.join(self.obspack_dir, 'summary', '%s_dataset_summary.txt' % (self.obspack_id,))
#        infile = "/store/empa/em05/parsenov/obspack/summary/obspack_co2_1_GLOBALVIEWplus_v3.2_2017-11-02_dataset_summary.txt"
#        f = open(infile, 'r')
#        lines = f.readlines()
#        f.close()
#        ncfilelist = []

#        for line in lines:
#            if not line.startswith('# dataset:'): continue

#            items = line.split(':')
#            ncfile = items[1].strip()

#            ncfilelist += [ncfile]

#        for ncfile in ncfilelist:
#            infile = os.path.join(ncfile + '.nc')

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 # UNCOMMENT FROM HERE

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#        co2_bg = np.empty(self.forecast_nmembers)
#
 #       logging.info('Multiplying emissions with parameters for lag %d' % (lag))
  #      for dt in rrule.rrule(rrule.HOURLY, dtstart=dacycle['time.start']+timedelta(hours=24*lag*int(dacycle['time.cycle'])), until=dacycle['time.start']+timedelta(hours=(lag+1)*24*int(dacycle['time.cycle']))):
   #         for ens in range(0,self.forecast_nmembers):
    #            dthh = dt.strftime('%H')
     #           co2_bg[ens] = members[ens].param_values[-1]
      #          ens = str(ens).zfill(3)
       #         cdo.setunit("'kg m-2 s-1' -expr,GPP_"+ens+"_F=CO2_GPP_F*parametermap -merge "+os.path.join(dacycle['da.bio.input'], 'gpp_%s.nc' % dt.strftime('%Y%m%d%H')), input = os.path.join(dacycle['dir.input'],"parameters_gpp_lag"+str(lag)+"."+ens+".nc"), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "gpp_"+ens+"_%s.nc" % dt.strftime('%Y%m%d%H')))
        #        cdo.setunit("'kg m-2 s-1' -expr,RESP_"+ens+"_F=CO2_RESP_F*parametermap -merge "+os.path.join(dacycle['da.bio.input'], 'ra_%s.nc' % dt.strftime('%Y%m%d%H')), input = os.path.join(dacycle['dir.input'],"parameters_resp_lag"+str(lag)+"."+ens+".nc"), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "ra_"+ens+"_%s.nc" % dt.strftime('%Y%m%d%H')))
#        #    logging.debug('Background CO2 params are (%s)' % co2_bg)
          #  if dthh=='00':
           #     ct(dt.strftime('%Y%m%d'), co2_bg)
#
 #           cdo.merge(input = os.path.join(dacycle['da.bio.input'], 'ensemble', "gpp_???_%s.nc" % dt.strftime('%Y%m%d%H')), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "gpp_%s.nc" % dt.strftime('%Y%m%d%H')))
  #          cdo.merge(input = os.path.join(dacycle['da.bio.input'], 'ensemble', "ra_???_%s.nc" % dt.strftime('%Y%m%d%H')), output = os.path.join(dacycle['da.bio.input'], 'ensemble', "ra_%s.nc" % dt.strftime('%Y%m%d%H')))
#
 #       os.chdir(dacycle['da.obsoperator.home'])
#
        if os.path.exists(dacycle['dir.da_run']+'/'+absolute_start_time+"_"+str(starth+lag*168)+"_"+str(endh+lag*168)+"/cosmo/output/"):
            if os.path.exists(dacycle['dir.da_run']+"/non_opt_"+absolute_start_time+"_"+str(starth+lag*168)+"_"+str(endh+lag*168)+"/cosmo/output/"):
                os.rename(dacycle['dir.da_run']+"/"+absolute_start_time+"_"+str(starth+lag*168)+"_"+str(endh+lag*168), dacycle['dir.da_run']+"/old_non_opt_"+dacycle['time.start'].strftime('%Y%m%d%H')+"_"+str(starth+lag*168)+"_"+str(endh+lag*168))
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            else:
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                os.rename(dacycle['dir.da_run']+"/"+absolute_start_time+"_"+str(starth+lag*168)+"_"+str(endh+lag*168), dacycle['dir.da_run']+"/non_opt_"+dacycle['time.start'].strftime('%Y%m%d%H')+"_"+str(starth+lag*168)+"_"+str(endh+lag*168))
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        os.system('python run_chain.py 21ens '+absolute_start_time_ch+' '+str(starth+lag*168)+' '+str(endh+lag*168)+' -j meteo icbc emissions biofluxes int2lm post_int2lm cosmo')
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        os.chdir(dacycle['dir.da_run'])

        args = [
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            (dacycle, starth+168*lag, endh+168*lag-1, n)
            for n in range(0,self.forecast_nmembers)
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        ]

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        with Pool(self.forecast_nmembers) as pool:
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            pool.starmap(self.extract_model_data, args)
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   #         pool.close()  
    #        pool.join()  
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        for i in range(0,self.forecast_nmembers):
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            idx = str(i).zfill(3)
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#            cosmo_file = os.path.join('/store/empa/em05/parsenov/cosmo_data/51ens/model_'+idx+'_%s.nc' % dacycle['time.sample.stamp'])
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            cosmo_file = os.path.join('/store/empa/em05/parsenov/cosmo_data/model_'+idx+'_%s.nc' % dacycle['time.sample.stamp'])
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            ifile = Dataset(cosmo_file, mode='r')
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            model_data[i,:] = (np.squeeze(ifile.variables['CO2'][:])*29./44.01)*1E6   # in ppm
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            ifile.close()

        for j,data in enumerate(zip(ids,obs,mdm)):
            f.variables['obs_num'][j] = data[0]		
            f.variables['flask'][j,:] = model_data[:,j]
        f.close()
#### WARNING ACHTUNG PAZNJA POZOR VNEMANIE data[2] is model data mismatch (=1000) by default in tools/io4.py!!! pavle


        logging.info('ObservationOperator finished successfully, output file written (%s)' % self.simulated_file)

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    def run_forecast_model(self, lag, dacycle, statevector):
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        self.prepare_run()
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        self.run(lag, dacycle, statevector)
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    def extract_model_data(self,dacycle,hstart,hstop,ensnum):
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        self.dacycle = dacycle
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        time_stamp = dacycle['time.sample.stamp']
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        abs_start_time = str((to_datetime(dacycle['abs.time.start'])).strftime('%Y%m%d%H'))
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        cosmo_out = dacycle['dir.da_run']+"/"+abs_start_time+"_"+str(hstart)+"_"+str(hstop+1)+"/cosmo/output/"
        hhl_cosmo_out = dacycle['dir.da_run']+"/"+abs_start_time+"_0_168/cosmo/output/"
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        cosmo_save = "/store/empa/em05/parsenov/cosmo_data/"
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        hhl_fn = hhl_cosmo_out+'lffd'+abs_start_time+'c.nc'
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        ens = str(ensnum).zfill(3)
        files2cat_jfj=[]
        files2cat_lhw=[]
        files2cat_brm=[]
        files2cat_ssl=[]
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        if ens == "000":
            cdo.selname("HHL", input = hhl_fn, output = cosmo_out+"hhl.nc")
            cdo.remapnn("lon=7.99_lat=46.54,", input = cosmo_out+"hhl.nc", output = cosmo_out+"hhl_jfj.nc")
            cdo.remapnn("lon=8.40_lat=47.48,", input = cosmo_out+"hhl.nc", output = cosmo_out+"hhl_lhw.nc")
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            cdo.remapnn("lon=8.18_lat=47.19,", input = cosmo_out+"hhl.nc", output = cosmo_out+"hhl_brm.nc")
            cdo.remapnn("lon=7.92_lat=47.92,", input = cosmo_out+"hhl.nc", output = cosmo_out+"hhl_ssl.nc")
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        for dt in rrule.rrule(rrule.HOURLY, dtstart=to_datetime(dacycle['abs.time.start'])+timedelta(hours=hstart), until=to_datetime(dacycle['abs.time.start'])+timedelta(hours=hstop)):
            dt=dt.strftime('%Y%m%d%H')
            logging.info('Extracting output for ens %s, time %s' % (str(ens),str(dt)))
            co2_in_fn = cosmo_out+'lffd'+dt+'.nc'
            co2_out_jfj = cosmo_out+'CO2_jfj_'+ens+'_'+dt+'.nc'
            co2_out_lhw = cosmo_out+'CO2_lhw_'+ens+'_'+dt+'.nc'
            co2_out_brm = cosmo_out+'CO2_brm_'+ens+'_'+dt+'.nc'
            co2_out_ssl = cosmo_out+'CO2_ssl_'+ens+'_'+dt+'.nc'
            cdo.expr("'CO2=(BG_"+ens+"-GPP_"+ens+"+RESP_"+ens+"+CO2_A_CH+CO2_A)/(1.-QV)'", input = "-remapnn,lon=7.99_lat=46.54 -selname,QV,BG_"+ens+",GPP_"+ens+",RESP_"+ens+",CO2_A_CH,CO2_A "+co2_in_fn, output = co2_out_jfj)
            cdo.expr("'CO2=(BG_"+ens+"-GPP_"+ens+"+RESP_"+ens+"+CO2_A_CH+CO2_A)/(1.-QV)'", input = "-remapnn,lon=8.40_lat=47.48 -selname,QV,BG_"+ens+",GPP_"+ens+",RESP_"+ens+",CO2_A_CH,CO2_A "+co2_in_fn, output = co2_out_lhw)
            cdo.expr("'CO2=(BG_"+ens+"-GPP_"+ens+"+RESP_"+ens+"+CO2_A_CH+CO2_A)/(1.-QV)'", input = "-remapnn,lon=8.18_lat=47.19 -selname,QV,BG_"+ens+",GPP_"+ens+",RESP_"+ens+",CO2_A_CH,CO2_A "+co2_in_fn, output = co2_out_brm)
            cdo.expr("'CO2=(BG_"+ens+"-GPP_"+ens+"+RESP_"+ens+"+CO2_A_CH+CO2_A)/(1.-QV)'", input = "-remapnn,lon=7.92_lat=47.92 -selname,QV,BG_"+ens+",GPP_"+ens+",RESP_"+ens+",CO2_A_CH,CO2_A "+co2_in_fn, output = co2_out_ssl)
            files2cat_jfj.append(co2_out_jfj)
            files2cat_lhw.append(co2_out_lhw)
            files2cat_brm.append(co2_out_brm)
            files2cat_ssl.append(co2_out_ssl)

        cdo.cat(input = files2cat_jfj, output = cosmo_out+"CO2_jfj_"+ens+"_"+time_stamp+".nc")
        cdo.cat(input = files2cat_lhw, output = cosmo_out+"CO2_lhw_"+ens+"_"+time_stamp+".nc")
        cdo.cat(input = files2cat_brm, output = cosmo_out+"CO2_brm_"+ens+"_"+time_stamp+".nc")
        cdo.cat(input = files2cat_ssl, output = cosmo_out+"CO2_ssl_"+ens+"_"+time_stamp+".nc")

        sites = ("lhw","brm","jfj","ssl")
        for s,ss in enumerate(sites):
            site_height.main(cosmo_out, str(ens), ss, time_stamp)

        cdo.intlevel("860", input = cosmo_out+"CO2_60lev_"+ens+"_lhw_"+time_stamp+".nc", output = cosmo_out+"modelled_"+ens+"_lhw_"+time_stamp+".nc")
        cdo.intlevel("797", input = cosmo_out+"CO2_60lev_"+ens+"_brm_"+time_stamp+".nc", output = cosmo_out+"modelled_"+ens+"_brm_"+time_stamp+".nc") # this needs changing to 1009 (797 + 212)
        cdo.intlevel("3580", input = cosmo_out+"CO2_60lev_"+ens+"_jfj_"+time_stamp+".nc", output = cosmo_out+"modelled_"+ens+"_jfj_"+time_stamp+".nc")
        cdo.intlevel("1205", input = cosmo_out+"CO2_60lev_"+ens+"_ssl_"+time_stamp+".nc", output = cosmo_out+"modelled_"+ens+"_ssl_"+time_stamp+".nc")

        cdo.cat(input = cosmo_out+"modelled_"+ens+"_brm_"+time_stamp+".nc "+cosmo_out+"modelled_"+ens+"_jfj_"+time_stamp+".nc "+cosmo_out+"modelled_"+ens+"_lhw_"+time_stamp+".nc "+cosmo_out+"modelled_"+ens+"_ssl_"+time_stamp+".nc ", output = cosmo_save+"model_"+ens+"_"+time_stamp+".nc")
        logging.info('Extracting done for ens %s' % (ens))
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################### End Class ObservationOperator ###################

class RandomizerObservationOperator(ObservationOperator):
    """ This class holds methods and variables that are needed to use a random number generated as substitute
        for a true observation operator. It takes observations and returns values for each obs, with a specified 
        amount of white noise added 
    """



if __name__ == "__main__":
    pass