Bugs arisen while using external simulator fixed

optimizer/Core.py

@@ -484,7 +484,7 @@ def FourthStep(self,args={}):
                         for line in in_handler:
                             self.model_handler.spike_times.append(int(float(line) / (1000.0 / self.option_handler.input_freq)))
                         in_handler.close();
-                    except OSError:
+                    except (OSError, IOError):
                         pass
 
 
@@ -583,16 +583,3 @@ def callGrid(self,resolution):
         self.grid_result=self.optimizer.final_pop
         self.optimizer.final_pop=self.prev_result
 
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optimizer/fitnessFunctions.py

@@ -162,11 +162,12 @@ def modelRunner(self, candidates, act_trace_idx):
             try:
                 in_handler = open(self.option.base_dir + "/spike.dat", "r")
                 self.model.spike_times = []
-            except OSError:
+
+                for line in in_handler:
+                    self.model.spike_times.append(int(float(line) / (1000.0 / self.option.input_freq)))
+                    #print self.model.spike_times[1:10]
+            except (OSError, IOError): # IOError for latest python versions
                 pass
-            for line in in_handler:
-                self.model.spike_times.append(int(float(line) / (1000.0 / self.option.input_freq)))
-                #print self.model.spike_times[1:10]
 
         else:
             section = self.option.GetObjTOOpt()

optimizer/graphic.py

@@ -450,7 +450,7 @@ def __init__(self, parent, ID, size, title, core, path):
         import optimizer
         path = os.path.dirname(optimizer.__file__)
 
-        self.path = path
+        self.path = os.path.abspath(path)
         self.layer = None
         self.panel = wx.Panel(self)
         self.Center()
@@ -721,23 +721,18 @@ def __init__(self, parent, ID, size, title, core, path):
         self.parent = parent
         self.core = core
         self.layer = None
-
+        
         #this will need to be wrapped in a try statement later:
         import optimizer
         print optimizer.__file__
-        path = os.path.dirname(optimizer.__file__)
+        #path = os.path.dirname(optimizer.__file__)
 
         self.path = path
         #print "path",self.path
         self.Center()
         self.ToolbarCreator()
         self.Design()
         #self.is_loaded=False
-
-
-
-
-
 
     def ToolbarCreator(self):
 
@@ -748,6 +743,7 @@ def ToolbarCreator(self):
         self.Bind(wx.EVT_TOOL, self.Next, button_toolbar_fward)
         self.Bind(wx.EVT_TOOL, self.Prev, button_toolbar_bward)
         self.toolbar.EnableTool(button_toolbar_fward.GetId(), False)     
+
     def Design(self):
 
         self.horizontal_box1 = wx.BoxSizer(wx.HORIZONTAL)
@@ -1104,7 +1100,7 @@ def __init__(self, parent, ID, size, title, core, path):
         #this will need to be wrapped in a try statement later:
         import optimizer
         print optimizer.__file__
-        path = os.path.dirname(optimizer.__file__)
+        #path = os.path.dirname(optimizer.__file__)
 
         self.path = path
         #print "path",self.path
@@ -1381,15 +1377,14 @@ def __init__(self, parent, ID, size, title, core, path, kwargs):
         #this will need to be wrapped in a try statement later:
         import optimizer
         print optimizer.__file__        
-        path = os.path.dirname(optimizer.__file__)
+        #path = os.path.dirname(optimizer.__file__)
 
         self.path = path
         self.Center()
         self.ToolbarCreator()
         self.Design()
         self.seed = None
         self.kwargs = kwargs
-
         #print "ffun",kwargs
         self.layer = None
 
@@ -1815,7 +1810,7 @@ def __init__(self, parent, ID, size, title, core, path,kwargs):
         #this will need to be wrapped in a try statement later:
         import optimizer
         print optimizer.__file__        
-        path = os.path.dirname(optimizer.__file__)
+        #path = os.path.dirname(optimizer.__file__)
 
         self.path = path
         self.panel = wx.Panel(self)
@@ -1945,7 +1940,7 @@ def __init__(self, parent, ID, size, title, core, path):
         #this will need to be wrapped in a try statement later:
         import optimizer
         print optimizer.__file__
-        path = os.path.dirname(optimizer.__file__)
+        #path = os.path.dirname(optimizer.__file__)
 
         self.path = path
         self.Center()

optimizer/traceHandler.py

@@ -183,7 +183,7 @@ def get_type(self):
 
 
 
-    def detect_format(self,line):
+    def detect_format(self,line,contains_time):
         """
         Automatically detects the format of the file and returns a reader functions which can process it correctly.
         The recognized formats are the following:
@@ -206,11 +206,16 @@ def detect_format(self,line):
         spike_times_rule=re.compile("# variable = spikes")
         rules=[pynn_rule,neuron_rule_time,neuron_rule,spike_times_rule]
         result=[n!=None for n in [re.match(k,line) for k in rules ] ]
+        #print line
         #print result
-        #print result.index(True)
-        return [self.PyNNReader,self.traceReaderTime,self.traceReader,self.spikeTimeReader][result.index(True)]
+        # FIXED: if no time specified, the second true option
+        # (traceReader) should be chosen
+        index = result.index(True)
+        if not contains_time and index == 1:
+            index += 1
+        return [self.PyNNReader,self.traceReaderTime,self.traceReader,self.spikeTimeReader][index]
 
-    def Read(self,path=[os.getcwd()+"/inputTrace.txt"],no_traces=1,scale="mV",t_length=1000,freq=1000,trace_type="voltage"):
+    def Read(self,path=[os.getcwd()+"/inputTrace.txt"],no_traces=1,scale="mV",t_length=1000,freq=1000,trace_type="voltage", contains_time=False):
         """
         The main reader function. This calls the recognition function ``detect_format``
         and uses the obtained reader function to read the data.
@@ -232,7 +237,7 @@ def Read(self,path=[os.getcwd()+"/inputTrace.txt"],no_traces=1,scale="mV",t_leng
             tmp.append(f.readline())
             i+=1
         if trace_type!="spike":
-            self.data=self.detect_format(tmp[4])(path,no_traces,scale,t_length,freq,trace_type)
+            self.data=self.detect_format(tmp[4],contains_time)(path,no_traces,scale,t_length,freq,trace_type)
         else:
             self.additional_data=self.spikeTimeReader(path, no_traces, scale, t_length, freq, trace_type)
 
@@ -436,9 +441,3 @@ def Write(self):
                 f.write(self.separator.join(string.strip(k,"[]") for k in temp))
                 f.write("\n")
 
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