/[escript]/trunk/escript/py_src/util.py
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revision 587 by gross, Fri Mar 10 02:26:50 2006 UTC revision 804 by gross, Thu Aug 10 01:12:16 2006 UTC
# Line 1  Line 1 
1  # $Id$  # $Id$
 #  
 #      COPYRIGHT ACcESS 2004 -  All Rights Reserved  
 #  
 #   This software is the property of ACcESS.  No part of this code  
 #   may be copied in any form or by any means without the expressed written  
 #   consent of ACcESS.  Copying, use or modification of this software  
 #   by any unauthorised person is illegal unless that  
 #   person has a software license agreement with ACcESS.  
 #  
2    
3  """  """
4  Utility functions for escript  Utility functions for escript
5    
 @remark:  This module is under construction and is still tested!!!  
   
6  @var __author__: name of author  @var __author__: name of author
7  @var __licence__: licence agreement  @var __copyright__: copyrights
8    @var __license__: licence agreement
9  @var __url__: url entry point on documentation  @var __url__: url entry point on documentation
10  @var __version__: version  @var __version__: version
11  @var __date__: date of the version  @var __date__: date of the version
12  """  """
13                                                                                                                                                                                                                                                                                                                                                                                                            
14  __author__="Lutz Gross, l.gross@uq.edu.au"  __author__="Lutz Gross, l.gross@uq.edu.au"
15  __licence__="contact: esys@access.uq.edu.au"  __copyright__="""  Copyright (c) 2006 by ACcESS MNRF
16                        http://www.access.edu.au
17                    Primary Business: Queensland, Australia"""
18    __license__="""Licensed under the Open Software License version 3.0
19                 http://www.opensource.org/licenses/osl-3.0.php"""
20  __url__="http://www.iservo.edu.au/esys/escript"  __url__="http://www.iservo.edu.au/esys/escript"
21  __version__="$Revision$"  __version__="$Revision$"
22  __date__="$Date$"  __date__="$Date$"
# Line 30  __date__="$Date$" Line 24  __date__="$Date$"
24    
25  import math  import math
26  import numarray  import numarray
 import numarray.linear_algebra  
27  import escript  import escript
28  import os  import os
29    
 # missing tests:  
   
 # def pokeShape(arg):  
 # def pokeDim(arg):  
 # def commonShape(arg0,arg1):  
 # def commonDim(*args):  
 # def testForZero(arg):  
 # def matchType(arg0=0.,arg1=0.):  
 # def matchShape(arg0,arg1):  
   
 # def reorderComponents(arg,index):  
   
 #  
 # slicing: get  
 #          set  
 #  
 # and derivatives  
   
30  #=========================================================  #=========================================================
31  #   some helpers:  #   some helpers:
32  #=========================================================  #=========================================================
# Line 59  def saveVTK(filename,domain=None,**data) Line 34  def saveVTK(filename,domain=None,**data)
34      """      """
35      writes a L{Data} objects into a files using the the VTK XML file format.      writes a L{Data} objects into a files using the the VTK XML file format.
36    
37      Example:      Example::
38    
39         tmp=Scalar(..)         tmp=Scalar(..)
40         v=Vector(..)         v=Vector(..)
# Line 87  def saveDX(filename,domain=None,**data): Line 62  def saveDX(filename,domain=None,**data):
62      """      """
63      writes a L{Data} objects into a files using the the DX file format.      writes a L{Data} objects into a files using the the DX file format.
64    
65      Example:      Example::
66    
67         tmp=Scalar(..)         tmp=Scalar(..)
68         v=Vector(..)         v=Vector(..)
# Line 118  def kronecker(d=3): Line 93  def kronecker(d=3):
93     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
94     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}
95     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise
96     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 2.     @rtype: L{numarray.NumArray} or L{escript.Data} of rank 2.
97     """     """
98     return identityTensor(d)     return identityTensor(d)
99    
# Line 154  def identityTensor(d=3): Line 129  def identityTensor(d=3):
129     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
130     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}
131     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise     @return: the object u of rank 2 with M{u[i,j]=1} for M{i=j} and M{u[i,j]=0} otherwise
132     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 2     @rtype: L{numarray.NumArray} or L{escript.Data} of rank 2
133     """     """
134     if isinstance(d,escript.FunctionSpace):     if isinstance(d,escript.FunctionSpace):
135         return escript.Data(identity((d.getDim(),)),d)         return escript.Data(identity((d.getDim(),)),d)
# Line 170  def identityTensor4(d=3): Line 145  def identityTensor4(d=3):
145     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
146     @type d: C{int} or any object with a C{getDim} method     @type d: C{int} or any object with a C{getDim} method
147     @return: the object u of rank 4 with M{u[i,j,k,l]=1} for M{i=k and j=l} and M{u[i,j,k,l]=0} otherwise     @return: the object u of rank 4 with M{u[i,j,k,l]=1} for M{i=k and j=l} and M{u[i,j,k,l]=0} otherwise
148     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 4.     @rtype: L{numarray.NumArray} or L{escript.Data} of rank 4.
149     """     """
150     if isinstance(d,escript.FunctionSpace):     if isinstance(d,escript.FunctionSpace):
151         return escript.Data(identity((d.getDim(),d.getDim())),d)         return escript.Data(identity((d.getDim(),d.getDim())),d)
# Line 188  def unitVector(i=0,d=3): Line 163  def unitVector(i=0,d=3):
163     @param d: dimension or an object that has the C{getDim} method defining the dimension     @param d: dimension or an object that has the C{getDim} method defining the dimension
164     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}     @type d: C{int}, L{escript.Domain} or L{escript.FunctionSpace}
165     @return: the object u of rank 1 with M{u[j]=1} for M{j=i} and M{u[i]=0} otherwise     @return: the object u of rank 1 with M{u[j]=1} for M{j=i} and M{u[i]=0} otherwise
166     @rtype d: L{numarray.NumArray} or L{escript.Data} of rank 1     @rtype: L{numarray.NumArray} or L{escript.Data} of rank 1
167     """     """
168     return kronecker(d)[i]     return kronecker(d)[i]
169    
# Line 244  def inf(arg): Line 219  def inf(arg):
219    
220      @param arg: argument      @param arg: argument
221      @type arg: C{float}, C{int}, L{escript.Data}, L{numarray.NumArray}.      @type arg: C{float}, C{int}, L{escript.Data}, L{numarray.NumArray}.
222      @return : minimum value of arg over all components and all data points      @return: minimum value of arg over all components and all data points
223      @rtype: C{float}      @rtype: C{float}
224      @raise TypeError: if type of arg cannot be processed      @raise TypeError: if type of arg cannot be processed
225      """      """
# Line 333  def commonDim(*args): Line 308  def commonDim(*args):
308      """      """
309      identifies, if possible, the spatial dimension across a set of objects which may or my not have a spatial dimension.      identifies, if possible, the spatial dimension across a set of objects which may or my not have a spatial dimension.
310    
311      @param *args: given objects      @param args: given objects
312      @return: the spatial dimension of the objects with identifiable dimension (see L{pokeDim}). If none the objects has      @return: the spatial dimension of the objects with identifiable dimension (see L{pokeDim}). If none the objects has
313               a spatial dimension C{None} is returned.               a spatial dimension C{None} is returned.
314      @rtype: C{int} or C{None}      @rtype: C{int} or C{None}
# Line 355  def testForZero(arg): Line 330  def testForZero(arg):
330    
331      @param arg: a given object      @param arg: a given object
332      @type arg: typically L{numarray.NumArray},L{escript.Data},C{float}, C{int}      @type arg: typically L{numarray.NumArray},L{escript.Data},C{float}, C{int}
333      @return : True if the argument is identical to zero.      @return: True if the argument is identical to zero.
334      @rtype : C{bool}      @rtype: C{bool}
335      """      """
336      if isinstance(arg,numarray.NumArray):      if isinstance(arg,numarray.NumArray):
337         return not Lsup(arg)>0.         return not Lsup(arg)>0.
# Line 459  def matchType(arg0=0.,arg1=0.): Line 434  def matchType(arg0=0.,arg1=0.):
434    
435  def matchShape(arg0,arg1):  def matchShape(arg0,arg1):
436      """      """
437            return representations of arg0 amd arg1 which ahve the same shape
438    
439      If shape is not given the shape "largest" shape of args is used.      @param arg0: a given object
440        @type arg0: L{numarray.NumArray},L{escript.Data},C{float}, C{int}, L{Symbol}
441      @param args: a given ob      @param arg1: a given object
442      @type arg: typically L{numarray.NumArray},L{escript.Data},C{float}, C{int}      @type arg1: L{numarray.NumArray},L{escript.Data},C{float}, C{int}, L{Symbol}
443      @return: True if the argument is identical to zero.      @return: C{arg0} and C{arg1} where copies are returned when the shape has to be changed.
444      @rtype: C{list} of C{int}      @rtype: C{tuple}
445      """      """
446      sh=commonShape(arg0,arg1)      sh=commonShape(arg0,arg1)
447      sh0=pokeShape(arg0)      sh0=pokeShape(arg0)
# Line 494  class Symbol(object): Line 469  class Symbol(object):
469         Creates an instance of a symbol of a given shape. The symbol may depending on a list of arguments args which may be         Creates an instance of a symbol of a given shape. The symbol may depending on a list of arguments args which may be
470         symbols or any other object.         symbols or any other object.
471    
472         @param arg: the arguments of the symbol.         @param args: the arguments of the symbol.
473         @type arg: C{list}         @type args: C{list}
474         @param shape: the shape         @param shape: the shape
475         @type shape: C{tuple} of C{int}         @type shape: C{tuple} of C{int}
476         @param dim: spatial dimension of the symbol. If dim=C{None} the spatial dimension is undefined.           @param dim: spatial dimension of the symbol. If dim=C{None} the spatial dimension is undefined.  
# Line 538  class Symbol(object): Line 513  class Symbol(object):
513         """         """
514         the shape of the symbol.         the shape of the symbol.
515    
516         @return : the shape of the symbol.         @return: the shape of the symbol.
517         @rtype: C{tuple} of C{int}         @rtype: C{tuple} of C{int}
518         """         """
519         return self.__shape         return self.__shape
# Line 547  class Symbol(object): Line 522  class Symbol(object):
522         """         """
523         the spatial dimension         the spatial dimension
524    
525         @return : the spatial dimension         @return: the spatial dimension
526         @rtype: C{int} if the dimension is defined. Otherwise C{None} is returned.         @rtype: C{int} if the dimension is defined. Otherwise C{None} is returned.
527         """         """
528         return self.__dim         return self.__dim
# Line 571  class Symbol(object): Line 546  class Symbol(object):
546         """         """
547         substitutes symbols in the arguments of this object and returns the result as a list.         substitutes symbols in the arguments of this object and returns the result as a list.
548    
549         @param argvals: L{Symbols} and their substitutes. The L{Symbol} u in the expression defining this object is replaced by argvals[u].         @param argvals: L{Symbol} and their substitutes. The L{Symbol} u in the expression defining this object is replaced by argvals[u].
550         @type argvals: C{dict} with keywords of type L{Symbol}.         @type argvals: C{dict} with keywords of type L{Symbol}.
551         @rtype: C{list} of objects         @rtype: C{list} of objects
552         @return: list of the object assigned to the arguments through substitution or for the arguments which are not L{Symbols} the value assigned to the argument at instantiation.         @return: list of the object assigned to the arguments through substitution or for the arguments which are not L{Symbol} the value assigned to the argument at instantiation.
553         """         """
554         out=[]         out=[]
555         for a in self.getArgument():         for a in self.getArgument():
# Line 698  class Symbol(object): Line 673  class Symbol(object):
673         """         """
674         returns -self.         returns -self.
675    
676         @return:  a S{Symbol} representing the negative of the object         @return:  a L{Symbol} representing the negative of the object
677         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
678         """         """
679         return self*(-1.)         return self*(-1.)
# Line 707  class Symbol(object): Line 682  class Symbol(object):
682         """         """
683         returns +self.         returns +self.
684    
685         @return:  a S{Symbol} representing the positive of the object         @return:  a L{Symbol} representing the positive of the object
686         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
687         """         """
688         return self*(1.)         return self*(1.)
689    
690     def __abs__(self):     def __abs__(self):
691         """         """
692         returns a S{Symbol} representing the absolute value of the object.         returns a L{Symbol} representing the absolute value of the object.
693         """         """
694         return Abs_Symbol(self)         return Abs_Symbol(self)
695    
# Line 724  class Symbol(object): Line 699  class Symbol(object):
699    
700         @param other: object to be added to this object         @param other: object to be added to this object
701         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
702         @return:  a S{Symbol} representing the sum of this object and C{other}         @return:  a L{Symbol} representing the sum of this object and C{other}
703         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
704         """         """
705         return add(self,other)         return add(self,other)
# Line 735  class Symbol(object): Line 710  class Symbol(object):
710    
711         @param other: object this object is added to         @param other: object this object is added to
712         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
713         @return: a S{Symbol} representing the sum of C{other} and this object object         @return: a L{Symbol} representing the sum of C{other} and this object object
714         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
715         """         """
716         return add(other,self)         return add(other,self)
# Line 746  class Symbol(object): Line 721  class Symbol(object):
721    
722         @param other: object to be subtracted from this object         @param other: object to be subtracted from this object
723         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
724         @return: a S{Symbol} representing the difference of C{other} and this object         @return: a L{Symbol} representing the difference of C{other} and this object
725         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
726         """         """
727         return add(self,-other)         return add(self,-other)
# Line 757  class Symbol(object): Line 732  class Symbol(object):
732    
733         @param other: object this object is been subtracted from         @param other: object this object is been subtracted from
734         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
735         @return: a S{Symbol} representing the difference of this object and C{other}.         @return: a L{Symbol} representing the difference of this object and C{other}.
736         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
737         """         """
738         return add(-self,other)         return add(-self,other)
# Line 768  class Symbol(object): Line 743  class Symbol(object):
743    
744         @param other: object to be mutiplied by this object         @param other: object to be mutiplied by this object
745         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
746         @return: a S{Symbol} representing the product of the object and C{other}.         @return: a L{Symbol} representing the product of the object and C{other}.
747         @rtype: L{DependendSymbol} or 0 if other is identical to zero.         @rtype: L{DependendSymbol} or 0 if other is identical to zero.
748         """         """
749         return mult(self,other)         return mult(self,other)
# Line 779  class Symbol(object): Line 754  class Symbol(object):
754    
755         @param other: object this object is multiplied with         @param other: object this object is multiplied with
756         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
757         @return: a S{Symbol} representing the product of C{other} and the object.         @return: a L{Symbol} representing the product of C{other} and the object.
758         @rtype: L{DependendSymbol} or 0 if other is identical to zero.         @rtype: L{DependendSymbol} or 0 if other is identical to zero.
759         """         """
760         return mult(other,self)         return mult(other,self)
# Line 790  class Symbol(object): Line 765  class Symbol(object):
765    
766         @param other: object dividing this object         @param other: object dividing this object
767         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
768         @return: a S{Symbol} representing the quotient of this object and C{other}         @return: a L{Symbol} representing the quotient of this object and C{other}
769         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
770         """         """
771         return quotient(self,other)         return quotient(self,other)
# Line 801  class Symbol(object): Line 776  class Symbol(object):
776    
777         @param other: object dividing this object         @param other: object dividing this object
778         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
779         @return: a S{Symbol} representing the quotient of C{other} and this object         @return: a L{Symbol} representing the quotient of C{other} and this object
780         @rtype: L{DependendSymbol} or 0 if C{other} is identical to zero.         @rtype: L{DependendSymbol} or 0 if C{other} is identical to zero.
781         """         """
782         return quotient(other,self)         return quotient(other,self)
# Line 812  class Symbol(object): Line 787  class Symbol(object):
787    
788         @param other: exponent         @param other: exponent
789         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
790         @return: a S{Symbol} representing the power of this object to C{other}         @return: a L{Symbol} representing the power of this object to C{other}
791         @rtype: L{DependendSymbol} or 1 if C{other} is identical to zero.         @rtype: L{DependendSymbol} or 1 if C{other} is identical to zero.
792         """         """
793         return power(self,other)         return power(self,other)
# Line 823  class Symbol(object): Line 798  class Symbol(object):
798    
799         @param other: basis         @param other: basis
800         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type other: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
801         @return: a S{Symbol} representing the power of C{other} to this object         @return: a L{Symbol} representing the power of C{other} to this object
802         @rtype: L{DependendSymbol} or 0 if C{other} is identical to zero.         @rtype: L{DependendSymbol} or 0 if C{other} is identical to zero.
803         """         """
804         return power(other,self)         return power(other,self)
# Line 834  class Symbol(object): Line 809  class Symbol(object):
809    
810         @param index: defines a         @param index: defines a
811         @type index: C{slice} or C{int} or a C{tuple} of them         @type index: C{slice} or C{int} or a C{tuple} of them
812         @return: a S{Symbol} representing the slice defined by index         @return: a L{Symbol} representing the slice defined by index
813         @rtype: L{DependendSymbol}         @rtype: L{DependendSymbol}
814         """         """
815         return GetSlice_Symbol(self,index)         return GetSlice_Symbol(self,index)
# Line 844  class DependendSymbol(Symbol): Line 819  class DependendSymbol(Symbol):
819     DependendSymbol extents L{Symbol} by modifying the == operator to allow two instances to be equal.     DependendSymbol extents L{Symbol} by modifying the == operator to allow two instances to be equal.
820     Two DependendSymbol are equal if they have the same shape, the same arguments and one of them has an unspecified spatial dimension or the spatial dimension is identical       Two DependendSymbol are equal if they have the same shape, the same arguments and one of them has an unspecified spatial dimension or the spatial dimension is identical  
821        
822     Example:     Example::
823        
824     u1=Symbol(shape=(3,4),dim=2,args=[4.])       u1=Symbol(shape=(3,4),dim=2,args=[4.])
825     u2=Symbol(shape=(3,4),dim=2,args=[4.])       u2=Symbol(shape=(3,4),dim=2,args=[4.])
826     print u1==u2       print u1==u2
827     False       False
828        
829        but       but::
830    
831     u1=DependendSymbol(shape=(3,4),dim=2,args=[4.])       u1=DependendSymbol(shape=(3,4),dim=2,args=[4.])
832     u2=DependendSymbol(shape=(3,4),dim=2,args=[4.])       u2=DependendSymbol(shape=(3,4),dim=2,args=[4.])
833     u3=DependendSymbol(shape=(2,),dim=2,args=[4.])         u3=DependendSymbol(shape=(2,),dim=2,args=[4.])  
834     print u1==u2, u1==u3       print u1==u2, u1==u3
835     True False       True False
836    
837     @note: DependendSymbol should be used as return value of functions with L{Symbol} arguments. This will allow the optimizer to remove redundant function calls.     @note: DependendSymbol should be used as return value of functions with L{Symbol} arguments. This will allow the optimizer to remove redundant function calls.
838     """     """
# Line 947  class GetSlice_Symbol(DependendSymbol): Line 922  class GetSlice_Symbol(DependendSymbol):
922        @type format: C{str}        @type format: C{str}
923        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
924        @rtype: C{str}        @rtype: C{str}
925        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
926        """        """
927        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
928           return "%s.__getitem__(%s)"%(argstrs[0],argstrs[1])           return "%s.__getitem__(%s)"%(argstrs[0],argstrs[1])
# Line 983  def log10(arg): Line 958  def log10(arg):
958    
959     @param arg: argument     @param arg: argument
960     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
961     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
962     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
963     """     """
964     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1005  def wherePositive(arg): Line 980  def wherePositive(arg):
980    
981     @param arg: argument     @param arg: argument
982     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
983     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
984     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
985     """     """
986     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1051  class WherePositive_Symbol(DependendSymb Line 1026  class WherePositive_Symbol(DependendSymb
1026        @type format: C{str}        @type format: C{str}
1027        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1028        @rtype: C{str}        @rtype: C{str}
1029        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1030        """        """
1031        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1032            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1087  def whereNegative(arg): Line 1062  def whereNegative(arg):
1062    
1063     @param arg: argument     @param arg: argument
1064     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1065     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1066     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1067     """     """
1068     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1133  class WhereNegative_Symbol(DependendSymb Line 1108  class WhereNegative_Symbol(DependendSymb
1108        @type format: C{str}        @type format: C{str}
1109        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1110        @rtype: C{str}        @rtype: C{str}
1111        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1112        """        """
1113        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1114            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1169  def whereNonNegative(arg): Line 1144  def whereNonNegative(arg):
1144    
1145     @param arg: argument     @param arg: argument
1146     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1147     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1148     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1149     """     """
1150     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1199  def whereNonPositive(arg): Line 1174  def whereNonPositive(arg):
1174    
1175     @param arg: argument     @param arg: argument
1176     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1177     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1178     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1179     """     """
1180     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1231  def whereZero(arg,tol=0.): Line 1206  def whereZero(arg,tol=0.):
1206     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1207     @param tol: tolerance. values with absolute value less then tol are accepted as zero.     @param tol: tolerance. values with absolute value less then tol are accepted as zero.
1208     @type tol: C{float}     @type tol: C{float}
1209     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1210     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1211     """     """
1212     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1239  def whereZero(arg,tol=0.): Line 1214  def whereZero(arg,tol=0.):
1214        if isinstance(out,float): out=numarray.array(out,type=numarray.Float64)        if isinstance(out,float): out=numarray.array(out,type=numarray.Float64)
1215        return out        return out
1216     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1217        if tol>0.:        return arg._whereZero(tol)
          return whereNegative(abs(arg)-tol)  
       else:  
          return arg._whereZero()  
1218     elif isinstance(arg,float):     elif isinstance(arg,float):
1219        if abs(arg)<=tol:        if abs(arg)<=tol:
1220          return 1.          return 1.
# Line 1280  class WhereZero_Symbol(DependendSymbol): Line 1252  class WhereZero_Symbol(DependendSymbol):
1252        @type format: C{str}        @type format: C{str}
1253        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1254        @rtype: C{str}        @rtype: C{str}
1255        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1256        """        """
1257        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
1258           return "whereZero(%s,tol=%s)"%(argstrs[0],argstrs[1])           return "whereZero(%s,tol=%s)"%(argstrs[0],argstrs[1])
# Line 1314  def whereNonZero(arg,tol=0.): Line 1286  def whereNonZero(arg,tol=0.):
1286    
1287     @param arg: argument     @param arg: argument
1288     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1289     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1290     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1291     """     """
1292     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1322  def whereNonZero(arg,tol=0.): Line 1294  def whereNonZero(arg,tol=0.):
1294        if isinstance(out,float): out=numarray.array(out,type=numarray.Float64)        if isinstance(out,float): out=numarray.array(out,type=numarray.Float64)
1295        return out        return out
1296     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
1297        if tol>0.:        return arg._whereNonZero(tol)
          return 1.-whereZero(arg,tol)  
       else:  
          return arg._whereNonZero()  
1298     elif isinstance(arg,float):     elif isinstance(arg,float):
1299        if abs(arg)>tol:        if abs(arg)>tol:
1300          return 1.          return 1.
# Line 1347  def sin(arg): Line 1316  def sin(arg):
1316    
1317     @param arg: argument     @param arg: argument
1318     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1319     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1320     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1321     """     """
1322     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1385  class Sin_Symbol(DependendSymbol): Line 1354  class Sin_Symbol(DependendSymbol):
1354        @type format: C{str}        @type format: C{str}
1355        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1356        @rtype: C{str}        @rtype: C{str}
1357        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1358        """        """
1359        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1360            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1437  def cos(arg): Line 1406  def cos(arg):
1406    
1407     @param arg: argument     @param arg: argument
1408     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1409     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1410     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1411     """     """
1412     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1475  class Cos_Symbol(DependendSymbol): Line 1444  class Cos_Symbol(DependendSymbol):
1444        @type format: C{str}        @type format: C{str}
1445        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1446        @rtype: C{str}        @rtype: C{str}
1447        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1448        """        """
1449        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1450            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1527  def tan(arg): Line 1496  def tan(arg):
1496    
1497     @param arg: argument     @param arg: argument
1498     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1499     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1500     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1501     """     """
1502     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1565  class Tan_Symbol(DependendSymbol): Line 1534  class Tan_Symbol(DependendSymbol):
1534        @type format: C{str}        @type format: C{str}
1535        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1536        @rtype: C{str}        @rtype: C{str}
1537        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1538        """        """
1539        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1540            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1617  def asin(arg): Line 1586  def asin(arg):
1586    
1587     @param arg: argument     @param arg: argument
1588     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1589     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1590     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1591     """     """
1592     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1655  class Asin_Symbol(DependendSymbol): Line 1624  class Asin_Symbol(DependendSymbol):
1624        @type format: C{str}        @type format: C{str}
1625        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1626        @rtype: C{str}        @rtype: C{str}
1627        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1628        """        """
1629        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1630            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1707  def acos(arg): Line 1676  def acos(arg):
1676    
1677     @param arg: argument     @param arg: argument
1678     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1679     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1680     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1681     """     """
1682     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1745  class Acos_Symbol(DependendSymbol): Line 1714  class Acos_Symbol(DependendSymbol):
1714        @type format: C{str}        @type format: C{str}
1715        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1716        @rtype: C{str}        @rtype: C{str}
1717        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1718        """        """
1719        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1720            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1797  def atan(arg): Line 1766  def atan(arg):
1766    
1767     @param arg: argument     @param arg: argument
1768     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1769     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1770     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1771     """     """
1772     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1835  class Atan_Symbol(DependendSymbol): Line 1804  class Atan_Symbol(DependendSymbol):
1804        @type format: C{str}        @type format: C{str}
1805        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1806        @rtype: C{str}        @rtype: C{str}
1807        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1808        """        """
1809        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1810            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1887  def sinh(arg): Line 1856  def sinh(arg):
1856    
1857     @param arg: argument     @param arg: argument
1858     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1859     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1860     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1861     """     """
1862     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 1925  class Sinh_Symbol(DependendSymbol): Line 1894  class Sinh_Symbol(DependendSymbol):
1894        @type format: C{str}        @type format: C{str}
1895        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1896        @rtype: C{str}        @rtype: C{str}
1897        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1898        """        """
1899        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1900            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 1977  def cosh(arg): Line 1946  def cosh(arg):
1946    
1947     @param arg: argument     @param arg: argument
1948     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
1949     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
1950     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
1951     """     """
1952     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2015  class Cosh_Symbol(DependendSymbol): Line 1984  class Cosh_Symbol(DependendSymbol):
1984        @type format: C{str}        @type format: C{str}
1985        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
1986        @rtype: C{str}        @rtype: C{str}
1987        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
1988        """        """
1989        if isinstance(argstrs,list):        if isinstance(argstrs,list):
1990            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2067  def tanh(arg): Line 2036  def tanh(arg):
2036    
2037     @param arg: argument     @param arg: argument
2038     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2039     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2040     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2041     """     """
2042     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2105  class Tanh_Symbol(DependendSymbol): Line 2074  class Tanh_Symbol(DependendSymbol):
2074        @type format: C{str}        @type format: C{str}
2075        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2076        @rtype: C{str}        @rtype: C{str}
2077        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2078        """        """
2079        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2080            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2157  def asinh(arg): Line 2126  def asinh(arg):
2126    
2127     @param arg: argument     @param arg: argument
2128     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2129     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2130     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2131     """     """
2132     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2195  class Asinh_Symbol(DependendSymbol): Line 2164  class Asinh_Symbol(DependendSymbol):
2164        @type format: C{str}        @type format: C{str}
2165        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2166        @rtype: C{str}        @rtype: C{str}
2167        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2168        """        """
2169        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2170            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2247  def acosh(arg): Line 2216  def acosh(arg):
2216    
2217     @param arg: argument     @param arg: argument
2218     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2219     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2220     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2221     """     """
2222     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2285  class Acosh_Symbol(DependendSymbol): Line 2254  class Acosh_Symbol(DependendSymbol):
2254        @type format: C{str}        @type format: C{str}
2255        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2256        @rtype: C{str}        @rtype: C{str}
2257        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2258        """        """
2259        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2260            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2337  def atanh(arg): Line 2306  def atanh(arg):
2306    
2307     @param arg: argument     @param arg: argument
2308     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2309     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2310     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2311     """     """
2312     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2375  class Atanh_Symbol(DependendSymbol): Line 2344  class Atanh_Symbol(DependendSymbol):
2344        @type format: C{str}        @type format: C{str}
2345        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2346        @rtype: C{str}        @rtype: C{str}
2347        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2348        """        """
2349        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2350            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2427  def exp(arg): Line 2396  def exp(arg):
2396    
2397     @param arg: argument     @param arg: argument
2398     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2399     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2400     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2401     """     """
2402     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2465  class Exp_Symbol(DependendSymbol): Line 2434  class Exp_Symbol(DependendSymbol):
2434        @type format: C{str}        @type format: C{str}
2435        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2436        @rtype: C{str}        @rtype: C{str}
2437        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2438        """        """
2439        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2440            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2517  def sqrt(arg): Line 2486  def sqrt(arg):
2486    
2487     @param arg: argument     @param arg: argument
2488     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2489     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2490     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2491     """     """
2492     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2555  class Sqrt_Symbol(DependendSymbol): Line 2524  class Sqrt_Symbol(DependendSymbol):
2524        @type format: C{str}        @type format: C{str}
2525        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2526        @rtype: C{str}        @rtype: C{str}
2527        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2528        """        """
2529        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2530            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2607  def log(arg): Line 2576  def log(arg):
2576    
2577     @param arg: argument     @param arg: argument
2578     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2579     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2580     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2581     """     """
2582     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2645  class Log_Symbol(DependendSymbol): Line 2614  class Log_Symbol(DependendSymbol):
2614        @type format: C{str}        @type format: C{str}
2615        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2616        @rtype: C{str}        @rtype: C{str}
2617        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2618        """        """
2619        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2620            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2697  def sign(arg): Line 2666  def sign(arg):
2666    
2667     @param arg: argument     @param arg: argument
2668     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2669     @rtype:C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
2670     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2671     """     """
2672     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2745  class Abs_Symbol(DependendSymbol): Line 2714  class Abs_Symbol(DependendSymbol):
2714        @type format: C{str}        @type format: C{str}
2715        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2716        @rtype: C{str}        @rtype: C{str}
2717        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2718        """        """
2719        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2720            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2797  def minval(arg): Line 2766  def minval(arg):
2766    
2767     @param arg: argument     @param arg: argument
2768     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2769     @rtype:C{float}, L{escript.Data}, L{Symbol} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol} depending on the type of arg.
2770     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2771     """     """
2772     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2838  class Minval_Symbol(DependendSymbol): Line 2807  class Minval_Symbol(DependendSymbol):
2807        @type format: C{str}        @type format: C{str}
2808        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2809        @rtype: C{str}        @rtype: C{str}
2810        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2811        """        """
2812        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2813            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2874  def maxval(arg): Line 2843  def maxval(arg):
2843    
2844     @param arg: argument     @param arg: argument
2845     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2846     @rtype:C{float}, L{escript.Data}, L{Symbol} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol} depending on the type of arg.
2847     @raises TypeError: if the type of the argument is not expected.     @raises TypeError: if the type of the argument is not expected.
2848     """     """
2849     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
# Line 2915  class Maxval_Symbol(DependendSymbol): Line 2884  class Maxval_Symbol(DependendSymbol):
2884        @type format: C{str}        @type format: C{str}
2885        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
2886        @rtype: C{str}        @rtype: C{str}
2887        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
2888        """        """
2889        if isinstance(argstrs,list):        if isinstance(argstrs,list):
2890            argstrs=argstrs[0]            argstrs=argstrs[0]
# Line 2951  def length(arg): Line 2920  def length(arg):
2920    
2921     @param arg: argument     @param arg: argument
2922     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: C{float}, L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2923     @rtype:C{float}, L{escript.Data}, L{Symbol} depending on the type of arg.     @rtype: C{float}, L{escript.Data}, L{Symbol} depending on the type of arg.
2924     """     """
2925     return sqrt(inner(arg,arg))     return sqrt(inner(arg,arg))
2926    
# Line 2961  def trace(arg,axis_offset=0): Line 2930  def trace(arg,axis_offset=0):
2930    
2931     @param arg: argument     @param arg: argument
2932     @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}.     @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
2933     @param axis_offset: axis_offset to components to sum over. C{axis_offset} must be non-negative and less than the rank of arg +1. The dimensions on component     @param axis_offset: C{axis_offset} to components to sum over. C{axis_offset} must be non-negative and less than the rank of arg +1. The dimensions on component
2934                    axis_offset and axis_offset+1 must be equal.                    C{axis_offset} and axis_offset+1 must be equal.
2935     @type axis_offset: C{int}     @type axis_offset: C{int}
2936     @return: trace of arg. The rank of the returned object is minus 2 of the rank of arg.     @return: trace of arg. The rank of the returned object is minus 2 of the rank of arg.
2937     @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.     @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
# Line 2970  def trace(arg,axis_offset=0): Line 2939  def trace(arg,axis_offset=0):
2939     if isinstance(arg,numarray.NumArray):     if isinstance(arg,numarray.NumArray):
2940        sh=arg.shape        sh=arg.shape
2941        if len(sh)<2:        if len(sh)<2:
2942          raise ValueError,"trace: rank of argument must be greater than 1"          raise ValueError,"rank of argument must be greater than 1"
2943        if axis_offset<0 or axis_offset>len(sh)-2:        if axis_offset<0 or axis_offset>len(sh)-2:
2944          raise ValueError,"trace: axis_offset must be between 0 and %s"%len(sh)-2          raise ValueError,"axis_offset must be between 0 and %s"%len(sh)-2
2945        s1=1        s1=1
2946        for i in range(axis_offset): s1*=sh[i]        for i in range(axis_offset): s1*=sh[i]
2947        s2=1        s2=1
2948        for i in range(axis_offset+2,len(sh)): s2*=sh[i]        for i in range(axis_offset+2,len(sh)): s2*=sh[i]
2949        if not sh[axis_offset] == sh[axis_offset+1]:        if not sh[axis_offset] == sh[axis_offset+1]:
2950          raise ValueError,"trace: dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)          raise ValueError,"dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)
2951        arg_reshaped=numarray.reshape(arg,(s1,sh[axis_offset],sh[axis_offset],s2))        arg_reshaped=numarray.reshape(arg,(s1,sh[axis_offset],sh[axis_offset],s2))
2952        out=numarray.zeros([s1,s2],numarray.Float64)        out=numarray.zeros([s1,s2],numarray.Float64)
2953        for i1 in range(s1):        for i1 in range(s1):
# Line 2987  def trace(arg,axis_offset=0): Line 2956  def trace(arg,axis_offset=0):
2956        out.resize(sh[:axis_offset]+sh[axis_offset+2:])        out.resize(sh[:axis_offset]+sh[axis_offset+2:])
2957        return out        return out
2958     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
2959        return escript_trace(arg,axis_offset)        if arg.getRank()<2:
2960            raise ValueError,"rank of argument must be greater than 1"
2961          if axis_offset<0 or axis_offset>arg.getRank()-2:
2962            raise ValueError,"axis_offset must be between 0 and %s"%arg.getRank()-2
2963          s=list(arg.getShape())        
2964          if not s[axis_offset] == s[axis_offset+1]:
2965            raise ValueError,"dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)
2966          return arg._trace(axis_offset)
2967     elif isinstance(arg,float):     elif isinstance(arg,float):
2968        raise TypeError,"trace: illegal argument type float."        raise TypeError,"illegal argument type float."
2969     elif isinstance(arg,int):     elif isinstance(arg,int):
2970        raise TypeError,"trace: illegal argument type int."        raise TypeError,"illegal argument type int."
2971     elif isinstance(arg,Symbol):     elif isinstance(arg,Symbol):
2972        return Trace_Symbol(arg,axis_offset)        return Trace_Symbol(arg,axis_offset)
2973     else:     else:
2974        raise TypeError,"trace: Unknown argument type."        raise TypeError,"Unknown argument type."
2975    
 def escript_trace(arg,axis_offset): # this should be escript._trace  
       "arg si a Data objects!!!"  
       if arg.getRank()<2:  
         raise ValueError,"escript_trace: rank of argument must be greater than 1"  
       if axis_offset<0 or axis_offset>arg.getRank()-2:  
         raise ValueError,"escript_trace: axis_offset must be between 0 and %s"%arg.getRank()-2  
       s=list(arg.getShape())          
       if not s[axis_offset] == s[axis_offset+1]:  
         raise ValueError,"escript_trace: dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)  
       out=escript.Data(0.,tuple(s[0:axis_offset]+s[axis_offset+2:]),arg.getFunctionSpace())  
       if arg.getRank()==2:  
          for i0 in range(s[0]):  
             out+=arg[i0,i0]  
       elif arg.getRank()==3:  
          if axis_offset==0:  
             for i0 in range(s[0]):  
                   for i2 in range(s[2]):  
                          out[i2]+=arg[i0,i0,i2]  
          elif axis_offset==1:  
             for i0 in range(s[0]):  
                for i1 in range(s[1]):  
                          out[i0]+=arg[i0,i1,i1]  
       elif arg.getRank()==4:  
          if axis_offset==0:  
             for i0 in range(s[0]):  
                   for i2 in range(s[2]):  
                      for i3 in range(s[3]):  
                          out[i2,i3]+=arg[i0,i0,i2,i3]  
          elif axis_offset==1:  
             for i0 in range(s[0]):  
                for i1 in range(s[1]):  
                      for i3 in range(s[3]):  
                          out[i0,i3]+=arg[i0,i1,i1,i3]  
          elif axis_offset==2:  
             for i0 in range(s[0]):  
                for i1 in range(s[1]):  
                   for i2 in range(s[2]):  
                          out[i0,i1]+=arg[i0,i1,i2,i2]  
       return out  
2976  class Trace_Symbol(DependendSymbol):  class Trace_Symbol(DependendSymbol):
2977     """     """
2978     L{Symbol} representing the result of the trace function     L{Symbol} representing the result of the trace function
# Line 3045  class Trace_Symbol(DependendSymbol): Line 2982  class Trace_Symbol(DependendSymbol):
2982        initialization of trace L{Symbol} with argument arg        initialization of trace L{Symbol} with argument arg
2983        @param arg: argument of function        @param arg: argument of function
2984        @type arg: L{Symbol}.        @type arg: L{Symbol}.
2985        @param axis_offset: axis_offset to components to sum over. C{axis_offset} must be non-negative and less than the rank of arg +1. The dimensions on component        @param axis_offset: C{axis_offset} to components to sum over. C{axis_offset} must be non-negative and less than the rank of arg +1. The dimensions on component
2986                    axis_offset and axis_offset+1 must be equal.                    C{axis_offset} and axis_offset+1 must be equal.
2987        @type axis_offset: C{int}        @type axis_offset: C{int}
2988        """        """
2989        if arg.getRank()<2:        if arg.getRank()<2:
2990          raise ValueError,"Trace_Symbol: rank of argument must be greater than 1"          raise ValueError,"rank of argument must be greater than 1"
2991        if axis_offset<0 or axis_offset>arg.getRank()-2:        if axis_offset<0 or axis_offset>arg.getRank()-2:
2992          raise ValueError,"Trace_Symbol: axis_offset must be between 0 and %s"%arg.getRank()-2          raise ValueError,"axis_offset must be between 0 and %s"%arg.getRank()-2
2993        s=list(arg.getShape())                s=list(arg.getShape())        
2994        if not s[axis_offset] == s[axis_offset+1]:        if not s[axis_offset] == s[axis_offset+1]:
2995          raise ValueError,"Trace_Symbol: dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)          raise ValueError,"dimensions of component %s and %s must match."%(axis_offset.axis_offset+1)
2996        super(Trace_Symbol,self).__init__(args=[arg,axis_offset],shape=tuple(s[0:axis_offset]+s[axis_offset+2:]),dim=arg.getDim())        super(Trace_Symbol,self).__init__(args=[arg,axis_offset],shape=tuple(s[0:axis_offset]+s[axis_offset+2:]),dim=arg.getDim())
2997    
2998     def getMyCode(self,argstrs,format="escript"):     def getMyCode(self,argstrs,format="escript"):
# Line 3068  class Trace_Symbol(DependendSymbol): Line 3005  class Trace_Symbol(DependendSymbol):
3005        @type format: C{str}        @type format: C{str}
3006        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3007        @rtype: C{str}        @rtype: C{str}
3008        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3009        """        """
3010        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
3011           return "trace(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])           return "trace(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])
# Line 3112  class Trace_Symbol(DependendSymbol): Line 3049  class Trace_Symbol(DependendSymbol):
3049    
3050  def transpose(arg,axis_offset=None):  def transpose(arg,axis_offset=None):
3051     """     """
3052     returns the transpose of arg by swaping the first axis_offset and the last rank-axis_offset components.     returns the transpose of arg by swaping the first C{axis_offset} and the last rank-axis_offset components.
3053    
3054     @param arg: argument     @param arg: argument
3055     @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}, C{float}, C{int}     @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}, C{float}, C{int}
3056     @param axis_offset: the first axis_offset components are swapped with rest. If C{axis_offset} must be non-negative and less or equal the rank of arg.     @param axis_offset: the first C{axis_offset} components are swapped with rest. If C{axis_offset} must be non-negative and less or equal the rank of arg.
3057                         if axis_offset is not present C{int(r/2)} where r is the rank of arg is used.                         if C{axis_offset} is not present C{int(r/2)} where r is the rank of arg is used.
3058     @type axis_offset: C{int}     @type axis_offset: C{int}
3059     @return: transpose of arg     @return: transpose of arg
3060     @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray},C{float}, C{int} depending on the type of arg.     @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray},C{float}, C{int} depending on the type of arg.
# Line 3126  def transpose(arg,axis_offset=None): Line 3063  def transpose(arg,axis_offset=None):
3063        if axis_offset==None: axis_offset=int(arg.rank/2)        if axis_offset==None: axis_offset=int(arg.rank/2)
3064        return numarray.transpose(arg,axes=range(axis_offset,arg.rank)+range(0,axis_offset))        return numarray.transpose(arg,axes=range(axis_offset,arg.rank)+range(0,axis_offset))
3065     elif isinstance(arg,escript.Data):     elif isinstance(arg,escript.Data):
3066        if axis_offset==None: axis_offset=int(arg.getRank()/2)        r=arg.getRank()
3067        return escript_transpose(arg,axis_offset)        if axis_offset==None: axis_offset=int(r/2)
3068          if axis_offset<0 or axis_offset>r:
3069            raise ValueError,"axis_offset must be between 0 and %s"%r
3070          return arg._transpose(axis_offset)
3071     elif isinstance(arg,float):     elif isinstance(arg,float):
3072        if not ( axis_offset==0 or axis_offset==None):        if not ( axis_offset==0 or axis_offset==None):
3073          raise ValueError,"transpose: axis_offset must be 0 for float argument"          raise ValueError,"axis_offset must be 0 for float argument"
3074        return arg        return arg
3075     elif isinstance(arg,int):     elif isinstance(arg,int):
3076        if not ( axis_offset==0 or axis_offset==None):        if not ( axis_offset==0 or axis_offset==None):
3077          raise ValueError,"transpose: axis_offset must be 0 for int argument"          raise ValueError,"axis_offset must be 0 for int argument"
3078        return float(arg)        return float(arg)
3079     elif isinstance(arg,Symbol):     elif isinstance(arg,Symbol):
3080        if axis_offset==None: axis_offset=int(arg.getRank()/2)        if axis_offset==None: axis_offset=int(arg.getRank()/2)
3081        return Transpose_Symbol(arg,axis_offset)        return Transpose_Symbol(arg,axis_offset)
3082     else:     else:
3083        raise TypeError,"transpose: Unknown argument type."        raise TypeError,"Unknown argument type."
3084    
 def escript_transpose(arg,axis_offset): # this should be escript._transpose  
       "arg si a Data objects!!!"  
       r=arg.getRank()  
       if axis_offset<0 or axis_offset>r:  
         raise ValueError,"escript_transpose: axis_offset must be between 0 and %s"%r  
       s=arg.getShape()  
       s_out=s[axis_offset:]+s[:axis_offset]  
       out=escript.Data(0.,s_out,arg.getFunctionSpace())  
       if r==4:  
          if axis_offset==1:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                      for i3 in range(s_out[3]):  
                          out[i0,i1,i2,i3]=arg[i3,i0,i1,i2]  
          elif axis_offset==2:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                      for i3 in range(s_out[3]):  
                          out[i0,i1,i2,i3]=arg[i2,i3,i0,i1]  
          elif axis_offset==3:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                      for i3 in range(s_out[3]):  
                          out[i0,i1,i2,i3]=arg[i1,i2,i3,i0]  
          else:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                      for i3 in range(s_out[3]):  
                          out[i0,i1,i2,i3]=arg[i0,i1,i2,i3]  
       elif r==3:  
          if axis_offset==1:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                          out[i0,i1,i2]=arg[i2,i0,i1]  
          elif axis_offset==2:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                          out[i0,i1,i2]=arg[i1,i2,i0]  
          else:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                   for i2 in range(s_out[2]):  
                          out[i0,i1,i2]=arg[i0,i1,i2]  
       elif r==2:  
          if axis_offset==1:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                          out[i0,i1]=arg[i1,i0]  
          else:  
             for i0 in range(s_out[0]):  
                for i1 in range(s_out[1]):  
                          out[i0,i1]=arg[i0,i1]  
       elif r==1:  
           for i0 in range(s_out[0]):  
                out[i0]=arg[i0]  
       elif r==0:  
              out=arg+0.  
       return out  
3085  class Transpose_Symbol(DependendSymbol):  class Transpose_Symbol(DependendSymbol):
3086     """     """
3087     L{Symbol} representing the result of the transpose function     L{Symbol} representing the result of the transpose function
# Line 3216  class Transpose_Symbol(DependendSymbol): Line 3092  class Transpose_Symbol(DependendSymbol):
3092    
3093        @param arg: argument of function        @param arg: argument of function
3094        @type arg: L{Symbol}.        @type arg: L{Symbol}.
3095         @param axis_offset: the first axis_offset components are swapped with rest. If C{axis_offset} must be non-negative and less or equal the rank of arg.        @param axis_offset: the first C{axis_offset} components are swapped with rest. If C{axis_offset} must be non-negative and less or equal the rank of arg.
3096                         if axis_offset is not present C{int(r/2)} where r is the rank of arg is used.                         if C{axis_offset} is not present C{int(r/2)} where r is the rank of arg is used.
3097        @type axis_offset: C{int}        @type axis_offset: C{int}
3098        """        """
3099        if axis_offset==None: axis_offset=int(arg.getRank()/2)        if axis_offset==None: axis_offset=int(arg.getRank()/2)
3100        if axis_offset<0 or axis_offset>arg.getRank():        if axis_offset<0 or axis_offset>arg.getRank():
3101          raise ValueError,"escript_transpose: axis_offset must be between 0 and %s"%r          raise ValueError,"axis_offset must be between 0 and %s"%arg.getRank()
3102        s=arg.getShape()        s=arg.getShape()
3103        super(Transpose_Symbol,self).__init__(args=[arg,axis_offset],shape=s[axis_offset:]+s[:axis_offset],dim=arg.getDim())        super(Transpose_Symbol,self).__init__(args=[arg,axis_offset],shape=s[axis_offset:]+s[:axis_offset],dim=arg.getDim())
3104    
# Line 3236  class Transpose_Symbol(DependendSymbol): Line 3112  class Transpose_Symbol(DependendSymbol):
3112        @type format: C{str}        @type format: C{str}
3113        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3114        @rtype: C{str}        @rtype: C{str}
3115        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3116        """        """
3117        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
3118           return "transpose(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])           return "transpose(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])
# Line 3277  class Transpose_Symbol(DependendSymbol): Line 3153  class Transpose_Symbol(DependendSymbol):
3153           return identity(self.getShape())           return identity(self.getShape())
3154        else:        else:
3155           return transpose(self.getDifferentiatedArguments(arg)[0],axis_offset=self.getArgument()[1])           return transpose(self.getDifferentiatedArguments(arg)[0],axis_offset=self.getArgument()[1])
3156    
3157    def swap_axes(arg,axis0=0,axis1=1):
3158       """
3159       returns the swap of arg by swaping the components axis0 and axis1
3160    
3161       @param arg: argument
3162       @type arg: L{escript.Data}, L{Symbol}, L{numarray.NumArray}.
3163       @param axis0: axis. C{axis0} must be non-negative and less than the rank of arg.
3164       @type axis0: C{int}
3165       @param axis1: axis. C{axis1} must be non-negative and less than the rank of arg.
3166       @type axis1: C{int}
3167       @return: C{arg} with swaped components
3168       @rtype: L{escript.Data}, L{Symbol}, L{numarray.NumArray} depending on the type of arg.
3169       """
3170       if axis0 > axis1:
3171          axis0,axis1=axis1,axis0
3172       if isinstance(arg,numarray.NumArray):
3173          return numarray.swapaxes(arg,axis0,axis1)
3174       elif isinstance(arg,escript.Data):
3175          return arg._swap_axes(axis0,axis1)
3176       elif isinstance(arg,float):
3177          raise TyepError,"float argument is not supported."
3178       elif isinstance(arg,int):
3179          raise TyepError,"int argument is not supported."
3180       elif isinstance(arg,Symbol):
3181          return SwapAxes_Symbol(arg,axis0,axis1)
3182       else:
3183          raise TypeError,"Unknown argument type."
3184    
3185    class SwapAxes_Symbol(DependendSymbol):
3186       """
3187       L{Symbol} representing the result of the swap function
3188       """
3189       def __init__(self,arg,axis0=0,axis1=1):
3190          """
3191          initialization of swap L{Symbol} with argument arg
3192    
3193          @param arg: argument
3194          @type arg: L{Symbol}.
3195          @param axis0: axis. C{axis0} must be non-negative and less than the rank of arg.
3196          @type axis0: C{int}
3197          @param axis1: axis. C{axis1} must be non-negative and less than the rank of arg.
3198          @type axis1: C{int}
3199          """
3200          if arg.getRank()<2:
3201             raise ValueError,"argument must have at least rank 2."
3202          if axis0<0 or axis0>arg.getRank()-1:
3203             raise ValueError,"axis0 must be between 0 and %s"%arg.getRank()-1
3204          if axis1<0 or axis1>arg.getRank()-1:
3205             raise ValueError,"axis1 must be between 0 and %s"%arg.getRank()-1
3206          if axis0 == axis1:
3207             raise ValueError,"axis indices must be different."
3208          if axis0 > axis1:
3209             axis0,axis1=axis1,axis0
3210          s=arg.getShape()
3211          s_out=[]
3212          for i in range(len(s)):
3213             if i == axis0:
3214                s_out.append(s[axis1])
3215             elif i == axis1:
3216                s_out.append(s[axis0])
3217             else:
3218                s_out.append(s[i])
3219          super(SwapAxes_Symbol,self).__init__(args=[arg,axis0,axis1],shape=tuple(s_out),dim=arg.getDim())
3220    
3221       def getMyCode(self,argstrs,format="escript"):
3222          """
3223          returns a program code that can be used to evaluate the symbol.
3224    
3225          @param argstrs: gives for each argument a string representing the argument for the evaluation.
3226          @type argstrs: C{str} or a C{list} of length 1 of C{str}.
3227          @param format: specifies the format to be used. At the moment only "escript" ,"text" and "str" are supported.
3228          @type format: C{str}
3229          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3230          @rtype: C{str}
3231          @raise NotImplementedError: if the requested format is not available
3232          """
3233          if format=="escript" or format=="str"  or format=="text":
3234             return "swap(%s,axis_offset=%s)"%(argstrs[0],argstrs[1])
3235          else:
3236             raise NotImplementedError,"SwapAxes_Symbol does not provide program code for format %s."%format
3237    
3238       def substitute(self,argvals):
3239          """
3240          assigns new values to symbols in the definition of the symbol.
3241          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
3242    
3243          @param argvals: new values assigned to symbols
3244          @type argvals: C{dict} with keywords of type L{Symbol}.
3245          @return: result of the substitution process. Operations are executed as much as possible.
3246          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
3247          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
3248          """
3249          if argvals.has_key(self):
3250             arg=argvals[self]
3251             if self.isAppropriateValue(arg):
3252                return arg
3253             else:
3254                raise TypeError,"%s: new value is not appropriate."%str(self)
3255          else:
3256             arg=self.getSubstitutedArguments(argvals)
3257             return swap_axes(arg[0],axis0=arg[1],axis1=arg[2])
3258    
3259       def diff(self,arg):
3260          """
3261          differential of this object
3262    
3263          @param arg: the derivative is calculated with respect to arg
3264          @type arg: L{escript.Symbol}
3265          @return: derivative with respect to C{arg}
3266          @rtype: typically L{Symbol} but other types such as C{float}, L{escript.Data}, L{numarray.NumArray}  are possible.
3267          """
3268          if arg==self:
3269             return identity(self.getShape())
3270          else:
3271             return swap_axes(self.getDifferentiatedArguments(arg)[0],axis0=self.getArgument()[1],axis1=self.getArgument()[2])
3272    
3273  def symmetric(arg):  def symmetric(arg):
3274      """      """
3275      returns the symmetric part of the square matrix arg. This is (arg+transpose(arg))/2      returns the symmetric part of the square matrix arg. This is (arg+transpose(arg))/2
# Line 3289  def symmetric(arg): Line 3282  def symmetric(arg):
3282      if isinstance(arg,numarray.NumArray):      if isinstance(arg,numarray.NumArray):
3283        if arg.rank==2:        if arg.rank==2:
3284          if not (arg.shape[0]==arg.shape[1]):          if not (arg.shape[0]==arg.shape[1]):
3285             raise ValueError,"symmetric: argument must be square."             raise ValueError,"argument must be square."
3286        elif arg.rank==4:        elif arg.rank==4:
3287          if not (arg.shape[0]==arg.shape[2] and arg.shape[1]==arg.shape[3]):          if not (arg.shape[0]==arg.shape[2] and arg.shape[1]==arg.shape[3]):
3288             raise ValueError,"symmetric: argument must be square."             raise ValueError,"argument must be square."
3289        else:        else:
3290          raise ValueError,"symmetric: rank 2 or 4 is required."          raise ValueError,"rank 2 or 4 is required."
3291        return (arg+transpose(arg))/2        return (arg+transpose(arg))/2
3292      elif isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
3293        return escript_symmetric(arg)        if arg.getRank()==2:
3294            if not (arg.getShape()[0]==arg.getShape()[1]):
3295               raise ValueError,"argument must be square."
3296            return arg._symmetric()
3297          elif arg.getRank()==4:
3298            if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3299               raise ValueError,"argument must be square."
3300            return arg._symmetric()
3301          else:
3302            raise ValueError,"rank 2 or 4 is required."
3303      elif isinstance(arg,float):      elif isinstance(arg,float):
3304        return arg        return arg
3305      elif isinstance(arg,int):      elif isinstance(arg,int):
# Line 3305  def symmetric(arg): Line 3307  def symmetric(arg):
3307      elif isinstance(arg,Symbol):      elif isinstance(arg,Symbol):
3308        if arg.getRank()==2:        if arg.getRank()==2:
3309          if not (arg.getShape()[0]==arg.getShape()[1]):          if not (arg.getShape()[0]==arg.getShape()[1]):
3310             raise ValueError,"symmetric: argument must be square."             raise ValueError,"argument must be square."
3311        elif arg.getRank()==4:        elif arg.getRank()==4:
3312          if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):          if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3313             raise ValueError,"symmetric: argument must be square."             raise ValueError,"argument must be square."
3314        else:        else:
3315          raise ValueError,"symmetric: rank 2 or 4 is required."          raise ValueError,"rank 2 or 4 is required."
3316        return (arg+transpose(arg))/2        return (arg+transpose(arg))/2
3317      else:      else:
3318        raise TypeError,"symmetric: Unknown argument type."        raise TypeError,"symmetric: Unknown argument type."
3319    
 def escript_symmetric(arg): # this should be implemented in c++  
       if arg.getRank()==2:  
         if not (arg.getShape()[0]==arg.getShape()[1]):  
            raise ValueError,"escript_symmetric: argument must be square."  
         out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())  
         for i0 in range(arg.getShape()[0]):  
            for i1 in range(arg.getShape()[1]):  
               out[i0,i1]=(arg[i0,i1]+arg[i1,i0])/2.  
       elif arg.getRank()==4:  
         if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):  
            raise ValueError,"escript_symmetric: argument must be square."  
         out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())  
         for i0 in range(arg.getShape()[0]):  
            for i1 in range(arg.getShape()[1]):  
               for i2 in range(arg.getShape()[2]):  
                  for i3 in range(arg.getShape()[3]):  
                      out[i0,i1,i2,i3]=(arg[i0,i1,i2,i3]+arg[i2,i3,i0,i1])/2.  
       else:  
         raise ValueError,"escript_symmetric: rank 2 or 4 is required."  
       return out  
   
3320  def nonsymmetric(arg):  def nonsymmetric(arg):
3321      """      """
3322      returns the nonsymmetric part of the square matrix arg. This is (arg-transpose(arg))/2      returns the nonsymmetric part of the square matrix arg. This is (arg-transpose(arg))/2
# Line 3356  def nonsymmetric(arg): Line 3337  def nonsymmetric(arg):
3337          raise ValueError,"nonsymmetric: rank 2 or 4 is required."          raise ValueError,"nonsymmetric: rank 2 or 4 is required."
3338        return (arg-transpose(arg))/2        return (arg-transpose(arg))/2
3339      elif isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
3340        return escript_nonsymmetric(arg)        if arg.getRank()==2:
3341            if not (arg.getShape()[0]==arg.getShape()[1]):
3342               raise ValueError,"argument must be square."
3343            return arg._nonsymmetric()
3344          elif arg.getRank()==4:
3345            if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):
3346               raise ValueError,"argument must be square."
3347            return arg._nonsymmetric()
3348          else:
3349            raise ValueError,"rank 2 or 4 is required."
3350      elif isinstance(arg,float):      elif isinstance(arg,float):
3351        return arg        return arg
3352      elif isinstance(arg,int):      elif isinstance(arg,int):
# Line 3374  def nonsymmetric(arg): Line 3364  def nonsymmetric(arg):
3364      else:      else:
3365        raise TypeError,"nonsymmetric: Unknown argument type."        raise TypeError,"nonsymmetric: Unknown argument type."
3366    
 def escript_nonsymmetric(arg): # this should be implemented in c++  
       if arg.getRank()==2:  
         if not (arg.getShape()[0]==arg.getShape()[1]):  
            raise ValueError,"escript_nonsymmetric: argument must be square."  
         out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())  
         for i0 in range(arg.getShape()[0]):  
            for i1 in range(arg.getShape()[1]):  
               out[i0,i1]=(arg[i0,i1]-arg[i1,i0])/2.  
       elif arg.getRank()==4:  
         if not (arg.getShape()[0]==arg.getShape()[2] and arg.getShape()[1]==arg.getShape()[3]):  
            raise ValueError,"escript_nonsymmetric: argument must be square."  
         out=escript.Data(0.,arg.getShape(),arg.getFunctionSpace())  
         for i0 in range(arg.getShape()[0]):  
            for i1 in range(arg.getShape()[1]):  
               for i2 in range(arg.getShape()[2]):  
                  for i3 in range(arg.getShape()[3]):  
                      out[i0,i1,i2,i3]=(arg[i0,i1,i2,i3]-arg[i2,i3,i0,i1])/2.  
       else:  
         raise ValueError,"escript_nonsymmetric: rank 2 or 4 is required."  
       return out  
   
   
3367  def inverse(arg):  def inverse(arg):
3368      """      """
3369      returns the inverse of the square matrix arg.      returns the inverse of the square matrix arg.
3370    
3371      @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.      @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.
3372      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3373      @return: inverse arg_inv of the argument. It will be matrixmul(inverse(arg),arg) almost equal to kronecker(arg.getShape()[0])      @return: inverse arg_inv of the argument. It will be matrix_mult(inverse(arg),arg) almost equal to kronecker(arg.getShape()[0])
3374      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
3375      @remark: for L{escript.Data} objects the dimension is restricted to 3.      @note: for L{escript.Data} objects the dimension is restricted to 3.
3376      """      """
3377        import numarray.linear_algebra # This statement should be after the next statement but then somehow numarray is gone.
3378      if isinstance(arg,numarray.NumArray):      if isinstance(arg,numarray.NumArray):
3379        return numarray.linear_algebra.inverse(arg)        return numarray.linear_algebra.inverse(arg)
3380      elif isinstance(arg,escript.Data):      elif isinstance(arg,escript.Data):
# Line 3498  class Inverse_Symbol(DependendSymbol): Line 3467  class Inverse_Symbol(DependendSymbol):
3467        @type format: C{str}        @type format: C{str}
3468        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3469        @rtype: C{str}        @rtype: C{str}
3470        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3471        """        """
3472        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
3473           return "inverse(%s)"%argstrs[0]           return "inverse(%s)"%argstrs[0]
# Line 3538  class Inverse_Symbol(DependendSymbol): Line 3507  class Inverse_Symbol(DependendSymbol):
3507        if arg==self:        if arg==self:
3508           return identity(self.getShape())           return identity(self.getShape())
3509        else:        else:
3510           return -matrixmult(matrixmult(self,self.getDifferentiatedArguments(arg)[0]),self)           return -matrix_mult(matrix_mult(self,self.getDifferentiatedArguments(arg)[0]),self)
3511    
3512  def eigenvalues(arg):  def eigenvalues(arg):
3513      """      """
# Line 3549  def eigenvalues(arg): Line 3518  def eigenvalues(arg):
3518      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
3519      @return: the eigenvalues in increasing order.      @return: the eigenvalues in increasing order.
3520      @rtype: L{numarray.NumArray},L{escript.Data}, L{Symbol} depending on the input.      @rtype: L{numarray.NumArray},L{escript.Data}, L{Symbol} depending on the input.
3521      @remark: for L{escript.Data} and L{Symbol} objects the dimension is restricted to 3.      @note: for L{escript.Data} and L{Symbol} objects the dimension is restricted to 3.
3522      """      """
3523      if isinstance(arg,numarray.NumArray):      if isinstance(arg,numarray.NumArray):
3524        out=numarray.linear_algebra.eigenvalues((arg+numarray.transpose(arg))/2.)        out=numarray.linear_algebra.eigenvalues((arg+numarray.transpose(arg))/2.)
# Line 3610  def eigenvalues(arg): Line 3579  def eigenvalues(arg):
3579    
3580  def eigenvalues_and_eigenvectors(arg):  def eigenvalues_and_eigenvectors(arg):
3581      """      """
3582      returns the eigenvalues of the square matrix arg.      returns the eigenvalues and eigenvectors of the square matrix arg.
3583    
3584      @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.      @param arg: square matrix. Must have rank 2 and the first and second dimension must be equal.
3585                  arg must be symmetric, ie. transpose(arg)==arg (this is not checked).                  arg must be symmetric, ie. transpose(arg)==arg (this is not checked).
3586      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}      @type arg: L{escript.Data}
3587      @return: the eigenvalues in increasing order.      @return: the eigenvalues and eigenvectors. The eigenvalues are ordered by increasing value. The
3588      @rtype: L{numarray.NumArray},L{escript.Data}, L{Symbol} depending on the input.               eigenvectors are orthogonal and normalized. If V are the eigenvectors than V[:,i] is
3589      @remark: for L{escript.Data} and L{Symbol} objects the dimension is restricted to 3.               the eigenvector coresponding to the i-th eigenvalue.
3590        @rtype: L{tuple} of L{escript.Data}.
3591        @note: The dimension is restricted to 3.
3592      """      """
3593      if isinstance(arg,numarray.NumArray):      if isinstance(arg,numarray.NumArray):
3594        raise TypeError,"eigenvalues_and_eigenvectors is not supporting numarray arguments"        raise TypeError,"eigenvalues_and_eigenvectors is not supporting numarray arguments"
# Line 3690  class Add_Symbol(DependendSymbol): Line 3661  class Add_Symbol(DependendSymbol):
3661        @type format: C{str}        @type format: C{str}
3662        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3663        @rtype: C{str}        @rtype: C{str}
3664        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3665        """        """
3666        if format=="str" or format=="text":        if format=="str" or format=="text":
3667           return "(%s)+(%s)"%(argstrs[0],argstrs[1])           return "(%s)+(%s)"%(argstrs[0],argstrs[1])
# Line 3789  class Mult_Symbol(DependendSymbol): Line 3760  class Mult_Symbol(DependendSymbol):
3760        @type format: C{str}        @type format: C{str}
3761        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3762        @rtype: C{str}        @rtype: C{str}
3763        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3764        """        """
3765        if format=="str" or format=="text":        if format=="str" or format=="text":
3766           return "(%s)*(%s)"%(argstrs[0],argstrs[1])           return "(%s)*(%s)"%(argstrs[0],argstrs[1])
# Line 3894  class Quotient_Symbol(DependendSymbol): Line 3865  class Quotient_Symbol(DependendSymbol):
3865        @type format: C{str}        @type format: C{str}
3866        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3867        @rtype: C{str}        @rtype: C{str}
3868        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3869        """        """
3870        if format=="str" or format=="text":        if format=="str" or format=="text":
3871           return "(%s)/(%s)"%(argstrs[0],argstrs[1])           return "(%s)/(%s)"%(argstrs[0],argstrs[1])
# Line 3998  class Power_Symbol(DependendSymbol): Line 3969  class Power_Symbol(DependendSymbol):
3969        @type format: C{str}        @type format: C{str}
3970        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
3971        @rtype: C{str}        @rtype: C{str}
3972        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
3973        """        """
3974        if format=="escript" or format=="str" or format=="text":        if format=="escript" or format=="str" or format=="text":
3975           return "(%s)**(%s)"%(argstrs[0],argstrs[1])           return "(%s)**(%s)"%(argstrs[0],argstrs[1])
# Line 4087  def clip(arg,minval=0.,maxval=1.): Line 4058  def clip(arg,minval=0.,maxval=1.):
4058      @param arg: argument      @param arg: argument
4059      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float}      @type arg: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float}
4060      @param minval: lower range      @param minval: lower range
4061      @type arg: C{float}      @type minval: C{float}
4062      @param maxval: upper range      @param maxval: upper range
4063      @type arg: C{float}      @type maxval: C{float}
4064      @return: is on object with all its value between minval and maxval. value of the argument that greater then minval and      @return: is on object with all its value between minval and maxval. value of the argument that greater then minval and
4065               less then maxval are unchanged.               less then maxval are unchanged.
4066      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float} depending on the input      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{int} or C{float} depending on the input
# Line 4114  def inner(arg0,arg1): Line 4085  def inner(arg0,arg1):
4085      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4086      @param arg1: second argument      @param arg1: second argument
4087      @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}      @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4088      @return : the inner product of arg0 and arg1 at each data point      @return: the inner product of arg0 and arg1 at each data point
4089      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float} depending on the input      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float} depending on the input
4090      @raise ValueError: if the shapes of the arguments are not identical      @raise ValueError: if the shapes of the arguments are not identical
4091      """      """
# Line 4124  def inner(arg0,arg1): Line 4095  def inner(arg0,arg1):
4095          raise ValueError,"inner: shape of arguments does not match"          raise ValueError,"inner: shape of arguments does not match"
4096      return generalTensorProduct(arg0,arg1,axis_offset=len(sh0))      return generalTensorProduct(arg0,arg1,axis_offset=len(sh0))
4097    
4098    def outer(arg0,arg1):
4099        """
4100        the outer product of the two argument:
4101    
4102        out[t,s]=arg0[t]*arg1[s]
4103    
4104        where
4105    
4106            - s runs through arg0.Shape
4107            - t runs through arg1.Shape
4108    
4109        @param arg0: first argument
4110        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4111        @param arg1: second argument
4112        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4113        @return: the outer product of arg0 and arg1 at each data point
4114        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4115        """
4116        return generalTensorProduct(arg0,arg1,axis_offset=0)
4117    
4118  def matrixmult(arg0,arg1):  def matrixmult(arg0,arg1):
4119      """      """
4120        see L{matrix_mult}
4121        """
4122        return matrix_mult(arg0,arg1)
4123    
4124    def matrix_mult(arg0,arg1):
4125        """
4126      matrix-matrix or matrix-vector product of the two argument:      matrix-matrix or matrix-vector product of the two argument:
4127    
4128      out[s0]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0]      out[s0]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0]
4129    
4130            or      or
4131    
4132      out[s0,s1]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0,s1]      out[s0,s1]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0,s1]
4133    
4134      The second dimension of arg0 and the length of arg1 must match.      The second dimension of arg0 and the first dimension of arg1 must match.
4135    
4136      @param arg0: first argument of rank 2      @param arg0: first argument of rank 2
4137      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
# Line 4152  def matrixmult(arg0,arg1): Line 4149  def matrixmult(arg0,arg1):
4149          raise ValueError,"second argument must have rank 1 or 2"          raise ValueError,"second argument must have rank 1 or 2"
4150      return generalTensorProduct(arg0,arg1,axis_offset=1)      return generalTensorProduct(arg0,arg1,axis_offset=1)
4151    
4152  def outer(arg0,arg1):  def tensormult(arg0,arg1):
4153      """      """
4154      the outer product of the two argument:      use L{tensor_mult}
   
     out[t,s]=arg0[t]*arg1[s]  
   
     where s runs through arg0.Shape  
           t runs through arg1.Shape  
   
     @param arg0: first argument  
     @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}  
     @param arg1: second argument  
     @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}  
     @return: the outer product of arg0 and arg1 at each data point  
     @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input  
4155      """      """
4156      return generalTensorProduct(arg0,arg1,axis_offset=0)      return tensor_mult(arg0,arg1)
4157    
4158    def tensor_mult(arg0,arg1):
 def tensormult(arg0,arg1):  
4159      """      """
4160      the tensor product of the two argument:      the tensor product of the two argument:
   
4161            
4162      for arg0 of rank 2 this is      for arg0 of rank 2 this is
4163    
4164      out[s0]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0]        out[s0]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0]  
4165    
4166                   or      or
4167    
4168      out[s0,s1]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0,s1]      out[s0,s1]=S{Sigma}_{r0} arg0[s0,r0]*arg1[r0,s1]
4169    
# Line 4189  def tensormult(arg0,arg1): Line 4172  def tensormult(arg0,arg1):
4172    
4173      out[s0,s1,s2,s3]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[r0,r1,s2,s3]      out[s0,s1,s2,s3]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[r0,r1,s2,s3]
4174                                
4175                   or      or
4176    
4177      out[s0,s1,s2]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[r0,r1,s2]      out[s0,s1,s2]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[r0,r1,s2]
4178    
4179                   or      or
4180    
4181      out[s0,s1]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[r0,r1]      out[s0,s1]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[r0,r1]
4182    
4183      In the first case the the second dimension of arg0 and the length of arg1 must match and        In the first case the the second dimension of arg0 and the last dimension of arg1 must match and  
4184      in the second case the two last dimensions of arg0 must match the shape of arg1.      in the second case the two last dimensions of arg0 must match the two first dimensions of arg1.
4185    
4186      @param arg0: first argument of rank 2 or 4      @param arg0: first argument of rank 2 or 4
4187      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
# Line 4214  def tensormult(arg0,arg1): Line 4197  def tensormult(arg0,arg1):
4197      elif len(sh0)==4 and (len(sh1)==2 or len(sh1)==3 or len(sh1)==4):      elif len(sh0)==4 and (len(sh1)==2 or len(sh1)==3 or len(sh1)==4):
4198         return generalTensorProduct(arg0,arg1,axis_offset=2)         return generalTensorProduct(arg0,arg1,axis_offset=2)
4199      else:      else:
4200          raise ValueError,"tensormult: first argument must have rank 2 or 4"          raise ValueError,"tensor_mult: first argument must have rank 2 or 4"
4201    
4202  def generalTensorProduct(arg0,arg1,axis_offset=0):  def generalTensorProduct(arg0,arg1,axis_offset=0):
4203      """      """
# Line 4222  def generalTensorProduct(arg0,arg1,axis_ Line 4205  def generalTensorProduct(arg0,arg1,axis_
4205    
4206      out[s,t]=S{Sigma}_r arg0[s,r]*arg1[r,t]      out[s,t]=S{Sigma}_r arg0[s,r]*arg1[r,t]
4207    
4208      where s runs through arg0.Shape[:arg0.Rank-axis_offset]      where
           r runs trough arg0.Shape[:axis_offset]  
           t runs through arg1.Shape[axis_offset:]  
4209    
4210      In the first case the the second dimension of arg0 and the length of arg1 must match and            - s runs through arg0.Shape[:arg0.Rank-axis_offset]
4211      in the second case the two last dimensions of arg0 must match the shape of arg1.          - r runs trough arg0.Shape[:axis_offset]
4212            - t runs through arg1.Shape[axis_offset:]
4213    
4214      @param arg0: first argument      @param arg0: first argument
4215      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}      @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4216      @param arg1: second argument of shape greater of 1 or 2 depending on rank of arg0      @param arg1: second argument
4217      @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}      @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4218      @return: the general tensor product of arg0 and arg1 at each data point.      @return: the general tensor product of arg0 and arg1 at each data point.
4219      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input      @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
# Line 4244  def generalTensorProduct(arg0,arg1,axis_ Line 4226  def generalTensorProduct(arg0,arg1,axis_
4226             return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)             return GeneralTensorProduct_Symbol(arg0,arg1,axis_offset)
4227         else:         else:
4228             if not arg0.shape[arg0.rank-axis_offset:]==arg1.shape[:axis_offset]:             if not arg0.shape[arg0.rank-axis_offset:]==arg1.shape[:axis_offset]:
4229                 raise ValueError,"generalTensorProduct: dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)                 raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4230             arg0_c=arg0.copy()             arg0_c=arg0.copy()
4231             arg1_c=arg1.copy()             arg1_c=arg1.copy()
4232             sh0,sh1=arg0.shape,arg1.shape             sh0,sh1=arg0.shape,arg1.shape
# Line 4270  def generalTensorProduct(arg0,arg1,axis_ Line 4252  def generalTensorProduct(arg0,arg1,axis_
4252                                    
4253  class GeneralTensorProduct_Symbol(DependendSymbol):  class GeneralTensorProduct_Symbol(DependendSymbol):
4254     """     """
4255     Symbol representing the quotient of two arguments.     Symbol representing the general tensor product of two arguments
4256     """     """
4257     def __init__(self,arg0,arg1,axis_offset=0):     def __init__(self,arg0,arg1,axis_offset=0):
4258         """         """
4259         initialization of L{Symbol} representing the quotient of two arguments         initialization of L{Symbol} representing the general tensor product of two arguments.
4260    
4261         @param arg0: numerator         @param arg0: first argument
4262         @type arg0: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type arg0: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
4263         @param arg1: denominator         @param arg1: second argument
4264         @type arg1: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.         @type arg1: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
4265         @raise ValueError: if both arguments do not have the same shape.         @raise ValueError: illegal dimension
4266         @note: if both arguments have a spatial dimension, they must equal.         @note: if both arguments have a spatial dimension, they must equal.
4267         """         """
4268         sh_arg0=pokeShape(arg0)         sh_arg0=pokeShape(arg0)
# Line 4303  class GeneralTensorProduct_Symbol(Depend Line 4285  class GeneralTensorProduct_Symbol(Depend
4285        @type format: C{str}        @type format: C{str}
4286        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4287        @rtype: C{str}        @rtype: C{str}
4288        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
4289        """        """
4290        if format=="escript" or format=="str" or format=="text":        if format=="escript" or format=="str" or format=="text":
4291           return "generalTensorProduct(%s,%s,axis_offset=%s)"%(argstrs[0],argstrs[1],argstrs[2])           return "generalTensorProduct(%s,%s,axis_offset=%s)"%(argstrs[0],argstrs[1],argstrs[2])
# Line 4331  class GeneralTensorProduct_Symbol(Depend Line 4313  class GeneralTensorProduct_Symbol(Depend
4313           args=self.getSubstitutedArguments(argvals)           args=self.getSubstitutedArguments(argvals)
4314           return generalTensorProduct(args[0],args[1],args[2])           return generalTensorProduct(args[0],args[1],args[2])
4315    
4316    def escript_generalTensorProductNew(arg0,arg1,axis_offset):
4317        "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"
4318        # calculate the return shape:
4319        shape0=arg0.getShape()[:arg0.getRank()-axis_offset]
4320        shape01=arg0.getShape()[arg0.getRank()-axis_offset:]
4321        shape10=arg1.getShape()[:axis_offset]
4322        shape1=arg1.getShape()[axis_offset:]
4323        if not shape01==shape10:
4324            raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4325        # Figure out which functionspace to use (look at where operator+ is defined maybe in BinaryOp.h to get the logic for this)
4326        # fs=(escript.Scalar(0.,arg0.getFunctionSpace())+escript.Scalar(0.,arg1.getFunctionSpace())).getFunctionSpace()
4327        out=GeneralTensorProduct(arg0, arg1, axis_offset)
4328        return out
4329    
4330  def escript_generalTensorProduct(arg0,arg1,axis_offset): # this should be escript._generalTensorProduct  def escript_generalTensorProduct(arg0,arg1,axis_offset): # this should be escript._generalTensorProduct
4331      "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"      "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"
4332      # calculate the return shape:      # calculate the return shape:
# Line 4374  def escript_generalTensorProduct(arg0,ar Line 4370  def escript_generalTensorProduct(arg0,ar
4370      return out      return out
4371    
4372    
4373    def transposed_matrix_mult(arg0,arg1):
4374        """
4375        transposed(matrix)-matrix or transposed(matrix)-vector product of the two argument:
4376    
4377        out[s0]=S{Sigma}_{r0} arg0[r0,s0]*arg1[r0]
4378    
4379        or
4380    
4381        out[s0,s1]=S{Sigma}_{r0} arg0[r0,s0]*arg1[r0,s1]
4382    
4383        The function call transposed_matrix_mult(arg0,arg1) is equivalent to matrix_mult(transpose(arg0),arg1).
4384    
4385        The first dimension of arg0 and arg1 must match.
4386    
4387        @param arg0: first argument of rank 2
4388        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4389        @param arg1: second argument of at least rank 1
4390        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4391        @return: the product of the transposed of arg0 and arg1 at each data point
4392        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4393        @raise ValueError: if the shapes of the arguments are not appropriate
4394        """
4395        sh0=pokeShape(arg0)
4396        sh1=pokeShape(arg1)
4397        if not len(sh0)==2 :
4398            raise ValueError,"first argument must have rank 2"
4399        if not len(sh1)==2 and not len(sh1)==1:
4400            raise ValueError,"second argument must have rank 1 or 2"
4401        return generalTransposedTensorProduct(arg0,arg1,axis_offset=1)
4402    
4403    def transposed_tensor_mult(arg0,arg1):
4404        """
4405        the tensor product of the transposed of the first and the second argument
4406        
4407        for arg0 of rank 2 this is
4408    
4409        out[s0]=S{Sigma}_{r0} arg0[r0,s0]*arg1[r0]  
4410    
4411        or
4412    
4413        out[s0,s1]=S{Sigma}_{r0} arg0[r0,s0]*arg1[r0,s1]
4414    
4415      
4416        and for arg0 of rank 4 this is
4417    
4418        out[s0,s1,s2,s3]=S{Sigma}_{r0,r1} arg0[r0,r1,s0,s1]*arg1[r0,r1,s2,s3]
4419                  
4420        or
4421    
4422        out[s0,s1,s2]=S{Sigma}_{r0,r1} arg0[r0,r1,s0,s1]*arg1[r0,r1,s2]
4423    
4424        or
4425    
4426        out[s0,s1]=S{Sigma}_{r0,r1} arg0[r0,r1,s0,s1]*arg1[r0,r1]
4427    
4428        In the first case the the first dimension of arg0 and the first dimension of arg1 must match and  
4429        in the second case the two first dimensions of arg0 must match the two first dimension of arg1.
4430    
4431        The function call transposed_tensor_mult(arg0,arg1) is equivalent to tensor_mult(transpose(arg0),arg1).
4432    
4433        @param arg0: first argument of rank 2 or 4
4434        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4435        @param arg1: second argument of shape greater of 1 or 2 depending on rank of arg0
4436        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4437        @return: the tensor product of tarnsposed of arg0 and arg1 at each data point
4438        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4439        """
4440        sh0=pokeShape(arg0)
4441        sh1=pokeShape(arg1)
4442        if len(sh0)==2 and ( len(sh1)==2 or len(sh1)==1 ):
4443           return generalTransposedTensorProduct(arg0,arg1,axis_offset=1)
4444        elif len(sh0)==4 and (len(sh1)==2 or len(sh1)==3 or len(sh1)==4):
4445           return generalTransposedTensorProduct(arg0,arg1,axis_offset=2)
4446        else:
4447            raise ValueError,"first argument must have rank 2 or 4"
4448    
4449    def generalTransposedTensorProduct(arg0,arg1,axis_offset=0):
4450        """
4451        generalized tensor product of transposed of arg0 and arg1:
4452    
4453        out[s,t]=S{Sigma}_r arg0[r,s]*arg1[r,t]
4454    
4455        where
4456    
4457            - s runs through arg0.Shape[axis_offset:]
4458            - r runs trough arg0.Shape[:axis_offset]
4459            - t runs through arg1.Shape[axis_offset:]
4460    
4461        The function call generalTransposedTensorProduct(arg0,arg1,axis_offset) is equivalent
4462        to generalTensorProduct(transpose(arg0,arg0.rank-axis_offset),arg1,axis_offset).
4463    
4464        @param arg0: first argument
4465        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4466        @param arg1: second argument
4467        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4468        @return: the general tensor product of transposed(arg0) and arg1 at each data point.
4469        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4470        """
4471        if isinstance(arg0,float) and isinstance(arg1,float): return arg1*arg0
4472        arg0,arg1=matchType(arg0,arg1)
4473        # at this stage arg0 and arg0 are both numarray.NumArray or escript.Data or Symbols
4474        if isinstance(arg0,numarray.NumArray):
4475           if isinstance(arg1,Symbol):
4476               return GeneralTransposedTensorProduct_Symbol(arg0,arg1,axis_offset)
4477           else:
4478               if not arg0.shape[:axis_offset]==arg1.shape[:axis_offset]:
4479                   raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4480               arg0_c=arg0.copy()
4481               arg1_c=arg1.copy()
4482               sh0,sh1=arg0.shape,arg1.shape
4483               d0,d1,d01=1,1,1
4484               for i in sh0[axis_offset:]: d0*=i
4485               for i in sh1[axis_offset:]: d1*=i
4486               for i in sh0[:axis_offset]: d01*=i
4487               arg0_c.resize((d01,d0))
4488               arg1_c.resize((d01,d1))
4489               out=numarray.zeros((d0,d1),numarray.Float64)
4490               for i0 in range(d0):
4491                        for i1 in range(d1):
4492                             out[i0,i1]=numarray.sum(arg0_c[:,i0]*arg1_c[:,i1])
4493               out.resize(sh0[axis_offset:]+sh1[axis_offset:])
4494               return out
4495        elif isinstance(arg0,escript.Data):
4496           if isinstance(arg1,Symbol):
4497               return GeneralTransposedTensorProduct_Symbol(arg0,arg1,axis_offset)
4498           else:
4499               return escript_generalTransposedTensorProduct(arg0,arg1,axis_offset) # this calls has to be replaced by escript._generalTensorProduct(arg0,arg1,axis_offset)
4500        else:      
4501           return GeneralTransposedTensorProduct_Symbol(arg0,arg1,axis_offset)
4502                    
4503    class GeneralTransposedTensorProduct_Symbol(DependendSymbol):
4504       """
4505       Symbol representing the general tensor product of the transposed of arg0 and arg1
4506       """
4507       def __init__(self,arg0,arg1,axis_offset=0):
4508           """
4509           initialization of L{Symbol} representing tensor product of the transposed of arg0 and arg1
4510    
4511           @param arg0: first argument
4512           @type arg0: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
4513           @param arg1: second argument
4514           @type arg1: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
4515           @raise ValueError: inconsistent dimensions of arguments.
4516           @note: if both arguments have a spatial dimension, they must equal.
4517           """
4518           sh_arg0=pokeShape(arg0)
4519           sh_arg1=pokeShape(arg1)
4520           sh01=sh_arg0[:axis_offset]
4521           sh10=sh_arg1[:axis_offset]
4522           sh0=sh_arg0[axis_offset:]
4523           sh1=sh_arg1[axis_offset:]
4524           if not sh01==sh10:
4525               raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4526           DependendSymbol.__init__(self,dim=commonDim(arg0,arg1),shape=sh0+sh1,args=[arg0,arg1,axis_offset])
4527    
4528       def getMyCode(self,argstrs,format="escript"):
4529          """
4530          returns a program code that can be used to evaluate the symbol.
4531    
4532          @param argstrs: gives for each argument a string representing the argument for the evaluation.
4533          @type argstrs: C{list} of length 2 of C{str}.
4534          @param format: specifies the format to be used. At the moment only "escript", "str" and "text" are supported.
4535          @type format: C{str}
4536          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4537          @rtype: C{str}
4538          @raise NotImplementedError: if the requested format is not available
4539          """
4540          if format=="escript" or format=="str" or format=="text":
4541             return "generalTransposedTensorProduct(%s,%s,axis_offset=%s)"%(argstrs[0],argstrs[1],argstrs[2])
4542          else:
4543             raise NotImplementedError,"%s does not provide program code for format %s."%(str(self),format)
4544    
4545       def substitute(self,argvals):
4546          """
4547          assigns new values to symbols in the definition of the symbol.
4548          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
4549    
4550          @param argvals: new values assigned to symbols
4551          @type argvals: C{dict} with keywords of type L{Symbol}.
4552          @return: result of the substitution process. Operations are executed as much as possible.
4553          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4554          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4555          """
4556          if argvals.has_key(self):
4557             arg=argvals[self]
4558             if self.isAppropriateValue(arg):
4559                return arg
4560             else:
4561                raise TypeError,"%s: new value is not appropriate."%str(self)
4562          else:
4563             args=self.getSubstitutedArguments(argvals)
4564             return generalTransposedTensorProduct(args[0],args[1],args[2])
4565    
4566    def escript_generalTransposedTensorProduct(arg0,arg1,axis_offset): # this should be escript._generalTransposedTensorProduct
4567        "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"
4568        # calculate the return shape:
4569        shape01=arg0.getShape()[:axis_offset]
4570        shape10=arg1.getShape()[:axis_offset]
4571        shape0=arg0.getShape()[axis_offset:]
4572        shape1=arg1.getShape()[axis_offset:]
4573        if not shape01==shape10:
4574            raise ValueError,"dimensions of first %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4575    
4576        # whatr function space should be used? (this here is not good!)
4577        fs=(escript.Scalar(0.,arg0.getFunctionSpace())+escript.Scalar(0.,arg1.getFunctionSpace())).getFunctionSpace()
4578        # create return value:
4579        out=escript.Data(0.,tuple(shape0+shape1),fs)
4580        #
4581        s0=[[]]
4582        for k in shape0:
4583              s=[]
4584              for j in s0:
4585                    for i in range(k): s.append(j+[slice(i,i)])
4586              s0=s
4587        s1=[[]]
4588        for k in shape1:
4589              s=[]
4590              for j in s1:
4591                    for i in range(k): s.append(j+[slice(i,i)])
4592              s1=s
4593        s01=[[]]
4594        for k in shape01:
4595              s=[]
4596              for j in s01:
4597                    for i in range(k): s.append(j+[slice(i,i)])
4598              s01=s
4599    
4600        for i0 in s0:
4601           for i1 in s1:
4602             s=escript.Scalar(0.,fs)
4603             for i01 in s01:
4604                s+=arg0.__getitem__(tuple(i01+i0))*arg1.__getitem__(tuple(i01+i1))
4605             out.__setitem__(tuple(i0+i1),s)
4606        return out
4607    
4608    
4609    def matrix_transposed_mult(arg0,arg1):
4610        """
4611        matrix-transposed(matrix) product of the two argument:
4612    
4613        out[s0,s1]=S{Sigma}_{r0} arg0[s0,r0]*arg1[s1,r0]
4614    
4615        The function call matrix_transposed_mult(arg0,arg1) is equivalent to matrix_mult(arg0,transpose(arg1)).
4616    
4617        The last dimensions of arg0 and arg1 must match.
4618    
4619        @param arg0: first argument of rank 2
4620        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4621        @param arg1: second argument of rank 2
4622        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4623        @return: the product of arg0 and the transposed of arg1 at each data point
4624        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4625        @raise ValueError: if the shapes of the arguments are not appropriate
4626        """
4627        sh0=pokeShape(arg0)
4628        sh1=pokeShape(arg1)
4629        if not len(sh0)==2 :
4630            raise ValueError,"first argument must have rank 2"
4631        if not len(sh1)==2 and not len(sh1)==1:
4632            raise ValueError,"second argument must have rank 1 or 2"
4633        return generalTensorTransposedProduct(arg0,arg1,axis_offset=1)
4634    
4635    def tensor_transposed_mult(arg0,arg1):
4636        """
4637        the tensor product of the first and the transpose of the second argument
4638        
4639        for arg0 of rank 2 this is
4640    
4641        out[s0,s1]=S{Sigma}_{r0} arg0[s0,r0]*arg1[s1,r0]
4642    
4643        and for arg0 of rank 4 this is
4644    
4645        out[s0,s1,s2,s3]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[s2,s3,r0,r1]
4646                  
4647        or
4648    
4649        out[s0,s1,s2]=S{Sigma}_{r0,r1} arg0[s0,s1,r0,r1]*arg1[s2,r0,r1]
4650    
4651        In the first case the the second dimension of arg0 and arg1 must match and  
4652        in the second case the two last dimensions of arg0 must match the two last dimension of arg1.
4653    
4654        The function call tensor_transpose_mult(arg0,arg1) is equivalent to tensor_mult(arg0,transpose(arg1)).
4655    
4656        @param arg0: first argument of rank 2 or 4
4657        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4658        @param arg1: second argument of shape greater of 1 or 2 depending on rank of arg0
4659        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}
4660        @return: the tensor product of tarnsposed of arg0 and arg1 at each data point
4661        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4662        """
4663        sh0=pokeShape(arg0)
4664        sh1=pokeShape(arg1)
4665        if len(sh0)==2 and ( len(sh1)==2 or len(sh1)==1 ):
4666           return generalTensorTransposedProduct(arg0,arg1,axis_offset=1)
4667        elif len(sh0)==4 and (len(sh1)==2 or len(sh1)==3 or len(sh1)==4):
4668           return generalTensorTransposedProduct(arg0,arg1,axis_offset=2)
4669        else:
4670            raise ValueError,"first argument must have rank 2 or 4"
4671    
4672    def generalTensorTransposedProduct(arg0,arg1,axis_offset=0):
4673        """
4674        generalized tensor product of transposed of arg0 and arg1:
4675    
4676        out[s,t]=S{Sigma}_r arg0[s,r]*arg1[t,r]
4677    
4678        where
4679    
4680            - s runs through arg0.Shape[:arg0.Rank-axis_offset]
4681            - r runs trough arg0.Shape[arg1.Rank-axis_offset:]
4682            - t runs through arg1.Shape[arg1.Rank-axis_offset:]
4683    
4684        The function call generalTensorTransposedProduct(arg0,arg1,axis_offset) is equivalent
4685        to generalTensorProduct(arg0,transpose(arg1,arg1.Rank-axis_offset),axis_offset).
4686    
4687        @param arg0: first argument
4688        @type arg0: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4689        @param arg1: second argument
4690        @type arg1: L{numarray.NumArray}, L{escript.Data}, L{Symbol}, C{float}, C{int}
4691        @return: the general tensor product of transposed(arg0) and arg1 at each data point.
4692        @rtype: L{numarray.NumArray}, L{escript.Data}, L{Symbol} depending on the input
4693        """
4694        if isinstance(arg0,float) and isinstance(arg1,float): return arg1*arg0
4695        arg0,arg1=matchType(arg0,arg1)
4696        # at this stage arg0 and arg0 are both numarray.NumArray or escript.Data or Symbols
4697        if isinstance(arg0,numarray.NumArray):
4698           if isinstance(arg1,Symbol):
4699               return GeneralTensorTransposedProduct_Symbol(arg0,arg1,axis_offset)
4700           else:
4701               if not arg0.shape[arg0.rank-axis_offset:]==arg1.shape[arg1.rank-axis_offset:]:
4702                   raise ValueError,"dimensions of last %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4703               arg0_c=arg0.copy()
4704               arg1_c=arg1.copy()
4705               sh0,sh1=arg0.shape,arg1.shape
4706               d0,d1,d01=1,1,1
4707               for i in sh0[:arg0.rank-axis_offset]: d0*=i
4708               for i in sh1[:arg1.rank-axis_offset]: d1*=i
4709               for i in sh1[arg1.rank-axis_offset:]: d01*=i
4710               arg0_c.resize((d0,d01))
4711               arg1_c.resize((d1,d01))
4712               out=numarray.zeros((d0,d1),numarray.Float64)
4713               for i0 in range(d0):
4714                        for i1 in range(d1):
4715                             out[i0,i1]=numarray.sum(arg0_c[i0,:]*arg1_c[i1,:])
4716               out.resize(sh0[:arg0.rank-axis_offset]+sh1[:arg1.rank-axis_offset])
4717               return out
4718        elif isinstance(arg0,escript.Data):
4719           if isinstance(arg1,Symbol):
4720               return GeneralTensorTransposedProduct_Symbol(arg0,arg1,axis_offset)
4721           else:
4722               return escript_generalTensorTransposedProduct(arg0,arg1,axis_offset) # this calls has to be replaced by escript._generalTensorProduct(arg0,arg1,axis_offset)
4723        else:      
4724           return GeneralTensorTransposedProduct_Symbol(arg0,arg1,axis_offset)
4725                    
4726    class GeneralTensorTransposedProduct_Symbol(DependendSymbol):
4727       """
4728       Symbol representing the general tensor product of arg0 and the transpose of arg1
4729       """
4730       def __init__(self,arg0,arg1,axis_offset=0):
4731           """
4732           initialization of L{Symbol} representing the general tensor product of arg0 and the transpose of arg1
4733    
4734           @param arg0: first argument
4735           @type arg0: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
4736           @param arg1: second argument
4737           @type arg1: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray}.
4738           @raise ValueError: inconsistent dimensions of arguments.
4739           @note: if both arguments have a spatial dimension, they must equal.
4740           """
4741           sh_arg0=pokeShape(arg0)
4742           sh_arg1=pokeShape(arg1)
4743           sh0=sh_arg0[:len(sh_arg0)-axis_offset]
4744           sh01=sh_arg0[len(sh_arg0)-axis_offset:]
4745           sh10=sh_arg1[len(sh_arg1)-axis_offset:]
4746           sh1=sh_arg1[:len(sh_arg1)-axis_offset]
4747           if not sh01==sh10:
4748               raise ValueError,"dimensions of last %s components in left argument don't match the last %s components in the right argument."%(axis_offset,axis_offset)
4749           DependendSymbol.__init__(self,dim=commonDim(arg0,arg1),shape=sh0+sh1,args=[arg0,arg1,axis_offset])
4750    
4751       def getMyCode(self,argstrs,format="escript"):
4752          """
4753          returns a program code that can be used to evaluate the symbol.
4754    
4755          @param argstrs: gives for each argument a string representing the argument for the evaluation.
4756          @type argstrs: C{list} of length 2 of C{str}.
4757          @param format: specifies the format to be used. At the moment only "escript", "str" and "text" are supported.
4758          @type format: C{str}
4759          @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4760          @rtype: C{str}
4761          @raise NotImplementedError: if the requested format is not available
4762          """
4763          if format=="escript" or format=="str" or format=="text":
4764             return "generalTensorTransposedProduct(%s,%s,axis_offset=%s)"%(argstrs[0],argstrs[1],argstrs[2])
4765          else:
4766             raise NotImplementedError,"%s does not provide program code for format %s."%(str(self),format)
4767    
4768       def substitute(self,argvals):
4769          """
4770          assigns new values to symbols in the definition of the symbol.
4771          The method replaces the L{Symbol} u by argvals[u] in the expression defining this object.
4772    
4773          @param argvals: new values assigned to symbols
4774          @type argvals: C{dict} with keywords of type L{Symbol}.
4775          @return: result of the substitution process. Operations are executed as much as possible.
4776          @rtype: L{escript.Symbol}, C{float}, L{escript.Data}, L{numarray.NumArray} depending on the degree of substitution
4777          @raise TypeError: if a value for a L{Symbol} cannot be substituted.
4778          """
4779          if argvals.has_key(self):
4780             arg=argvals[self]
4781             if self.isAppropriateValue(arg):
4782                return arg
4783             else:
4784                raise TypeError,"%s: new value is not appropriate."%str(self)
4785          else:
4786             args=self.getSubstitutedArguments(argvals)
4787             return generalTensorTransposedProduct(args[0],args[1],args[2])
4788    
4789    def escript_generalTensorTransposedProduct(arg0,arg1,axis_offset): # this should be escript._generalTensorTransposedProduct
4790        "arg0 and arg1 are both Data objects but not neccesrily on the same function space. they could be identical!!!"
4791        # calculate the return shape:
4792        shape01=arg0.getShape()[arg0.getRank()-axis_offset:]
4793        shape0=arg0.getShape()[:arg0.getRank()-axis_offset]
4794        shape10=arg1.getShape()[arg1.getRank()-axis_offset:]
4795        shape1=arg1.getShape()[:arg1.getRank()-axis_offset]
4796        if not shape01==shape10:
4797            raise ValueError,"dimensions of first %s components in left argument don't match the first %s components in the right argument."%(axis_offset,axis_offset)
4798    
4799        # whatr function space should be used? (this here is not good!)
4800        fs=(escript.Scalar(0.,arg0.getFunctionSpace())+escript.Scalar(0.,arg1.getFunctionSpace())).getFunctionSpace()
4801        # create return value:
4802        out=escript.Data(0.,tuple(shape0+shape1),fs)
4803        #
4804        s0=[[]]
4805        for k in shape0:
4806              s=[]
4807              for j in s0:
4808                    for i in range(k): s.append(j+[slice(i,i)])
4809              s0=s
4810        s1=[[]]
4811        for k in shape1:
4812              s=[]
4813              for j in s1:
4814                    for i in range(k): s.append(j+[slice(i,i)])
4815              s1=s
4816        s01=[[]]
4817        for k in shape01:
4818              s=[]
4819              for j in s01:
4820                    for i in range(k): s.append(j+[slice(i,i)])
4821              s01=s
4822    
4823        for i0 in s0:
4824           for i1 in s1:
4825             s=escript.Scalar(0.,fs)
4826             for i01 in s01:
4827                s+=arg0.__getitem__(tuple(i0+i01))*arg1.__getitem__(tuple(i1+i01))
4828             out.__setitem__(tuple(i0+i1),s)
4829        return out
4830    
4831    
4832  #=========================================================  #=========================================================
4833  #  functions dealing with spatial dependency  #  functions dealing with spatial dependency
4834  #=========================================================  #=========================================================
# Line 4394  def grad(arg,where=None): Line 4849  def grad(arg,where=None):
4849                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
4850      @type where: C{None} or L{escript.FunctionSpace}      @type where: C{None} or L{escript.FunctionSpace}
4851      @return: gradient of arg.      @return: gradient of arg.
4852      @rtype:  L{escript.Data} or L{Symbol}      @rtype: L{escript.Data} or L{Symbol}
4853      """      """
4854      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4855         return Grad_Symbol(arg,where)         return Grad_Symbol(arg,where)
# Line 4434  class Grad_Symbol(DependendSymbol): Line 4889  class Grad_Symbol(DependendSymbol):
4889        @type format: C{str}        @type format: C{str}
4890        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4891        @rtype: C{str}        @rtype: C{str}
4892        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
4893        """        """
4894        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
4895           return "grad(%s,where=%s)"%(argstrs[0],argstrs[1])           return "grad(%s,where=%s)"%(argstrs[0],argstrs[1])
# Line 4487  def integrate(arg,where=None): Line 4942  def integrate(arg,where=None):
4942                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
4943      @type where: C{None} or L{escript.FunctionSpace}      @type where: C{None} or L{escript.FunctionSpace}
4944      @return: integral of arg.      @return: integral of arg.
4945      @rtype:  C{float}, C{numarray.NumArray} or L{Symbol}      @rtype: C{float}, C{numarray.NumArray} or L{Symbol}
4946      """      """
4947      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
4948         return Integrate_Symbol(arg,where)         return Integrate_Symbol(arg,where)
# Line 4525  class Integrate_Symbol(DependendSymbol): Line 4980  class Integrate_Symbol(DependendSymbol):
4980        @type format: C{str}        @type format: C{str}
4981        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
4982        @rtype: C{str}        @rtype: C{str}
4983        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
4984        """        """
4985        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
4986           return "integrate(%s,where=%s)"%(argstrs[0],argstrs[1])           return "integrate(%s,where=%s)"%(argstrs[0],argstrs[1])
# Line 4577  def interpolate(arg,where): Line 5032  def interpolate(arg,where):
5032      @param where: FunctionSpace to be interpolated to      @param where: FunctionSpace to be interpolated to
5033      @type where: L{escript.FunctionSpace}      @type where: L{escript.FunctionSpace}
5034      @return: interpolated argument      @return: interpolated argument
5035      @rtype:  C{escript.Data} or L{Symbol}      @rtype: C{escript.Data} or L{Symbol}
5036      """      """
5037      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
5038         return Interpolate_Symbol(arg,where)         return Interpolate_Symbol(arg,where)
# Line 4608  class Interpolate_Symbol(DependendSymbol Line 5063  class Interpolate_Symbol(DependendSymbol
5063        @type format: C{str}        @type format: C{str}
5064        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.        @return: a piece of program code which can be used to evaluate the expression assuming the values for the arguments are available.
5065        @rtype: C{str}        @rtype: C{str}
5066        @raise: NotImplementedError: if the requested format is not available        @raise NotImplementedError: if the requested format is not available
5067        """        """
5068        if format=="escript" or format=="str"  or format=="text":        if format=="escript" or format=="str"  or format=="text":
5069           return "interpolate(%s,where=%s)"%(argstrs[0],argstrs[1])           return "interpolate(%s,where=%s)"%(argstrs[0],argstrs[1])
# Line 4661  def div(arg,where=None): Line 5116  def div(arg,where=None):
5116                    If not present or C{None} an appropriate default is used.                    If not present or C{None} an appropriate default is used.
5117      @type where: C{None} or L{escript.FunctionSpace}      @type where: C{None} or L{escript.FunctionSpace}
5118      @return: divergence of arg.      @return: divergence of arg.
5119      @rtype:  L{escript.Data} or L{Symbol}      @rtype: L{escript.Data} or L{Symbol}
5120      """      """
5121      if isinstance(arg,Symbol):      if isinstance(arg,Symbol):
5122          dim=arg.getDim()          dim=arg.getDim()
# Line 4683  def jump(arg,domain=None): Line 5138  def jump(arg,domain=None):
5138                     the domain of arg is used. If arg is a L{Symbol} the domain must be present.                     the domain of arg is used. If arg is a L{Symbol} the domain must be present.
5139      @type domain: C{None} or L{escript.Domain}      @type domain: C{None} or L{escript.Domain}
5140      @return: jump of arg      @return: jump of arg
5141      @rtype:  L{escript.Data} or L{Symbol}      @rtype: L{escript.Data} or L{Symbol}
5142      """      """
5143      if domain==None: domain=arg.getDomain()      if domain==None: domain=arg.getDomain()
5144      return interpolate(arg,escript.FunctionOnContactOne(domain))-interpolate(arg,escript.FunctionOnContactZero(domain))      return interpolate(arg,escript.FunctionOnContactOne(domain))-interpolate(arg,escript.FunctionOnContactZero(domain))
# Line 4695  def L2(arg): Line 5150  def L2(arg):
5150      @param arg: function which L2 to be calculated.      @param arg: function which L2 to be calculated.
5151      @type arg: L{escript.Data} or L{Symbol}      @type arg: L{escript.Data} or L{Symbol}
5152      @return: L2 norm of arg.      @return: L2 norm of arg.
5153      @rtype:  L{float} or L{Symbol}      @rtype: L{float} or L{Symbol}
5154      @note: L2(arg) is equivalent to sqrt(integrate(inner(arg,arg)))      @note: L2(arg) is equivalent to sqrt(integrate(inner(arg,arg)))
5155      """      """
5156      return sqrt(integrate(inner(arg,arg)))      return sqrt(integrate(inner(arg,arg)))

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