tags 478463 + patch thanks Please find attached a preliminary patch to fix this bug. More testing is needed to ensure that I have used the correct numpy functions.
Thanks. Kumar -- Kumar Appaiah
diff -u sixpack-0.66/lsqfitter.py sixpack-0.66/lsqfitter.py
--- sixpack-0.66/lsqfitter.py
+++ sixpack-0.66/lsqfitter.py
@@ -3,7 +3,7 @@
from spdirvars import *
from spglobalfuncs import *
import spplotter
-from Numeric import *
+from numpy import *
from Tkinter import *
from Ifeffit import *
import Pmw
diff -u sixpack-0.66/spsamview.py sixpack-0.66/spsamview.py
--- sixpack-0.66/spsamview.py
+++ sixpack-0.66/spsamview.py
@@ -3,7 +3,7 @@
import xasinput
from spdirvars import *
from spglobalfuncs import *
-from Numeric import *
+from numpy import *
from Tkinter import *
import Pmw
import Tix
@@ -13,7 +13,6 @@
import os
import math
from string import *
-import MLab
from Scientific.Functions.LeastSquares import leastSquaresFit
#root=Tix.Tk()
@@ -714,8 +713,8 @@
def getderiv(self,x,y):
#returns deriv in ans(x,y)
ans=[]
- difx=MLab.diff(x,n=1)
- dify=MLab.diff(y,n=1)
+ difx=diff(x,n=1)
+ dify=diff(y,n=1)
ans.append(self.dxdata(x))
ans.append(dify/difx)
return ans
diff -u sixpack-0.66/debian/control sixpack-0.66/debian/control
--- sixpack-0.66/debian/control
+++ sixpack-0.66/debian/control
@@ -11,7 +11,7 @@
Package: sixpack
Architecture: all
Depends: ${misc:Depends}, ${python:Depends}, ifeffit, python-tk, python-pmw,
- tix, python-ifeffit, python-numeric, blt, python-scientific
+ tix, python-ifeffit, python-numpy, blt, python-scientific
XB-Python-Version: ${python:Versions}
Provides: ${python:Provides}
Description: full-featured package for XAS analysis
only in patch2:
unchanged:
--- sixpack-0.66.orig/func.py
+++ sixpack-0.66/func.py
@@ -1,11 +1,11 @@
-import Numeric
-from Numeric import *
+import numpy
+from numpy import *
import operator
import math
from types import *
ArrayType = type(asarray(1.0))
-UfuncType = type(Numeric.add)
+UfuncType = type(numpy.add)
# unary function objects (maybe rename to UN_FUNC?)
@@ -19,22 +19,22 @@
return UnCompose(self, f)
def __add__(self, f):
- return BinCompose(Numeric.add, self, f)
+ return BinCompose(numpy.add, self, f)
def __sub__(self, f):
- return BinCompose(Numeric.subtract, self, f)
+ return BinCompose(numpy.subtract, self, f)
def __mul__(self, f):
- return BinCompose(Numeric.multiply, self, f)
+ return BinCompose(numpy.multiply, self, f)
def __div__(self, f):
- return BinCompose(Numeric.divide, self, f)
+ return BinCompose(numpy.divide, self, f)
def __neg__(self):
- return UnCompose(Numeric.negative, self)
+ return UnCompose(numpy.negative, self)
def __pow__(self, f):
- return BinCompose(Numeric.power, self, f)
+ return BinCompose(numpy.power, self, f)
def __coerce__(self, x):
if type(x) in [IntType, FloatType, LongType, ComplexType]:
@@ -50,10 +50,10 @@
return self.call(arg)
def exp(self):
- return UnCompose(Numeric.exp, self)
+ return UnCompose(numpy.exp, self)
def log(self):
- return UnCompose(Numeric.log, self)
+ return UnCompose(numpy.log, self)
only in patch2:
unchanged:
--- sixpack-0.66.orig/spkpca.py
+++ sixpack-0.66/spkpca.py
@@ -3,7 +3,7 @@
import xasinput
from spdirvars import *
from spglobalfuncs import *
-from Numeric import *
+from numpy import *
from Tkinter import *
#from Ifeffit import *
import Pmw
@@ -15,7 +15,6 @@
import math
import types
from string import *
-import LinearAlgebra
import spline
import varimax
@@ -736,7 +735,7 @@
#reshape datmat
datmat=transpose(datmat)
#do svd and eigens for pca
- (evect,eval,weight)=LinearAlgebra.singular_value_decomposition(datmat)
+ (evect,eval,weight)=linalg.singular_value_decomposition(datmat)
evalmat=identity(len(eval))*eval
#prop=matrixmultiply(evalmat,weight)
prop=weight
only in patch2:
unchanged:
--- sixpack-0.66.orig/xasinput.py
+++ sixpack-0.66/xasinput.py
@@ -17,7 +17,7 @@
# self.iF -- will be array if multielement is used
# self.ICR -- data for Ge13's, else array of ones
-from Numeric import *
+from numpy import *
from string import *
from struct import *
import Pmw
@@ -1582,4 +1582,4 @@
# return generic(fn,master)
-
\ No newline at end of file
+
only in patch2:
unchanged:
--- sixpack-0.66.orig/spline.py
+++ sixpack-0.66/spline.py
@@ -1,5 +1,5 @@
import func
-from Numeric import *
+from numpy import *
BadInput = "Bad xa input to routine splint."
only in patch2:
unchanged:
--- sixpack-0.66.orig/varimax.py
+++ sixpack-0.66/varimax.py
@@ -4,10 +4,8 @@
#Adapted from MATLAB code modified by Tevor Park in 2002 from original code by J.O. Ramsay
#
-from Numeric import *
+from numpy import *
from math import *
-import MLab
-import LinearAlgebra
def angle(z):
a=z.real
@@ -15,7 +13,7 @@
return arctan2(b,a)
def var(z):
- s=MLab.std(z)
+ s=std(z)
return s**2
def vcomplex(a,b):
@@ -41,7 +39,7 @@
if len(target_basis.shape)!=2:
raise ValueError, 'TARGET_BASIS must be 2-dimensional'
if alltrue(target_basis.shape==(n,n)):
- amat=LinearAlgebra.solve_linear_equations(target_basis,amat)
+ amat=linalg.solve(target_basis,amat)
else:
raise ValueError, 'TARGET_BASIS must be a basis for the column space'
else:
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