Changeset 490 for trunk

Timestamp:

08/23/11 15:18:35 (9 months ago)

Author:

emuller

Message:

Added AnalogSignal?.slice_exclude_events to cut out (remove) spikes

Location:

trunk

Files:

• src/signals/analogs.py (modified) (1 diff)
• test/test_analogs.py (modified) (1 diff)

trunk/src/signals/analogs.py

@@ -386 +386 @@
                 result[index] = self.time_slice(t_start_new, t_stop_new)
         return result
-        
-            
-
+
+    def slice_exclude_events(self,events,t_min=100,t_max=100):
+        """
+        yields new AnalogSignals with events cutout (useful for removing spikes).
+
+        Events should be sorted in chronological order
+
+        Inputs:
+            events  - Can be a SpikeTrain object (and events will be the spikes) or just a list 
+                      of times
+            t_min   - Time (>0) to cut the signal before an event, in ms (default 100)
+            t_max   - Time (>0) to cut the signal after an event, in ms  (default 100)
+        
+        Examples:
+            >> res = aslist.slice_by_events([100,200,300], t_min=0, t_max =10)
+            >> print len(res)
+                4
+        """
+        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"
+        
+        t_last = self.t_start
+        for spike in events:
+            t_min_local = numpy.max([t_last, spike-t_min])
+            t_max_local = numpy.min([self.t_stop, spike+t_max])
+            if t_min_local>t_last:
+                yield self.time_slice(t_last, t_min_local)
+            t_last = t_max_local
+
+        if t_last<self.t_stop:
+            yield self.time_slice(t_last, self.t_stop)
 
 

trunk/test/test_analogs.py

@@ -56 +56 @@
         res2 = sig.slice_by_events(analogs.SpikeTrain([0, 50, 100]),t_min=0, t_max=50)
         assert len(res1) == 3 and len(res2) == 3
+
+    def testSliceExcludeEvents(self):
+        sig = analogs.AnalogSignal(numpy.sin(numpy.arange(10000.)), 0.1)
+        # check something in the middle splits in 2
+        res0 = list(sig.slice_exclude_events([500.0],t_min=0., t_max=0.))
+        assert len(res0)==2
+        assert res0[0].t_stop == res0[1].t_start
+        assert res0[0].t_start == sig.t_start
+        assert res0[1].t_stop == sig.t_stop
+
+        # check that event at t_start yields only one slice, removing t_max
+        res1 = list(sig.slice_exclude_events([0.0],t_min=10., t_max=10.))
+        assert len(res1)==1
+        assert res1[0].t_start == sig.t_start+10.0
+        assert res1[0].duration() == 990.0      
+
+
+        # check something in the middle splits in 2
+        res2 = list(sig.slice_exclude_events([250.0, 750.0], t_min=50., t_max=50.))
+        assert len(res2)==3
+        assert res2[0].duration() == 200.0
+        assert res2[1].duration() == 400.0
+        assert res2[2].duration() == 200.0
+
+        # check behaviour at the end (t_stop)
+        res3 = list(sig.slice_exclude_events([1000.0], t_min=50., t_max=50.))
+        assert len(res3)==1
+        assert res3[0].duration() == 950.0
+
+        
         
     def testThresholdDetection(self):