Changeset 416

Timestamp:

07/16/08 10:40:43 (1 month ago)

Author:

apdavison

Message:

Harmonization of logging setup across simulators (see #66). Also fixes bug #105.

Files:

• trunk/src/nest1/__init__.py (modified) (3 diffs)
• trunk/src/nest2/__init__.py (modified) (3 diffs)
• trunk/src/neuron/__init__.py (modified) (3 diffs)
• trunk/src/neuron2/__init__.py (modified) (1 diff)
• trunk/src/recording.py (modified) (2 diffs)
• trunk/src/utility.py (modified) (1 diff)

trunk/src/nest1/__init__.py

@@ -7 +7 @@
-
-import pynest
-
+, utility
-from pyNN.random import *
-import numpy, types, sys, shutil, os, logging, copy, tempfile
@@ -88 +88 @@
-    global tempdir
-    
+    # Initialisation of the log module. To write in the logfile, simply enter
+    # logging.critical(), logging.debug(), logging.info(), logging.warning() 
+    log_file = "nest1.log"
+    if debug:
+        if isinstance(debug, basestring):
+            log_file = debug
+    utility.init_logging(log_file, debug, num_processes(), rank())
+    logging.info("Initialization of Nest")
+    
-    tempdir = tempfile.mkdtemp()
-    tempdirs.append(tempdir) # append tempdir to tempdirs list
@@ -111 +120 @@
-                        'rng_seeds'   : rng_seeds[0:num_threads],
-                        'buffsize'    : batchsize})
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
-    return 0
-

trunk/src/nest2/__init__.py

@@ -7 +7 @@
-
-import nest
-
+, utility
-from pyNN.random import *
-from pyNN import recording
@@ -290 +290 @@
-    simulator but not by others.
-    """
+    global tempdir
+    log_file = "nest2.log"
+    if debug:
+        if isinstance(debug, basestring):
+            log_file = debug
+    utility.init_logging(log_file, debug, num_processes(), rank())
+    logging.info("Initialization of Nest")
-    common.setup(timestep, min_delay, max_delay, debug, **extra_params)
-    global tempdir
-    assert min_delay >= timestep, "min_delay (%g) must be greater than timestep (%g)" % (min_delay, timestep)
-
@@ -327 +333 @@
-                                                'max_delay': max_delay})
-
-    # Initialisation of the log module. To write in the logfile, simply enter
-    # logging.critical(), logging.debug(), logging.info(), logging.warning()
-    if debug:
-        if isinstance(debug, basestring):
-            filename = debug
-        else:
-            filename = "nest.log"
-        logging.basicConfig(level=logging.DEBUG,
-                    format='%(asctime)s %(levelname)s %(message)s',
-                    filename=filename,
-                    filemode='w')
-    else:
-        logging.basicConfig(level=logging.INFO,
-                    format='%(asctime)s %(levelname)s %(message)s',
-                    filename='nest.log',
-                    filemode='w')
-
-    logging.info("Initialization of Nest")
-    return nest.Rank()
-

trunk/src/neuron/__init__.py

@@ -13 +13 @@
-from pyNN.random import *
-from math import *
-
+, utility
-from pyNN.neuron.cells import *
-from pyNN.neuron.connectors import *
@@ -414 +414 @@
-    simulator but not by others.
-    """
-logger, 
+
-    load_mechanisms()
-    if 'quit_on_end' in extra_params:
-        quit_on_end = extra_params['quit_on_end']
-    # Initialisation of the log module. To write in the logfile, simply enter
-    # logging.critical(), logging.debug(), logging.info(), logging.warning() 
-    if debug:
-        logging.basicConfig(level=logging.DEBUG,
-                    format='%(asctime)s %(levelname)s %(message)s',
-                    filename='neuron.log',
-                    filemode='w')
-    else:
-        logging.basicConfig(level=logging.INFO,
-                    format='%(asctime)s %(levelname)s %(message)s',
-                    filename='neuron.log',
-                    filemode='w')
-        
-    logging.info("Initialization of NEURON (use setup(.., debug=True) to see a full logfile)")
-    
-    # All the objects that will be used frequently in the hoc code are declared in the setup
@@ -462 +448 @@
-            h('cvode = new CVode()')
-            h.cvode.active(1)
-
+
+
+
+
+
+
+
+
+
+
-    nhost = int(h.pc.nhost())
-    if nhost < 2:

trunk/src/neuron2/__init__.py

@@ -37 +37 @@
-    global quit_on_end
-    if not simulator.state.initialized:
-.%d" % rank(), debug
+", debug, num_processes(), rank()
-        logging.info("Initialization of NEURON (use setup(.., debug=True) to see a full logfile)")
-        simulator.state.initialized = True

trunk/src/recording.py

@@ -124 +124 @@
-    saved by the simulators).
-    """
-    logging.debug(filename)
-    myfile = open(filename, "r", DEFAULT_BUFFER_SIZE)
-    contents = myfile.readlines()
-    myfile.close()
-    logging.debug(contents)
-    data = []
-    for line in contents:
@@ -139 +137 @@
-    if a.size > 0:
-        (Nrow, Ncol) = a.shape
-
+#
-        #if ((Nrow == 1) or (Ncol == 1)): a = numpy.ravel(a)
-    return a

trunk/src/utility.py

@@ -44 +44 @@
-    return args
-    
-
+
+
+
-    if debug:
-        logging.basicConfig(level=logging.DEBUG,