Changeset 365

Timestamp:

06/13/08 18:17:09 (5 months ago)

Author:

apdavison

Message:

Began updating the neuron module to use the new features of NEURON (HocObject, etc)

Files:

• trunk/src/neuron/__init__.py (modified) (8 diffs)

trunk/src/neuron/__init__.py

@@ -48 +48 @@
-    hit is it to replace integers with ID objects?
-    """
-
-
-
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+
-    def __init__(self, n):
-        int.__init__(n)
@@ -66 +63 @@
-    
-    def _hoc_cell(self):
+        """Returns the hoc object corresponding to the cell with this id."""
-        assert self in gidlist, "Cell %d does not exist on this node" % self
-        if self.parent:
-            hoc_cell_list = getattr(h, self.parent.label)
-            try:
-                #cell = hoc_cell_list.object(self - self.parent.gid_start)
-                list_index = self.parent.gidlist.index(self)
-                cell = hoc_cell_list.object(list_index)
@@ -313 +310 @@
-        new_ids = list( ids.difference(self.recorded) )
-        self.recorded = self.recorded.union(ids)
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-        if self.variable == 'spikes':
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-        
-    def get(self, gather=False):
-        """Returns the recorded data."""
+        # not implemented yet
-        data = recording.readArray(filename, sepchar=None)
-        data = recording.convert_compatible_output(data, self.population, variable)
@@ -440 +432 @@
-    
-    if initialised:
-oc_commands = ['dt = %f' % timestep,
-                'min_delay = %g' % min_delay]
+.dt = timestep
+h.min_delay = min_delay
-        running = False
-    else:
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-        #---Experimental--- Optimize the simulation time ? / Reduce inter-processors exchanges ?
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-        if extra_params.has_key('use_cvode') and extra_params['use_cvode'] == True:
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-    nhost = int(h.pc.nhost())
-    if nhost < 2:
-        nhost = 1; myid = 0
-    else:
-        #myid = HocToPy.get('pc.id()','int')
-        myid = int(h.pc.id())
-    #print "\nHost #%d of %d" % (myid+1, nhost)
-    vfilelist = {}
-    spikefilelist = {}
-    
-    initialised = True
@@ -492 +474 @@
-    for recorder in recorder_list:
-        recorder.write(gather=False, compatible_output=compatible_output)
-
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+
-    if quit_on_end:
-oc.execute('tmp = quit()') # sometimes needed, sometimes not wanted. Maybe a 'quit_on_end' kwarg for setup?
+.quit()
-        logging.info("Finishing up with NEURON.")
-        sys.exit(0)
@@ -504 +484 @@
-    """Run the simulation for simtime ms."""
-    global running
-
+
-    if not running:
-        running = True
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-        logging.debug("local_minimum_delay on host #%d = %g" % (myid, h.local_minimum_delay))
-        if nhost > 1:
-            assert h.local_minimum_delay >= get_min_delay(),\
-                   "There are connections with delays (%g) shorter than the minimum delay (%g)" % (h.local_minimum_delay, get_min_delay())
-
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-    return get_current_time()
-
@@ -572 +550 @@
-                         #'nc = new NetCon(cell%d.source, nil)' % cell_id,
-                         'tmp = pc.cell(%d, nc)' % cell_id]
+        #h('tmp = pc.set_gid2node(%d,%d)' % (cell_id, myid))
+        #h('objref cell%d' % cell_id)
+        #h('cell%d = new %s(%s)' % (cell_id, hoc_name, argstr))
+        #h('tmp = cell%d.connect2target(nil, nc)' % cell_id)
+        #h('tmp = pc.cell(%d, nc)' % cell_id)
-    hoc_execute(hoc_commands, "--- create() ---")
-
@@ -971 +954 @@
-            # Each node will record N/nhost cells...
-            nrec = int(record_from/nhost)
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-        else:
-            raise Exception("record_from must be either a list of cells or the number of cells to record from")