init sparse

gof/compile.py

-
 import env
 import tools
 import utils
 
 class Compiler:
+    """ What is this?  Please document.
+
+    """
 
     def __init__(self, optimizer, features):
         self.features = set(features)

gof/env.py

@@ -2,7 +2,6 @@
 from copy import copy
 
 import graph
-## from value import Value, AsValue
 from utils import ClsInit
 from err import GofError, GofTypeError, PropagationError
 from op import Op
@@ -46,6 +45,7 @@ __all__ = ['InconsistencyError',
 
 
 
+#TODO: why is this not in err.py? -James
 class InconsistencyError(GofError):
     """
     This exception is raised by Env whenever one of the listeners marks
@@ -71,6 +71,14 @@ class Env(graph.Graph):
     time and whenever there is a replacement). In addition to that, each listener can
     implement the 'consistent' and 'ordering' methods (see EnvListener) in order to
     restrict how ops in the subgraph can be related.
+
+    Regarding inputs and orphans:
+    In the context of a computation graph, the inputs and orphans are both
+    results that are the source nodes of computation.  Those results that are
+    named as inputs will be assumed to contain fresh.  In other words, the
+    backward search from outputs will stop at any node that has been explicitly
+    named as an input.
+
     """
 
     ### Special ###
@@ -79,6 +87,11 @@ class Env(graph.Graph):
         """
         Create an Env which operates on the subgraph bound by the inputs and outputs
         sets. If consistency_check is False, an illegal graph will be tolerated.
+
+        Features are class types derived from things in the tools file.  These
+        can be listeners, constraints, orderings, etc.  Features add much
+        (most?) functionality to an Env.
+
         """
 
         self._features = {}

gof/err.py

-
+"""
+This file defines the Exceptions that may be raised by graph manipulations.
+"""
 
 class GofError(Exception):
     pass

gof/op.py

@@ -30,17 +30,21 @@ class Op(object):
     __slots__ = ['_inputs', '_outputs']
     __require__ = []
 
+    #create inputs and outputs as read-only attributes
     inputs = property(lambda self: self._inputs, doc = "The list of this Op's input Results.")
     outputs = property(lambda self: self._outputs, doc = "The list of this Op's output Results.")
 
-    """
-    If true, self.default_output() or self.out can be used to access
-    self.outputs[0]
-    """
-    has_default_output = True
-    
-    out = property(lambda self: self.default_output(), doc = "Same as self.outputs[0] if this Op's has_default_output field is True.")
+    _default_output_idx = 0
 
+    def default_output(self):
+        """Returns the default output of this Op instance, typically self.outputs[0]."""
+        try:
+            return self.outputs[self._default_output_idx]
+        except (IndexError, TypeError):
+            raise AttributeError("Op does not have a default output.")
+    
+    out = property(default_output, 
+            doc = "Same as self.outputs[0] if this Op's has_default_output field is True.")
 
     def __init__(self, inputs, outputs, use_self_setters = False):
         """
@@ -72,14 +76,6 @@ class Op(object):
         self.validate()
 
         
-    def default_output(self):
-        """
-        Returns the default output of this Op instance, typically self.outputs[0].
-        """
-        if self.has_default_output:
-            return self.outputs[0]
-        else:
-            raise AttributeError("Op does not have a default output.")
 
 
     def set_input(self, i, input, allow_changes = False, validate = True):
@@ -153,7 +149,7 @@ class Op(object):
                 self.set_output(i, previous, False)
 
 
-    def repair(self, allow_changes = False):
+    def _dontuse_repair(self, allow_changes = False):
         """
         This function attempts to repair all inputs that are broken
         links by calling set_input on the new Result that replaced

gof/result.py

@@ -2,6 +2,7 @@
 """
 Contains the Result class, which is the base interface for a
 value that is the input or the output of an Op.
+
 """
 
 
@@ -43,10 +44,9 @@ class Result(object):
     The Result class represents a datum for use in a graph of Ops. It
     has two slots:
 
-    - owner: represents the Op which computes this Result. It is
-    assumed to be an instance of Op. If owner raises an
-    AttributeError, the Result is assumed to be an input.
-    - index: the index this Result holds in its owner's outputs.
+    - owner: represents the Op which computes this Result. Contains either None
+      or an instance of Op.
+    - index: the index of this Result in owner.outputs.
 
     Result has no __init__ or __new__ routine. It is the Op's
     responsibility to set the owner field of its results.

gof/utils.py

@@ -30,6 +30,8 @@ def all_bases_collect(cls, raw_name):
 
 
 def uniq_features(_features, *_rest):
+    """Return a list such that no element is a subclass of another"""
+    # used in Env.__init__ to 
     features = [x for x in _features]
     for other in _rest:
         features += [x for x in other]

sparse.py

+import unittest
+
+import numpy
+from scipy import sparse
+
+import gof.lib
+import core
+import grad
+
+# Wrapper type
+
+class SparseR(gof.PythonR):
+    """
+    Attribute:
+    format - a subclass of sparse.spmatrix indicating self.data.__class__
+    """
+    def __init__(self, x = core.UNCOMPUTED, constant = False, 
+            format = sparse.csr_matrix):
+        gof.PythonR.__init__(self, x, constant)
+        self.format = isinstance(x, sparse.spmatrix) and x.__class__ or format
+
+    def set_value(self, value):
+        """Extend base impl, assert value is sparse matrix"""
+        gof.PythonR.set_value(self,value)
+        if self.data is not core.UNCOMPUTED:
+            if not isinstance(self.data, sparse.spmatrix):
+                print self.data.__class__
+                print self.owner.__class__
+                raise TypeError(('hrm',value))
+
+    def __add__(left, right): return add(left, right)
+    def __radd__(right, left): return add(left, right)
+
+    T = property(lambda self: transpose(self), doc = "Return aliased transpose")
+
+# convenience base class
+class op(gof.PythonOp, grad.update_gradient_via_grad):
+    pass
+
+#
+# Conversion
+#
+
+# convert a sparse matrix to an ndarray
+class sparse2dense(op):
+    def gen_outputs(self): return [core.NumpyR()]
+    def impl(x): return numpy.asarray(x.todense())
+    def grad(self, x, gz): 
+        if x.format is sparse.coo_matrix:
+            return dense2coo(gz)
+        if x.format is sparse.csc_matrix:
+            return dense2csc(gz)
+        if x.format is sparse.csr_matrix:
+            return dense2csr(gz)
+        if x.format is sparse.dok_matrix:
+            return dense2dok(gz)
+        if x.format is sparse.lil_matrix:
+            return dense2lil(gz)
+
+# convert an ndarray to various sorts of sparse matrices.
+class _dense2sparse(op):
+    def gen_outputs(self): return [SparseR()]
+    def grad(self, x, gz): return sparse2dense(gz)
+class dense2coo(_dense2sparse):
+    def impl(x): return sparse.coo_matrix(x)
+class dense2csc(_dense2sparse):
+    def impl(x): return sparse.csc_matrix(x)
+class dense2csr(_dense2sparse):
+    def impl(x): return sparse.csr_matrix(x)
+class dense2dok(_dense2sparse):
+    def impl(x): return sparse.dok_matrix(x)
+class dense2lil(_dense2sparse):
+    def impl(x): return sparse.lil_matrix(x)
+
+
+# Linear Algebra
+
+class add(op):
+    def gen_outputs(self): return [SparseR()]
+    def impl(csr,y): return csr + y
+
+class transpose(op):
+    def gen_outputs(self): return [SparseR()]
+    def impl(x): return x.transpose() 
+    def grad(self, x, gz): return transpose(gz)
+
+class _testCase_transpose(unittest.TestCase):
+    def setUp(self):
+        core.build_eval_mode()
+        numpy.random.seed(44)
+    def tearDown(self):
+        core.pop_mode()
+    def test_transpose(self):
+        a = SparseR(sparse.csr_matrix(sparse.speye(5,3)))
+        self.failUnless(a.data.shape == (5,3))
+        ta = transpose(a)
+        self.failUnless(ta.data.shape == (3,5))
+
+class dot(op):
+    """
+    Attributes:
+    grad_preserves_dense - an array of boolean flags (described below)
+
+
+    grad_preserves_dense controls whether gradients with respect to inputs are
+    converted to dense matrices when the corresponding inputs are not in a
+    SparseR wrapper.  This can be a good idea when dot is in the middle of a
+    larger graph, because the types of gx and gy will match those of x and y.
+    This conversion might be annoying if the gradients are graph outputs though,
+    hence this mask.
+    """
+    def __init__(self, *args, **kwargs):
+        op.__init__(self, *args, **kwargs)
+        self.grad_preserves_dense = [True, True]
+    def gen_outputs(self): return [SparseR()]
+    def impl(x,y):
+        if hasattr(x, 'getnnz'):
+            return x.dot(y)
+        else:
+            return y.transpose().dot(x.transpose()).transpose()
+
+    def grad(self, x, y, gz):
+        rval = [dot(gz, y.T), dot(x.T, gz)]
+        for i in 0,1:
+            if not isinstance(self.inputs[i], SparseR):
+                #assume it is a dense matrix
+                if self.grad_preserves_dense[i]:
+                    rval[i] = sparse2dense(rval[i])
+        return rval
+
+class _testCase_dot(unittest.TestCase):
+    def setUp(self):
+        core.build_eval_mode()
+        numpy.random.seed(44)
+    def tearDown(self):
+        core.pop_mode()
+    def test_basic0(self):
+        for mtype in [sparse.csc_matrix, sparse.csr_matrix]:
+            x = SparseR(mtype(sparse.speye(5,3)))
+            y = core.NumpyR(numpy.random.rand(3, 2))
+
+            z = dot(x,y)
+            self.failUnless(z.data.shape == (5,2))
+            self.failUnless(type(z.data) is mtype)
+    def test_basic1(self):
+        """dot: sparse left"""
+        a = numpy.asarray([[1, 0, 3, 0, 5], [0, 0, -2, 0, 0]],
+                dtype='float64')
+        b = numpy.random.rand(5, 3)
+        for mtype in [sparse.csr_matrix, sparse.csc_matrix, sparse.dok_matrix,
+                sparse.lil_matrix]:#, sparse.coo_matrix]:
+            #print type(a), mtype
+            m = mtype(a)
+            ab = m.dot(b)
+            try:
+                z = dot(SparseR(m),gof.lib.PythonR(b))
+                self.failUnless(z.data.shape == ab.shape)
+                self.failUnless(type(z.data) == type(ab))
+            except Exception, e:
+                print mtype, e, str(e)
+                raise
+    def test_basic2(self):
+        """dot: sparse right"""
+        a = numpy.random.rand(2, 5)
+        b = numpy.asarray([[1, 0, 3, 0, 5], [0, 0, -2, 0, 0]],
+                dtype='float64').transpose()
+
+        for mtype in [sparse.csr_matrix, sparse.csc_matrix, sparse.dok_matrix,
+                sparse.lil_matrix]:#, sparse.coo_matrix]:
+            m = mtype(b)
+            ab = m.transpose().dot(a.transpose()).transpose()
+            z = dot(gof.lib.PythonR(a),SparseR(mtype(b)))
+            self.failUnless(z.data.shape == ab.shape)
+            self.failUnless(type(z.data) == type(ab))
+    def test_graph_bprop0(self):
+        x = core.NumpyR(numpy.random.rand(10,2))
+        w = SparseR(sparse.csr_matrix(numpy.asarray([[1, 0, 3, 0, 5], [0, 0, -2, 0,
+            0]],dtype='float64')))
+
+        for epoch in xrange(50):
+            xw = sparse2dense(dot(x, w))
+            y = sparse2dense(dot(xw, transpose(w)))
+            loss = core.sum(core.sqr(x-y))
+            gy = y-x
+            g = grad.Grad({y:gy})
+            g.bprop()
+            lr = 0.002
+            g(w).data[1,0] = 0
+            g(w).data[1,4] = 0
+            w.data = -lr * g(w).data + w.data
+
+        self.failUnless('3.08560636025' == str(loss))
+
+    def test_graph_bprop1(self):
+        x = core.NumpyR(numpy.random.rand(10,2))
+        w = SparseR(sparse.csr_matrix(numpy.asarray([[1, 0, 3, 0, 5], [0, 0, -2, 0,
+            0]],dtype='float64')))
+
+        for epoch in xrange(50):
+            xw = sparse2dense(dot(x, w))
+            y = sparse2dense(dot(xw, transpose(w)))
+            loss = core.sum(core.sqr(x-y))
+            g = grad.grad(loss)
+            lr = 0.001
+
+            g(w).data[1,0] = 0
+            g(w).data[1,4] = 0
+            w.data = -lr * g(w).data + w.data
+
+        self.failUnless('3.08560636025' == str(loss))
+        
+if __name__ == '__main__':
+    unittest.main()
+