Changeset 401 for trunk

Timestamp:

06/16/09 16:45:16 (3 years ago)

Author:

pierre

Message:

Fix a bug in psth, do some improvement on the interval.py file

Location:

trunk/src

Files:

• io.py (modified) (1 diff)
• signals/intervals.py (modified) (4 diffs)
• signals/spikes.py (modified) (4 diffs)

trunk/src/io.py

@@ -160 +160 @@
         try:
             import TableIO
-            data = TableIO.readTableAsArray(self.filename, skipchar)
+            data = numpy.fliplr(TableIO.readTableAsArray(self.filename, skipchar))
         except ImportError:
             myfile = open(self.filename, "r", DEFAULT_BUFFER_SIZE)

trunk/src/signals/intervals.py

@@ -1 +1 @@
 from NeuroTools import check_dependency
 
-if check_dependency('interval'):
+HAVE_INTERVAL = check_dependency('interval')
+
+if HAVE_INTERVAL:
     from interval import * 
 
@@ -25 +27 @@
 
         """
-        self.start_times = start_times
-        self.end_times   = end_times
-        # write the intervals to an interval object (pyinterval)
-        if len(start_times) != len(end_times) :
-            raise Exception("There sould be an equal number of starts and stops")
-        self.interval_data = interval(*numpy.transpose(numpy.array([start_times,end_times])))
-        
+        if HAVE_INTERVAL:
+            self.start_times = start_times
+            self.end_times   = end_times
+            # write the intervals to an interval object (pyinterval)
+            test = isinstance(start_times, int) or isinstance(start_times, float)
+            if test:
+                start_times = [start_times]
+            test = isinstance(end_times, int) or isinstance(end_times, float)
+            if test:
+                end_times = [end_times]
+            if len(start_times) != len(end_times) :
+                raise Exception("There sould be an equal number of starts and stops")
+            self.interval_data = interval(*numpy.transpose(numpy.array([start_times,end_times])))
+        else:
+            test = isinstance(start_times, int) or isinstance(start_times, float)
+            assert test, "Interval package not present, start_times should be a number !"
+            test = isinstance(end_times, int) or isinstance(end_times, float)
+            assert test, "Interval package not present, end_times should be a number !"
+            self.start_times = start_times
+            self.end_times   = end_times
+
     def intersect(self, itv) :
         self.interval_data = self.interval_data & itv.interval_data
@@ -56 +72 @@
         bounds = self.interval_data.extrema
         return (bounds[0][0],bounds[-1][0])
+    
+    def t_start(self):
+        if HAVE_INTERVAL:
+            return self.interval_data.extrema[0][0]
+        else:
+            return self.start_times[0]
+    
+    def t_stop(self):
+        if HAVE_INTERVAL:
+            return self.interval_data.extrema[-1][0]
+        else:
+            return self.end_times[0]
     
     def copy(self):
@@ -106 +134 @@
         return tot_duration
 
+
+    def slice_times(self, times):
+        spikes_selector = numpy.zeros(len(times), dtype=numpy.bool)
+        if HAVE_INTERVAL:
+            for itv in self.interval_data :
+                spikes_selector = spikes_selector + (times > itv[0])*(times <= itv[1])
+        else:
+            spikes_selector = (times >= self.t_start()) & (times <= self.t_stop())
+        return numpy.extract(spikes_selector, times)
+
+
+
 #def build_psth(spiketrain, eventtrain, before_Dt, after_Dt, intervals=None):
     #"""         

trunk/src/signals/spikes.py

@@ -401 +401 @@
         return axis
 
-    def raster_plot(self, t_start=None, t_stop=None, display=True, kwargs={}):
+    def raster_plot(self, t_start=None, t_stop=None, interval=None, display=True, kwargs={}):
         """
         Generate a raster plot with the SpikeTrain in a subwindow of interest,
@@ -422 +422 @@
         if t_start is None: t_start = self.t_start
         if t_stop is None:  t_stop = self.t_stop
-        spikes = numpy.extract((self.spike_times >= t_start) & (self.spike_times <= t_stop), self.spike_times)
+        
+        if interval is None:
+            interval = Interval(t_start, t_stop)
+        
+        spikes  = interval.slice_times(self.spike_times)
         subplot = get_display(display)
         if not subplot or not HAVE_PYLAB:
@@ -488 +492 @@
                 100
         """
-        spikes_selector = numpy.zeros(len(self.spike_times), dtype=numpy.bool)
+        times           = interval.slice_times(self.spike_times)
         t_start, t_stop = interval.time_parameters()
-        for itv in interval.interval_data :
-            spikes_selector = spikes_selector + (self.spike_times > itv[0])*(self.spike_times <= itv[1])   
-        return SpikeTrain(numpy.extract(spikes_selector, self.spike_times), t_start, t_stop)
+        return SpikeTrain(times, t_start, t_stop)
+        
 
     def time_histogram(self, time_bin=10, normalized=True):
@@ -2007 +2010 @@
         t_min_l  = numpy.floor(t_min/time_bin)
         t_max_l  = numpy.floor(t_max/time_bin)
+        t_start  = numpy.floor(self.t_start/time_bin)
+        t_stop   = numpy.floor(self.t_stop/time_bin)
         for ev in events:
-           ev = int((ev-self.t_start)/time_bin)
-           if (ev > self.t_start + t_min_l) and ev < self.t_stop-t_max_l:
+           ev = int((ev-t_start)/time_bin)
+           if ((ev -t_min_l )> t_start) and (ev +t_max_l ) < t_stop:
                count  += 1
                result += spk_hist[:,(ev-t_min_l):ev+t_max_l]