Added a forgotten file. Minor changes elsewhere

pycif/plugins/controlvects/standard/__init__.py

@@ -94,3 +94,4 @@ def ini_data(plugin, **kwargs):
     # Initializing the product of chi by B^(1/2), only if components specified
     if hasattr(plugin, 'components'):
         init_bprod(plugin, **kwargs)
+

pycif/plugins/controlvects/standard/background_xb.py

+import numpy as np
+from scipy import ndimage
+from pycif.utils import dates
+from .utils.dimensions import hresol2dim, vresol2dim
+from .utils.scalemaps import map2scale, vmap2vaggreg
+import xarray as xr
+
+
+def background_xb(cntrlv, **kwargs):
+    """Extends the prior control vector to include background components.
+    Is called if the obsvect has a background plugin.
+    
+    
+    Args:
+        cntrlv (Plugin): definition of the control vector.
+        datei (datetime): initial date of the inversion window
+        datei (datetime): end date of the inversion window
+        
+    """
+
+    datei = getattr(cntrlv, 'datei')
+    datef = getattr(cntrlv, 'datef')
+    
+    
+    # If no definition is specified for the control vector in the Yaml,
+    # return empty control vector
+    if not hasattr(cntrlv, 'components'):
+        return cntrlv
+
+    # Else, carry on initializing
+    components = cntrlv.components
+    for comp in components.attributes:
+        component = getattr(components, comp)
+        for trcr in component.parameters.attributes:
+            tracer = getattr(component.parameters, trcr)
+             
+            # Keeping a pointer to the correct location in the whole control
+            # tracer.xpointer = cntrlv.dim
+            
+            # Updating dimension
+            
+            
+            # Time stamp for initial mixing ratio scalars
+            cinidim = cntrlv.background.ntcini * cntrlv.background.ncini
+
+            # ESO: update tracer.dim?
+            # tracer.dim = tracer.ndates * tracer.hresoldim * tracer.vresoldim
+            # tracer.dim += cinidim
+            
+            cntrlv.dim += cinidim
+            
+            
+            # Filling Xbb and uncertainties
+            xbb = np.ones(cinidim)
+            stdb = np.ones(cinidim) * \
+                   float(cntrlv.background.cini_err)
+            
+            # Appending local xb to the control vector
+            cntrlv.xb = np.append(cntrlv.xb, xbb)
+            cntrlv.std = np.append(cntrlv.std, stdb)
+
+            # Extending chi
+            # TODO: this is temporary solution to deal with background opt.
+            # would also need to change tracer.chi_dim etc.
+            cntrlv.chi = np.append(cntrlv.chi, np.zeros(cinidim))
+            cntrlv.chi_dim += cinidim
+
+
+    # Finished initializing controlvect
+    cntrlv.background.updated_controlvect = True
+            
+    return cntrlv

pycif/plugins/controlvects/standard/init_bprod.py

@@ -114,7 +114,9 @@ def init_bprod(cntrlv, options={}, **kwargs):
                     errscalar = glob_err/toterr
                     #cntrlv.std = cntrlv.std*errscalar**2
                     verbose("Total error scaled by "+ str(errscalar))
-                    # TODO: rework this based on most recent flexinvert version
+                    verbose("errsum "+ str(errsum))
+                    # TODO: rework this based on most recent flexinvert version,
+                    #       including using xerr (time avg error)
 
 
 

pycif/plugins/controlvects/standard/init_xb.py

@@ -151,5 +151,5 @@ def init_xb(cntrlv, **kwargs):
             # Appending local xb to the control vector
             cntrlv.xb = np.append(cntrlv.xb, xb)
             cntrlv.std = np.append(cntrlv.std, std)
-            
+
     return cntrlv

pycif/plugins/obsoperators/fp/obsoper.py

@@ -81,13 +81,13 @@ def obsoper(self, inputs, mode,
     
     fp_header_glob = model.utils.flexpart_header.Flexpartheader()
     fp_header_glob.read_header(
-        os.path.join(model.run_dir_glob, obsvect.datastore.head(1)['station'][0].upper(),
+        os.path.join(model.run_dir_glob, obsvect.datastore.head(1)['station'][0].decode().upper(),
                      subdir, 'header'))
     
     if model.plugin.nested:
         fp_header_nest = model.utils.flexpart_header.Flexpartheader()
         fp_header_nest.read_header(
-            os.path.join(model.run_dir_nest, obsvect.datastore.head(1)['station'][0].upper(),
+            os.path.join(model.run_dir_nest, obsvect.datastore.head(1)['station'][0].decode().upper(),
                          subdir, 'header_nest'))
 
     # Trajectory life time
@@ -150,9 +150,9 @@ def obsoper(self, inputs, mode,
             station = row.station
             
             runsubdir_nest = os.path.join(
-                model.run_dir_nest, station.upper(), subdir)
+                model.run_dir_nest, station.decode().upper(), subdir)
             runsubdir_glob = os.path.join(
-                model.run_dir_glob, station.upper(), subdir)
+                model.run_dir_glob, station.decode().upper(), subdir)
             
             file_date = row.Index.strftime('%Y%m%d%H%M%S')
 

pycif/plugins/obsvects/standard/init_background.py

@@ -74,7 +74,8 @@ def init_background(obsvect, **kwargs):
 
         # Subdirectory for FLEXPART grid_initial files
         subdir = row.Index.strftime("%Y%m")
-        station = row.station
+        # station = row.station
+        station = row.station.decode()
         runsubdir_glob = os.path.join(
             model.run_dir_glob, station.upper(), subdir)
         file_date = row.Index.strftime('%Y%m%d%H%M%S')