Changeset 266

Timestamp:

11/02/08 17:42:18 (5 years ago)

Author:

JensKremkow

Message:

minor changes in signals, spikes and add IF-Curve example for spike2

Location:

trunk

Files:

• examples/spike2 (added)
• examples/spike2/IF-Curve.py (added)
• src/signals.py (modified) (6 diffs)
• src/spike2/sonpy/son.py (modified) (1 diff)

trunk/src/signals.py

@@ -1990 +1990 @@
         self.t_start = t_start
         self.t_stop  = t_stop
-
+        
         # If t_start is not None, we resize the signal keeping only
         # elements with t >= t_start
-        if self.t_start is not None:
-            self.signal = self.signal[(self.t_start/self.dt):]
+        #if self.t_start is not None:
+        #    self.signal = self.signal[(self.t_start/self.dt):]
 
         # If t_stop is not None, we resize the signal keeping only
         # elements with t <= t_stop
-        if self.t_stop is not None:
-            self.signal = self.signal[:(self.t_stop-self.t_start)/self.dt]
+        #if self.t_stop is not None:
+        #    self.signal = self.signal[:(self.t_stop-self.t_start)/self.dt]
 
         if len(self.signal) > 0: # spike list may be empty
@@ -2032 +2032 @@
         return len(self.signal)
 
+    def max(self):
+        return self.signal.max()
+
+    def min(self):
+        return self.signal.min()
+
     def copy(self):
         """
@@ -2038 +2044 @@
         return AnalogSignal(self.signal, self.dt, self.t_start, self.t_stop)
 
-    def time_axis(self):
+    def time_axis(self,normalized=False):
         """
         Return the time axis of the AnalogSignal
         """
-        return numpy.linspace(self.t_start, self.t_stop, len(self.signal))
+        if normalized:
+            norm = self.t_start
+        else:
+            norm = 0.
+        return numpy.linspace(self.t_start-norm, self.t_stop-norm, len(self.signal))
 
     def time_parameters(self):
@@ -2069 +2079 @@
         Inputs:
              threshold - Threshold
-             format - when 'spiketrain' a SpikeTrain object is returned, else a numpy.array
+             format - when 'raw' the raw events array is returned, otherwise a SpikeTrain object
         
         """
@@ -2076 +2086 @@
         
         above = numpy.where(self.signal > threshold)[0]
-        take = numpy.where(numpy.diff(above)>1)[0]+1
-        take = numpy.append(0,take)
-                
-        time = self.time_axis()
-        events = time[above][take]
-
-        if format is 'spiketrain':
+        if len(above) <= 0:
+            events = []
+        else:
+            take = numpy.where(numpy.diff(above)>1)[0]+1
+            take = numpy.append(0,take)
+            
+            time = self.time_axis()
+            events = time[above][take]
+
+        if format is 'raw':
+            return events
+        else:
             return SpikeTrain(events,t_start=self.t_start,t_stop=self.t_stop)
-        else:
-            return events
-    
+            
                     
     def event_triggered_average(self, events, average = True, t_min = 0, t_max = 100, display = False, kwargs={}):
@@ -2169 +2182 @@
             set_axis_limits(subplot, -t_min, t_max, ymin, ymax)
             pylab.draw()
+
+    def slice_by_events(self,events,t_min=100,t_max=100):
+        """
+        
+        """
+        if isinstance(events, SpikeTrain):
+            events = events.spike_times
+        else:
+            assert numpy.iterable(events), "events should be a SpikeTrain object or an iterable object"
+        assert (t_min >= 0) and (t_max >= 0), "t_min and t_max should be greater than 0"
+        assert len(events) > 0, "events should not be empty and should contained at least one element"
+        
+        # in timesteps
+        events = numpy.floor(numpy.array(events)/self.dt)
+        t_min_l = numpy.floor(t_min/self.dt)
+        t_max_l = numpy.floor(t_max/self.dt)
+        t_start = numpy.floor(self.t_start/self.dt)
+        t_stop = numpy.floor(self.t_stop/self.dt)
+        
+        result = {}
+        for index, spike in enumerate(events):
+            if ((spike-t_min_l) > t_start) and ((spike+t_max_l) < t_stop):
+                spike = spike - t_start
+                signal = self.signal[(spike-t_min_l):(spike+t_max_l)]
+                t_start_new = (spike-t_min_l)*self.dt
+                t_stop_new = (spike+t_max_l)*self.dt
+                result[index] = AnalogSignal(signal, self.dt, t_start=t_start_new, t_stop=t_stop_new)
+
+        return result
+        
+            
 
 

trunk/src/spike2/sonpy/son.py

@@ -208 +208 @@
                 if interval == 0: interval = 1.
                 # in milliseconds
-                self.dt = interval*fhead.usPerTime*fhead.dTimeBase*1e3
+                # have to multiply by 2, I dont know why, I have to check that
+                self.dt = interval*fhead.usPerTime*fhead.dTimeBase*1e3*2
                 
         def type(self):