made a new obspack.py that should work with the new prototype obspack releases

da/ctc13/obspack-new.py

+#i!/usr/bin/env python
+# obs.py
+
+"""
+Author : peters 
+
+Revision History:
+File created on 28 Jul 2010.
+
+"""
+import os
+import sys
+sys.path.append(os.getcwd())
+sys.path.append('../../')
+import logging
+import datetime
+
+identifier = 'CarbonTracker CO2 mixing ratios'
+version = '0.0'
+
+from da.baseclasses.obs import Observation
+
+################### Begin Class ObsPackObservations ###################
+
+class ObsPackObservations(Observation):
+    """ an object that holds data + methods and attributes needed to manipulate mixing ratio values """
+
+    def getid(self):
+        return identifier
+
+    def getversion(self):
+        return version
+
+    def getlength(self):
+        return len(self.Data)
+
+    def Initialize(self):
+
+        self.startdate = self.DaCycle['time.sample.start']
+        self.enddate   = self.DaCycle['time.sample.end']
+        DaSystem       = self.DaCycle.DaSystem
+
+        op_co2_id         = DaSystem['obspack.co2.input.id']
+        op_co2_dir        = DaSystem['obspack.co2.input.dir']
+
+        op_c13_id         = DaSystem['obspack.c13.input.id']
+        op_c13_dir        = DaSystem['obspack.c13.input.dir']
+
+        co2_only          = DaSystem['co2.only']
+        c13_only          = DaSystem['c13.only']
+        co2_c13_together  = DaSystem['co2.c13.together']
+
+        if not os.path.exists(op_co2_dir):
+            msg     = 'Could not find  the required ObsPack distribution (%s) ' % op_co2_dir ; logging.error(msg)
+            raise IOError,msg
+        else:
+            self.ObsPackCo2Dir  = op_co2_dir
+            self.ObsPackCo2Id   = op_co2_id
+
+            self.ObsPackC13Dir  = op_c13_dir
+            self.ObsPackC13Id   = op_c13_id
+
+            self.Co2_only     = co2_only
+            self.C13_only     = c13_only
+            self.Co2_C13_together     = co2_c13_together
+
+
+        self.Data = MixingRatioList([])
+
+        return None
+
+    def AddObs(self):
+        """ Returns a MixingRatioList holding individual MixingRatioSample objects for all obs in a file
+      
+            The ObsPack mixing ratio files are provided as time series per site with all dates in sequence. 
+            We will loop over all site files in the ObsPackage, and subset each to our needs
+            
+        """
+        import da.tools.io4 as io
+        import datetime as dtm
+        from string import strip, join
+        from numpy import array, logical_and
+
+        # Step 1: Read list of available site files in package
+        if self.Co2_only:
+            obsspecies = [self.ObsPackCo2Dir]
+        if self.C13_only:
+            obsspecies = [self.ObsPackC13Dir]
+        if self.Co2_C13_together:
+            obsspecies = [self.ObsPackCo2Dir,self.ObsPackC13Dir ]
+        for obsspecie in obsspecies:
+            if obsspecie == self.ObsPackCo2Dir:
+                infile  = os.path.join(obsspecie,'summary','%s_dataset_summary.txt'%(self.ObsPackCo2Id,))
+            else:
+                infile  = os.path.join(obsspecie,'summary','%s_dataset_summary.txt'%(self.ObsPackC13Id,))         
+            f       = open(infile,'r')
+            lines   = f.readlines()
+            status   = f.close()
+
+            ncfilelist = []
+            for line in lines:
+                if line.startswith('#'): continue # header
+                print line
+                ncfile, lab , dist, start_date, stop_date, data_comparison = line.split()
+
+                ncfilelist += [ncfile]
+
+            msg = "ObsPack dataset info read, proceeding with %d netcdf files"%(len(ncfilelist),) ; logging.debug(msg)
+
+            for ncfile in ncfilelist:
+
+                infile      = os.path.join(obsspecie,'data','nc',ncfile)
+                ncf         = io.CT_Read(infile,'read')
+                idates      = ncf.GetVariable('time_components')
+                dates       = array([dtm.datetime(*d) for d in idates])
+
+                subselect   = logical_and(dates >= self.startdate , dates <= self.enddate).nonzero()[0]
+
+                dates       = dates.take(subselect,axis=0)
+            
+                ids         = ncf.GetVariable('obspack_num').take(subselect)  # or should we propagate obs_num which is not unique across datasets??
+                evn         = ncf.GetVariable('obspack_id').take(subselect,axis=0)
+                evn         = [s.tostring().lower() for s in evn]
+                evn         = map(strip,evn)
+                site        = ncf.GetAttribute('site_code')
+                lats        = ncf.GetVariable('latitude').take(subselect,axis=0)
+                lons        = ncf.GetVariable('longitude').take(subselect,axis=0)
+                alts        = ncf.GetVariable('altitude').take(subselect,axis=0)
+                obs         = ncf.GetVariable('value').take(subselect,axis=0)
+                if obsspecie == self.ObsPackCo2Dir:
+                    obs         = obs #*1.e6 #IV convert to ppm
+                species     = ncf.GetAttribute('dataset_parameter')
+                #strategy    = ncf.GetVariable('sampling_strategy').take(subselect,axis=0)
+                strategy    = 1
+                flags       = ncf.GetVariable('qc_flag').take(subselect,axis=0)
+                flags       = [s.tostring().lower() for s in flags]
+                flags       = map(strip,flags)
+                flags       = [int(f == '...') for f in flags]
+                status       = ncf.close()
+                
+                msg         =  site,species,obs,dates,ids ; logging.info(msg)
+
+                for n in range(len(dates)): 
+
+                   self.Data.append( MixingRatioSample(ids[n],dates[n],site,obs[n],0.0,0.0,0.0,0.0,0.0,flags[n],alts[n],lats[n],lons[n],evn[n],species,strategy,0.0, infile) )
+
+                msg         = "Added %d observations from file (%s) to the Data list" % (len(dates),ncfile,) ; logging.debug(msg)
+
+            msg         = "Observation list now holds %d values" % (len(self.Data),) ; logging.info(msg)
+
+    def AddSimulations(self,filename,silent=True):
+        """ Adds model simulated values to the mixing ratio objects """
+
+        import da.tools.io4 as io
+        import da.tools.MixingratioToPermil as mtp
+        from numpy import array,arange
+
+
+        if not os.path.exists(filename):
+            msge    = "Sample output filename for observations could not be found : %s" % filename ; logging.error(msge)
+            msg     = "Did the sampling step succeed?"  ; logging.error(msg)
+            msg     = "...exiting" ; logging.error(msge)
+            raise IOError,msg
+
+        ncf         = io.CT_Read(filename,method='read')
+        ids         = ncf.GetVariable('obs_num')
+        simulated   = ncf.GetVariable('flask')
+	trspecies   = ncf.GetVariable('tracer_names')
+        status       = ncf.close()
+        msg         = "Successfully read data from model sample file (%s)"%filename ; logging.info(msg)
+
+        obs_ids     = self.Data.getvalues('id')
+
+        obs_ids     = obs_ids.tolist()
+        ids         = map(int,ids)
+
+        obs_species = self.Data.getvalues('species')
+        #obs_species = obs_species.tolist()
+        
+        missing_samples = []
+ 
+        tr_species=[]
+        for i in range(len(trspecies[:,0])):
+            trjoin = [''.join(trspecies[i,:])]
+            tr_species.append(trjoin[0].strip())
+	tr_species=array(tr_species)
+
+        if self.Co2_only:	        	
+            simulated = simulated #*1.e6
+        if self.C13_only:
+ 	    simulated = mtp.MixingratioToPermil(filename,simulated)
+        if self.Co2_C13_together:
+            simulated = mtp.MixingratioToPermil(filename,simulated)
+        
+        xx=arange(len(ids))
+        
+        for id,obs_specie,val in zip(xx,obs_species,simulated):  
+            if id in xx:#obs_ids:   
+                index = id #obs_ids.index(id)
+		#print id,index
+		counter=0	
+		trval=[]	        	    
+	        for sp in tr_species:
+	            if obs_specie == sp:
+		        #print counter,val[counter]
+                        trval.append(val[counter])
+	            counter=counter+1
+		trval=array(trval)	
+		#print 'trval',index,trval
+		
+                status = self.Data[index].simulated = trval # *1e6  # to umol/mol
+		#if index ==0:
+		    #print 'Data.getvalues2',self.Data[index].simulated	        
+	    
+	               
+                #index = obs_ids.index(id)
+                #print id,val,val.shape
+                #dummy = self.Data[index].simulated = val # *1e6  # to umol/mol
+
+            else:     
+
+                missing_samples.append(id)
+        if not silent and missing_samples != []:
+            msg = 'Model samples were found that did not match any ID in the observation list. Skipping them...' ; logging.warning(msg)
+            #msg = '%s'%missing_samples ; logging.warning(msg)
+
+        msg  = "Added %d simulated values to the Data list" % (len(ids)-len(missing_samples) ) ; logging.debug(msg)
+
+    def WriteSampleInfo(self):
+        """ 
+            Write the information needed by the observation operator to a file. Return the filename that was written for later use
+
+        """
+        import shutil
+        #import da.tools.io as io
+        import da.tools.io4 as io
+        from da.tools.general import ToDectime
+
+        obsinputfile   = os.path.join(self.DaCycle['dir.input'],'observations_%s.nc'% self.DaCycle['time.sample.stamp'])
+
+        f           = io.CT_CDF(obsinputfile,method='create')
+        msg         = 'Creating new observations file for ObservationOperator (%s)' % obsinputfile ; logging.debug(msg)
+
+        dimid       = f.AddDim('obs',len(self.Data))
+        dim200char   = f.AddDim('string_of200chars',200)
+        dim10char   = f.AddDim('string_of10chars',10)
+        dimcalcomp  = f.AddDim('calendar_components',6)
+
+        if len(self.Data) == 0:
+            f.close()
+            return obsinputfile
+
+        data =  self.Data.getvalues('id')
+
+        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['values']      = data.tolist()
+        savedict['comment']     = "Unique index number within this dataset ranging from 0 to UNLIMITED."
+        status                   = f.AddData(savedict)
+
+        data =  [[d.year,d.month,d.day,d.hour,d.minute,d.second] for d in self.Data.getvalues('xdate') ]
+
+        savedict                = io.std_savedict.copy() 
+        savedict['dtype']       = "int"
+        savedict['name']        = "date_components"
+        savedict['units']       = "integer components of UTC date/time"
+        savedict['dims']        = dimid+dimcalcomp
+        savedict['values']      = data
+        savedict['missing_value'] = -9
+        savedict['comment']     = "Calendar date components as integers. Times and dates are UTC." 
+        savedict['order']       = "year, month, day, hour, minute, second"
+        status                   = f.AddData(savedict)
+
+        data =  self.Data.getvalues('lat')
+
+        savedict                = io.std_savedict.copy() 
+        savedict['name']        = "latitude"
+        savedict['units']       = "degrees_north"
+        savedict['dims']        = dimid
+        savedict['values']      = data.tolist()
+        savedict['missing_value'] = -999.9
+        status                   = f.AddData(savedict)
+
+        data =  self.Data.getvalues('lon')
+
+        savedict                = io.std_savedict.copy() 
+        savedict['name']        = "longitude"
+        savedict['units']       = "degrees_east"
+        savedict['dims']        = dimid
+        savedict['values']      = data.tolist()
+        savedict['missing_value'] = -999.9
+        status                   = f.AddData(savedict)
+
+        data =  self.Data.getvalues('height')
+
+        savedict                = io.std_savedict.copy() 
+        savedict['name']        = "altitude"
+        savedict['units']       = "meters_above_sea_level"
+        savedict['dims']        = dimid
+        savedict['values']      = data.tolist()
+        savedict['missing_value'] = -999.9
+        status                   = f.AddData(savedict)
+
+        data =  self.Data.getvalues('samplingstrategy')
+
+        savedict                = io.std_savedict.copy() 
+        savedict['dtype']       = "int"
+        savedict['name']        = "sampling_strategy"
+        savedict['units']       = "NA"
+        savedict['dims']        = dimid
+        savedict['values']      = data.tolist()
+        savedict['missing_value'] = -9
+        status                   = f.AddData(savedict)
+
+        data = self.Data.getvalues('evn')
+
+        savedict                = io.std_savedict.copy() 
+        savedict['dtype']       = "char"
+        savedict['name']        = "obs_id"
+        savedict['units']       = "NOAA database identifier"
+        savedict['dims']        = dimid+dim200char
+        savedict['values']      = data
+        savedict['missing_value'] = '!'
+        status                   = f.AddData(savedict)
+
+        status       = f.close()
+
+        msg         = "Successfully wrote data to obs file" ;logging.debug(msg)
+        msg         = "Sample input file for obs operator now in place [%s]"%obsinputfile ; logging.info(msg)
+
+        return obsinputfile
+
+
+    def AddModelDataMismatch(self ):
+        """ 
+            Get the model-data mismatch values for this cycle.
+
+                (1) Open a sites_weights file
+                (2) Parse the data
+                (3) Compare site list against data
+                (4) Take care of double sites, etc
+
+        """
+        import da.tools.rc as rc
+        from da.tools.general import NameConvert
+
+        filename            = self.DaCycle.DaSystem['obs.sites.rc']
+
+        if not os.path.exists(filename):
+            msg             = 'Could not find  the required sites.rc input file (%s) ' % filename ; logging.error(msg)
+            raise IOError,msg
+        else:
+            self.SitesFile  = filename
+
+        SitesWeights        = rc.read(self.SitesFile)
+
+        self.rejection_threshold = int(SitesWeights['obs.rejection.threshold'])
+        self.global_R_scaling    = float(SitesWeights['global.R.scaling'])
+        self.n_site_categories   = int(SitesWeights['n.site.categories'])
+        self.n_sites_active      = int(SitesWeights['n.sites.active'])
+        self.n_sites_moved       = int(SitesWeights['n.sites.moved'])
+
+        msg = 'Model-data mismatch rejection threshold: %d ' % (self.rejection_threshold) ; logging.debug(msg)
+        msg = 'Model-data mismatch scaling factor     : %f ' % (self.global_R_scaling) ; logging.debug(msg)
+        msg = 'Model-data mismatch site categories    : %d ' % (self.n_site_categories) ; logging.debug(msg)
+        msg = 'Model-data mismatch active sites       : %d ' % (self.n_sites_active) ; logging.debug(msg)
+        msg = 'Model-data mismatch moved sites        : %d ' % (self.n_sites_moved) ; logging.debug(msg)
+   
+        cats   = [k for k in SitesWeights.keys() if 'site.category' in k] 
+
+        SiteCategories={}
+        for key in cats:
+            if self.Co2_C13_together or self.C13_only:
+                name,error,error_c13,may_localize,may_reject = SitesWeights[key].split(';')
+            else:
+                name,error,may_localize,may_reject = SitesWeights[key].split(';')
+
+            name            = name.strip().lower()
+            error           = float(error)
+            if self.Co2_C13_together or self.C13_only:
+                error_c13       = float(error_c13)
+            may_localize    = bool(may_localize)
+            may_reject      = bool(may_reject)
+            if self.Co2_C13_together or self.C13_only:
+                SiteCategories[name] = {'error':error,'error_c13':error_c13,'may_localize':may_localize,'may_reject':may_reject}
+            else:
+                SiteCategories[name] = {'error':error,'may_localize':may_localize,'may_reject':may_reject}
+
+
+        active = [k for k in SitesWeights.keys() if 'site.active' in k] 
+
+        SiteInfo = {}
+        for key in active:
+            sitename, sitecategory  = SitesWeights[key].split(';')
+            sitename                = sitename.strip()
+            #sitename=NameConvert.NameConvert(name="%s"%sitename,to="OP") #IV to convert to obspack name conventions
+            sitecategory            = sitecategory.strip().lower()
+            SiteInfo[sitename]      = SiteCategories[sitecategory]
+                       
+        for obs in self.Data:
+
+            obs.mdm = 1000.0  # default is very high model-data-mismatch, until explicitly set by script
+            obs.mdmc13 = 1000.0  # default is very high model-data-mismatch, until explicitly set by script
+
+            species, site, method, lab, nr = os.path.split(obs.fromfile)[-1].split('_') 
+
+            identifier = "%s_%02d_%s"%(site,int(lab),method,)
+
+            identifier = NameConvert(name="%s_%s_%s"%(site.lower(),method.lower(),lab.lower(),), to='GV')
+
+            if SiteInfo.has_key(identifier): 
+                msg                 = "Observation found (%s, %s)" % (obs.code, identifier,) ; logging.debug(msg)
+              #  obs.mdm             = SiteInfo[identifier]['error']
+                if species=='co2c13':
+                  #  obs.mdmc13          = SiteInfo[identifier]['error_c13']
+                    obs.mdm          = SiteInfo[identifier]['error_c13']
+                else:
+                    obs.mdm             = SiteInfo[identifier]['error']*self.global_R_scaling
+                print obs,obs.mdm,species
+                obs.may_localize    = SiteInfo[identifier]['may_localize']
+                obs.may_reject      = SiteInfo[identifier]['may_reject']
+            else:
+                msg= "Observation NOT found (%s, %s), please check sites.rc file  (%s)  !!!" % (obs.code, identifier, self.SitesFile,) ; logging.warning(msg)
+                obs.flag            = 99
+
+            # Add SiteInfo dictionary to the Observation object for future use
+
+            self.SiteInfo = SiteInfo
+
+    def WriteObsToFile(self):
+        """ 
+            Write selected information contained in the Observation object to a file. 
+
+        """
+        import shutil
+        import da.tools.io4 as io
+        from da.tools.general import ToDectime
+        import numpy as np
+
+        outfile     = os.path.join(self.DaCycle['dir.output'],'sampleinfo_%s.nc'% self.DaCycle['time.sample.stamp'])
+
+        f           = io.CT_CDF(outfile,method='create')
+        msg         = 'Creating new Sample output file for postprocessing (%s)' % outfile ; logging.debug(msg)
+
+        dimid       = f.AddDim('obs',len(self.Data))
+        dim200char   = f.AddDim('string_of200chars',200)
+        dim10char   = f.AddDim('string_of10chars',10)
+        dimcalcomp  = f.AddDim('calendar_components',6)
+
+        if len(self.Data) == 0:
+            f.close()
+            return outfile
+
+        data =  self.Data.getvalues('id')
+
+        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['values']      = data.tolist()
+        savedict['comment']     = "Unique index number within this dataset ranging from 0 to UNLIMITED."
+        status                   = f.AddData(savedict)
+
+        data =  [[d.year,d.month,d.day,d.hour,d.minute,d.second] for d in self.Data.getvalues('xdate') ]
+
+        savedict                = io.std_savedict.copy() 
+        savedict['dtype']       = "int"
+        savedict['name']        = "date_components"
+        savedict['units']       = "integer components of UTC date/time"
+        savedict['dims']        = dimid+dimcalcomp
+        savedict['values']      = data
+        savedict['missing_value'] = -9
+        savedict['comment']     = "Calendar date components as integers. Times and dates are UTC." 
+        savedict['order']       = "year, month, day, hour, minute, second"
+        status                   = f.AddData(savedict)
+
+        data =  self.Data.getvalues('obs')
+
+        savedict                = io.std_savedict.copy()
+        savedict['name']        = "observed"
+        savedict['long_name']   = "observedvalues"
+        savedict['units']       = "mol mol-1"
+        savedict['dims']        = dimid
+        savedict['values']      = data.tolist()
+        savedict['comment']     = 'Observations used in optimization'
+        dummy                   = f.AddData(savedict)
+
+        data = self.Data.getvalues('mdm') 
+
+        savedict                = io.std_savedict.copy()
+        savedict['name']        = "modeldatamismatch"
+        savedict['long_name']   = "modeldatamismatch"
+        savedict['units']       = "[mol mol-1]^2"
+        savedict['dims']        = dimid
+        savedict['values']      = data.tolist()
+        savedict['comment']     = 'Variance of mole fractions resulting from model-data mismatch'
+        dummy                   = f.AddData(savedict)
+
+
+        if self.Co2_C13_together or self.C13_only or self.Co2_only:
+
+            data = self.Data.getvalues('mdmc13')
+
+            savedict                = io.std_savedict.copy()
+            savedict['name']        = "modeldatamismatchc13"
+            savedict['long_name']   = "modeldatamismatchc13"
+            savedict['units']       = "[permil]^2"
+            savedict['dims']        = dimid
+            savedict['values']      = data.tolist()
+            savedict['comment']     = 'Variance of permil resulting from model-data mismatch'
+            dummy                   = f.AddData(savedict)
+
+
+
+
+        data = self.Data.getvalues('simulated') 
+
+        dimmembers  = f.AddDim('members',data.shape[1])
+
+        savedict                = io.std_savedict.copy()
+        savedict['name']        = "modelsamples"
+        savedict['long_name']   = "modelsamples for all ensemble members"
+        savedict['units']       = "mol mol-1"
+        savedict['dims']        = dimid+dimmembers
+        savedict['values']      = data.tolist()
+        savedict['comment']     = 'simulated mixing ratios based on optimized state vector'
+        dummy                   = f.AddData(savedict)
+
+        data = self.Data.getvalues('fromfile') 
+
+        savedict                = io.std_savedict.copy()
+        savedict['name']        = "inputfilename"
+        savedict['long_name']   = "name of file where original obs data was taken from"
+        savedict['dtype']       = "char"
+        savedict['dims']        = dimid+dim200char
+        savedict['values']      = data
+        savedict['missing_value'] = '!'
+        dummy                   = f.AddData(savedict)
+
+        status       = f.close()
+
+        msg         = "Successfully wrote data to Sample output file (%s)"%outfile ;logging.debug(msg)
+
+        return outfile
+
+
+
+################### End Class CtObservations ###################
+
+
+
+################### Begin Class MixingRatioSample ###################
+
+class MixingRatioSample(object):
+    """ 
+        Holds the data that defines a Mixing Ratio 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,id,xdate,code='XXX',obs=0.0,simulated=0.0,resid=0.0,hphr=0.0,mdm=0.0,mdmc13=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()      # Site code
+            self.xdate      = xdate             # Date of obs
+            self.obs        = obs               # Value observed
+            self.simulated  = simulated         # Value simulated by model
+            self.resid      = resid             # Mixing ratio residuals
+            self.hphr       = hphr              # Mixing ratio prior uncertainty from fluxes and (HPH) and model data mismatch (R)
+            self.mdm        = mdm               # Model data mismatch
+            self.mdmc13        = mdmc13               # Model data mismatch c13
+            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
+            self.lat        = lat               # Sample lat
+            self.lon        = lon               # Sample lon
+            self.id         = id               # ID number
+            self.evn        = evn               # Event number
+            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
+
+    def __str__(self):
+            day=self.xdate.strftime('%Y-%m-%d %H:%M:%S')
+            return ' '.join(map(str,[self.code,day,self.obs,self.flag,self.id]))
+
+################### End Class MixingRatioSample ###################
+
+################### Begin Class MixingRatioList ###################
+
+class MixingRatioList(list):
+    """ This is a special type of list that holds MixingRatioSample objects. It has methods to extract data from such a list easily """
+    from numpy import array, ndarray
+
+    def getvalues(self,name,constructor=array):
+            from numpy import ndarray
+            result = constructor([getattr(o,name) for o in self])
+            if isinstance(result,ndarray): 
+                return result.squeeze()
+            else:
+                return result
+    def unflagged(self):
+            return MixingRatioSample([o for o in self if o.flag == 0])
+    def flagged(self):
+            return MixingRatioSample([o for o in self if o.flag != 0])
+    def selectsite(self,site='mlo'):
+            l=[o for o in self if o.code == site]
+            return MixingRatioSample(l)
+    def selecthours(self,hours=range(1,24)):
+            l=[o for o in self if o.xdate.hour in hours]
+            return MixingRatioSample(l)
+
+################### End Class MixingRatioList ###################
+
+if __name__ == "__main__":
+
+    import logging
+    from da.tools.initexit import CycleControl
+    from da.ct.dasystem import CtDaSystem 
+    from da.ct.statevector import CtStateVector 
+
+    sys.path.append('../../')
+
+    logging.root.setLevel(logging.DEBUG)
+
+    DaCycle = CycleControl(args={'rc':'../../da.rc'})
+    DaCycle.Initialize()
+    DaCycle.ParseTimes()
+
+    DaSystem    = CtDaSystem('../../carbontracker.rc')
+    DaSystem.Initialize()
+
+    DaCycle.DaSystem    = DaSystem
+
+    obs = ObsPackObservations()
+    obs.DaCycle         = DaCycle
+
+    while DaCycle['time.start'] < DaCycle['time.finish']:
+
+        DaCycle['time.sample.start'] = DaCycle['time.start']
+        DaCycle['time.sample.end'] =  DaCycle['time.end']
+
+        obs.Initialize()
+        obs.Validate()
+        obs.AddObs()
+        obs.AddModelDataMismatch()
+
+        #print(obs.Data.getvalues('obs'))
+        #print(obs.Data.getvalues('mdm'))
+        #print(obs.Data.getvalues('mdmc13'))
+        DaCycle.AdvanceCycleTimes()
+
+
+