Changeset 1042

Timestamp:

12/22/11 01:45:18 (5 months ago)

Author:

pierre

Message:

Add a new way of handling the CurrentSource? objects. Now everything is moved into standardmodels, and those objects are now inheriting from the StandardCurrentSource? object in the standardmodels, allowing to get parameters translations. Moreover, objects are now dynamically modified each time a parameter is changed. Will work on the tests later to be sure everything is fine. Note that parameters of the CurrentSource? objects should now be given as a dictionary, as for StandardCellType?. Pcsim compatibility will follow

Location:

trunk

Files:

• examples/StepCurrentSource.py (modified) (1 diff)
• src/brian/__init__.py (modified) (1 diff)
• src/brian/standardmodels/electrodes.py (added)
• src/models.py (modified) (1 diff)
• src/nemo/__init__.py (modified) (1 diff)
• src/nemo/simulator.py (modified) (1 diff)
• src/nemo/standardmodels/electrodes.py (added)
• src/nest/__init__.py (modified) (1 diff)
• src/nest/standardmodels/electrodes.py (added)
• src/neuron/__init__.py (modified) (1 diff)
• src/neuron/standardmodels/electrodes.py (added)
• src/standardmodels/__init__.py (modified) (1 diff)
• src/standardmodels/electrodes.py (added)
• test/system/test_nest.py (modified) (1 diff)
• test/unittests/test_neuron.py (modified) (3 diffs)
• test/unittests/test_population.py (modified) (1 diff)

trunk/examples/StepCurrentSource.py

@@ -16 +16 @@
 
 cell = create(IF_curr_exp, {'v_thresh': -55.0, 'tau_refrac': 5.0})
-current_source = StepCurrentSource([50.0, 110.0, 150.0, 210.0],
-                                   [0.4, 0.6, -0.2, 0.2])
+current_source = StepCurrentSource({'times' : [50.0, 110.0, 150.0, 210.0],
+                                    'amplitudes' : [0.4, 0.6, -0.2, 0.2]})
 cell.inject(current_source)
 

trunk/src/brian/__init__.py

@@ -17 +17 @@
 from pyNN.recording import files
 from pyNN.brian.standardmodels.cells import *
+from pyNN.brian.standardmodels.electrodes import *
 from pyNN.brian.connectors import *
 from pyNN.brian.standardmodels.synapses import *
-from pyNN.brian.electrodes import *
 from pyNN.brian import electrodes
 from pyNN.brian.recording import *

trunk/src/models.py

@@ -95 +95 @@
     injectable = True # override for spike sources
 
+class BaseCurrentSource(BaseModelType):
+    """Base class for current source model classes."""
 
 class BaseSynapseDynamics(object):

trunk/src/nemo/__init__.py

@@ -19 +19 @@
 from pyNN.nemo.connectors import *
 from pyNN.nemo.standardmodels.synapses import *
-from pyNN.nemo.electrodes import *
+from pyNN.nemo.standardmodels.electrodes import *
 from pyNN.nemo import electrodes
 from pyNN.nemo.recording import *

trunk/src/nemo/simulator.py

@@ -129 +129 @@
 def reset():
     """Reset the state of the current network to time t = 0."""
-    state.net.reset_timer()    
-    self.time   = 0
-    self._fired = []
+    state.time   = 0
+    state._fired = []
     
 # --- For implementation of access to individual neurons' parameters -----------

trunk/src/nest/__init__.py

@@ -27 +27 @@
 from pyNN.nest.standardmodels.synapses import *
 from pyNN.nest.electrodes import *
+from pyNN.nest.standardmodels.electrodes import *
 from pyNN.nest.recording import *
 from pyNN.random import RandomDistribution

trunk/src/neuron/__init__.py

@@ -17 +17 @@
 from pyNN.neuron.connectors import *
 from pyNN.neuron.standardmodels.synapses import *
-from pyNN.neuron.electrodes import *
+from pyNN.neuron.standardmodels.electrodes import *
 from pyNN.neuron.recording import Recorder
 from pyNN import standardmodels

trunk/src/standardmodels/__init__.py

@@ -129 +129 @@
 class StandardCellType(StandardModelType, models.BaseCellType):
     """Base class for standardized cell model classes."""
-    recordable = ['spikes', 'v', 'gsyn']
+    recordable    = ['spikes', 'v', 'gsyn']
     synapse_types = ('excitatory', 'inhibitory')
-    always_local = False # override for NEST spike sources
-
+    always_local  = False # override for NEST spike sources
+
+
+class StandardCurrentSource(StandardModelType, models.BaseCurrentSource):
+    """Base class for standardized current source model classes."""             
+    
+    def inject_into(self, cells):
+        raise Exception("Should be redefined in the local simulator electrodes")
+
+    def __getattr__(self, name):
+        try:
+            val = self.__getattribute__(name)
+        except AttributeError:
+            try:
+                val = self.get_parameters()[name]
+            except KeyError:
+                raise errors.NonExistentParameterError(name,
+                                                       self.__class__.__name__,
+                                                       self.get_parameter_names())
+        return val
+
+    def __setattr__(self, name, value):
+        if self.has_parameter(name):
+            self.set_parameters(**{name: value})
+        else:
+            object.__setattr__(self, name, value)
+
+    def set_parameters(self, **parameters):
+        """
+        Set current source parameters, given as a sequence of parameter=value arguments.
+        """
+        # if some of the parameters are computed from the values of other
+        # parameters, need to get and translate all parameters
+        computed_parameters = self.computed_parameters()
+        have_computed_parameters = numpy.any([p_name in computed_parameters
+                                              for p_name in parameters])
+        if have_computed_parameters:
+            all_parameters = self.get_parameters()
+            all_parameters.update(parameters)
+            parameters = all_parameters
+            parameters = self.translate(parameters)
+        self.set_native_parameters(parameters)
+
+    def get_parameters(self):
+        """Return a dict of all current source parameters."""
+        parameters = self.get_native_parameters()
+        parameters = self.reverse_translate(parameters)
+        return parameters
+
+    def set_native_parameters(self, parameters):
+        pass
+
+    def get_native_parameters(self):    
+        pass
 
 class ModelNotAvailable(object):

trunk/test/system/test_nest.py

@@ -39 +39 @@
     print p1.get('Tau_m')
     
-    current_source = nest.StepCurrentSource([50.0, 110.0, 150.0, 210.0],
-                                            [0.01, 0.02, -0.02, 0.01])
+    current_source = nest.StepCurrentSource({'times' : [50.0, 110.0, 150.0, 210.0],
+                                            'amplitudes' : [0.01, 0.02, -0.02, 0.01]})
     p1.inject(current_source)
     

trunk/test/unittests/test_neuron.py

@@ -30 +30 @@
         self.foo_init = -99.9
 
+class MockStepCurrentSource(object):
+    parameter_names = ['amplitudes', 'times']
+    def __init__(self, parameters):
+        self._devices = []
+
+    def inject_into(self, cell_list):
+        for cell in cell_list:
+            if cell.local:
+               self._devices += [cell]
+
+class MockDCSource(object):
+    parameter_names = ['amplitude', 'start', 'stop']
+    parameters      = {'amplitude' : 0, 'start' : 0, 'stop' : 1e12}
+    def __init__(self, parameters):
+        self._devices = []
+
+    def inject_into(self, cell_list):
+        for cell in cell_list:
+            if cell.local:
+               self._devices += [cell]
+
+
 class MockID(int):
     def __init__(self, n):
@@ -222 +244 @@
 
     def test_inject_dc(self):
-        cs = electrodes.DCSource()
+        cs = electrodes.DCSource({})
         cs.inject_into(self.cells)
         assert_equal(cs.stop, 1e12)
@@ -228 +250 @@
 
     def test_inject_step_current(self):
-        cs = electrodes.StepCurrentSource([1,2,3], [0.5, 1.5, 2.5])
+        cs = MockStepCurrentSource({'amplitudes' : [1,2,3], 'times' : [0.5, 1.5, 2.5]})
         cs.inject_into(self.cells)
         assert_equal(len(cs._devices), 2)# 2 local cells

trunk/test/unittests/test_population.py

@@ -30 +30 @@
     def _create_cells(self, cellclass, cellparams, size):
         self.all_cells = numpy.array([MockID(i) for i in range(999, 999+size)], MockID)
+        self.cell      = self.all_cells
         self._mask_local = numpy.arange(size)%5==3 # every 5th cell, starting with the 4th, is on this node
         self.first_id = self.all_cells[0]