Changeset 403

Timestamp:

06/26/08 17:17:12 (5 months ago)

Author:

apdavison

Message:

More modifications to neuron2 to pass generictests.py

Files:

• trunk/src/nest1/cells.py (modified) (2 diffs)
• trunk/src/nest2/__init__.py (modified) (1 diff)
• trunk/src/neuron2/cells.py (modified) (13 diffs)
• trunk/src/neuron2/simulator.py (modified) (4 diffs)
• trunk/test/unittests/generictests.py (modified) (1 diff)
• trunk/test/unittests/neuron2tests.py (modified) (1 diff)

trunk/src/nest1/cells.py

@@ -66 +66 @@
-        ('e_rev_I',    'V_reversal_I'),
-    )
-
+2
-    
-
@@ -96 +96 @@
-    https://facets.kip.uni-heidelberg.de/private/wiki/index.php/WP7_NNM
-    """
-    # in 'iaf_sfa_neuron', the dimension of C is pF,
-    # while in the pyNN context, cm is given in nF
-    translations = common.build_translations(
-        ('v_reset',    'Vreset'),

trunk/src/nest2/__init__.py

@@ -146 +146 @@
-            os.remove(nest_filename)
-            if data.size > 0:
+                # the following returns indices, not IDs. I'm not sure this is what we want.
-                if self.population is not None:
-                    padding = self.population.cell.flatten()[0]

trunk/src/neuron2/cells.py

@@ -35 +35 @@
-
-
-
-
+
-    """docstring"""
-    
@@ -43 +42 @@
-        'conductance' : { 'exp': neuron.ExpSyn,  'alpha': AlphaSyn },
-    }
-
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-        # initialise Section object with 'pas' mechanism
-        neuron.nrn.Section.__init__(self)
@@ -68 +61 @@
-        self.excitatory = self.esyn # } aliases
-        self.inhibitory = self.isyn # }
-
+
-        # insert current source
-        self.stim = neuron.IClamp(self, 0.5, delay=0, dur=1e12, amp=i_offset)
-
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-        self.spiketimes = neuron.Vector(0)
+
+    def area(self):
+        return pi*self.L*self.seg.diam
-
-    def __set_tau_m(self, value):
@@ -92 +76 @@
-    def __get_tau_m(self):
-        return 1e-3*self.seg.cm/self.seg.pas.g
-
+
-    tau_m    = property(fget=__get_tau_m, fset=__set_tau_m)
-    cm       = _new_property('seg', 'cm')
@@ -101 +85 @@
-    e_i      = _new_property('isyn', 'e')
-    v_rest   = _new_property('seg.pas', 'e')
-    v_thresh = _new_property('spike_reset', 'vthresh')
-    v_reset  = _new_property('spike_reset', 'vreset')
-    t_refrac = _new_property('spike_reset', 'trefrac')
-    
-    # what about v_init?
-
@@ -127 +107 @@
-        self.seg.v = self.v_init
-
-    
-    def use_Tsodyks_Markram_synapses(ei, U, tau_rec, tau_facil, u0):
-        if self.syn_type == 'current':
@@ -146 +125 @@
-        syn.u0 = u0
-
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-class SpikeSource(object):
-    
@@ -178 +226 @@
-                self.rec.record(self.spiketimes.hoc_obj)
-            
+# == Standard cells ============================================================
-
-class IF_curr_alpha(common.IF_curr_alpha):
@@ -290 +339 @@
-
-    translations = common.build_translations(
-        ('cm',         'cm'),
-        ('v_rest',     'v_rest'),
-        ('v_thresh',   'v_thresh'),
-        ('v_reset',    'v_reset'),
-
-
+
-        ('tau_syn_E',  'tau_e'),
-        ('tau_syn_I',  'tau_i'),
-
-
-
+
+
-    model = StandardIF
-
@@ -308 +354 @@
-        self.parameters['syn_shape'] = 'exp'
-        self.parameters['i_offset']  = 0.0
-
+
+
+
+
-
-class SpikeSourcePoisson(common.SpikeSourcePoisson):
@@ -350 +399 @@
-    """
-    
-
+common.build_translations
-        ('v_init',     'v_init'),
-        ('w_init',     'w_init'),
-        ('cm',         'cm'),
-Ref
-V
-Vbo
-EL
-GL',       "cm/tau_m", "CM/GL"), # uS
+t_refrac
+v_
+v_rese
+v_rest
+tau_m'),
-        ('i_offset',   'i_offset'), 
-        ('a',          'a',        0.001), # nS --> uS
@@ -364 +413 @@
-        ('delta_T',    'delta'), 
-        ('tau_w',      'tau_w'), 
-Vtr
+v_thresh
-        ('e_rev_E',    'e_e'),
-        ('tau_syn_E',  'tau_e'), 
@@ -370 +419 @@
-        ('tau_syn_I',  'tau_i'),
-    )
-hoc_name = "IF_BG_alpha"
+model = BretteGerstnerIF
-    
-    def __init__(self, parameters):

trunk/src/neuron2/simulator.py

@@ -31 +31 @@
-    numpy1_0_formats = {'spikes': "%g", # only later versions of numpy support different
-                        'v': "%g"}      # formats for different columns
-t id
+id t
-               'v': 't v id'}
-    
@@ -67 +67 @@
-    def get(self, gather=False):
-        """Returns the recorded data."""
+        if self.population:  # we return indices (always starting at 0), not IDs. This is what the other modules do, but I think we should really return IDs.
+            offset = self.population.first_id
+        else:
+            offset = 0
-        if self.variable == 'spikes':
-            data = numpy.empty((0,2))
@@ -73 +77 @@
-                spikes = spikes[spikes<=state.t+1e-9]
-                if len(spikes) > 0:
-spikes, numpy.ones(spikes.shape)*id
+numpy.ones(spikes.shape)*(id-offset), spikes
-                    data = numpy.concatenate((data, new_data))
-        elif self.variable == 'v':
@@ -80 +84 @@
-                v = id._cell.vtrace.toarray()
-                t = id._cell.record_times.toarray()
-id
+(id-offset)
-                data = numpy.concatenate((data, new_data))
-        return data

trunk/test/unittests/generictests.py

@@ -45 +45 @@
-                        i = [1.0, 2.0]
-                        cell.__setattr__(name, i)
-cell.__getattr__(name
+list(cell.__getattr__(name)
-                        self.assertEqual(i, o)
-                    else:

trunk/test/unittests/neuron2tests.py

@@ -496 +496 @@
-        neuron.run(100.0)
-        spikes = spike_source.getSpikes()
-0
+1
-        if neuron.rank() == 0:
-            self.assert_( max(spikes) == 100.0, str(spikes) )