Changeset 372

Timestamp:

06/18/08 14:47:45 (5 months ago)

Author:

apdavison

Message:

recording.write_compatible_output() now takes an input_format argument, specifying the order of time, id, voltage, etc columns.

Note, in nest2, reintroduced the use of recording_device.interval, since that seems to have reappeared (I'm using NEST version 1.9-7295 Jun 11 2008).

Files:

• trunk/src/nest2/__init__.py (modified) (3 diffs)
• trunk/src/neuron/__init__.py (modified) (1 diff)
• trunk/src/neuron2/utility.py (modified) (4 diffs)
• trunk/src/recording.py (modified) (3 diffs)

trunk/src/nest2/__init__.py

@@ -99 +99 @@
-    """Encapsulates data and functions related to recording model variables."""
-    
+    formats = {'spikes': 'id t',
+               'v': 'id t v'}
+    
-    def __init__(self, variable, population=None, file=None):
-        """
@@ -115 +118 @@
-        self._device = nest.Create(device_name)
-        device_parameters = {"withgid": True, "withtime": True,
-
+
+
-        if file is False:
-            device_parameters.update(to_file=False, to_memory=True)
@@ -158 +162 @@
-                user_filename += '.%d' % rank()
-            if gather == False or rank() == 0: # if we gather, only do this on the master node
-
+ Recorder.formats[self.variable],
-                                                  self.population, get_time_step())
-        else:

trunk/src/neuron/__init__.py

@@ -400 +400 @@
-                write_data()
-        else:
-
+
+
-            write_data()
-                

trunk/src/neuron2/utility.py

@@ -1 +1 @@
-from pyNN import __path__ as pyNN_path
-
+, recording
-import platform
-import logging
@@ -27 +27 @@
-    """Encapsulates data and functions related to recording model variables."""
-    
-
+numpy_
-               'v': "%g\t%g\t%d"}
+    formats = {'spikes': 't id',
+               'v': 't v id'}
-    
-    def __init__(self, variable, population=None, file=None):
@@ -40 +42 @@
-        self.filename = file or None
-        self.population = population # needed for writing header information
-
+
+
-
-    def record(self, ids):
@@ -80 +83 @@
-    def write(self, file=None, gather=False, compatible_output=True):
-        data = self.get(gather)
-
+
+
+
+
+
-        
-class Initializer(object):

trunk/src/recording.py

@@ -57 +57 @@
-            
-    
-
+input_format, 
-    """
-    Rewrite simulation data in a standard format:
@@ -63 +63 @@
-    """
-    logging.info("Writing %s in compatible format (was %s)" % (user_filename, sim_filename))
-    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.id_start)
-        result.write("# last_id = %d\n" % (population.id_start+len(population)-1,))
-        padding = population.id_start
-    else:
-        padding = 0
-    result.write("# dt = %g\n" % dt)
-                    
-    # Writing spiketimes, cell_id-min(cell_id)                    
@@ -79 +68 @@
-    if os.path.getsize(sim_filename) > 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.id_start)
+            result.write("# last_id = %d\n" % (population.id_start+len(population)-1,))
+            padding = population.id_start
+        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?
-        #data = data[indx]
+        input_format = input_format.split()
+        time_column = input_format.index('t')
+        id_column = input_format.index('id')
+        
-        if data.shape[1] == 4: # conductance files
+            ge_column = input_format.index('ge')
+            gi_column = input_format.index('gi')
-            raise Exception("Not yet implemented")
-        elif data.shape[1] == 3: # voltage files
+            v_column = input_format.index('v')
-            #result.write("# n = %d\n" % int(nest.GetStatus([0], "time")[0]/dt))
-            result.write("# n = %d\n" % len(data))
-            for idx in xrange(len(data)):
-2], data[idx][0
+v_column], data[idx][id_column
-        elif data.shape[1] == 2: # spike files
-            for idx in xrange(len(data)):
-1], data[idx][0
+t_column], data[idx][id_column
-        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)
-
-
-
+
-def readArray(filename, sepchar=None, skipchar='#'):
-    """