Merge remote-tracking branch 'origin/master' into develop

mldrugdiscovery · May 24, 2019 · 16a7209 · 16a7209
2 parents 658214d + 535fa79
commit 16a7209
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Showing 4 changed files with 32 additions and 8 deletions.
diff --git a/similarity_search/apps/report_intr_dim.cc b/similarity_search/apps/report_intr_dim.cc
@@ -75,7 +75,8 @@ void TestSpace(
                 string dataFile,
                 bool compMuDeffect,
                 unsigned maxNumData,
-                unsigned sampleQty
+                unsigned sampleQty,
+                string sampleFile
                ) {
   string          spaceType;
   vector<string>  vSpaceArgs;
@@ -90,9 +91,21 @@ void TestSpace(
   vector<string>  tmp;
   unique_ptr<DataFileInputState> inpState(space->ReadDataset(data, tmp, dataFile, maxNumData));
   space->UpdateParamsFromFile(*inpState);
+  vector<double>  dist;
 
   // Prints the report
-  ReportIntrinsicDimensionality("********", *space, data, sampleQty);
+  ReportIntrinsicDimensionality("********", *space, data, dist, sampleQty);
+  if (!sampleFile.empty()) {
+    ofstream of(sampleFile);
+    CHECK_MSG(of, "Cannot open for writing file: " + sampleFile);
+    of.exceptions ( std::ifstream::failbit | std::ifstream::badbit );
+
+    for (size_t i = 0; i < dist.size(); ++i) {
+      if (i) of << ",";
+      of << dist[i];
+    } 
+    of << std::endl;
+  }
   if (compMuDeffect) {
     double    dleft, dright;
     ComputeMuDeffect<dist_t>(
@@ -108,6 +121,7 @@ void TestSpace(
 int main(int argc, char* argv[]) {
   string    spaceDesc, distType;
   string    dataFile;
+  string    sampleFile;
   unsigned  maxNumData;
   unsigned  sampleQty;
   bool      compMuDeffect;
@@ -126,6 +140,8 @@ int main(int argc, char* argv[]) {
                                &sampleQty, false, defaultSampleQty));
   cmd_options.Add(new CmdParam("muDeffect,m", "estimate the left and the right mu deffectiveness",
                                &compMuDeffect, false, false));
+  cmd_options.Add(new CmdParam("sampleFile", "optional output sample file",
+                               &sampleFile, false, ""));
 
   try {
     cmd_options.Parse(argc, argv);
@@ -143,23 +159,26 @@ int main(int argc, char* argv[]) {
                   dataFile,
                   compMuDeffect,
                   maxNumData,
-                  sampleQty
+                  sampleQty,
+                  sampleFile
                 );
     } else if (DIST_TYPE_FLOAT == distType) {
       TestSpace<float>(
                   spaceDesc,
                   dataFile,
                   compMuDeffect,
                   maxNumData,
-                  sampleQty
+                  sampleQty,
+                  sampleFile
                  );
     } else if (DIST_TYPE_DOUBLE == distType) {
       TestSpace<double>(
                   spaceDesc,
                   dataFile,
                   compMuDeffect,
                   maxNumData,
-                  sampleQty
+                  sampleQty,
+                  sampleFile
                  );
     }
 

diff --git a/similarity_search/include/report_intr_dim.h b/similarity_search/include/report_intr_dim.h
@@ -33,9 +33,10 @@ void ComputeIntrinsicDimensionality(const Space<dist_t>& space,
                                double& IntrDim,
                                double& DistMean,
                                double& DistSigma,
+                               std::vector<double>& dist,
                                size_t SampleQty = 1000000) {
-  std::vector<double> dist;
   DistMean = 0;
+  dist.clear();
   for (size_t n = 0; n < SampleQty; ++n) {
     size_t r1 = RandomInt() % dataset.size();
     size_t r2 = RandomInt() % dataset.size();
@@ -70,13 +71,15 @@ template <typename dist_t>
 void ReportIntrinsicDimensionality(const string& reportName,
                                    const Space<dist_t>& space, 
                                    const ObjectVector& dataset,
+                                   std::vector<double>& dist,
                                    size_t SampleQty = 1000000) {
     double DistMean, DistSigma, IntrDim;
 
     ComputeIntrinsicDimensionality(space, dataset,
                                   IntrDim,
                                   DistMean,
                                   DistSigma,
+                                  dist,
                                   SampleQty);
 
     LOG(LIB_INFO) << "### " << reportName;

diff --git a/similarity_search/src/method/perm_bin_vptree.cc b/similarity_search/src/method/perm_bin_vptree.cc
@@ -72,7 +72,8 @@ void PermBinVPTree<dist_t, RankCorrelDistFunc>::CreateIndex(const AnyParams& Ind
     BinPermData_[i] = VPTreeSpace_->CreateObjFromVect(i, -1, binPivot);
   }
 
-  ReportIntrinsicDimensionality("Set of permutations" , *VPTreeSpace_, BinPermData_);
+  vector<double> dist;
+  ReportIntrinsicDimensionality("Set of permutations" , *VPTreeSpace_, BinPermData_, dist);
   VPTreeIndex_.reset(new VPTree<int, PolynomialPruner<int>>(
                                           PrintProgress_,
                                           *VPTreeSpace_,

diff --git a/similarity_search/src/method/proj_vptree.cc b/similarity_search/src/method/proj_vptree.cc
@@ -167,7 +167,8 @@ void ProjectionVPTree<dist_t>::CreateIndex(const AnyParams& IndexParams) {
     projData_[id] = ProjectOneVect(id, NULL, this->data_[id]);
   }
 
-  ReportIntrinsicDimensionality("Set of projections" , *VPTreeSpace_, projData_);
+  vector<double> dist;
+  ReportIntrinsicDimensionality("Set of projections" , *VPTreeSpace_, projData_, dist);
 
   VPTreeIndex_.reset(new VPTree<float, PolynomialPruner<float>>(
                                           PrintProgress_,