Merge pull request #888 from nouiz/view_map

doc/library/tensor/nnet/conv.txt

@@ -21,5 +21,11 @@
 
 TODO: Give examples for how to use these things! They are pretty complicated.
 
-.. autofunction:: theano.tensor.nnet.conv.conv2d
+- Conv implemented
+    - :func:`signal.conv2d <theano.tensor.signal.conv.conv2d>`.
+    - :func:`nnet.conv2d <theano.tensor.nnet.conv.conv2d>`.
+    - :func:`conv3D <theano.tensor.nnet.Conv3D.conv3D>`.
 
+.. autofunction:: theano.tensor.signal.conv.conv2d
+.. autofunction:: theano.tensor.nnet.conv.conv2d
+.. autofunction:: theano.tensor.nnet.Conv3D.conv3D

doc/tutorial/extending_theano.txt

@@ -319,6 +319,56 @@ Exercises 8
 
   - Our current element-wise fusion generates computation with only 1 output.
 
+SciPy
+-----
+
+We can wrap SciPy function in Theano. But Scipy is an optional dependency.
+Here is some code that allow to make the op Optional:
+
+.. code-block:: python
+
+    try:
+        import scipy.linalg
+        imported_scipy = True
+    except ImportError:
+        # some ops (e.g. Cholesky, Solve, A_Xinv_b) won't work
+        imported_scipy = False
+
+    class SomeOp(Op):
+        ...
+        def make_node(self, x):
+            assert imported_scipy, (
+            "Scipy not available. Scipy is needed for the SomeOp op.")
+
+    from nose.plugins.skip import SkipTest
+    class test_Solve(utt.InferShapeTester):
+        ...
+        def test_infer_shape(self):
+            if not imported_scipy:
+                raise SkipTest("Scipy needed for the Cholesky op.")
+
+Random number in tests
+----------------------
+
+Making test errors more reproducable is a good practice. To make your
+tests more reproducable, you need a way to get the same random
+number. You can do this by seeding NumPy's randon number
+generator. There is the Theano flag unittest.rseed that specify the
+seed that should be used to init random number generators. There is 2
+ways to do this it numpy, here is one:
+
+.. code-block:: python
+
+    # You can set NumPy's internal random number generator state with
+    numpy.random.seed(utt.fetch_seed())
+    # All following call to numpy.random.*() function will get affected.
+
+    # Or you can create a new RandomState separate from the others
+    rng = numpy.random.RandomState(utt.fetch_seed())
+    # You can call all numpy's random number generator function's on rng
+    rng.rand(5, 5)
+
+
 GPU Op
 ------
 

theano/compile/debugmode.py

@@ -780,13 +780,6 @@ def _check_viewmap(node, storage_map):
         outstorage = storage_map[onode][0]
         instorage_id = [id(storage_map[i][0]) for i in node.inputs]
 
-        # TODO: investigate ways in which other Types may be aliased
-        # TODO: consider adding a function to Type to detect aliasing
-        danger_flag = id(outstorage) in instorage_id or\
-                      (type(outstorage)==numpy.ndarray and
-                       outstorage.flags['OWNDATA']==False)
-
-        if danger_flag:
         # first find out which input it aliases
         view_map = getattr(node.op, 'view_map', {})
         destroy_map = getattr(node.op, 'destroy_map', {})
@@ -803,8 +796,8 @@ def _check_viewmap(node, storage_map):
                 bad_alias[nodeid] = ii
 
                 # check that the aliasing was declared in [view|destroy]_map
-                    if ([ii]==view_map.get(oi,None) or\
-                        [ii]==destroy_map.get(oi,None)):
+                if ([ii] == view_map.get(oi, None) or
+                    [ii] == destroy_map.get(oi, None)):
 
                     good_alias[nodeid] = bad_alias.pop(nodeid)
 
@@ -819,7 +812,8 @@ def _check_viewmap(node, storage_map):
         #if its not aliased to input, check output->output aliasing
         if not good_alias and _is_used_in_graph(onode):
             for other_oi, other_onode in enumerate(node.outputs):
-                if other_oi == oi: continue
+                if other_oi == oi:
+                    continue
 
                 other_storage = storage_map[other_onode][0]
                 # check to see if we share memory with this other output
@@ -1547,7 +1541,8 @@ class _VariableEquivalenceTracker(object):
 #List of default version of make thunk.
 #This is needed to know if the user overrided it.
 #The GpuOp will be added here when theano.sandbox.cuda is imported.
-default_make_thunk = [theano.gof.Op.make_thunk.im_func]
+default_make_thunk = [theano.gof.Op.make_thunk.im_func,
+                      theano.gof.OpenMPOp.make_thunk.im_func]
 
 
 class _Linker(gof.link.LocalLinker):

theano/sandbox/cuda/elemwise.py

@@ -905,16 +905,22 @@ nd_collapse_[i]=0;
         //std::cerr << "C_CODE %(opname)s checking input %(iname)s\\n";
         if (%(nd)s != %(iname)s->nd)
         {
-            PyErr_Format(PyExc_TypeError, "need %(nd)s dims, not %%i", %(iname)s->nd);
+            PyErr_Format(PyExc_TypeError,
+                         "need %(nd)s dims, not %%i", %(iname)s->nd);
             %(fail)s;
         }
         for (int i = 0; i< %(nd)s; ++i)
         {
             dims[i] = (dims[i] == 1) ? CudaNdarray_HOST_DIMS(%(iname)s)[i] : dims[i];
-            if ((!(broadcasts_%(iname)s[i] && CudaNdarray_HOST_DIMS(%(iname)s)[i] == 1))&& (dims[i] != CudaNdarray_HOST_DIMS(%(iname)s)[i]))
+            if ((!(broadcasts_%(iname)s[i] &&
+                 CudaNdarray_HOST_DIMS(%(iname)s)[i] == 1)) &&
+                (dims[i] != CudaNdarray_HOST_DIMS(%(iname)s)[i]))
             {
                 //std::cerr << "C_CODE %(opname)s checking input %(iname)s failed\\n";
-                PyErr_Format(PyExc_ValueError, "GpuElemwise. Input dimension mis-match. One of your inputs has shape[%%i] == %%i, but the output's size on that axis is %%i.",
+                PyErr_Format(PyExc_ValueError,
+                             "GpuElemwise. Input dimension mis-match. Input"
+                             " %(id)d (index start at 0 has shape[%%i] == %%i"
+                             ", but the output's size on that axis is %%i.",
                              i,
                              CudaNdarray_HOST_DIMS(%(iname)s)[i],
                              dims[i]

theano/sandbox/cuda/opt.py

@@ -62,7 +62,7 @@ optdb.register('gpu_after_fusion',
 def register_opt(*tags, **kwargs):
     def f(local_opt):
         name = (kwargs and kwargs.pop('name')) or local_opt.__name__
-        gpu_optimizer.register(name, local_opt, 'fast_run', 'inplace', *tags)
+        gpu_optimizer.register(name, local_opt, 'fast_run', *tags)
         return local_opt
     return f
 

theano/sandbox/cuda/tests/test_cuda_ndarray.py

@@ -380,6 +380,7 @@ def test_reshape():
         #print n_bb
 
         assert numpy.all(aa == n_bb)
+        assert aa.shape == n_bb.shape
 
         # Test the not contiguous case
         shape_1_2x = (shape_1[0] * 2,) + shape_1[1:]
@@ -396,6 +397,7 @@ def test_reshape():
         #print n_bb
 
         assert numpy.all(aa == n_bb)
+        assert aa.shape == n_bb.shape
 
     def bad_subtest(shape_1, shape_2, rng):
         a = theano._asarray(rng.randn(*shape_1), dtype='float32')

theano/sparse/basic.py

@@ -679,10 +679,6 @@ class CSM(gof.Op):
            a regular grad.
     """
 
-    # should view the other inputs too, but viewing multiple inputs is not
-    view_map = {0: [0]}
-    #currently supported by the destroyhandler
-
     kmap = None
     """Indexing to speficied what part of the data parameter
     should be use to construct the sparse matrix."""
@@ -701,6 +697,11 @@ class CSM(gof.Op):
 
         self.kmap = kmap
 
+        if not isinstance(self.kmap, numpy.ndarray):
+            # should view the other inputs too, but viewing multiple
+            # inputs is not currently supported by the destroyhandler
+            self.view_map = {0: [0]}
+
         self._hashval = (hash(type(self)) ^ hash(self.format) ^
                          _kmap_hash(self.kmap))
 
@@ -711,6 +712,11 @@ class CSM(gof.Op):
     def __hash__(self):
         return self._hashval
 
+    def __str__(self):
+        if self.kmap is not None:
+            return "%s{%s}" %(self.__class__.__name__, str(self.kmap))
+        return self.__class__.__name__
+
     def make_node(self, data, indices, indptr, shape):
         data = tensor.as_tensor_variable(data)
 
@@ -802,8 +808,10 @@ class CSMGrad(gof.op.Op):
 
     def __init__(self, kmap=None):
         self.kmap = kmap
-        if self.kmap is None:
-            self.view_map = {0: [1]}
+        #This class always allocate a new output.
+        #I keep this here to help GD understand what this kmap think is.
+        #if self.kmap is None:
+        #    self.view_map = {0: [1]}
 
     def __eq__(self, other):
         return type(self) == type(other) and _kmap_eq(self.kmap, other.kmap)
@@ -1224,6 +1232,7 @@ class Transpose(gof.op.Op):
            matrix.
     :note: The grad is regular, i.e. not structured.
     """
+    view_map = {0: [0]}
 
     format_map = {'csr': 'csc',
                   'csc': 'csr'}
@@ -1355,6 +1364,8 @@ class RowScaleCSC(gof.op.Op):
 
     # :note: The grad implemented is structured.
 
+    view_map = {0: [0]}
+
     def __eq__(self, other):
         return type(self) == type(other)
 

theano/sparse/tests/test_basic.py

@@ -2070,6 +2070,7 @@ def _hv_switch(op, expected_function):
 
         def expected_f(self, a, format=None, dtype=None):
             return expected_function(a, format, dtype)
+    XStackTester.__name__ = op.__name__ + "Tester"
     return XStackTester
 
 HStackTester = _hv_switch(HStack, sp.hstack)
@@ -2385,6 +2386,7 @@ def elemwise_checker(op, expected_f, gap=None, test_dtypes=None,
                         verify_grad_sparse(self.op,
                                            data,
                                            structured=True)
+    Tester.__name__ = op.__name__ + "Tester"
     return Tester
 
 

theano/tensor/elemwise.py

@@ -817,8 +817,7 @@ class Elemwise(Op):
                             min_informative_str(output) + '\n'
                 errormsg += 'original exception was: ' + '\n'.join(
                         traceback.format_exception_only(*sys.exc_info()[0:2]))
-                raise Exception(errormsg)
-            else:
+
             e.args = e.args + (errormsg, )
             raise
 

theano/tensor/nnet/Conv3D.py

@@ -549,6 +549,20 @@ class Conv3D(theano.Op):
 
 global conv3D
 conv3D = Conv3D()
+"""
+3D "convolution" of multiple filters on a minibatch
+(does not flip the kernel, moves kernel with a user specified stride)
+
+:param V: Visible unit, input.
+    dimensions: (batch, row, column, time, in channel)
+:param W: Weights, filter.
+    dimensions: (out channel, row, column, time ,in channel)
+:param b: bias, shape == (W.shape[0],)
+:param d: strides when moving the filter over the input(dx, dy, dt)
+
+:note: The order of dimensions do not correspond with the one in `conv2d`.
+       This is for optimization.
+"""
 
 def computeH(V,W,b,d):
     assert len(W.shape) == 5

theano/tensor/nnet/conv.py

@@ -690,8 +690,8 @@ class ConvOp(OpenMPOp):
             fulloutshp = tuple(ConvOp.getOutputShape(imshp_logical[
                 1:], kshp_logical, (1, 1), self.out_mode))
 
-        if z[0] is None or z[0].shape != (bsize,) + (nkern,) + fulloutshp:
-            z[0] = numpy.zeros((bsize,) + (nkern,) + fulloutshp,
+        if z[0] is None or z[0].shape != (bsize, nkern,) + fulloutshp:
+            z[0] = numpy.zeros((bsize, nkern,) + fulloutshp,
                                dtype=img2d.dtype)
         zz = z[0]
 

theano/tensor/tests/test_basic.py

@@ -1397,12 +1397,8 @@ _good_broadcast_unary_gammaln = dict(
     normal=(rand_ranged(-1 + 1e-2, 10, (2, 3)),),
     empty=(numpy.asarray([]),),)
 _grad_broadcast_unary_gammaln = dict(
-    normal=(rand_ranged(1e-8, 10, (2, 3)),),)
-
-if theano.config.floatX == 'float32':
-    gamma_eps = 3e-4
-else:
-    gamma_eps = 2e-10
+    # smaler range as our grad method don't estimate it good enough.
+    normal=(rand_ranged(1e-8, 8, (2, 3)),),)
 
 GammaTester = makeBroadcastTester(
     op=tensor.gamma,
@@ -1410,7 +1406,6 @@ GammaTester = makeBroadcastTester(
     good=_good_broadcast_unary_gammaln,
     grad=_grad_broadcast_unary_gammaln,
     mode=mode_no_scipy,
-    eps=gamma_eps,
     skip=skip_scipy)
 GammaInplaceTester = makeBroadcastTester(
     op=inplace.gamma_inplace,
@@ -1418,7 +1413,6 @@ GammaInplaceTester = makeBroadcastTester(
     good=_good_broadcast_unary_gammaln,
     grad=_grad_broadcast_unary_gammaln,
     mode=mode_no_scipy,
-    eps=gamma_eps,
     inplace=True,
     skip=skip_scipy)