Changeset 878 for branches

Timestamp:

12/17/10 08:07:44 (17 months ago)

Author:

apdavison

Message:

In reorganization branch, fixed nest.Population.set() for computed parameters and for NativeCellType.

Location:

branches/reorganization

Files:

• src/common.py (modified) (3 diffs)
• src/nest/__init__.py (modified) (4 diffs)
• src/standardmodels/__init__.py (modified) (2 diffs)
• test/system/test_nest.py (modified) (3 diffs)
• test/unittests/test_basepopulation.py (modified) (3 diffs)
• test/unittests/test_nest.py (added)
• test/unittests/test_standardmodels.py (modified) (1 diff)

branches/reorganization/src/common.py

@@ -506 +506 @@
         else:
             raise errors.InvalidParameterValueError
-        for name, val in param_dict.items():
-            if name not in self.celltype.get_parameter_names():
-                raise errors.NonExistentParameterError(name, self.celltype, self.celltype.get_parameter_names())
-            if isinstance(val, (float, int)):
-                param_dict[name] = float(val)
-            elif isinstance(val, (list, numpy.ndarray)):
-                pass  # ought to check list/array only contains numeric types
-            else:
-                raise errors.InvalidParameterValueError
+        param_dict = self.celltype.checkParameters(param_dict, with_defaults=False)
         logger.debug("%s.set(%s)", self.label, param_dict)
         if hasattr(self, "_set_array"):
@@ -865 +857 @@
         for variable, value in self.celltype.default_initial_values.items():
             self.initialize(variable, value)
-#        # should only create recorders for recordable variables: pointless creating a 'v' recorder for a spike source
-#        self.recorders = {'spikes': self.recorder_class('spikes', population=self),
-#                          'v'     : self.recorder_class('v', population=self),
-#                          'gsyn'  : self.recorder_class('gsyn', population=self)}
         self.recorders = {}
         Population.nPop += 1
@@ -975 +963 @@
 
 class PopulationView(BasePopulation):
+    """
+    docstring needed
+    """
 
     def __init__(self, parent, selector, label=None):

branches/reorganization/src/nest/__init__.py

@@ -7 +7 @@
 import nest
 from pyNN.nest import simulator
-from pyNN import common, recording, errors, space, standardmodels, __doc__
+from pyNN import common, recording, errors, space, __doc__
 common.simulator = simulator
 recording.simulator = simulator
@@ -24 +24 @@
 from pyNN.nest.recording import *
 from pyNN.random import RandomDistribution
+from pyNN import standardmodels
 
 Set = set
@@ -222 +223 @@
         else:
             raise errors.InvalidParameterValueError
-        
+        param_dict = self.celltype.checkParameters(param_dict, with_defaults=False)
         # The default implementation in common is is not very efficient for
         # simple and scaled parameters.
@@ -231 +232 @@
         # in the computation vary between cells, since if this is not the case
         # we can do the computation here and use nest.SetStatus.
-        to_be_set = {}
-        for key, value in param_dict.items():
-            if not isinstance(self.celltype, str):
-                # Here we check the consistency of the given parameters
-                try:
-                    self.celltype.default_parameters[key]
-                except Exception:
-                    raise errors.NonExistentParameterError(key, self.celltype.__class__)
-                if type(value) != type(self.celltype.default_parameters[key]):
-                    if isinstance(value, int) and isinstance(self.celltype.default_parameters[key], float):
-                        value = float(value)
-                    elif (isinstance(value, numpy.ndarray) and len(value.shape) == 1) and isinstance(self.celltype.default_parameters[key], list):
-                        pass
-                    else:
-                        raise errors.InvalidParameterValueError("The parameter %s should be a %s, you supplied a %s" % (key,
-                                                                                                                        type(self.celltype.default_parameters[key]),
-                                                                                                                        type(value)))
-                # Then we do the call to SetStatus
-                if key in self.celltype.scaled_parameters() or key in self.celltype.computed_parameters():
+        
+        if isinstance(self.celltype, standardmodels.StandardCellType):
+            to_be_set = {}
+            for key, value in param_dict.items():
+                if key in self.celltype.scaled_parameters():
                     translation = self.celltype.translations[key]
                     value = eval(translation['forward_transform'], globals(), {key:value})
-                    to_be_set[translation['translated_name']] = value
+                    to_be_set[translation['translated_name']] = value                
                 elif key in self.celltype.simple_parameters():
                     translation = self.celltype.translations[key]
                     to_be_set[translation['translated_name']] = value                    
                 else:
-                    to_be_set[key] = value
-            else:
-                try:
-                    nest.SetStatus(self.local_cells, key, value)
-                except Exception:
-                    raise errors.InvalidParameterValueError
+                    assert key in self.celltype.computed_parameters()
             nest.SetStatus(self.local_cells.tolist(), to_be_set)
+            for key, value in param_dict.items():
+                if key in self.celltype.computed_parameters():
+                    for cell in self:
+                        cell.set_parameters(**{key:value})
+        else:
+            nest.SetStatus(self.local_cells.tolist(), param_dict)
 
     def initialize(self, variable, value):

branches/reorganization/src/standardmodels/__init__.py

@@ -58 +58 @@
     
     def __init__(self, parameters):
+        assert set(self.translations.keys()) == set(self.default_parameters.keys()), \
+               "%s != %s" % (self.translations.keys(), self.default_parameters.keys())
         self.parameters = self.__class__.checkParameters(parameters, with_defaults=True)
         self.parameters = self.__class__.translate(self.parameters)
@@ -122 +124 @@
 
 
-
-
 class StandardCellType(StandardModelType, models.BaseCellType):
     """Base class for standardized cell model classes."""

branches/reorganization/test/system/test_nest.py

@@ -28 +28 @@
     
     class ht_neuron(nest.NativeCellType):
-        default_initial_values = {
-            'V_m': -65.0,
-            'Theta': -51.0
-        }
-        default_parameters = {
-            'Tau_m': 16.0,
-            'Theta_eq': -51.0,
-        }
         nest_model = 'ht_neuron'
         conductance_based = True
-        synapse_types = ['AMPA']
         standard_receptor_type = False
     
@@ -44 +35 @@
         injectable = False
         nest_model = "poisson_generator"
-        default_parameters = {
-            'rate': 0.0,
-            'start': 0.0,
-            'stop': 1e12
-        }
     
     parameters = {'Tau_m': 17.0}
@@ -54 +40 @@
     p1.initialize('V_m', -70.0)
     p1.initialize('Theta', -50.0)
+    p1.set('Theta_eq', -51.5)
+    assert_equal(p1.get('Theta_eq'), [-51.5]*10)
     print p1.get('Tau_m')
     p1.rset('Tau_m', RandomDistribution('uniform', [15.0, 20.0]))

branches/reorganization/test/unittests/test_basepopulation.py

@@ -11 +11 @@
 class MockStandardCell(standardmodels.StandardCellType):
     recordable = ['v', 'spikes']
-    default_parameters = {'tau_m': 999.9, 'i_offset': 321, 'spike_times': [0,1,2], 'foo': 33.3}
+    default_parameters = {'tau_m': 999.9, 'i_offset': 321.0, 'spike_times': [0,1,2], 'foo': 33.3}
+    translations = {'tau_m': None, 'i_offset': None, 'spike_times': None, 'foo': None}
     @classmethod
     def translate(cls, parameters):
@@ -202 +203 @@
     assert_raises(errors.InvalidParameterValueError, p.set, {'foo': 'bar'})
 
+def test_set_inconsistent_type():
+    p = MockPopulation()
+    p._set_array = Mock()
+    assert_raises(errors.InvalidParameterValueError, p.set, 'tau_m', [12.34, 56.78])
+
 def test_set_with_no_get_array():
     mock_cell = Mock()
@@ -214 +220 @@
     p = MockPopulation()
     p._set_array = Mock()
-    p.set('foo', range(10))
-    p._set_array.assert_called_with(**{'foo': range(10)})
+    p.set('spike_times', range(10))
+    p._set_array.assert_called_with(**{'spike_times': range(10)})
     
 def test_tset_with_numeric_values():

branches/reorganization/test/unittests/test_standardmodels.py

@@ -48 +48 @@
     """
     M = StandardModelType
+    M.default_parameters = {'a': 0.0, 'b': 0.0}
+    M.translations = {'a': None, 'b': None}
     P1 = {'a': 22.2, 'b': 33.3}
     P2 = {'A': 22.2, 'B': 333}