SDR replaces VectorHelpers

src/CMakeLists.txt

@@ -190,7 +190,6 @@ set(utils_files
     nupic/utils/Random.cpp
     nupic/utils/Random.hpp
     nupic/utils/SlidingWindow.hpp
-    nupic/utils/VectorHelpers.hpp
     nupic/utils/SdrMetrics.cpp
     nupic/utils/SdrMetrics.hpp
     nupic/utils/MurmurHash3.hpp

src/nupic/algorithms/SpatialPooler.cpp

@@ -31,7 +31,6 @@
 
 #include <nupic/algorithms/SpatialPooler.hpp>
 #include <nupic/utils/Topology.hpp>
-#include <nupic/utils/VectorHelpers.hpp>
 
 using namespace std;
 using namespace nupic;
@@ -450,18 +449,17 @@ void SpatialPooler::initialize(
   inhibitionRadius_ = 0;
 
   connections_.initialize(numColumns_, synPermConnected_);
-  for (Size i = 0; i < numColumns_; ++i) {
-    connections_.createSegment( (CellIdx)i );
-
-    // Note: initMapPotential_ & initPermanence_ return dense arrays.
-    vector<UInt> potential = initMapPotential_((UInt)i, wrapAround_);
-    vector<Real> perm = initPermanence_(potential, initConnectedPct_);
-    for(UInt presyn = 0; presyn < numInputs_; presyn++) {
-      if( potential[presyn] )
-        connections_.createSynapse( (Segment)i, presyn, perm[presyn] );
+  for (Size column = 0; column < numColumns_; column++) {
+    connections_.createSegment( static_cast<CellIdx>(column) );
+
+    SDR potential({numInputs_});
+    initMapPotential_(static_cast<UInt>(column), wrapAround_, potential);
+    const vector<Real> perm = initPermanence_(potential, initConnectedPct_);
+    for(const auto presyn : potential.getSparse()) {
+        connections_.createSynapse( static_cast<Segment>(column), presyn, perm[presyn] );
     }
 
-    connections_.raisePermanencesToThreshold( (Segment)i, stimulusThreshold_ );
+    connections_.raisePermanencesToThreshold( static_cast<Segment>(column), stimulusThreshold_ );
   }
 
   updateInhibitionRadius_();
@@ -505,6 +503,7 @@ void SpatialPooler::compute(const SDR &input, const bool learn, SDR &active) {
 
 void SpatialPooler::boostOverlaps_(const vector<SynapseIdx> &overlaps, //TODO use Eigen sparse vector here
                                    vector<Real> &boosted) const {
+  NTA_ASSERT(overlaps.size() == numColumns_);
   for (UInt i = 0; i < numColumns_; i++) {
     boosted[i] = overlaps[i] * boostFactors_[i];
   }
@@ -530,8 +529,10 @@ UInt SpatialPooler::initMapColumn_(UInt column) const {
 }
 
 
-vector<UInt> SpatialPooler::initMapPotential_(UInt column, bool wrapAround) {
-  NTA_ASSERT(column < numColumns_);
+void SpatialPooler::initMapPotential_(UInt column, bool wrapAround, SDR& potential) {
+  NTA_CHECK(potential.size == numInputs_);
+  NTA_CHECK(column < numColumns_);
+
   const UInt centerInput = initMapColumn_(column);
 
   vector<UInt> columnInputs;
@@ -547,9 +548,9 @@ vector<UInt> SpatialPooler::initMapPotential_(UInt column, bool wrapAround) {
   }
 
   const UInt numPotential = (UInt)round(columnInputs.size() * potentialPct_);
-  const auto selectedInputs = rng_.sample<UInt>(columnInputs, numPotential);
-  const vector<UInt> potential = VectorHelpers::sparseToBinary<UInt>(selectedInputs, numInputs_);
-  return potential;
+  auto selectedInputs = rng_.sample<UInt>(columnInputs, numPotential);
+  std::sort(selectedInputs.begin(), selectedInputs.end()); 
+  potential.setSparse(selectedInputs);
 }
 
 
@@ -563,14 +564,9 @@ Real SpatialPooler::initPermNonConnected_() {
 }
 
 
-vector<Real> SpatialPooler::initPermanence_(const vector<UInt> &potential, //TODO make potential sparse
-                                            Real connectedPct) {
+const vector<Real> SpatialPooler::initPermanence_(const SDR &potential, const Real connectedPct) {
   vector<Real> perm(numInputs_, 0);
-  for (UInt i = 0; i < numInputs_; i++) {
-    if (potential[i] < 1) {
-      continue;
-    }
-
+  for (const auto i : potential.getSparse()) {
     if (rng_.getReal64() <= connectedPct) {
       perm[i] = initPermConnected_();
     } else {

src/nupic/algorithms/SpatialPooler.hpp

@@ -839,8 +839,10 @@ class SpatialPooler : public Serializable
 
     @param wrapAround  A boolean value indicating that boundaries should be
                        ignored.
+    @param potential  A SDR (sized as input), the return values are written to
+    this field
   */
-  vector<UInt> initMapPotential_(UInt column, bool wrapAround);
+  void initMapPotential_(UInt column, bool wrapAround, SDR& potential);
 
   /**
   Returns a randomly generated permanence value for a synapses that is
@@ -880,7 +882,7 @@ class SpatialPooler : public Serializable
     @param connectedPct   A real value between 0 or 1 specifying the percent of
     the input bits that will start off in a connected state.
   */
-  vector<Real> initPermanence_(const vector<UInt> &potential, Real connectedPct);
+  const vector<Real> initPermanence_(const SDR &potential, const Real connectedPct);
 
   void clip_(vector<Real> &perm) const;
 

src/nupic/regions/TMRegion.cpp

@@ -34,7 +34,6 @@
 #include <nupic/engine/Spec.hpp>
 #include <nupic/ntypes/Array.hpp>
 #include <nupic/utils/Log.hpp>
-#include <nupic/utils/VectorHelpers.hpp>
 
 #define VERSION 1
 

src/test/CMakeLists.txt

@@ -104,7 +104,6 @@ set(utils_tests
 	   unit/utils/GroupByTest.cpp
 	   unit/utils/MovingAverageTest.cpp
 	   unit/utils/RandomTest.cpp
-	   unit/utils/VectorHelpersTest.cpp
 	   unit/utils/SdrMetricsTest.cpp
 	   )
 

src/test/unit/algorithms/SpatialPoolerTest.cpp

@@ -60,7 +60,7 @@ bool almost_eq(Real a, Real b) {
   return (diff > -1e-5 && diff < 1e-5);
 }
 
-bool check_vector_eq(UInt arr[], vector<UInt> vec) {  //TODO replace with ArrayBase, VectorHelpers or teplates
+bool check_vector_eq(UInt arr[], vector<UInt> vec) {  //TODO replace with ArrayBase, or teplates
   for (UInt i = 0; i < vec.size(); i++) {
     if (arr[i] != vec[i]) {
       return false;
@@ -127,6 +127,14 @@ bool check_vector_eq(vector<Real> vec1, vector<Real> vec2) {
   return true;
 }
 
+bool check_vector_eq(UInt arr[], SDR &sdr) {
+  const auto vec = sdr.getSparse();
+  for(UInt i = 0; i < vec.size(); i++) {
+    if(arr[i] != vec[i]) return false;
+  }
+  return true;
+}
+
 void check_spatial_eq(const SpatialPooler& sp1, const SpatialPooler& sp2) {
   UInt numColumns = sp1.getNumColumns();
   UInt numInputs = sp2.getNumInputs();
@@ -1615,39 +1623,39 @@ TEST(SpatialPoolerTest, testinitMapPotential1D) {
   sp.initialize(inputDim, columnDim);
   sp.setPotentialRadius(potentialRadius);
 
-  vector<UInt> mask;
+  SDR mask({sp.getNumInputs()});
 
   // Test without wrapAround and potentialPct = 1
   sp.setPotentialPct(1.0);
 
   UInt expectedMask1[12] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0};
-  mask = sp.initMapPotential_(0, false);
+  sp.initMapPotential_(0, false, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask1, mask));
 
   UInt expectedMask2[12] = {0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0};
-  mask = sp.initMapPotential_(2, false);
+  sp.initMapPotential_(2, false, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask2, mask));
 
   // Test with wrapAround and potentialPct = 1
   sp.setPotentialPct(1.0);
 
   UInt expectedMask3[12] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1};
-  mask = sp.initMapPotential_(0, true);
+  sp.initMapPotential_(0, true, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask3, mask));
 
   UInt expectedMask4[12] = {1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1};
-  mask = sp.initMapPotential_(3, true);
+  sp.initMapPotential_(3, true, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask4, mask));
 
   // Test with potentialPct < 1
   sp.setPotentialPct(0.5);
   UInt supersetMask1[12] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1};
-  mask = sp.initMapPotential_(0, true);
-  ASSERT_TRUE(accumulate(mask.begin(), mask.end(), 0.0f) == 3u);
+  sp.initMapPotential_(0, true, mask);
+  ASSERT_TRUE(mask.getSum() == 3u);
 
   UInt unionMask1[12] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
   for (UInt i = 0; i < 12; i++) {
-    unionMask1[i] = supersetMask1[i] | mask.at(i);
+    unionMask1[i] = supersetMask1[i] | mask.getDense().at(i);
   }
 
   ASSERT_TRUE(check_vector_eq(unionMask1, supersetMask1, 12));
@@ -1667,21 +1675,21 @@ TEST(SpatialPoolerTest, testinitMapPotential2D) {
   sp.setPotentialRadius(potentialRadius);
   sp.setPotentialPct(potentialPct);
 
-  vector<UInt> mask;
+  SDR mask({sp.getNumInputs()});
 
   // Test without wrapAround
   UInt expectedMask1[72] = {
       1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
-  mask = sp.initMapPotential_(0, false);
+  sp.initMapPotential_(0, false, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask1, mask));
 
   UInt expectedMask2[72] = {
       0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
-  mask = sp.initMapPotential_(2, false);
+  sp.initMapPotential_(2, false, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask2, mask));
 
   // Test with wrapAround
@@ -1691,14 +1699,14 @@ TEST(SpatialPoolerTest, testinitMapPotential2D) {
       1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1,
       1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1};
-  mask = sp.initMapPotential_(0, true);
+  sp.initMapPotential_(0, true, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask3, mask));
 
   UInt expectedMask4[72] = {
       1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1,
       1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1,
       0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1};
-  mask = sp.initMapPotential_(3, true);
+  sp.initMapPotential_(3, true, mask);
   ASSERT_TRUE(check_vector_eq(expectedMask4, mask));
 }
 

src/test/unit/regions/TMRegionTest.cpp

@@ -60,7 +60,6 @@
 #include <nupic/os/Timer.hpp>
 #include <nupic/regions/TMRegion.hpp>
 #include <nupic/types/Exception.hpp>
-#include <nupic/utils/VectorHelpers.hpp>
 
 #include <cmath>   // fabs/abs
 #include <cstdlib> // exit
@@ -75,6 +74,8 @@
 #include "yaml-cpp/yaml.h"
 #include "gtest/gtest.h"
 
+namespace testing {
+
 #define VERBOSE if (verbose) std::cerr << "[          ] "
 static bool verbose = false; // turn this on to print extra stuff for debugging the test.
 
@@ -84,7 +85,6 @@ static bool verbose = false; // turn this on to print extra stuff for debugging
 
 using namespace nupic;
 
-namespace testing {
 
 // Verify that all parameters are working.
 // Assumes that the default value in the Spec is the same as the default when
@@ -277,9 +277,9 @@ TEST(TMRegionTest, testLinking) {
       << r3InputArray.getCount();
   EXPECT_TRUE(r3InputArray.getType() == NTA_BasicType_SDR);
   VERBOSE << "   " << r3InputArray << "\n";
-  std::vector<Byte> expected3in = VectorHelpers::sparseToBinary<Byte>(
-    { 1, 2, 3, 5, 6, 8, 11, 13, 17, 19 }, (UInt32)r3InputArray.getCount());
-  EXPECT_TRUE(r3InputArray == expected3in);
+  SDR expectedR3Input({(UInt32)r3InputArray.getCount()});
+  expectedR3Input.setSparse(SDR_sparse_t{ 1, 2, 3, 5, 6, 8, 11, 13, 17, 19 });
+  EXPECT_EQ(r3InputArray.getSDR(), expectedR3Input);
 
   VERBOSE << "  TMRegion output "
           << region3->getOutputDimensions("bottomUpOut") << "\n";
@@ -293,13 +293,13 @@ TEST(TMRegionTest, testLinking) {
       << r3InputArray.getCount();
   EXPECT_TRUE(r3OutputArray.getType() == NTA_BasicType_SDR);
   VERBOSE << "   " << r3OutputArray << "\n";
-  std::vector<Byte> expected3out = VectorHelpers::sparseToBinary<Byte>(
-            { 5u, 6u, 7u, 8u, 9u, 10u, 11u, 12u, 13u, 14u, 15u, 16u, 17u, 18u, 19u,
+  SDR expectedR3Out({(UInt32)r3OutputArray.getCount()});
+  expectedR3Out.setSparse( SDR_sparse_t{ 5u, 6u, 7u, 8u, 9u, 10u, 11u, 12u, 13u, 14u, 15u, 16u, 17u, 18u, 19u,
              25u, 26u, 27u, 28u, 29u, 30u, 31u, 32u, 33u, 34u, 40u, 41u, 42u, 43u,
              44u, 55u, 56u, 57u, 58u, 59u, 65u, 66u, 67u, 68u, 69u, 85u, 86u, 87u,
-             88u, 89u, 95u, 96u, 97u, 98u, 99u }, (UInt32)r3OutputArray.getCount());
-  EXPECT_TRUE(r3OutputArray == expected3out);
-  EXPECT_EQ(r3OutputArray.getSDR().getSparse().size(), 50u);
+             88u, 89u, 95u, 96u, 97u, 98u, 99u });
+  EXPECT_EQ(r3OutputArray.getSDR(), expectedR3Out);
+  EXPECT_EQ(r3OutputArray.getSDR().getSum(), 50u);
 
   // execute TMRegion several more times and check that it has output.
   VERBOSE << "Execute 9 times." << std::endl;
@@ -313,20 +313,20 @@ TEST(TMRegionTest, testLinking) {
       << r3OutputArray.getCount() << ", should be ("
       << numberOfCols << " * " << cellsPerColumn;
   VERBOSE << "   " << r3OutputArray << ")\n";
-  std::vector<Byte> expected3outa = VectorHelpers::sparseToBinary<Byte>(
-            {20u, 21u, 22u, 23u, 24u, 25u, 26u, 27u, 28u, 29u, 35u, 36u, 37u, 38u,
+  expectedR3Out.setSparse(
+            SDR_sparse_t{20u, 21u, 22u, 23u, 24u, 25u, 26u, 27u, 28u, 29u, 35u, 36u, 37u, 38u,
              39u, 45u, 46u, 47u, 48u, 49u, 50u, 51u, 52u, 53u, 54u, 60u, 61u, 62u,
              63u, 64u, 70u, 71u, 72u, 73u, 74u, 80u, 81u, 82u, 83u, 84u, 90u, 91u,
-             92u, 93u, 94u, 95u, 96u, 97u, 98u, 99u}, (UInt32)r3OutputArray.getCount());
-  EXPECT_TRUE(r3OutputArray == expected3outa);
+             92u, 93u, 94u, 95u, 96u, 97u, 98u, 99u});
+  EXPECT_EQ(r3OutputArray, expectedR3Out.getDense());
 
 
   VERBOSE << "   Input to VectorFileEffector "
           << region4->getInputDimensions("dataIn") << "\n";
   Array r4InputArray = region4->getInputData("dataIn");
   EXPECT_TRUE(r4InputArray.getType() == NTA_BasicType_Real32);
   VERBOSE << "   " << r4InputArray << "\n";
-  EXPECT_TRUE(r4InputArray == expected3outa);
+  EXPECT_TRUE(r4InputArray == expectedR3Out.getDense());
 
   // cleanup
   region3->executeCommand({"closeFile"});