Changeset 3514 for inundation-numpy-branch/pyvolution

Timestamp:

Aug 21, 2006, 4:10:14 PM (19 years ago)

Author:

duncan

Message:

Hi all,
I'm doing a change in the anuga structure, moving the code to

\anuga_core\source\anuga

After you have done an svn update, the PYTHONPATH has to be changed to;
PYTHONPATH = anuga_core/source/

This is part of changes required to make installation of anuga quicker and reducing the size of our sandpits.

If any imports are broken, try fixing them. With adding anuga. to them for example. If this seems to have really broken things, email/phone me.

Cheers
Duncan

Location:

inundation-numpy-branch/pyvolution

Files:

• _test_sww2domain.py (modified) (1 diff)
• _test_sww2domain2.py (modified) (1 diff)
• bed_w_file_boundary.py (modified) (1 diff)
• check_sww_tsh.py (modified) (1 diff)
• combine_pts.py (modified) (1 diff)
• data_manager.py (modified) (4 diffs)
• data_manager_obsolete_stuff.py (modified) (1 diff)
• domain.py (modified) (1 diff)
• flatbed.py (modified) (1 diff)
• general_mesh.py (modified) (1 diff)
• generic_boundary_conditions.py (modified) (2 diffs)
• island.py (modified) (1 diff)
• least_squares.py (modified) (3 diffs)
• mesh.py (modified) (2 diffs)
• mesh_factory.py (modified) (2 diffs)
• mesh_factory_all.py (modified) (2 diffs)
• pressure_force.py (modified) (1 diff)
• quantity.py (modified) (4 diffs)
• realtime_visualisation.py (modified) (1 diff)
• shallow_water.py (modified) (3 diffs)
• shallow_water_kinetic.py (modified) (4 diffs)
• test_data_manager.py (modified) (6 diffs)
• test_generic_boundary_conditions.py (modified) (2 diffs)
• test_interpolate_sww.py (modified) (1 diff)
• test_least_squares.py (modified) (1 diff)
• test_mesh.py (modified) (1 diff)
• test_quantity.py (modified) (5 diffs)
• test_shallow_water.py (modified) (4 diffs)
• test_util.py (modified) (5 diffs)
• tsh2sww.py (modified) (1 diff)
• twolevels.py (modified) (1 diff)
• util.py (modified) (11 diffs)
• view_tsh.py (modified) (1 diff)

inundation-numpy-branch/pyvolution/_test_sww2domain.py

@@ -61 +61 @@
 ##NOW TEST IT!!!
 
-from data_manager import sww2domain
+from anuga.pyvolution.data_manager import sww2domain
 from Numeric import allclose
 

inundation-numpy-branch/pyvolution/_test_sww2domain2.py

@@ -59 +59 @@
 ##NOW TEST IT!!!
 
-from data_manager import sww2domain
+from anuga.pyvolution.data_manager import sww2domain
 from Numeric import allclose
 

inundation-numpy-branch/pyvolution/bed_w_file_boundary.py

@@ -57 +57 @@
 
 #Convert ASCII file to NetCDF (Which is what we really like!)
-from data_manager import timefile2swww        
+from anuga.pyvolution.data_manager import timefile2swww        
 timefile2swww(filename, quantity_names = domain.conserved_quantities)
 

inundation-numpy-branch/pyvolution/check_sww_tsh.py

@@ -5 +5 @@
 from os import sep, path
 
-import data_manager
+import anuga.pyvolution.data_manager
 from load_mesh.loadASCII import import_mesh_file
 from shallow_water import Domain

inundation-numpy-branch/pyvolution/combine_pts.py

@@ -5 +5 @@
 """
 
-from utilities.polygon import outside_polygon, inside_polygon
+from anuga.utilities.polygon import outside_polygon, inside_polygon
 from Numeric import take, concatenate
 import time

inundation-numpy-branch/pyvolution/data_manager.py

@@ -248 +248 @@
             #Create new file
             fid.institution = 'Geoscience Australia'
-            fid.description = 'Output from pyvolution suitable for plotting'
+            fid.description = 'Output from anuga.pyvolution suitable for plotting'
 
             if domain.smooth:
@@ -1572 +1572 @@
     from Numeric import array2string
 
-    from utilities.polygon import inside_polygon, outside_polygon, separate_points_by_polygon
-    from util import apply_expression_to_dictionary
+    from anuga.utilities.polygon import inside_polygon, outside_polygon, separate_points_by_polygon
+    from anuga.pyvolution.util import apply_expression_to_dictionary
 
     msg = 'Format must be either asc or ers'
@@ -2571 +2571 @@
     from Numeric import array
     from config import time_format
-    from utilities.numerical_tools import ensure_numeric    
+    from anuga.utilities.numerical_tools import ensure_numeric    
 
 
@@ -3093 +3093 @@
     from pmesh2domain import pmesh_to_domain_instance
     import time, os
-    from data_manager import get_dataobject
+    from anuga.pyvolution.data_manager import get_dataobject
     from os import sep, path
-    from utilities.numerical_tools import mean
+    from anuga.utilities.numerical_tools import mean
 
     if verbose == True:print 'Creating domain from', filename

inundation-numpy-branch/pyvolution/data_manager_obsolete_stuff.py

@@ -221 +221 @@
     from Numeric import array, Float, concatenate, NewAxis, zeros,\
          sometrue
-    from utilities.polygon import inside_polygon
+    from anuga.utilities.polygon import inside_polygon
 
     #FIXME: Should be variable

inundation-numpy-branch/pyvolution/domain.py

@@ -238 +238 @@
         """
 
-        from util import apply_expression_to_dictionary
+        from anuga.pyvolution.util import apply_expression_to_dictionary
         return apply_expression_to_dictionary(expression, self.quantities)
 

inundation-numpy-branch/pyvolution/flatbed.py

@@ -13 +13 @@
      Constant_height
 from Numeric import array
-from util import Polygon_function, read_polygon
+from anuga.pyvolution.util import Polygon_function, read_polygon
 
 

inundation-numpy-branch/pyvolution/general_mesh.py

@@ -50 +50 @@
 
 
-        This is a cut down version of mesh from pyvolution mesh.py
+        This is a cut down version of mesh from anuga.pyvolution mesh.py
     """
 

inundation-numpy-branch/pyvolution/generic_boundary_conditions.py

@@ -131 +131 @@
         from Numeric import array
         from config import time_format
-        from util import File_function
+        from anuga.pyvolution.util import File_function
 
         Boundary.__init__(self)
@@ -181 +181 @@
         from Numeric import array, zeros, Float
         from config import time_format
-        from util import file_function
+        from anuga.pyvolution.util import file_function
 
         Boundary.__init__(self)

inundation-numpy-branch/pyvolution/island.py

@@ -13 +13 @@
      Constant_height
 from Numeric import array
-from util import Polygon_function, read_polygon
+from anuga.pyvolution.util import Polygon_function, read_polygon
 from math import exp
 

inundation-numpy-branch/pyvolution/least_squares.py

@@ -25 +25 @@
 
 #FIXME (Ole): Meshes to move somewhere else
-from pyvolution.mesh import Mesh
-from utilities.sparse import Sparse, Sparse_CSR
-from utilities.cg_solve import conjugate_gradient, VectorShapeError
-from utilities.numerical_tools import ensure_numeric, mean, gradient
+from anuga.pyvolution.mesh import Mesh
+from anuga.utilities.sparse import Sparse, Sparse_CSR
+from anuga.utilities.cg_solve import conjugate_gradient, VectorShapeError
+from anuga.utilities.numerical_tools import ensure_numeric, mean, gradient
 
 
@@ -441 +441 @@
         #Maybe we need some sort of blocking
 
-        from pyvolution.quad import build_quadtree
-        from utilities.polygon import inside_polygon
+        from anuga.pyvolution.quad import build_quadtree
+        from anuga.utilities.polygon import inside_polygon
         
 
@@ -1134 +1134 @@
         from math import pi, cos, sin, sqrt
         from Numeric import zeros, Float
-        from utilities.numerical_tools import mean        
+        from anuga.utilities.numerical_tools import mean        
 
         if self.spatial is True:

inundation-numpy-branch/pyvolution/mesh.py

@@ -492 +492 @@
         from config import epsilon
         from math import pi
-        from utilities.numerical_tools import anglediff
+        from anuga.utilities.numerical_tools import anglediff
 
         N = self.number_of_elements
@@ -616 +616 @@
         """
 
-        from utilities.numerical_tools import histogram
+        from anuga.utilities.numerical_tools import histogram
 
         vertex_coordinates = self.vertex_coordinates

inundation-numpy-branch/pyvolution/mesh_factory.py

@@ -334 +334 @@
     """
 
-    from util import anglediff
+    from anuga.pyvolution.util import anglediff
     from math import pi
     import os.path
@@ -449 +449 @@
 
     from math import pi
-    from util import anglediff
+    from anuga.pyvolution.util import anglediff
 
 

inundation-numpy-branch/pyvolution/mesh_factory_all.py

@@ -351 +351 @@
     """
 
-    from util import anglediff
+    from anuga.pyvolution.util import anglediff
     from math import pi
     import os.path
@@ -466 +466 @@
 
     from math import pi
-    from util import anglediff
+    from anuga.pyvolution.util import anglediff
 
 

inundation-numpy-branch/pyvolution/pressure_force.py

@@ -49 +49 @@
 def cyclone(domain):
     from config import rho_w 
-    from util import gradient
+    from anuga.pyvolution.util import gradient
 
     xmom = domain.quantities['xmomentum'].explicit_update

inundation-numpy-branch/pyvolution/quantity.py

@@ -267 +267 @@
         """
 
-        from geospatial_data.geospatial_data import Geospatial_data
+        from anuga.geospatial_data.geospatial_data import Geospatial_data
         from types import FloatType, IntType, LongType, ListType, NoneType
 
@@ -613 +613 @@
 
 
-        from utilities.numerical_tools import ensure_numeric
+        from anuga.utilities.numerical_tools import ensure_numeric
         from least_squares import fit_to_mesh
         from coordinate_transforms.geo_reference import Geo_reference
@@ -685 +685 @@
 
         from load_mesh.loadASCII import import_points_file
-        from geospatial_data.geospatial_data import points_dictionary2geospatial_data
+        from anuga.geospatial_data.geospatial_data import points_dictionary2geospatial_data
 
         from types import StringType
@@ -1296 +1296 @@
 
 
-from utilities import compile
+from anuga.utilities import compile
 if compile.can_use_C_extension('quantity_ext.c'):
     #Replace python version with c implementations

inundation-numpy-branch/pyvolution/realtime_visualisation.py

@@ -200 +200 @@
 
     #print scene.forward
-    #FIXME: Use smoother from pyvolution instead
+    #FIXME: Use smoother from anuga.pyvolution instead
     if domain.smooth:
         #Get all average point values

inundation-numpy-branch/pyvolution/shallow_water.py

@@ -62 +62 @@
 from generic_boundary_conditions import Transmissive_boundary
 
-from utilities.numerical_tools import gradient, mean
+from anuga.utilities.numerical_tools import gradient, mean
 
 
@@ -285 +285 @@
         """
 
-        import data_manager
+        import anuga.pyvolution.data_manager
 
         #Initialise writer
@@ -1779 +1779 @@
 
 
-from utilities import compile
+from anuga.utilities import compile
 if compile.can_use_C_extension('shallow_water_ext.c'):
     #Replace python version with c implementations

inundation-numpy-branch/pyvolution/shallow_water_kinetic.py

@@ -94 +94 @@
 
         #Reduction operation for get_vertex_values
-        from util import mean
+        from anuga.pyvolution.util import mean
         self.reduction = mean
         #self.reduction = min  #Looks better near steep slopes
@@ -245 +245 @@
         """
 
-        import data_manager
+        import anuga.pyvolution.data_manager
 
         #Initialise writer
@@ -1169 +1169 @@
     """
 
-    from util import gradient
+    from anuga.pyvolution.util import gradient
     from Numeric import zeros, Float, array, sum
 
@@ -1772 +1772 @@
 
 
-from utilities import compile
+from anuga.utilities import compile
 if compile.can_use_C_extension('shallow_water_kinetic_ext.c'):
     #Replace python version with c implementations

inundation-numpy-branch/pyvolution/test_data_manager.py

@@ -5 +5 @@
 import copy
 from Numeric import zeros, array, allclose, Float
-from utilities.numerical_tools import mean
+from anuga.utilities.numerical_tools import mean
 import tempfile
 import os
 from Scientific.IO.NetCDF import NetCDFFile
 
-from data_manager import *
+from anuga.pyvolution.data_manager import *
 from shallow_water import *
 from config import epsilon
-import data_manager
+import anuga.pyvolution.data_manager
 
 from coordinate_transforms.geo_reference import Geo_reference
@@ -2528 +2528 @@
         #Import the example's file as a new domain
         ##########################################
-        from data_manager import sww2domain
+        from anuga.pyvolution.data_manager import sww2domain
         from Numeric import allclose
         import os
@@ -2665 +2665 @@
         #Import the file as a new domain
         ##################################
-        from data_manager import sww2domain
+        from anuga.pyvolution.data_manager import sww2domain
         from Numeric import allclose
         import os
@@ -2703 +2703 @@
 
     #def test_weed(self):
-        from data_manager import weed
+        from anuga.pyvolution.data_manager import weed
 
         coordinates1 = [[0.,0.],[1.,0.],[1.,1.],[1.,0.],[2.,0.],[1.,1.]]
@@ -2776 +2776 @@
         #Import the example's file as a new domain
         ##########################################
-        from data_manager import sww2domain
+        from anuga.pyvolution.data_manager import sww2domain
         from Numeric import allclose
         import os
@@ -3077 +3077 @@
         from Scientific.IO.NetCDF import NetCDFFile
 
-        import data_manager
+        import anuga.pyvolution.data_manager
         #Write test asc file
         filename = tempfile.mktemp(".000")

inundation-numpy-branch/pyvolution/test_generic_boundary_conditions.py

@@ -152 +152 @@
         #Convert ASCII file to NetCDF (Which is what we really like!)
         
-        from data_manager import timefile2netcdf                
+        from anuga.pyvolution.data_manager import timefile2netcdf                
         timefile2netcdf(filename, quantity_names = ['stage', 'ymomentum'])
         
@@ -246 +246 @@
 
         #Convert ASCII file to NetCDF (Which is what we really like!)
-        from data_manager import timefile2netcdf               
+        from anuga.pyvolution.data_manager import timefile2netcdf               
         timefile2netcdf(filename, quantity_names = ['stage', 'xmomentum'])
 

inundation-numpy-branch/pyvolution/test_interpolate_sww.py

@@ -8 +8 @@
 import unittest
 from Numeric import zeros, array, allclose, Float
-from util import mean
+from anuga.pyvolution.util import mean
 
 from interpolate_sww import *
 from shallow_water import *
-from data_manager import *
+from anuga.pyvolution.data_manager import *
 #from config import epsilon
 

inundation-numpy-branch/pyvolution/test_least_squares.py

@@ -1085 +1085 @@
         #Check basic interpolation of one quantity using averaging
         #(no interpolation points or spatial info)
-        from utilities.numerical_tools import mean        
+        from anuga.utilities.numerical_tools import mean        
         I = Interpolation_function(time, [mean(Q[0,:]),
                                           mean(Q[1,:]),

inundation-numpy-branch/pyvolution/test_mesh.py

@@ -15 +15 @@
 from numpy import allclose, array, zeros, Float
 
-from utilities.polygon import inside_polygon
+from anuga.utilities.polygon import inside_polygon
 
 def distance(x, y):

inundation-numpy-branch/pyvolution/test_quantity.py

@@ -280 +280 @@
     def test_set_values_using_least_squares(self):
 
-        from geospatial_data.geospatial_data import Geospatial_data
+        from anuga.geospatial_data.geospatial_data import Geospatial_data
         
         quantity = Quantity(self.mesh4)
@@ -331 +331 @@
 
         from domain import Domain
-        from geospatial_data.geospatial_data import Geospatial_data        
+        from anuga.geospatial_data.geospatial_data import Geospatial_data        
         from coordinate_transforms.geo_reference import Geo_reference
         from least_squares import fit_to_mesh
@@ -389 +389 @@
         quantity.vertex_values[:] = 0.0
         
-        from geospatial_data.geospatial_data import Geospatial_data
+        from anuga.geospatial_data.geospatial_data import Geospatial_data
         geo = Geospatial_data(data_points, z, data_georef)
 
@@ -1062 +1062 @@
         from mesh_factory import rectangular
         from shallow_water import Domain, Transmissive_boundary
-        from utilities.numerical_tools import mean
+        from anuga.utilities.numerical_tools import mean
 
         #Create basic mesh
@@ -1151 +1151 @@
         from mesh_factory import rectangular
         from shallow_water import Domain, Transmissive_boundary
-        from utilities.numerical_tools import mean
+        from anuga.utilities.numerical_tools import mean
 
 

inundation-numpy-branch/pyvolution/test_shallow_water.py

@@ -6 +6 @@
 from config import g, epsilon
 from Numeric import allclose, array, zeros, ones, Float, take
-from utilities.numerical_tools import mean
+from anuga.utilities.numerical_tools import mean
 
 from shallow_water import *
@@ -967 +967 @@
         from math import pi, cos, sin, sqrt
         from config import time_format
-        from util import file_function
+        from anuga.pyvolution.util import file_function
         import time
 
@@ -1014 +1014 @@
 
         #Convert ASCII file to NetCDF (Which is what we really like!)
-        from data_manager import timefile2netcdf        
+        from anuga.pyvolution.data_manager import timefile2netcdf        
         timefile2netcdf(filename)
         os.remove(filename + '.txt')
@@ -2169 +2169 @@
 
     def test_flatbed_second_order_distribute(self):
-        #Use real data from pyvolution 2
+        #Use real data from anuga.pyvolution 2
         #painfully setup and extracted.
         from mesh_factory import rectangular

inundation-numpy-branch/pyvolution/test_util.py

@@ -6 +6 @@
 from math import sqrt, pi
 
-from util import *
+from anuga.pyvolution.util import *
 from config import epsilon
-from data_manager import timefile2netcdf
+from anuga.pyvolution.data_manager import timefile2netcdf
 
 
@@ -26 +26 @@
     #Geometric
     #def test_distance(self):
-    #    from util import distance#
+    #    from anuga.pyvolution.util import distance#
     #
     #    self.failUnless( distance([4,2],[7,6]) == 5.0,
@@ -119 +119 @@
         domain1 = Domain(points, vertices, boundary)
 
-        from utilities.numerical_tools import mean
+        from anuga.utilities.numerical_tools import mean
         domain1.reduction = mean
         domain1.smooth = True #NOTE: Mimic sww output where each vertex has
@@ -319 +319 @@
         
 
-        from utilities.numerical_tools import mean      
+        from anuga.utilities.numerical_tools import mean        
         domain1.reduction = mean
         domain1.smooth = True #NOTE: Mimic sww output where each vertex has
@@ -522 +522 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        import data_manager
+        import anuga.pyvolution.data_manager
 
         finaltime = 1200

inundation-numpy-branch/pyvolution/tsh2sww.py

@@ -13 +13 @@
 from pmesh2domain import pmesh_to_domain_instance
 import time, os 
-from data_manager import get_dataobject   
-from util import mean
+from anuga.pyvolution.data_manager import get_dataobject   
+from anuga.pyvolution.util import mean
 
 def tsh2sww(infilename, sww_file_name = None, verbose = False):

inundation-numpy-branch/pyvolution/twolevels.py

@@ -13 +13 @@
      Constant_height
 from Numeric import array
-from util import Polygon_function, read_polygon
+from anuga.pyvolution.util import Polygon_function, read_polygon
 
 

inundation-numpy-branch/pyvolution/util.py

@@ -6 +6 @@
 
 
-import utilities.polygon
+import anuga.utilities.polygon
 from warnings import warn
 
@@ -173 +173 @@
     from Scientific.IO.NetCDF import NetCDFFile
     from Numeric import array, zeros, Float, alltrue, concatenate, reshape
-    from utilities.numerical_tools import ensure_numeric    
+    from anuga.utilities.numerical_tools import ensure_numeric    
 
     #Open NetCDF file
@@ -401 +401 @@
     """Temporary Interface to new location"""
 
-    import utilities.numerical_tools as NT      
+    import anuga.utilities.numerical_tools as NT        
     
     msg = 'angle has moved from util.py.  '
-    msg += 'Please use "from utilities.numerical_tools import angle"'
+    msg += 'Please use "from anuga.utilities.numerical_tools import angle"'
     warn(msg, DeprecationWarning) 
 
@@ -412 +412 @@
     """Temporary Interface to new location"""
 
-    import utilities.numerical_tools as NT
+    import anuga.utilities.numerical_tools as NT
     
     msg = 'anglediff has moved from util.py.  '
-    msg += 'Please use "from utilities.numerical_tools import anglediff"'
+    msg += 'Please use "from anuga.utilities.numerical_tools import anglediff"'
     warn(msg, DeprecationWarning) 
 
@@ -424 +424 @@
     """Temporary Interface to new location"""
 
-    import utilities.numerical_tools as NT    
+    import anuga.utilities.numerical_tools as NT    
     
     msg = 'mean has moved from util.py.  '
-    msg += 'Please use "from utilities.numerical_tools import mean"'
+    msg += 'Please use "from anuga.utilities.numerical_tools import mean"'
     warn(msg, DeprecationWarning) 
 
@@ -436 +436 @@
 
     msg = 'point_on_line has moved from util.py.  '
-    msg += 'Please use "from utilities.polygon import point_on_line"'
+    msg += 'Please use "from anuga.utilities.polygon import point_on_line"'
     warn(msg, DeprecationWarning) 
 
@@ -445 +445 @@
 
     print 'inside_polygon has moved from util.py.  ',
-    print 'Please use "from utilities.polygon import inside_polygon"'
+    print 'Please use "from anuga.utilities.polygon import inside_polygon"'
 
     return utilities.polygon.inside_polygon(*args, **kwargs)    
@@ -453 +453 @@
 
     print 'outside_polygon has moved from util.py.  ',
-    print 'Please use "from utilities.polygon import outside_polygon"'
+    print 'Please use "from anuga.utilities.polygon import outside_polygon"'
 
     return utilities.polygon.outside_polygon(*args, **kwargs)    
@@ -462 +462 @@
 
     print 'separate_points_by_polygon has moved from util.py.  ',
-    print 'Please use "from utilities.polygon import separate_points_by_polygon"'
+    print 'Please use "from anuga.utilities.polygon import separate_points_by_polygon"'
 
     return utilities.polygon.separate_points_by_polygon(*args, **kwargs)    
@@ -472 +472 @@
 
     print 'read_polygon has moved from util.py.  ',
-    print 'Please use "from utilities.polygon import read_polygon"'
+    print 'Please use "from anuga.utilities.polygon import read_polygon"'
 
     return utilities.polygon.read_polygon(*args, **kwargs)    
@@ -481 +481 @@
 
     print 'populate_polygon has moved from util.py.  ',
-    print 'Please use "from utilities.polygon import populate_polygon"'
+    print 'Please use "from anuga.utilities.polygon import populate_polygon"'
 
     return utilities.polygon.populate_polygon(*args, **kwargs)    

inundation-numpy-branch/pyvolution/view_tsh.py

@@ -9 +9 @@
 from shallow_water import Domain
 from pmesh2domain import pmesh_to_domain_instance
-from util import file_function, Polygon_function, read_polygon
+from anuga.pyvolution.util import file_function, Polygon_function, read_polygon
 from Numeric import zeros, Float, maximum, minimum
 from realtime_visualisation_new import *