merged r1186 and r1218 into new version that works under current trunk

da/ct/obspack_geocarbon.py

@@ -24,13 +24,13 @@ from da.baseclasses.obs import Observation
 class ObsPackObservations(Observation):
     """ an object that holds data + methods and attributes needed to manipulate mixing ratio values """
 
-    def Initialize(self, start, end, params):
+    def Initialize(self):
 
-        self.startdate = start
-        self.enddate = end
+        self.startdate = self.DaCycle['time.sample.start']
+        self.enddate = self.DaCycle['time.sample.end']
 
-        op_id = params['obspack.input.id']
-        op_dir = params['obspack.input.dir']
+        op_id = self.DaCycle.DaSystem['obspack.input.id']
+        op_dir = self.DaCycle.DaSystem['obspack.input.dir']
 
         if not os.path.exists(op_dir):
             msg = 'Could not find  the required ObsPack distribution (%s) ' % op_dir
@@ -67,7 +67,7 @@ class ObsPackObservations(Observation):
 
             items = line.split()
             #ncfile, lab , start_date, stop_date, data_comparison = items[0:5]
-            ncfile, lab, start_date, stop_date, data_comparison= line[:105].split()
+            ncfile, lab , start_date, stop_date, data_comparison= line[:105].split()
 
 
             ncfilelist += [ncfile]
@@ -133,6 +133,7 @@ class ObsPackObservations(Observation):
         for idx, val in zip(ids, simulated): 
             if idx in obs_ids:
                 index = obs_ids.index(idx)
+
                 self.datalist[index].simulated = val  # in mol/mol
             else:     
                 missing_samples.append(idx)
@@ -143,14 +144,14 @@ class ObsPackObservations(Observation):
 
         logging.debug("Added %d simulated values to the Data list" % (len(ids) - len(missing_samples)))
 
-    def write_sample_info(self, dirinput, timestamp):
+    def write_sample_info(self):
         """ 
             Write the information needed by the observation operator to a file. Return the filename that was written for later use
 
         """
         import da.tools.io4 as io
 
-        obsinputfile = os.path.join(dirinput, 'observations_%s.nc' % timestamp)
+        obsinputfile = os.path.join(self.DaCycle['dir.input'], 'observations_%s.nc' % self.DaCycle['time.sample.stamp'])
 
         f = io.CT_CDF(obsinputfile, method='create')
         logging.debug('Creating new observations file for ObservationOperator (%s)' % obsinputfile)
@@ -252,7 +253,7 @@ class ObsPackObservations(Observation):
 
         return obsinputfile
 
-    def add_model_data_mismatch(self, filename):
+    def add_model_data_mismatch(self):
         """ 
             Get the model-data mismatch values for this cycle.
 
@@ -264,7 +265,7 @@ class ObsPackObservations(Observation):
         """
         import da.tools.rc as rc
 
-        
+        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
@@ -359,14 +360,14 @@ class ObsPackObservations(Observation):
 
         logging.debug("Added Model Data Mismatch to all samples ")
 
-    def write_obs_to_file(self, outdir, timestamp, filenam="oldstyle"):
+    def write_obs_to_file(self,filenam="oldstyle"):
         """ 
             Write selected information contained in the Observation object to a file. 
 
         """
         import da.tools.io4 as io
 
-        outfile = os.path.join(outdir, 'sampleinfo_%s__%s.nc' % (timestamp, filenam))
+        outfile = os.path.join(self.DaCycle['dir.output'], 'sampleinfo_%s__%s.nc' % (self.DaCycle['time.sample.stamp'], filenam))
 
         f = io.CT_CDF(outfile, method='create')
         logging.debug('Creating new Sample output file for postprocessing (%s)' % outfile)