Changeset 5745

Timestamp:

Sep 8, 2008, 3:55:57 PM (16 years ago)

Author:

ole

Message:

Arranged for permutation passed in to urs2sts to also be stored in
the NetCDF file.
Updated tests and user manual as well.

Location:

anuga_core

Files:

• documentation/user_manual/anuga_user_manual.tex (modified) (2 diffs)
• source/anuga/shallow_water/data_manager.py (modified) (3 diffs)
• source/anuga/shallow_water/test_data_manager.py (modified) (5 diffs)

anuga_core/documentation/user_manual/anuga_user_manual.tex

@@ -3030 +3030 @@
 \begin{itemize}
     \item \code{x} and \code{y}: coordinates of the points, represented as Numeric arrays
+    \item \code{permutation}: Original indices of the points as specified by
+    the optional \code{ordering\_file} 
+    (see the function \code{urs2sts} in Section \ref{sec:basicfileconversions}).
+    
     \item \code{elevation}, a Numeric array storing bed-elevations
     % Refer here to the example to be provided in describing the simple example
@@ -3178 +3182 @@
   Module: \module{shallow\_water.data\_manager}
 
-  Takes urs data in (timeseries data in mux2 format) and converts it to STS format.
+  Takes urs data in (timeseries data in mux2 format) and converts it to STS format. The optional filename \code{ordering\_filename} specifies the permutation of indices of points to select along with their longitudes and latitudes. This permutation will also be
+  stored in the STS file. If absent, all points are taken and the permutation will be trivial, i.e. $0, 1, \ldots, N-1$, where $N$ is the total number of points stored.  
   \end{funcdesc}
 

anuga_core/source/anuga/shallow_water/data_manager.py

@@ -5207 +5207 @@
     number_of_longitudes = longitudes.shape[0] # Number longitudes
 
+    
+    # The permutation vector of contains original indices 
+    # as given in ordering file or None in which case points 
+    # are assigned the trivial indices enumerating them from 
+    # 0 to number_of_points-1
+    if permutation is None:
+        permutation = arange(number_of_points, typecode=Int)
+    
+    
     # NetCDF file definition
     outfile = NetCDFFile(stsname, 'w')
@@ -5254 +5263 @@
 
     elevation = resize(elevation,outfile.variables['elevation'][:].shape)
+    outfile.variables['permutation'][:] = permutation
     outfile.variables['x'][:] = x - geo_ref.get_xllcorner()
     outfile.variables['y'][:] = y - geo_ref.get_yllcorner()
@@ -5768 +5778 @@
 
         # Variable definitions
+        outfile.createVariable('permutation', Int, ('number_of_points',))        
         outfile.createVariable('x', sts_precision, ('number_of_points',))
         outfile.createVariable('y', sts_precision, ('number_of_points',))

anuga_core/source/anuga/shallow_water/test_data_manager.py

@@ -6822 +6822 @@
         elevation = fid.variables['elevation'][:]
         time=fid.variables['time'][:]+fid.starttime
+        
+        
+        # Check that stored permutation is as per default
+        permutation = range(len(x))
+        stored_permutation = fid.variables['permutation'][:]
+        msg = 'Permutation was not stored correctly. I got '
+        msg += str(stored_permutation)
+        assert allclose(stored_permutation, permutation), msg        
 
         # get quantity data from sts file
@@ -7020 +7028 @@
         # Note, the sts info is not gridded.  It is point data.
         fid = NetCDFFile(sts_file)
+        
+        # Check that original indices have been stored
+        stored_permutation = fid.variables['permutation'][:]
+        msg = 'Permutation was not stored correctly. I got '
+        msg += str(stored_permutation)
+        assert allclose(stored_permutation, permutation), msg
+        
 
         # Make x and y absolute
@@ -7359 +7374 @@
 
         #------------------------------------------------------------
-        # Now read the mux files one by one with out weights and test
+        # Now read the mux files one by one without weights and test
         
         # Call urs2sts with mux file #0
@@ -7372 +7387 @@
         fid = NetCDFFile(sts_file)
 
+        # Check that original indices have been stored
+        stored_permutation = fid.variables['permutation'][:]
+        msg = 'Permutation was not stored correctly. I got '
+        msg += str(stored_permutation)
+        assert allclose(stored_permutation, permutation), msg
+        
+
+        
+        
         # Make x and y absolute
         x = fid.variables['x'][:]
@@ -7476 +7500 @@
         sts_file = base_nameI + '.sts'
         fid = NetCDFFile(sts_file)
-
+        
+        # Check that original indices have been stored
+        stored_permutation = fid.variables['permutation'][:]
+        msg = 'Permutation was not stored correctly. I got '
+        msg += str(stored_permutation)
+        assert allclose(stored_permutation, permutation), msg
+        
         # Make x and y absolute
         x = fid.variables['x'][:]