Changeset 99

Timestamp:

06/07/07 15:31:43 (1 year ago)

Author:

apdavison

Message:

Improved ID class now working with pcsim module.

Files:

• branches/improved-ID/common.py (modified) (1 diff)
• branches/improved-ID/nest.py (modified) (1 diff)
• branches/improved-ID/neuron.py (modified) (1 diff)
• branches/improved-ID/pcsim.py (modified) (7 diffs)
• branches/improved-ID/test/pcsimtests_population.py (modified) (2 diffs)

branches/improved-ID/common.py

@@ -37 +37 @@
-class ID(int):
-    """
-This class is experimental. The idea is that instead of storing ids as
-integers, we store them as ID objects, 
-p[3,4].set('tau_m',20.0)
+Instead of storing ids as integers, we store them as ID objects,
+
+  p[3,4].tau_m = 20.0
-    where p is a Population object. The question is, how big a memory/performance
-    hit is it to replace integers with ID objects?

branches/improved-ID/nest.py

@@ -27 +27 @@
-class ID(common.ID):
-    """
-This class is experimental. The idea is that instead of storing ids as
-integers, we store them as ID objects, 
-p[3,4].set('tau_m',20.0)
+Instead of storing ids as integers, we store them as ID objects,
+
+  p[3,4].tau_m = 20.0
-    where p is a Population object. The question is, how big a memory/performance
-    hit is it to replace integers with ID objects?

branches/improved-ID/neuron.py

@@ -33 +33 @@
-class ID(common.ID):
-    """
-This class is experimental. The idea is that instead of storing ids as
-integers, we store them as ID objects, 
-p[3,4].set('tau_m',20.0)
+Instead of storing ids as integers, we store them as ID objects,
+
+  p[3,4].tau_m = 20.0
-    where p is a Population object. The question is, how big a memory/performance
-    hit is it to replace integers with ID objects?

branches/improved-ID/pcsim.py

@@ -227 +227 @@
-        f.close()
-
-common.ID
+long
-    """
-This class is experimental. The idea is that instead of storing ids as
-integers, we store them as ID objects, 
-p[3,4].set('tau_m',20.0)
+Instead of storing ids as integers, we store them as ID objects,
+
+  p[3,4].tau_m = 20.0
-    where p is a Population object. The question is, how big a memory/performance
-    hit is it to replace integers with ID objects?
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-        #if hasattr(self,'in_population'):
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-    
-# ==============================================================================
@@ -532 +553 @@
-        else:
-            raise exceptions.AttributeError('Trying to create non-existent cellclass ' + cellclass.__name__ )
-
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+
-    if n == 1:
-        cell_list = cell_list[0]
@@ -704 +728 @@
-                raise exceptions.AttributeError('Trying to create non-existent cellclass ' + cellclass.__name__ )
-            cellclass = eval(cellclass)
-
+    
-        if issubclass(cellclass, common.StandardCellType):
-
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-            if issubclass(cellclass, SimObject):
-                self.cellfactory = apply(cellclass, (), cellparams)
@@ -716 +742 @@
-        # CuboidGridPopulation(SimNetwork &net, GridPoint3D origin, Volume3DSize dims, SimObjectFactory &objFactory)
-        self.pcsim_population = CuboidGridObjectPopulation(pcsim_globals.net, GridPoint3D(0,0,0), Volume3DSize(dims[0], dims[1], dims[2]), self.cellfactory)
+        self.cell = numpy.array(self.pcsim_population.idVector())
+        self.cell -= self.cell[0]
-        
-        if not self.label:
@@ -743 +771 @@
-        assert index == pcsim_index, " index = %s, pcsim_index = %s" % (index, pcsim_index)
-        id = ID(pcsim_index)
-
-
+
-        if orig_addr != self.locate(id):
-            raise IndexError, 'Invalid cell address %s' % str(addr)
@@ -830 +857 @@
-        """PCSIM: iteration through all elements """
-        paramDict = checkParams(param, val)
-subclass
-({})
+instance
+
-                 
-        for index in range(0,len(self)):
@@ -849 +876 @@
-            values = numpy.copy(valueArray) # we do not wish to change the original valueArray in case it needs to be reused in user code
-            values = numpy.reshape(values, values.size)                          
-subclass
+instance
-                try:
-({})
+
-                except TypeError:
-                    raise common.InvalidParameterValueError(values[0])
-({})
+
-                values *= unit_scale_factor
-            for i, val in enumerate(values):

branches/improved-ID/test/pcsimtests_population.py

@@ -400 +400 @@
-         
-
-# #class ProjectionConnectionTest(unittest.TestCase):
-# #    """Tests of the connection attribute and connections() method of the Projection class."""
-# #    
-# #    def setUp(self):
-# #        neuron.Population.nPop = 0
-# #        self.pop1 = neuron.Population((5,),neuron.IF_curr_alpha)
-# #        self.pop2 = neuron.Population((4,4),neuron.IF_curr_alpha)    
-# #        self.pop3 = neuron.Population((3,3,3),neuron.IF_curr_alpha)
-# #        self.prj23 = neuron.Projection(self.pop2,self.pop3,"allToAll")
-# #        self.prj11 = neuron.Projection(self.pop1,self.pop1,"fixedProbability",0.5)
-# #        
-# #    def testFullAddress(self):
-# #        assert self.prj23.connection[(3,1),(2,0,1)] == "[3][1][2][0][1]"
-# #        assert self.prj23.connection[(3,3),(2,2,2)] == "[3][3][2][2][2]"
-# #        
-# #    def testPreIDPostID(self):
-# #        assert self.prj23.connection[0,0] == "[0][0][0][0][0]"
-# #        assert self.prj23.connection[0,26] == "[0][0][2][2][2]"
-# #        assert self.prj23.connection[0,25] == "[0][0][2][2][1]"
-# #        assert self.prj23.connection[15,0] == "[3][3][0][0][0]"
-# #        assert self.prj23.connection[14,0] == "[3][2][0][0][0]"
-# #        assert self.prj23.connection[13,19] == "[3][1][2][0][1]"
-# #        
-# #    def testSingleID(self):
-# #        assert self.prj23.connection[0] == "[0][0][0][0][0]"
-# #        assert self.prj23.connection[26] == "[0][0][2][2][2]"
-# #        assert self.prj23.connection[25] == "[0][0][2][2][1]"
-# #        assert self.prj23.connection[27] == "[0][1][0][0][0]"
-# #        assert self.prj23.connection[53] == "[0][1][2][2][2]"
-# #        assert self.prj23.connection[52] == "[0][1][2][2][1]"
-# #        assert self.prj23.connection[431] == "[3][3][2][2][2]"
-# #        assert self.prj23.connection[377] == "[3][1][2][2][2]"
-# #        assert self.prj23.connection[370] == "[3][1][2][0][1]"
-# #        
-# #        assert self.prj11.connection[0] == "[0][0]"
-
-
-class IDTest(unittest.TestCase):
-    """Tests of the ID class."""
@@ -442 +405 @@
-    def setUp(self):
-        setup(max_delay=0.5)
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-# ==============================================================================