Fixes to make tests run on Python 3.5 (issue 1)

Author: gb119

Stoner/Analysis.py

@@ -94,8 +94,9 @@ def _threshold(threshold, data, rising=True, falling=False):
 
     intr=interp1d(index,data.ravel()-threshold,kind="cubic")
     roots=[]
-    for ix,x in enumerate(sdat):
-        if expr(x) and ix>0 and ix<len(data)-1: # There's a root somewhere here !
+    for ix in range(sdat.shape[0]):
+        x=sdat[ix]
+        if expr(x): # There's a root somewhere here !
             try:
                 roots.append(newton(intr,ix))
             except ValueError: # fell off the end here
@@ -257,6 +258,7 @@ def SG_Filter(self, col=None, points=15, poly=1, order=0, result=None, replace=F
             User guide section :ref:`smoothing_guide`
         """
         from Stoner.Util import ordinal
+        points=int(round(points))
         if points % 2 == 0:  #Ensure window length is odd
             points += 1
         if col is None:
@@ -702,7 +704,7 @@ def curve_fit(self, func, xcol=None, ycol=None, p0=None, sigma=None, **kargs):
             kargs["full_output"] = True
 
         _=self._col_args(xcol=xcol,ycol=ycol,yerr=sigma,scalar=False)
-
+        
         xcol,ycol,sigma=_.xcol,_.ycol,_.yerr
 
         working = self.search(xcol, bounds)

Stoner/Core.py

@@ -353,7 +353,7 @@ def __call__(self, *args, **kargs):
             for i, v in enumerate(list(value)):
                 if v.lower() not in "xyzedfuvw.-":
                     raise ValueError("Set as column element is invalid: {}".format(v))
-                if v != "-":
+                if v != "-" and i<len(self.setas):
                     self.setas[i] = v.lower()
         else:
             raise ValueError("Set as column string ended with a number")
@@ -1079,7 +1079,7 @@ def __getitem__(self,ix):
         """
 
         #Is this goign to be a single row ?
-        single_row=isinstance(ix,int) or (isinstance(ix,tuple) and isinstance(ix[0],int))
+        single_row=isinstance(ix,int) or (isinstance(ix,tuple) and len(ix)>0 and isinstance(ix[0],int))
         #If the index is a single string type, then build a column accessing index
         if isinstance(ix,string_types):
             if self.ndim>1:
@@ -1088,15 +1088,17 @@ def __getitem__(self,ix):
                 ix=(self._setas.find_col(ix),)
         if isinstance(ix,(int,slice)):
                 ix=(ix,)
-        elif isinstance(ix,tuple) and isinstance(ix[-1],string_types): # index still has a string type in it
+        elif isinstance(ix,tuple) and len(ix)>0 and isinstance(ix[-1],string_types): # index still has a string type in it
             ix=list(ix)
             ix[-1]=self._setas.find_col(ix[-1])
             ix=tuple(ix)
-        elif isinstance(ix,tuple) and isinstance(ix[0],string_types): # oops! backwards indexing
+        elif isinstance(ix,tuple) and len(ix)>0 and isinstance(ix[0],string_types): # oops! backwards indexing
             c=ix[0]
             ix=list(ix[1:])
             ix.append(self._setas.find_col(c))
             ix=tuple(ix)
+        elif isinstance(ix,list): # indexing with a list in here
+            ix=(ix,)
 
         # Now can index with our constructed multidimesnional indexer
         ret=super(DataArray,self).__getitem__(ix)
@@ -1137,7 +1139,7 @@ def __getitem__(self,ix):
                 ret.i=self.i[ix[0]]
             else: #This is a single element?
                 ret.i=self.i
-            if not single_row:
+            if not single_row and len(ix)>0:
                 ret.name=self.column_headers[ix[-1]]
         return ret
 

Stoner/Util.py

@@ -37,6 +37,7 @@ def _up_down(data):
         for d in f[grp][1:]:
             ret[i]=ret[i]+d
         ret[i].sort(data.setas._get_cols('xcol'))
+        ret[i].setas=data.setas.clone
     return ret
 
 
@@ -166,12 +167,11 @@ def split_up_down(data, col=None, folder=None):
     """
     if col is None:
         col = data.setas["x"]
-    a = _AF_(data)
-    width = len(a) / 10
+    width = len(data) / 10
     if width % 2 == 0:  # Ensure the window for Satvisky Golay filter is odd
         width += 1
-    peaks = list(a.peaks(col, width,xcol=False, peaks=True, troughs=False))
-    troughs = list(a.peaks(col, width, xcol=False, peaks=False, troughs=True))
+    peaks = list(data.peaks(col, width,xcol=False, peaks=True, troughs=False))
+    troughs = list(data.peaks(col, width, xcol=False, peaks=False, troughs=True))
     if len(peaks) > 0 and len(troughs) > 0:  #Ok more than up down here
         order = peaks[0] < troughs[0]
     elif len(peaks) > 0:  #Rise then fall
@@ -180,7 +180,7 @@ def split_up_down(data, col=None, folder=None):
         order = False
     else:  #No peaks or troughs so just return a single rising
         return ([data], [])
-    splits = [0, len(a)]
+    splits = [0, len(data)]
     splits.extend(peaks)
     splits.extend(troughs)
     splits.sort()
@@ -348,7 +348,7 @@ def hysteresis_correct(data, **kargs):
     #Get xcol and ycols from kargs if specified
     xc = kargs.pop("xcol",data.find_col(data.setas["x"]))
     yc = kargs.pop("ycol",data.find_col(data.setas["y"]))
-    setas=data.setas
+    setas=data.setas.clone
     setas[xc]="x"
     setas[yc]="y"
     data.setas=setas
@@ -385,6 +385,8 @@ def hysteresis_correct(data, **kargs):
     Ms=array([p1[0],p2[0]])
     Ms=list(Ms-mean(Ms))
 
+
+
     data["Ms"] = Ms #mean(Ms)
     data["Ms Error"] = perr[0]/2
     data["Offset Moment"] = pm[0]
@@ -406,6 +408,7 @@ def hysteresis_correct(data, **kargs):
     m_sat=[p1[0]+perr[0],p2[0]-perr[0]]
     Mr=[None,None]
     Mr_err=[None,None]
+
     for i,(d,sat) in enumerate(zip([up,down],m_sat)):
         hc=d.threshold(0.,all_vals=True,rising=True,falling=True) # Get the Hc value
         Hc[i]=mean(hc)
@@ -438,14 +441,7 @@ def hysteresis_correct(data, **kargs):
     i = argmax(bh)
     data["BH_Max"] = max(bh)
     data["BH_Max_H"] = data.x[i]
-    mr1 = data.threshold(0.0, col=xc, xcol=yc, rising=True, falling=False)
-    mr2 = data.threshold(0.0, col=xc, xcol=yc, rising=False, falling=True)
-
-    data["Remenance"] = abs((mr2 - mr1) / 2)
-
-    h_sat_data = data.search(data.setas["y"], lambda x, r: low_m <= x <= high_m)[:, xc]
-    if len(h_sat_data)>0:
-        data["H_sat"] = (min(h_sat_data), max(h_sat_data))
 
     data["Area"] = data.integrate()
     return cls(data)
+    return cls(data)

Stoner/__init__.py

@@ -10,6 +10,6 @@
 from .Util import Data
 from Stoner.Folders import DataFolder
 
-__version_info__ = ('0', '6', '3')
+__version_info__ = ('0', '6', '4')
 __version__ = '.'.join(__version_info__)
 

tests/Stoner/test_Util.py

@@ -0,0 +1,50 @@
+# -*- coding: utf-8 -*-
+"""
+Test_Util.py
+Created on Mon Jul 18 14:13:39 2016
+@author: phygbu
+"""
+
+
+import unittest
+import sys
+import os.path as path
+import os
+import numpy as np
+import re
+from Stoner.compat import *
+import Stoner.Util as SU
+
+from Stoner import Data
+
+pth=path.dirname(__file__)
+pth=path.realpath(path.join(pth,"../../"))
+sys.path.insert(0,pth)
+
+def is_2tuple(x):
+    """Return tru if x is a length two tuple of floats."""
+    return isinstance(x,tuple) and len(x)==2 and isinstance(x[0],float) and isinstance(x[1],float)
+
+
+class Utils_test(unittest.TestCase):
+
+    """Path to sample Data File"""
+    datadir=path.join(pth,"sample-data")
+
+    def setUp(self):
+        pass
+
+    def test_hysteresis(self):
+        """Test the hysteresis analysis code."""
+        x=SU.hysteresis_correct(path.join(pth,"./sample-data/QD-SQUID-VSM.dat"))
+        self.assertTrue("Hc" in x and "Area" in x and
+                       "Hsat" in x and "BH_Max" in x and
+                       "BH_Max_H" in x,"Hystersis loop analysis keys not present.")
+
+        self.assertTrue(is_2tuple(x["Hc"]) and x["Hc"][0]+578<1.0,"Failed to find correct Hc in a SQUID loop")
+        self.assertTrue(isinstance(x["Area"],float) and 0.0136<x["Area"]<0.0137,"Incorrect calculation of area under loop")
+
+if __name__=="__main__": # Run some tests manually to allow debugging
+    test=Utils_test("test_hysteresis")
+    test.setUp()
+    test.test_hysteresis()