renamed package ct to carbondioxide and ctgridded to co2gridded

renamed class names Ct- to CO2-
changed class name Observation to Observations 
small cleanup changes to template.py

da/analysis/expand_fluxes.py

@@ -117,7 +117,7 @@ def save_weekly_avg_1x1_data(DaCycle, StateVector):
                 for n in range(nlag, 0, -1):
                     priordate = enddate - timedelta(dt.days * n)
                     savedir = DaCycle['dir.output'].replace(startdate.strftime('%Y%m%d'), priordate.strftime('%Y%m%d'))
-                    filename = os.path.join(savedir, 'savestate.nc')#LU i suppose that it would be priordate (savestate gets same stamp as dir.output=
+                    filename = os.path.join(savedir, 'savestate_%s.nc' % priordate.strftime('%Y%m%d'))
                     if os.path.exists(filename):
                         StateVector.read_from_file(filename, qual=qual_short)
                         gridmean, gridensemble = StateVector.state_to_grid(lag=n)
@@ -131,7 +131,7 @@ def save_weekly_avg_1x1_data(DaCycle, StateVector):
             else:
                 qual_short = 'opt'
                 savedir = DaCycle['dir.output']
-                filename = os.path.join(savedir, 'savestate.nc')
+                filename = os.path.join(savedir, 'savestate_%s.nc' % startdate.strftime('%Y%m%d'))
                 StateVector.read_from_file(filename, qual=qual_short)
                 gridmean, gridensemble = StateVector.state_to_grid(lag=1)
 
@@ -301,7 +301,7 @@ def save_weekly_avg_state_data(DaCycle, StateVector):
                 for n in range(nlag, 0, -1):
                     priordate = enddate - timedelta(dt.days * n)
                     savedir = DaCycle['dir.output'].replace(startdate.strftime('%Y%m%d'), priordate.strftime('%Y%m%d'))
-                    filename = os.path.join(savedir, 'savestate.nc')
+                    filename = os.path.join(savedir,'savestate_%s.nc' % priordate.strftime('%Y%m%d'))
                     if os.path.exists(filename):
                         StateVector.read_from_file(filename, qual=qual_short)
 
@@ -316,7 +316,7 @@ def save_weekly_avg_state_data(DaCycle, StateVector):
             else:
                 qual_short = 'opt'
                 savedir = DaCycle['dir.output']
-                filename = os.path.join(savedir, 'savestate.nc')
+                filename = os.path.join(savedir, 'savestate_%s.nc' % startdate.strftime('%Y%m%d'))
                 StateVector.read_from_file(filename)
                 choicelag = 1
                 statemean = StateVector.EnsembleMembers[choicelag - 1][0].ParameterValues
@@ -1027,8 +1027,8 @@ if __name__ == "__main__":
 
     import logging
     from da.tools.initexit import CycleControl
-    from da.ct.dasystem import CtDaSystem 
-    from da.ct.statevector import CtStateVector 
+    from da.carbondioxide.dasystem import CO2DaSystem 
+    from da.carbondioxide.statevector import CO2StateVector 
 
     sys.path.append('../../')
 
@@ -1038,11 +1038,11 @@ if __name__ == "__main__":
     DaCycle.initialize()
     DaCycle.parse_times()
 
-    DaSystem = CtDaSystem('../rc/carbontracker_ct09_opfnew.rc')
+    DaSystem = CO2DaSystem('../rc/carbontracker_ct09_opfnew.rc')
 
     DaCycle.DaSystem = DaSystem
 
-    StateVector = CtStateVector()
+    StateVector = CO2StateVector()
     StateVector.initialize(DaCycle)
 
     while DaCycle['time.end'] < DaCycle['time.finish']:

da/analysis/expand_mixingratios.py

@@ -315,10 +315,9 @@ def write_mixing_ratios(DaCycle):
 
 
 if __name__ == "__main__":
-
     import logging
     from da.tools.initexit import CycleControl
-    from da.ct.dasystem import CtDaSystem
+    from da.carbondioxide.dasystem import CO2DaSystem
 
     sys.path.append('../../')
 
@@ -328,7 +327,7 @@ if __name__ == "__main__":
     DaCycle.initialize()
     DaCycle.parse_times()
 
-    DaSystem = CtDaSystem('../rc/carbontracker_ct09_opf.rc')
+    DaSystem = CO2DaSystem('../rc/carbontracker_ct09_opf.rc')
     DaSystem.initialize()
 
     DaCycle.DaSystem = DaSystem

da/analysis/siteseries.py

@@ -745,8 +745,8 @@ def residuals_new(fig, infile):
 if __name__ == '__main__':    # started as script
 
     from da.tools.initexit import CycleControl
-    from da.ct.dasystem import CtDaSystem 
-    from da.ct.statevector import CtStateVector 
+    from da.carbondioxide.dasystem import CO2DaSystem 
+    from da.carbondioxide.statevector import CO2StateVector 
 
     sys.path.append('../../')
 
@@ -756,7 +756,7 @@ if __name__ == '__main__':    # started as script
     DaCycle.initialize()
     DaCycle.parse_times()
 
-    DaSystem = CtDaSystem('../rc/carbontracker_ct09_opf.rc')
+    DaSystem = CO2DaSystem('../rc/carbontracker_ct09_opf.rc')
     DaSystem.initialize()
 
     DaCycle.DaSystem = DaSystem

da/analysis/summarize_obs.py

@@ -332,7 +332,7 @@ def grep(pattern, fil):
 
 if __name__ == '__main__':    # started as script
     from da.tools.initexit import CycleControl
-    from da.ct.dasystem import CtDaSystem 
+    from da.carbondioxide.dasystem import CO2DaSystem 
 
     sys.path.append('../../')
 
@@ -342,7 +342,7 @@ if __name__ == '__main__':    # started as script
     DaCycle.initialize()
     DaCycle.parse_times()
 
-    DaSystem = CtDaSystem('../rc/carbontracker_ct09_opf.rc')
+    DaSystem = CO2DaSystem('../rc/carbontracker_ct09_opf.rc')
     DaSystem.initialize()
 
     DaCycle.DaSystem = DaSystem

da/baseclasses/obs.py

@@ -8,7 +8,7 @@
 Revision History:
 File created on 28 Jul 2010.
 
-.. autoclass:: da.baseclasses.obs.Observation 
+.. autoclass:: da.baseclasses.obs.Observations 
    :members: initialize, Validate, add_observations, add_simulations, add_model_data_mismatch, write_sample_info  
 
 .. autoclass:: da.baseclasses.obs.ObservationList 
@@ -19,14 +19,14 @@ File created on 28 Jul 2010.
 import logging
 from numpy import array, ndarray
 
-identifier = 'Observation baseclass'
+identifier = 'Observations baseclass'
 version = '0.0'
 
-################### Begin Class Observation ###################
+################### Begin Class Observations ###################
 
-class Observation(object):
+class Observations(object):
     """ 
-    The baseclass Observation is a generic object that provides a number of methods required for any type of observations used in 
+    The baseclass Observations is a generic object that provides a number of methods required for any type of observations used in 
     a data assimilation system. These methods are called from the CarbonTracker pipeline. 
 
     .. note:: Most of the actual functionality will need to be provided through a derived Observations class with the methods 
@@ -35,17 +35,17 @@ class Observation(object):
 
     Upon initialization of the class, an object is created that holds no actual data, but has a placeholder attribute `self.Data` 
     which is an empty list of type :class:`~da.baseclasses.obs.ObservationList`. An ObservationList object is created when the 
-    method :meth:`~da.baseclasses.obs.Observation.add_observations` is invoked in the pipeline. 
+    method :meth:`~da.baseclasses.obs.Observations.add_observations` is invoked in the pipeline. 
 
     From the list of observations, a file is written  by method 
-    :meth:`~da.baseclasses.obs.Observation.write_sample_info`
+    :meth:`~da.baseclasses.obs.Observations.write_sample_info`
     with the sample info needed by the 
     :class:`~da.baseclasses.observationoperator.ObservationOperator` object. The values returned after sampling 
-    are finally added by :meth:`~da.baseclasses.obs.Observation.add_simulations`
+    are finally added by :meth:`~da.baseclasses.obs.Observations.add_simulations`
 
     """ 
 
-    def __init__(self, DaCycle=None):#LU to sie nigdy nie wywola, prawda?
+    def __init__(self):
         """
         create an object with an identifier, version, and an empty ObservationList
         """
@@ -56,12 +56,7 @@ class Observation(object):
         # The following code allows the object to be initialized with a DaCycle object already present. Otherwise, it can
         # be added at a later moment.
 
-        if DaCycle != None:
-            self.DaCycle = DaCycle
-        else:
-            self.DaCycle = {}
-
-        logging.info('Observation object initialized: %s' % self.Identifier)
+        logging.info('Observations object initialized: %s' % self.Identifier)
 
     def getlength(self):
         return len(self.datalist)
@@ -73,7 +68,7 @@ class Observation(object):
 
     def add_observations(self):
         """ 
-        Add actual observation data to the Observation object. This is in a form of an 
+        Add actual observation data to the Observations object. This is in a form of an 
         :class:`~da.baseclasses.obs.ObservationList` that is contained in self.Data. The 
         list has as only requirement that it can return the observed+simulated values 
         through the method :meth:`~da.baseclasses.obs.ObservationList.getvalues`
@@ -81,7 +76,7 @@ class Observation(object):
         """
 
     def add_simulations(self):
-        """ Add the simulation data to the Observation object. 
+        """ Add the simulation data to the Observations object. 
         """
 
     def add_model_data_mismatch(self):

da/baseclasses/optimizer.py

@@ -116,7 +116,7 @@ class Optimizer(object):
 
                 simulatedensemble = Samples.getvalues('simulated')
 
-                if allsimulated == None :           #LU if allsimulated: np.concatenate; else: np.array
+                if allsimulated == None :     
                     allsimulated = np.array(simulatedensemble)
                 else:
                     allsimulated = np.concatenate((allsimulated, np.array(simulatedensemble)), axis=0)

da/ct/dasystem.py → da/carbondioxide/dasystem.py

@@ -11,11 +11,11 @@ File created on 26 Aug 2010.
 
 import logging
 
-################### Begin Class CtDaSystem ###################
+################### Begin Class CO2DaSystem ###################
 
 from da.baseclasses.dasystem import DaSystem
 
-class CtDaSystem(DaSystem):
+class CO2DaSystem(DaSystem):
     """ Information on the data assimilation system used. This is normally an rc-file with settings.
     """
     def validate(self):
@@ -43,7 +43,7 @@ class CtDaSystem(DaSystem):
                 logging.warning('Missing a required value in rc-file : %s' % key)
         logging.debug('DA System Info settings have been validated succesfully')
 
-################### End Class CtDaSystem ###################
+################### End Class CO2DaSystem ###################
 
 
 if __name__ == "__main__":

da/ct/obs.py → da/carbondioxide/obs.py

@@ -22,13 +22,13 @@ sys.path.append('../../')
 identifier = 'CarbonTracker CO2 mixing ratios'
 version = '0.0'
 
-from da.baseclasses.obs import Observation
+from da.baseclasses.obs import Observations
 import da.tools.io4 as io
 import da.tools.rc as rc
 
-################### Begin Class CtObservations ###################
+################### Begin Class CO2Observations ###################
 
-class CtObservations(Observation):
+class CO2Observations(Observations):
     """ an object that holds data + methods and attributes needed to manipulate mixing ratio values """
 
     def initialize(self, DaCycle):
@@ -305,13 +305,13 @@ class CtObservations(Observation):
                 logging.warning("Observation NOT found (%s, %s), please check sites.rc file  (%s)  !!!" % (obs.code, identifier, self.SitesFile))
                 obs.flag = 99
 
-            # Add SiteInfo dictionary to the Observation object for future use
+            # Add SiteInfo dictionary to the Observations object for future use
 
             self.SiteInfo = SiteInfo
 
     def write_obs_to_file(self, outfile):
         """ 
-            Write selected information contained in the Observation object to a file. 
+            Write selected information contained in the Observations object to a file. 
 
         """
         
@@ -415,7 +415,7 @@ class CtObservations(Observation):
         #return outfile
 
 
-################### End Class CtObservations ###################
+################### End Class CO2Observations ###################
 
 
 

da/ct/obspack.py → da/carbondioxide/obspack.py

@@ -20,7 +20,7 @@ sys.path.append('../../')
 
 import da.tools.io4 as io
 import da.tools.rc as rc
-from da.baseclasses.obs import Observation
+from da.baseclasses.obs import Observations
 from da.tools.general import name_convert
 
 identifier = 'CarbonTracker CO2 mixing ratios'
@@ -30,7 +30,7 @@ version = '0.0'
 
 ################### Begin Class ObsPackObservations ###################
 
-class ObsPackObservations(Observation):
+class ObsPackObservations(Observations):
     """ an object that holds data + methods and attributes needed to manipulate mixing ratio values """
 
     def initialize(self, DaCycle):
@@ -111,7 +111,7 @@ class ObsPackObservations(Observation):
 
             logging.debug("Added %d observations from file (%s) to the Data list" % (len(dates), ncfile))
 
-        logging.info("Observation list now holds %d values" % len(self.datalist))
+        logging.info("Observations list now holds %d values" % len(self.datalist))
 
     def add_simulations(self, filename, silent=False):
         """ Adds model simulated values to the mixing ratio objects """
@@ -330,13 +330,13 @@ class ObsPackObservations(Observation):
                 logging.warning("Observation found (%s, %s), but not used in assimilation !!!" % (obs.code, identifier))
                 obs.flag = 99
 
-            # Add SiteInfo dictionary to the Observation object for future use
+            # Add SiteInfo dictionary to the Observations object for future use
 
             self.SiteInfo = SiteInfo
 
     def write_obs_to_file(self, outfile):
         """ 
-            Write selected information contained in the Observation object to a file. 
+            Write selected information contained in the Observations object to a file. 
 
         """
 

da/ct/obspack_geocarbon.py → da/carbondioxide/obspack_geocarbon.py

@@ -21,12 +21,12 @@ sys.path.append('../../')
 identifier = 'CarbonTracker CO2 mixing ratios'
 version = '0.0'
 
-from da.baseclasses.obs import Observation
+from da.baseclasses.obs import Observations
 import da.tools.io4 as io
 import da.tools.rc as rc
 ################### Begin Class ObsPackObservations ###################
 
-class ObsPackObservations(Observation):
+class ObsPackObservations(Observations):
     """ an object that holds data + methods and attributes needed to manipulate mixing ratio values """
 
     def initialize(self, DaCycle):
@@ -104,7 +104,7 @@ class ObsPackObservations(Observation):
 
             logging.debug("Added %d observations from file (%s) to the Data list" % (len(dates), ncfile)) 
 
-        logging.info("Observation list now holds %d values" % len(self.datalist))
+        logging.info("Observations list now holds %d values" % len(self.datalist))
 
     def add_simulations(self, filename, silent=False):
         """ Adds model simulated values to the mixing ratio objects """
@@ -318,7 +318,7 @@ class ObsPackObservations(Observation):
                 if SiteHourly.has_key(identifier):
                     hourf, hourt = SiteHourly[identifier]
                     if int(obs.xdate.hour) >= hourf and int(obs.xdate.hour) <= hourt:
-                        logging.warning("Observation in hourly dataset INCLUDED, while sampling time %s was between %s:00-%s:00"%(obs.xdate.time(),hourf,hourt))
+                        logging.warning("Observations in hourly dataset INCLUDED, while sampling time %s was between %s:00-%s:00"%(obs.xdate.time(),hourf,hourt))
                     else:
                         logging.warning("Observation in hourly dataset EXCLUDED, while sampling time %s was outside %s:00-%s:00"%(obs.xdate.time(),hourf,hourt))
                         exclude_hourly = True
@@ -346,7 +346,7 @@ class ObsPackObservations(Observation):
 
                 logging.warning("Observation location for (%s, %d), is moved by %3.2f degrees latitude and %3.2f degrees longitude" % (identifier, obs.id, movelat, movelon))
 
-        # Add SiteInfo dictionary to the Observation object for future use
+        # Add SiteInfo dictionary to the Observations object for future use
 
         self.SiteInfo = SiteInfo
         self.SiteMove = SiteMove
@@ -356,7 +356,7 @@ class ObsPackObservations(Observation):
 
     def write_obs_to_file(self, outfile):
         """ 
-            Write selected information contained in the Observation object to a file. 
+            Write selected information contained in the Observations object to a file. 
 
         """
 

da/ct/optimizer.py → da/carbondioxide/optimizer.py

@@ -19,12 +19,12 @@ from da.baseclasses.optimizer import Optimizer
 identifier = 'Ensemble Square Root Filter'
 version = '0.0'
 
-################### Begin Class CtOptimizer ###################
+################### Begin Class CO2Optimizer ###################
 
-class CtOptimizer(Optimizer):
+class CO2Optimizer(Optimizer):
     """
         This creates an instance of a CarbonTracker optimization object. The base class it derives from is the optimizer object.
-        Additionally, this CtOptimizer implements a special localization option following the CT2007 method.
+        Additionally, this CO2Optimizer implements a special localization option following the CT2007 method.
 
         All other methods are inherited from the base class Optimizer.
     """
@@ -83,7 +83,7 @@ class CtOptimizer(Optimizer):
     
         logging.info("Current minimum least squares algorithm is set to %s" % self.algorithm)
 
-################### End Class CtOptimizer ###################
+################### End Class CO2Optimizer ###################
 
 if __name__ == "__main__":
     pass

da/ct/statevector.py → da/carbondioxide/statevector.py

@@ -22,9 +22,9 @@ import da.tools.io4 as io
 identifier = 'CarbonTracker Statevector '
 version = '0.0'
 
-################### Begin Class CtStateVector ###################
+################### Begin Class CO2StateVector ###################
 
-class CtStateVector(StateVector):
+class CO2StateVector(StateVector):
     """ This is a StateVector object for CarbonTracker. It has a private method to make new ensemble members """
 
     def get_covariance(self, date, DaCycle):
@@ -40,7 +40,7 @@ class CtStateVector(StateVector):
         # Get the needed matrices from the specified covariance files
 
         file_ocn_cov = DaCycle.DaSystem['ocn.covariance'] 
-        file_bio_cov = DaCycle.DaSystem['bio.covariance']   #LU logika tego to powrot do dacycle zeby potem z systemu(CT) pobrac parametr
+        file_bio_cov = DaCycle.DaSystem['bio.covariance'] 
 
         # replace YYYY.MM in the ocean covariance file string
 
@@ -136,7 +136,7 @@ class CtStateVector(StateVector):
 
         logging.info('Successfully read the State Vector from file (%s) ' % filename)
 
-################### End Class CtStateVector ###################
+################### End Class CO2StateVector ###################
 
 
 if __name__ == "__main__":

da/ctgridded/dasystem.py → da/co2gridded/dasystem.py

@@ -16,7 +16,7 @@ import logging
 
 from da.baseclasses.dasystem import DaSystem
 
-class CtGriddedDaSystem(DaSystem):
+class CO2GriddedDaSystem(DaSystem):
     """ Information on the data assimilation system used. This is normally an rc-file with settings.
     """
 

da/ctgridded/statevector.py → da/co2gridded/statevector.py

@@ -24,7 +24,7 @@ version = '0.0'
 
 ################### Begin Class CtStateVector ###################
 
-class CtGriddedStateVector(StateVector):
+class CO2GriddedStateVector(StateVector):
     """ This is a StateVector object for CarbonTracker. It has a private method to make new ensemble members """
 
     def get_covariance(self, date, DaCycle):

da/examples/das.py

@@ -16,12 +16,12 @@ sys.path.append(os.getcwd())
 from da.tools.initexit import start_logger, validate_opts_args, parse_options, CycleControl
 from da.tools.pipeline import ensemble_smoother_pipeline
 from da.platform.maunaloa import MaunaloaPlatForm 
-from da.ct.dasystem import CtDaSystem 
-from da.ct.statevector import CtStateVector 
-#from da.ct.obspack import ObsPackObservations 
-from da.ct.obs import CtObservations 
+from da.carbondioxide.dasystem import CO2DaSystem 
+from da.carbondioxide.statevector import CO2StateVector 
+#from da.carbondioxide.obspack import ObsPackObservations 
+from da.carbondioxide.obs import CO2Observations 
 from da.tm5.observationoperator import TM5ObservationOperator 
-from da.ct.optimizer import CtOptimizer
+from da.carbondioxide.optimizer import CO2Optimizer
 
 from da.analysis.expand_fluxes import save_weekly_avg_1x1_data, save_weekly_avg_state_data, save_weekly_avg_tc_data, save_weekly_avg_ext_tc_data
 from da.analysis.expand_mixingratios import write_mixing_ratios
@@ -43,12 +43,12 @@ DaCycle = CycleControl(opts, args)
 
 
 PlatForm = MaunaloaPlatForm()
-DaSystem = CtDaSystem(DaCycle['da.system.rc'])
+DaSystem = CO2DaSystem(DaCycle['da.system.rc'])
 ObsOperator = TM5ObservationOperator(DaCycle['da.obsoperator.rc'])
 #Samples     = ObsPackObservations()
-Samples = CtObservations()
-StateVector = CtStateVector()
-Optimizer = CtOptimizer()
+Samples = CO2Observations()
+StateVector = CO2StateVector()
+Optimizer = CO2Optimizer()
 
 ##########################################################################################
 ################### ENTER THE PIPELINE WITH THE OBJECTS PASSED BY THE USER ###############

da/examples/dasgridded.py

@@ -18,12 +18,12 @@ from da.tools.initexit import start_logger, parse_options, validate_opts_args, C
 
 from da.tools.pipeline import ensemble_smoother_pipeline
 from da.platform.maunaloa import MaunaloaPlatForm 
-from da.ctgridded.dasystem import CtGriddedDaSystem 
-from da.ctgridded.statevector import CtGriddedStateVector 
-from da.ct.obs import CtObservations 
+from da.co2gridded.dasystem import CO2GriddedDaSystem 
+from da.co2gridded.statevector import CO2GriddedStateVector 
+from da.carbondioxide.obs import CO2Observations 
 
 from da.tm5.observationoperator import TM5ObservationOperator 
-from da.ct.optimizer import CtOptimizer
+from da.carbondioxide.optimizer import CO2Optimizer
 from da.tools.pipeline import header, footer
 
 from da.analysis.expand_fluxes import save_weekly_avg_1x1_data, save_weekly_avg_state_data, save_weekly_avg_tc_data, save_weekly_avg_ext_tc_data
@@ -44,11 +44,11 @@ opts, args = validate_opts_args(parse_options())
 DaCycle = CycleControl(opts, args)
 
 PlatForm = MaunaloaPlatForm()
-DaSystem = CtGriddedDaSystem(DaCycle['da.system.rc'])
+DaSystem = CO2GriddedDaSystem(DaCycle['da.system.rc'])
 ObsOperator = TM5ObservationOperator(DaCycle['da.obsoperator.rc'])
-Samples = CtObservations()
-StateVector = CtGriddedStateVector()
-Optimizer = CtOptimizer()
+Samples = CO2Observations()
+StateVector = CO2GriddedStateVector()
+Optimizer = CO2Optimizer()
 
 ##########################################################################################
 ################### ENTER THE PIPELINE WITH THE OBJECTS PASSED BY THE USER ###############

da/examples/dasjet.py

@@ -16,11 +16,11 @@ sys.path.append(os.getcwd())
 from da.tools.initexit import start_logger, validate_opts_args, parse_options, CycleControl
 from da.tools.pipeline import ensemble_smoother_pipeline
 from da.platform.jet import JetPlatForm 
-from da.ct.dasystem import CtDaSystem 
-from da.ct.statevector import CtStateVector 
-from da.ct.obs import CtObservations 
+from da.carbondioxide.dasystem import CO2DaSystem 
+from da.carbondioxide.statevector import CO2StateVector 
+from da.carbondioxide.obs import CO2Observations 
 from da.tm5.observationoperator import TM5ObservationOperator 
-from da.ct.optimizer import CtOptimizer
+from da.carbondioxide.optimizer import CO2Optimizer
 from da.tools.pipeline import header, footer
 
 
@@ -38,11 +38,11 @@ opts, args = validate_opts_args(parse_options())
 DaCycle = CycleControl(opts, args)
 
 PlatForm = JetPlatForm()
-DaSystem = CtDaSystem(DaCycle['da.system.rc'])
+DaSystem = CO2DaSystem(DaCycle['da.system.rc'])
 ObsOperator = TM5ObservationOperator(DaCycle['da.obsoperator.rc'])
-Samples = CtObservations()
-StateVector = CtStateVector()
-Optimizer = CtOptimizer()
+Samples = CO2Observations()
+StateVector = CO2StateVector()
+Optimizer = CO2Optimizer()
 
 ##########################################################################################
 ################### ENTER THE PIPELINE WITH THE OBJECTS PASSED BY THE USER ###############