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Commit 396e0df5 authored by JJDHooghiem's avatar JJDHooghiem
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molefractionsample and totalcolumnsample moved to baseclass and inherit from... 

molefractionsample and totalcolumnsample moved to baseclass and inherit from new observation object. Added the appropriate imports to obs_column_xco2 and obs_gvp_co2.py.
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da/observations/obs_baseclass.py
+ 137
− 33
View file @ 396e0df5
......@@ -278,11 +278,15 @@ class Observations(object):
Write selected additional information contained in the Observations object to a file for later processing.
"""
#FLAG this doesn't do anything should we remove this from the baseclass
#FLAG add documenation
def getvalues(self, name, constructor=array):
#FLAG add documenation
"""getvalues.
:param name:
:param constructor: datatype that can be initialized by passing a list
"""
result = constructor([getattr(o, name) for o in self.datalist])
if isinstance(result, ndarray):
return result.squeeze()
......@@ -291,39 +295,139 @@ class Observations(object):
################### End Class Observations ###################
################### Begin Classes for Sample ###################
class Observation(object):
""" Observation."""
def __init__(self,idx,xdate,obs=0.0,simulated=0.0,lat=-999.,lon=-999.,height=0.0,mdm=0.0,hphr=0.0,resid=0.0,species='co2',flag=0,loc_L=0,may_localize=False,may_reject=False,sdev=0.0):
"""__init__.
:param idx: Observation id by which it can distinguished from the others
:param xdate: datetime of the observation
:param obs: observed value
:param simulated: nd.array, (nmembers,), simulated values of the ensemble
:param lat: float, latitude
:param lon: float, longitude
:param height: float, height
:param mdm: float, model-data-mismatch
:param hphr: float, Mole fraction prior uncertainty from fluxes and (HPH) and model data mismatch (R)
:param resid: float, Mole fraction residuals
:param species: species string, e.g. co2 or co2c13
:param flag: float, observation flag that specifies whether to assimilate, 0, or ignore, 99. Wil be moddifed by the kalman filter. 1 means assimilated 2 means rejected
:param loc_L: localization length
:param may_localize: If the observation may be localized
:param may_reject: If the observation may be rejected
:param sdev:
"""
#FLAG should we add the rejection_threshold here?
self.id = idx
self.xdate = xdate
self.obs = obs
self.simulated = simulated
self.lat = lat
self.lon = lon
self.height = height
self.mdm = mdm
self.hphr = hphr
self.resid = resid
self.species = species.strip()
self.flag = flag
self.loc_L = loc_L # Whether sample may be localized in optimizer
self.may_localize = may_localize # Whether sample may be rejected if outside threshold
self.may_reject = may_reject
self.sdev = sdev
return
class MoleFractionSample(Observation):
"""MoleFractionSample."""
def __init__(self, idx, xdate, code='XXX', obs=0.0, simulated=0.0, resid=0.0, hphr=0.0, mdm=0.0, flag=0, height=0.0, lat= -999., lon= -999.,
evn='0000', species='co2', samplingstrategy=1, sdev=0.0, fromfile='none.nc', loc_L=0,may_reject=False,u=None,v=None,blh=None,q=None,p=None,T=None):
"""__init__.
:param idx:
:param xdate:
:param code: dataset identifier, i.e., co2_lef_tower_insitu_1_99
:param obs:
:param simulated:
:param resid:
:param hphr:
:param mdm:
:param flag:
:param height:
:param lat:
:param lon:
:param evn: Obspack Number within distrution (string), e.g., obspack_co2_1_PROTOTYPE_v0.9.2_2012-07-26_99_82536
:param species:
:param samplingstrategy:
:param sdev:
:param fromfile:
:param loc_L:
:param u: float, eastward or longitudinal wind component
:param v:
:param blh:
:param q:
:param p:
:param T:
"""
super().__init__(idx,xdate,obs,simulated,lat,lon,height,mdm,hphr,resid,species,flag,loc_L,may_localize,may_reject,sdev)
self.code = code.strip()
self.evn = evn
#FLAG seems to be always true
self.masl = True
self.mag = not self.masl
self.samplingstrategy = samplingstrategy #
self.fromfile = fromfile
self.u = u
self.v = v
self.blh = blh
self.q = p
self.p = p
self.T = T
class TotalColumnSample(Observation):
"""TotalColumnSample."""
def __init__(self, idx, codex, xdate, obs=0.0, simulated=0.0, lat=-999., lon=-999., mdm=0.0, prior=0.0, prior_profile=0.0, av_kernel=0.0, pressure=0.0, \
level_def = "pressure_boundary", psurf = float('nan'), resid=0.0, hphr=0.0, flag=0, species='co2', sdev=0.0, h=0.0, moderr=0.0, loc_L=0, may_localize=False,may_reject=False):
"""__init__.
:param idx:
:param codex: Retrieval ID
:param xdate:
:param obs:
:param simulated:
:param lat: :param lon:
:param mdm:
:param prior :A priori column value used in retrieval
:param prior_profile: A priori profile used in retrieval
:param av_kernel:
:param pressure: Pressure levels of retrieval
:param level_def:Are prior and averaging kernel defined as layer averages?
:param psurf: Surface pressure (only needed if level_def is "layer_average")
:param resid:
:param hphr:
:param flag:
:param species:
:param sdev:
:param h: Sounding pressure level weights
:param moderr: Model error, NaN unless mdm_calculation = read_from_file
:param loc_L:
:param may_localize:
:param may_reject:
"""
super().__init__(idx,xdate,obs,simulated,lat,lon,height,mdm,hphr,resid,species,flag,loc_L,may_localize,may_reject,sdev)
self.code = codex
self.prior = prior
self.prior_profile = prior_profile
self.av_kernel = av_kernel
self.pressure = pressure
self.level_def = level_def
self.psurf = psurf
#FLAG poor name
self.h = h
self.modelunc = moderr
################### Begin Class MoleFractionSample ###################
class MoleFractionSample(object):
"""
Holds the data that defines a mole fraction Sample in the data assimilation framework. Sor far, this includes all
attributes listed below in the __init__ method. One can additionally make more types of data, or make new
objects for specific projects.
"""
def __init__(self, idx, xdate, code='XXX', obs=0.0, simulated=0.0, resid=0.0, hphr=0.0, mdm=0.0, flag=0, height=0.0, lat= -999., lon= -999., evn='0000', species='co2', samplingstrategy=1, sdev=0.0, fromfile='none.nc'):
self.code = code.strip() # dataset identifier, i.e., co2_lef_tower_insitu_1_99
self.xdate = xdate # Date of obs
self.obs = obs # Value observed
self.simulated = simulated # Value simulated by model
self.resid = resid # Mole fraction residuals
self.hphr = hphr # Mole fraction prior uncertainty from fluxes and (HPH) and model data mismatch (R)
self.mdm = mdm # Model data mismatch
self.may_localize = True # Whether sample may be localized in optimizer
self.may_reject = True # Whether sample may be rejected if outside threshold
self.flag = flag # Flag
self.height = height # Sample height in masl
self.lat = lat # Sample lat
self.lon = lon # Sample lon
self.id = idx # Obspack ID within distrution (integer), e.g., 82536
self.evn = evn # Obspack Number within distrution (string), e.g., obspack_co2_1_PROTOTYPE_v0.9.2_2012-07-26_99_82536
self.sdev = sdev # standard deviation of ensemble
self.masl = True # Sample is in Meters Above Sea Level
self.mag = not self.masl # Sample is in Meters Above Ground
self.species = species.strip()
self.samplingstrategy = samplingstrategy
self.fromfile = fromfile # netcdf filename inside ObsPack distribution, to write back later
################### End Class MoleFractionSample ###################
......
da/observations/obs_column_xco2.py
+ 1
− 42
View file @ 396e0df5
......@@ -34,52 +34,11 @@ sys.path.append('../../')
identifier = 'CarbonTracker total column-averaged mole fractions'
version = '0.0'
from da.observations.obs_baseclass import Observations
from da.observations.obs_baseclass import Observations, TotalColumnSample
import da.tools.io4 as io
import da.tools.rc as rc
################### Begin Class TotalColumnSample ###################
class TotalColumnSample(object):
"""
Holds the data that defines a total column sample in the data assimilation framework. Sor far, this includes all
attributes listed below in the __init__ method. One can additionally make more types of data, or make new
objects for specific projects.
This file may contain OCO-2 specific parts...
"""
def __init__(self, idx, codex, xdate, obs=0.0, simulated=0.0, lat=-999., lon=-999., mdm=None, prior=0.0, prior_profile=0.0, av_kernel=0.0, pressure=0.0, \
level_def = "pressure_boundary", psurf = float('nan'), resid=0.0, hphr=0.0, flag=0, species='co2', sdev=0.0, h=0.0, moderr=0.0, loc_L=0):
self.id = idx # Sounding ID
self.code = codex # Retrieval ID
self.xdate = xdate # Date of obs
self.obs = obs # Value observed
self.simulated = simulated # Value simulated by model, fillvalue = -9999
self.lat = lat # Sample lat
self.lon = lon # Sample lon
self.mdm = mdm # Model data mismatch
self.prior = prior # A priori column value used in retrieval
self.prior_profile = prior_profile # A priori profile used in retrieval
self.av_kernel = av_kernel # Averaging kernel
self.pressure = pressure # Pressure levels of retrieval
self.level_def = level_def # Are prior and averaging kernel defined as layer averages?
self.psurf = psurf # Surface pressure (only needed if level_def is "layer_average")
self.h = h # Sounding pressure level weights
self.modelunc = moderr # Model error, NaN unless mdm_calculation = read_from_file
self.loc_L = loc_L # localization length
self.resid = resid # Mole fraction residuals
self.hphr = hphr # Mole fraction prior uncertainty from fluxes and (HPH) and model data mismatch (R)
self.may_localize = True # Whether sample may be localized in optimizer
self.may_reject = True # Whether sample may be rejected if outside threshold
self.flag = flag # Flag
self.sdev = sdev # standard deviation of ensemble
self.species = species.strip()
################### End Class TotalColumnSample ###################
################### Begin Class TotalColumnObservations ###################
......
da/observations/obs_gvp_co2.py
+ 1
− 41
View file @ 396e0df5
......@@ -33,7 +33,7 @@ sys.path.append('../../')
identifier = 'CarbonTracker CO2 mole fractions'
version = '2.0'
from da.observations.obs_baseclass import Observations
from da.observations.obs_baseclass import Observations, MoleFractionSample
import da.tools.io4 as io
import da.tools.rc as rc
......@@ -563,45 +563,5 @@ class ObsPackObservations(Observations):
################### End Class CtObservations ###################
################### Begin Class MoleFractionSample ###################
#FLAG: this MoleFractionSample is a direct copy from the obs_baseclass class.
class MoleFractionSample(object):
"""
Holds the data that defines a mole fraction Sample in the data assimilation framework. Sor far, this includes all
attributes listed below in the __init__ method. One can additionally make more types of data, or make new
objects for specific projects.
"""
def __init__(self, idx, xdate, code='XXX', obs=0.0, simulated=0.0, resid=0.0, hphr=0.0, mdm=0.0, flag=0, height=0.0, lat= -999., lon= -999.,
evn='0000', species='co2', samplingstrategy=1, sdev=0.0, fromfile='none.nc', loc_L=0):
self.code = code.strip() # dataset identifier, i.e., co2_lef_tower_insitu_1_99
self.xdate = xdate # Date of obs
self.obs = obs # Value observed
self.simulated = simulated # Value simulated by model
self.resid = resid # Mole fraction residuals
self.hphr = hphr # Mole fraction prior uncertainty from fluxes and (HPH) and model data mismatch (R)
self.mdm = mdm # Model data mismatch
self.may_localize = True # Whether sample may be localized in optimizer
self.loc_L = loc_L # localization length for observation
self.may_reject = True # Whether sample may be rejected if outside threshold
self.flag = flag # Flag
self.height = height # Sample height in masl
self.lat = lat # Sample lat
self.lon = lon # Sample lon
self.id = idx # Obspack ID within distrution (integer), e.g., 82536
self.evn = evn # Obspack Number within distrution (string), e.g., obspack_co2_1_PROTOTYPE_v0.9.2_2012-07-26_99_82536
self.sdev = sdev # standard deviation of ensemble
self.masl = True # Sample is in Meters Above Sea Level
self.mag = not self.masl # Sample is in Meters Above Ground
self.species = species.strip()
self.samplingstrategy = samplingstrategy
self.fromfile = fromfile # netcdf filename inside ObsPack distribution, to write back later
################### End Class MoleFractionSample ###################
if __name__ == "__main__":
pass
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