merge

README.1st

 THEANO
 
 Documentation et al is in Trac:
-   http://lgcm:8000/testenv/wiki/WikiStart
+   http://lgcm.iro.umontreal.ca:8000/theano/wiki/WikiStart
 
 The lisa twiki is deprecated for documenting Theano.
 

__init__.py

 
 import gof
-import base_tensor
 import tensor
 import sparse
 import compile
 import gradient
 import opt
 
-from base_tensor import *
 from tensor import *
 from compile import *
 from opt import *

_test_base_tensor.py

-from base_tensor import *
-
-import unittest
-from copy import copy
-from compile import Function
-import gof
-
-def _tensor(data, broadcastable=None, name=None):
-    """Return a BaseTensor containing given data"""
-    data = numpy.asarray(data)
-    if broadcastable is None:
-        broadcastable = [s==1 for s in data.shape]
-    elif broadcastable in [0, 1]:
-        broadcastable = [broadcastable] *  len(data.shape)
-    rval = BaseTensor(data.dtype, broadcastable, name)
-    rval.data = data # will raise if broadcastable was mis-specified
-    return rval
-
-
-
-class T_tensor(unittest.TestCase):
-    def test0(self): # allocate from a scalar float
-        t = _tensor(1.0)
-        self.failUnless(isinstance(t, BaseTensor))
-        self.failUnless(t.dtype == 'float64')
-        self.failUnless(t.broadcastable == ())
-        self.failUnless(t.role == None)
-        self.failUnless(isinstance(t.data, numpy.ndarray))
-        self.failUnless(str(t.data.dtype) == 'float64')
-        self.failUnless(t.data == 1.0)
-    def test0_int(self): # allocate from a scalar float
-        t = _tensor(1)
-        self.failUnless(isinstance(t, BaseTensor))
-        self.failUnless(t.dtype == 'int64' or t.dtype == 'int32')
-    def test1(self): # allocate from a vector of ints, not broadcastable
-        t = _tensor(numpy.ones(5,dtype='int32'))
-        self.failUnless(isinstance(t, BaseTensor))
-        self.failUnless(t.dtype == 'int32')
-        self.failUnless(t.broadcastable == (0,))
-        self.failUnless(isinstance(t.data, numpy.ndarray))
-        self.failUnless(str(t.data.dtype) == 'int32')
-    def test2(self): # allocate from a column matrix of complex with name
-        t = _tensor(numpy.ones((5,1),dtype='complex64'),name='bart')
-        self.failUnless(isinstance(t, BaseTensor))
-        self.failUnless(t.dtype == 'complex64')
-        self.failUnless(t.broadcastable == (0,1))
-        self.failUnless(isinstance(t.data, numpy.ndarray))
-        self.failUnless(t.name == 'bart')
-    def test2b(self): # allocate from a column matrix, not broadcastable
-        t = _tensor(numpy.ones((5,1),dtype='complex64'),broadcastable=0)
-        self.failUnless(isinstance(t, BaseTensor))
-        self.failUnless(t.dtype == 'complex64')
-        self.failUnless(t.broadcastable == (0,0))
-        self.failUnless(isinstance(t.data, numpy.ndarray))
-        f = Function([t], [t], linker_cls=gof.CLinker)
-        self.failUnless(numpy.all(t.data == f(t.data)))
-    def test_data_normal(self): #test that assigning to .data works when it should
-        t = _tensor(numpy.ones((5,1),dtype='complex64'), broadcastable=0)
-        o27 = numpy.ones((2,7), dtype='complex64')
-        t.data = o27
-        lst = t._data
-        self.failUnless(t.data.shape == (2,7))
-        self.failUnless(t.data is o27)
-        self.failUnless(t._data is lst)
-    def test_data_badrank0(self):
-        t = _tensor(numpy.ones((5,1),dtype='complex64'), broadcastable=0)
-        try:
-            t.data = numpy.ones((2,7,1))
-            self.fail()
-        except ValueError, e:
-            self.failUnless(e[0] is BaseTensor.filter.E_rank)
-        try:
-            t.data = numpy.ones(1)
-            self.fail()
-        except ValueError, e:
-            self.failUnless(e[0] is BaseTensor.filter.E_rank)
-    def test_data_badrank1(self):
-        t = _tensor(numpy.ones((1,1),dtype='complex64'), broadcastable=1)
-        try:
-            t.data = numpy.ones((1,1,1))
-            self.fail()
-        except ValueError, e:
-            self.failUnless(e[0] is BaseTensor.filter.E_rank)
-        try:
-            t.data = numpy.ones(1)
-            self.fail()
-        except ValueError, e:
-            self.failUnless(e[0] is BaseTensor.filter.E_rank)
-    def test_data_badshape0(self):
-        t = _tensor(numpy.ones((1,1),dtype='complex64'), broadcastable=1)
-        try:
-            t.data = numpy.ones((1,2))
-            self.fail()
-        except ValueError, e:
-            self.failUnless(e[0] is BaseTensor.filter.E_shape)
-        try:
-            t.data = numpy.ones((0,1))
-            self.fail()
-        except ValueError, e:
-            self.failUnless(e[0] is BaseTensor.filter.E_shape)
-
-    def test_cast0(self):
-        t = BaseTensor('float32', [0])
-        t.data = numpy.random.rand(4) > 0.5
-        self.failUnless(str(t.data.dtype) == t.dtype)
-
-class T_stdlib(unittest.TestCase):
-    def test0(self):
-        t = _tensor(1.0)
-        tt = t.clone(False)
-        self.failUnless(t.dtype == tt.dtype)
-        self.failUnless(t.broadcastable is tt.broadcastable)
-        self.failUnless(tt.data is None)
-        self.failUnless(t.data == 1.0)
-    def test0b(self):
-        t = _tensor(1.0)
-        tt = t.clone()
-        self.failUnless(t.dtype == tt.dtype)
-        self.failUnless(t.broadcastable is tt.broadcastable)
-        self.failUnless(tt.data is None)
-        self.failUnless(t.data == 1.0)
-
-    def test1(self):
-        t = _tensor(1.0)
-        tt = t.clone(True)
-        self.failUnless(t.dtype == tt.dtype)
-        self.failUnless(t.broadcastable is tt.broadcastable)
-        self.failUnless(tt.data == 1.0)
-        self.failUnless(t.data == 1.0)
-        self.failUnless(t.data is not tt.data)
-    def test1b(self):
-        t = _tensor(1.0)
-        tt = copy(t)
-        self.failUnless(t.dtype == tt.dtype)
-        self.failUnless(t.broadcastable is tt.broadcastable)
-        self.failUnless(tt.data == 1.0)
-        self.failUnless(t.data == 1.0)
-        self.failUnless(t.data is not tt.data)
-
-if __name__ == '__main__':
-    unittest.main()
-

_test_tensor.py

@@ -1280,5 +1280,142 @@ class t_gemm(unittest.TestCase):
         self.fail()
 
 
+
+
+def _tensor(data, broadcastable=None, name=None):
+    """Return a Tensor containing given data"""
+    data = numpy.asarray(data)
+    if broadcastable is None:
+        broadcastable = [s==1 for s in data.shape]
+    elif broadcastable in [0, 1]:
+        broadcastable = [broadcastable] *  len(data.shape)
+    rval = Tensor(data.dtype, broadcastable, name)
+    rval.data = data # will raise if broadcastable was mis-specified
+    return rval
+
+
+
+class T_tensor(unittest.TestCase):
+    def test0(self): # allocate from a scalar float
+        t = _tensor(1.0)
+        self.failUnless(isinstance(t, Tensor))
+        self.failUnless(t.dtype == 'float64')
+        self.failUnless(t.broadcastable == ())
+        self.failUnless(t.role == None)
+        self.failUnless(isinstance(t.data, numpy.ndarray))
+        self.failUnless(str(t.data.dtype) == 'float64')
+        self.failUnless(t.data == 1.0)
+    def test0_int(self): # allocate from a scalar float
+        t = _tensor(1)
+        self.failUnless(isinstance(t, Tensor))
+        self.failUnless(t.dtype == 'int64' or t.dtype == 'int32')
+    def test1(self): # allocate from a vector of ints, not broadcastable
+        t = _tensor(numpy.ones(5,dtype='int32'))
+        self.failUnless(isinstance(t, Tensor))
+        self.failUnless(t.dtype == 'int32')
+        self.failUnless(t.broadcastable == (0,))
+        self.failUnless(isinstance(t.data, numpy.ndarray))
+        self.failUnless(str(t.data.dtype) == 'int32')
+    def test2(self): # allocate from a column matrix of complex with name
+        t = _tensor(numpy.ones((5,1),dtype='complex64'),name='bart')
+        self.failUnless(isinstance(t, Tensor))
+        self.failUnless(t.dtype == 'complex64')
+        self.failUnless(t.broadcastable == (0,1))
+        self.failUnless(isinstance(t.data, numpy.ndarray))
+        self.failUnless(t.name == 'bart')
+    def test2b(self): # allocate from a column matrix, not broadcastable
+        t = _tensor(numpy.ones((5,1),dtype='complex64'),broadcastable=0)
+        self.failUnless(isinstance(t, Tensor))
+        self.failUnless(t.dtype == 'complex64')
+        self.failUnless(t.broadcastable == (0,0))
+        self.failUnless(isinstance(t.data, numpy.ndarray))
+        f = Function([t], [t], linker_cls=gof.CLinker)
+        self.failUnless(numpy.all(t.data == f(t.data)))
+    def test_data_normal(self): #test that assigning to .data works when it should
+        t = _tensor(numpy.ones((5,1),dtype='complex64'), broadcastable=0)
+        o27 = numpy.ones((2,7), dtype='complex64')
+        t.data = o27
+        lst = t._data
+        self.failUnless(t.data.shape == (2,7))
+        self.failUnless(t.data is o27)
+        self.failUnless(t._data is lst)
+    def test_data_badrank0(self):
+        t = _tensor(numpy.ones((5,1),dtype='complex64'), broadcastable=0)
+        try:
+            t.data = numpy.ones((2,7,1))
+            self.fail()
+        except ValueError, e:
+            self.failUnless(e[0] is Tensor.filter.E_rank)
+        try:
+            t.data = numpy.ones(1)
+            self.fail()
+        except ValueError, e:
+            self.failUnless(e[0] is Tensor.filter.E_rank)
+    def test_data_badrank1(self):
+        t = _tensor(numpy.ones((1,1),dtype='complex64'), broadcastable=1)
+        try:
+            t.data = numpy.ones((1,1,1))
+            self.fail()
+        except ValueError, e:
+            self.failUnless(e[0] is Tensor.filter.E_rank)
+        try:
+            t.data = numpy.ones(1)
+            self.fail()
+        except ValueError, e:
+            self.failUnless(e[0] is Tensor.filter.E_rank)
+    def test_data_badshape0(self):
+        t = _tensor(numpy.ones((1,1),dtype='complex64'), broadcastable=1)
+        try:
+            t.data = numpy.ones((1,2))
+            self.fail()
+        except ValueError, e:
+            self.failUnless(e[0] is Tensor.filter.E_shape)
+        try:
+            t.data = numpy.ones((0,1))
+            self.fail()
+        except ValueError, e:
+            self.failUnless(e[0] is Tensor.filter.E_shape)
+
+    def test_cast0(self):
+        t = Tensor('float32', [0])
+        t.data = numpy.random.rand(4) > 0.5
+        self.failUnless(str(t.data.dtype) == t.dtype)
+
+class T_stdlib(unittest.TestCase):
+    def test0(self):
+        t = _tensor(1.0)
+        tt = t.clone(False)
+        self.failUnless(t.dtype == tt.dtype)
+        self.failUnless(t.broadcastable is tt.broadcastable)
+        self.failUnless(tt.data is None)
+        self.failUnless(t.data == 1.0)
+    def test0b(self):
+        t = _tensor(1.0)
+        tt = t.clone()
+        self.failUnless(t.dtype == tt.dtype)
+        self.failUnless(t.broadcastable is tt.broadcastable)
+        self.failUnless(tt.data is None)
+        self.failUnless(t.data == 1.0)
+
+    def test1(self):
+        t = _tensor(1.0)
+        tt = t.clone(True)
+        self.failUnless(t.dtype == tt.dtype)
+        self.failUnless(t.broadcastable is tt.broadcastable)
+        self.failUnless(tt.data == 1.0)
+        self.failUnless(t.data == 1.0)
+        self.failUnless(t.data is not tt.data)
+    def test1b(self):
+        t = _tensor(1.0)
+        tt = copy(t)
+        self.failUnless(t.dtype == tt.dtype)
+        self.failUnless(t.broadcastable is tt.broadcastable)
+        self.failUnless(tt.data == 1.0)
+        self.failUnless(t.data == 1.0)
+        self.failUnless(t.data is not tt.data)
+
+
+
+
 if __name__ == '__main__':
     unittest.main()

_test_opt.py → _test_tensor_opt.py

@@ -2,7 +2,7 @@
 import unittest
 
 import gof
-from opt import *
+from tensor_opt import *
 import tensor
 from tensor import Tensor
 from gof import Env

cutils.py

-
-try:
-    from cutils_ext import *
-
-except ImportError:
-
-    from scipy import weave
-
-    single_runner = """
-        if (!PyCObject_Check(py_cthunk)) {
-            PyErr_SetString(PyExc_ValueError,
-                            "Argument to run_cthunk must be a PyCObject returned by the c_thunk method of an omega_op.");
-            return NULL;
-        }
-        void * ptr_addr = PyCObject_AsVoidPtr(py_cthunk);
-        int (*fn)(void*) = reinterpret_cast<int (*)(void*)>(ptr_addr);
-        //int (*fn)(void*) = static_cast<int (*)(void*)>(PyCObject_AsVoidPtr(py_cthunk));
-        //int (*fn)(void*) = NULL;
-        //fn += PyCObject_AsVoidPtr(py_cthunk);
-        //int (*fn)(void*) = 
-
-        void* it = PyCObject_GetDesc(py_cthunk);
-        int failure = fn(it);
-        if (failure) {
-            return NULL;
-        }
-        """
-
-    
-    
-    cthunk = object()
-    mod = weave.ext_tools.ext_module('cutils_ext')
-    fun =weave.ext_tools.ext_function('run_cthunk', single_runner, ['cthunk'])
-    fun.customize.add_extra_compile_arg('--permissive')
-    mod.add_function(fun)
-    mod.compile()
-
-    from cutils_ext import *

elemwise.py

@@ -3,7 +3,6 @@ import elemwise_cgen as cgen
 
 import numpy
 from gof import Op, Viewer, Destroyer
-#from base_tensor import BaseTensor as Tensor
 import scalar
 from scalar import upcast, Scalar
 import gof

gof/op.py

@@ -17,7 +17,9 @@ __all__ = ['Op',
 
 
 def constructor(op_cls, name = None):
-    """Make an Op look like a L{Result}-valued function."""
+    """
+    Make an L{Op} look like a L{Result}-valued function.
+    """
     def f(*args, **kwargs):
         op = op_cls(*args, **kwargs)
         if len(op.outputs) > 1:

gradient.py

@@ -27,27 +27,14 @@ def grad_sources_inputs(sources, graph_inputs):
     calling L{Op.grad}(...) when it is provided by an L{Op}, and at least one of the
     outputs of the L{Op} has an associated gradient.
 
-    The L{Op.grad}(...) functions may be called in several ways (for the
-    convenience of the L{Op} implementer) depending on the number of inputs and
-    outputs.  
-
-    If there is one input and one output::
+    The L{Op.grad}(...) functions are called as such:
         op.grad( op.inputs[0], grad(op.outputs[0]))
 
-    If there are several inputs and one output::
-        op.grad( op.inputs, grad(op.outputs[0]))
-
-    If there is one input and several outputs::
-        op.grad( op.inputs[0], [grad(o) for o in op.outputs[0]])
-
-    If there are multiple inputs and outputs::
-        op.grad( op.inputs, [grad(o) for o in op.outputs[0]])
-
     This function expects the L{Op.grad}(...) function to return the gradient
-    expression [results] associated with the inputs of the L{Op}.  If the L{Op} has a
-    single input, it should return a single result; if the L{Op} has multiple
-    inputs, it should return a list of results corresponding to the gradients in
-    the same order as the inputs.
+    expression [results] associated with the inputs of the L{Op}. The L{Op} should
+    return a list of results corresponding to the gradients in the same order
+    as the inputs. If it has a single output it should return a list or tuple
+    of length 1.
 
     For each input wrt to which an L{Op} is not differentiable, it should return
     None instead of a result instance.
@@ -79,9 +66,6 @@ def grad_sources_inputs(sources, graph_inputs):
         #if all output gradients are None, continue
         if all(map(lambda x:x is None, g_outputs)): continue
         
-#         output_arg = _unpack_result(g_outputs)
-#         input_arg = _unpack_result(op.inputs)
-        
         output_arg = g_outputs
         input_arg = op.inputs
 
@@ -90,8 +74,6 @@ def grad_sources_inputs(sources, graph_inputs):
         except AttributeError:
             dinputs = []
 
-#        input_arg = [input in dinputs and input.copy() or input for input in input_arg]
-
         new_input_arg = []
         for input in input_arg:
             if input in dinputs:

sparse.py

@@ -11,7 +11,7 @@ import numpy
 from scipy import sparse
 
 import gof.op, gof.result
-import tensor, base_tensor
+import tensor
 
 
 
@@ -20,19 +20,19 @@ import tensor, base_tensor
 def _is_sparse_result(x):
     """
     @rtype: boolean
-    @return: True iff x is a L{SparseResult} (and not a L{base_tensor.BaseTensor})
+    @return: True iff x is a L{SparseResult} (and not a L{tensor.Tensor})
     """
-    if not isinstance(x, SparseResult) and not isinstance(x, base_tensor.BaseTensor):
-        raise NotImplementedError("_is_sparse should only be called on sparse.SparseResult or base_tensor.BaseTensor, not,", x)
+    if not isinstance(x, SparseResult) and not isinstance(x, tensor.Tensor):
+        raise NotImplementedError("_is_sparse should only be called on sparse.SparseResult or tensor.Tensor, not,", x)
     return isinstance(x, SparseResult)
 def _is_dense_result(x):
     """
     @rtype: boolean
-    @return: True unless x is a L{SparseResult} (and not a L{base_tensor.BaseTensor})
+    @return: True unless x is a L{SparseResult} (and not a L{tensor.Tensor})
     """
-    if not isinstance(x, SparseResult) and not isinstance(x, base_tensor.BaseTensor):
-        raise NotImplementedError("_is_sparse should only be called on sparse.SparseResult or base_tensor.BaseTensor, not,", x)
-    return isinstance(x, base_tensor.BaseTensor)
+    if not isinstance(x, SparseResult) and not isinstance(x, tensor.Tensor):
+        raise NotImplementedError("_is_sparse should only be called on sparse.SparseResult or tensor.Tensor, not,", x)
+    return isinstance(x, tensor.Tensor)
 
 def _is_sparse(x):
     """