revised additive scheme

da/stilt/statevector.py

-"""CarbonTracker Data Assimilation Shell (CTDAS) Copyright (C) 2017 Wouter Peters. 
-Users are recommended to contact the developers (wouter.peters@wur.nl) to receive
-updates of the code. See also: http://www.carbontracker.eu. 
-
-This program is free software: you can redistribute it and/or modify it under the
-terms of the GNU General Public License as published by the Free Software Foundation, 
-version 3. This program is distributed in the hope that it will be useful, but 
-WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS 
-FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. 
-
-You should have received a copy of the GNU General Public License along with this 
-program. If not, see <http://www.gnu.org/licenses/>."""
 #!/usr/bin/env python
 # ct_statevector_tools.py
 
@@ -83,20 +71,19 @@ class CO2GriddedStateVector(StateVector):
             else:
                 cov = f.get_variable('covariance')
                 #cov_sf      = 10.0/np.sqrt(cov.diagonal().sum())  # this scaling factor makes the total variance close to the value of a single ecoregion
-                cov_sf = 20.0 / np.sqrt(cov.diagonal().sum())  # this scaling factor makes the total variance close to the value of a single ecoregion
-                cov = cov * cov_sf
+                cov_sf = 360. / np.sqrt(cov.diagonal().sum())  # this scaling factor makes the total variance close to the value of a single ecoregion #I use 360 to boost up the P matrix uncertainty
+                cov1 = cov * cov_sf * (1.e-6)**2  # here you assume that your P matrix has units of mol m-2 s-1 squared.
 
             f.close()
-            covariancematrixlist.append(cov)
+            covariancematrixlist.append(cov1)
 
         # Boundary conditions covariance
 
-        cov = np.array([[2]]) #np.ones((1,1),)
+        cov = np.array([[2*2]])
+        covariancematrixlist.append(cov)
+        covariancematrixlist.append(cov)
+        covariancematrixlist.append(cov)
         covariancematrixlist.append(cov)
-
-
-
-
 
         logging.debug("Succesfully closed files after retrieving prior covariance matrices")
 
@@ -168,34 +155,32 @@ class CO2GriddedStateVector(StateVector):
             npoints = matrix.shape[0]
 
             istop = istop + npoints
-            logging.info('i %s,%s'%(i,matrix ))
-
-
-            if i < len(covariancematrixlist)-1:
 
+            #if i < len(covariancematrixlist)-1:
+            if i < len(covariancematrixlist)-4:
                 for member in range(1, self.nmembers):
                     rands = np.random.randn(npoints)
                     deviations = np.dot(C, rands)
                     dev_matrix[istart:istop, member - 1] = deviations
                     #dev_matrix[istop, member - 1] = 1.e-10 * np.random.randn()
-                    logging.info('deviation %s,%s,%s'%(deviations[0],istart,istop))
 
-            #cov2 = np.dot(dev_matrix[istart:istop,:],np.transpose(dev_matrix[istart:istop,:])) / (self.nmembers-1)
-            #print matrix.sum(),cov2.sum(),abs(matrix.diagonal()-cov2.diagonal()).max(), matrix.shape,cov2.shape
 
-            #istart = istart + npoints
 
-            #logging.info('i %s,%s'%(i,len(covariancematrixlist)-1), )
-            if i == len(covariancematrixlist)-1:
+            #if i == len(covariancematrixlist)-1:
+            if i >= len(covariancematrixlist)-4 and i <= len(covariancematrixlist)-1:
                 for member in range(1, self.nmembers):
                     rands = np.random.randn(npoints)
                     deviations = np.dot(C, rands)
-                    logging.info('deviation boundary conditions %s,%s,%s'%(deviations,istart,istop))
+                    #logging.info('deviation boundary conditions %s,%s,%s'%(deviations,istart,istop))
                     dev_matrix[istart:istop, member - 1] = deviations
 
             istart = istart + npoints
 
 
+        #for i in range(self.nparams):
+            #logging.info('i=%s,deviation=%s'%(i,dev_matrix[i,:]))
+
+
         logging.debug('Successfully constructed a deviation matrix from covariance structure')
         logging.info('Appr. degrees of freedom in full covariance matrix is %s' % (int(dof)))
 
@@ -204,8 +189,12 @@ class CO2GriddedStateVector(StateVector):
 
         # Create mean values
 
-        new_mean = np.ones(self.nparams, float) # standard value for a new time step is 1.0
-        new_mean[-1] = np.zeros((1),float) # standard value for boundary conditions for new time step is 0.0
+        #new_mean = np.ones(self.nparams, float) # standard value for a new time step is 1.0
+        new_mean = np.zeros(self.nparams, float)
+        new_mean[-4] = np.zeros((1),float) # standard value for boundary conditions for new time step is 0.0
+        new_mean[-3] = np.zeros((1),float)
+        new_mean[-2] = np.zeros((1),float)
+        new_mean[-1] = np.zeros((1),float)
 
         # If this is not the start of the filter, average previous two optimized steps into the mix
 
@@ -226,7 +215,6 @@ class CO2GriddedStateVector(StateVector):
             new_member = EnsembleMember(member)
             new_member.param_values = dev_matrix[:, member - 1] + new_mean
             self.ensemble_members[lag].append(new_member)
-
         logging.debug('%d new ensemble members were added to the state vector # %d' % (self.nmembers, (lag + 1)))
 
 
@@ -259,8 +247,10 @@ class CO2GriddedStateVector(StateVector):
         for mem in members:
             filename = os.path.join(outdir, 'parameters.%03d%s' % (mem.membernumber, endswith))
             ncf = io.CT_CDF(filename, method='create')
-            dimparams = ncf.add_params_dim(self.nparams-1)
-            dimparams_bc       = ncf.add_dim('nparameters_bc',1)
+            #dimparams = ncf.add_params_dim(self.nparams-1)
+            dimparams = ncf.add_params_dim(self.nparams-4)
+            #dimparams_bc  = ncf.add_dim('nparameters_bc',1)
+            dimparams_bc  = ncf.add_dim('nparameters_bc',4)
             dimgrid = ncf.add_latlon_dim()
 
             data = mem.param_values
@@ -270,7 +260,8 @@ class CO2GriddedStateVector(StateVector):
             savedict['long_name'] = "parameter_values_for_member_%d" % mem.membernumber
             savedict['units'] = "unitless"
             savedict['dims'] = dimparams
-            savedict['values'] = data[:self.nparams-1]
+            #savedict['values'] = data[:self.nparams-1]
+            savedict['values'] = data[:self.nparams-4]
             savedict['comment'] = 'These are parameter values to use for member %d' % mem.membernumber
             ncf.add_data(savedict)
 
@@ -290,7 +281,8 @@ class CO2GriddedStateVector(StateVector):
             savedict['long_name'] = "parameter_values_for_member_%d" % mem.membernumber
             savedict['units'] = "unitless"
             savedict['dims'] = dimparams_bc
-            savedict['values'] = data[-1]
+            #savedict['values'] = data[-1]
+            savedict['values'] = data[-4:]   #data[-4:-1]
             savedict['comment'] = 'These are parameter values to use for member %d' % mem.membernumber
             ncf.add_data(savedict)