# [Scipy-svn] r4565 - branches/Interpolate1D

scipy-svn@scip... scipy-svn@scip...
Mon Jul 28 15:48:17 CDT 2008

```Author: fcady
Date: 2008-07-28 15:48:16 -0500 (Mon, 28 Jul 2008)
New Revision: 4565

branches/Interpolate1D/interpolate1d.py
Removed:
branches/Interpolate1D/interpolate1d.py
Modified:
branches/Interpolate1D/Interpolate1D.py
branches/Interpolate1D/TODO.txt
branches/Interpolate1D/example_script.py
branches/Interpolate1D/fitpack_wrapper.py
branches/Interpolate1D/interpolate_wrapper.py
branches/Interpolate1D/setup.py
Log:
trying to fix a problem with file names

Modified: branches/Interpolate1D/Interpolate1D.py
===================================================================
--- branches/Interpolate1D/Interpolate1D.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/Interpolate1D.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -268,10 +268,10 @@
elif interp_arg in ['cubic', 'Cubic', 'Quadratic', \
# specify specific kinds of splines
-            if interp_arg in ['cubic', 'Cubic']:
-                result = Spline(self._x, self._y, k=3)
result = Spline(self._x, self._y, k=2)
+            elif interp_arg in ['cubic', 'Cubic']:
+                result = Spline(self._x, self._y, k=3)
elif interp_arg in ['Quintic', 'quintic']:
result = Spline(self._x, self._y, k=4)

@@ -296,14 +296,11 @@
result.set_xy(self._x, self._y)

# user passes a function to be called
-        # FIXME : I think there is too much flexibility allowed here; it makes
-        #       there be more pathological side cases to consider.  Functions
-        #       should perhaps be reqired to be of the form f(x, y, newx, **kw)
-        elif isfunction(interp_arg) and interp.func_code.argcount >= 3:
+        # Assume function has form of f(x, y, newx, **kw)
+        # FIXME : should other function forms be allowed?
+        elif isfunction(interp_arg):
# assume x, y and newx are all passed to interp_arg
result = lambda new_x : interp_arg(self._x, self._y, new_x, **kw)
-        elif isfunction(interp_arg):
-            result = lambda new_x : interp_arg(new_x, **kw)

# default : user has passed a default value to always be returned
else:

Modified: branches/Interpolate1D/TODO.txt
===================================================================
--- branches/Interpolate1D/TODO.txt	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/TODO.txt	2008-07-28 20:48:16 UTC (rev 4565)
@@ -94,8 +94,11 @@
I believe vectorize is supposed to handle arrays of
length 0, but it's not working on my computer.

+
+**allow newx to be in non-sorted order
+    This requires rethinking the partition of newx into
+    low, high and mid

-
********* LONGER TERM ************

**update for 2D and ND

Modified: branches/Interpolate1D/example_script.py
===================================================================
--- branches/Interpolate1D/example_script.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/example_script.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -1,41 +1,97 @@
-# sample operation script
+""" sample operation script
+    Note that in the plot, quadratic, cubic and
+    quintic lines blur together.  You can comment
+    two out to see one clearly.
+"""
import numpy as np
import interpolate1d as I
import matplotlib.pyplot as P
+import interpolate_wrapper
+import fitpack_wrapper
+import time

-N = 10.0
-x = np.arange(N)
-y = np.sin(x)
+## Interpolating in-range data.  Basic operation
+if True:
+
+    N = 10.0
+    x = np.arange(N)
+    x[1] = 1.2 # make it grid non-regular
+    y = np.sin(x)
+    newx = np.arange(.05, N, .05)

+    # block interpolation
+    interp = I.Interpolate1d(x, y, 'block')
+    y_block = interp(newx)

-## Interpolating in-range data
-newx = np.arange(.05, N, .05)
+    # linear interpolation
+    interp = I.Interpolate1d(x, y, 'linear')
+    y_linear = interp(newx)

-# block interpolation
-interp = I.Interpolate1d(x, y, 'block')
-y_block = interp(newx)
+    # 2nd order spline
+    interp = I.Interpolate1d(x, y, 'quad')

-# linear interpolation
-interp = I.Interpolate1d(x, y, 'linear')
-y_linear = interp(newx)
+    # 3rd order spline
+    interp = I.Interpolate1d(x, y, 'cubic')
+    y_cubic = interp(newx)
+
+    # 4th order spline
+    interp = I.Interpolate1d(x, y, 'quintic')
+    y_quintic = interp(newx)

-# 2nd order spline
+    # plot result
+    print "plotting results"
+    P.hold(True)
+    P.plot(newx, y_block, 'g')
+    P.plot(newx, y_linear, 'b')
+    P.plot(newx, y_cubic, 'm')
+    P.plot(newx, y_quintic, 'y')
+    P.title( "interpolating in-range data with Interpolate1d class" )
+    P.show()
+    print "plotted results"
+
+    time.sleep(3)

-# 3rd order spline
-interp = I.Interpolate1d(x, y, 'cubic')
-y_cubic = interp(newx)
+## demoing some of the other interfac features
+if True:
+    N = 10.0
+    x = np.arange(N)
+    x[1] = 1.2 # make it grid non-regular
+    y = np.sin(x)
+    newx = np.arange(.05, N, .05)

+    # block interpolation with interp1d class
+    y_block2 = I.interp1d(x, y, newx, 'block')

-# plot result
-print "plotting results"
-P.hold(True)
-P.plot(newx, y_block)
-P.plot(newx, y_linear)
-P.plot(newx, y_cubic)
-P.show()
-print "plotted results"
+    # linear interpolation with a function passed in
+    interp = I.Interpolate1d(x, y, interpolate_wrapper.linear)
+    y_linear2 = interp(newx)

+    # 2nd order spline, with partially-instantiated class
+    interp = I.Interpolate1d(x, y, fitpack_wrapper.Spline(k=2))
+
+    # 3rd order spline with additional keyword arguments
+    interp = I.Interpolate1d(x, y, fitpack_wrapper.Spline, kindkw = {'k':3})
+    y_cubic2 = interp(newx)
+
+    # 4th order spline
+    interp = I.Interpolate1d(x, y, 'quintic')
+    y_quintic2 = interp(newx)
+
+    # plot result
+    print "plotting results"
+    P.hold(True)
+    P.plot(newx, y_block2, 'g')
+    P.plot(newx, y_linear2, 'b')
+    P.plot(newx, y_cubic2, 'm')
+    P.plot(newx, y_quintic2, 'y')
+    P.title( "same data through different interface" )
+    P.show()
+    print "plotted results"
+
+    #time.sleep(20)
+

Modified: branches/Interpolate1D/fitpack_wrapper.py
===================================================================
--- branches/Interpolate1D/fitpack_wrapper.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/fitpack_wrapper.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -1,8 +1,7 @@
"""
This module is used for spline interpolation, and functions
as a wrapper around the FITPACK Fortran interpolation
-package.  It is not intended to be directly accessed by
-the user, but rather through the class Interpolate1d.
+package.

The code has been modified from an older version of
scipy.interpolate, where it was directly called by the
@@ -11,10 +10,15 @@
under the hood.

"""
+# FIXME : clean up this file!  scipy.interpolate contained a lot of
+#       nice functionality that is only partially in this file.
+#       The question is whether to copy over the full functionality
+#       to the point where we may as well include fitting.py form
+#       scipy.interpolate, or whether we should strip is down some.

import numpy as np

-import dfitpack # extension module containing FITPACK subroutines
+import dfitpack # extension module containing FITPACK subroutines in Fortran

class Spline(object):

Deleted: branches/Interpolate1D/interpolate1d.py
===================================================================
--- branches/Interpolate1D/interpolate1d.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/interpolate1d.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -1,487 +0,0 @@
-"""
-    Interpolation of 1D data
-
-    This module provides several functions and classes for interpolation
-    and extrapolation of 1D data (1D in both input and output).  The
-    primary function provided is:
-
-        interp1d(x, y, new_x) : from data points x and y, interpolates
-                                        values for points in new_x and
-                                        returns them as an array.
-
-    Classes provided include:
-
-        Interpolate1d  :   an object for interpolation of
-                                various kinds.  interp1d is a wrapper
-                                around this class.
-
-        Spline : an object for spline interpolation
-
-    Functions provided include:
-
-        linear : linear interpolation
-        logarithmic :  logarithmic interpolation
-        block : block interpolation
-        block_average_above : block average above interpolation
-
-"""
-
-# FIXME: information strings giving mathematical descriptions of the actions
-#     of the functions.
-
-from interpolate_wrapper import linear, logarithmic, block, block_average_above
-from fitpack_wrapper import Spline
-import numpy as np
-from numpy import array, arange, empty, float64, NaN
-
-def make_array_safe(ary, typecode=np.float64):
-    """Used to make sure that inputs and outputs are
-    properly formatted.
-    """
-    ary = np.atleast_1d(np.asarray(ary, typecode))
-    if not ary.flags['CONTIGUOUS']:
-        ary = ary.copy()
-    return ary
-
-def interp1d(x, y, new_x, kind='linear', low=np.NaN, high=np.NaN, \
-                    kindkw={}, lowkw={}, highkw={}, \
-    """ A function for interpolation of 1D data.
-
-        Parameters
-        -----------
-
-        x -- list or NumPy array
-            x includes the x-values for the data set to
-            interpolate from.  It must be sorted in
-            ascending order
-
-        y -- list or NumPy array
-            y includes the y-values for the data set  to
-            interpolate from.  Note that y must be
-            one-dimensional.
-
-        new_x -- list or NumPy array
-            points whose value is to be interpolated from x and y.
-            new_x must be in sorted order, lowest to highest.
-
-        Optional Arguments
-        -------------------
-
-        kind -- Usu. function or string.  But can be any type.
-            Specifies the type of extrapolation to use for values within
-            the range of x.  If a string is passed, it will look for an object
-            or function with that name and call it when evaluating.  If
-            a function or object is passed, it will be called when interpolating.
-            If nothing else, assumes the argument is intended as a value
-            to be returned for all arguments.  Defaults to linear interpolation.
-
-        kindkw -- dictionary
-            If kind is a class, function or string, additional keyword arguments
-            may be needed (example: if you want a 2nd order spline, kind = 'spline'
-            and kindkw = {'k' : 2}.
-
-        low (high) -- same as for kind
-            Same options as for 'kind'.  Defaults to returning numpy.NaN ('not
-            a number') for all values outside the range of x.
-
-            indicates whether to remove bad data.
-
-            List of values (in x or y) which indicate unacceptable data. All points
-            that have x or y value in missing_data will be removed before
-            any interpolatin is performed if remove_bad_data is true.
-
-            numpy.NaN is always considered bad data.
-
-        Acceptable Input Strings
-        ------------------------
-
-            "linear" -- linear interpolation : default
-            "logarithmic" -- logarithmic interpolation : linear in log space?
-            "block" --
-            "block_average_above' -- block average above
-            "Spline" -- spline interpolation.  keyword k (defaults to 3)
-                indicates order of spline
-            numpy.NaN -- return numpy.NaN
-
-        Examples
-        ---------
-
-            >>> import numpy
-            >>> from Interpolate1D import interp1d
-            >>> x = range(5)        # note list is permitted
-            >>> y = numpy.arange(5.)
-            >>> new_x = [.2, 2.3, 5.6]
-            >>> interp1d(x, y, new_x)
-            array([.2, 2.3, 5.6, NaN])
-    """
-    return Interpolate1d(x, y, kind=kind, low=low, high=high, \
-                                    kindkw=kindkw, lowkw=lowkw, highkw=highkw, \
-
-class Interpolate1d(object):
-    """ A class for interpolation of 1D data.
-
-        Parameters
-        -----------
-
-        x -- list or NumPy array
-            x includes the x-values for the data set to
-            interpolate from.  It must be sorted in
-            ascending order.
-
-        y -- list or NumPy array
-            y includes the y-values for the data set  to
-            interpolate from.  Note that y must be
-            one-dimensional.
-
-        Optional Arguments
-        -------------------
-
-        kind -- Usu. function or string.  But can be any type.
-            Specifies the type of extrapolation to use for values within
-            the range of x.  If a string is passed, it will look for an object
-            or function with that name and call it when evaluating.  If
-            a function or object is passed, it will be called when interpolating.
-            A constant signifies a function which returns that constant
-            (e.g. val and lambda x : val are equivalent).  Defaults to linear
-            interpolation.
-
-        kindkw -- dictionary
-            If kind is a class, function or string, additional keyword arguments
-            may be needed (example: if you want a 2nd order spline, kind = 'spline'
-            and kindkw = {'k' : 2}.
-
-        low (high) -- same as for kind
-            Same options as for 'kind'.  Defaults to returning numpy.NaN ('not
-            a number') for all values outside the range of x.
-
-            indicates whether to remove bad data points from x and y.
-
-            List of values (in x or y) which indicate unacceptable data. All points
-            that have x or y value in missing_data will be removed before
-            any interpolatin is performed if remove_bad_data is true.
-
-            numpy.NaN is always considered bad data.
-
-        Some Acceptable Input Strings
-        ------------------------
-
-            "linear" -- linear interpolation : default
-            "logarithmic" -- logarithmic interpolation : linear in log space?
-            "block" --
-            "block_average_above' -- block average above
-            "Spline" -- spline interpolation.  keyword k (defaults to 3)
-                indicates order of spline
-            numpy.NaN -- return numpy.NaN
-
-        Examples
-        ---------
-
-            >>> import numpy
-            >>> from Interpolate1D import interp1d
-            >>> x = range(5)        # note list is permitted
-            >>> y = numpy.arange(5.)
-            >>> new_x = [.2, 2.3, 5.6]
-            >>> interp1d(x, y, new_x)
-            array([.2, 2.3, 5.6, NaN])
-    """
-    # FIXME: examples in doc string
-    # FIXME : Allow copying or not of arrays.  non-copy + remove_bad_data should flash
-    #           a warning (esp if we interpolate missing values), but work anyway.
-
-    def __init__(self, x, y, kind='linear', low=np.NaN, high=np.NaN, \
-                        kindkw={}, lowkw={}, highkw={}, \
-        # FIXME: don't allow copying multiple times.
-        # FIXME : allow no copying, in case user has huge dataset
-
-        # check acceptable size and dimensions
-        x = np.array(x)
-        y = np.array(y)
-        assert len(x) > 0 and len(y) > 0 , "Arrays cannot be of zero length"
-        assert x.ndim == 1 , "x must be one-dimensional"
-        assert y.ndim == 1 , "y must be one-dimensional"
-        assert len(x) == len(y) , "x and y must be of the same length"
-
-        # remove bad data, is there is any
-
-        # store data
-        # FIXME : may be good to let x and y be initialized later, or changed after-the-fact
-        self._init_xy(x, y)
-
-        # store interpolation functions for each range
-        self.kind = self._init_interp_method(kind, kindkw)
-        self.low = self._init_interp_method(low, lowkw)
-        self.high = self._init_interp_method(high, highkw)
-
-        """ removes data points whose x or y coordinate is
-            either in bad_data or is a NaN.
-        """
-        # FIXME : In the future, it may be good to just replace the bad points with good guesses.
-        #       Especially in generalizing the higher dimensions
-        # FIXME : This step is very inefficient because it iterates over the array
-        mask = np.array([  (xi not in bad_data) and (not np.isnan(xi)) and \
-                                    (y[i] not in bad_data) and (not np.isnan(y[i])) \
-                                for i, xi in enumerate(x) ])
-        return x, y
-
-    def _init_xy(self, x, y):
-        # select proper dataypes and make arrays
-        self._xdtype = {np.float32 : np.float32}.setdefault(type(x[0]), np.float64) # unless data is float32,  cast to float64
-        self._ydtype = {np.float32 : np.float32}.setdefault(type(y[0]), np.float64)
-        self._x = make_array_safe(x, self._xdtype).copy()
-        self._y = make_array_safe(y, self._ydtype).copy()
-
-    def _init_interp_method(self, interp_arg, kw):
-        """
-            User provides interp_arg and dictionary kw.  _init_interp_method
-            returns the interpolating function from x and y specified by interp_arg,
-            possibly with extra keyword arguments given in kw.
-
-        """
-        # FIXME : error checking specific to interpolation method.  x and y long
-        #   enough for order-3 spline if that's indicated, etc.  Functions should throw
-        #   errors themselves, but errors at instantiation would be nice.
-
-        from inspect import isclass, isfunction
-
-        # primary usage : user passes a string indicating a known function
-        if interp_arg in ['linear', 'logarithmic', 'block', 'block_average_above']:
-            # string used to indicate interpolation method,  Select appropriate function
-            func = {'linear':linear, 'logarithmic':logarithmic, 'block':block, \
-                        'block_average_above':block_average_above}[interp_arg]
-            result = lambda new_x : func(self._x, self._y, new_x, **kw)
-        elif interp_arg in ['Spline', Spline, 'spline']:
-            # use the Spline class from fitpack_wrapper
-            result = Spline(self._x, self._y, **kw)
-        elif interp_arg in ['cubic', 'Cubic', 'Quadratic', \
-            # specify specific kinds of splines
-            if interp_arg in ['cubic', 'Cubic']:
-                result = Spline(self._x, self._y, k=3)
-                result = Spline(self._x, self._y, k=2)
-            elif interp_arg in ['Quintic', 'quintic']:
-                result = Spline(self._x, self._y, k=4)
-
-        # secondary usage : user passes a callable class
-        elif isclass(interp_arg) and hasattr(interp_arg, '__call__'):
-            if hasattr(interp_arg, 'init_xy'):
-                result = interp_arg(**kw)
-                result.init_xy(self._x, self._y)
-            elif hasattr(interp_arg, 'set_xy'):
-                result = interp_arg(**kw)
-                result.set_xy(self._x, self._y)
-            else:
-                result = interp_arg(x, y, **kw)
-
-        # user passes an instance of a callable class which has yet
-        # to have its x and y initialized.
-        elif hasattr(interp_arg, 'init_xy') and hasattr(interp_arg, '__call__'):
-            result = interp_arg
-            result.init_xy(self._x, self._y)
-        elif hasattr(interp_arg, 'set_xy') and hasattr(interp_arg, '__call__'):
-            result = interp_arg
-            result.set_xy(self._x, self._y)
-
-        # user passes a function to be called
-        # FIXME : I think there is too much flexibility allowed here; it makes
-        #       there be more pathological side cases to consider.  Functions
-        #       should perhaps be reqired to be of the form f(x, y, newx, **kw)
-        elif isfunction(interp_arg) and interp.func_code.argcount >= 3:
-            # assume x, y and newx are all passed to interp_arg
-            result = lambda new_x : interp_arg(self._x, self._y, new_x, **kw)
-        elif isfunction(interp_arg):
-            result = lambda new_x : interp_arg(new_x, **kw)
-
-        # default : user has passed a default value to always be returned
-        else:
-            result = np.vectorize(lambda new_x : interp_arg)
-
-        return result
-
-    def __call__(self, newx):
-        """
-            Input x must be in sorted order.
-            Breaks x into pieces in-range, below-range, and above range.
-            Performs appropriate operation on each and concatenates results.
-        """
-        # FIXME : make_array_safe may also be called within the interpolation technique.
-        #   waste of time, but ok for the time being.
-        newx = make_array_safe(newx)
-
-        # masks indicate which elements fall into which interpolation region
-
-        # use correct function for x values in each region
-        if len(newx[low_mask]) == 0: new_low=np.array([])  # FIXME : remove need for if/else.
-                                                                            # if/else is a hack, since vectorize is failing
-                                                                            # to work on lists/arrays of length 0
-                                                                            # on the computer where this is being
-                                                                            # developed
-        if len(newx[high_mask]) == 0: new_high = np.array([])
-
-        result = np.concatenate((new_low, new_interp, new_high)) # FIXME : deal with mixed datatypes
-                                                                                          # Would be nice to say result = zeros(dtype=?)
-                                                                                          # and fill in
-
-        return result
-
-# unit testing
-import unittest, time
-class Test(unittest.TestCase):
-
-    def assertAllclose(self, x, y):
-        self.assert_(np.allclose(make_array_safe(x), make_array_safe(y)))
-
-    def test_interpolate_wrapper(self):
-        """ run unit test contained in interpolate_wrapper.py
-        """
-        #print "\n\nTESTING _interpolate_wrapper MODULE"
-        from interpolate_wrapper import Test
-        T = Test()
-        T.runTest()
-
-    def test_fitpack_wrapper(self):
-        """ run unit test contained in fitpack_wrapper.py
-        """
-        #print "\n\nTESTING _fitpack_wrapper MODULE"
-        from fitpack_wrapper import Test
-        T = Test()
-        T.runTest()
-
-    def test_instantiationFormat(self):
-        """ make sure : all allowed instantiation formats are supported
-        """
-
-        # make sure : an instance of a callable class in which
-        #   x and y haven't been initiated works
-        N = 7 #must be > 5
-        x = np.arange(N)
-        y = np.arange(N)
-        interp_func = Interpolate1d(x, y, kind=Spline(k=2), low=Spline(k=2), high=Spline(k=2))
-        new_x = np.arange(N+1)-0.5
-        new_y = interp_func(new_x)
-        self.assertAllclose(new_x, new_y)
-
-    def test_callFormat(self):
-        """ make sure : all allowed calling formats are supported
-        """
-        # make sure : having no out-of-range elements in new_x is fine
-        # There was a bug with this earlier.
-        N = 5
-        x = arange(N)
-        y = arange(N)
-        new_x = arange(1,N-1)+.2
-        interp_func = Interpolate1d(x, y, kind='linear', low='linear', high=np.NaN)
-        new_y = interp_func(new_x)
-        self.assertAllclose(new_x, new_y)
-
-        """make sure : interp1d works with bad data
-        """
-        N = 7.0 # must be >=5
-        x = arange(N); x[2] = np.NaN
-        y = arange(N); y[4] = None; y[0]=np.NaN
-        new_x = arange(N+1)-0.5
-        new_y = interp1d(x, y, new_x, kind='linear', low='linear', high='linear', \
-        self.assertAllclose(new_x, new_y)
-
-    def test_intper1d(self):
-        """ make sure : interp1d works, at least in the linear case
-        """
-        N = 7
-        x = arange(N)
-        y = arange(N)
-        new_x = arange(N+1)-0.5
-        new_y = interp1d(x, y, new_x, kind='linear', low='linear', high='linear')
-        self.assertAllclose(new_x, new_y)
-
-    def test_spline1_defaultExt(self):
-        """ make sure : spline order 1 (linear) interpolation works correctly
-            make sure : default extrapolation works
-        """
-        #print "\n\nTESTING LINEAR (1st ORDER) SPLINE"
-        N = 7 # must be > 5
-        x = np.arange(N)
-        y = np.arange(N)
-        interp_func = Interpolate1d(x, y, kind='Spline', kindkw={'k':1}, low=None, high=599.73)
-        new_x = np.arange(N+1)-0.5
-        new_y = interp_func(new_x)
-
-        self.assertAllclose(new_y[1:5], [0.5, 1.5, 2.5, 3.5])
-        self.assert_(new_y[0] == None)
-        self.assert_(new_y[-1] == 599.73)
-
-    def test_spline2(self):
-        """ make sure : order-2 splines work on linear data
-            make sure : order-2 splines work on non-linear data
-            make sure : 'cubic' and 'quad' as arguments yield
-                                the desired spline
-        """
-        #print "\n\nTESTING 2nd ORDER SPLINE"
-        N = 7 #must be > 5
-        x = np.arange(N)
-        y = np.arange(N)
-        T1 = time.clock()
-        interp_func = Interpolate1d(x, y, kind='Spline', kindkw={'k':2}, low='spline', high='spline')
-        T2 = time.clock()
-        print "time to create 2nd order spline interp function with N = %i: " % N, T2 - T1
-        new_x = np.arange(N+1)-0.5
-        t1 = time.clock()
-        new_y = interp_func(new_x)
-        t2 = time.clock()
-        print "time to evaluate 2nd order spline interp function with N = %i: " % N, t2 - t1
-        self.assertAllclose(new_x, new_y)
-
-        # make sure for non-linear data
-        N = 7
-        x = np.arange(N)
-        y = x**2
-        interp_func = Interpolate1d(x, y, kind='Spline', kindkw={'k':2}, low='quad', high='cubic')
-        new_x = np.arange(N+1)-0.5
-        new_y = interp_func(new_x)
-        self.assertAllclose(new_x**2, new_y)
-
-
-    def test_linear(self):
-        """ make sure : linear interpolation works
-            make sure : linear extrapolation works
-        """
-        #print "\n\nTESTING LINEAR INTERPOLATION"
-        N = 7
-        x = arange(N)
-        y = arange(N)
-        new_x = arange(N+1)-0.5
-        T1 = time.clock()
-        interp_func = Interpolate1d(x, y, kind='linear', low='linear', high='linear')
-        T2 = time.clock()
-        print "time to create linear interp function with N = %i: " % N, T2 - T1
-        t1 = time.clock()
-        new_y = interp_func(new_x)
-        t2 = time.clock()
-        print "time to create linear interp function with N = %i: " % N, t2 - t1
-
-        self.assertAllclose(new_x, new_y)
-
-
-if __name__ == '__main__':
-    unittest.main()
\ No newline at end of file

===================================================================
--- branches/Interpolate1D/interpolate1d.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/interpolate1d.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -0,0 +1,484 @@
+"""
+    Interpolation of 1D data
+
+    This module provides several functions and classes for interpolation
+    and extrapolation of 1D data (1D in both input and output).  The
+    primary function provided is:
+
+        interp1d(x, y, new_x) : from data points x and y, interpolates
+                                        values for points in new_x and
+                                        returns them as an array.
+
+    Classes provided include:
+
+        Interpolate1d  :   an object for interpolation of
+                                various kinds.  interp1d is a wrapper
+                                around this class.
+
+        Spline : an object for spline interpolation
+
+    Functions provided include:
+
+        linear : linear interpolation
+        logarithmic :  logarithmic interpolation
+        block : block interpolation
+        block_average_above : block average above interpolation
+
+"""
+
+# FIXME: information strings giving mathematical descriptions of the actions
+#     of the functions.
+
+from interpolate_wrapper import linear, logarithmic, block, block_average_above
+from fitpack_wrapper import Spline
+import numpy as np
+from numpy import array, arange, empty, float64, NaN
+
+def make_array_safe(ary, typecode=np.float64):
+    """Used to make sure that inputs and outputs are
+    properly formatted.
+    """
+    ary = np.atleast_1d(np.asarray(ary, typecode))
+    if not ary.flags['CONTIGUOUS']:
+        ary = ary.copy()
+    return ary
+
+def interp1d(x, y, new_x, kind='linear', low=np.NaN, high=np.NaN, \
+                    kindkw={}, lowkw={}, highkw={}, \
+    """ A function for interpolation of 1D data.
+
+        Parameters
+        -----------
+
+        x -- list or NumPy array
+            x includes the x-values for the data set to
+            interpolate from.  It must be sorted in
+            ascending order
+
+        y -- list or NumPy array
+            y includes the y-values for the data set  to
+            interpolate from.  Note that y must be
+            one-dimensional.
+
+        new_x -- list or NumPy array
+            points whose value is to be interpolated from x and y.
+            new_x must be in sorted order, lowest to highest.
+
+        Optional Arguments
+        -------------------
+
+        kind -- Usu. function or string.  But can be any type.
+            Specifies the type of extrapolation to use for values within
+            the range of x.  If a string is passed, it will look for an object
+            or function with that name and call it when evaluating.  If
+            a function or object is passed, it will be called when interpolating.
+            If nothing else, assumes the argument is intended as a value
+            to be returned for all arguments.  Defaults to linear interpolation.
+
+        kindkw -- dictionary
+            If kind is a class, function or string, additional keyword arguments
+            may be needed (example: if you want a 2nd order spline, kind = 'spline'
+            and kindkw = {'k' : 2}.
+
+        low (high) -- same as for kind
+            Same options as for 'kind'.  Defaults to returning numpy.NaN ('not
+            a number') for all values outside the range of x.
+
+            indicates whether to remove bad data.
+
+            List of values (in x or y) which indicate unacceptable data. All points
+            that have x or y value in missing_data will be removed before
+            any interpolatin is performed if remove_bad_data is true.
+
+            numpy.NaN is always considered bad data.
+
+        Acceptable Input Strings
+        ------------------------
+
+            "linear" -- linear interpolation : default
+            "logarithmic" -- logarithmic interpolation : linear in log space?
+            "block" --
+            "block_average_above' -- block average above
+            "Spline" -- spline interpolation.  keyword k (defaults to 3)
+                indicates order of spline
+            numpy.NaN -- return numpy.NaN
+
+        Examples
+        ---------
+
+            >>> import numpy
+            >>> from Interpolate1D import interp1d
+            >>> x = range(5)        # note list is permitted
+            >>> y = numpy.arange(5.)
+            >>> new_x = [.2, 2.3, 5.6]
+            >>> interp1d(x, y, new_x)
+            array([.2, 2.3, 5.6, NaN])
+    """
+    return Interpolate1d(x, y, kind=kind, low=low, high=high, \
+                                    kindkw=kindkw, lowkw=lowkw, highkw=highkw, \
+
+class Interpolate1d(object):
+    """ A class for interpolation of 1D data.
+
+        Parameters
+        -----------
+
+        x -- list or NumPy array
+            x includes the x-values for the data set to
+            interpolate from.  It must be sorted in
+            ascending order.
+
+        y -- list or NumPy array
+            y includes the y-values for the data set  to
+            interpolate from.  Note that y must be
+            one-dimensional.
+
+        Optional Arguments
+        -------------------
+
+        kind -- Usu. function or string.  But can be any type.
+            Specifies the type of extrapolation to use for values within
+            the range of x.  If a string is passed, it will look for an object
+            or function with that name and call it when evaluating.  If
+            a function or object is passed, it will be called when interpolating.
+            A constant signifies a function which returns that constant
+            (e.g. val and lambda x : val are equivalent).  Defaults to linear
+            interpolation.
+
+        kindkw -- dictionary
+            If kind is a class, function or string, additional keyword arguments
+            may be needed (example: if you want a 2nd order spline, kind = 'spline'
+            and kindkw = {'k' : 2}.
+
+        low (high) -- same as for kind
+            Same options as for 'kind'.  Defaults to returning numpy.NaN ('not
+            a number') for all values outside the range of x.
+
+            indicates whether to remove bad data points from x and y.
+
+            List of values (in x or y) which indicate unacceptable data. All points
+            that have x or y value in missing_data will be removed before
+            any interpolatin is performed if remove_bad_data is true.
+
+            numpy.NaN is always considered bad data.
+
+        Some Acceptable Input Strings
+        ------------------------
+
+            "linear" -- linear interpolation : default
+            "logarithmic" -- logarithmic interpolation : linear in log space?
+            "block" --
+            "block_average_above' -- block average above
+            "Spline" -- spline interpolation.  keyword k (defaults to 3)
+                indicates order of spline
+            numpy.NaN -- return numpy.NaN
+
+        Examples
+        ---------
+
+            >>> import numpy
+            >>> from Interpolate1D import interp1d
+            >>> x = range(5)        # note list is permitted
+            >>> y = numpy.arange(5.)
+            >>> new_x = [.2, 2.3, 5.6]
+            >>> interp1d(x, y, new_x)
+            array([.2, 2.3, 5.6, NaN])
+    """
+    # FIXME: examples in doc string
+    # FIXME : Allow copying or not of arrays.  non-copy + remove_bad_data should flash
+    #           a warning (esp if we interpolate missing values), but work anyway.
+
+    def __init__(self, x, y, kind='linear', low=np.NaN, high=np.NaN, \
+                        kindkw={}, lowkw={}, highkw={}, \
+        # FIXME: don't allow copying multiple times.
+        # FIXME : allow no copying, in case user has huge dataset
+
+        # check acceptable size and dimensions
+        x = np.array(x)
+        y = np.array(y)
+        assert len(x) > 0 and len(y) > 0 , "Arrays cannot be of zero length"
+        assert x.ndim == 1 , "x must be one-dimensional"
+        assert y.ndim == 1 , "y must be one-dimensional"
+        assert len(x) == len(y) , "x and y must be of the same length"
+
+        # remove bad data, is there is any
+
+        # store data
+        # FIXME : may be good to let x and y be initialized later, or changed after-the-fact
+        self._init_xy(x, y)
+
+        # store interpolation functions for each range
+        self.kind = self._init_interp_method(kind, kindkw)
+        self.low = self._init_interp_method(low, lowkw)
+        self.high = self._init_interp_method(high, highkw)
+
+        """ removes data points whose x or y coordinate is
+            either in bad_data or is a NaN.
+        """
+        # FIXME : In the future, it may be good to just replace the bad points with good guesses.
+        #       Especially in generalizing the higher dimensions
+        # FIXME : This step is very inefficient because it iterates over the array
+        mask = np.array([  (xi not in bad_data) and (not np.isnan(xi)) and \
+                                    (y[i] not in bad_data) and (not np.isnan(y[i])) \
+                                for i, xi in enumerate(x) ])
+        return x, y
+
+    def _init_xy(self, x, y):
+        # select proper dataypes and make arrays
+        self._xdtype = {np.float32 : np.float32}.setdefault(type(x[0]), np.float64) # unless data is float32,  cast to float64
+        self._ydtype = {np.float32 : np.float32}.setdefault(type(y[0]), np.float64)
+        self._x = make_array_safe(x, self._xdtype).copy()
+        self._y = make_array_safe(y, self._ydtype).copy()
+
+    def _init_interp_method(self, interp_arg, kw):
+        """
+            User provides interp_arg and dictionary kw.  _init_interp_method
+            returns the interpolating function from x and y specified by interp_arg,
+            possibly with extra keyword arguments given in kw.
+
+        """
+        # FIXME : error checking specific to interpolation method.  x and y long
+        #   enough for order-3 spline if that's indicated, etc.  Functions should throw
+        #   errors themselves, but errors at instantiation would be nice.
+
+        from inspect import isclass, isfunction
+
+        # primary usage : user passes a string indicating a known function
+        if interp_arg in ['linear', 'logarithmic', 'block', 'block_average_above']:
+            # string used to indicate interpolation method,  Select appropriate function
+            func = {'linear':linear, 'logarithmic':logarithmic, 'block':block, \
+                        'block_average_above':block_average_above}[interp_arg]
+            result = lambda new_x : func(self._x, self._y, new_x, **kw)
+        elif interp_arg in ['Spline', Spline, 'spline']:
+            # use the Spline class from fitpack_wrapper
+            result = Spline(self._x, self._y, **kw)
+        elif interp_arg in ['cubic', 'Cubic', 'Quadratic', \
+            # specify specific kinds of splines
+                result = Spline(self._x, self._y, k=2)
+            elif interp_arg in ['cubic', 'Cubic']:
+                result = Spline(self._x, self._y, k=3)
+            elif interp_arg in ['Quintic', 'quintic']:
+                result = Spline(self._x, self._y, k=4)
+
+        # secondary usage : user passes a callable class
+        elif isclass(interp_arg) and hasattr(interp_arg, '__call__'):
+            if hasattr(interp_arg, 'init_xy'):
+                result = interp_arg(**kw)
+                result.init_xy(self._x, self._y)
+            elif hasattr(interp_arg, 'set_xy'):
+                result = interp_arg(**kw)
+                result.set_xy(self._x, self._y)
+            else:
+                result = interp_arg(x, y, **kw)
+
+        # user passes an instance of a callable class which has yet
+        # to have its x and y initialized.
+        elif hasattr(interp_arg, 'init_xy') and hasattr(interp_arg, '__call__'):
+            result = interp_arg
+            result.init_xy(self._x, self._y)
+        elif hasattr(interp_arg, 'set_xy') and hasattr(interp_arg, '__call__'):
+            result = interp_arg
+            result.set_xy(self._x, self._y)
+
+        # user passes a function to be called
+        # Assume function has form of f(x, y, newx, **kw)
+        # FIXME : should other function forms be allowed?
+        elif isfunction(interp_arg):
+            # assume x, y and newx are all passed to interp_arg
+            result = lambda new_x : interp_arg(self._x, self._y, new_x, **kw)
+
+        # default : user has passed a default value to always be returned
+        else:
+            result = np.vectorize(lambda new_x : interp_arg)
+
+        return result
+
+    def __call__(self, newx):
+        """
+            Input x must be in sorted order.
+            Breaks x into pieces in-range, below-range, and above range.
+            Performs appropriate operation on each and concatenates results.
+        """
+        # FIXME : make_array_safe may also be called within the interpolation technique.
+        #   waste of time, but ok for the time being.
+        newx = make_array_safe(newx)
+
+        # masks indicate which elements fall into which interpolation region
+
+        # use correct function for x values in each region
+        if len(newx[low_mask]) == 0: new_low=np.array([])  # FIXME : remove need for if/else.
+                                                                            # if/else is a hack, since vectorize is failing
+                                                                            # to work on lists/arrays of length 0
+                                                                            # on the computer where this is being
+                                                                            # developed
+        if len(newx[high_mask]) == 0: new_high = np.array([])
+
+        result = np.concatenate((new_low, new_interp, new_high)) # FIXME : deal with mixed datatypes
+                                                                                          # Would be nice to say result = zeros(dtype=?)
+                                                                                          # and fill in
+
+        return result
+
+# unit testing
+import unittest, time
+class Test(unittest.TestCase):
+
+    def assertAllclose(self, x, y):
+        self.assert_(np.allclose(make_array_safe(x), make_array_safe(y)))
+
+    def test_interpolate_wrapper(self):
+        """ run unit test contained in interpolate_wrapper.py
+        """
+        #print "\n\nTESTING _interpolate_wrapper MODULE"
+        from interpolate_wrapper import Test
+        T = Test()
+        T.runTest()
+
+    def test_fitpack_wrapper(self):
+        """ run unit test contained in fitpack_wrapper.py
+        """
+        #print "\n\nTESTING _fitpack_wrapper MODULE"
+        from fitpack_wrapper import Test
+        T = Test()
+        T.runTest()
+
+    def test_instantiationFormat(self):
+        """ make sure : all allowed instantiation formats are supported
+        """
+
+        # make sure : an instance of a callable class in which
+        #   x and y haven't been initiated works
+        N = 7 #must be > 5
+        x = np.arange(N)
+        y = np.arange(N)
+        interp_func = Interpolate1d(x, y, kind=Spline(k=2), low=Spline(k=2), high=Spline(k=2))
+        new_x = np.arange(N+1)-0.5
+        new_y = interp_func(new_x)
+        self.assertAllclose(new_x, new_y)
+
+    def test_callFormat(self):
+        """ make sure : all allowed calling formats are supported
+        """
+        # make sure : having no out-of-range elements in new_x is fine
+        # There was a bug with this earlier.
+        N = 5
+        x = arange(N)
+        y = arange(N)
+        new_x = arange(1,N-1)+.2
+        interp_func = Interpolate1d(x, y, kind='linear', low='linear', high=np.NaN)
+        new_y = interp_func(new_x)
+        self.assertAllclose(new_x, new_y)
+
+        """make sure : interp1d works with bad data
+        """
+        N = 7.0 # must be >=5
+        x = arange(N); x[2] = np.NaN
+        y = arange(N); y[4] = None; y[0]=np.NaN
+        new_x = arange(N+1)-0.5
+        new_y = interp1d(x, y, new_x, kind='linear', low='linear', high='linear', \
+        self.assertAllclose(new_x, new_y)
+
+    def test_intper1d(self):
+        """ make sure : interp1d works, at least in the linear case
+        """
+        N = 7
+        x = arange(N)
+        y = arange(N)
+        new_x = arange(N+1)-0.5
+        new_y = interp1d(x, y, new_x, kind='linear', low='linear', high='linear')
+        self.assertAllclose(new_x, new_y)
+
+    def test_spline1_defaultExt(self):
+        """ make sure : spline order 1 (linear) interpolation works correctly
+            make sure : default extrapolation works
+        """
+        #print "\n\nTESTING LINEAR (1st ORDER) SPLINE"
+        N = 7 # must be > 5
+        x = np.arange(N)
+        y = np.arange(N)
+        interp_func = Interpolate1d(x, y, kind='Spline', kindkw={'k':1}, low=None, high=599.73)
+        new_x = np.arange(N+1)-0.5
+        new_y = interp_func(new_x)
+
+        self.assertAllclose(new_y[1:5], [0.5, 1.5, 2.5, 3.5])
+        self.assert_(new_y[0] == None)
+        self.assert_(new_y[-1] == 599.73)
+
+    def test_spline2(self):
+        """ make sure : order-2 splines work on linear data
+            make sure : order-2 splines work on non-linear data
+            make sure : 'cubic' and 'quad' as arguments yield
+                                the desired spline
+        """
+        #print "\n\nTESTING 2nd ORDER SPLINE"
+        N = 7 #must be > 5
+        x = np.arange(N)
+        y = np.arange(N)
+        T1 = time.clock()
+        interp_func = Interpolate1d(x, y, kind='Spline', kindkw={'k':2}, low='spline', high='spline')
+        T2 = time.clock()
+        print "time to create 2nd order spline interp function with N = %i: " % N, T2 - T1
+        new_x = np.arange(N+1)-0.5
+        t1 = time.clock()
+        new_y = interp_func(new_x)
+        t2 = time.clock()
+        print "time to evaluate 2nd order spline interp function with N = %i: " % N, t2 - t1
+        self.assertAllclose(new_x, new_y)
+
+        # make sure for non-linear data
+        N = 7
+        x = np.arange(N)
+        y = x**2
+        interp_func = Interpolate1d(x, y, kind='Spline', kindkw={'k':2}, low='quad', high='cubic')
+        new_x = np.arange(N+1)-0.5
+        new_y = interp_func(new_x)
+        self.assertAllclose(new_x**2, new_y)
+
+
+    def test_linear(self):
+        """ make sure : linear interpolation works
+            make sure : linear extrapolation works
+        """
+        #print "\n\nTESTING LINEAR INTERPOLATION"
+        N = 7
+        x = arange(N)
+        y = arange(N)
+        new_x = arange(N+1)-0.5
+        T1 = time.clock()
+        interp_func = Interpolate1d(x, y, kind='linear', low='linear', high='linear')
+        T2 = time.clock()
+        print "time to create linear interp function with N = %i: " % N, T2 - T1
+        t1 = time.clock()
+        new_y = interp_func(new_x)
+        t2 = time.clock()
+        print "time to create linear interp function with N = %i: " % N, t2 - t1
+
+        self.assertAllclose(new_x, new_y)
+
+
+if __name__ == '__main__':
+    unittest.main()
\ No newline at end of file

Modified: branches/Interpolate1D/interpolate_wrapper.py
===================================================================
--- branches/Interpolate1D/interpolate_wrapper.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/interpolate_wrapper.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -1,9 +1,10 @@
-""" helper_funcs.py
+""" helper_funcs.py.
+    scavenged from enthought,interpolate
"""

import numpy as np
import sys
-import _interpolate
+import _interpolate # C extension.  Does all the real work.

def make_array_safe(ary, typecode = np.float64):
ary = np.atleast_1d(np.asarray(ary, typecode))
@@ -104,7 +105,10 @@
return new_y

def block(x, y, new_x):
-        """ Used when only one element is available in the log.
+        """ Essentially a step function.
+
+            For each new_x[i], finds largest j such that
+            x[j] < new_x[j], and returns y[j].
"""

# find index of values in x that preceed values in x
@@ -119,21 +123,6 @@
indices = np.atleast_1d(np.clip(indices, 0, np.Inf).astype(np.int))
new_y = np.take(y, indices, axis=-1)
return new_y
-def test_helper():
-    """ use numpy.allclose to test
-    """
-
-    print "now testing accuracy of interpolation of linear data"
-
-    x = np.arange(10.)
-    y = 2.0*x
-    c = np.array([-1.0, 2.3, 10.5])
-
-    assert np.allclose( linear(x, y, c) , [-2.0, 4.6, 21.0] ), "problem in linear"
-    assert np.allclose( logarithmic(x, y, c) , [0. , 4.51738774 , 21.47836848] ), \
-                    "problem with logarithmic"
-    assert np.allclose( block_average_above(x, y, c) , [0., 2., 4.] ), \
-                    "problem with block_average_above"

# Unit Test

Modified: branches/Interpolate1D/setup.py
===================================================================
--- branches/Interpolate1D/setup.py	2008-07-28 19:41:44 UTC (rev 4564)
+++ branches/Interpolate1D/setup.py	2008-07-28 20:48:16 UTC (rev 4565)
@@ -9,19 +9,25 @@
config = Configuration('', parent_package, top_path)

+    # C++ extension for several basic interpolation types
['_interpolate.cpp'],
include_dirs = ['.'],
depends = ['interpolate.h'])

+    # used by dfitpack extension
sources=[join('fitpack', '*.f')],
)

+    # Fortran routines (collectively "FITPACK" for spline interpolation)
sources=['fitpack.pyf'],
libraries=['fitpack'],
)
+
+    # FIXME : add documentation files