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Commit e79032dc authored by Woude, Auke van der's avatar Woude, Auke van der
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write true, prior and optimised fluxes to file

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da/ccffdas/category_info.py
View file @ e79032dc
......@@ -59,7 +59,7 @@ categories = {
'CO2.uncertainty': 'n',
'CO': -4.32,
'CO.uncertainty': 'l'},
'heavy duty': {'name': 'heavy duty highway',
'heavy duty': {'name': 'heavy duty',
'model': 1,
'spatial': 'Road transport',
'temporal': 't_road',
......
da/ccffdas/emissionmodel.py
View file @ e79032dc
......@@ -92,7 +92,6 @@ class EmisModel(object):
key = station + '.' + cat
else:
key = station + '.' + cat + '.' + name
#print('Looking for {}'.format(key))
if key in self.paramdict:
i_in_state = int(self.paramdict[key])
......@@ -103,7 +102,7 @@ class EmisModel(object):
elif return_index: return False
else: return 1
def get_emis(self, dacycle, samples, indices, do_pseudo):
def get_emis(self, dacycle, indices):
"""set up emission information for pseudo-obs (do_pseudo=1) and ensemble runs (do_pseudo=0)"""
self.timestartkey = self.dacycle['time.sample.start']
......@@ -149,10 +148,19 @@ class EmisModel(object):
def get_emissions(self, dacycle, time_profiles, member):
"""read in proxy data used for spatial distribution of the gridded emissions, disaggregate yearly totals for the area"""
prmfile=os.path.join(dacycle['dir.input'],'parameters.%03d.nc'%member)
f = io.ct_read(prmfile, 'read')
params = f.get_variable('parametervalues')
f.close()
if isinstance(member, int) or member == 'optimised':
if isinstance(member, int):
prmfile = os.path.join(dacycle['dir.input'],'parameters.%03d.nc'%member)
prmname = 'parametervalues'
elif member == 'optimised':
prmfile = os.path.join(dacycle['dir.output'], 'optimizer.%s.nc' % dacycle['time.start'].strftime('%Y%m%d'))
prmname = 'statevectormean_optimized'
f = io.ct_read(prmfile, 'read')
params = f.get_variable(prmname)
f.close()
elif member == 'true':
params = np.ones(100)
yremis = self.get_yearly_emissions(params)
# Create a recalculation factor from kg/km2/yr to umol/m2/sec
M_mass = np.array([44e-9, 28e-9][:self.nrspc])
......@@ -188,32 +196,77 @@ class EmisModel(object):
emissions.append(spatial_emissions[i, :, :, :] * temporal_profile[None, :, :, :])
self.emissions = emissions
emissions = np.array(emissions)
emissions = np.swapaxes(emissions, 0,1) # Indices: species, category, time, lat, lon
emissions = np.array(emissions) # [cat, species, time, lat, lon]
emissions = np.swapaxes(emissions, 0, 2) # [time, cat, species, lat, lon]
emissions = np.swapaxes(emissions, 1, 2) # [time, species, cat, lat, lon]
# Recalculate spatial emissions to umol/sec/m2
emissions = emissions / kgperkmperyr2umolperm2pers[:, None, None, :, :]
emissions = emissions / kgperkmperyr2umolperm2pers[None, :, None, :, :]
## create output file
prior_file = os.path.join(self.inputdir, 'prior_spatial_{0:03d}.nc'.format(member))
f = io.CT_CDF(prior_file, method='create')
dimid = f.add_dim('ncat', self.nrcat)
dimid2 = f.add_dim('ops',2 )
dimtime= f.add_dim('time', emissions.shape[2])
dimlat = f.add_dim('lat', self.area.shape[0])
dimlon = f.add_dim('lon', self.area.shape[1])
#loop over all tracers
for i, species in enumerate(self.species):
savedict = io.std_savedict.copy()
savedict['name'] = species
savedict['long_name'] = "Spatially distributed emissions"
savedict['units'] = "micromole/m2/s"
savedict['dims'] = dimid + dimtime + dimlat + dimlon
savedict['values'] = emissions[i, :, :, :]
savedict['dtype'] = 'float'
f.add_data(savedict)
f.close()
if not isinstance(member, str):
prior_file = os.path.join(self.inputdir, 'prior_spatial_{0:03d}.nc'.format(member))
f = io.CT_CDF(prior_file, method='create')
if self.dacycle.dasystem['cat.sum_emissions']:
emissions = emissions.sum(axis=2) # [time, species, lat, lon]
logging.debug('Summed emissions')
else:
dimid = f.add_dim('ncat', self.nrcat)
dimid2 = f.add_dim('ops',2 )
dimtime= f.add_dim('time', emissions.shape[0])
dimlat = f.add_dim('lat', self.area.shape[0])
dimlon = f.add_dim('lon', self.area.shape[1])
#loop over all tracers
for i, species in enumerate(self.species):
savedict = io.std_savedict.copy()
savedict['name'] = species
savedict['long_name'] = "Spatially distributed emissions"
savedict['units'] = "micromole/m2/s"
if self.dacycle.dasystem['cat.sum_emissions']:
dims = dimtime + dimlat + dimlon
else: dims = dimtime + dimid + dimlat + dimlon
savedict['dims'] = dims
if self.dacycle.dasystem['cat.sum_emissions']:
savedict['values'] = emissions[:, i]
else: savedict['values'] = emissions[:, :, i]
savedict['dtype'] = 'float'
f.add_data(savedict)
f.close()
if member == 0 or isinstance(member, str):
if member == 0: qual = 'prior'
elif member == 'optimised': qual = 'optimised'
elif member == 'true': qual = 'true'
name = 'ff_emissions_{}_{}.nc'.format(qual, self.dacycle['time.sample.start'].strftime('%Y%m%d'))
emisfile = os.path.join(dacycle['dir.output'], name)
f = io.CT_CDF(emisfile, method='create')
if self.dacycle.dasystem['cat.sum_emissions']:
emissions = emissions.sum(axis=2) # [time, species, lat, lon]
else:
dimid = f.add_dim('ncat', self.nrcat)
dimid2 = f.add_dim('ops',2 )
backtime = int(dacycle.dasystem['run.backtime'])
dimtime= f.add_dim('time', emissions.shape[0]-backtime)
dimlat = f.add_dim('lat', self.area.shape[0])
dimlon = f.add_dim('lon', self.area.shape[1])
#loop over all tracers
for i, species in enumerate(self.species):
savedict = io.std_savedict.copy()
savedict['name'] = species
savedict['long_name'] = "Spatially distributed emissions"
savedict['units'] = "micromole/m2/s"
if self.dacycle.dasystem['cat.sum_emissions']:
dims = dimtime + dimlat + dimlon
else: dims = dimtime + dimid + dimlat + dimlon
savedict['dims'] = dims
if self.dacycle.dasystem['cat.sum_emissions']:
savedict['values'] = emissions[backtime:, i]
else: savedict['values'] = emissions[backtime:, :, i]
savedict['dtype'] = 'float'
f.add_data(savedict)
f.close()
def make_time_profiles(self, indices):
"""Function that calculates the time profiles based on pre-specified
monthly, daily and hourly profiles. Temperature and radiation affect
......@@ -232,6 +285,7 @@ class EmisModel(object):
times = times[indices]
self.times = times
numdays = (times[-1] - times[0]).days + 1
day_start = times[0].timetuple().tm_yday
datapath = '/projects/0/ctdas/RINGO/EmissionInventories/DynEmMod_TimeProfiles'
infilename = '{}/RINGO_ECMWF_DailyMeteo{}.nc'.format(datapath, year)
with nc.Dataset(infilename) as infile:
......@@ -274,10 +328,10 @@ class EmisModel(object):
HC_coal = HDC_coal.mean(axis=0)
HC_gas = HDC_gas.mean(axis=0)
t_consd = (HDC_cons + fr_cons * HC_cons) / ((1 + fr_cons) * HC_cons) # daily time profile for consumer/household heating
t_glsd = (HDC_gls + fr_gls * HC_gls) / ((1 + fr_gls ) * HC_gls) # glasshouse
t_coald = (HDC_coal + fr_coal * HC_coal) / ((1 + fr_coal) * HC_coal) # coal-fired powerplant
t_gasd = (HDC_gas + fr_gas * HC_gas) / ((1 + fr_gas ) * HC_gas) # gas-fired powerplant
t_consd = ((HDC_cons + fr_cons * HC_cons) / ((1 + fr_cons) * HC_cons))[day_start-1:]# daily time profile for consumer/household heating, starting from the day of the inversion
t_glsd = ((HDC_gls + fr_gls * HC_gls) / ((1 + fr_gls ) * HC_gls))[day_start-1:] # glasshouse
t_coald = ((HDC_coal + fr_coal * HC_coal) / ((1 + fr_coal) * HC_coal))[day_start-1:] # coal-fired powerplant
t_gasd = ((HDC_gas + fr_gas * HC_gas) / ((1 + fr_gas ) * HC_gas))[day_start-1:] # gas-fired powerplant
#### Get the time profiles for all sectors:
with nc.Dataset(self.time_prof_file) as ds:
......@@ -310,14 +364,16 @@ class EmisModel(object):
t_road = np.zeros_like(t_public_power_coal)
t_ship = np.zeros_like(t_public_power_coal)
for i, t in enumerate(times_add1):
month = t.month -1 # Make index
day = (t.day -1) % 7 # Make weekly index
day_ind = t.day - 1 # Make index, starting at time 0
day_ind = t.timetuple().tm_yday - day_start
hour = t.hour # Hours start at 0
weekday = t.weekday() < 6
saturday = t.weekday() == 6
sunday = t.weekday() == 7
self.t = t
# Monthly time profiles
public_power_month_mul = public_power_monthly[month, :, :]
......@@ -330,8 +386,8 @@ class EmisModel(object):
public_power_day_mul_coal = t_coald[day_ind, :, :]
public_power_day_mul_gas = t_gasd[day_ind, :, :]
industry_day_mul = industry_weekly[day]
other_stat_day_mul_cons = t_consd[t.day, :, :] # Index should start at startday, check!
other_stat_day_mul_gls = t_glsd[t.day, :, :]
other_stat_day_mul_cons = t_consd[day_ind, :, :] # Index should start at startday, check!
other_stat_day_mul_gls = t_glsd[day_ind, :, :]
road_transport_day_mul = road_transport_weekly[day, :, :]
shipping_day_mul = shipping_weekly
......@@ -367,7 +423,8 @@ class EmisModel(object):
't_cons': t_other_stat_cons,
't_gls': t_other_stat_gls,
't_road': t_road,
't_ship': t_ship}
't_ship': t_ship
}
# Roll the time profiles to be consisten with time zones
with nc.Dataset(self.country_mask_file) as ds:
......
da/ccffdas/observationoperator.py
View file @ e79032dc
......@@ -30,8 +30,6 @@ from numpy import array, logical_and
import glob
import subprocess
import netCDF4 as nc
import rasterio
from rasterio.enums import Resampling
from functools import partial
from multiprocessing import Process, Pool
......@@ -43,6 +41,8 @@ from da.tools.general import create_dirs, to_datetime
from da.ccffdas.emissionmodel import EmisModel
from da.baseclasses.observationoperator import ObservationOperator
#import matplotlib.pyplot as plt
try: # Import memoization. This speeds up the functions a lot.
from memoization import cached
except: # The memoization package is not always included. Import the memoization from #functools
......@@ -101,7 +101,6 @@ def run_STILT(dacycle, footprint, datepoint, species, i_member):
footprint : np.array: the footprint of the station
datepoint : datetime: the datepoint for which the concentrations should be calculated
species : str: the species
path : path: path to the files containing the emissions
i_member : int: index of the ensemblemember
Returns:
float: the concentration increase at the respective location due to the emissions from the respective species"""
......@@ -109,7 +108,10 @@ def run_STILT(dacycle, footprint, datepoint, species, i_member):
spatial_emissions = get_spatial_emissions(dacycle, i_member, species, datepoint)
# multiply footprint with emissions for each hour in the back trajectory. Indices: Time, Category, lat, lon
foot_flux = (footprint[None, :, :, :] * spatial_emissions[:, :, :, :]).sum()
if dacycle.dasystem['cat.sum_emissions']:
foot_flux = (footprint * spatial_emissions).sum()
else:
foot_flux = (footprint[:, None, :, :] * spatial_emissions[:, :, :, :]).sum()
concentration_increase = float(recalc_factors[species]) * foot_flux
return concentration_increase
......@@ -133,15 +135,14 @@ def get_spatial_emissions(dacycle, i_member, species, datepoint):
emisfile = path +'prior_spatial_{0:03d}.nc'.format(i_member) #format: species[SNAP, time, lon, lat]
f = io.ct_read(emisfile,method='read')
emis=f.get_variable(species)
emis = emis[:, indices, :, :].astype(np.float32) # index the interesting times
emis = emis[indices].astype(np.float32) # index the interesting times
f.close()
#plt.figure()
#plt.imshow(np.log(emis[0, 0, :, :]), cmap='binary')
#plt.savefig('ff.png')
return emis
#def average2d(arr, new_shape):
# """ Function to average the paint-by-colour NEE to the domain size"""
# shape = (new_shape[0], arr.shape[0] // new_shape[0],
# new_shape[1], arr.shape[1] // new_shape[1])
# return arr.reshape(shape).mean(-1).mean(1)
def get_time_index_nc(time=None, startdate=None):
"""Function that gets the time index from the flux files
......@@ -205,11 +206,7 @@ class STILTObservationOperator(ObservationOperator):
self.categories = categories # Imported from file at top
self.inputdir = dacycle.dasystem['inputdir']
self.paramdict = rc.read(dacycle.dasystem['paramdict'])
self.pftfile = dacycle.dasystem['file.pft']
with rasterio.Env(logging.getLogger().setLevel(logging.INFO)):
with rasterio.open(self.pftfile) as dataset:
self.pft_shape_orig = dataset.read().shape[-2:]
logging.getLogger().setLevel(logging.DEBUG)
self.lon_start = float(dacycle.dasystem['domain.lon.start'])
......@@ -293,35 +290,16 @@ class STILTObservationOperator(ObservationOperator):
emismodel = EmisModel()
emismodel.setup(self.dacycle)
self.emismodel = emismodel
emismodel.get_emis(self.dacycle, self.allsamples, indices=self.indices, do_pseudo=0)
emismodel.get_emis(self.dacycle, indices=self.indices)
logging.info('Emissions calculated')
def get_biosphere_emissions(self):
with nc.Dataset(self.dacycle.dasystem['biosphere_fluxdir']) as biosphere_fluxes:
lonsib = biosphere_fluxes['lonsib'][:]
latsib = biosphere_fluxes['latsib'][:]
nee = biosphere_fluxes['nee'][self.indices, :, :]
nee = np.array(nee, dtype=np.float32)
lu_pref = biosphere_fluxes['lu_pref'][:]
lon_ind_start = st.lonindex(self.lon_start)
lon_ind_end = st.lonindex(self.lon_end)
lat_ind_start = st.latindex(self.lat_start)
lat_ind_end = st.latindex(self.lat_end)
# The SiB data is read in correctly, whilst the remainder
# Of the data is read in upside down. THerefore, we flip
# The SiB data also upside down.
nee_2d = np.flip(st.convert_2d(nee, latsib, lonsib), axis=2)
nee_2d = nee_2d[:, :,
lat_ind_end: lat_ind_start,
lon_ind_start: lon_ind_end].astype(np.float32)
nee_2d = np.flip(nee_2d, axis=2)
self.nee = nee_2d
lu_pref = np.flip(st.convert_2d(lu_pref, latsib, lonsib), axis=1)
self.lu_pref = np.flip(lu_pref[:,
lat_ind_end: lat_ind_start,
lon_ind_start: lon_ind_end],
axis=1)
nee = np.flip(biosphere_fluxes['NEE'][self.indices, :, :].astype(np.float32), axis=1)
self.nee = nee
#plt.figure()
#plt.imshow(nee[0, :, :], cmap='binary')
#plt.savefig('nee.png')
def prepare_biosphere(self):
"""Function that prepares the biosphere fluxes on a map
......@@ -334,54 +312,51 @@ class STILTObservationOperator(ObservationOperator):
# First, get the time indices
indices = self.indices
# We cannot, because of memory, use all detail of CORINE.
# The grids have to be compatible with eachother
# Therefore, we will coarsen it, by the following factors:
# Coarsen in x and y:
sibshape = self.lu_pref.shape[1:]
coarsen = [None, None]
for i in range(15, 100):
COARSEN_x = i
COARSEN_y = i
new_shape = tuple(int(self.pft_shape_orig[i] / COARSEN_x -
(self.pft_shape_orig[i] / COARSEN_y % sibshape[i]))
for i in range(2))
scaling_factors = np.array(np.array(new_shape) / np.array(self.domain_shape))
for j, k in enumerate(scaling_factors):
if k % 1 == 0:
if not coarsen[j]:
coarsen[j] = i
if not None in coarsen:
break
new_shape = tuple([int(self.pft_shape_orig[i] / coarsen[i] -
(self.pft_shape_orig[i] / coarsen[i] % sibshape[i]))
for i in range(2)])
logging.debug('Shape for paint-by-number: {}'.format(new_shape))
with rasterio.Env(logging.getLogger().setLevel(logging.INFO)):
with rasterio.open(self.pftfile) as dataset:
pftdata = dataset.read(out_shape=new_shape,
resampling=Resampling.mode)
pftdata = np.flipud(pftdata.reshape(pftdata.shape[1:]))
logging.getLogger().setLevel(logging.DEBUG)
scaling_factors = np.array(np.array(new_shape) / np.array(self.lu_pref[0].shape), dtype=int)
with nc.Dataset(self.pftfile) as ds:
pftdata = np.flipud(ds['pft'][:]).astype(int)
self.pftdata = pftdata
#plt.figure()
#plt.imshow(pftdata[:, :], cmap='binary')
#plt.savefig('pft.png')
logging.debug('Starting paint-by-number')
times = len(self.nee)
timeslist = list(range(times))
lus_prefs = np.kron(self.lu_pref, np.ones((scaling_factors), dtype=self.lu_pref.dtype))
pool = Pool(times)
pool = Pool(self.forecast_nmembers)
# Create the function that calculates the conentration
func = partial(self.paint_by_number, self.nee, self.param_values, scaling_factors, lus_prefs,
func = partial(self.paint_by_number, self.nee, self.param_values,
pftdata, self.emismodel.find_in_state, self.average2d, self.domain_shape)
scaled_nees = pool.map(func, timeslist)
scaled_nees = pool.map(func, list(range(self.forecast_nmembers)))
pool.close()
pool.join()
self.nee_mem = np.asarray(scaled_nees).swapaxes(0, 1) # Indices: mem, time, *domain_shape
self.nee_mem = np.asarray(scaled_nees) # Indices: mem, time, *domain_shape
logging.debug('Paint-by-number done, biosphere prepared')
self.write_biosphere_fluxes(self.nee_mem[0, self.btime:, :, :])
def write_biosphere_fluxes(self, values, qual='prior'):
# Write the biosphere fluxes to a file
bio_emis_file = os.path.join(self.outputdir, 'bio_emissions_{}_{}.nc'.format(qual, self.dacycle['time.sample.start'].strftime('%Y%m%d')))
f = io.CT_CDF(bio_emis_file, method='create')
dimtime= f.add_dim('time', values.shape[0])
dimlat = f.add_dim('lat', values.shape[1])
dimlon = f.add_dim('lon', values.shape[2])
savedict = io.std_savedict.copy()
savedict['name'] = 'CO2'
savedict['long_name'] = 'Biosphere CO2 emissions'
savedict['units'] = "micromole/m2/s"
dims = dimtime + dimlat + dimlon
savedict['dims'] = dims
savedict['values'] = values
savedict['dtype'] = 'float'
f.add_data(savedict)
f.close()
#plt.figure()
#plt.imshow(np.log(self.nee_mem[0, 0, :, :]), cmap='binary')
#plt.savefig('bio.png')
@staticmethod
def average2d(arr, new_shape):
......@@ -391,26 +366,23 @@ class STILTObservationOperator(ObservationOperator):
return arr.reshape(shape).mean(-1).mean(1)
@staticmethod
def paint_by_number(nee, all_param_values, scaling_factors, lus_prefs, pftdata,
find_in_state, average2d, domain_shape, time_ind):
nmembers = len(all_param_values)
scaled_nees_time = np.zeros((nmembers, *domain_shape), dtype=np.float32)
def paint_by_number(nee, all_param_values, pftdata,
find_in_state, average2d, domain_shape, member):
scaled_nees = np.zeros((len(nee), *domain_shape), dtype=np.float32)
all_lutypes = np.unique(pftdata.reshape(-1))
nee_time = nee[time_ind]
nee = np.kron(nee_time, np.ones((scaling_factors), dtype=np.float32))
param_values = all_param_values[member]
newnee = np.zeros_like(nee)
for lutype_ind, lutype in enumerate(all_lutypes):
mask = np.where(pftdata==lutype, 1, 0)
nee_lut = np.where(lus_prefs==lutype, nee, 0)
for mem, values in enumerate(all_param_values):
param_values = all_param_values[mem]
index_in_state = find_in_state(param_values, 'BIO', str(lutype), return_index=True)
if index_in_state:
param_value = param_values[index_in_state]
else: param_value = 1
nee_lut_mem = (nee_lut.sum(axis=0) * mask) * param_value
nee_lut_mem_scaled = average2d(nee_lut_mem, domain_shape)
scaled_nees_time[mem] += nee_lut_mem_scaled
return(scaled_nees_time)
index_in_state = find_in_state(param_values, 'BIO', str(lutype), return_index=True)
if index_in_state:
param_value = param_values[index_in_state]
else: param_value = 1
mask = np.where(pftdata == lutype, 1, 0)
newnee += (nee * mask * param_value)
for i, n in enumerate(newnee):
scaled_nees[i] = average2d(n, domain_shape)
return scaled_nees
def prepare_c14(self):
"""Function that loads the nuclear power temporal variation"""
......@@ -444,6 +416,12 @@ class STILTObservationOperator(ObservationOperator):
f = glob.glob(fname)[0]
footprint = nc.Dataset(f)['foot']
#plt.figure()
#plt.imshow(np.log(footprint[0, :, :]), cmap='binary')
#plt.title(site)
#plt.savefig('foot.png')
# Flip, because the times are negative
return np.flipud(footprint).astype(np.float32)
......@@ -553,11 +531,31 @@ class STILTObservationOperator(ObservationOperator):
def run_forecast_model(self,dacycle,do_pseudo,adv):
logging.info('Preparing run...')
#self.make_observations(dacycle)
self.prepare_run(do_pseudo,adv)
logging.info('Starting to simulate concentrations...')
self.run(dacycle,do_pseudo)
self.save_data()
def make_observations(self, dacycle, do_pseudo=0, adv=0):
logging.info('Prepare run...')
self.prepare_run(do_pseudo, adv)
logging.info('Starting to simulate concentrations...')
import pandas as pd
import copy
all_samples = copy.deepcopy(self.samples)
sites = set([sample.code.split('/')[1].split('_')[1] for sample in all_samples])
print(sites)
for site in sites:
current_samples = [sample for sample in all_samples if site in sample.code]
self.samples = current_samples
self.run(dacycle, do_pseudo)
times = [sample.xdate for sample in current_samples]
df = pd.DataFrame(self.calculated_concentrations, times, columns=['concentration'])
df.to_csv(site + dtm.datetime.strftime(dacycle['time.sample.start'], "%Y%m%d") + '.csv')
save_and_submit(dacycle, statevector)
def run(self, dacycle, do_pseudo):
"""Function that calculates the simulated concentrations for all samples
Loops over all samples, looks for relevant information (e.g. footprint)
......@@ -604,7 +602,6 @@ class STILTObservationOperator(ObservationOperator):
previous_day = datepoint.day
previously_done_site = site
logging.debug('Cache info: {}'.format(get_spatial_emissions.cache_info()))
# This is how ingrid did it, so I will too...
self.mod = np.array(calculated_concentrations)
......@@ -635,6 +632,7 @@ class STILTObservationOperator(ObservationOperator):
# First, add noise (this represents errors in the transport model
noise = np.random.normal(0, sample.mdm)
#noise = 0
# Some different cases for different species.
# First case: Species is not c14:
......
da/ccffdas/pipeline.py
View file @ e79032dc
......@@ -16,6 +16,7 @@ import os
import sys
import datetime
import copy
import numpy as np
header = '\n\n *************************************** '
footer = ' *************************************** \n '
......@@ -32,7 +33,7 @@ def ensemble_smoother_pipeline(dacycle, platform, dasystem, samples, statevector
invert(dacycle, statevector, optimizer, obsoperator)
#advance(dacycle, samples, statevector, obsoperator)
advance(dacycle, samples, statevector, obsoperator, optimizer)
save_and_submit(dacycle, statevector)
logging.info("Cycle finished...exiting pipeline")
......@@ -115,7 +116,7 @@ def forward_pipeline(dacycle, platform, dasystem, samples, statevector, obsopera
# Finally, we run forward with these parameters
advance(dacycle, samples, statevector, obsoperator)
advance(dacycle, samples, statevector, obsoperator, optimizer)
# In save_and_submit, the posterior statevector will be added to the savestate.nc file, and it is added to the copy list.
# This way, we have both the prior and posterior data from another run copied into this assimilation, for later analysis.
......@@ -400,31 +401,41 @@ def invert(dacycle, statevector, optimizer, obsoperator):
def advance(dacycle, samples, statevector, obsoperator):
def advance(dacycle, samples, statevector, obsoperator, optimizer):
""" Advance the filter state to the next step """
# This is the advance of the modeled CO2 state. Optionally, routines can be added to advance the state vector (mean+covariance)
# Then, restore model state from the start of the filter
logging.info(header + "starting advance" + footer)
logging.info("Sampling model will be run over 1 cycle")
obsoperator.get_initial_data(samples)
sample_step(dacycle, samples, statevector, obsoperator, 0, True)
dacycle.restart_filelist.extend(obsoperator.restart_filelist)
dacycle.output_filelist.extend(obsoperator.output_filelist)
logging.debug("Appended ObsOperator restart and output file lists to dacycle for collection ")