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Commit 3d76c114 authored by Ingrid Luijkx's avatar Ingrid Luijkx
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Deleted duplicate of methane_2lambdas

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da/methane_2lambdas/__init__.py deleted 100755 → 0
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da/methane_2lambdas/analysis/__init__.py deleted 100755 → 0
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da/methane_2lambdas/analysis/expand_fluxes.py deleted 100755 → 0
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#!/usr/bin/env python
# expand_fluxes.py
import sys
sys.path.append('../../')
import os
from datetime import datetime, timedelta
import logging
import numpy as np
from da.tools.general import date2num, num2date
import da.methane.io4 as io
from da.methane.analysis.tools_regions import globarea,state_to_grid
from da.tools.general import create_dirs
"""
Author: aki
Revision History:
File created on April 2016 by Aki T.
"""
def save_weekly_avg_1x1_data(dacycle, statevector):
"""
Function creates a NetCDF file with output on 1x1 degree grid. It uses the flux data written by the
:class:`~da.baseclasses.obsoperator.ObsOperator.py`, and multiplies these with the mapped parameters and
variance (not covariance!) from the :class:`~da.baseclasses.statevector.StateVector`.
:param dacycle: a :class:`~da.tools.initexit.CycleControl` object
:param statevector: a :class:`~da.baseclasses.statevector.StateVector`
:rtype: None
"""
#
dirname = create_dirs(os.path.join(dacycle['dir.analysis'], 'data_flux1x1_weekly'))
#
# Some help variables
#
dectime0 = date2num(datetime(2000, 1, 1))
dt = dacycle['cyclelength']
startdate = dacycle['time.start']
enddate = dacycle['time.end']
nlag = statevector.nlag
logging.debug("DA Cycle start date is %s" % startdate.strftime('%Y-%m-%d %H:%M'))
logging.debug("DA Cycle end date is %s" % enddate.strftime('%Y-%m-%d %H:%M'))
#
# Region bio_land and fossil_land
#
region_land_file = dacycle.dasystem['regionsfile']
nfcr = io.CT_CDF(region_land_file, 'read')
logging.info('region land file read: %s' %region_land_file)
bio_land = nfcr.variables['bio_land'][:]
fossil_land = nfcr.variables['fossil_land'][:]
#logging.debug("bio_land %s" %bio_land[25,205])
#logging.debug("ff_land %s" %fossil_land[25,205])
#
# Create or open NetCDF output file
#
logging.debug("Create NetCDF output file: flux_1x1.%s.nc" % startdate.strftime('%Y-%m-%d'))
saveas = os.path.join(dirname, 'flux_1x1.%s.nc' % startdate.strftime('%Y-%m-%d'))
ncf = io.CT_CDF(saveas, 'write')
#
# Create dimensions and lat/lon grid
#
dimgrid = ncf.add_latlon_dim()
dimensemble = ncf.add_dim('members', statevector.nmembers)
dimdate = ncf.add_date_dim()
#
# set title and tell GMT that we are using "pixel registration"
#
setattr(ncf, 'Title', 'CarbonTracker fluxes')
setattr(ncf, 'node_offset', 1)
#
# skip dataset if already in file
#
ncfdate = date2num(startdate) - dectime0 + dt.days / 2.0
skip = ncf.has_date(ncfdate)
if skip:
logging.warning('Skipping writing of data for date %s : already present in file %s' % (startdate.strftime('%Y-%m-%d'), saveas))
else:
#
# if not, process this cycle. Start by getting flux input data from CTDAS
#
filename = os.path.join(dacycle['dir.output'], 'flux1x1_%s_%s.nc' % (startdate.strftime('%Y%m%d%H'), enddate.strftime('%Y%m%d%H')))
file = io.ct_read(filename, 'read')
bio = np.array(file.get_variable(dacycle.dasystem['background.ch4.bio.flux']))
ocean = np.array(file.get_variable(dacycle.dasystem['background.ch4.ocean.flux']))
fire = np.array(file.get_variable(dacycle.dasystem['background.ch4.fires.flux']))
fossil = np.array(file.get_variable(dacycle.dasystem['background.ch4.fossil.flux']))
term = np.array(file.get_variable(dacycle.dasystem['background.ch4.term.flux']))
#mapped_parameters = np.array(file.get_variable(dacycle.dasystem['final.param.mean.1x1']))
file.close()
next = ncf.inq_unlimlen()[0]
# Start adding datasets from here on, both prior and posterior datasets for bio and ocn
for prior in [True, False]:
#
# Now fill the statevector with the prior values for this time step. Note that the prior value for this time step
# occurred nlag time steps ago, so we make a shift in the output directory, but only if we are more than nlag cycle away from the start date..
#
if prior:
logging.debug("prior")
qual_short = 'prior'
for n in range(nlag, 0, -1):
priordate = enddate - timedelta(dt.days * n)
savedir = dacycle['dir.output'].replace(startdate.strftime('%Y%m%d'), priordate.strftime('%Y%m%d'))
filename = os.path.join(savedir, 'savestate_%s.nc' % priordate.strftime('%Y%m%d'))
if os.path.exists(filename):
statevector.read_from_file(filename, qual=qual_short)
gridmean, gridensemble = statevector.state_to_grid(lag=n)
# Replace the mean statevector by all ones (assumed priors)
gridmean = statevector.vector2grid(vectordata=np.ones(statevector.nparams,))
logging.debug('Read prior dataset from file %s, sds %d: ' % (filename, n))
break
else:
logging.debug("opt")
qual_short = 'opt'
savedir = dacycle['dir.output']
filename = os.path.join(savedir, 'savestate_%s.nc' % startdate.strftime('%Y%m%d'))
statevector.read_from_file(filename, qual=qual_short)
gridmean, gridensemble = statevector.state_to_grid(lag=1)
logging.debug('Read posterior dataset from file %s, sds %d: ' % (filename, 1))
#
# if prior, do not multiply fluxes with parameters, otherwise do
#
logging.debug("gridmean %s" %gridmean[25,205])
logging.debug("bio land %s" %bio_land[25,205])
w = np.where(bio_land == 0)
s = gridmean.shape
gridmean_bio = np.zeros(shape=s)
gridmean_bio[:,:] = gridmean[:,:]
gridmean_bio[w] = 1.0
biomapped = bio * gridmean_bio
s = gridensemble.shape
gridensemble_bio = np.zeros(shape=s)
gridensemble_bio[:,:,:] = gridensemble[:,:,:]
gridensemble_bio[:, w[0],w[1]] = 0.0
biovarmapped = bio * gridensemble_bio
w = np.where(fossil_land == 0)
gridmean_fossil = gridmean
gridmean_fossil[w] = 1.0
fossilmapped = fossil * gridmean_fossil
gridensemble_fossil = gridensemble
gridensemble_fossil[:, w[0],w[1]] = 0.0
fossilvarmapped = fossil * gridensemble_fossil
logging.debug("gridmean %s" %gridmean[25,205])
logging.debug("gridmean bio %s" %gridmean_bio[25,205])
logging.debug("gridmean ff %s" %gridmean_fossil[25,205])
#
#
# For each dataset, get the standard definitions from the module mysettings, add values, dimensions, and unlimited count, then write
#
savedict = ncf.standard_var(varname='bio_flux_' + qual_short)
savedict['values'] = biomapped.tolist()
savedict['dims'] = dimdate + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
#
savedict = ncf.standard_var(varname='fossil_flux_' + qual_short)
savedict['values'] = fossilmapped.tolist()
savedict['dims'] = dimdate + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
#print biovarmapped.shape
savedict = ncf.standard_var(varname='bio_flux_%s_ensemble' % qual_short)
savedict['values'] = biovarmapped.tolist()
savedict['dims'] = dimdate + dimensemble + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
#
savedict = ncf.standard_var(varname='fossil_flux_%s_ensemble' % qual_short)
savedict['values'] = fossilvarmapped.tolist()
savedict['dims'] = dimdate + dimensemble + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
# End prior/posterior block
savedict = ncf.standard_var(varname='fire_flux_imp')
savedict['values'] = fire.tolist()
savedict['dims'] = dimdate + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
#
savedict = ncf.standard_var(varname='ocn_flux_imp')
savedict['values'] = ocean.tolist()
savedict['dims'] = dimdate + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
savedict = ncf.standard_var(varname='term_flux_imp')
savedict['values'] = term.tolist()
savedict['dims'] = dimdate + dimgrid
savedict['count'] = next
ncf.add_data(savedict)
#area = globarea()
#savedict = ncf.standard_var(varname='cell_area')
#savedict['values'] = area.tolist()
#savedict['dims'] = dimgrid
#ncf.add_data(savedict)
#
savedict = ncf.standard_var(varname='date')
savedict['values'] = date2num(startdate) - dectime0 + dt.days / 2.0
savedict['dims'] = dimdate
savedict['count'] = next
ncf.add_data(savedict)
sys.stdout.write('.')
sys.stdout.flush()
#
# Done, close the new NetCDF file
#
ncf.close()
#
# Return the full name of the NetCDF file so it can be processed by the next routine
#
logging.info("Gridded weekly average fluxes now written")
return saveas
def save_weekly_avg_state_data(dacycle, statevector):
"""
Function creates a NetCDF file with output for all parameters. It uses the flux data written by the
:class:`~da.baseclasses.obsoperator.ObsOperator.py`, and multiplies these with the mapped parameters and
variance (not covariance!) from the :class:`~da.baseclasses.statevector.StateVector`.
:param dacycle: a :class:`~da.tools.initexit.CycleControl` object
:param statevector: a :class:`~da.baseclasses.statevector.StateVector`
:rtype: None
"""
logging.debug('start: save weekly avg state data')
dirname = create_dirs(os.path.join(dacycle['dir.analysis'], 'data_state_weekly'))
#
# Some help variables
#
dectime0 = date2num(datetime(2000, 1, 1))
dt = dacycle['cyclelength']
startdate = dacycle['time.start']
enddate = dacycle['time.end']
nlag = statevector.nlag
area = globarea()
vectorarea = statevector.grid2vector(griddata=area, method='sum')
logging.debug("DA Cycle start date is %s" % startdate.strftime('%Y-%m-%d %H:%M'))
logging.debug("DA Cycle end date is %s" % enddate.strftime('%Y-%m-%d %H:%M'))
#
# Create or open NetCDF output file
#
saveas = os.path.join(dirname, 'statefluxes.nc')
ncf = io.CT_CDF(saveas, 'write')
logging.debug('save weekly avg state data to file %s' %saveas)
#
# Create dimensions and lat/lon grid
#
dimregs = ncf.add_dim('nparameters', statevector.nparams)
dimmembers = ncf.add_dim('nmembers', statevector.nmembers)
dimdate = ncf.add_date_dim()
#
# set title and tell GMT that we are using "pixel registration"
#
setattr(ncf, 'Title', 'CarbonTracker fluxes')
setattr(ncf, 'node_offset', 1)
#
# skip dataset if already in file
#
ncfdate = date2num(startdate) - dectime0 + dt.days / 2.0
skip = ncf.has_date(ncfdate)
if skip:
logging.warning('Skipping writing of data for date %s : already present in file %s' % (startdate.strftime('%Y-%m-%d'), saveas))
else:
next = ncf.inq_unlimlen()[0]
logging.debug('Writing of data for date %s: file %s' % (startdate.strftime('%Y-%m-%d'), saveas))
#
# if not, process this cycle. Start by getting flux input data from CTDAS
#
filename = os.path.join(dacycle['dir.output'], 'flux1x1_%s_%s.nc' % (startdate.strftime('%Y%m%d%H'), enddate.strftime('%Y%m%d%H')))
file = io.ct_read(filename, 'read')
bio = np.array(file.get_variable(dacycle.dasystem['background.ch4.bio.flux']))
ocean = np.array(file.get_variable(dacycle.dasystem['background.ch4.ocean.flux']))
fire = np.array(file.get_variable(dacycle.dasystem['background.ch4.fires.flux']))
fossil = np.array(file.get_variable(dacycle.dasystem['background.ch4.fossil.flux']))
term = np.array(file.get_variable(dacycle.dasystem['background.ch4.term.flux']))
#mapped_parameters = np.array(file.get_variable(dacycle.dasystem['final.param.mean.1x1']))
file.close()
next = ncf.inq_unlimlen()[0]
vectorbio = statevector.grid2vector(griddata=bio * area, method='sum')
vectorocn = statevector.grid2vector(griddata=ocean * area, method='sum')
vectorfire = statevector.grid2vector(griddata=fire * area, method='sum')
vectorfossil = statevector.grid2vector(griddata=fossil * area, method='sum')
vectorterm = statevector.grid2vector(griddata=term * area, method='sum')
# Start adding datasets from here on, both prior and posterior datasets for bio and ocn
for prior in [True, False]:
#
# Now fill the statevector with the prior values for this time step. Note that the prior value for this time step
# occurred nlag time steps ago, so we make a shift in the output directory, but only if we are more than nlag cycle away from the start date..
#
if prior:
qual_short = 'prior'
for n in range(nlag, 0, -1):
priordate = enddate - timedelta(dt.days * n)
savedir = dacycle['dir.output'].replace(startdate.strftime('%Y%m%d'), priordate.strftime('%Y%m%d'))
filename = os.path.join(savedir,'savestate_%s.nc' % priordate.strftime('%Y%m%d'))
if os.path.exists(filename):
statevector.read_from_file(filename, qual=qual_short)
# Replace the mean statevector by all ones (assumed priors)
statemean = np.ones((statevector.nparams,))
choicelag = n
logging.debug('Read prior dataset from file %s, lag %d: ' % (filename, choicelag))
break
else:
qual_short = 'opt'
savedir = dacycle['dir.output']
filename = os.path.join(savedir, 'savestate_%s.nc' % startdate.strftime('%Y%m%d'))
statevector.read_from_file(filename)
choicelag = 1
statemean = statevector.ensemble_members[choicelag - 1][0].param_values
logging.debug('Read posterior dataset from file %s, lag %d: ' % (filename, choicelag))
#
# if prior, do not multiply fluxes with parameters, otherwise do
#
data = statemean * vectorbio # units of mole region-1 s-1
savedict = ncf.standard_var(varname='bio_flux_%s' % qual_short)
savedict['values'] = data
savedict['dims'] = dimdate + dimregs
savedict['count'] = next
ncf.add_data(savedict)
#
# Here comes a special provision for the posterior flux covariances: these are calculated relative to the prior flux covariance to
# ensure they are indeed smaller due to the data assimilation. If they would be calculated relative to the mean posterior flux, the
# uncertainties would shift just because the mean flux had increased or decreased, which is not what we want.
#
# The implementation is done by multiplying the ensemble with the vectorbio only, and not with the statemean values
# which are assumed 1.0 in the prior always.
#
members = statevector.ensemble_members[choicelag - 1]
deviations = np.array([mem.param_values * vectorbio for mem in members])
deviations = deviations - deviations[0, :]
savedict = ncf.standard_var(varname='bio_flux_%s_ensemble' % qual_short)
savedict['values'] = deviations.tolist()
savedict['dims'] = dimdate + dimmembers + dimregs
savedict['comment'] = "This is the matrix square root, use (M x M^T)/(nmembers-1) to make covariance"
savedict['units'] = "mol region-1 s-1"
savedict['count'] = next
ncf.add_data(savedict)
savedict = ncf.standard_var('unknown')
savedict['name'] = 'bio_flux_%s_std' % qual_short
savedict['long_name'] = 'Biosphere flux standard deviation, %s' % qual_short
savedict['values'] = deviations.std(axis=0)
savedict['dims'] = dimdate + dimregs
savedict['comment'] = "This is the standard deviation on each parameter"
savedict['units'] = "mol region-1 s-1"
savedict['count'] = next
ncf.add_data(savedict)
data = statemean * vectorfossil # units of mole region-1 s-1
savedict = ncf.standard_var(varname='fossil_flux_%s' % qual_short)
savedict['values'] = data
savedict['dims'] = dimdate + dimregs
savedict['count'] = next
ncf.add_data(savedict)
#
# Here comes a special provision for the posterior flux covariances: these are calculated relative to the prior flux covariance to
# ensure they are indeed smaller due to the data assimilation. If they would be calculated relative to the mean posterior flux, the
# uncertainties would shift just because the mean flux had increased or decreased, which is not what we want.
#
# The implementation is done by multiplying the ensemble with the vectorocn only, and not with the statemean values
# which are assumed 1.0 in the prior always.
#
deviations = np.array([mem.param_values * vectorfossil for mem in members])
deviations = deviations - deviations[0, :]
savedict = ncf.standard_var(varname='fossil_flux_%s_ensemble' % qual_short)
savedict['values'] = deviations.tolist()
savedict['dims'] = dimdate + dimmembers + dimregs
savedict['comment'] = "This is the matrix square root, use (M x M^T)/(nmembers-1) to make covariance"
savedict['units'] = "mol region-1 s-1"
savedict['count'] = next
ncf.add_data(savedict)
savedict = ncf.standard_var('unknown')
savedict['name'] = 'fossil_flux_%s_std' % qual_short
savedict['long_name'] = 'Fossil flux standard deviation, %s' % qual_short
savedict['values'] = deviations.std(axis=0)
savedict['dims'] = dimdate + dimregs
savedict['comment'] = "This is the standard deviation on each parameter"
savedict['units'] = "mol region-1 s-1"
savedict['count'] = next
ncf.add_data(savedict)
data = vectorfire
savedict = ncf.standard_var(varname='fire_flux_imp')
savedict['values'] = data
savedict['dims'] = dimdate + dimregs
savedict['count'] = next
ncf.add_data(savedict)
data = vectorterm
savedict = ncf.standard_var(varname='term_flux_imp')
savedict['values'] = data
savedict['dims'] = dimdate + dimregs
savedict['count'] = next
ncf.add_data(savedict)
data = vectorocn
savedict = ncf.standard_var(varname='ocn_flux_imp')
savedict['values'] = data
savedict['dims'] = dimdate + dimregs
savedict['count'] = next
ncf.add_data(savedict)
savedict = ncf.standard_var(varname='date')
savedict['values'] = ncfdate
savedict['dims'] = dimdate
savedict['count'] = next
ncf.add_data(savedict)
sys.stdout.write('.')
sys.stdout.flush()
#
# Done, close the new NetCDF file
#
ncf.close()
#
# Return the full name of the NetCDF file so it can be processed by the next routine
#
logging.info("Vector weekly average fluxes now written")
return saveas
da/methane_2lambdas/statevector.py deleted 100755 → 0
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