Changeset 859 for trunk

Timestamp:

12/10/10 16:41:57 (2 years ago)

Author:

apdavison

Message:

More unit tests, and some minor changes in common.

Location:

trunk

Files:

• src/common.py (modified) (4 diffs)
• test/unittests/test_assembly.py (modified) (5 diffs)
• test/unittests/test_basepopulation.py (modified) (1 diff)
• test/unittests/test_population.py (modified) (4 diffs)
• test/unittests/test_populationview.py (modified) (1 diff)
• test/unittests/test_projection.py (modified) (2 diffs)

trunk/src/common.py

@@ -471 +471 @@
         
         if hasattr(self, "_get_array"):
-            values = self._get_array(parameter_name)
+            values = self._get_array(parameter_name).tolist()
         else:
             values = [getattr(cell, parameter_name) for cell in self]  # list or array?
         
         if gather == True and num_processes() > 1:
-            all_values = { rank(): values }
-            all_index  = { rank(): self.local_cells.tolist()}
-            all_values = recording.gather_dict(all_values)
-            all_index  = recording.gather_dict(all_index)
+            all_values  = { rank(): values }
+            all_indices = { rank(): self.local_cells.tolist()}
+            all_values  = recording.gather_dict(all_values)
+            all_indices = recording.gather_dict(all_indices)
             if rank() == 0:
-                values = reduce(operator.add, all_values.values())
-                index  = reduce(operator.add, all_index.values())
-            idx    = argsort(index)
+                values  = reduce(operator.add, all_values.values())
+                indices = reduce(operator.add, all_indices.values())
+            idx    = numpy.argsort(indices)
             values = numpy.array(values)[idx]
         return values
@@ -912 +912 @@
         if isinstance(id, IDMixin):
             if not self.first_id <= id <= self.last_id:
-                raise IndexError("id should be in the range [%d,%d], actually %d" % (self.first_id, self.last_id, id))
+                raise ValueError("id should be in the range [%d,%d], actually %d" % (self.first_id, self.last_id, id))
+            return int(id - self.first_id)  # this assumes ids are consecutive
         else:
             id = numpy.array(id, IDMixin)
             if (self.first_id > id.min()) or (self.last_id < id.max()):
-                raise IndexError("ids should be in the range [%d,%d], actually [%d, %d]" % (self.first_id, self.last_id, id.min(), id.max()))
-        return id - self.first_id  # this assumes ids are consecutive
+                raise ValueError("ids should be in the range [%d,%d], actually [%d, %d]" % (self.first_id, self.last_id, id.min(), id.max()))
+            return (id - self.first_id).astype(int)  # this assumes ids are consecutive
 
     def id_to_local_index(self, id):
@@ -1161 +1162 @@
         result[:,1:4] = self.positions.T 
         if rank() == 0:
-            file.write(result, {'population' : self.label})
+            file.write(result, {'assembly' : self.label})
             file.close()
 
@@ -1413 +1414 @@
         # it is arguable whether functions operating on the set of weights
         # should be put here or in an external module.
+        weights = self.getWeights(format='list', gather=True)
+        if min is None:
+            min = weights.min()
+        if max is None:
+            max = weights.max()
         bins = numpy.linspace(min, max, nbins+1)
-        return numpy.histogram(self.getWeights(format='list', gather=True), bins)  # returns n, bins
+        return numpy.histogram(weights, bins, new=True)  # returns n, bins
 
     def describe(self, template='projection_default.txt', engine='default'):

trunk/test/unittests/test_assembly.py

@@ -1 @@
-
+from pyNN import common
 from pyNN.common import Assembly, BasePopulation
 from nose.tools import assert_equal, assert_raises
@@ -18 +18 @@
     _mask_local = numpy.arange(10)%2 == 1
     initialize = Mock()
+    positions = numpy.arange(3*size).reshape(3,size)
     def describe(self, template='abcd', engine=None):
         if template is None:
@@ -45 +46 @@
     a = Assembly(p1, p2, label="test")
     assert_equal(a.size, p1.size + p2.size)
+
+def test_positions_property():
+    p1 = MockPopulation()
+    p2 = MockPopulation()
+    a = Assembly(p1, p2, label="test")
+    assert_arrays_equal(a.positions, numpy.concatenate((p1.positions, p2.positions), axis=1))
 
 def test__len__():
@@ -103 +110 @@
     a1 += a2
     assert_equal(a1.populations, [p1, p2, p2, p3])
-    
+
+def test_add_invalid_object():
+    p1 = MockPopulation()
+    p2 = MockPopulation()
+    a = Assembly(p1, p2)
+    assert_raises(TypeError, a.__add__, 42)
+    assert_raises(TypeError, a.__iadd__, 42)
+
 def test_initialize():
     p1 = MockPopulation()
@@ -164 +178 @@
     assert_arrays_equal(a._mask_local, numpy.append(p1._mask_local, (p2._mask_local, p3._mask_local)))
     assert_arrays_equal(a.local_cells, a.all_cells[a._mask_local])
+
+def test_save_positions():
+    import os
+    orig_rank = common.rank
+    common.rank = lambda: 0
+    p1 = MockPopulation()
+    p2 = MockPopulation()
+    p1.all_cells = numpy.array([34, 45])
+    p2.all_cells = numpy.array([56, 67])
+    p1.positions = numpy.arange(0,6).reshape((2,3)).T
+    p2.positions = numpy.arange(6,12).reshape((2,3)).T
+    a = Assembly(p1, p2, label="test")
+    output_file = Mock()
+    a.save_positions(output_file)
+    assert_arrays_equal(output_file.write.call_args[0][0],
+                        numpy.array([[34, 0, 1, 2], [45, 3, 4, 5], [56, 6, 7, 8], [67, 9, 10, 11]]))
+    assert_equal(output_file.write.call_args[0][1], {'assembly': a.label})
+    # arguably, the first column should contain indices, not ids.
+    common.rank = orig_rank

trunk/test/unittests/test_basepopulation.py

@@ -158 +158 @@
     MockPopulation.__iter__ = orig_iter
 
-#def test_get_with_gather():
-#    np_orig = common.num_processes
-#    rank_orig = common.rank
-#    gd_orig = common.recording.gather_dict
-#    common.num_processes = lambda: 2
-#    common.rank = 0
-#    common.recording.gather_dict = Mock(return_value={0: 
-#    
-#    p = MockPopulation()
-#    p._get_array = Mock(return_value=numpy.arange(10.0, 23.0, 1.0))
-#    p.get("tau_m")
-#    
-#    common.num_processes = np_orig
-#    common.rank = rank_orig
-#    common.recording.gather_dict = gd_orig
+def test_get_with_gather():
+    np_orig = common.num_processes
+    rank_orig = common.rank
+    gd_orig = common.recording.gather_dict
+    common.num_processes = lambda: 2
+    common.rank = lambda: 0
+    def mock_gather_dict(D): # really hacky
+        assert isinstance(D[0], list)
+        D[1] = [i-1 for i in D[0]] + [D[0][-1] + 1]
+        return D
+    common.recording.gather_dict = mock_gather_dict
+    
+    p = MockPopulation()
+    p._get_array = Mock(return_value=numpy.arange(11.0, 23.0, 2.0))
+    assert_arrays_equal(p.get("tau_m", gather=True),
+                        numpy.arange(10.0, 23.0))
+    
+    common.num_processes = np_orig
+    common.rank = rank_orig
+    common.recording.gather_dict = gd_orig
 
 def test_set_from_dict():

trunk/test/unittests/test_population.py

@@ -6 +6 @@
 
 
-class MockID(object):
-    def __init__(self, i, parent):
-        self.label = str(i)
-        self.parent = parent
+class MockID(int, common.IDMixin):
+    def __init__(self, n):
+        int.__init__(n)
+        common.IDMixin.__init__(self)
     def get_parameters(self):
         return {}
@@ -16 +16 @@
     recorder_class = Mock()
     initialize = Mock()
-    first_id = 999
-    last_id = 7777
     
     def _create_cells(self, cellclass, cellparams, size):
-        self.all_cells = numpy.array([MockID(i, self) for i in range(size)], MockID)
-        self._mask_local = numpy.arange(size)%5==3
+        self.all_cells = numpy.array([MockID(i) for i in range(999, 999+size)], MockID)
+        self._mask_local = numpy.arange(size)%5==3 # every 5th cell, starting with the 4th, is on this node
+        self.first_id = self.all_cells[0]
+        self.last_id = self.all_cells[-1]
 
 class MockStandardCell(standardmodels.StandardCellType):
@@ -77 +77 @@
     assert_arrays_equal(p.cell, p.all_cells)
 
-#def test_id_to_index():
+def test_id_to_index():
+    p = MockPopulation(11, MockStandardCell)
+    assert isinstance(p[0], common.IDMixin)
+    assert_equal(p.id_to_index(p[0]), 0)
+    assert_equal(p.id_to_index(p[10]), 10)
 
-# test id_to_local_index
+def test_id_to_index_with_array():
+    p = MockPopulation(11, MockStandardCell)
+    assert isinstance(p[0], common.IDMixin)
+    assert_arrays_equal(p.id_to_index(p.all_cells[3:9:2]), numpy.arange(3,9,2))
+
+def test_id_to_index_with_populationview():
+    p = MockPopulation(11, MockStandardCell)
+    assert isinstance(p[0], common.IDMixin)
+    view = p[3:7]
+    assert isinstance(view, common.PopulationView)
+    assert_arrays_equal(p.id_to_index(view), numpy.arange(3,7))
+
+def test_id_to_index_with_invalid_id():
+    p = MockPopulation(11, MockStandardCell)
+    assert isinstance(p[0], common.IDMixin)
+    assert_raises(ValueError, p.id_to_index, MockID(p.last_id+1))
+    assert_raises(ValueError, p.id_to_index, MockID(p.first_id-1))
+    
+def test_id_to_index_with_invalid_ids():
+    p = MockPopulation(11, MockStandardCell)
+    assert_raises(ValueError, p.id_to_index, [MockID(p.first_id-1)] + p.all_cells[0:3].tolist())
+
+def test_id_to_local_index():
+    orig_np = common.num_processes
+    common.num_processes = lambda: 5
+    p = MockPopulation(11, MockStandardCell)
+    # every 5th cell, starting with the 4th, is on this node.
+    assert_equal(p.id_to_local_index(p[3]), 0)
+    assert_equal(p.id_to_local_index(p[8]), 1)
+    
+    common.num_processes = lambda: 1
+    # only one node
+    assert_equal(p.id_to_local_index(p[3]), 3)
+    assert_equal(p.id_to_local_index(p[8]), 8)
+    common.num_processes = orig_np
+
+def test_id_to_local_index_with_invalid_id():
+    orig_np = common.num_processes
+    common.num_processes = lambda: 5
+    p = MockPopulation(11, MockStandardCell)
+    # every 5th cell, starting with the 4th, is on this node.
+    assert_raises(ValueError, p.id_to_local_index, p[0])
+    common.num_processes = orig_np
 
 # test structure property
@@ -114 +160 @@
     assert p.positions[0,0] != 99.9
 
+def test_position_generator():
+    p = MockPopulation(11, MockStandardCell)
+    assert_arrays_equal(p.position_generator(0), p.positions[:,0])
+    assert_arrays_equal(p.position_generator(10), p.positions[:,10])
+    assert_arrays_equal(p.position_generator(-1), p.positions[:,10])
+    assert_arrays_equal(p.position_generator(-11), p.positions[:,0])
+    assert_raises(IndexError, p.position_generator, 11)
+    assert_raises(IndexError, p.position_generator, -12)
+
 # test describe method
 def test_describe():

trunk/test/unittests/test_populationview.py

@@ -74 +74 @@
 # test initial values property
 
-# test structure property
+def test_structure_property():
+    p = MockPopulation(11, MockStandardCell)
+    mask = slice(3,9,2)
+    pv = common.PopulationView(parent=p, selector=mask)
+    assert_equal(pv.structure, p.structure)
 
 # test positions property

trunk/test/unittests/test_projection.py

@@ -4 +4 @@
 import numpy
 import os
+from pyNN.utility import assert_arrays_equal
 
 orig_rank = common.rank
@@ -190 +191 @@
     os.remove(filename)
 
+def test_weight_histogram_with_args():
+    p1 = MockPopulation()
+    p2 = MockPopulation()
+    prj = common.Projection(p1, p2, method=Mock())
+    prj.getWeights = Mock(return_value=numpy.array(range(10)*42))
+    n, bins = prj.weightHistogram(min=0.0, max=9.0, nbins=10)
+    assert_equal(n.size, 10)
+    assert_equal(bins.size, n.size+1)
+    assert_arrays_equal(n, 42*numpy.ones(10))
+    assert_equal(n.sum(), 420)
+    assert_arrays_equal(bins, numpy.arange(0.0, 9.1, 0.9))
+
+def test_weight_histogram_no_args():
+    p1 = MockPopulation()
+    p2 = MockPopulation()
+    prj = common.Projection(p1, p2, method=Mock())
+    prj.getWeights = Mock(return_value=numpy.array(range(10)*42))
+    n, bins = prj.weightHistogram(nbins=10)
+    assert_equal(n.size, 10)
+    assert_equal(bins.size, n.size+1)
+    assert_arrays_equal(n, 42*numpy.ones(10))
+    assert_equal(n.sum(), 420)
+    assert_arrays_equal(bins, numpy.arange(0.0, 9.1, 0.9))
+
 def test_describe():
     p1 = MockPopulation()