Cereal for TMRegion

src/nupic/engine/Link.hpp

@@ -478,24 +478,22 @@ class Link : public Serializable
   void save_ar(Archive& ar) const {
     ar(cereal::make_nvp("srcRegionName", srcRegionName_),
        cereal::make_nvp("srcOutputName", srcOutputName_),
-       cereal::make_nvp("destRegionName",destRegionName_),
+       cereal::make_nvp("destRegionName", destRegionName_),
        cereal::make_nvp("destInputName", destInputName_),
-       cereal::make_nvp("destOffset",    destOffset_),
-       cereal::make_nvp("is_FanIn",      is_FanIn_),
-       cereal::make_nvp("propagationDelayBuffer", propagationDelayBuffer_)
-      );
+       cereal::make_nvp("destOffset", destOffset_),
+       cereal::make_nvp("is_FanIn", is_FanIn_));
+    ar(cereal::make_nvp("propagationDelayBuffer", propagationDelayBuffer_));
   }
   // FOR Cereal Deserialization
   template<class Archive>
   void load_ar(Archive& ar) {
     ar(cereal::make_nvp("srcRegionName", srcRegionName_),
        cereal::make_nvp("srcOutputName", srcOutputName_),
-       cereal::make_nvp("destRegionName",destRegionName_),
+       cereal::make_nvp("destRegionName", destRegionName_),
        cereal::make_nvp("destInputName", destInputName_),
-       cereal::make_nvp("destOffset",    destOffset_),
-       cereal::make_nvp("is_FanIn",      is_FanIn_),
-       cereal::make_nvp("propagationDelayBuffer", propagationDelayBuffer_)
-      );
+       cereal::make_nvp("destOffset", destOffset_),
+       cereal::make_nvp("is_FanIn", is_FanIn_));
+    ar(cereal::make_nvp("propagationDelayBuffer", propagationDelayBuffer_));
     propagationDelay_ = propagationDelayBuffer_.size();
     initialized_ = false;
   }

src/nupic/engine/Region.cpp

@@ -662,7 +662,7 @@ bool Region::isParameter(const std::string &name) const {
   return (spec_->parameters.contains(name));
 }
 
-// Some functions used to prevent symbles from being in Region.hpp
+// Some functions used to prevent symbols from being in Region.hpp
 void Region::getDims_(std::map<std::string,Dimensions>& outDims,
                       std::map<std::string,Dimensions>& inDims) const {
   for(auto out: outputs_) {

src/nupic/regions/TMRegion.hpp

@@ -72,6 +72,70 @@ class TMRegion : public RegionImpl, Serializable {
   void serialize(BundleIO &bundle) override;
   void deserialize(BundleIO &bundle) override;
 
+	CerealAdapter;  // see Serializable.hpp
+  // FOR Cereal Serialization
+  template<class Archive>
+  void save_ar(Archive& ar) const {
+    bool init = ((tm_) ? true : false);
+    ar(cereal::make_nvp("numberOfCols", args_.numberOfCols));
+    ar(cereal::make_nvp("cellsPerColumn", args_.cellsPerColumn));
+    ar(cereal::make_nvp("activationThreshold", args_.activationThreshold));
+    ar(cereal::make_nvp("initialPermanence", args_.initialPermanence));
+    ar(cereal::make_nvp("connectedPermanence", args_.connectedPermanence));
+    ar(cereal::make_nvp("maxNewSynapseCount", args_.maxNewSynapseCount));
+    ar(cereal::make_nvp("permanenceIncrement", args_.permanenceIncrement));
+    ar(cereal::make_nvp("permanenceDecrement", args_.permanenceDecrement));
+    ar(cereal::make_nvp("predictedSegmentDecrement", args_.predictedSegmentDecrement));
+    ar(cereal::make_nvp("seed", args_.seed));
+    ar(cereal::make_nvp("maxSegmentsPerCell", args_.maxSegmentsPerCell));
+    ar(cereal::make_nvp("maxSynapsesPerSegment", args_.maxSynapsesPerSegment));
+    ar(cereal::make_nvp("extra", args_.extra));
+    ar(cereal::make_nvp("checkInputs", args_.checkInputs));
+    ar(cereal::make_nvp("learningMode", args_.learningMode));
+    ar(cereal::make_nvp("sequencePos", args_.sequencePos));
+    ar(cereal::make_nvp("iter", args_.iter));
+    ar(cereal::make_nvp("orColumnOutputs", args_.orColumnOutputs));
+		ar(cereal::make_nvp("dim", dim_));  // from RegionImpl
+    ar(cereal::make_nvp("init", init));
+    if (init) {
+      // Save the algorithm state
+      ar(cereal::make_nvp("TM", tm_));
+    }
+  }
+
+  // FOR Cereal Deserialization
+  template<class Archive>
+  void load_ar(Archive& ar) {
+    ar(cereal::make_nvp("numberOfCols", args_.numberOfCols));
+    ar(cereal::make_nvp("cellsPerColumn", args_.cellsPerColumn));
+    ar(cereal::make_nvp("activationThreshold", args_.activationThreshold));
+    ar(cereal::make_nvp("initialPermanence", args_.initialPermanence));
+    ar(cereal::make_nvp("connectedPermanence", args_.connectedPermanence));
+    ar(cereal::make_nvp("maxNewSynapseCount", args_.maxNewSynapseCount));
+    ar(cereal::make_nvp("permanenceIncrement", args_.permanenceIncrement));
+    ar(cereal::make_nvp("permanenceDecrement", args_.permanenceDecrement));
+    ar(cereal::make_nvp("predictedSegmentDecrement", args_.predictedSegmentDecrement));
+    ar(cereal::make_nvp("seed", args_.seed));
+    ar(cereal::make_nvp("maxSegmentsPerCell", args_.maxSegmentsPerCell));
+    ar(cereal::make_nvp("maxSynapsesPerSegment", args_.maxSynapsesPerSegment));
+    ar(cereal::make_nvp("extra", args_.extra));
+    ar(cereal::make_nvp("checkInputs", args_.checkInputs));
+    ar(cereal::make_nvp("learningMode", args_.learningMode));
+    ar(cereal::make_nvp("sequencePos", args_.sequencePos));
+    ar(cereal::make_nvp("iter", args_.iter));
+    ar(cereal::make_nvp("orColumnOutputs", args_.orColumnOutputs));
+    args_.outputWidth = (args_.orColumnOutputs)?args_.numberOfCols
+                      : (args_.numberOfCols * args_.cellsPerColumn);
+		ar(cereal::make_nvp("dim", dim_));  // from RegionImpl
+    ar(cereal::make_nvp("init", args_.init));
+    if (args_.init) {
+      // Restore algorithm state
+      nupic::algorithms::temporal_memory::TemporalMemory* tm = new nupic::algorithms::temporal_memory::TemporalMemory();
+      tm_.reset(tm);
+      ar(cereal::make_nvp("TM", tm_));
+    }
+  }
+
   // Per-node size (in elements) of the given output.
   // For per-region outputs, it is the total element count.
   // This method is called only for outputs whose size is not

src/test/unit/regions/SPRegionTest.cpp

@@ -237,10 +237,6 @@ namespace testing
             << "actual type is " << BasicType::getName(r1OutputArray.getType());
 
     Real32 *buffer1 = (Real32*) r1OutputArray.getBuffer();
-	  //for (size_t i = 0; i < r1OutputArray.getCount(); i++)
-	  //{
-		//VERBOSE << "  [" << i << "]=    " << buffer1[i] << "" << std::endl;
-	  //}
 
     VERBOSE << "  SPRegion input" << std::endl;
     Array r2InputArray = region2->getInputData("bottomUpIn");
@@ -324,11 +320,6 @@ TEST(SPRegionTest, testSerialization)
     std::map<std::string, std::string> parameterMap;
     EXPECT_TRUE(captureParameters(n1region2, parameterMap)) << "Capturing parameters before save.";
 
-    // TODO: JSON serialization does not work.
-    //    returns 3 (not really a crash)
-    // It fails returning from SpatialPooler, in rapidjson::PrettyWriter.h line 128
-    // It is apparently checking that it is not in array mode.
-
     Directory::removeTree("TestOutputDir", true);
     VERBOSE << "Writing stream to " << Path::makeAbsolute("TestOutputDir/spRegionTest.stream") << "\n";
 	  net1.saveToFile_ar("TestOutputDir/spRegionTest.stream", SerializableFormat::JSON);

src/test/unit/regions/TMRegionTest.cpp

@@ -335,110 +335,85 @@ TEST(TMRegionTest, testLinking) {
 }
 
 TEST(TMRegionTest, testSerialization) {
-  // use default parameters the first time
-  Network *net1 = new Network();
-  Network *net2 = nullptr;
-  Network *net3 = nullptr;
-
-  try {
-
-    VERBOSE << "Setup first network and save it" << std::endl;
-    std::shared_ptr<Region> n1region1 = net1->addRegion( "region1", "ScalarSensor",
-                                             "{n: 48,w: 10,minValue: 0.05,maxValue: 10}");
-    n1region1->setParameterReal64("sensedValue", 5.0);
-
-    std::shared_ptr<Region> n1region2 =  net1->addRegion("region2", "TMRegion", "{numberOfCols: 48}");
-
-    net1->link("region1", "region2", "", "", "encoded", "bottomUpIn");
-    VERBOSE << "Initialize" << std::endl;
-    net1->initialize();
-
-    VERBOSE << "compute region1" << std::endl;
-    n1region1->prepareInputs();
-    n1region1->compute();
-
-    VERBOSE << "compute region2" << std::endl;
-    n1region2->prepareInputs();
-    n1region2->compute();
-
-    // take a snapshot of everything in TMRegion at this point
-    // save to a bundle.
-    std::map<std::string, std::string> parameterMap;
-    EXPECT_TRUE(captureParameters(n1region2, parameterMap))
-        << "Capturing parameters before save.";
-
-    VERBOSE << "saveToFile" << std::endl;
-    Directory::removeTree("TestOutputDir", true);
-    net1->saveToFile("TestOutputDir/tmRegionTest.stream");
-
-    VERBOSE << "Restore from bundle into a second network and compare." << std::endl;
-    net2 = new Network();
-    net2->loadFromFile("TestOutputDir/tmRegionTest.stream");
-
-
-    VERBOSE << "checked restored network" << std::endl;
-    std::shared_ptr<Region> n2region2 = net2->getRegion("region2");
-    ASSERT_TRUE(n2region2->getType() == "TMRegion")
-        << " Restored TMRegion region does not have the right type.  Expected "
-           "TMRegion, found "
-        << n2region2->getType();
-
-    EXPECT_FLOAT_EQ(n2region2->getParameterReal32("anomaly"), 1.0f);
-    EXPECT_TRUE(compareParameters(n2region2, parameterMap))
-        << "Conflict when comparing TMRegion parameters after restore with "
-           "before save.";
-
-    VERBOSE << "continue with execution." << std::endl;
-    // can we continue with execution?  See if we get any exceptions.
-    n1region1->setParameterReal64("sensedValue", 0.12);
-    n1region1->prepareInputs();
-    n1region1->compute();
-
-    n2region2->prepareInputs();
-    VERBOSE << "continue 4." << std::endl;
-    n2region2->compute();
-    VERBOSE << "continue 5." << std::endl;
-
-    // Change a parameters and see if it is retained after a restore.
-    n2region2->setParameterReal32("permanenceDecrement", 0.099f);
-    n2region2->compute();
-
-    parameterMap.clear();
-    EXPECT_TRUE(captureParameters(n2region2, parameterMap))
-        << "Capturing parameters before second save.";
-    // serialize using a stream to a single file
-    VERBOSE << "save second network." << std::endl;
-    net2->saveToFile("TestOutputDir/tmRegionTest.stream");
-
-    VERBOSE << "Restore into a third network and compare changed parameters." << std::endl;
-    net3 = new Network();
-    net3->loadFromFile("TestOutputDir/tmRegionTest.stream");
-    std::shared_ptr<Region> n3region2 = net3->getRegion("region2");
-    EXPECT_TRUE(n3region2->getType() == "TMRegion")
-        << "Failure: Restored region does not have the right type. "
-           " Expected \"TMRegion\", found \""
-        << n3region2->getType() << "\".";
-
-    EXPECT_TRUE(compareParameters(n3region2, parameterMap))
-        << "Comparing parameters after second restore with before save.";
-  } catch (nupic::Exception &ex) {
-    FAIL() << "Failure: Exception: " << ex.getFilename() << "("
-           << ex.getLineNumber() << ") " << ex.getMessage() << "" << std::endl;
-  } catch (std::exception &e) {
-    FAIL() << "Failure: Exception: " << e.what() << "" << std::endl;
-  }
+  Network net1;
+  Network net2;
+  Network net3;
+
+  VERBOSE << "Setup first network and save it" << std::endl;
+  std::shared_ptr<Region> n1region1 = net1.addRegion( "region1", "ScalarSensor",
+                                            "{n: 48,w: 10,minValue: 0.05,maxValue: 10}");
+  n1region1->setParameterReal64("sensedValue", 5.0);
+
+  std::shared_ptr<Region> n1region2 =  net1.addRegion("region2", "TMRegion", "{numberOfCols: 48}");
+
+  net1.link("region1", "region2", "", "", "encoded", "bottomUpIn");
+  VERBOSE << "Initialize" << std::endl;
+  net1.initialize();
+
+  VERBOSE << "compute region1" << std::endl;
+  n1region1->prepareInputs();
+  n1region1->compute();
+
+  VERBOSE << "compute region2" << std::endl;
+  n1region2->prepareInputs();
+  n1region2->compute();
+
+  // take a snapshot of everything in TMRegion at this point
+  // save to a bundle.
+  std::map<std::string, std::string> parameterMap;
+  EXPECT_TRUE(captureParameters(n1region2, parameterMap))
+      << "Capturing parameters before save.";
+
+  VERBOSE << "saveToFile" << std::endl;
+  Directory::removeTree("TestOutputDir", true);
+  net1.saveToFile_ar("TestOutputDir/tmRegionTest.stream");
+
+  VERBOSE << "Restore from bundle into a second network and compare." << std::endl;
+  net2.loadFromFile_ar("TestOutputDir/tmRegionTest.stream");
+
+  VERBOSE << "checked restored network" << std::endl;
+  std::shared_ptr<Region> n2region2 = net2.getRegions().getByName("region2");
+  ASSERT_TRUE(n2region2->getType() == "TMRegion")
+      << " Restored TMRegion region does not have the right type.  Expected "
+          "TMRegion, found "
+      << n2region2->getType();
+
+  EXPECT_TRUE(compareParameters(n2region2, parameterMap))
+      << "Conflict when comparing TMRegion parameters after restore with "
+          "before save.";
+
+  VERBOSE << "continue with execution." << std::endl;
+  // can we continue with execution?  See if we get any exceptions.
+  n1region1->setParameterReal64("sensedValue", 0.12);
+  n1region1->prepareInputs();
+  n1region1->compute();
+
+  n2region2->prepareInputs();
+  n2region2->compute();
+
+  // Change a parameters and see if it is retained after a restore.
+  n2region2->setParameterReal32("permanenceDecrement", 0.099f);
+  n2region2->compute();
+
+  parameterMap.clear();
+  EXPECT_TRUE(captureParameters(n2region2, parameterMap))
+      << "Capturing parameters before second save.";
+  // serialize using a stream to a single file
+  VERBOSE << "save second network." << std::endl;
+  net2.saveToFile_ar("TestOutputDir/tmRegionTest.stream");
+
+  VERBOSE << "Restore into a third network and compare changed parameters." << std::endl;
+  net3.loadFromFile_ar("TestOutputDir/tmRegionTest.stream");
+  std::shared_ptr<Region> n3region2 = net3.getRegions().getByName("region2");
+  EXPECT_TRUE(n3region2->getType() == "TMRegion")
+      << "Failure: Restored region does not have the right type. "
+          " Expected \"TMRegion\", found \""
+      << n3region2->getType() << "\".";
+
+  EXPECT_TRUE(compareParameters(n3region2, parameterMap))
+      << "Comparing parameters after second restore with before save.";
 
   VERBOSE << "Cleanup" << std::endl;
-  // cleanup
-  if (net1 != nullptr) {
-    delete net1;
-  }
-  if (net2 != nullptr) {
-    delete net2;
-  }
-  if (net3 != nullptr) {
-    delete net3;
-  }
   Directory::removeTree("TestOutputDir", true);
 }