Changeset 397 for trunk

Timestamp:

06/12/09 09:17:12 (3 years ago)

Author:

pierre

Message:

Minor modifications

Location:

trunk/src

Files:

• io.py (modified) (3 diffs)
• signals/spikes.py (modified) (6 diffs)

trunk/src/io.py

@@ -27 +27 @@
 
 import os, logging, cPickle, numpy
-DEFAULT_BUFFER_SIZE = 10000
-
+DEFAULT_BUFFER_SIZE = -1
 
 class FileHandler(object):
@@ -157 +156 @@
     def get_data(self, sepchar = "\t", skipchar = "#"):
         """
-        Load data from a text file and returns a list of data
+        Load data from a text file and returns an array of the data
         """
         myfile = open(self.filename, "r", DEFAULT_BUFFER_SIZE)
@@ -164 +163 @@
         data = []
         for line in contents:
-            line = line.strip()
-            if (len(line) != 0):
-                if (line[0] != skipchar):
-                    line = line.split(sepchar)
-                    id    = [int(float(line[-1]))]
-                    id.extend(map(float, line[0:-1]))
-                    data.append(id)
+            if (line[0] != skipchar):
+                line = line.strip().split(sepchar)
+                id   = [int(float(line[-1]))]
+                id.extend(map(float, line[0:-1]))
+                data.append(id)
         logging.debug("Loaded %d lines of data from %s" % (len(data), self))
         return numpy.array(data, numpy.float32)
+    
+    #def get_data(self, sepchar = "\t", skipchar = "#"):
+        #return numpy.loadtxt(self.filename, dtype=numpy.float32)
 
     def write(self, object):

trunk/src/signals/spikes.py

@@ -559 +559 @@
             
         if nspk_1 > 0 and nspk_2 > 0:
-            for i in xrange(1,nspk_1+1):
-                for j in xrange(1,nspk_2+1):
+            for i in xrange(1, nspk_1+1):
+                for j in xrange(1, nspk_2+1):
                     scr[i,j] = min(scr[i-1,j]+1,scr[i,j-1]+1)
                     scr[i,j] = min(scr[i,j],scr[i-1,j-1]+cost*abs(self.spike_times[i-1]-spktrain.spike_times[j-1]))
@@ -591 +591 @@
         if len(idx_spikes) > 0:
             for spike in idx_spikes[1:]:
-                vec_1[previous_spike:spike] = (spike-previous_spike)*dt
+                vec_1[previous_spike:spike] = (spike-previous_spike)
                 previous_spike = spike
         idx_spikes     = numpy.array(spktrain.spike_times/dt,int)
@@ -597 +597 @@
         if len(idx_spikes) > 0:
             for spike in idx_spikes[1:]:
-                vec_2[previous_spike:spike] = (spike-previous_spike)*dt
+                vec_2[previous_spike:spike] = (spike-previous_spike)
                 previous_spike = spike
         idx = numpy.where(vec_1 < vec_2)[0]
@@ -1547 +1547 @@
         The 'dimensions' attribute of the SpikeList must be defined
         
+        Examples:
+            >> spklist.id2position(2536)
+                (25, 35)
+        
         See also
             activity_map, activity_movie
@@ -1560 +1564 @@
 
 
-    #def position2id(self, id):
-        #"""
-        #Return the id  of the cell at position (x,y) if the cells are aranged on a
-        #grid of size dims, as defined in the dims attribute of the SpikeList object
-        
-        #Inputs:
-            #id - the id of the cell
-        
-        #The 'dimensions' attribute of the SpikeList must be defined
-        
-        #See also
-            #activity_map, activity_movie
-        #"""
-        #if self.dimensions is None:
-            #raise Exception("Dimensions of the population are not defined ! Set spikelist.dimensions")
-        #if len(self.dimensions) == 1:
-            #return id
-        #if len(self.dimensions) == 2:
-            #x = id % self.dimensions[0]
-            #y = numpy.floor(id/self.dimensions[0])
-            #return (x,y)
+    def position2id(self, position):
+        """
+        Return the id of the cell at position (x,y) if the cells are aranged on a
+        grid of size dims, as defined in the dims attribute of the SpikeList object
+        
+        Inputs:
+            position - a tuple with the position of the cell
+                    
+        The 'dimensions' attribute of the SpikeList must be defined and have the same shape
+        as the position argument
+        
+        Examples:
+            >> spklist.position2id((25,35))
+                2536
+        
+        See also
+            activity_map, activity_movie, id2position
+        """
+        if self.dimensions is None:
+            raise Exception("Dimensions of the population are not defined ! Set spikelist.dimensions")
+        assert array(position).shape == self.dimensions.shape, "position does not have the correct shape !"
+        if len(self.dimensions) == 1:
+            return position
+        if len(self.dimensions) == 2:
+            return position[0]*self.dimensions[0] + position[1]
 
 
@@ -1835 +1843 @@
         pairs = pairs_generator.get_pairs(nb_pairs)
         N     = len(pairs)
-        
         distance   = 0.
-        
         for idx in xrange(N):
             idx_1 = pairs[idx,0]