Changeset 96

Timestamp:

06/07/07 11:35:13 (1 year ago)

Author:

apdavison

Message:

:

• Improved ID class now working with neuron module
  
• Renamed ID.set() method to setParameters(), and added getParameters()
  

The reason for not having a parameters property, is that setParameters() should allow setting only a sub-set of the cell parameters and so parameters would have behave in some ways like a dict and in other ways not, which could be confusing.

Files:

• branches/improved-ID/common.py (modified) (3 diffs)
• branches/improved-ID/nest.py (modified) (2 diffs)
• branches/improved-ID/neuron.py (modified) (9 diffs)
• branches/improved-ID/test/neurontests.py (modified) (2 diffs)

branches/improved-ID/common.py

@@ -44 +44 @@
-    """
-    
+    non_parameter_attributes = ('parent','_cellclass','cellclass','_position','position','hocname')
+    
-    def __init__(self,n):
-        int.__init__(n)
-        self.parent = None
-        self._cellclass = None
-        #self._hocname   = None
-
-    def __getattr__(self,name):
@@ -55 +56 @@
-    
-    def __setattr__(self,name,value):
-('parent','_cellclass','cellclass','_position','position')
+ID.non_parameter_attributes
-            object.__setattr__(self,name,value)
-        else:
-
+Parameters
-
-    def _set_cellclass(self, cellclass):
@@ -96 +97 @@
-    position = property(_get_position, _set_position)
-
-
+Parameters
-        """Set cell parameters, given as a sequence of parameter=value arguments."""
+        return _abstractMethod(self)
+    
+    def getParameters(self):
+        """Return a dict of all cell parameters."""
-        return _abstractMethod(self)
-

branches/improved-ID/nest.py

@@ -39 +39 @@
-        return pynest.getDict([int(self)])[0][translated_name]
-    
-
+Parameters
-        # We perform a call to the low-level function set() of the API.
-        # If the cellclass is not defined in the ID object :
@@ -48 +48 @@
-            set(self, self.cellclass, parameters) 
-
+    def getParameters(self):
+        """Note that this currently does not translate units."""
+        pynest_params = pynest.getDict([int(self)])[0]
+        params = {}
+        for k,v in self.cellclass.translations.items():
+            params[k] = pynest_params[v[0]]
+        return params
+            
-
-# ==============================================================================

branches/improved-ID/neuron.py

@@ -40 +40 @@
-    """
-    
+    def __init__(self,n):
+        common.ID.__init__(self,n)
+        self.hocname = None
+    
-    def __getattr__(self,name):
-        """Note that this currently does not translate units."""
-_
-_
-_
+
+
+
-        else:
-            return HocToPy.get('cell%d.%s' % (int(self), translated_name),'float')
-    
-(self,param,val=None
+Parameters(self,**parameters
-        # We perform a call to the low-level function set() of the API.
- (?) 
-_
+
+
-            raise Exception("Unknown cellclass")
-        else:
@@ -58 +62 @@
-            #several nodes. Then a call like cell[i,j].set() should be performed only on the
-            #node who owns the cell. To do that, if the node doesn't have the cell, a call to set()
-
-
-
-
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-
-# ==============================================================================
@@ -499 +495 @@
-    cell_list = [ID(i) for i in range(gid,gid+n)]
-    for id in cell_list:
-setCellClass(cellclass)
+cellclass = cellclass
-    gid = gid+n
-    if n == 1:
@@ -544 +540 @@
-    return range(nc_start,ncid)
-
- #,hocname=None):
+
-    """Set one or more parameters of an individual cell or list of cells.
-    param can be a dict, in which case val should not be supplied, or a string
@@ -560 +556 @@
-    for param,val in paramDict.items():
-        if isinstance(val,str):
-            ## If we know the hoc name of the object (set() applied to a population object), we use it
-            #if (hocname != None):
-            #    fmt = '%s.%s = "%s"'
-            #else:
-            #    fmt = 'cell%d.%s = "%s"'
-            fmt = 'pc.gid2cell(%d).%s = "%s"'
-        elif isinstance(val,list):
-            cmds,argstr = _hoc_arglist([val])
-            hoc_commands += cmds
-            ## If we know the hoc name of the object (set() applied to a population object), we use it
-            #if (hocname != None):
-            #    fmt = '%s.%s = %s'
-            #else:
-            #    fmt = 'cell%d.%s = %s'
-            fmt = 'pc.gid2cell(%d).%s = %s'
-            val = argstr
-        else:
-            ## If we know the hoc name of the object (set() applied to a population object), we use it
-            #if (hocname != None):
-            #    fmt = '%s.%s = %g'
-            #else:
-            #    fmt = 'cell%d.%s = %g'
-            fmt = 'pc.gid2cell(%d).%s = %g'
-        for cell in cells:
-            if cell in gidlist:
-                ## If we know the hoc name of the object (set() applied to a population object), we use it
-                #if (hocname != None):
-                #    hoc_commands += [fmt % (hocname,param,val),
-                #                     'tmp = %s.param_update()' %hocname]
-                #else:
-                #    hoc_commands += [fmt % (cell,param,val),
-                #                     'tmp = cell%d.param_update()' %cell]
-                hoc_commands += [fmt % (cell,param,val),
-                                 'tmp = pc.gid2cell(%d).param_update()' % cell]
@@ -699 +673 @@
-        # each population should store what we call a "fullgidlist" with the ID of all the cells in the populations 
-        # (and therefore their positions)
-
+
+
-        
-        # self.gidlist is now derived from self.fullgidlist since it contains only the cells of the population located on
@@ -728 +703 @@
-        # in the population
-        for cell_id in self.fullgidlist:
-setCellClass(cellclass)
-
+parent = self
+#
-                    
-        # On the opposite, each node has to know only the precise hocname of its cells, if we
-        # want to be able to use the low level set() function
-        for cell_id in self.gidlist:
-setHocName("%s.o(%d)" %(self.hoc_label, self.gidlist.index(cell_id)
+hocname = "%s.o(%d)" % (self.hoc_label, self.gidlist.index(cell_id
-
-    def __getitem__(self,addr):
@@ -1182 +1157 @@
-        population is scaled to the size of the source population."""
-        dist = 0.0
-getPosition()
-getPosition()
+position
+position
-        if (len(src_position) == len(tgt_position)):
-            for i in xrange(len(src_position)):
@@ -1581 +1556 @@
-                tgt = self.connections[i][1]
-                # calculate the distance between the two cells
-self.pre.fullgidlist.index(src)
-self.post.fullgidlist.index(tgt)
+numpy.where(self.pre.fullgidlist == src)[0][0]
+numpy.where(self.post.fullgidlist == tgt)[0][0]
-                dist = self._distance(self.pre, self.post, self.pre.fullgidlist[idx_src], self.post.fullgidlist[idx_tgt])
-                # then evaluate the delay according to the delay rule

branches/improved-ID/test/neurontests.py

@@ -595 +595 @@
-        assert (mean_weight_before < mean_weight_after)
-        
-    def testSetAndGetID(self):
-        # Small test to see if the ID class is working
-        self.target[0,2].set({'tau_m' : 15.1})
-        assert (self.target[0,2].get('tau_m') == 15.1)
-        
-    def testSetAndGetPositionID(self):
-        # Small test to see if the position of the ID class is working
-        self.target[0,2].setPosition((0.5,1.5))
-        assert (self.target[0,2].getPosition() == (0.5,1.5))
-        
-    def testSetTopographicDelay(self):
-        # We fix arbitrarily the positions of 2 cells in 2 populations and check 
-        # the topographical delay between them is linked to the distance
-setPosition((0,0)
-setPosition((0,10)
+position = (0,0,0
+position = (0,10,0
-        prj1 = neuron.Projection(self.source, self.target, 'allToAll')
-        rule="5.432*d"
@@ -661 +651 @@
-    def setUp(self):
-        neuron.Population.nPop = 0
-
-
-
-
-
-
-
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-if __name__ == "__main__":
-    sys.argv = ['./nrnpython']