Changeset 418

Timestamp:

08/17/09 21:30:58 (3 years ago)

Author:

lestebanez

Message:

spikes.py : fixes several bugs

Files:

• branches/interval/src/signals/spikes.py (modified) (10 diffs)

branches/interval/src/signals/spikes.py

@@ -26 +26 @@
 
 import os, re, numpy
+import copy
 import logging
 from NeuroTools import check_dependency, check_numpy_version, analysis
@@ -111 +112 @@
 
 
-
     def __str__(self):
         return str(self.spike_times)
+
+    def __format__(self):
+        return 'hella'
 
     def __len__(self):
@@ -393 +396 @@
             spikes  = interval.slice_times(self.spike_times)
         else:
-            spikes = self
+            spikes = self.spike_times
 
         subplot = get_display(display)
@@ -401 +404 @@
         else:
             if len(spikes) > 0:
-                subplot.plot(spikes,numpy.ones(len(spikes)),',', **kwargs)
+                subplot.plot(spikes,numpy.ones(len(spikes)),',', **kwargs)
                 xlabel = "Time (ms)"
                 ylabel = "Neurons #"
@@ -466 +469 @@
         """
         Bin the spikes with the specified bin width. The first and last bins
-        are calculated from `self.t_start` and `self.t_stop`.
+        are calculated from the interval of the spike train.
         
         Inputs:
@@ -576 +579 @@
     
     
-    def psth(self, events, time_bin=2, t_min=50, t_max=50, display = False, kwargs={}):
+    def psth(self, events, time_bin=2, t_min=50, t_max=50, display = False, labels=True, kwargs={}):
         """
         Return the psth of the spike times contained in the SpikeTrain according to selected events, 
@@ -587 +590 @@
             t_min   - Time (>0) to average the signal before an event, in ms (default 0)
             t_max   - Time (>0) to average the signal after an event, in ms  (default 100)
-            display - if True, a new figure is created. Could also be a subplot.
+            display - if True, the psth is displayed in a new figure. If a Matplotlib Axes name,
+                      the psth is displayed inside this Axes.
+            labels  - if True, psth plot has full labels. If not, the plot is shown 'raw' 
             kwargs  - dictionary contening extra parameters that will be sent to the plot 
                       function
@@ -603 +608 @@
             events = events.spike_times
         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"
-
+        assert len(events) > 0, "events should not be empty"
         spk_hist = self.time_histogram(time_bin)
         subplot  = get_display(display)
         count    = 0
-        t_min_l  = numpy.floor(t_min/time_bin)
-        t_max_l  = numpy.floor(t_max/time_bin)
+        t_min_l  = numpy.floor(t_min/float(time_bin))
+        t_max_l  = numpy.floor(t_max/float(time_bin))
         result   = numpy.zeros((t_min_l+t_max_l), numpy.float32)
+        events_interval = copy.copy(self.interval)
+        events_interval.offset_start(t_min, colapse=True)
+        events_interval.offset_stop(-t_max, colapse=True)
+        events = events_interval.slice_times(events)
+        assert len(events) > 0, "the PSTH windows [event-t_min, event+t_max] should be included within the spike train interval"
         for ev in events:
-           itv = Interval((ev-t_min,ev+t_max))
-           ev  = numpy.floor(ev/time_bin)
-           if itv.intersect(self.interval).total_duration() == (t_max+t_min):
-               count  += 1
-               result += spk_hist[(ev-t_min_l):ev+t_max_l]
+            ev  = numpy.floor((ev - self.interval.t_start())/float(time_bin))
+            count  += 1.    
+            result += spk_hist[(ev-t_min_l):ev+t_max_l]
         result /= count
         
@@ -622 +629 @@
             return result
         else:
-            xlabel = "Time (ms)"
-            ylabel = "PSTH"
-            time   = numpy.linspace(-t_min, t_max, (t_min+t_max)/time_bin)
-            set_labels(subplot, xlabel, ylabel)
+            if labels :
+                xlabel = "Time (ms)"
+                ylabel = "PSTH"
+                set_labels(subplot, xlabel, ylabel)
+            else :
+                subplot.xaxis.set_major_locator(pylab.NullLocator())
+                subplot.yaxis.set_major_locator(pylab.NullLocator())
+            time   = numpy.linspace(-t_min, t_max, (t_min+t_max)/time_bin)
             subplot.plot(time, result, c='k', **kwargs)
             xmin, xmax, ymin, ymax = subplot.axis()
-            subplot.plot([0,0],[ymin, ymax], c='r')
+            subplot.axvline(0, c='r')
             set_axis_limits(subplot, -t_min, t_max, ymin, ymax)
             pylab.draw()
@@ -795 +806 @@
                 [0,1,2,3,....,9999]
         """
+        print self.spiketrains.keys()
         return numpy.array(self.spiketrains.keys(), int)