Changeset 2608 for inundation-numpy-branch

Timestamp:

Mar 27, 2006, 3:49:00 PM (19 years ago)

Author:

ole

Message:

Played with custom exceptions for ANUGA

Location:

inundation-numpy-branch

Files:

• coordinate_transforms/geo_reference.py (modified) (1 diff)
• geospatial_data/geospatial_data.py (modified) (1 diff)
• geospatial_data/test_geospatial_data.py (modified) (1 diff)
• load_mesh/loadASCII.py (modified) (2 diffs)
• load_mesh/test_loadASCII.py (modified) (2 diffs)
• pyvolution/domain.py (modified) (3 diffs)
• pyvolution/general_mesh.py (modified) (7 diffs)
• pyvolution/least_squares.py (modified) (2 diffs)
• pyvolution/mesh.py (modified) (8 diffs)
• pyvolution/mesh_factory.py (modified) (1 diff)
• pyvolution/quad.py (modified) (1 diff)
• pyvolution/quantity.py (modified) (17 diffs)
• pyvolution/test_domain.py (modified) (3 diffs)
• pyvolution/test_general_mesh.py (modified) (4 diffs)
• pyvolution/test_mesh.py (modified) (6 diffs)
• pyvolution/test_quad.py (modified) (1 diff)
• pyvolution/test_quantity.py (modified) (11 diffs)

inundation-numpy-branch/coordinate_transforms/geo_reference.py

@@ -7 +7 @@
 
 import types
-from Numeric import array,Float,ArrayType
+from numpy import array, Float, ArrayType
+
 
 DEFAULT_ZONE = 56

inundation-numpy-branch/geospatial_data/geospatial_data.py

@@ -7 +7 @@
 from utilities.numerical_tools import ensure_numeric
 
-from Numeric import concatenate
+from numpy import concatenate
 
 from coordinate_transforms.geo_reference import Geo_reference

inundation-numpy-branch/geospatial_data/test_geospatial_data.py

@@ -4 +4 @@
 import unittest
 import os
-from Numeric import zeros, array, allclose, concatenate
+from numpy import zeros, array, allclose, concatenate
 from math import sqrt, pi
 

inundation-numpy-branch/load_mesh/loadASCII.py

@@ -79 +79 @@
 
 from string import  find, rfind
-from Numeric import array, Float, Int16, Int32, Character,reshape, concatenate, take
+from numpy import array, Float, Int16, Int32, Character, reshape, concatenate, take
 from os.path import splitext
 
@@ -1174 +1174 @@
     # consider format change
 
-
     legal_keys = ['pointlist', 'attributelist', 'geo_reference']
     for key in point_atts.keys():
         msg = 'Key %s is illegal. Valid keys are %s' %(key, legal_keys) 
         assert key in legal_keys, msg
-    
+
     from Scientific.IO.NetCDF import NetCDFFile
     point_atts2array(point_atts)
     # NetCDF file definition
+
     outfile = NetCDFFile(file_name, 'w')
-    
+
     #Create new file
     outfile.institution = 'Geoscience Australia'

inundation-numpy-branch/load_mesh/test_loadASCII.py

@@ -10 +10 @@
 from os.path import splitext
 
-from Numeric import array, allclose 
+from numpy import array, allclose 
     
 from loadASCII import *
@@ -1048 +1048 @@
 if __name__ == "__main__":
 
-    suite = unittest.makeSuite(loadASCIITestCase,'test')
-    #suite = unittest.makeSuite(loadASCIITestCase,'test_writepts')
+    #suite = unittest.makeSuite(loadASCIITestCase,'test')
+    suite = unittest.makeSuite(loadASCIITestCase,'test_writepts')
     runner = unittest.TextTestRunner(verbosity=0)
     runner.run(suite)

inundation-numpy-branch/pyvolution/domain.py

@@ -27 +27 @@
                       tagged_elements, geo_reference, use_inscribed_circle)
 
-        from Numeric import zeros, Float, Int
+        from numpy import zeros, Float, Int
         from quantity import Quantity, Conserved_quantity
 
@@ -125 +125 @@
         """
 
-        from Numeric import zeros, Float
+        from numpy import zeros, Float
 
         if not (vertex is None or edge is None):
@@ -737 +737 @@
         """
 
-        from Numeric import ones, sum, equal, Float
+        from numpy import ones, sum, equal, Float
 
         N = self.number_of_elements

inundation-numpy-branch/pyvolution/general_mesh.py

@@ +1 @@
+
+from numpy import array, reshape, zeros, Int, Float, maximum, sqrt, sum, take
+
 
 from coordinate_transforms.geo_reference import Geo_reference
@@ -63 +66 @@
         """
 
-        from Numeric import array, zeros, Int, Float, maximum, sqrt, sum
-
         self.triangles = array(triangles).astype(Int)
         self.coordinates = array(coordinates)
@@ -81 +82 @@
 
         msg = 'Vertex indices reference non-existing coordinate sets'
-        assert max(max(self.triangles)) <= self.coordinates.shape[0], msg
-
+        
+        assert max(self.triangles.flat[:]) <= self.coordinates.shape[0], msg
 
         #Register number of elements (N)
@@ -192 +193 @@
 
         if obj is True:
-            from Numeric import concatenate, reshape
             V = self.vertex_coordinates
-            #return concatenate( (V[:,0:2], V[:,2:4], V[:,4:6]), axis=0)
 
             N = V.shape[0]
@@ -218 +217 @@
         #FIXME (Ole) - oh yes they should
 
-        from Numeric import zeros, Float
 
         N = self.number_of_elements
@@ -236 +234 @@
         indices is the set of element ids of interest
         """
-
-        from Numeric import take
 
         if (indices ==  None):
@@ -255 +251 @@
 
         if obj is True:
-            from Numeric import array, reshape, Int        
             m = len(self)  #Number of triangles
             M = 3*m        #Total number of unique vertices

inundation-numpy-branch/pyvolution/least_squares.py

@@ -22 +22 @@
 
 #from general_mesh import General_mesh
-from Numeric import zeros, array, Float, Int, dot, transpose, concatenate, ArrayType
+from numpy import zeros, take, array, Float, Int, dot, transpose, concatenate, ArrayType
+
+#FIXME (Ole): Meshes to move somewhere else
 from pyvolution.mesh import Mesh
-
-from Numeric import zeros, take, array, Float, Int, dot, transpose, concatenate, ArrayType
 from utilities.sparse import Sparse, Sparse_CSR
 from utilities.cg_solve import conjugate_gradient, VectorShapeError
@@ -499 +499 @@
         
         if precrop is True:
-            from Numeric import take
+            #from Numeric import take
 
             if verbose: print 'Getting boundary polygon'

inundation-numpy-branch/pyvolution/mesh.py

@@ -5 +5 @@
 """
 
+from numpy import array, zeros, Int, Float, minimum, maximum, sum, arange
+from math import sqrt
 from general_mesh import General_mesh
+
 
 class Mesh(General_mesh):
@@ -68 +71 @@
 
 
-
-        from Numeric import array, zeros, Int, Float, maximum, sqrt, sum
+        from math import sqrt
+
 
         General_mesh.__init__(self, coordinates, triangles, geo_reference)
@@ -125 +128 @@
                 #of inscribed circle is computed
 
-                from math import sqrt
                 a = sqrt((x0-x1)**2+(y0-y1)**2)
                 b = sqrt((x1-x2)**2+(y1-y2)**2)
@@ -165 +167 @@
     def set_to_inscribed_circle(self,safety_factor = 1):
         #FIXME phase out eventually
-        from math import sqrt
         N = self.number_of_elements
         V = self.vertex_coordinates
@@ -349 +350 @@
             self.element_tag is defined
         """
-        from Numeric import array, Int
 
         if tagged_elements is None:
@@ -421 +421 @@
         this may not work as expected.
         """
-        from Numeric import allclose, sqrt, array, minimum, maximum
-
-
 
         #V = self.get_vertex_coordinates()
@@ -538 +535 @@
 
                 #Normalise
-                from math import sqrt
                 l_u = sqrt(u[0]*u[0] + u[1]*u[1])
                 l_v = sqrt(v[0]*v[0] + v[1]*v[1])                
@@ -620 +616 @@
         """
 
-        from Numeric import arange
         from utilities.numerical_tools import histogram
 

inundation-numpy-branch/pyvolution/mesh_factory.py

@@ -73 +73 @@
 
     from config import epsilon
-    from Numeric import zeros, Float, Int
+    from numpy import zeros, Float, Int
 
     delta1 = float(len1)/m

inundation-numpy-branch/pyvolution/quad.py

@@ -387 +387 @@
     """
 
-    from Numeric import minimum, maximum
+    from numpy import minimum, maximum
 
     #Initialise

inundation-numpy-branch/pyvolution/quantity.py

@@ -15 +15 @@
 """
 
+from numpy import concatenate, zeros, Float, Int, array, reshape, ArrayType, allclose, take, sum, equal
+
 
 class Quantity:
@@ -21 +23 @@
 
         from mesh import Mesh
-        from Numeric import array, zeros, Float
+        #from Numeric import array, zeros, Float
 
         msg = 'First argument in Quantity.__init__ '
@@ -267 +269 @@
         from geospatial_data.geospatial_data import Geospatial_data
         from types import FloatType, IntType, LongType, ListType, NoneType
-        from Numeric import ArrayType
 
         #General input checks
@@ -449 +450 @@
         """
 
-        from Numeric import array, Float, Int, allclose
-
         values = array(values).astype(Float)
 
@@ -529 +528 @@
         A = q.vertex_values
 
-        from Numeric import allclose
         msg = 'Quantities are defined on different meshes. '+\
               'This might be a case for implementing interpolation '+\
@@ -555 +553 @@
 
         #FIXME: Should supply absolute coordinates
-
-        from Numeric import take
 
         if (indices is None):
@@ -617 +613 @@
 
 
-        from Numeric import Float
         from utilities.numerical_tools import ensure_numeric
         from least_squares import fit_to_mesh
@@ -773 +768 @@
 
         """
-        from Numeric import take
 
         if location not in ['vertices', 'centroids', 'edges', 'unique vertices']:
@@ -779 +773 @@
             raise msg
 
-        import types, Numeric
+        import types
         assert type(indices) in [types.ListType, types.NoneType,
-                                 Numeric.ArrayType],\
+                                 ArrayType],\
                                  'Indices must be a list or None'
 
@@ -811 +805 @@
                     sum += self.vertex_values[triangle_id, vertex_id]
                 vert_values.append(sum/len(triangles))
-            return Numeric.array(vert_values)
+            return array(vert_values)
         else:
             if (indices ==  None):
@@ -829 +823 @@
         This function is used by set_values_from_array
         """
-
-        from Numeric import array, Float
 
         #Assert that A can be converted to a Numeric array of appropriate dim
@@ -869 +861 @@
                Maybe it should be removed..-DSG
         """
-
-        from Numeric import concatenate, zeros, Float, Int, array, reshape
 
 
@@ -928 +918 @@
         """
 
-        from Numeric import concatenate, zeros, Float, Int, array, reshape
-
-
         if smooth is None:
             smooth = self.domain.smooth
@@ -1037 +1024 @@
         Quantity.__init__(self, domain, vertex_values)
 
-        from Numeric import zeros, Float
 
         #Allocate space for boundary values
@@ -1110 +1096 @@
     """
 
-    from Numeric import sum, equal, ones, Float
+    #from Numeric import sum, equal, ones, Float
 
     N = quantity.centroid_values.shape[0]
@@ -1188 +1174 @@
     """
 
-    from Numeric import zeros, Float
     from utilitites.numerical_tools import gradient
 
@@ -1262 +1247 @@
     """
 
-    from Numeric import zeros, Float
-
     N = quantity.domain.number_of_elements
 

inundation-numpy-branch/pyvolution/test_domain.py

@@ -6 +6 @@
 from domain import *
 from config import epsilon
-from Numeric import allclose, array, ones, Float
+from numpy import allclose, array, zeros, ones, Float
 
 
@@ -64 +64 @@
 
 
-        assert domain.get_conserved_quantities(0, edge=1) == 0.
+        assert (domain.get_conserved_quantities(0, edge=1) == 0.).all()
 
 
@@ -495 +495 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh

inundation-numpy-branch/pyvolution/test_general_mesh.py

@@ -6 +6 @@
 import unittest
 from math import sqrt, pi
+from numpy import allclose, array, zeros, ones, Float
 
 
 from quantity import *
 from config import epsilon
-from Numeric import allclose, array, ones, Float
+
 
 
@@ -26 +27 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -40 +40 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -55 +54 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh

inundation-numpy-branch/pyvolution/test_mesh.py

@@ -13 +13 @@
 from mesh_factory import rectangular
 from config import epsilon
-from Numeric import allclose, array
+from numpy import allclose, array, zeros, Float
 
 from utilities.polygon import inside_polygon
@@ -691 +691 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -710 +709 @@
         from mesh_factory import rectangular
         from mesh import Mesh
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -730 +728 @@
     def test_boundary_polygon_II(self):
         from mesh import Mesh
-        from Numeric import zeros, Float
-        
 
         #Points
@@ -770 +766 @@
 
         from mesh import Mesh
-        from Numeric import zeros, Float
-
 
         #Points
@@ -811 +805 @@
 
         from mesh import Mesh
-        from Numeric import zeros, Float
         from mesh_factory import rectangular        
 

inundation-numpy-branch/pyvolution/test_quad.py

@@ -2 +2 @@
 from quad import Cell, build_quadtree
 
-#from domain import *
 from general_mesh import General_mesh as Mesh
 

inundation-numpy-branch/pyvolution/test_quantity.py

@@ -7 +7 @@
 from quantity import *
 from config import epsilon
-from Numeric import allclose, array, ones, Float
+from numpy import allclose, array, zeros, ones, Float, sum
 
 
@@ -891 +891 @@
 
         #Assert that quantities are conserved
-        from Numeric import sum
+        from numpy import sum
         for k in range(quantity.centroid_values.shape[0]):
             assert allclose (quantity.centroid_values[k],
@@ -923 +923 @@
 
         #Assert that quantities are conserved
-        from Numeric import sum
         for k in range(quantity.centroid_values.shape[0]):
             assert allclose (quantity.centroid_values[k],
@@ -952 +951 @@
 
         #Assert that quantities are conserved
-        from Numeric import sum
         for k in range(quantity.centroid_values.shape[0]):
             assert allclose (quantity.centroid_values[k],
@@ -1064 +1062 @@
         from mesh_factory import rectangular
         from shallow_water import Domain, Transmissive_boundary
-        from Numeric import zeros, Float
         from utilities.numerical_tools import mean
 
@@ -1154 +1151 @@
         from mesh_factory import rectangular
         from shallow_water import Domain, Transmissive_boundary
-        from Numeric import zeros, Float
         from utilities.numerical_tools import mean
 
@@ -1223 +1219 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -1253 +1248 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -1329 +1323 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -1356 +1349 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh
@@ -1397 +1389 @@
         from mesh_factory import rectangular
         from shallow_water import Domain
-        from Numeric import zeros, Float
 
         #Create basic mesh