Merge pull request #1351 from scottpurdy/nup-2356

Add Cells4 read/write SWIG wrapping and fix bug in Cells4 deserialization

src/nupic/algorithms/Cells4.cpp

@@ -2000,25 +2000,26 @@ void Cells4::write(Cells4Proto::Builder& proto) const
 void Cells4::read(Cells4Proto::Reader& proto)
 {
   NTA_CHECK(proto.getVersion() == 2);
-  _ownsMemory = proto.getOwnsMemory();
+
+  initialize(proto.getNColumns(),
+             proto.getNCellsPerCol(),
+             proto.getActivationThreshold(),
+             proto.getMinThreshold(),
+             proto.getNewSynapseCount(),
+             proto.getSegUpdateValidDuration(),
+             proto.getPermInitial(),
+             proto.getPermConnected(),
+             proto.getPermMax(),
+             proto.getPermDec(),
+             proto.getPermInc(),
+             proto.getGlobalDecay(),
+             proto.getDoPooling(),
+             proto.getOwnsMemory());
   auto randomProto = proto.getRng();
   _rng.read(randomProto);
-  _nColumns = proto.getNColumns();
-  _nCellsPerCol = proto.getNCellsPerCol();
-  _activationThreshold = proto.getActivationThreshold();
-  _minThreshold = proto.getMinThreshold();
-  _newSynapseCount = proto.getNewSynapseCount();
   _nIterations = proto.getNIterations();
   _nLrnIterations = proto.getNLrnIterations();
-  _segUpdateValidDuration = proto.getSegUpdateValidDuration();
   _initSegFreq = proto.getInitSegFreq();
-  _permInitial = proto.getPermInitial();
-  _permConnected = proto.getPermConnected();
-  _permMax = proto.getPermMax();
-  _permDec = proto.getPermDec();
-  _permInc = proto.getPermInc();
-  _globalDecay = proto.getGlobalDecay();
-  _doPooling = proto.getDoPooling();
   _pamLength = proto.getPamLength();
   _maxInfBacktrack = proto.getMaxInfBacktrack();
   _maxLrnBacktrack = proto.getMaxLrnBacktrack();

src/nupic/algorithms/Cells4.hpp

@@ -525,9 +525,9 @@ namespace nupic {
         UInt getMaxSeqLength() const        { return _maxSeqLength;}
         Real getAvgLearnedSeqLength() const { return _avgLearnedSeqLength;}
         UInt getNLrnIterations() const      { return _nLrnIterations;}
-        Int  getmaxSegmentsPerCell() const  { return _maxSegmentsPerCell;}
-        Int  getMaxSynapsesPerCell() const  { return _maxSynapsesPerSegment;}
-        bool getCheckSynapseConsistency()   { return _checkSynapseConsistency;}
+        Int  getMaxSegmentsPerCell() const  { return _maxSegmentsPerCell;}
+        Int  getMaxSynapsesPerSegment() const  { return _maxSynapsesPerSegment;}
+        bool getCheckSynapseConsistency() const   { return _checkSynapseConsistency;}
 
 
         //----------------------------------------------------------------------

src/nupic/bindings/algorithms.i

@@ -34,10 +34,11 @@ try:
 except ImportError:
   capnp = None
 else:
-  from nupic.proto.SpatialPoolerProto_capnp import SpatialPoolerProto
+  from nupic.proto.Cells4_capnp import Cells4Proto
   from nupic.proto.ClaClassifier_capnp import ClaClassifierProto
-  from nupic.proto.SdrClassifier_capnp import SdrClassifierProto
   from nupic.proto.ConnectionsProto_capnp import ConnectionsProto
+  from nupic.proto.SdrClassifier_capnp import SdrClassifierProto
+  from nupic.proto.SpatialPoolerProto_capnp import SpatialPoolerProto
   from nupic.proto.TemporalMemoryProto_capnp import TemporalMemoryProto
 
 
@@ -97,6 +98,7 @@ _ALGORITHMS = _algorithms
 #include <nupic/algorithms/OutSynapse.hpp>
 #include <nupic/algorithms/SegmentUpdate.hpp>
 
+#include <nupic/proto/Cells4.capnp.h>
 #include <nupic/proto/ConnectionsProto.capnp.h>
 #include <nupic/proto/SpatialPoolerProto.capnp.h>
 #include <nupic/proto/TemporalMemoryProto.capnp.h>
@@ -804,8 +806,33 @@ void forceRetentionOfImageSensorLiteLibrary(void) {
     def __setstate__(self, inString):
       self.this = _ALGORITHMS.new_Cells4()
       self.loadFromString(inString)
+
+    @classmethod
+    def read(cls, proto):
+      instance = cls()
+      instance._initFromCapnpPyBytes(proto.as_builder().to_bytes()) # copy * 2
+      return instance
+
+    def write(self, pyBuilder):
+      """Serialize the Cells4 instance using capnp.
+
+      :param: Destination Cells4Proto message builder
+      """
+      reader = Cells4Proto.from_bytes(self._writeAsCapnpPyBytes()) # copy
+      pyBuilder.from_dict(reader.to_dict())  # copy
+
   %}
 
+  inline PyObject* _writeAsCapnpPyBytes() const
+  {
+    return nupic::PyCapnpHelper::writeAsPyBytes(*self);
+  }
+
+  inline void _initFromCapnpPyBytes(PyObject* pyBytes)
+  {
+    nupic::PyCapnpHelper::initFromPyBytes(*self, pyBytes);
+  }
+
   void loadFromString(const std::string& inString)
   {
     std::istringstream inStream(inString);

src/test/unit/algorithms/Cells4Test.cpp

@@ -82,20 +82,74 @@ std::vector<UInt> _getOrderedSynapseIndexesForSrcCells(const Segment& segment,
 }
 
 
+/**
+ * Simple comparison function that does the easy checks. It can be expanded to
+ * cover more of the attributes of Cells4 in the future.
+ */
+bool checkCells4Attributes(const Cells4& c1, const Cells4& c2)
+{
+  if (c1.nSegments() != c2.nSegments() ||
+      c1.nCells() != c2.nCells() ||
+      c1.nColumns() != c2.nColumns() ||
+      c1.nCellsPerCol() != c2.nCellsPerCol() ||
+      c1.getMinThreshold() != c2.getMinThreshold() ||
+      c1.getPermConnected() != c2.getPermConnected() ||
+      c1.getVerbosity() != c2.getVerbosity() ||
+      c1.getMaxAge() != c2.getMaxAge() ||
+      c1.getPamLength() != c2.getPamLength() ||
+      c1.getMaxInfBacktrack() != c2.getMaxInfBacktrack() ||
+      c1.getMaxLrnBacktrack() != c2.getMaxLrnBacktrack() ||
+
+      c1.getPamCounter() != c2.getPamCounter() ||
+      c1.getMaxSeqLength() != c2.getMaxSeqLength() ||
+      c1.getAvgLearnedSeqLength() != c2.getAvgLearnedSeqLength() ||
+      c1.getNLrnIterations() != c2.getNLrnIterations() ||
+
+      c1.getMaxSegmentsPerCell() != c2.getMaxSegmentsPerCell() ||
+      c1.getMaxSynapsesPerSegment() != c2.getMaxSynapsesPerSegment() ||
+      c1.getCheckSynapseConsistency() != c2.getCheckSynapseConsistency())
+  {
+    return false;
+  }
+  return true;
+}
+
+
 TEST(Cells4Test, capnpSerialization)
 {
   Cells4 cells(
       10, 2, 1, 1, 1, 1, 0.5, 0.8, 1, 0.1, 0.1, 0, false, -1, true, false);
-  std::vector<Real> input(10, 0.0);
-  input[1] = 1.0;
-  input[4] = 1.0;
-  input[5] = 1.0;
-  input[9] = 1.0;
+  std::vector<Real> input1(10, 0.0);
+  input1[1] = 1.0;
+  input1[4] = 1.0;
+  input1[5] = 1.0;
+  input1[9] = 1.0;
+  std::vector<Real> input2(10, 0.0);
+  input2[0] = 1.0;
+  input2[2] = 1.0;
+  input2[5] = 1.0;
+  input2[6] = 1.0;
+  std::vector<Real> input3(10, 0.0);
+  input3[1] = 1.0;
+  input3[3] = 1.0;
+  input3[6] = 1.0;
+  input3[7] = 1.0;
+  std::vector<Real> input4(10, 0.0);
+  input4[2] = 1.0;
+  input4[4] = 1.0;
+  input4[7] = 1.0;
+  input4[8] = 1.0;
   std::vector<Real> output(10*2);
-  cells.compute(&input.front(), &output.front(), true, true);
+  for (UInt i = 0; i < 10; ++i)
+  {
+    cells.compute(&input1.front(), &output.front(), true, true);
+    cells.compute(&input2.front(), &output.front(), true, true);
+    cells.compute(&input3.front(), &output.front(), true, true);
+    cells.compute(&input4.front(), &output.front(), true, true);
+    cells.reset();
+  }
 
-  Cells4 secondCells(
-      10, 2, 1, 1, 1, 1, 0.5, 0.8, 1, 0.1, 0.1, 0, false, -1, true, false);
+  Cells4 secondCells;
   {
     capnp::MallocMessageBuilder message1;
     Cells4Proto::Builder cells4Builder = message1.initRoot<Cells4Proto>();
@@ -110,13 +164,16 @@ TEST(Cells4Test, capnpSerialization)
     secondCells.read(cells4Reader);
   }
 
+  NTA_CHECK(checkCells4Attributes(cells, secondCells));
+
   std::vector<Real> secondOutput(10*2);
-  cells.compute(&input.front(), &output.front(), true, true);
-  secondCells.compute(&input.front(), &secondOutput.front(), true, true);
+  cells.compute(&input1.front(), &output.front(), true, true);
+  secondCells.compute(&input1.front(), &secondOutput.front(), true, true);
   for (UInt i = 0; i < 10; ++i)
   {
     ASSERT_EQ(output[i], secondOutput[i]) << "Outputs differ at index " << i;
   }
+  NTA_CHECK(checkCells4Attributes(cells, secondCells));
 }