Changeset 465

Timestamp:

10/02/08 11:38:28 (2 months ago)

Author:

apdavison

Message:

Various minor bug-fixes

Files:

• trunk/src/__init__.py (modified) (1 diff)
• trunk/src/nest2/__init__.py (modified) (7 diffs)
• trunk/src/neuron/__init__.py (modified) (2 diffs)
• trunk/src/neuron2/__init__.py (modified) (1 diff)
• trunk/src/pcsim/__init__.py (modified) (1 diff)
• trunk/src/pcsim/cells.py (modified) (2 diffs)
• trunk/src/random.py (modified) (1 diff)
• trunk/src/recording.py (modified) (1 diff)
• trunk/test/rngtests.py (modified) (1 diff)

trunk/src/__init__.py

@@ -2 +2 @@
-__all__ = ["common", "random", "nest1", "nest2", "neuron", "neuron2", "pcsim", 'brian' ]
-
+#

trunk/src/nest2/__init__.py

@@ -2 +2 @@
-"""
-PyNEST v2 implementation of the PyNN API.
-:__init__.py 188 2008-01-29 10:03:59Z apdavison 
+
-"""
-__version__ = "$Rev:188 $"
-
-import nest
@@ -174 +173 @@
-        return data
-    
+    def _get_header(self, file_name):
+        header = {}
+        if os.path.exists(file_name):
+            f = open(file_name, 'r')
+            for line in f:
+                if line[0] == '#':
+                    key, value = line[1:].split("=")
+                    header[key.strip()] = value.strip()
+        else:
+            logging.warning("File %s does not exist, so could not get header." % file_name)
+        return header
+    
+    def _strip_header(self, input_file_name, output_file_name):
+        if os.path.exists(input_file_name):
+            fin = open(input_file_name, 'r')
+            fout = open(output_file_name, 'a')
+            for line in fin:
+                if line[0] != '#':
+                    fout.write(line)
+            fin.close()
+            fout.close()
+    
-    def write(self, file=None, gather=False, compatible_output=True):
-        if self._device is None:
@@ -182 +203 @@
-                user_file += '.%d' % rank()
-            recording.rename_existing(user_file)
+        logging.debug("Recorder is writing '%s' to file '%s' with gather=%s and compatible_output=%s" % (self.variable,
+                                                                                                         user_file,
+                                                                                                         gather,
+                                                                                                         compatible_output))
-        nest_filename = _merge_files(self._device, gather)
-        if compatible_output:
@@ -189 +214 @@
-            # is escaped while reading the file, there is no problem
-           recording.write_compatible_output(nest_filename, user_file,
- 
- 
- 
+
+
+
-        else:
-            if isinstance(user_file, basestring):
@@ -201 +226 @@
-            else:
-                raise Exception('Must provide a filename or an open file')
-
+
+
+
-            root_file = file or self.filename
+            logging.debug("Gathering files generated by different nodes into %s" % root_file)
+            n_cells = 0
-            recording.rename_existing(root_file)
-
-
+
+
+
-                if os.path.exists(node_file):
-
+
+
+
+
+
+
+
-                    os.system('rm %s' % node_file)
+            # write header for gathered file
+            f = open("tmp_header", 'w')
+            header['n'] = n_cells
+            for k,v in header.items():
+                f.write("# %s = %s\n" % (k,v))
+            f.close()
+            os.system('cat %s >> tmp_header' % root_file)
+            os.system('mv tmp_header %s' % root_file)
-        # don't want to remove nest_filename at this point in case the user wants to access the data
-        # a second time (e.g. with both getSpikes() and printSpikes()), but we should
@@ -340 +384 @@
-    except nest.NESTError:    
-        nest.SetStatus([0], {'data_path':tempdir,})
-
-
+
-
-    # set kernel RNG seeds
@@ -363 +406 @@
-                                                'max_delay': max_delay})
-
+    # set resolution
+    nest.SetStatus([0], {'resolution': timestep})
-    return nest.Rank()
-

trunk/src/neuron/__init__.py

@@ -8 +8 @@
-__version__ = "$Rev$"
-
-, Vector
+
-h = hoc.HocObject()
-from pyNN import __path__ as pyNN_path
@@ -113 +113 @@
-        for name, val in parameters.items():
-            if hasattr(val, '__len__'):
-
+
+
-            else:
-                setattr(cell, name, val)

trunk/src/neuron2/__init__.py

@@ -135 +135 @@
-    all_ids = numpy.array([id for id in range(first_id, last_id+1)], ID)
-    # mask_local is used to extract those elements from arrays that apply to the cells on the current node
-0
+rank()
-    for i,(id,is_local) in enumerate(zip(all_ids, mask_local)):
-        if is_local:

trunk/src/pcsim/__init__.py

@@ -921 +921 @@
-    nProj = 0
-    
-    #class ConnectionDict:
-    #        
-    #    def __init__(self, parent):
-    #        self.parent = parent
-    #
-    #    def __getitem__(self, id):
-    #        """Returns a connection id.
-    #        Suppose we have a 2D Population (5x3) projecting to a 3D Population (4x5x7).
-    #        Total number of possible connections is 5x3x4x5x7 = 2100.
-    #        Therefore valid calls are:
-    #        connection[2099] - 2099th possible connection (may not exist)
-    #        connection[14,139] - connection between 14th pre- and 139th postsynaptic neuron (may not exist)
-    #        connection[(4,2),(3,4,6)] - connection between presynaptic neuron with address (4,2)
-    #        and post-synaptic neuron with address (3,4,6) (may not exist).
-    #        """
-    #        if isinstance(id, int): # linear mapping
-    #            preID = id/self.parent.post.size; postID = id%self.parent.post.size
-    #            return self.__getitem__((preID, postID))
-    #        elif isinstance(id, tuple): # (pre, post)
-    #            if len(id) == 2:
-    #                pre = id[0]
-    #                post = id[1]
-    #                if isinstance(pre, int) and isinstance(post, int):
-    #                    pre_coords = self.parent.pre.locate(pre)
-    #                    post_coords = self.parent.post.locate(post)
-    #                    return self.__getitem__((pre_coords, post_coords))
-    #                elif isinstance(pre, tuple) and isinstance(post, tuple): # should also allow lists
-    #                    if len(pre) == self.parent.pre.ndim and len(post) == self.parent.post.ndim:
-    #                        fmt = "[%d]"*(len(pre)+len(post))
-    #                        address = fmt % (pre+post)
-    #                    else:
-    #                        raise common.InvalidDimensionsError
-    #                else:
-    #                    raise KeyError
-    #            else:
-    #                raise common.InvalidDimensionsError
-    #        else:
-    #            raise KeyError #most appropriate?
-    #        
-    #        return address
-    #
-    
-    def __init__(self, presynaptic_population, postsynaptic_population, method='allToAll', method_parameters=None, source=None, target=None, synapse_dynamics=None, label=None, rng=None):
-        """

trunk/src/pcsim/cells.py

@@ -89 +89 @@
-
-
-alpha
+exp
-    """Leaky integrate and fire model with fixed threshold and 
-    exponentially-decaying post-synaptic conductance."""
@@ -112 +112 @@
-        
-    def __init__(self, parameters):
-alpha
+exp
-        self.parameters['Inoise'] = 0.0
-        self.simObjFactory = LIFCondExpNeuron(**self.parameters)

trunk/src/random.py

@@ -99 +99 @@
-            # This assumption is not true for NEST
-            rarr = rarr[numpy.arange(self.rank, len(rarr), self.num_processes)]
-
+
+
+
+
-
-class GSLRNG(AbstractRNG):

trunk/src/recording.py

@@ -186 +186 @@
-        user_file.write(data_array, metadata)
-    else:
-sim_filenam
+data_sourc
-
-def readArray(filename, sepchar=None, skipchar='#'):

trunk/test/rngtests.py

@@ -29 +29 @@
-            
-    def testNonPositiveN(self):
-=
+
-        for rng in self.rnglist:
-            self.assertRaises(ValueError,rng.next,0)
-            self.assertRaises(ValueError,rng.next,-1)
+
+    def testNZero(self):
+        """Calling next(0) should return an empty array."""
+        for rng in self.rnglist:
+            self.assertEqual(len(rng.next(0)), 0)
-
-# ==============================================================================