- Start UnitTest framework

- make scipy import optional for peakfinder
- fix errors from refactoring

Author: aglavic

mime_types/mbe.xml

@@ -4,10 +4,6 @@
      <comment>MBE Log File</comment>
      <glob pattern="*.log"/>
    </mime-type>
-   <mime-type type="text/aes">
-     <comment>MBE AES File</comment>
-     <glob pattern="*.dat"/>
-   </mime-type>
    <mime-type type="image/png">
      <comment>PNG image</comment>
      <glob pattern="*.png"/>

plot_script/fit_data.py

@@ -3149,8 +3149,9 @@ def simulate(self):
         data_x=[d[0] for d in data_xy]
         # only interpolate if the number of points isn't too large
         use_interpolate=min(5, 5000/len(data_x))
-        fit_x, fit_y=function[0].simulate(data_x, inside_fitrange=getattr(self, 'restrict_to_region', False),
-                                          interpolate=use_interpolate)
+        fit_x, fit_y=function[0].simulate(data_x,
+                    inside_fitrange=getattr(self, 'restrict_to_region', False),
+                    interpolate=use_interpolate)
         for i in range(len(fit_x)):
           result.append((fit_x[i], fit_y[i]))
         function_text=function[0].fit_function_text_eval

plot_script/gtkgui/dialogs.py

@@ -435,7 +435,8 @@ def __init__(self, title, entries, *args, **opts):
     '''
     # Initialize this dialog
     opts['title']=title
-    opts['buttons']=('OK', 1, 'Cancel', 0)
+    if not 'buttons' in opts:
+      opts['buttons']=('OK', 1, 'Cancel', 0)
     if 'description' in opts:
       description=gtk.Label(opts['description'])
       del(opts['description'])

plot_script/measurement_data_structure.py

@@ -684,8 +684,8 @@ def list(self): #@ReservedAssignment
     zd=self.zdata
     if (xd>=0) and (yd>=0):
       if (zd<0):
-        return data[numpy.array([xd, yd])].tolist()
-      return data[numpy.array([xd, yd, zd])].tolist()
+        return data[numpy.array([xd, yd])].transpose().tolist()
+      return data[numpy.array([xd, yd, zd])].transpose().tolist()
     elif yd>=0:
       return numpy.vstack([numpy.arange(len(data[0])), data[yd]]).transpose().tolist()
     elif xd>=0:
@@ -706,8 +706,8 @@ def list_err(self):
       return [point+[0] for point in self.list()]
     if (xd>=0) and (yd>=0):
       if (zd<0):
-        return data[numpy.array([xd, yd, ye])].tolist()
-      return data[numpy.array([xd, yd, zd, ye])].tolist()
+        return data[numpy.array([xd, yd, ye])].transpose().tolist()
+      return data[numpy.array([xd, yd, zd, ye])].transpose().tolist()
     elif yd>=0:
       return numpy.vstack([numpy.arange(len(data[0])),
                            data[numpy.array([yd, ye])]]).transpose().tolist()
@@ -2865,7 +2865,8 @@ def _propagate_errors(self, out_arr, context):
     try:
       if len(context[1])==1:
         # only a function of one parameter
-        out_arr.error=abs(derivatives[context[0].__str__()](self.view(numpy.ndarray))*self.error)
+        out_arr.error=abs(derivatives[context[0].__str__()](
+                                      self.view(numpy.ndarray))*self.error)
       elif context[0].__name__ in compare_functions:
         other=context[1][1]
         # if both arguments to compare function have an error value
@@ -2892,7 +2893,8 @@ def _propagate_errors(self, out_arr, context):
                                     )
           # only the first argument has an error value
           else:
-            out_arr.error=abs(derivatives[context[0].__str__()][0](self.view(numpy.ndarray), numpy.array(other))*self.error)
+            out_arr.error=abs(derivatives[context[0].__str__()][0](self.view(numpy.ndarray),
+                                                                   numpy.array(other))*self.error)
         else:
           # the second argument is self, so the first is no PhysicalProperty instance
           out_arr.error=abs(derivatives[context[0].__str__()][1](numpy.array(context[1][0]), self.view(numpy.ndarray))*self.error)

plot_script/peakfinder.py

@@ -12,7 +12,10 @@
 '''
 
 import numpy
-from scipy.stats.mstats import mquantiles
+try:
+  from scipy.stats.mstats import mquantiles
+except ImportError:
+  pass
 
 class PeakFinder(object):
   '''

plot_script/sessions/dns.py

@@ -532,7 +532,7 @@ def read_argument_add(self, argument, last_argument_option=[False, ''], input_fi
           file_postfix=str(last_argument_option[2][3][0])+last_argument_option[2][4]
           try:
             first_file=sorted([file_ for file_ in os.listdir(directory) \
-                               if file.startswith(file_prefix) and file.endswith(file_postfix)])[0]
+                               if file_.startswith(file_prefix) and file_.endswith(file_postfix)])[0]
           except IndexError:
             erg=last_argument_option[2]
             print """No file found for the -files options:
@@ -639,18 +639,18 @@ def read_files(self, file_name):
     if len(file_list)==0:
       return None
     file_list.sort()
-    # Read the raw data
-    self.file_data[file_name+'|raw_data']=[]
     print "Reading files %s{num}%s with num from %i to %i."%(prefix, postfix, num_range[0], num_range[1])
-    for file_name in file_list:
+    self.file_data[file_name+'|raw_data']=[]
+    for file_i in file_list:
+      # Read the raw data
       # get integer number of the file_name, catch errors form wrong file_name selection
       try:
-        active_number=int(os.path.join(folder, file_name).rsplit(postfix)[0].split(prefix, 1)[1])
+        active_number=int(os.path.join(folder, file_i).rsplit(postfix)[0].split(prefix, 1)[1])
       except ValueError:
         continue
       if (active_number>=num_range[0]) and (active_number<=num_range[1] or num_range[1]==-1):
         # read the datafile into a MeasurementData object.
-        dataset=read_data.read_data(os.path.join(folder, file_name))
+        dataset=read_data.read_data(os.path.join(folder, file_i))
         dataset.number=str(active_number)
         self.file_data[file_name+'|raw_data'].append(dataset)
     print "\tRead, creating map."

tests/__init__.py

@@ -0,0 +1,3 @@
+'''
+  Package providing unit tests for the plot_script package.
+'''

tests/datatype.py

@@ -0,0 +1,90 @@
+#-*- coding: utf8 -*-
+'''
+  Testing the datatype framewok.
+'''
+
+from plot_script.measurement_data_structure import PhysicalProperty
+from numpy import *
+import unittest
+
+class TestPhysicalProperty(unittest.TestCase):
+  '''
+    Check the behavior of the base data holding array type.
+  '''
+
+  def setUp(self):
+    self.error=array([2. for ignore in range(100)], dtype=float32)
+    self.values=arange(1., 101., 1.0, dtype=float32)
+    self.data=PhysicalProperty('x', '°', self.values, self.error)
+
+  def test_add(self):
+    # test the base calculations with addition
+    add_res=self.data+self.data
+    self.assertEqual(add_res.view(ndarray).tolist(),
+                      (2.*self.values).tolist(),
+                     "Add results")
+    self.assertEqual(add_res.error.tolist(),
+                     (sqrt(2.)*self.error).tolist(),
+                     "Add errors")
+
+  def test_sub(self):
+    # test the base calculations with subtraction
+    sub_res=self.data-self.data
+    self.assertEqual(sub_res.view(ndarray).tolist(),
+                     (zeros_like(self.values)).tolist(),
+                     "Subtract results")
+    self.assertEqual(sub_res.error.tolist(),
+                     (sqrt(2.)*self.error).tolist(),
+                     "Subtract errors")
+
+  def test_mul(self):
+    # test the base calculations with multiplication
+    mul_res=self.data*self.data
+    self.assertEqual(mul_res.view(ndarray).tolist(),
+                     (self.values**2).tolist(),
+                     "Multiply results")
+    self.assertEqual(mul_res.error.tolist(),
+                     (sqrt((self.error*self.values)**2+
+                           (self.error*self.values)**2)).tolist(),
+                     "Multiply errors")
+
+  def test_div(self):
+    # test the base calculations with division
+    div_res=self.data/self.data
+    self.assertEqual(div_res.view(ndarray).tolist(),
+                     (ones_like(self.values)).tolist(),
+                     "Devision results")
+    self.assertEqual(div_res.error.tolist(),
+                     (sqrt((self.error/self.values)**2+
+                           (self.error/self.values)**2)).tolist(),
+                     "Devision errors")
+
+  def test_unit_conversions(self):
+    # test automatic and manual unit conversion
+    deg=self.data
+    rad=deg%'rad'
+    self.assertEqual(rad.unit, 'rad',
+                     "Unit conversion from ° to rad - Unit")
+    self.assertEqual((deg*(pi/180.)).tolist(),
+                     rad.tolist(),
+                     "Unit conversion from ° to rad - Value")
+    # automatic conversion when added
+    degrad=deg+rad
+    self.assertEqual(degrad.tolist(), (2.*deg).tolist(),
+                     "Unit auto conversion in addition")
+    # automatic conversion for angle functions
+    degsin=sin(deg)
+    radsin=sin(rad)
+    self.assertEqual(degsin.tolist(), radsin.tolist(),
+                     "Unit auto conversion in sin(x)")
+
+
+class TestBla(unittest.TestCase):
+  pass
+
+if __name__=='__main__':
+  #unittest.main()
+  loader=unittest.TestLoader()
+  suite=loader.loadTestsFromTestCase(TestPhysicalProperty)
+  suite.addTest(loader.loadTestsFromTestCase(TestBla))
+  unittest.TextTestRunner(verbosity=2).run(suite)