Data attribute of Obs class now obsolete, code changes needed

da/baseclasses/optimizer.py

@@ -80,6 +80,8 @@ class Optimizer(object):
         self.KG = np.zeros((self.nlag * self.nparams, self.nobs,), float)
 
     def state_to_matrix(self, StateVector):
+        import numpy as np
+
         allsites = []      # collect all obs for n=1,..,nlag
         allobs = []      # collect all obs for n=1,..,nlag
         allmdm = []      # collect all mdm for n=1,..,nlag
@@ -99,16 +101,16 @@ class Optimizer(object):
             if Samples != None:
                 self.rejection_threshold = Samples.rejection_threshold
 
-                allreject.extend(Samples.Data.getvalues('may_reject'))
-                alllocalize.extend(Samples.Data.getvalues('may_localize'))
-                allflags.extend(Samples.Data.getvalues('flag'))
-                allspecies.extend(Samples.Data.getvalues('species'))
-                allobs.extend(Samples.Data.getvalues('obs'))
-                allsites.extend(Samples.Data.getvalues('code'))
-                allmdm.extend(Samples.Data.getvalues('mdm'))
-                allids.extend(Samples.Data.getvalues('id'))
+                allreject.extend(Samples.getvalues('may_reject'))
+                alllocalize.extend(Samples.getvalues('may_localize'))
+                allflags.extend(Samples.getvalues('flag'))
+                allspecies.extend(Samples.getvalues('species'))
+                allobs.extend(Samples.getvalues('obs'))
+                allsites.extend(Samples.getvalues('code'))
+                allmdm.extend(Samples.getvalues('mdm'))
+                allids.extend(Samples.getvalues('id'))
 
-                simulatedensemble = Samples.Data.getvalues('simulated')
+                simulatedensemble = Samples.getvalues('simulated')
 
                 if allsimulated == None :
                     allsimulated = np.array(simulatedensemble)
@@ -428,7 +430,7 @@ if __name__ == "__main__":
     samples.add_simulations('/Users/peters/tmp/test_da/output/20050305/samples.000.nc')
 
 
-    nobs = len(samples.Data)
+    nobs = len(samples.datalist)
     dims = (int(DaCycle['time.nlag']),
                   int(DaCycle['da.optimizer.nmembers']),
                   int(DaCycle.DaSystem['nparameters']),