renamed directories

1 files changed, 536 insertions, 0 deletions

diff --git a/base/function_base.py b/base/function_base.py
new file mode 100644
index 000000000..369dd9f92
--- /dev/null
+++ b/base/function_base.py
@@ -0,0 +1,536 @@
+import types
+import numerix as _nx
+from numerix import ravel, nonzero, array, choose, ones, zeros, \
+     sometrue, alltrue, reshape, alter_numeric, restore_numeric, arraymap, \
+     pi, _insert, multiply, add, arctan2, maximum, minimum, any, all
+from type_check import ScalarType, isscalar, asarray
+from shape_base import squeeze, atleast_1d
+
+__all__ = ['round','logspace','linspace','fix','mod',
+           'select','trim_zeros','amax','amin', 'alen',
+           'ptp','cumsum','take', 'copy',
+           'prod','cumprod','diff','gradient','angle','unwrap','sort_complex',
+           'disp','unique','extract','insert','nansum','nanmax','nanargmax',
+           'nanargmin','nanmin','sum','vectorize','asarray_chkfinite',
+           'alter_numeric', 'restore_numeric','isaltered']
+
+def isaltered():
+    val = str(type(_nx.array([1])))
+    return 'scipy' in val
+
+round = _nx.around
+
+def asarray_chkfinite(x):
+    """Like asarray except it checks to be sure no NaNs or Infs are present.
+    """
+    x = asarray(x)
+    if not all(_nx.isfinite(x)):
+        raise ValueError, "Array must not contain infs or nans."
+    return x    
+
+# Need this to change array type for low precision values
+def sum(x,axis=0):  # could change default axis here
+    x = asarray(x)
+    if x.typecode() in ['1','s','b','w']:
+        x = x.astype('l')
+    return _nx.sum(x,axis)
+    
+
+def logspace(start,stop,num=50,endpoint=1):
+    """ Evenly spaced samples on a logarithmic scale.
+
+        Return num evenly spaced samples from 10**start to 10**stop.  If
+        endpoint=1 then last sample is 10**stop.
+    """
+    if num <= 0: return array([])
+    if endpoint:
+        step = (stop-start)/float((num-1))
+        y = _nx.arange(0,num) * step + start
+    else:
+        step = (stop-start)/float(num)
+        y = _nx.arange(0,num) * step + start
+    return _nx.power(10.0,y)
+
+def linspace(start,stop,num=50,endpoint=1,retstep=0):
+    """ Evenly spaced samples.
+    
+        Return num evenly spaced samples from start to stop.  If endpoint=1 then
+        last sample is stop. If retstep is 1 then return the step value used.
+    """
+    if num <= 0: return array([])
+    if endpoint:
+        step = (stop-start)/float((num-1))
+        y = _nx.arange(0,num) * step + start        
+    else:
+        step = (stop-start)/float(num)
+        y = _nx.arange(0,num) * step + start
+    if retstep:
+        return y, step
+    else:
+        return y
+
+def fix(x):
+    """ Round x to nearest integer towards zero.
+    """
+    x = asarray(x)
+    y = _nx.floor(x)
+    return _nx.where(x<0,y+1,y)
+
+def mod(x,y):
+    """ x - y*floor(x/y)
+    
+        For numeric arrays, x % y has the same sign as x while
+        mod(x,y) has the same sign as y.
+    """
+    return x - y*_nx.floor(x*1.0/y)
+
+def select(condlist, choicelist, default=0):
+    """ Returns an array comprised from different elements of choicelist
+        depending on the list of conditions.
+
+        condlist is a list of condition arrays containing ones or zeros
+    
+        choicelist is a list of choice matrices (of the "same" size as the
+        arrays in condlist).  The result array has the "same" size as the
+        arrays in choicelist.  If condlist is [c0,...,cN-1] then choicelist
+        must be of length N.  The elements of the choicelist can then be
+        represented as [v0,...,vN-1]. The default choice if none of the
+        conditions are met is given as the default argument. 
+    
+        The conditions are tested in order and the first one statisfied is
+        used to select the choice. In other words, the elements of the
+        output array are found from the following tree (notice the order of
+        the conditions matters):
+    
+        if c0: v0
+        elif c1: v1
+        elif c2: v2
+        ...
+        elif cN-1: vN-1
+        else: default
+    
+        Note, that one of the condition arrays must be large enough to handle
+        the largest array in the choice list.
+    """
+    n = len(condlist)
+    n2 = len(choicelist)
+    if n2 != n:
+        raise ValueError, "List of cases, must be same length as the list of conditions."
+    choicelist.insert(0,default)    
+    S = 0
+    pfac = 1
+    for k in range(1,n+1):
+        S += k * pfac * asarray(condlist[k-1])
+        if k < n:
+            pfac *= (1-asarray(condlist[k-1]))
+    # handle special case of a 1-element condition but
+    #  a multi-element choice
+    if type(S) in ScalarType or max(asarray(S).shape)==1:
+        pfac = asarray(1)
+        for k in range(n2+1):
+            pfac = pfac + asarray(choicelist[k])            
+        S = S*ones(asarray(pfac).shape)
+    return choose(S, tuple(choicelist))
+
+def _asarray1d(arr):
+    """Ensure 1d array for one array.
+    """
+    m = asarray(arr)
+    if len(m.shape)==0:
+        m = reshape(m,(1,))
+    return m
+
+def copy(a):
+    """Return an array copy of the object.
+    """
+    return array(a,copy=1)
+
+def take(a, indices, axis=0):
+    """Selects the elements in indices from array a along given axis.
+    """
+    try:
+        a = _nx.take(a,indices,axis)
+    except ValueError:  # a is scalar
+        pass
+    return a
+
+def _no_axis_is_all(function, m, axis):
+    if axis is None:
+        m = ravel(m)
+        axis = 0
+    else:
+        m = _asarray1d(m)
+    if _nx.which[0] == "numeric":
+        r = function(m, axis)
+    else:
+        import numarray as _na
+        _na.Error.pushMode(overflow="raise")
+        try:
+            r = function(m, axis)
+        finally:
+            _na.Error.popMode()
+    return r
+    
+# Basic operations
+def amax(m,axis=-1): 
+    """Returns the maximum of m along dimension axis. 
+    """
+    return _no_axis_is_all(maximum.reduce, m, axis)
+
+def amin(m,axis=-1):
+    """Returns the minimum of m along dimension axis.
+    """
+    return _no_axis_is_all(minimum.reduce, m, axis)
+
+def alen(m):
+    """Returns the length of a Python object interpreted as an array
+    """
+    return len(asarray(m))
+
+# Actually from Basis, but it fits in so naturally here...
+
+def _amin_amax(m, axis):
+    return amax(m,axis)-amin(m,axis)
+
+def ptp(m,axis=-1):
+    """Returns the maximum - minimum along the the given dimension
+    """
+    return _no_axis_is_all(_amin_amax, m, axis)
+
+def cumsum(m,axis=-1):
+    """Returns the cumulative sum of the elements along the given axis
+    """
+    return _no_axis_is_all(add.accumulate, m, axis)
+
+def prod(m,axis=-1):
+    """Returns the product of the elements along the given axis
+    """
+    return _no_axis_is_all(multiply.reduce, m, axis)
+
+def cumprod(m,axis=-1):
+    """Returns the cumulative product of the elments along the given axis
+    """
+    return _no_axis_is_all(multiply.accumulate, m, axis)
+
+def gradient(f,*varargs):
+    """Calculate the gradient of an N-dimensional scalar function.
+
+    Uses central differences on the interior and first differences on boundaries
+    to give the same shape.
+
+    Inputs:
+
+      f -- An N-dimensional array giving samples of a scalar function
+
+      varargs -- 0, 1, or N scalars giving the sample distances in each direction
+
+    Outputs:
+
+      N arrays of the same shape as f giving the derivative of f with respect
+       to each dimension.
+    """
+    N = len(f.shape)  # number of dimensions
+    n = len(varargs)
+    if n==0:
+        dx = [1.0]*N
+    elif n==1:
+        dx = [varargs[0]]*N
+    elif n==N:
+        dx = list(varargs)
+    else:
+        raise SyntaxError, "Invalid number of arguments"
+
+    # use central differences on interior and first differences on endpoints
+
+    print dx
+    outvals = []
+
+    # create slice objects --- initially all are [:,:,...,:]
+    slice1 = [slice(None)]*N
+    slice2 = [slice(None)]*N
+    slice3 = [slice(None)]*N
+
+    otype = f.typecode()
+    if otype not in ['f','d','F','D']:
+        otype = 'd'
+
+    for axis in range(N):
+        # select out appropriate parts for this dimension
+        out = zeros(f.shape, f.typecode())
+        slice1[axis] = slice(1,-1)
+        slice2[axis] = slice(2,None)
+        slice3[axis] = slice(None,-2)
+        # 1d equivalent -- out[1:-1] = (f[2:] - f[:-2])/2.0
+        out[slice1] = (f[slice2] - f[slice3])/2.0   
+        slice1[axis] = 0
+        slice2[axis] = 1
+        slice3[axis] = 0
+        # 1d equivalent -- out[0] = (f[1] - f[0])
+        out[slice1] = (f[slice2] - f[slice3])
+        slice1[axis] = -1
+        slice2[axis] = -1
+        slice3[axis] = -2
+        # 1d equivalent -- out[-1] = (f[-1] - f[-2])
+        out[slice1] = (f[slice2] - f[slice3])
+        
+        # divide by step size
+        outvals.append(out / dx[axis])
+        
+        # reset the slice object in this dimension to ":"
+        slice1[axis] = slice(None)
+        slice2[axis] = slice(None)
+        slice3[axis] = slice(None)
+
+    if N == 1:
+        return outvals[0]
+    else:
+        return outvals
+    
+
+def diff(x, n=1,axis=-1):
+    """Calculates the nth order, discrete difference along given axis.
+    """
+    if n==0:
+        return x
+    if n<0:
+        raise ValueError,'Order must be non-negative but got ' + `n`
+    x = _asarray1d(x)
+    nd = len(x.shape)
+    slice1 = [slice(None)]*nd
+    slice2 = [slice(None)]*nd
+    slice1[axis] = slice(1,None)
+    slice2[axis] = slice(None,-1)
+    if n > 1:
+        return diff(x[slice1]-x[slice2], n-1, axis=axis)
+    else:
+        return x[slice1]-x[slice2]
+    
+def angle(z,deg=0):
+    """Return the angle of complex argument z."""
+    if deg:
+        fact = 180/pi
+    else:
+        fact = 1.0
+    z = asarray(z)
+    if z.typecode() in ['D','F']:
+       zimag = z.imag
+       zreal = z.real
+    else:
+       zimag = 0
+       zreal = z
+    return arctan2(zimag,zreal) * fact
+
+def unwrap(p,discont=pi,axis=-1):
+    """unwraps radian phase p by changing absolute jumps greater than
+       discont to their 2*pi complement along the given axis.
+    """
+    p = asarray(p)
+    nd = len(p.shape)
+    dd = diff(p,axis=axis)
+    slice1 = [slice(None,None)]*nd     # full slices
+    slice1[axis] = slice(1,None)
+    ddmod = mod(dd+pi,2*pi)-pi
+    _nx.putmask(ddmod,(ddmod==-pi) & (dd > 0),pi)
+    ph_correct = ddmod - dd;
+    _nx.putmask(ph_correct,abs(dd)<discont,0)
+    up = array(p,copy=1,typecode='d')
+    up[slice1] = p[slice1] + cumsum(ph_correct,axis)
+    return up
+
+def sort_complex(a):
+    """ Doesn't currently work for integer arrays -- only float or complex.
+    """
+    a = asarray(a,typecode=a.typecode().upper())
+    def complex_cmp(x,y):
+        res = cmp(x.real,y.real)
+        if res == 0:
+            res = cmp(x.imag,y.imag)
+        return res
+    l = a.tolist()                
+    l.sort(complex_cmp)
+    return array(l)
+
+def trim_zeros(filt,trim='fb'):
+    """ Trim the leading and trailing zeros from a 1D array.
+    
+        Example:
+            >>> import scipy
+            >>> a = array((0,0,0,1,2,3,2,1,0))
+            >>> scipy.trim_zeros(a)
+            array([1, 2, 3, 2, 1])
+    """
+    first = 0
+    if 'f' in trim or 'F' in trim:
+        for i in filt:
+            if i != 0.: break
+            else: first = first + 1
+    last = len(filt)
+    if 'b' in trim or 'B' in trim:
+        for i in filt[::-1]:
+            if i != 0.: break
+            else: last = last - 1
+    return filt[first:last]
+
+def unique(inseq):
+    """Returns unique items in 1-dimensional sequence.
+    """
+    set = {}
+    for item in inseq:
+        set[item] = None
+    return asarray(set.keys())
+
+def where(condition,x=None,y=None):
+    """If x and y are both None, then return the (1-d equivalent) indices
+    where condition is true.  Otherwise, return an array shaped like
+    condition with elements of x and y in the places where condition is
+    true or false respectively.
+    """
+    if (x is None) and (y is None):
+             # Needs work for multidimensional arrays
+        return nonzero(ravel(condition))
+    else:
+        return choose(not_equal(condition, 0), (y,x))
+    
+def extract(condition, arr):
+    """Elements of ravel(condition) where ravel(condition) is true (1-d)
+
+    Equivalent of compress(ravel(condition), ravel(arr))
+    """
+    return _nx.take(ravel(arr), nonzero(ravel(condition)))
+
+def insert(arr, mask, vals):
+    """Similar to putmask arr[mask] = vals but 1d array vals has the
+    same number of elements as the non-zero values of mask. Inverse of extract.
+    """
+    return _nx._insert(arr, mask, vals)
+
+def nansum(x,axis=-1):
+    """Sum the array over the given axis treating nans as missing values.
+    """
+    x = _asarray1d(x).copy()
+    _nx.putmask(x,isnan(x),0)
+    return _nx.sum(x,axis)
+
+def nanmin(x,axis=-1):
+    """Find the minimium over the given axis ignoring nans.
+    """
+    x = _asarray1d(x).copy()
+    _nx.putmask(x,isnan(x),inf)
+    return amin(x,axis)
+
+def nanargmin(x,axis=-1):
+    """Find the indices of the minimium over the given axis ignoring nans.
+    """
+    x = _asarray1d(x).copy()
+    _nx.putmask(x,isnan(x),inf)
+    return argmin(x,axis)
+    
+
+def nanmax(x,axis=-1):
+    """Find the maximum over the given axis ignoring nans.
+    """
+    x = _asarray1d(x).copy()
+    _nx.putmask(x,isnan(x),-inf)
+    return amax(x,axis)
+
+def nanargmax(x,axis=-1):
+    """Find the maximum over the given axis ignoring nans.
+    """
+    x = _asarray1d(x).copy()
+    _nx.putmask(x,isnan(x),-inf)
+    return argmax(x,axis)
+
+def disp(mesg, device=None, linefeed=1):
+    """Display a message to device (default is sys.stdout) with(out) linefeed.
+    """
+    if device is None:
+        import sys
+        device = sys.stdout
+    if linefeed:
+        device.write('%s\n' % mesg)
+    else:
+        device.write('%s' % mesg)
+    device.flush()
+    return
+
+class vectorize:
+    """
+ vectorize(somefunction)  Generalized Function class.
+
+  Description:
+ 
+    Define a vectorized function which takes nested sequence
+    objects or numerix arrays as inputs and returns a
+    numerix array as output, evaluating the function over successive
+    tuples of the input arrays like the python map function except it uses
+    the broadcasting rules of numerix Python.
+
+  Input:
+
+    somefunction -- a Python function or method
+
+  Example:
+
+    def myfunc(a,b):
+        if a > b:
+            return a-b
+        else
+            return a+b
+
+    vfunc = vectorize(myfunc)
+
+    >>> vfunc([1,2,3,4],2)
+    array([3,4,1,2])
+
+    """
+    def __init__(self,pyfunc,otypes=None,doc=None):
+        if not callable(pyfunc) or type(pyfunc) is types.ClassType:
+            raise TypeError, "Object is not a callable Python object."
+        self.thefunc = pyfunc
+        if doc is None:
+            self.__doc__ = pyfunc.__doc__
+        else:
+            self.__doc__ = doc
+        if otypes is None:
+            self.otypes=''
+        else:
+            if isinstance(otypes,types.StringType):
+                self.otypes=otypes
+            else:
+                raise ValueError, "Output types must be a string."
+
+    def __call__(self,*args):
+        try:
+            return squeeze(arraymap(self.thefunc,args,self.otypes))
+        except IndexError:
+            return self.zerocall(*args)
+
+    def zerocall(self,*args):
+        # one of the args was a zeros array
+        #  return zeros for each output
+        #  first --- find number of outputs
+        #  get it from self.otypes if possible
+        #  otherwise evaluate function at 0.9
+        N = len(self.otypes)
+        if N==1:
+            return zeros((0,),'d')
+        elif N !=0:
+            return (zeros((0,),'d'),)*N
+        newargs = []
+        args = atleast_1d(args)
+        for arg in args:
+            if arg.typecode() != 'O':
+                newargs.append(0.9)
+            else:
+                newargs.append(arg[0])
+        newargs = tuple(newargs)
+        try:
+            res = self.thefunc(*newargs)
+        except:
+            raise ValueError, "Zerocall is failing.  "\
+                  "Try using otypes in vectorize."
+        if isscalar(res):
+            return zeros((0,),'d')
+        else:
+            return (zeros((0,),'d'),)*len(res)
+