Changeset 1000 for trunk

Timestamp:

10/30/11 15:45:23 (7 months ago)

Author:

apdavison

Message:

No longer store a global reference to the current simulator module in common. Now each class that needs it stores its own reference as the attribute _simulator. This will make it much easier to use more than one simulator at the same time, once Connector classes have been fixed up to use the simulator module only during connect(), not on creation

Location:

trunk

Files:

• src/brian/__init__.py (modified) (6 diffs)
• src/brian/connectors.py (modified) (3 diffs)
• src/brian/recording.py (modified) (1 diff)
• src/common/__init__.py (modified) (1 diff)
• src/common/control.py (modified) (1 diff)
• src/common/populations.py (modified) (13 diffs)
• src/common/projections.py (modified) (3 diffs)
• src/connectors.py (modified) (14 diffs)
• src/moose/__init__.py (modified) (6 diffs)
• src/multisim.py (modified) (2 diffs)
• src/nemo/__init__.py (modified) (8 diffs)
• src/nemo/connectors.py (modified) (1 diff)
• src/nemo/recording.py (modified) (1 diff)
• src/nest/__init__.py (modified) (7 diffs)
• src/nest/connectors.py (modified) (2 diffs)
• src/nest/recording.py (modified) (3 diffs)
• src/neuron/__init__.py (modified) (8 diffs)
• src/neuron/connectors.py (modified) (2 diffs)
• src/neuron/recording.py (modified) (1 diff)
• src/pcsim/__init__.py (modified) (7 diffs)
• src/pcsim/connectors.py (modified) (1 diff)
• src/pcsim/recording.py (modified) (1 diff)
• src/recording/__init__.py (modified) (4 diffs)
• test/system/scenarios.py (modified) (8 diffs)
• test/unittests/test_assembly.py (modified) (4 diffs)
• test/unittests/test_basepopulation.py (modified) (12 diffs)
• test/unittests/test_connectors.py (modified) (10 diffs)
• test/unittests/test_population.py (modified) (5 diffs)
• test/unittests/test_projection.py (modified) (1 diff)
• test/unittests/test_recording.py (modified) (2 diffs)
• test/unittests/test_simulation_control.py (modified) (2 diffs)
• test/unittests/test_utility_functions.py (modified) (1 diff)

trunk/src/brian/__init__.py

@@ -14 +14 @@
 from pyNN.brian import simulator
 from pyNN import common, recording, space, core, __doc__
-common.control.simulator = simulator
-recording.simulator = simulator
 from pyNN.random import *
 from pyNN.recording import files
@@ -89 +87 @@
 # ==============================================================================
 
-get_time_step = common.get_time_step
-get_min_delay = common.get_min_delay
-get_max_delay = common.get_max_delay
-num_processes = common.num_processes
-rank = common.rank
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+            num_processes, rank = common.control.build_state_queries(simulator)
 
 # ==============================================================================
@@ -99 +94 @@
 #   neurons.
 # ==============================================================================
+
+class Assembly(common.Assembly):
+    _simulator = simulator
+
+
+class PopulationView(common.PopulationView):
+    _simulator = simulator
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
+
 
 class Population(common.Population, common.BasePopulation):
@@ -105 +112 @@
     term intended to include layers, columns, nuclei, etc., of cells.
     """
+    _simulator = simulator
     recorder_class = Recorder
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
 
     def _create_cells(self, cellclass, cellparams=None, n=1):
@@ -187 +199 @@
 
 
-PopulationView = common.PopulationView
-Assembly = common.Assembly
-
 class Projection(common.Projection):
     """
@@ -196 +205 @@
     parameters of those connections, including of plasticity mechanisms.
     """
+    _simulator = simulator
     
     def __init__(self, presynaptic_population, postsynaptic_population, method,

trunk/src/brian/connectors.py

@@ -10 +10 @@
 from pyNN.random import RandomDistribution
 import numpy
-from pyNN import random, common, core
+from pyNN import core
 from pyNN.connectors import AllToAllConnector, \
                             ProbabilisticConnector, \
@@ -24 +24 @@
                             WeightGenerator, \
                             DelayGenerator, \
-                            ProbaGenerator
+                            ProbaGenerator, Connector
+from pyNN.brian import simulator
+
+Connector._simulator = simulator
+
 
 class FastProbabilisticConnector(ProbabilisticConnector):
@@ -125 +129 @@
                 raise Exception('Expression for weights or delays is not supported for OneToOneConnector !')
             weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
-            delays_generator  = DelayGenerator(self.delays, local, self.safe)                
+            delays_generator  = DelayGenerator(self.delays, local, kernel=projection._simulator.state, safe=self.safe)                
             weights           = weights_generator.get(N)
             delays            = delays_generator.get(N)

trunk/src/brian/recording.py

@@ -21 +21 @@
 class Recorder(recording.Recorder):
     """Encapsulates data and functions related to recording model variables."""
+    _simulator = simulator
   
     def __init__(self, variable, population=None, file=None):

trunk/src/common/__init__.py

@@ -49 +49 @@
 
 from populations import IDMixin, BasePopulation, Population, PopulationView, Assembly, is_conductance
-from projections import Projection, check_weight, check_delay, DEFAULT_WEIGHT
+from projections import Projection, check_weight, DEFAULT_WEIGHT
 from procedural_api import build_create, build_connect, set, build_record, initialize
-from control import setup, end, run, reset, get_current_time, get_time_step, \
-                    get_min_delay, get_max_delay, num_processes, rank
+from control import setup

trunk/src/common/control.py

@@ -40 +40 @@
     raise NotImplementedError
 
-def reset():
-    """
-    Reset the time to zero, neuron membrane potentials and synaptic weights to
-    their initial values, and delete any recorded data. The network structure
-    is not changed, nor is the specification of which neurons to record from.
-    """
-    simulator.reset()
+def build_reset(simulator):
+    def reset():
+        """
+        Reset the time to zero, neuron membrane potentials and synaptic weights to
+        their initial values, and delete any recorded data. The network structure
+        is not changed, nor is the specification of which neurons to record from.
+        """
+        simulator.reset()
+    return reset
 
-def get_current_time():
-    """Return the current time in the simulation."""
-    return simulator.state.t
-
-def get_time_step():
-    """Return the integration time step."""
-    return simulator.state.dt
-
-def get_min_delay():
-    """Return the minimum allowed synaptic delay."""
-    return simulator.state.min_delay
-
-def get_max_delay():
-    """Return the maximum allowed synaptic delay."""
-    return simulator.state.max_delay
-
-def num_processes():
-    """Return the number of MPI processes."""
-    return simulator.state.num_processes
-
-def rank():
-    """Return the MPI rank of the current node."""
-    return simulator.state.mpi_rank
+def build_state_queries(simulator):
+    def get_current_time():
+        """Return the current time in the simulation."""
+        return simulator.state.t
+    
+    def get_time_step():
+        """Return the integration time step."""
+        return simulator.state.dt
+    
+    def get_min_delay():
+        """Return the minimum allowed synaptic delay."""
+        return simulator.state.min_delay
+    
+    def get_max_delay():
+        """Return the maximum allowed synaptic delay."""
+        return simulator.state.max_delay
+    
+    def num_processes():
+        """Return the number of MPI processes."""
+        return simulator.state.num_processes
+    
+    def rank():
+        """Return the MPI rank of the current node."""
+        return simulator.state.mpi_rank
+    
+    return get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank

trunk/src/common/populations.py

@@ -166 +166 @@
             return self.all_cells[index]
         elif isinstance(index, (slice, list, numpy.ndarray)):
-            return PopulationView(self, index)
+            return self._get_view(index)
         elif isinstance(index, tuple):
-            return PopulationView(self, list(index))
+            return self._get_view(list(index))
         else:
             raise TypeError("indices must be integers, slices, lists, arrays or tuples, not %s" % type(index).__name__)
@@ -206 +206 @@
         """
         assert isinstance(other, BasePopulation)
-        return Assembly(self, other)
+        return self.assembly_class(self, other)
 
     def _get_cell_position(self, id):
@@ -248 +248 @@
         logger.debug("The %d cells recorded have indices %s" % (n, indices))
         logger.debug("%s.sample(%s)", self.label, n)
-        return PopulationView(self, indices)
+        return self._get_view(indices)
 
     def get(self, parameter_name, gather=False):
@@ -262 +262 @@
             values = [getattr(cell, parameter_name) for cell in self]  # list or array?
         
-        if gather == True and control.num_processes() > 1:
-            all_values  = { control.rank(): values }
-            all_indices = { control.rank(): self.local_cells.tolist()}
+        if gather == True and self._simulator.state.num_processes > 1:
+            all_values  = { self._simulator.state.mpi_rank: values }
+            all_indices = { self._simulator.state.mpi_rank: self.local_cells.tolist()}
             all_values  = recording.gather_dict(all_values)
             all_indices = recording.gather_dict(all_indices)
-            if control.rank() == 0:
+            if self._simulator.state.mpi_rank == 0:
                 values  = reduce(operator.add, all_values.values())
                 indices = reduce(operator.add, all_indices.values())
@@ -582 +582 @@
         spike_counts = self.recorders['spikes'].count(gather, self.record_filter)
         total_spikes = sum(spike_counts.values())
-        if control.rank() == 0 or not gather:  # should maybe use allgather, and get the numbers on all nodes
+        if self._simulator.state.mpi_rank == 0 or not gather:  # should maybe use allgather, and get the numbers on all nodes
             if len(spike_counts) > 0:
                 return float(total_spikes)/len(spike_counts)
@@ -610 +610 @@
         result[:,0]   = cells
         result[:,1:4] = self.positions.T 
-        if control.rank() == 0:
+        if self._simulator.state.mpi_rank == 0:
             file.write(result, {'population' : self.label})
             file.close()
@@ -707 +707 @@
         (order in the Population), counting only cells on the local MPI node.
         """
-        if control.num_processes() > 1:
+        if self._simulator.state.num_processes > 1:
             return self.local_cells.tolist().index(id)          # probably very slow
             #return numpy.nonzero(self.local_cells == id)[0][0] # possibly faster?
@@ -1098 +1098 @@
             pindices = boundaries[1:].searchsorted(indices, side='right')
             views = (self.populations[i][indices[pindices==i] - boundaries[i]] for i in numpy.unique(pindices))
-            return Assembly(*views)
+            return self.__class__(*views)
         else:
             raise TypeError("indices must be integers, slices, lists, arrays, not %s" % type(index).__name__)
@@ -1110 +1110 @@
         """
         if isinstance(other, BasePopulation):
-            return Assembly(*(self.populations + [other]))
+            return self.__class__(*(self.populations + [other]))
         elif isinstance(other, Assembly):
-            return Assembly(*(self.populations + other.populations))
+            return self.__class__(*(self.populations + other.populations))
         else:
             raise TypeError("can only add a Population or another Assembly to an Assembly")
@@ -1203 +1203 @@
         result[:,0]   = cells
         result[:,1:4] = self.positions.T 
-        if control.rank() == 0:
+        if self._simulator.state.mpi_rank == 0:
             file.write(result, {'assembly' : self.label})
             file.close()
@@ -1249 +1249 @@
         spike_counts = self.get_spike_counts()
         total_spikes = sum(spike_counts.values())
-        if control.rank() == 0 or not gather:  # should maybe use allgather, and get the numbers on all nodes
+        if self._simulator.state.mpi_rank() == 0 or not gather:  # should maybe use allgather, and get the numbers on all nodes
             return float(total_spikes)/len(spike_counts)
         else:
@@ -1301 +1301 @@
                     'last_id'     : self.last_id}
         
-        metadata['dt'] = control.simulator.state.dt # note that this has to run on all nodes (at least for NEST)
+        metadata['dt'] = self._simulator.state.dt # note that this has to run on all nodes (at least for NEST)
         data = numpy.zeros(format)
         for pop in filenames.keys():
             if filenames[pop][1] is True:
                 name     = filenames[pop][0]
-                if gather==False and control.simulator.state.num_processes > 1:
-                    name += '.%d' % control.simulator.state.mpi_rank            
+                if gather==False and self._simulator.state.num_processes > 1:
+                    name += '.%d' % self._simulator.state.mpi_rank            
                 p_file   = files.NumpyBinaryFile(name, mode='r') 
                 tmp_data = p_file.read()                    
@@ -1318 +1318 @@
         
         if isinstance(file, basestring):
-            if gather==False and control.simulator.state.num_processes > 1:
-                file += '.%d' % control.simulator.state.mpi_rank
+            if gather==False and self._simulator.state.num_processes > 1:
+                file += '.%d' % self._simulator.state.mpi_rank
             file = files.StandardTextFile(file, mode='w')
         
-        if control.simulator.state.mpi_rank == 0 or gather == False:
+        if self._simulator.state.mpi_rank == 0 or gather == False:
             file.write(data, metadata)
             file.close()

trunk/src/common/projections.py

@@ -13 +13 @@
 from pyNN.recording import files
 from populations import BasePopulation, Assembly, is_conductance
-from control import get_min_delay, get_max_delay, rank, num_processes
 
 logger = logging.getLogger("PyNN")
@@ -46 +45 @@
 
 
-def check_delay(delay):
-    if delay is None:
-        delay = get_min_delay()
-    # If the delay is too small , we have to throw an error
-    if delay < get_min_delay() or delay > get_max_delay():
-        raise errors.ConnectionError("delay (%s) is out of range [%s,%s]" % \
-                                     (delay, get_min_delay(), get_max_delay()))
-    return delay
-
-
 class Projection(object):
     """
@@ -301 +290 @@
             all_lines = { rank(): lines }
             all_lines = recording.gather_dict(all_lines)
-            if rank() == 0:
+            if self._simulator.state.mpi_rank == 0:
                 lines = reduce(operator.add, all_lines.values())
-        elif num_processes() > 1:
-            file.rename('%s.%d' % (file.name, rank()))
+        elif self._simulator.state.num_processes > 1:
+            file.rename('%s.%d' % (file.name, self._simulator.state.mpi_rank))
         
         logger.debug("--- Projection[%s].__saveConnections__() ---" % self.label)

trunk/src/connectors.py

@@ -178 +178 @@
     """Generator for synaptic delays. %s""" % ConnectionAttributeGenerator.__doc__
 
-    def __init__(self, source, local_mask, safe=True):
+    def __init__(self, source, local_mask, kernel, safe=True):
         ConnectionAttributeGenerator.__init__(self, source, local_mask, safe)
-        self.min_delay = common.get_min_delay()
-        self.max_delay = common.get_max_delay()
+        assert hasattr(kernel, "min_delay")
+        self.kernel = kernel
         
     def check(self, delay):
-        all_negative = (delay<=self.max_delay).all()
-        all_positive = (delay>=self.min_delay).all()# If the delay is too small , we have to throw an error
+        min_delay = self.kernel.min_delay
+        max_delay = self.kernel.max_delay
+        all_negative = (delay<=max_delay).all()
+        all_positive = (delay>=min_delay).all()# If the delay is too small , we have to throw an error
         if not (all_negative and all_positive):
-            raise errors.ConnectionError("delay (%s) is out of range [%s,%s]" % (delay, common.get_min_delay(), common.get_max_delay()))
+            raise errors.ConnectionError("delay (%s) is out of range [%s,%s]" % (delay, min_delay, max_delay))
         return delay    
 
@@ -232 +234 @@
         self.safe    = safe
         self.verbose = verbose
-        min_delay    = common.get_min_delay()
+        min_delay    = self._simulator.state.min_delay
         if delays is None:
             self.delays = min_delay
@@ -252 +254 @@
     def progression(self, count):
         self.prog.update_amount(count)
-        if self.verbose and common.rank() == 0:           
+        if self.verbose and self._simulator.state.mpi_rank == 0:           
             print self.prog, "\r",
             sys.stdout.flush()
@@ -293 +295 @@
         self.N                 = projection.post.size
         self.weights_generator = WeightGenerator(weights, self.local, projection, safe)
-        self.delays_generator  = DelayGenerator(delays, self.local, safe)
+        self.delays_generator  = DelayGenerator(delays, self.local, kernel=projection._simulator.state, safe=safe)
         self.probas_generator  = ProbaGenerator(RandomDistribution('uniform', (0,1), rng=self.rng), self.local)
         self._distance_matrix  = None
@@ -468 +470 @@
         proba_generator = ProbaGenerator(self.d_expression, connector.local)
         self.progressbar(len(projection.pre))
-        if (common.num_processes() > 1) and (self.n_connections is not None):
+        if (projection._simulator.state.num_processes > 1) and (self.n_connections is not None):
             raise Exception("n_connections not implemented yet for this connector in parallel !")
 
@@ -498 +500 @@
         """
         # needs extending for dynamic synapses.
-        Connector.__init__(self, 0., common.get_min_delay(), safe=safe, verbose=verbose)
+        Connector.__init__(self, 0.0, self._simulator.state.min_delay, safe=safe, verbose=verbose)
         self.conn_list  = numpy.array(conn_list)               
         
@@ -550 +552 @@
                          distributed simulations.
         """
-        Connector.__init__(self, 0., common.get_min_delay(), safe=safe, verbose=verbose)
+        Connector.__init__(self, 0.0, self._simulator.state.min_delay, safe=safe, verbose=verbose)
         
         if isinstance(file, basestring):
@@ -560 +562 @@
         """Connect-up a Projection."""
         if self.distributed:
-            self.file.rename("%s.%d" % (self.file.name, common.rank()))        
+            self.file.rename("%s.%d" % (self.file.name, projection._simulator.state.mpi_rank))        
         self.conn_list = self.file.read()
         FromListConnector.connect(self, projection)
@@ -614 +616 @@
         local             = numpy.ones(len(projection.post), bool)
         weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
-        delays_generator  = DelayGenerator(self.delays, local, self.safe)
+        delays_generator  = DelayGenerator(self.delays, local, kernel=projection._simulator.state, safe=self.safe)
         distance_matrix   = DistanceMatrix(projection.post.positions, self.space)
         candidates        = projection.post.all_cells
@@ -700 +702 @@
         local             = numpy.ones(len(projection.pre), bool)
         weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
-        delays_generator  = DelayGenerator(self.delays, local, self.safe)
+        delays_generator  = DelayGenerator(self.delays, local, kernel=projection._simulator.state, safe=self.safe)
         distance_matrix   = DistanceMatrix(projection.pre.positions, self.space)              
         candidates        = projection.pre.all_cells 
@@ -767 +769 @@
                 raise Exception('Expression for weights or delays is not supported for OneToOneConnector !')
             weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
-            delays_generator  = DelayGenerator(self.delays, local, self.safe)                
+            delays_generator  = DelayGenerator(self.delays, local, kernel=projection._simulator.state, safe=self.safe)                
             weights           = weights_generator.get(N)
             delays            = delays_generator.get(N)
@@ -871 +873 @@
             self.rng = projection.rng
         self.weights_generator = WeightGenerator(self.weights, local, projection, self.safe)
-        self.delays_generator  = DelayGenerator(self.delays, local, self.safe)
+        self.delays_generator  = DelayGenerator(self.delays, local, kernel=projection._simulator.state, safe=self.safe)
         self.probas_generator  = ProbaGenerator(RandomDistribution('uniform',(0,1), rng=self.rng), local)
         self.distance_matrix   = DistanceMatrix(projection.post.positions, self.space, local)
@@ -893 +895 @@
             """
             """
-            min_delay = common.get_min_delay()
+            min_delay = self._simulator.state.min_delay
             Connector.__init__(self, None, None, safe=safe, verbose=verbose)
             self.cset = cset
@@ -904 +906 @@
                 self.delays = delays
                 if delays is None:
-                    self.delays = common.get_min_delay()
+                    self.delays = self._simulator.state.min_delay
             else:
                 assert cset.arity == 2, 'must specify mask or connection-set with arity 2'

trunk/src/moose/__init__.py

@@ -17 +17 @@
 from pyNN.moose import simulator
 from pyNN import common, recording, core
-common.control.simulator = simulator
-recording.simulator = simulator
 
 from pyNN.connectors import FixedProbabilityConnector, AllToAllConnector, OneToOneConnector
@@ -58 +56 @@
     return get_current_time()
 
-reset = common.reset
+reset = common.control.build_reset(simulator)
 
 initialize = common.initialize
@@ -66 +64 @@
 # ==============================================================================
 
-get_current_time = common.get_current_time
-get_time_step = common.get_time_step
-get_min_delay = common.get_min_delay
-get_max_delay = common.get_max_delay
-num_processes = common.num_processes
-rank = common.rank
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+            num_processes, rank = common.control.build_state_queries(simulator)
 
 # ==============================================================================
@@ -78 +72 @@
 # ==============================================================================
 
+class Assembly(common.Assembly):
+    _simulator = simulator
+
+
+class PopulationView(common.PopulationView):
+    _simulator = simulator
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
+
+
 class Population(common.Population):
     """
@@ -83 +89 @@
     term intended to include layers, columns, nuclei, etc., of cells.
     """
+    _simulator = simulator
     recorder_class = Recorder
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
 
     def _create_cells(self, cellclass, cellparams, n):
@@ -118 +129 @@
     parameters of those connections, including of plasticity mechanisms.
     """
-
+    _simulator = simulator
     nProj = 0
 

trunk/src/multisim.py

@@ -8 +8 @@
 
 from multiprocessing import Process, Queue
-from pyNN import common, recording
 
 def run_simulation(network_model, sim, parameters, input_queue, output_queue):
@@ -17 +16 @@
     """
     print "Running simulation with %s" % sim.__name__
-    common.control.simulator = sim.simulator
-    recording.simulator = sim.simulator
     network = network_model(sim, parameters)
     print "Network constructed with %s." % sim.__name__

trunk/src/nemo/__init__.py

@@ -14 +14 @@
 from pyNN.nemo import simulator
 from pyNN import common, recording, space, core, __doc__
-common.control.simulator = simulator
-recording.simulator = simulator
 from pyNN.random import *
 from pyNN.recording import files
@@ -53 +51 @@
     simulator.spikes_array_list = []
     simulator.recorder_lise     = []
-    return rank()
+    return simulator.state.mpi_rank
 
 def end(compatible_output=True):
@@ -64 +62 @@
     electrodes.current_sources = []
 
-def get_current_time():
-    """Return the current time in the simulation."""
-    return simulator.state.t
     
 def run(simtime):    
     """Run the simulation for simtime ms."""
     simulator.state.run(simtime)
-    return get_current_time()
+    return simulator.state.t
 
 reset      = simulator.reset
@@ -80 +75 @@
 # ==============================================================================
 
-get_time_step = common.get_time_step
-get_min_delay = common.get_min_delay
-get_max_delay = common.get_max_delay
-num_processes = common.num_processes
-rank = common.rank
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+            num_processes, rank = common.control.build_state_queries(simulator)
 
 # ==============================================================================
@@ -91 +83 @@
 # ==============================================================================
 
+class Assembly(common.Assembly):
+    _simulator = simulator
+
+
+class PopulationView(common.PopulationView):
+    _simulator = simulator
+    assembly_class = Assembly
+    
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
+
+
 class Population(common.Population, common.BasePopulation):
     """
@@ -96 +100 @@
     term intended to include layers, columns, nuclei, etc., of cells.
     """
+    _simulator = simulator
     recorder_class = Recorder
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
 
     def _create_cells(self, cellclass, cellparams=None, n=1):
@@ -135 +144 @@
     def _set_initial_value_array(self, variable, value):
         if not hasattr(value, "__len__"):
-            value = value*numpy.ones((len(self),))        
-       
-PopulationView = common.PopulationView
-Assembly = common.Assembly
+            value = value*numpy.ones((len(self),))
+
 
 class Projection(common.Projection):
@@ -146 +153 @@
     parameters of those connections, including of plasticity mechanisms.
     """
+    _simulator = simulator
     
     def __init__(self, presynaptic_population, postsynaptic_population, method,

trunk/src/nemo/connectors.py

@@ -24 +24 @@
                             WeightGenerator, \
                             DelayGenerator, \
-                            ProbaGenerator
+                            ProbaGenerator, \
+                            Connector
+from pyNN.nemo import simulator
+
+Connector._simulator = simulator

trunk/src/nemo/recording.py

@@ -16 +16 @@
 class Recorder(recording.Recorder):
     """Encapsulates data and functions related to recording model variables."""
+    _simulator = simulator
   
     def __init__(self, variable, population=None, file=None):

trunk/src/nest/__init__.py

@@ -11 +11 @@
 from pyNN.nest import simulator
 from pyNN import common, recording, errors, space, __doc__
-common.control.simulator = simulator
-recording.simulator = simulator
 
 if recording.MPI and (nest.Rank() != recording.mpi_comm.rank):
@@ -154 +152 @@
     return get_current_time()
 
-reset = common.reset
+reset = common.control.build_reset(simulator)
 
 initialize = common.initialize
@@ -162 +160 @@
 # ==============================================================================
 
-get_current_time = common.get_current_time
-get_time_step = common.get_time_step
-get_min_delay = common.get_min_delay
-get_max_delay = common.get_max_delay
-num_processes = common.num_processes
-rank = common.rank
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+            num_processes, rank = common.control.build_state_queries(simulator)
+
 
 # ==============================================================================
@@ -173 +168 @@
 #   neurons.
 # ==============================================================================
+
+class Assembly(common.Assembly):
+    _simulator = simulator
+
+
+class PopulationView(common.PopulationView):
+    _simulator = simulator
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
+
 
 class Population(common.Population):
@@ -179 +186 @@
     term intended to include layers, columns, nuclei, etc., of cells.
     """
+    _simulator = simulator
     recorder_class = Recorder
+    assembly_class = Assembly
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
 
     def _create_cells(self, cellclass, cellparams, n):
@@ -280 +292 @@
         nest.SetStatus(self.local_cells.tolist(), variable, value)
 
-PopulationView = common.PopulationView
-Assembly = common.Assembly
-
 
 class Projection(common.Projection):
@@ -290 +299 @@
     parameters of those connections, including of plasticity mechanisms.
     """
-
+    _simulator = simulator
     nProj = 0
 

trunk/src/nest/connectors.py

@@ -13 +13 @@
                             FromListConnector, FromFileConnector, WeightGenerator, \
                             DelayGenerator, ProbaGenerator, DistanceMatrix, CSAConnector
-from pyNN.common import rank, num_processes
+from pyNN.nest import simulator
 import numpy
 from pyNN.space import Space
+
+Connector._simulator = simulator
 
 
@@ -35 +37 @@
         self.local_long[idx]   = True
         self.weights_generator = WeightGenerator(weights, self.local_long, projection, safe)
-        self.delays_generator  = DelayGenerator(delays, self.local_long, safe)
+        self.delays_generator  = DelayGenerator(delays, self.local_long, kernel=projection._simulator.state, safe=safe)
         self.probas_generator  = ProbaGenerator(random.RandomDistribution('uniform',(0,1), rng=self.rng), self.local_long)
         self.distance_matrix   = DistanceMatrix(projection.pre.positions, self.space, self.local)

trunk/src/nest/recording.py

@@ -5 +5 @@
 import warnings
 import nest
-from pyNN import recording, common, errors
+from pyNN import recording, errors
 from pyNN.nest import simulator
 
@@ -31 +31 @@
         device_parameters = {"withgid": True, "withtime": True}
         if self.type is 'multimeter':
-            device_parameters["interval"] = common.get_time_step()
+            device_parameters["interval"] = simulator.state.dt
         else:
             device_parameters["precise_times"] = True
@@ -237 +237 @@
 class Recorder(recording.Recorder):
     """Encapsulates data and functions related to recording model variables."""
-    
+    _simulator = simulator
     scale_factors = {'spikes': 1,
                      'v': 1,

trunk/src/neuron/__init__.py

@@ -12 +12 @@
 from pyNN.random import *
 from pyNN.neuron import simulator
-from pyNN import common, core, recording as base_recording, space, __doc__
-common.control.simulator = simulator
-base_recording.simulator = simulator
+from pyNN import common, core, space, __doc__
 
 from pyNN.neuron.standardmodels.cells import *
@@ -83 +81 @@
     return get_current_time()
     
-reset = common.reset
+reset = common.control.build_reset(simulator)
 
 initialize = common.initialize
@@ -91 +89 @@
 # ==============================================================================
 
-get_current_time = common.get_current_time
-get_time_step = common.get_time_step
-get_min_delay = common.get_min_delay
-get_max_delay = common.get_max_delay
-num_processes = common.num_processes
-rank = common.rank
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+            num_processes, rank = common.control.build_state_queries(simulator)
 
 
@@ -104 +98 @@
 # ==============================================================================
 
+class Assembly(common.Assembly):
+    _simulator = simulator
+
+
+class PopulationView(common.PopulationView):
+    _simulator = simulator
+    assembly_class = Assembly
+    
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
+    
+
 class Population(common.Population):
     """
@@ -109 +115 @@
     term intended to include layers, columns, nuclei, etc., of cells.
     """
+    _simulator = simulator
     recorder_class = Recorder
+    assembly_class = Assembly
     
     def __init__(self, size, cellclass, cellparams=None, structure=None,
@@ -116 +124 @@
         common.Population.__init__(self, size, cellclass, cellparams, structure, label)
         simulator.initializer.register(self)
+
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
 
     def _create_cells(self, cellclass, cellparams, n):
@@ -157 +168 @@
 
 
-PopulationView = common.PopulationView
-Assembly = common.Assembly
-
 class Projection(common.Projection):
     """
@@ -166 +174 @@
     parameters of those connections, including of plasticity mechanisms.
     """
-    
+    _simulator = simulator
     nProj = 0
     

trunk/src/neuron/connectors.py

@@ -8 +8 @@
 """
 
+from pyNN.neuron import simulator
 from pyNN.connectors import AllToAllConnector, \
                             OneToOneConnector, \
@@ -17 +18 @@
                             FixedNumberPostConnector, \
                             SmallWorldConnector, \
-                            CSAConnector
+                            CSAConnector, \
+                            Connector
 
-
-
-
+Connector._simulator = simulator

trunk/src/neuron/recording.py

@@ -17 +17 @@
 class Recorder(recording.Recorder):
     """Encapsulates data and functions related to recording model variables."""
-        
+    _simulator = simulator
+    
     def _record(self, new_ids):
         """Add the cells in `new_ids` to the set of recorded cells."""

trunk/src/pcsim/__init__.py

@@ -22 +22 @@
 from pyNN import common, recording, errors, space, core, __doc__
 from pyNN.pcsim import simulator
-common.control.simulator = simulator
-recording.simulator = simulator
 import os.path
 import types
@@ -206 +204 @@
     return simulator.state.t
 
-reset = common.reset
+reset = common.control.build_reset(simulator)
 
 initialize = common.initialize
 
-get_current_time = common.get_current_time
-get_time_step = common.get_time_step
-get_min_delay = common.get_min_delay
-get_max_delay = common.get_max_delay
-num_processes = common.num_processes
-rank = common.rank
+get_current_time, get_time_step, get_min_delay, get_max_delay, \
+            num_processes, rank = common.control.build_state_queries(simulator)
 
 
@@ -222 +216 @@
 #   neurons.
 # ==============================================================================
+
+class Assembly(common.Assembly):
+    _simulator = simulator
+    
+    
+class PopulationView(common.PopulationView):
+    _simulator = simulator
+    assembly_class = Assembly
+    
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
+
 
 class Population(common.Population):
@@ -228 +234 @@
     term intended to include layers, columns, nuclei, etc., of cells.
     """
+    _simulator = simulator
     recorder_class = Recorder
+    assembly_class = Assembly
     
     def __init__(self, size, cellclass, cellparams=None, structure=None,
@@ -234 +242 @@
         __doc__ = common.Population.__doc__
         common.Population.__init__(self, size, cellclass, cellparams, structure, label)
+    
+    def _get_view(self, selector, label=None):
+        return PopulationView(self, selector, label)
     
     def _create_cells(self, cellclass, cellparams, n):
@@ -406 +417 @@
             obj = simulator.net.object(self.pcsim_population[i])
             if obj: apply( obj, methodname, (), arguments)
-        
-PopulationView = common.PopulationView
-Assembly = common.Assembly
+
 
 class Projection(common.Projection, WDManager):
@@ -416 +425 @@
     parameters of those connections, including of plasticity mechanisms.
     """
-    
+    _simulator = simulator
     nProj = 0
     synapse_target_ids = { 'excitatory': 1, 'inhibitory': 2 }

trunk/src/pcsim/connectors.py

@@ -16 +16 @@
                             FixedNumberPreConnector, \
                             FixedNumberPostConnector, \
-                            SmallWorldConnector
+                            SmallWorldConnector, \
+                            Connector
+from pyNN.pcsim import simulator
 
 
-
-
+Connector._simulator = simulator

trunk/src/pcsim/recording.py

@@ -13 +13 @@
 class Recorder(recording.Recorder):
     """Encapsulates data and functions related to recording model variables."""
+    _simulator = simulator
     
     fieldnames = {'v': 'Vm',

trunk/src/recording/__init__.py

@@ -144 +144 @@
             filename = file
             #rename_existing(filename)
-            if gather==False and simulator.state.num_processes > 1:
-                filename += '.%d' % simulator.state.mpi_rank
+            if gather==False and self._simulator.state.num_processes > 1:
+                filename += '.%d' % self._simulator.state.mpi_rank
         else:
             filename = file.name
@@ -155 +155 @@
         metadata = self.metadata
         logger.debug("data has size %s" % str(data.size))
-        if simulator.state.mpi_rank == 0 or gather == False:
+        if self._simulator.state.mpi_rank == 0 or gather == False:
             if compatible_output:
                 data = self._make_compatible(data)
@@ -178 +178 @@
                 'label': self.population.label,
             })
-        metadata['dt'] = simulator.state.dt # note that this has to run on all nodes (at least for NEST)
+        metadata['dt'] = self._simulator.state.dt # note that this has to run on all nodes (at least for NEST)
         if not hasattr(self, '_data_size'):
             self.get()
@@ -229 +229 @@
         else:
             raise Exception("Only implemented for spikes.")
-        if gather and simulator.state.num_processes > 1:
+        if gather and self._simulator.state.num_processes > 1:
             N = gather_dict(N)
         return N

trunk/test/system/scenarios.py

@@ -5 +5 @@
 import numpy
 from pyNN.utility import init_logging, assert_arrays_equal, assert_arrays_almost_equal, sort_by_column
-
-
-def set_simulator(sim):
-    common.simulator = sim.simulator
-    recording.simulator = sim.simulator
 
 
@@ -28 +23 @@
     Balanced network of integrate-and-fire neurons.
     """
-    set_simulator(sim)
     cell_params = {
         'tau_m': 20.0, 'tau_syn_E': 5.0, 'tau_syn_I': 10.0, 'v_rest': -60.0,
@@ -95 +89 @@
     API.
     """
-    set_simulator(sim)
     cell_params = {
         'tau_m': 10.0, 'tau_syn_E': 2.0, 'tau_syn_I': 5.0, 'v_rest': -60.0,
@@ -155 +148 @@
     once (except neuron[0], which never reaches threshold).
     """
-    set_simulator(sim)
     n = 100
     t_start = 25.0
@@ -203 +195 @@
     connections should be potentiated more.
     """
-    set_simulator(sim)
 
     init_logging(logfile=None, debug=True)
@@ -301 +292 @@
         pylab.rcParams['interactive'] = interactive
     
-    set_simulator(sim)
     sim.setup(timestep=dt)
     
@@ -410 +400 @@
 @register(exclude=['pcsim', 'moose'])
 def test_EIF_cond_alpha_isfa_ista(sim):
-    set_simulator(sim)
     sim.setup(timestep=0.01, min_delay=0.1, max_delay=4.0)
     ifcell = sim.create(sim.EIF_cond_alpha_isfa_ista,
@@ -452 +441 @@
     from pyNN.utility import init_logging
     init_logging(logfile=None, debug=True)
-    set_simulator(sim)
     dt = 0.1
     tstop = 100.0

trunk/test/unittests/test_assembly.py

@@ -7 +7 @@
     
 
+class MockSimulator(object):
+    class MockState(object):
+        mpi_rank = 1
+        num_processes = 2
+    state = MockState()
+
 def test_create_with_zero_populations():
     a = Assembly()
@@ -13 +19 @@
 
 class MockPopulation(BasePopulation):
+    _simulator = MockSimulator
     size = 10
-    local_cells = numpy.arange(1,10,2)
-    all_cells = numpy.arange(10)
-    _mask_local = numpy.arange(10)%2 == 1
+    local_cells = numpy.arange(_simulator.state.mpi_rank,10,_simulator.state.num_processes)
+    all_cells = numpy.arange(size)
+    _mask_local = numpy.arange(size)%_simulator.state.num_processes == _simulator.state.mpi_rank
     initialize = Mock()
     positions = numpy.arange(3*size).reshape(3,size)
@@ -179 +186 @@
 def test_save_positions():
     import os
-    orig_rank = common.rank
-    common.rank = lambda: 0
+    Assembly._simulator = MockSimulator
+    Assembly._simulator.state.mpi_rank = 0
     p1 = MockPopulation()
     p2 = MockPopulation()
@@ -194 +201 @@
     assert_equal(output_file.write.call_args[0][1], {'assembly': a.label})
     # arguably, the first column should contain indices, not ids.
-    common.rank = orig_rank
+    del Assembly._simulator

trunk/test/unittests/test_basepopulation.py

@@ -1 +1 @@
 from pyNN import common, errors, random, standardmodels, recording
-from pyNN.common import populations, control
+from pyNN.common import populations
 from nose.tools import assert_equal, assert_raises
 import numpy
@@ -9 +9 @@
 builtin_open = open
 id_map = {'larry': 0, 'curly': 1, 'moe': 2, 'joe': 3, 'william': 4, 'jack': 5, 'averell': 6}
+
+
+class MockSimulator(object):
+    class MockState(object):
+        mpi_rank = 1
+        num_processes = 3
+    state = MockState()
 
 class MockStandardCell(standardmodels.StandardCellType):
@@ -19 +26 @@
 
 class MockPopulation(populations.BasePopulation):
+    _simulator = MockSimulator
     size = 13
     all_cells = numpy.arange(100, 113)
@@ -27 +35 @@
     celltype = MockStandardCell({})
     initial_values = {"foo": core.LazyArray(numpy.array((98, 100, 102)), shape=(3,))}
+    assembly_class = populations.Assembly
+
+    def _get_view(self, selector, label=None):
+        return populations.PopulationView(self, selector, label)
 
     def id_to_index(self, id):
@@ -61 +73 @@
     p = MockPopulation()
     pv = p[3:9]
-    populations.PopulationView.assert_called_with(p, slice(3,9,None))
+    populations.PopulationView.assert_called_with(p, slice(3,9,None), None)
     populations.PopulationView = orig_PV
 
@@ -69 +81 @@
     p = MockPopulation()
     pv = p[range(3,9)]
-    populations.PopulationView.assert_called_with(p, range(3,9))
+    populations.PopulationView.assert_called_with(p, range(3,9), None)
     populations.PopulationView = orig_PV
 
@@ -77 +89 @@
     p = MockPopulation()
     pv = p[(3,5,7)]
-    populations.PopulationView.assert_called_with(p, [3,5,7])
+    populations.PopulationView.assert_called_with(p, [3,5,7], None)
     populations.PopulationView = orig_PV
 
@@ -175 +187 @@
 
 def test_get_with_gather():
-    np_orig = control.num_processes
-    rank_orig = control.rank
+    np_orig = MockPopulation._simulator.state.num_processes
+    rank_orig = MockPopulation._simulator.state.mpi_rank
     gd_orig = recording.gather_dict
-    control.num_processes = lambda: 2
-    control.rank = lambda: 0
+    MockPopulation._simulator.state.num_processes = 2
+    MockPopulation._simulator.state.mpi_rank =  0
     def mock_gather_dict(D): # really hacky
         assert isinstance(D[0], list)
@@ -191 +203 @@
                         numpy.arange(10.0, 23.0))
     
-    control.num_processes = np_orig
-    control.rank = rank_orig
+    MockPopulation._simulator.state.num_processes = np_orig
+    MockPopulation._simulator.state.mpi_rank = rank_orig
     recording.gather_dict = gd_orig
 
@@ -437 +449 @@
     
 def test_meanSpikeCount():
-    orig_rank = control.rank
-    control.rank = lambda: 0
+    orig_rank = MockPopulation._simulator.state.mpi_rank
+    MockPopulation._simulator.state.mpi_rank = 0
     p = MockPopulation()
     p.recorders = {'spikes': Mock()}
     p.recorders['spikes'].count = Mock(return_value={0: 2, 1: 5})
     assert_equal(p.meanSpikeCount(), 3.5)
-    control.rank = orig_rank
+    MockPopulation._simulator.state.mpi_rank = orig_rank
 
 def test_meanSpikeCount_on_slave_node():
-    orig_rank = control.rank
-    control.rank = lambda: 1
+    orig_rank = MockPopulation._simulator.state.mpi_rank
+    MockPopulation._simulator.state.mpi_rank = 1
     p = MockPopulation()
     p.recorders = {'spikes': Mock()}
     p.recorders['spikes'].count = Mock(return_value={0: 2, 1: 5})
     assert p.meanSpikeCount() is numpy.NaN
-    control.rank = orig_rank
+    MockPopulation._simulator.state.mpi_rank = orig_rank
     
 def test_inject():
@@ -469 +481 @@
 def test_save_positions():
     import os
-    orig_rank = control.rank
-    control.rank = lambda: 0
+    orig_rank = MockPopulation._simulator.state.mpi_rank
+    MockPopulation._simulator.state.mpi_rank = 0
     p = MockPopulation()
     p.all_cells = numpy.array([34, 45, 56, 67])
@@ -480 +492 @@
     assert_equal(output_file.write.call_args[0][1], {'population': p.label})
     # arguably, the first column should contain indices, not ids.
-    control.rank = orig_rank
+    MockPopulation._simulator.state.mpi_rank = orig_rank

trunk/test/unittests/test_connectors.py

@@ -69 +69 @@
 
 class MockProjection(object):
+    _simulator = MockSimulator
     
     def __init__(self, pre, post):
@@ -102 +103 @@
 
 
+def setup():
+    connectors.Connector._simulator = MockSimulator
+    connectors.ConnectionAttributeGenerator._simulator = MockSimulator
+
+def teardown():
+    del connectors.Connector._simulator
+    del connectors.ConnectionAttributeGenerator._simulator
+
 class TestOneToOneConnector(object):
 
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(5), MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
 
@@ -129 +137 @@
 
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4), MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
 
@@ -182 +189 @@
         C = connectors.AllToAllConnector(weights=0.1, delays=None)
         assert_equal(C.weights, 0.1)
-        assert_equal(C.delays, common.get_min_delay())
+        assert_equal(C.delays, C._simulator.state.min_delay)
         assert C.safe
         assert C.allow_self_connections
@@ -202 +209 @@
 
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4),
                                   MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
@@ -222 +228 @@
 
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4),
                                   MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
@@ -243 +248 @@
     
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4),
                                   MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
@@ -282 +286 @@
     
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4),
                                   MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
@@ -321 +324 @@
     
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4),
                                   MockPost(numpy.array([0,1,0,1,0], dtype=bool)))
@@ -352 +354 @@
     
     def setup(self):
-        common.control.simulator = MockSimulator
         self.prj = MockProjection(MockPre(4),
                                   MockPost(numpy.array([0,1,0,1,0], dtype=bool)))

trunk/test/unittests/test_population.py

@@ -1 +1 @@
 from pyNN import errors, random, standardmodels, space
-from pyNN.common import control, populations
+from pyNN.common import populations
 from nose.tools import assert_equal, assert_raises
 import numpy
@@ -6 +6 @@
 from pyNN.utility import assert_arrays_equal
 
+
+class MockSimulator(object):
+    class MockState(object):
+        mpi_rank = 1
+        num_processes = 3
+    state = MockState()
 
 class MockID(int, populations.IDMixin):
@@ -15 +21 @@
 
 class MockPopulation(populations.Population):
+    _simulator = MockSimulator
     recorder_class = Mock()
     initialize = Mock()
+    
+    def _get_view(self, selector, label=None):
+        return populations.PopulationView(self, selector, label)
     
     def _create_cells(self, cellclass, cellparams, size):
@@ -107 +117 @@
 
 def test_id_to_local_index():
-    orig_np = control.num_processes
-    control.num_processes = lambda: 5
+    orig_np = MockPopulation._simulator.state.num_processes
+    MockPopulation._simulator.state.num_processes = 5
     p = MockPopulation(11, MockStandardCell)
     # every 5th cell, starting with the 4th, is on this node.
@@ -114 +124 @@
     assert_equal(p.id_to_local_index(p[8]), 1)
     
-    control.num_processes = lambda: 1
+    MockPopulation._simulator.state.num_processes = 1
     # only one node
     assert_equal(p.id_to_local_index(p[3]), 3)
     assert_equal(p.id_to_local_index(p[8]), 8)
-    control.num_processes = orig_np
+    MockPopulation._simulator.state.num_processes = orig_np
 
 def test_id_to_local_index_with_invalid_id():
-    orig_np = control.num_processes
-    control.num_processes = lambda: 5
+    orig_np = MockPopulation._simulator.state.num_processes
+    MockPopulation._simulator.state.num_processes = 5
     p = MockPopulation(11, MockStandardCell)
     # every 5th cell, starting with the 4th, is on this node.
     assert_raises(ValueError, p.id_to_local_index, p[0])
-    control.num_processes = orig_np
+    MockPopulation._simulator.state.num_processes = orig_np
 
 # test structure property

trunk/test/unittests/test_projection.py

@@ -7 +7 @@
 from pyNN.utility import assert_arrays_equal
 
-orig_rank = common.rank
-orig_np = common.num_processes
+
+class MockSimulator(object):
+    class MockState(object):
+        mpi_rank = 1
+        num_processes = 3
+    state = MockState()
+
 
 def setup():
-    common.rank = lambda: 1
-    common.num_processes = lambda: 3
+    common.Projection._simulator = MockSimulator
+
 
 def teardown():
-    common.rank = orig_rank
-    common.num_processes = orig_np
+    del common.Projection._simulator
+    
 
 class MockStandardCell(standardmodels.StandardCellType):

trunk/test/unittests/test_recording.py

@@ -9 +9 @@
 if MPI:
     mpi_comm = recording.mpi_comm
+
+def setup():
+    recording.Recorder._simulator = MockSimulator(mpi_rank=0)
+    
+def teardown():
+    del recording.Recorder._simulator
 
 #def test_rename_existing():
@@ -116 +122 @@
 
 def test_write__with_filename__compatible_output__gather__onroot():
-    recording.simulator = MockSimulator(mpi_rank=0)
     orig_metadata = recording.Recorder.metadata
     recording.Recorder.metadata = {'a': 2, 'b':3}

trunk/test/unittests/test_simulation_control.py

@@ -32 +32 @@
         
 def test_end():
-    assert_raises(NotImplementedError, common.end)
+    assert_raises(NotImplementedError, common.control.end)
         
 def test_run():
-    assert_raises(NotImplementedError, common.run, 10.0)
+    assert_raises(NotImplementedError, common.control.run, 10.0)
                
 def test_reset():
-    common.control.simulator = MockSimulator()
-    common.reset()
-    assert common.control.simulator.reset_called
+    simulator = MockSimulator()
+    reset = common.control.build_reset(simulator)
+    reset()
+    assert simulator.reset_called
     
 def test_initialize():
@@ -46 +47 @@
     common.initialize(p, 'v', -65.0)
     assert p.initializations == [('v', -65.0)]
-    
+
+
 def test_current_time():
-    common.control.simulator = MockSimulator()
-    common.get_current_time()
-    assert_equal(common.control.simulator.state.accesses, ['t'])
+    simulator = MockSimulator()
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_current_time()
+    assert_equal(simulator.state.accesses, ['t'])
     
 def test_time_step():
-    common.control.simulator = MockSimulator()
-    common.get_time_step()
-    assert_equal(common.control.simulator.state.accesses, ['dt'])
+    simulator = MockSimulator()
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_time_step()
+    assert_equal(simulator.state.accesses, ['dt'])
     
 def test_min_delay():
-    common.control.simulator = MockSimulator()
-    common.get_min_delay()
-    assert_equal(common.control.simulator.state.accesses, ['min_delay'])
+    simulator = MockSimulator()
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_min_delay()
+    assert_equal(simulator.state.accesses, ['min_delay'])
 
 def test_max_delay():
-    common.control.simulator = MockSimulator()
-    common.get_max_delay()
-    assert_equal(common.control.simulator.state.accesses, ['max_delay'])
+    simulator = MockSimulator()
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    get_max_delay()
+    assert_equal(simulator.state.accesses, ['max_delay'])
     
 def test_num_processes():
-    common.control.simulator = MockSimulator()
-    common.num_processes()
-    assert_equal(common.control.simulator.state.accesses, ['num_processes'])
+    simulator = MockSimulator()
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    num_processes()
+    assert_equal(simulator.state.accesses, ['num_processes'])
     
 def test_rank():
-    common.control.simulator = MockSimulator()
-    common.rank()
-    assert_equal(common.control.simulator.state.accesses, ['mpi_rank'])
+    simulator = MockSimulator()
+    get_current_time, get_time_step, get_min_delay, get_max_delay, num_processes, rank = common.control.build_state_queries(simulator)
+    rank()
+    assert_equal(simulator.state.accesses, ['mpi_rank'])

trunk/test/unittests/test_utility_functions.py

@@ -75 +75 @@
     # need to check that a log message was created
     assert_equal(4.3, common.check_weight(4.3, 'excitatory', is_conductance=None))
-    
-def test_check_delay():
-    assert_equal(common.check_delay(None), MIN_DELAY)
-    assert_equal(common.check_delay(2*MIN_DELAY), 2*MIN_DELAY)
-    assert_raises(errors.ConnectionError, common.check_delay, 0.5*MIN_DELAY)
-    assert_raises(errors.ConnectionError, common.check_delay, 2.0*MAX_DELAY)