Changeset 444

Timestamp:

08/20/08 11:42:21 (3 months ago)

Author:

apdavison

Message:

gather=True is working again for neuron.

When writing compatible output, if there are no spikes then an empty file (with just the header) is written. Before, no file was written.

Files:

• trunk/src/neuron/__init__.py (modified) (11 diffs)
• trunk/src/recording.py (modified) (2 diffs)

trunk/src/neuron/__init__.py

@@ -23 +23 @@
-import logging
-import platform
+import tempfile
-Set = set
-
@@ -330 +331 @@
-    
-    def write(self, file=None, gather=False, compatible_output=True):
-
-
+
+
+
-        vector_operation = ''
-        if self.variable == 'spikes':
@@ -338 +340 @@
-        if self.population is None:
-            cell_template = "cell%d"
-label = "node%d: post cellX.%s" % (myid, self.variable)
+fmt = "node%%d: post cellX.%s" % self.variable
-            id_list = gidlist
-            padding = 0
-        else:
-            cell_template = "%s.object(%s)" % (self.population.hoc_label, "%d")
-label = 'node%d: post_%s.%s' % (myid, 
+fmt = 'node%%d: post_%s.%s' % (
-            id_list = self.population.gidlist
-            padding = self.population.first_id
@@ -349 +351 @@
-        def post_data():
-            pack_template = 'tmp = pc.pack(%s.%s%s)' % (cell_template,
-
+S
-                                                        vector_operation)
+            hoc_commands = ['tmp = pc.pack(%d)' % len(self.recorded)]
-            for cell in self.recorded:
-
+cell, #
-                                 pack_template % id_list.index(cell)]
-post_label
-self
+(post_fmt % myid,)
+ self.population
-        def take_data():
-
+#
-            for node in range(1, num_processes()):
-
-
+
+
+
+
+
-        def write_data():
-            if self.population is None:
@@ -388 +394 @@
-                hoc_commands += ['fmt = "%s\\t%d\\n"' % (num_format, cell-padding),
-                                 write_template % id_list.index(cell)]
-            # writing gathered data is currently broken
-            #hoc_commands += ['while i < gathered_vec_list.count()-2 { gathered_vec_list.o(i+1).printf(fileobj, "%s broken") ' % num_format]
-            hoc_commands += ['tmp = fileobj.close()']
-            hoc_execute(hoc_commands, "Recorder.write()")
+            # write gathered data
+            for id, vec in zip(h.gathered_id_vec, h.gathered_vec_list):
+                fmt = "%s\t%d\n" % (num_format, int(id)-padding)
+                vec.printf(h.fileobj, fmt)
+            h.fileobj.close()
+            
-            
-        if gather:
@@ -401 +410 @@
-        else:
-            if num_processes() > 1:
-
+
+
+
+
-            write_data()
-                
@@ -585 +597 @@
-        if tgt > gid or tgt < 0 or not isinstance(tgt, int):
-            raise common.ConnectionError, "Postsynaptic cell id %s does not exist." % str(tgt)
-
+hasattr(tgt.cellclass, '__name__') and 
-            weight = abs(weight) # weights must be positive for conductance-based synapses
-        if tgt in gidlist: # only create connections to cells that exist on this machine
@@ -598 +610 @@
-                else:
-                    if p >= 1.0 or rarr[j] < p: # might be more efficient to vectorise the latter comparison
-#
-
+
+#
-                                         'nc.delay = %g' % delay,
-                                         'nc.weight = %g' % weight,
@@ -608 +620 @@
-                if src > gid or src < 0 or not isinstance(src, int):
-                    raise common.ConnectionError, "Presynaptic cell id %s does not exist." % str(src)
-    print hoc_commands
-    hoc_execute(hoc_commands, "--- connect(%s,%s) ---" % (str(source), str(target)))
-    return range(nc_start, ncid)
@@ -1041 +1052 @@
-        """
-        # This is a bit of a hack implemetation
-"neuron_tmpfile"
+os.path.join(tempfile.mkdtemp(prefix="pyNN_neuron"), "getSpikes_tmpfile")
-        self.recorders['spikes'].write(tmpfile, gather, compatible_output=False)
-
-
+ and num_processes()>1
+.
-        if myid==0 or not gather:
-            f = open(tmpfile, 'r')
@@ -1051 +1062 @@
-            spikes = numpy.array([line2spike(line.split()) for line in lines])
-            f.close()
-
+ # should also remove tmp parent directory
-            return spikes
-        else:

trunk/src/recording.py

@@ -79 +79 @@
-        N = 0
-    
+    result = open(user_filename,'w',DEFAULT_BUFFER_SIZE)    
+    # Write header info (e.g., dimensions of the population)
+    if population is not None:
+        result.write("# dimensions =" + "\t".join([str(d) for d in population.dim]) + "\n")
+        result.write("# first_id = %d\n" % population.first_id)
+        result.write("# last_id = %d\n" % (population.first_id+len(population)-1,))
+        padding = population.first_id
+    else:
+        padding = 0
+    result.write("# dt = %g\n" % dt)
+        
-    if N > 0:
-        data = readArray(sim_filename, sepchar=None)
-        
-        result = open(user_filename,'w',DEFAULT_BUFFER_SIZE)    
-        # Write header info (e.g., dimensions of the population)
-        if population is not None:
-            result.write("# dimensions =" + "\t".join([str(d) for d in population.dim]) + "\n")
-            result.write("# first_id = %d\n" % population.first_id)
-            result.write("# last_id = %d\n" % (population.first_id+len(population)-1,))
-            padding = population.first_id
-        else:
-            padding = 0
-        result.write("# dt = %g\n" % dt)
-        
-        data[:,0] = data[:,0] - padding
-        
-        # sort
-        #indx = data.argsort(axis=0, kind='mergesort')[:,0] # will quicksort (not stable) work?
@@ -119 +117 @@
-        else:
-            raise Exception("Data file should have 2,3 or 4 columns, actually has %d" % data.shape[1])
-        result.close()
-    else:
-        logging.info("%s is empty" % sim_filename)
+        result.write("# n = 0\n")
+    result.close()
-
-def write_compatible_output1(data_source, user_filename, variable, input_format, population, dt):