Changeset 424 for branches

Timestamp:

08/25/09 01:53:50 (3 years ago)

Author:

lestebanez

Message:

spikes.py : down to 6 failures and 25 errors

Location:

branches/interval

Files:

• src/signals/spikes.py (modified) (20 diffs)
• test/test_spikes.py (modified) (1 diff)

branches/interval/src/signals/spikes.py

@@ -94 +94 @@
         """
         self.spike_times = spike_times
-        if not (min(self.spike_times) >= 0) :
+        if len(self.spike_times) and not (min(self.spike_times) >= 0) :
             raise ValueError("spikes time stamps should be *positive* *numbers*")
 
@@ -100 +100 @@
         if not (self.interval.t_start() >= 0) and (self.interval.t_stop() >= 0) :
             raise ValueError("t_start and t_stop should be greater than 0")
+        self.update_t_start_and_t_stop()
 
         self.spike_times = self.interval.slice_times(numpy.array(self.spike_times, numpy.float32))
@@ -170 +171 @@
         """
         return (self.interval.t_start(), self.interval.t_stop())
+
+    def update_t_start_and_t_stop(self):
+        """
+        Update the t_start and t_stop constant to reflect the current t_start() and t_stop() methods
+        """
+        self.t_start = self.interval.t_start()
+        self.t_stop = self.interval.t_stop()
     
     def is_equal(self, spktrain):
@@ -220 +228 @@
                                         spiketrain.spike_times)
         self.interval = self.interval.union(spiketrain.interval)
+        self.update_t_start_and_t_stop()
 
     def format(self, relative=False, quantized=False):
@@ -294 +303 @@
                 34.2
         """
-        rate_interval = extract_intervals_from_SpikeTrain_arguments(t_start, t_stop, interval)
-
-        rate_interval = rate_interval.intersect(self.interval)
-        idx           = rate_interval.slice_times(self.spike_times)
+        if not (t_start==None and t_stop==None and interval==None) :
+            rate_interval = self.extract_intervals_from_SpikeTrain_arguments(t_start, t_stop, interval)
+            rate_interval = rate_interval.intersect(self.interval)
+            idx           = rate_interval.slice_times(self.spike_times)
+        else :
+            idx           = self.spike_times
+            rate_interval = self.interval
 
         return 1000.*len(idx)/rate_interval.total_duration()
@@ -320 +332 @@
             
         """
-        isi = self.isi(t_start, t_stop, interval)
+        isi = self.isi()
         if len(isi) > 0:
             return numpy.std(isi)/numpy.mean(isi)
@@ -350 +362 @@
             
         """
-        isi = self.isi(t_start, t_stop, interval) / 1000.
+        isi = self.isi() / 1000.
         if len(isi) < 2:
             logging.debug("Warning, a CV can't be computed because there are not enough spikes")
@@ -380 +392 @@
             isi, cv_isi
         """
-        isi = self.isi(t_start, t_stop, interval)
+        isi = self.isi()
         if len(isi) > 0:
             fano = numpy.var(isi)/numpy.mean(isi)
@@ -463 +475 @@
         self.interval.offset_full(offset)
         self.spike_times += offset
+        self.update_t_start_and_t_stop()
+
 
     def time_slice(self, t_start, t_stop):
@@ -481 +495 @@
         """
         interval = Interval((t_start, t_stop)) 
-        return SpikeTrain.interval_slice(interval)
+        sliced = self.interval_slice(interval)
+        sliced.update_t_start_and_t_stop()
+        return sliced
 
     def interval_slice(self, interval):
@@ -836 +852 @@
             for id in self.spiketrains.keys():
                 self.spiketrains[id].interval = self.interval
-
+        self.update_t_start_and_t_stop()
         
     def id_list(self):
@@ -870 +886 @@
             if t_start == None and t_stop == None :
                 try:
-                    start_times = numpy.array([self.spiketrains[idx].interval.t_start() for idx in self.id_list()], numpy.float32)
+                    start_times = numpy.array([self.spiketrains[idx].interval.t_start() for idx in self.id_list()], numpy.float64)
                     t_start = numpy.min(start_times)
                     logging.debug("Warning, t_start is infered from the data : %f" %t_start)
@@ -877 +893 @@
                     t_start = 0
                 try:
-                    stop_times = numpy.array([self.spiketrains[idx].interval.t_stop() for idx in self.id_list()], numpy.float32)
+                    stop_times = numpy.array([self.spiketrains[idx].interval.t_stop() for idx in self.id_list()], numpy.float64)
                     t_stop  = numpy.max(stop_times)
                     logging.debug("Warning, t_stop  is infered from the data : %f" %t_stop)     
@@ -887 +903 @@
                 if t_start == None :
                     try:
-                        start_times = numpy.array([self.spiketrains[idx].interval.t_start() for idx in self.id_list()], numpy.float32)
+                        start_times = numpy.array([self.spiketrains[idx].interval.t_start() for idx in self.id_list()], numpy.float64)
                         t_start = numpy.min(start_times)
                         logging.debug("Warning, t_start is infered from the data : %f" %t_start)
@@ -897 +913 @@
                     if t_start.__class__.__name__ == 'float' or t_start.__class__.__name__ == 'int' :
                         try:
-                            stop_times = numpy.array([self.spiketrains[idx].interval.t_stop() for idx in self.id_list()], numpy.float32)
+                            stop_times = numpy.array([self.spiketrains[idx].interval.t_stop() for idx in self.id_list()], numpy.float64)
                             t_stop  = numpy.max(stop_times)
                             logging.debug("Warning, t_stop  is infered from the data : %f" %t_stop)     
@@ -1009 +1025 @@
         return (self.interval.t_start(), self.interval.t_stop())
 
+    def update_t_start_and_t_stop(self):
+        """
+        Update the t_start and t_stop constant to reflect the current t_start() and t_stop() methods
+        """
+        self.t_start = self.interval.t_start()
+        self.t_stop = self.interval.t_stop()
+
     def time_axis(self, time_bin):
         """
@@ -1047 +1070 @@
             for id in sl.id_list():
                 self.append(id, sl.spiketrains[id])
+        self.update_t_start_and_t_stop()
+
 
     def merge(self, spikelist, relative=False):
@@ -1072 +1097 @@
                     spiketrain.relative_times()
                 self.append(id, spiketrain)
+        self.update_t_start_and_t_stop()
                 
     
@@ -1136 +1162 @@
         """
         interval = Interval((t_start, t_stop))
-        return self.interval_slice(interval)
+        sliced = self.interval_slice(interval)
+        sliced.update_t_start_and_t_stop()
+        return sliced
         
         
@@ -1173 +1201 @@
         for id in self.id_list():
             self.spiketrains[id].time_offset(offset)
-    
+        self.update_t_start_and_t_stop()
+
     def id_offset(self, offset):
         """

branches/interval/test/test_spikes.py

@@ -129 +129 @@
         assert   30 < spk1.mean_rate() < 50
         self.assertEqual(spk2.mean_rate(), 1000.0)
-        self.assertAlmostEqual(spk2.mean_rate(t_stop=4.99999999999), 1000.0, 6)
+        self.assertAlmostEqual(spk2.mean_rate(t_stop=4.999999)/1000., 1.0, 6)
         self.assertEqual(spk2.mean_rate(t_stop=5.0), 1200.0)