[Scipy-svn] r5060 - trunk/scipy/sparse/linalg/isolve

scipy-svn@scip... scipy-svn@scip...
Tue Nov 11 20:17:33 CST 2008


Author: wnbell
Date: 2008-11-11 20:17:26 -0600 (Tue, 11 Nov 2008)
New Revision: 5060

Modified:
   trunk/scipy/sparse/linalg/isolve/iterative.py
   trunk/scipy/sparse/linalg/isolve/minres.py
Log:
updated iterative solver docstrings
resolves ticket #652


Modified: trunk/scipy/sparse/linalg/isolve/iterative.py
===================================================================
--- trunk/scipy/sparse/linalg/isolve/iterative.py	2008-11-11 09:03:27 UTC (rev 5059)
+++ trunk/scipy/sparse/linalg/isolve/iterative.py	2008-11-12 02:17:26 UTC (rev 5060)
@@ -10,41 +10,67 @@
 
 _type_conv = {'f':'s', 'd':'d', 'F':'c', 'D':'z'}
 
-def bicg(A, b, x0=None, tol=1e-5, maxiter=None, xtype=None, M=None, callback=None):
-    """Use BIConjugate Gradient iteration to solve A x = b
 
-    Inputs:
+# Part of the docstring common to all iterative solvers
+common_doc = \
+"""
+Parameters
+----------
+A : {sparse matrix, dense matrix, LinearOperator}
+    The N-by-N matrix of the linear system.
+b : {array, matrix}
+    Right hand side of the linear system. Has shape (N,) or (N,1).
 
-    A --   An array or an object with matvec(x) and rmatvec(x) methods
-           to represent A * x and A^H * x respectively.  May also have
-           psolve(b) and rpsolve(b) methods for representing solutions
-           to the preconditioning equations M * x = b and
-           M^H * x = b respectively.
-    b --   An n-length vector
+Optional Parameters
+-------------------
+x0  : {array, matrix}
+    Starting guess for the solution.
+tol : float
+    Relative tolerance to achieve before terminating.
+maxiter : integer
+    Maximum number of iterations.  Iteration will stop after maxiter
+    steps even if the specified tolerance has not been achieved.
+M : {sparse matrix, dense matrix, LinearOperator}
+    Preconditioner for A.  The preconditioner should approximate the 
+    inverse of A.  Effective preconditioning dramatically improves the
+    rate of convergence, which implies that fewer iterations are needed
+    to reach a given error tolerance.
+callback : function
+    User-supplied function to call after each iteration.  It is called
+    as callback(xk), where xk is the current solution vector.
 
-    Outputs:
+Outputs
+-------
+x : {array, matrix}
+    The converged solution.
+info : integer
+    Provides convergence information:
+        0  : successful exit
+        >0 : convergence to tolerance not achieved, number of iterations
+        <0 : illegal input or breakdown
 
-    x  --  The converged solution
-    info -- output result
-            0  : successful exit
-            >0 : convergence to tolerance not achieved, number of iterations
-            <0 : illegal input or breakdown
+Deprecated Parameters
+----------------------
+xtype : {'f','d','F','D'}
+    The type of the result.  If None, then it will be determined from
+    A.dtype.char and b.  If A does not have a typecode method then it 
+    will compute A.matvec(x0) to get a typecode.   To save the extra 
+    computation when A does not have a typecode attribute use xtype=0 
+    for the same type as b or use xtype='f','d','F',or 'D'.
+    This parameter has been superceeded by LinearOperator.
+"""
 
-    Optional Inputs:
 
-    x0  -- (0) default starting guess.
-    tol -- (1e-5) relative tolerance to achieve
-    maxiter -- (10*n) maximum number of iterations
-    xtype  --  The type of the result.  If None, then it will be
-               determined from A.dtype.char and b.  If A does not have a
-               typecode method then it will compute A.matvec(x0) to get a
-               typecode.   To save the extra computation when A does not
-               have a typecode attribute use xtype=0 for the same type as
-               b or use xtype='f','d','F',or 'D'
-    callback -- an optional user-supplied function to call after each
-                iteration.  It is called as callback(xk), where xk is the
-                current parameter vector.
-    """
+def set_docstring(header, footer):
+    def combine(fn):
+        fn.__doc__ = header + '\n' + common_doc + '\n' + footer
+        return fn
+    return combine
+
+
+
+@set_docstring('Use BIConjugate Gradient iteration to solve A x = b','')
+def bicg(A, b, x0=None, tol=1e-5, maxiter=None, xtype=None, M=None, callback=None):
     A,M,x,b,postprocess = make_system(A,M,x0,b,xtype)
 
     n = len(b)
@@ -104,41 +130,8 @@
 
     return postprocess(x), info
 
-
+@set_docstring('Use BIConjugate Gradient STABilized iteration to solve A x = b','')
 def bicgstab(A, b, x0=None, tol=1e-5, maxiter=None, xtype=None, M=None, callback=None):
-    """Use BIConjugate Gradient STABilized iteration to solve A x = b
-
-    Inputs:
-
-    A --   An array or an object with a matvec(x) method
-           to represent A * x.  May also have a psolve(b) methods for
-           representing solution to the preconditioning equation
-           M * x = b.
-    b --   An n-length vector
-
-    Outputs:
-
-    x  --  The converged solution
-    info -- output result
-            0  : successful exit
-            >0 : convergence to tolerance not achieved, number of iterations
-            <0 : illegal input or breakdown
-
-    Optional Inputs:
-
-    x0  -- (0) default starting guess.
-    tol -- (1e-5) relative tolerance to achieve
-    maxiter -- (10*n) maximum number of iterations
-    xtype  --  The type of the result.  If None, then it will be
-               determined from A.dtype.char and b.  If A does not have a
-               typecode method then it will compute A.matvec(x0) to get a
-               typecode.   To save the extra computation when A does not
-               have a typecode attribute use xtype=0 for the same type as
-               b or use xtype='f','d','F',or 'D'
-    callback -- an optional user-supplied function to call after each
-                iteration.  It is called as callback(xk), where xk is the
-                current parameter vector.
-    """
     A,M,x,b,postprocess = make_system(A,M,x0,b,xtype)
 
     n = len(b)
@@ -199,42 +192,8 @@
 
     return postprocess(x), info
 
-
+@set_docstring('Use Conjugate Gradient iteration to solve A x = b','')
 def cg(A, b, x0=None, tol=1e-5, maxiter=None, xtype=None, M=None, callback=None):
-    """Use Conjugate Gradient iteration to solve A x = b (A^H = A)
-
-    Inputs:
-
-    A --   An array or an object with a matvec(x) method
-           to represent A * x.  May also have a psolve(b) methods for
-           representing solution to the preconditioning equation
-           M * x = b.
-    b --   An n-length vector
-
-
-    Outputs:
-
-    x  --  The converged solution
-    info -- output result
-            0  : successful exit
-            >0 : convergence to tolerance not achieved, number of iterations
-            <0 : illegal input or breakdown
-
-    Optional Inputs:
-
-    x0  -- (0) default starting guess.
-    tol -- (1e-5) relative tolerance to achieve
-    maxiter -- (10*n) maximum number of iterations
-    xtype  --  The type of the result.  If None, then it will be
-               determined from A.dtype.char and b.  If A does not have a
-               typecode method then it will compute A.matvec(x0) to get a
-               typecode.   To save the extra computation when A does not
-               have a typecode attribute use xtype=0 for the same type as
-               b or use xtype='f','d','F',or 'D'
-    callback -- an optional user-supplied function to call after each
-                iteration.  It is called as callback(xk), where xk is the
-                current parameter vector.
-    """
     A,M,x,b,postprocess = make_system(A,M,x0,b,xtype)
 
     n = len(b)
@@ -291,41 +250,8 @@
     return postprocess(x), info
 
 
+@set_docstring('Use Conjugate Gradient Squared iteration to solve A x = b','')
 def cgs(A, b, x0=None, tol=1e-5, maxiter=None, xtype=None, M=None, callback=None):
-    """Use Conjugate Gradient Squared iteration to solve A x = b
-
-    Inputs:
-
-    A --   An array or an object with a matvec(x) method
-           to represent A * x.  May also have a psolve(b) methods for
-           representing solution to the preconditioning equation
-           M * x = b.
-    b --   An n-length vector
-
-
-    Outputs:
-
-    x  --  The converged solution
-    info -- output result
-            0  : successful exit
-            >0 : convergence to tolerance not achieved, number of iterations
-            <0 : illegal input or breakdown
-
-    Optional Inputs:
-
-    x0  -- (0) default starting guess.
-    tol -- (1e-5) relative tolerance to achieve
-    maxiter -- (10*n) maximum number of iterations
-    xtype  --  The type of the result.  If None, then it will be
-               determined from A.dtype.char and b.  If A does not have a
-               typecode method then it will compute A.matvec(x0) to get a
-               typecode.   To save the extra computation when A does not
-               have a typecode attribute use xtype=0 for the same type as
-               b or use xtype='f','d','F',or 'D'
-    callback -- an optional user-supplied function to call after each
-                iteration.  It is called as callback(xk), where xk is the
-                current parameter vector.
-    """
     A,M,x,b,postprocess = make_system(A,M,x0,b,xtype)
 
     n = len(b)
@@ -379,44 +305,63 @@
         info = iter_
 
     return postprocess(x), info
+    
 
-
 def gmres(A, b, x0=None, tol=1e-5, restrt=20, maxiter=None, xtype=None, M=None, callback=None):
     """Use Generalized Minimal RESidual iteration to solve A x = b
-
-    Inputs:
-
-    A --   An array or an object with a matvec(x) method
-           to represent A * x.  May also have a psolve(b) methods for
-           representing solution to the preconditioning equation
-           M * x = b.
-    b --   An n-length vector
-
-
-    Outputs:
-
-    x  --  The converged solution
-    info -- output result
+    
+    Parameters
+    ----------
+    A : {sparse matrix, dense matrix, LinearOperator}
+        The N-by-N matrix of the linear system.
+    b : {array, matrix}
+        Right hand side of the linear system. Has shape (N,) or (N,1).
+    
+    Optional Parameters
+    -------------------
+    x0  : {array, matrix}
+        Starting guess for the solution.
+    tol : float
+        Relative tolerance to achieve before terminating.
+    restrt : integer
+        Number of iterations between restarts. Larger values increase
+        iteration cost, but may be necessary for convergence.
+    maxiter : integer
+        Maximum number of iterations.  Iteration will stop after maxiter
+        steps even if the specified tolerance has not been achieved.
+    M : {sparse matrix, dense matrix, LinearOperator}
+        Preconditioner for A.  The preconditioner should approximate the 
+        inverse of A.  Effective preconditioning dramatically improves the
+        rate of convergence, which implies that fewer iterations are needed
+        to reach a given error tolerance.
+    callback : function
+        User-supplied function to call after each iteration.  It is called
+        as callback(rk), where rk is the current residual vector.
+    
+    Outputs
+    -------
+    x : {array, matrix}
+        The converged solution.
+    info : integer
+        Provides convergence information:
             0  : successful exit
             >0 : convergence to tolerance not achieved, number of iterations
             <0 : illegal input or breakdown
-
-    Optional Inputs:
-
-    x0  -- (0) default starting guess.
-    tol -- (1e-5) relative tolerance to achieve
-    restrt -- (10) When to restart (change this to get faster performance -- but
-                   may not converge).
-    maxiter -- (10*n) maximum number of iterations
-    xtype  --  The type of the result.  If None, then it will be
-               determined from A.dtype.char and b.  If A does not have a
-               typecode method then it will compute A.matvec(x0) to get a
-               typecode.   To save the extra computation when A does not
-               have a typecode attribute use xtype=0 for the same type as
-               b or use xtype='f','d','F',or 'D'
-    callback -- an optional user-supplied function to call after each
-                iteration.  It is called as callback(rk), where rk is the
-                the current relative residual
+    
+    See Also
+    --------
+    LinearOperator
+    
+    Deprecated Parameters
+    ---------------------
+    xtype : {'f','d','F','D'}
+        The type of the result.  If None, then it will be determined from
+        A.dtype.char and b.  If A does not have a typecode method then it 
+        will compute A.matvec(x0) to get a typecode.   To save the extra 
+        computation when A does not have a typecode attribute use xtype=0 
+        for the same type as b or use xtype='f','d','F',or 'D'.
+        This parameter has been superceeded by LinearOperator.
+    
     """
     A,M,x,b,postprocess = make_system(A,M,x0,b,xtype)
 
@@ -499,38 +444,56 @@
 def qmr(A, b, x0=None, tol=1e-5, maxiter=None, xtype=None, M1=None, M2=None, callback=None):
     """Use Quasi-Minimal Residual iteration to solve A x = b
 
-    Inputs:
-
-    A --   An array or an object with matvec(x) and rmatvec(x) methods
-           to represent A * x and A^H * x respectively.  May also have
-           psolve(b,<which>) and rpsolve(b,<which>) methods for
-           representing solutions to the preconditioning equations
-           M * x = b and M^H * x = b respectively.   The <which> argument
-           may be given to specify 'left' or 'right' preconditioning.
-    b --   An n-length vector
-
-    Outputs:
-
-    x  --  The converged solution
-    info -- output result
+    Parameters
+    ----------
+    A : {sparse matrix, dense matrix, LinearOperator}
+        The N-by-N matrix of the linear system.
+    b : {array, matrix}
+        Right hand side of the linear system. Has shape (N,) or (N,1).
+    
+    Optional Parameters
+    -------------------
+    x0  : {array, matrix}
+        Starting guess for the solution.
+    tol : float
+        Relative tolerance to achieve before terminating.
+    maxiter : integer
+        Maximum number of iterations.  Iteration will stop after maxiter
+        steps even if the specified tolerance has not been achieved.
+    M1 : {sparse matrix, dense matrix, LinearOperator}
+        Left preconditioner for A.
+    M2 : {sparse matrix, dense matrix, LinearOperator}
+        Right preconditioner for A. Used together with the left
+        preconditioner M1.  The matrix M1*A*M2 should have better
+        conditioned than A alone.
+    callback : function
+        User-supplied function to call after each iteration.  It is called
+        as callback(xk), where xk is the current solution vector.
+    
+    Outputs
+    -------
+    x : {array, matrix}
+        The converged solution.
+    info : integer
+        Provides convergence information:
             0  : successful exit
             >0 : convergence to tolerance not achieved, number of iterations
             <0 : illegal input or breakdown
-
-    Optional Inputs:
-
-    x0  -- (0) default starting guess.
-    tol -- (1e-5) relative tolerance to achieve
-    maxiter -- (10*n) maximum number of iterations
-    xtype  --  The type of the result.  If None, then it will be
-               determined from A.dtype.char and b.  If A does not have a
-               typecode method then it will compute A.matvec(x0) to get a
-               typecode.   To save the extra computation when A does not
-               have a typecode attribute use xtype=0 for the same type as
-               b or use xtype='f','d','F',or 'D'
-    callback -- an optional user-supplied function to call after each
-                iteration.  It is called as callback(xk), where xk is the
-                current parameter vector.
+    
+    See Also
+    --------
+    LinearOperator
+    
+    Deprecated Parameters
+    ---------------------
+    xtype : {'f','d','F','D'}
+        The type of the result.  If None, then it will be determined from
+        A.dtype.char and b.  If A does not have a typecode method then it 
+        will compute A.matvec(x0) to get a typecode.   To save the extra 
+        computation when A does not have a typecode attribute use xtype=0 
+        for the same type as b or use xtype='f','d','F',or 'D'.
+        This parameter has been superceeded by LinearOperator.
+    
     """
     A_ = A
     A,M,x,b,postprocess = make_system(A,None,x0,b,xtype)

Modified: trunk/scipy/sparse/linalg/isolve/minres.py
===================================================================
--- trunk/scipy/sparse/linalg/isolve/minres.py	2008-11-11 09:03:27 UTC (rev 5059)
+++ trunk/scipy/sparse/linalg/isolve/minres.py	2008-11-12 02:17:26 UTC (rev 5060)
@@ -2,35 +2,40 @@
 from numpy.linalg import norm
 
 from utils import make_system
+from iterative import set_docstring
 
 __all__ = ['minres']
 
-def minres(A, b, x0=None, shift=0.0, tol=1e-5, maxiter=None, xtype=None,
-           M=None, callback=None, show=False, check=False):
-    """Use the Minimum Residual Method (MINRES) to solve Ax=b
+    
+header = \
+"""Use MINimum RESidual iteration to solve Ax=b
 
-    MINRES minimizes norm(A*x - b) for the symmetric matrix A.  Unlike
-    the Conjugate Gradient method, A can be indefinite or singular.
+MINRES minimizes norm(A*x - b) for the symmetric matrix A.  Unlike
+the Conjugate Gradient method, A can be indefinite or singular.
 
-    If shift != 0 then the method solves (A - shift*I)x = b
+If shift != 0 then the method solves (A - shift*I)x = b
+"""
 
+footer = \
+"""        
+Notes
+-----
+THIS FUNCTION IS EXPERIMENTAL AND SUBJECT TO CHANGE!
 
-    Parameters
-    ==========
-        TODO
+References
+----------
+Solution of sparse indefinite systems of linear equations,
+    C. C. Paige and M. A. Saunders (1975),
+    SIAM J. Numer. Anal. 12(4), pp. 617-629.
+    http://www.stanford.edu/group/SOL/software/minres.html
 
-    References
-    ==========
+This file is a translation of the following MATLAB implementation:
+    http://www.stanford.edu/group/SOL/software/minres/matlab/
+"""
 
-        Solution of sparse indefinite systems of linear equations,
-            C. C. Paige and M. A. Saunders (1975),
-            SIAM J. Numer. Anal. 12(4), pp. 617-629.
-            http://www.stanford.edu/group/SOL/software/minres.html
-
-        This file is a translation of the following MATLAB implementation:
-            http://www.stanford.edu/group/SOL/software/minres/matlab/
-
-    """
+@set_docstring(header,footer)
+def minres(A, b, x0=None, shift=0.0, tol=1e-5, maxiter=None, xtype=None,
+           M=None, callback=None, show=False, check=False):
     A,M,x,b,postprocess = make_system(A,M,x0,b,xtype)
 
     matvec = A.matvec



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