Changeset 817 for branches

Timestamp:

11/10/10 16:12:06 (19 months ago)

Author:

apdavison

Message:

Starting to reimplement native model support (in branch)

Location:

branches/nativemodels

Files:

• examples/native_nest.py (added)
• examples/native_neuron.py (added)
• src/common.py (modified) (4 diffs)
• src/nest/__init__.py (modified) (4 diffs)
• src/nest/electrodes.py (modified) (1 diff)
• src/nest/simulator.py (modified) (1 diff)
• src/neuron/__init__.py (modified) (2 diffs)
• src/neuron/electrodes.py (modified) (1 diff)
• src/neuron/simulator.py (modified) (2 diffs)

branches/nativemodels/src/common.py

@@ -70 +70 @@
     """
     if hasattr(target_cell, 'local') and target_cell.local and hasattr(target_cell, 'cellclass'):
-        if isinstance(target_cell.cellclass, type):
-            is_conductance = target_cell.cellclass.conductance_based
-        else: # where cellclass is a string, i.e. for native cell types in NEST
-            is_conductance = "cond" in target_cell.cellclass
+#        if isinstance(target_cell.cellclass, type):
+        is_conductance = target_cell.cellclass.conductance_based
+#        else: # where cellclass is a string, i.e. for native cell types in NEST
+#            is_conductance = "cond" in target_cell.cellclass
     else:
         is_conductance = None
@@ -759 +759 @@
         Connect a current source to all cells in the Population.
         """
-        if 'v' not in self.celltype.recordable:
+#        if 'v' not in self.celltype.recordable:
+        if not self.celltype.injectable:           
             raise TypeError("Can't inject current into a spike source.")
         current_source.inject_into(self)
@@ -786 +787 @@
     nPop = 0
     
-    def __init__(self, size, cellclass, cellparams=None, structure=None,
-                 label=None):
+    def __init__(self, size, celltype, structure=None, label=None):
         """
         Create a population of neurons all of the same type.
@@ -822 +822 @@
         self.size = size
         self.label = label or 'population%d' % Population.nPop         
-        if isinstance(cellclass, type) and issubclass(cellclass, standardmodels.StandardCellType):
-            self.celltype = cellclass(cellparams)
-        else:
-            self.celltype = cellclass
+#        if isinstance(cellclass, type) and issubclass(cellclass, standardmodels.StandardCellType):
+#            self.celltype = cellclass(cellparams)
+#        else:
+#            self.celltype = cellclass
+        self.celltype = celltype
         self._structure = structure or space.Line()
         self._positions = None
-        self.cellparams = cellparams
+#        self.cellparams = cellparams
         # Build the arrays of cell ids
         # Cells on the local node are represented as ID objects, other cells by integers
         # All are stored in a single numpy array for easy lookup by address
         # The local cells are also stored in a list, for easy iteration
-        self._create_cells(cellclass, cellparams, size)
+        self._create_cells(celltype, size)
         self.initial_values = {}
         for variable, value in self.celltype.default_initial_values.items():

branches/nativemodels/src/nest/__init__.py

@@ -167 +167 @@
     recorder_class = Recorder
 
-    def _create_cells(self, cellclass, cellparams, n):
+    def _create_cells(self, celltype, n):
         """
         Create cells in NEST.
@@ -178 +178 @@
         # perhaps should check for that
         assert n > 0, 'n must be a positive integer'
-        if isinstance(cellclass, basestring):  # celltype is not a standard cell
-            nest_model = cellclass
-            cell_parameters = cellparams or {}
-        elif isinstance(cellclass, type) and issubclass(cellclass, standardmodels.StandardCellType):
-            celltype = cellclass(cellparams)
-            nest_model = celltype.nest_name[simulator.state.spike_precision]
-            cell_parameters = celltype.parameters
-        else:
-            raise Exception("Invalid cell type: %s" % type(cellclass))
+#        if isinstance(cellclass, basestring):  # celltype is not a standard cell
+#            nest_model = cellclass
+#            cell_parameters = cellparams or {}
+#        elif isinstance(cellclass, type) and issubclass(cellclass, standardmodels.StandardCellType):
+        nest_model = celltype.nest_name[simulator.state.spike_precision]
+#        cell_parameters = celltype.parameters
+#        else:
+#            raise Exception("Invalid cell type: %s" % type(cellclass))
         try:
             self.all_cells = nest.Create(nest_model, n)
@@ -193 +192 @@
                 raise errors.InvalidModelError("%s Have you compiled NEST with the GSL (Gnu Scientific Library)?" % err)
             raise errors.InvalidModelError(err)
-        if cell_parameters:
-            try:
-                nest.SetStatus(self.all_cells, [cell_parameters])
-            except nest.NESTError:
-                print "NEST error when trying to set the following dictionary: %s" % cell_parameters
-                raise
+#        if cell_parameters:
+        try:
+            nest.SetStatus(self.all_cells, [celltype.parameters])
+        except nest.NESTError:
+            print "NEST error when trying to set the following dictionary: %s" % cell_parameters
+            raise
         self.first_id = self.all_cells[0]
         self.last_id = self.all_cells[-1]
@@ -283 +282 @@
             value = rarr #numpy.array(rarr)
             assert len(rarr) == len(self.local_cells), "%d != %d" % (len(rarr), len(self.local_cells))
-        nest.SetStatus(self.local_cells.tolist(), STATE_VARIABLE_MAP[variable], value)
+        if variable in STATE_VARIABLE_MAP:
+            variable = STATE_VARIABLE_MAP[variable]
+        nest.SetStatus(self.local_cells.tolist(), variable, value)
         self.initial_values[variable] = core.LazyArray(self.size, value)
 

branches/nativemodels/src/nest/electrodes.py

@@ -24 +24 @@
         """Inject this current source into some cells."""
         for id in cell_list:
-            if id.local and 'v' not in id.cellclass.recordable:
+            if id.local and not id.cellclass.injectable: #'v' not in id.cellclass.recordable:
                 raise TypeError("Can't inject current into a spike source.")
         if isinstance(cell_list, Population):

branches/nativemodels/src/nest/simulator.py

@@ -272 +272 @@
         
         try:
-            nest.DivergentConnect([source], targets, weights, delays, self.synapse_model)            
+            nest.DivergentConnect([source], targets, weights, delays, self.synapse_model)
+            raise
         except nest.NESTError, e:
             raise errors.ConnectionError("%s. source=%s, targets=%s, weights=%s, delays=%s, synapse model='%s'" % (

branches/nativemodels/src/neuron/__init__.py

@@ -105 +105 @@
     recorder_class = Recorder
     
-    def __init__(self, size, cellclass, cellparams=None, structure=None,
+    def __init__(self, size, celltype, structure=None,
                  label=None):
         __doc__ = common.Population.__doc__
-        common.Population.__init__(self, size, cellclass, cellparams, structure, label)
+        common.Population.__init__(self, size, celltype, structure, label)
         simulator.initializer.register(self)
 
-    def _create_cells(self, cellclass, cellparams, n):
+    def _create_cells(self, celltype, n):
         """
         Create cells in NEURON.
@@ -123 +123 @@
         # perhaps should check for that
         assert n > 0, 'n must be a positive integer'
-        if isinstance(cellclass, basestring): # cell defined in hoc template
-            try:
-                cell_model = getattr(h, cellclass)
-            except AttributeError:
-                raise errors.InvalidModelError("There is no hoc template called %s" % cellclass)
-            cell_parameters = cellparams or {}
-        elif isinstance(cellclass, type) and issubclass(cellclass, standardmodels.StandardCellType):
-            celltype = cellclass(cellparams)
-            cell_model = celltype.model
-            cell_parameters = celltype.parameters
-        else:
-            cell_model = cellclass
-            cell_parameters = cellparams
+#        if isinstance(cellclass, basestring): # cell defined in hoc template
+#            try:
+#                cell_model = getattr(h, cellclass)
+#            except AttributeError:
+#                raise errors.InvalidModelError("There is no hoc template called %s" % cellclass)
+#            cell_parameters = cellparams or {}
+#        elif isinstance(cellclass, type) and issubclass(cellclass, standardmodels.StandardCellType):
+#            celltype = cellclass(cellparams)
+        cell_model = celltype.model
+        cell_parameters = celltype.parameters
+#        else:
+#            cell_model = cellclass
+#            cell_parameters = cellparams
         self.first_id = simulator.state.gid_counter
         self.last_id = simulator.state.gid_counter + n - 1

branches/nativemodels/src/neuron/electrodes.py

@@ -67 +67 @@
         for id in cell_list:
             if id.local:
-                if 'v' not in id.cellclass.recordable:
+#                if 'v' not in id.cellclass.recordable:
+                if not id.cellclass.injectable:
                     raise TypeError("Can't inject current into a spike source.")
                 iclamp = h.IClamp(0.5, sec=id._cell.source_section)

branches/nativemodels/src/neuron/simulator.py

@@ -152 +152 @@
 class _State(object):
     """Represent the simulator state."""
+    max_delay = numpy.inf
     
     def __init__(self):
@@ -440 +441 @@
                 if self.synapse_model == 'Tsodyks-Markram' and 'TM' not in self.synapse_type:
                     self.synapse_type += '_TM'        
-                synapse_object = getattr(target._cell, self.synapse_type)
+                if "." in self.synapse_type:
+                    section, synapse_type = self.synapse_type.split(".")
+                    synapse_object = getattr(getattr(target._cell, section), synapse_type)
+                else:
+                    synapse_object = getattr(target._cell, self.synapse_type)
                 nc = state.parallel_context.gid_connect(int(source), synapse_object)
                 nc.weight[0] = weight