Changeset 726

Timestamp:

03/11/10 15:24:33 (2 years ago)

Author:

apdavison

Message:

Resumed implementation of the moose module. HH_cond_exp2.py example runs and gives the same results with moose as with neuron (nest is different - need to figure out why).

Location:

trunk

Files:

• examples/HH_cond_exp2.py (added)
• src/moose/__init__.py (modified) (2 diffs)
• src/moose/cells.py (modified) (3 diffs)
• src/moose/recording.py (added)
• src/moose/simple_example.py (added)
• src/moose/simulator.py (added)
• src/neuron/__init__.py (modified) (1 diff)
• src/neuron/simulator.py (modified) (1 diff)

trunk/src/moose/__init__.py

@@ -1 @@
-"""Interfacing MOOSE to PyNN"""
+# encoding: utf-8
+"""
+MOOSE implementation of the PyNN API
+
+Authors: Subhasis Ray and Andrew Davison
+
+$Id:$
+"""
+
 import moose
-import Neuron
-from cells import *
-from pyNN import common
+from pyNN.moose import simulator
+from pyNN import common, recording
+common.simulator = simulator
+recording.simulator = simulator
 
-def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, debug=False, **extra_params):
+from pyNN.moose.cells import *
+from pyNN.moose.recording import *
+
+import logging
+logger = logging.getLogger("PyNN")
+
+# ==============================================================================
+#   Functions for simulation set-up and control
+# ==============================================================================
+
+def setup(timestep=0.1, min_delay=0.1, max_delay=10.0, **extra_params):
     """
     Should be called at the very beginning of a script.
@@ -11 +30 @@
     simulator but not by others.
     """
-    common.setup(timestep, min_delay, max_delay, debug, **extra_params)
-    ctx = moose.PyMooseBase.getContext()
-    ctx.setClock(0, timestep, 0)
+    common.setup(timestep, min_delay, max_delay, **extra_params)
+    simulator.state.dt = timestep
     return 0
 
 def end(compatible_output=True):
     """Do any necessary cleaning up before exiting."""
+    for recorder in simulator.recorder_list:
+        recorder.write(gather=True, compatible_output=compatible_output)
     moose.PyMooseBase.endSimulation()
- 
-def create(cellclass, cellparams=None, n=1):
-    """
-    Create n cells all of the same type.
-    If n > 1, return a list of cell ids/references.
-    If n==1, return just the single id.
-    """
-    assert n > 0, 'n must be a positive integer'
-    cell_gids = []
-    if isinstance(cellclass, type):
-        for i in range(n):
-                print cellclass, cellparams
-                cell_type = cellclass(cellparams)
-                cell = eval("Neuron."+cell_type.moose_name)(**cell_type.parameters)
-                cell_gids.append(cell.id)
-        cell_gids = [ID(gid) for gid in cell_gids]
-    elif isinstance(cellclass, str):  # celltype is not a standard cell
-        cellclass = eval(cellclass)
-        for i in range(n):
-                cell = cellclass(**cellparams)
-                cell_gids.append(cell.id)
-        cell_gids = [ID(gid) for gid in cell_gids]
-    else:
-        raise Exception("Invalid cell type")
-    for id in cell_gids:
-        id.cellclass = cellclass
-    if n == 1:
-        return cell_gids[0]
-    else:
-        return cell_gids
 
-def record(source, filename):
-        dataDir = Neutral("/data")
-        probe = Table(source.name, dataDir)
-        probe.step_mode = 3
-        probe.connect("inputRequest", source, "Vm")
-        
 def run(simtime):
         """Run the simulation for simtime"""
-        moose.step(simtime)
+        simulator.run(simtime)
+
+
+# ==============================================================================
+#   Functions returning information about the simulation state
+# ==============================================================================
+
+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   
+
+# ==============================================================================
+#   Low-level API for creating, connecting and recording from individual neurons
+# ==============================================================================
+
+create = common.create
+
+#connect = common.connect
+
+#set = common.set
+
+record = common.build_record('spikes', simulator)
+
+record_v = common.build_record('v', simulator)
+
+record_gsyn = common.build_record('gsyn', simulator)
+        
+

trunk/src/moose/cells.py

@@ -1 @@
-from pyNN import common, cells
+import moose
+from pyNN import standardmodels, cells
+
+mV = 1e-3
+ms = 1e-3
+nA = 1e-9
+
+class SingleCompHH(moose.Neutral):
+    
+    def __init__(self, path, GbarNa=0.0, GbarK=0.0, GLeak=0.0, Cm=1.0,
+                 ENa=40*mV, EK=-90*mV, VLeak=-65*mV, Voff=-63*mV, ESynE=0*mV,
+                 ESynI=-70*mV, tauE=2*ms, tauI=5*ms, inject=0*nA, initVm=-65*mV):
+        moose.Neutral.__init__(self, path)
+        self.comp = moose.Compartment("compartment", self)
+        print "compartment is at %s" % self.comp.path
+        print locals()
+        self.comp.initVm = initVm
+        self.comp.Rm = 1/GLeak
+        self.comp.Cm = Cm
+        self.comp.Em = VLeak
+        self.comp.inject = inject
+        self.na = moose.HHChannel("na", self.comp)
+        self.na.Ek = ENa
+        self.na.Gbar = GbarNa
+        self.na.Xpower = 3
+        self.na.Ypower = 1
+        self.na.setupAlpha("X", 3.2e5 * (13*mV+Voff), -3.2e5, -1, -(13*mV+Voff), -4*mV, # alpha
+                               -2.8e5 * (40*mV+Voff),  2.8e5, -1, -(40*mV+Voff), 5*mV)  # beta
+        self.na.setupAlpha("Y", 128,                   0,      0, -(17*mV+Voff), 18*mV, # alpha
+                                4.0e3,                 0,      1, -(40*mV+Voff), -5*mV) # beta
+
+        self.k = moose.HHChannel("k", self.comp)
+        self.k.Ek = EK
+        self.k.Gbar = GbarK
+        self.k.Xpower = 4
+        self.k.setupAlpha("X", 3.2e4 * (15*mV+Voff), -3.2e4, -1, -(15*mV+Voff), -5*mV,
+                               500,                  0,       0, -(10*mV+Voff),  40*mV)
+
+        #self.synE = moose.SynChan("excitatory", self.comp)
+        #self.synE.Ek = ESynE
+        #self.synE.tau1 = 1e-6
+        #self.synE.tau2 = tauE
+        #self.synE.Gbar = 1e-9
+        #self.synI = moose.SynChan("inhibitory", self.comp)
+        #self.synI.Ek = ESynI
+        #self.synI.tau1 = 1e-6
+        #self.synI.tau2 = tauI
+        #self.synI.Gbar = 1e-9
+    
+        #self.comp.connect("channel", self.synE, "channel")
+        #self.comp.connect("channel", self.synI, "channel")
+        self.comp.connect("channel", self.na, "channel")
+        self.comp.connect("channel", self.k , "channel")
+        
+        self.comp.useClock(0)
+        self.comp.useClock(1, "init")
+
+    def record_v(self):
+        self.vmTable = moose.Table("Vm", self)
+        self.vmTable.stepMode = 3
+        self.vmTable.connect("inputRequest", self.comp, "Vm")
+        self.vmTable.useClock(2)
+        print "vmTable is at %s" % self.vmTable.path
+        #moose.PyMooseBase.getContext().useClock(0, self.comp.path+"/##")
+
+#a = SingleCompHH("/comp", 1e-9, 1e-9, 1e-9, 1e-12, -0.06, 0.08, -0.06, 0.001, 0.05, -0.05, 1e-2, 2e-2, 1e-9, -0.06)
+#print "Successfully setup SingleCompHH"
+
+
 
 class HH_cond_exp(cells.HH_cond_exp):
     """Single compartment cell with an Na channel and a K channel"""
-    translations = common.build_translations(
+    translations = standardmodels.build_translations(
         ('gbar_Na',    'GbarNa', 1e-9),   
         ('gbar_K',     'GbarK', 1e-9),    
@@ -11 +79 @@
         ('e_rev_Na',   'ENa', 1e-3),
         ('e_rev_K',    'EK', 1e-3), 
-        ('e_rev_leak', 'Vleak', 1e-3),
+        ('e_rev_leak', 'VLeak', 1e-3),
         ('e_rev_E',    'ESynE', 1e-3),
         ('e_rev_I',    'ESynI', 1e-3),
@@ -19 +87 @@
         ('v_init',     'initVm', 1e-3),
     )
-    moose_name = "SingleCompHH"
+    model = SingleCompHH
 
 

trunk/src/neuron/__init__.py

@@ -59 +59 @@
         simulator.state.cvode.active(int(extra_params['use_cvode']))
         if extra_params.has_key('rtol'):
-            simulator.state.cvode.rtol(float(extra_params['rtol']))
+            simulator.state.cvode.rtol(float(extra_params['rtol']))
         if extra_params.has_key('atol'):
             simulator.state.cvode.atol(float(extra_params['atol']))

trunk/src/neuron/simulator.py

@@ -2 +2 @@
 """
 Implementation of the "low-level" functionality used by the common
-implementation of the API.
+implementation of the API, for the NEURON simulator.
 
 Functions and classes useable by the common implementation: