Automated merge with ssh://p-omega1@lgcm/theano

_test_sparse.py

@@ -7,6 +7,8 @@ import gradient
 from sparse import _is_dense, _is_sparse, _is_dense_result, _is_sparse_result
 from sparse import _mtypes, _mtype_to_str
 
+import random
+
 class T_transpose(unittest.TestCase):
     def setUp(self):
         numpy.random.seed(44)

_test_tensor.py

@@ -566,6 +566,17 @@ def check_eq2_both(self, inputs, output, args_in, arg_out):
     val = fn(*args_in)
     self.failUnless( numpy.all(val == arg_out), (val, arg_out))
 
+class T_Shape(unittest.TestCase):
+    def test_basic0(self):
+        s = shape(numpy.ones((5, 3)))
+        self.failUnless((eval_outputs([s]) == [5, 3]).all())
+    def test_basic1(self):
+        s = shape(numpy.ones((2)))
+        self.failUnless((eval_outputs([s]) == [2]).all())
+    def test_basic2(self):
+        s = shape(numpy.ones((5, 3, 10)))
+        self.failUnless((eval_outputs([s]) == [5, 3, 10]).all())
+
 class T_argmax(unittest.TestCase):
     def setUp(self):
         numpy.random.seed(123784)
@@ -819,6 +830,21 @@ class T_subtensor(unittest.TestCase):
         self.failUnless(numpy.all(tval == 0))
 
 
+class T_Stack(unittest.TestCase):
+    def test_hstack(self):
+        a = astensor(numpy.array([[1, 2, 3], [4, 5, 6]]), broadcastable=[False,False])
+        b = astensor(numpy.array([[7], [8]]), broadcastable=[False,False])
+        s = horizontal_stack(a, b)
+        c = numpy.array([[1, 2, 3, 7], [4, 5, 6, 8]])
+        self.failUnless((eval_outputs([s]) == c).all())
+    def test_vstack(self):
+        a = astensor(numpy.array([[1, 2, 3], [4, 5, 6]]), broadcastable=[False,False])
+        b = astensor(numpy.array([[7, 8, 9]]), broadcastable=[False,False])
+        s = vertical_stack(a, b)
+        c = numpy.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+        self.failUnless((eval_outputs([s]) == c).all())
+
+
 class T_add(unittest.TestCase):
 
     def test_complex_all_ops(self):

_test_tensor_opt.py

@@ -25,37 +25,37 @@ class _test_inplace_opt(unittest.TestCase):
         x, y, z = inputs()
         e = x + y + z
         g = Env([x, y], [e])
-        assert str(g) == "[Broadcast{Add}(Broadcast{Add}(x, y), z)]"
+        self.failUnless(str(g) == "[Broadcast{Add}(Broadcast{Add}(x, y), z)]")
         inplace_optimizer.optimize(g)
-        assert str(g) == "[Broadcast{Add}{0: 0}(Broadcast{Add}{0: 0}(x, y), z)]"
+        self.failUnless(str(g) == "[Broadcast{Add}{0: 0}(Broadcast{Add}{0: 0}(x, y), z)]")
 
     def test_multiple_uses(self):
         x, y, z = inputs()
         e0 = x + y
         e1 = x * y
         g = Env([x, y], [e0, e1])
-        assert str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}(x, y)]"
+        self.failUnless(str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}(x, y)]")
         inplace_optimizer.optimize(g)
-        assert str(g) == "[Broadcast{Add}{0: 0}(x, y), Broadcast{Mul}(x, y)]" \
-            or str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, y)]"
+        self.failUnless(str(g) == "[Broadcast{Add}{0: 0}(x, y), Broadcast{Mul}(x, y)]" \
+            or str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, y)]")
 
     def test_user_inplace(self):
         x, y, z = inputs()
         e0 = x + y
         e1 = tensor.mul_inplace(x, y)
         g = Env([x, y], [e0, e1])
-        assert str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, y)]"
+        self.failUnless(str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, y)]")
         inplace_optimizer.optimize(g)
-        assert str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, y)]"
+        self.failUnless(str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, y)]")
 
     def test_inplace_on_second_argument(self):
         x, y, z = inputs()
         e0 = x + y
         e1 = tensor.mul_inplace(x, z)
         g = Env([x, y], [e0, e1])
-        assert str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, z)]"
+        self.failUnless(str(g) == "[Broadcast{Add}(x, y), Broadcast{Mul}{0: 0}(x, z)]")
         inplace_optimizer.optimize(g)
-        assert str(g) == "[Broadcast{Add}{0: 1}(x, y), Broadcast{Mul}{0: 0}(x, z)]"
+        self.failUnless(str(g) == "[Broadcast{Add}{0: 1}(x, y), Broadcast{Mul}{0: 0}(x, z)]")
 
 
 class _test_dimshuffle_lift(unittest.TestCase):
@@ -64,23 +64,23 @@ class _test_dimshuffle_lift(unittest.TestCase):
         x, y, z = inputs()
         e = ds(ds(x, (1, 0)), (1, 0))
         g = Env([x], [e])
-        assert str(g) == "[DimShuffle{10}(DimShuffle{10}(x))]"
+        self.failUnless(str(g) == "[InplaceDimShuffle{1,0}(InplaceDimShuffle{1,0}(x))]")
         lift_dimshuffle.optimize(g)
-        assert str(g) == "[x]"
+        self.failUnless(str(g) == "[x]")
 
     def test_merge2(self):
         x, y, z = inputs()
         e = ds(ds(x, (1, 'x', 0)), (2, 0, 'x', 1))
         g = Env([x], [e])
-        self.failUnless(str(g) == "[DimShuffle{20x1}(DimShuffle{1x0}(x))]", str(g))
+        self.failUnless(str(g) == "[InplaceDimShuffle{2,0,x,1}(InplaceDimShuffle{1,x,0}(x))]", str(g))
         lift_dimshuffle.optimize(g)
-        self.failUnless(str(g) == "[DimShuffle{01xx}(x)]", str(g))
+        self.failUnless(str(g) == "[InplaceDimShuffle{0,1,x,x}(x)]", str(g))
 
     def test_elim3(self):
         x, y, z = inputs()
         e = ds(ds(ds(x, (0, 'x', 1)), (2, 0, 'x', 1)), (1, 0))
         g = Env([x], [e])
-        self.failUnless(str(g) == "[DimShuffle{10}(DimShuffle{20x1}(DimShuffle{0x1}(x)))]", str(g))
+        self.failUnless(str(g) == "[InplaceDimShuffle{1,0}(InplaceDimShuffle{2,0,x,1}(InplaceDimShuffle{0,x,1}(x)))]", str(g))
         lift_dimshuffle.optimize(g)
         self.failUnless(str(g) == "[x]", str(g))
 
@@ -88,9 +88,9 @@ class _test_dimshuffle_lift(unittest.TestCase):
         x, y, z = inputs([0]*1, [0]*2, [0]*3)
         e = x + y + z
         g = Env([x, y, z], [e])
-        self.failUnless(str(g) == "[Broadcast{Add}(DimShuffle{x01}(Broadcast{Add}(DimShuffle{x0}(x), y)), z)]", str(g))
+        self.failUnless(str(g) == "[Broadcast{Add}(InplaceDimShuffle{x,0,1}(Broadcast{Add}(InplaceDimShuffle{x,0}(x), y)), z)]", str(g))
         lift_dimshuffle.optimize(g)
-        self.failUnless(str(g) == "[Broadcast{Add}(Broadcast{Add}(DimShuffle{xx0}(x), DimShuffle{x01}(y)), z)]", str(g))
+        self.failUnless(str(g) == "[Broadcast{Add}(Broadcast{Add}(InplaceDimShuffle{x,x,0}(x), InplaceDimShuffle{x,0,1}(y)), z)]", str(g))
 
 
 class _test_cliques(unittest.TestCase):
@@ -103,10 +103,10 @@ class _test_cliques(unittest.TestCase):
         e = x + y + d
         g = Env([x, y, z], [e])
         cliques = find_cliques(g)
-        assert len(cliques) == 2
+        self.failUnless(len(cliques) == 2)
         (i1, o1), (i2, o2) = cliques
-        assert str(Env(i1, o1)) == "[Broadcast{Add}(Broadcast{Add}(x, y), d)]"
-        assert str(Env(i2, o2)) == "[Broadcast{Mul}(y, z)]"
+        self.failUnless(str(Env(i1, o1)) == "[Broadcast{Add}(Broadcast{Add}(x, y), d)]")
+        self.failUnless(str(Env(i2, o2)) == "[Broadcast{Mul}(y, z)]")
 #         print g
 #         for i, o in find_cliques(g):
 #             print "-->", Env(i, [o])
@@ -116,8 +116,8 @@ class _test_cliques(unittest.TestCase):
         e = x + y + z
         g = Env([x, y, z], [e])
         lift_dimshuffle.optimize(g)
-        assert len(find_cliques(g, through_broadcast = True)) == 1
-        assert len(find_cliques(g, through_broadcast = False)) == 2
+        self.failUnless(len(find_cliques(g, through_broadcast = True)) == 1)
+        self.failUnless(len(find_cliques(g, through_broadcast = False)) == 2)
 #         print g
 #         for i, o in find_cliques(g, True):
 #             print "-->", Env(i, [o])

compile.py

@@ -189,6 +189,24 @@ def eval_outputs(outputs,
     return rval
 
 
+def infer_reuse_pattern(env, outputs_to_disown):
+    do_not_reuse = outputs_to_disown
+    seen = set()
+    def walk(r):
+        if env.edge(r) or r in seen:
+            return
+        seen.add(r)
+        do_not_reuse.append(r)
+        op = r.owner
+        dmap = op.destroy_map() if hasattr(op, 'destroy_map') else {}
+        vmap = op.view_map() if hasattr(op, 'view_map') else {}
+        cat = lambda x, y: list(x) + list(y)
+        for r2 in reduce(cat, dmap.values()) + reduce(cat, vmap.values()):
+            accumulate(r2)
+    for output in outputs_to_disown:
+        walk(output)
+    return do_not_reuse
+
 
 
 # StateFunction([x, y], [e], (w, w + lr * bla()))

elemwise.py

@@ -105,10 +105,13 @@ class DimShuffle(Op, Viewer):
             return {}
 
     def desc(self):
-        return (self.__class__, tuple(self.new_order))
+        return (self.__class__, tuple(self.new_order), self.inplace)
 
     def strdesc(self):
-        return "DimShuffle{%s}" % "".join(str(x) for x in self.new_order)
+        if self.inplace:
+            return "InplaceDimShuffle{%s}" % ",".join(str(x) for x in self.new_order)
+        else:
+            return "DimShuffle{%s}" % ",".join(str(x) for x in self.new_order)
 
     def perform(self):
         # drop
@@ -412,11 +415,14 @@ class Broadcast(Op, Destroyer):
          
 
 
-def make_broadcast(scalar_opclass, inplace_pattern = {}, name = None):
+def make_broadcast(scalar_opclass, inplace_pattern = {}, name = None, module_name = None):
+    scalar_name = scalar_opclass.__name__
     if name is None:
-        name = "Tensor" + scalar_opclass.__name__
+        name = scalar_name
+    if module_name is None:
+        module_name = 'elemwise.make_broadcast(%s, %s, %s)' % (scalar_name, inplace_pattern, repr(name))
+        name = "New"
         
-    scalar_name = scalar_opclass.__name__
     previous_doc = Broadcast.__doc__
 
     scalar_doc = scalar_opclass.__doc__ or ""
@@ -449,6 +455,7 @@ def make_broadcast(scalar_opclass, inplace_pattern = {}, name = None):
         def desc(cls):
             return (Broadcast, scalar_opclass, tuple(inplace_pattern.items()))
     New.__name__ = name
+    New.__module__ = module_name
     return New
 
 def wrap_broadcast(op):

gof/ext.py

@@ -493,4 +493,3 @@ def view_roots(r):
             return [r]
     else:
         return [r]
-

gof/link.py

@@ -115,8 +115,9 @@ class PerformLinker(Linker):
     the L{Env} in the order given by L{Env.toposort}.
     """
 
-    def __init__(self, env):
+    def __init__(self, env, no_recycling = []):
         self.env = env
+        self.no_recycling = no_recycling
 
     def make_thunk(self, inplace = False, profiler = None):
         if inplace:
@@ -125,8 +126,14 @@ class PerformLinker(Linker):
             env = self.env.clone(True)
         order = env.toposort()
         thunks = [op.perform for op in order]
+        no_recycling = self.no_recycling
+        if no_recycling is True:
+            no_recycling = list(env.results())
+        no_recycling = utils.difference(no_recycling, env.inputs)
         if profiler is None:
             def f():
+                for r in no_recycling:
+                    r.data = None
                 try:
                     for thunk, op in zip(thunks, order):
                         thunk()
@@ -134,6 +141,8 @@ class PerformLinker(Linker):
                     raise_with_op(op)
         else:
             def f():
+                for r in no_recycling:
+                    r.data = None
                 def g():
                     for thunk, op in zip(thunks, order):
                         profiler.profile_op(thunk, op)

sparse.py

@@ -320,3 +320,4 @@ def dot(x, y, grad_preserves_dense=True):
     else:
         assert y_is_sparse_result
         return transpose(Dot(y.T, x.T, grad_preserves_dense).outputs[0])
+

tensor.py

@@ -317,7 +317,7 @@ def astensor(data, broadcastable=None, name=None):
             raise ValueError("Cannot rename an existing Tensor.")
         return data
     elif isinstance(data, Result):
-        raise TypeError("Cannot make a Tensor out of a non-Tensor result:", data)
+        raise TypeError("Cannot make a Tensor out of a result that is not an instance of Tensor: %s (%s)" % (data, data.__class__.__name__), data)
         
     if data is None and broadcastable is None:
         raise TypeError("Cannot make a Tensor out of None.")
@@ -445,16 +445,38 @@ class _Op(Op):
 # Unary Operations
 ##########################
 
-def broadcast(scalar_opclass, name, inplace_versions = True):
-    C = s2t.make_broadcast(scalar_opclass, name = name)
+def broadcast(scalar_opclass, name, module_name = None, inplace_versions = True):
+    C = s2t.make_broadcast(scalar_opclass, name = name, module_name = module_name) # this returns a class
+    C.__module__ = module_name
     c = gof.op.constructor(s2t.wrap_broadcast(C))
     if inplace_versions:
         CInplace = s2t.make_broadcast(scalar_opclass, {0:0}, name = name+"Inplace")
+        CInplace.__module__ = module_name
         c_inplace = gof.op.constructor(s2t.wrap_broadcast(CInplace))
         return C, c, CInplace, c_inplace
     else:
         return C, c
-    
+
+def _broadcast(scalar_opclass, name, inplace_versions = True):
+    return broadcast(scalar_opclass, name, 'tensor', inplace_versions)
+
+class Shape(Op):
+    """
+    L{Op} to return the shape of a matrix.
+
+    @note: Non-differentiable.
+    """
+    def __init__(self, x, **kwargs):
+        Op.__init__(self, **kwargs)
+        x = astensor(x)
+        self.inputs = [x]
+        self.outputs = [Tensor("int64", [False])]
+    def impl(self, x):
+        return numpy.asarray(x.shape)
+    def grad(self, (x,), (gz,)):
+        raise ValueError
+shape = gof.op.constructor(Shape)
+
 class Argmax(Op):
     """Calculate the max and argmax over a given axis"""
     nin=2 # tensor, axis
@@ -487,32 +509,43 @@ def max(x, axis=None):
     # but when Argmax.c_impl() is in place, it should be fine.
     return argmax(x,axis)[0]
 
-Abs, _abs, AbsInplace, abs_inplace = broadcast(scal.Abs, 'Abs')
-Exp, exp, ExpInplace, exp_inplace = broadcast(scal.Exp, 'Exp')
-Neg, neg, NegInplace, neg_inplace = broadcast(scal.Neg, 'Neg')
-Log, log, LogInplace, log_inplace = broadcast(scal.Log, 'Log')
-Log2, log2, Log2Inplace, log2_inplace = broadcast(scal.Log2, 'Log2')
-Sgn, sgn, SgnInplace, sgn_inplace = broadcast(scal.Sgn, 'Sgn')
-Sqr, sqr, SqrInplace, sqr_inplace = broadcast(scal.Sqr, 'Sqr')
-Sqrt, sqrt, SqrtInplace, sqrt_inplace = broadcast(scal.Sqrt, 'Sqrt')
-Cos, cos, CosInplace, cos_inplace = broadcast(scal.Cos, 'Cos')
-Sin, sin, SinInplace, sin_inplace = broadcast(scal.Sin, 'Sin')
-Tan, tan, TanInplace, tan_inplace = broadcast(scal.Tan, 'Tan')
-Cosh, cosh, CoshInplace, cosh_inplace = broadcast(scal.Cosh, 'Cosh')
-Sinh, sinh, SinhInplace, sinh_inplace = broadcast(scal.Sinh, 'Sinh')
-Tanh, tanh, TanhInplace, tanh_inplace = broadcast(scal.Tanh, 'Tanh')
-
-Sum = s2t.Sum
-sum = gof.op.constructor(Sum)
-
-Fill, fill, FillInplace, fill_inplace = broadcast(scal.Second, 'Fill')
+Abs, _abs, AbsInplace, abs_inplace = _broadcast(scal.Abs, 'Abs')
+Exp, exp, ExpInplace, exp_inplace = _broadcast(scal.Exp, 'Exp')
+Neg, neg, NegInplace, neg_inplace = _broadcast(scal.Neg, 'Neg')
+Log, log, LogInplace, log_inplace = _broadcast(scal.Log, 'Log')
+Log2, log2, Log2Inplace, log2_inplace = _broadcast(scal.Log2, 'Log2')
+Sgn, sgn, SgnInplace, sgn_inplace = _broadcast(scal.Sgn, 'Sgn')
+Sqr, sqr, SqrInplace, sqr_inplace = _broadcast(scal.Sqr, 'Sqr')
+Sqrt, sqrt, SqrtInplace, sqrt_inplace = _broadcast(scal.Sqrt, 'Sqrt')
+Cos, cos, CosInplace, cos_inplace = _broadcast(scal.Cos, 'Cos')
+Sin, sin, SinInplace, sin_inplace = _broadcast(scal.Sin, 'Sin')
+Tan, tan, TanInplace, tan_inplace = _broadcast(scal.Tan, 'Tan')
+Cosh, cosh, CoshInplace, cosh_inplace = _broadcast(scal.Cosh, 'Cosh')
+Sinh, sinh, SinhInplace, sinh_inplace = _broadcast(scal.Sinh, 'Sinh')
+Tanh, tanh, TanhInplace, tanh_inplace = _broadcast(scal.Tanh, 'Tanh')
+
+Fill, fill, FillInplace, fill_inplace = _broadcast(scal.Second, 'Fill')
 
 def ones_like(model):
     return fill(model, 1.0)
 def zeros_like(model):
     return fill(model, 0.0)
 
-TensorCopy, tensor_copy = broadcast(scal.Identity, 'TensorCopy', False)
+TensorCopy, tensor_copy = _broadcast(scal.Identity, 'TensorCopy', inplace_versions = False)
+
+Sum = s2t.Sum
+sum = gof.op.constructor(Sum)
+
+
+##########################
+# Arithmetics
+##########################
+
+Add, add, AddInplace, add_inplace = _broadcast(scal.Add, 'Add')
+Sub, sub, SubInplace, sub_inplace = _broadcast(scal.Sub, 'Sub')
+Mul, mul, MulInplace, mul_inplace = _broadcast(scal.Mul, 'Mul')
+Div, div, DivInplace, div_inplace = _broadcast(scal.Div, 'Div')
+Pow, pow, PowInplace, pow_inplace = _broadcast(scal.Pow, 'Pow')
 
 
 ##########################
@@ -606,15 +639,59 @@ class Subtensor(Op, Viewer):
 subtensor = gof.op.constructor(Subtensor)
 
 
-##########################
-# Arithmetics
-##########################
+class VerticalStack(Op):
+    """
+    Vertically stack two L{Tensor}s.
+    Stack two L{Tensor}s along the first axis (row wise). These
+    L{Tensor}s must have the same shape along all dimensions but the
+    first.
+
+    @attention: Because we use vstack as the implementation, if the
+    inputs have 1-dimension, the output will have 2-dimensions.
+    """
+    def __init__(self, x, y, **kwargs):
+        Op.__init__(self, **kwargs)
+        x = astensor(x)
+        y = astensor(y)
+        assert x.dtype == y.dtype
+        if x.broadcastable[1:] != y.broadcastable[1:]:
+            raise NotImplementedError
+        self.inputs = [x, y]
+        bcastable = (False, ) + x.broadcastable[1:]
+        self.outputs = [Tensor(x.dtype, bcastable)]
+    def impl(self, x, y):
+        assert x.ndim == y.ndim
+        # Make sure every dimension (save the first) is the same
+        for i in range(x.ndim): assert i == 0 or x.shape[i] == y.shape[i]
 
-Add, add, AddInplace, add_inplace = broadcast(scal.Add, 'Add')
-Sub, sub, SubInplace, sub_inplace = broadcast(scal.Sub, 'Sub')
-Mul, mul, MulInplace, mul_inplace = broadcast(scal.Mul, 'Mul')
-Div, div, DivInplace, div_inplace = broadcast(scal.Div, 'Div')
-Pow, pow, PowInplace, pow_inplace = broadcast(scal.Pow, 'Pow')
+        return numpy.vstack([x, y])
+    def grad(self, (x, y), (gz,)):
+        """
+        @todo: Make VSplit (or this grad implementation) its own L{Op},
+        that way we can do more sanity-checking::
+            assert x.ndim == y.ndim
+            # Make sure every dimension (save the first) is the same
+            for i in range(x.data.ndim): assert i == 0 or x.data.shape[i] == y.shape[i]
+            etc...
+        """
+        xs = shape(x)
+        ys = shape(y)
+        return gz[:xs[0]], gz[xs[0]:]
+vertical_stack = gof.op.constructor(VerticalStack)
+
+def horizontal_stack(x, y, **kwargs):
+    """
+    Horizontally stack two L{Tensor}s.
+    Stack two L{Tensor}s along the second axis (column wise). These
+    L{Tensor}s must have the same shape along all dimensions but the
+    second.
+
+    @note: Unlike VerticalStack, we assume that the L{Tensor}s have
+    two dimensions.
+    """
+    assert x.ndim == 2
+    assert y.ndim == 2
+    return transpose(vertical_stack(x.T, y.T, **kwargs))
 
 
 #########################
@@ -624,8 +701,7 @@ Pow, pow, PowInplace, pow_inplace = broadcast(scal.Pow, 'Pow')
 class Dot(_Op):
     nin=2
     nout=1
-    @staticmethod 
-    def broadcastable_rule(bx,by):
+    def propagate_broadcastable(self, bx, by):
         if len(bx) == 0:     # x is a scalar
             rval = by
         else:
@@ -635,20 +711,11 @@ class Dot(_Op):
                 rval = bx[:-1]
             else:            #y is a scalar
                 rval = bx
-        return rval
-    def propagate_broadcastable(self, bx, by):
-        return [self.broadcastable_rule(bx,by)]
+        return [rval]
     def impl(self, x, y):
         return numpy.dot(x, y)
     def grad(self, (x, y), (gz,)):
         return dot(gz, y.T), dot(x.T, gz)
-    if 0:
-        def c_support_code(self):
-            return blas.cblas_header_text()
-        def c_libs(self):
-            return blas.ldflags()
-        def c_impl(self, (_x, _y), (_z, )):
-            return blas.gemm_code('', '1.0', '0.0')
 dot = gof.op.constructor(Dot)
 
 class Gemm(_Op):