Merge pull request #78 from benjamin-james/master

Added dot product from Annoy c++ source

ChangeLog

@@ -1,3 +1,11 @@
+2024-08-03  Benjamin James <[email protected]>
+
+        * R/annoy.R: Add AnnoyDotProduct to namespace
+	* inst/tinytest/testDotProduct.R: Unit tests for 'AnnoyDotProduct'
+
+	* src/init.c: Added new dot product distance measure (via template)
+	* src/annoy.cpp: Added template and module for AnnoyDotProduct
+
 2024-05-20  Dirk Eddelbuettel  <[email protected]>
 
 	* README.md: Use tinyverse.netlify.app for dependency badge

R/annoy.R

@@ -193,3 +193,4 @@ loadModule("AnnoyAngular", TRUE)
 loadModule("AnnoyEuclidean", TRUE)
 loadModule("AnnoyManhattan", TRUE)
 loadModule("AnnoyHamming", TRUE)
+loadModule("AnnoyDotProduct", TRUE)

inst/tinytest/testDotProduct.R

@@ -0,0 +1,76 @@
+
+suppressMessages(library(RcppAnnoy))
+
+f <- 3
+a <- new(AnnoyDotProduct, f)
+a$addItem(0, c(0,0,1))
+a$addItem(1, c(0,1,0))
+a$addItem(2, c(1,0,0))
+a$build(10)
+checkEqual(a$getNNsByVector(c(3,2,1), 3), c(2,1,0), msg="getNNsByVector check 1")
+checkEqual(a$getNNsByVector(c(1,2,3), 3), c(0,1,2), msg="getNNsByVector check 1")
+checkEqual(a$getNNsByVector(c(2,0,1), 3), c(2,0,1), msg="getNNsByVector check 1")
+
+
+f <- 3
+a <- new(AnnoyDotProduct, f)
+a$addItem(0, c(2,1,0))
+a$addItem(1, c(1,2,0))
+a$addItem(2, c(0,0,1))
+a$build(10)
+checkEqual(a$getNNsByItem(0, 3), c(0,1,2), msg="getNNsByItem check1")
+checkEqual(a$getNNsByItem(1, 3), c(1,0,2), msg="getNNsByItem check2")
+
+
+f <- 2
+a <- new(AnnoyDotProduct, f)
+a$addItem(0, c(0, 1))
+a$addItem(1, c(1, 1))
+checkEqual(a$getDistance(0, 1), 0 * 1 + 1 * 1, msg="distance 1", tolerance=1e-6)
+
+
+f <- 2
+a <- new(AnnoyDotProduct, f)
+a$addItem(0, c(1000, 0))
+a$addItem(1, c(10, 0))
+checkEqual(a$getDistance(0, 1), 1000 * 10 + 0 * 0, msg="distance 2", tolerance=1e-6)
+
+
+f <- 2
+a <- new(AnnoyDotProduct, f)
+a$addItem(0, c(97, 0))
+a$addItem(1, c(42, 42))
+d <- 97 * 42 + 0 * 42
+checkEqual(a$getDistance(0, 1), d, msg="distance 3", tolerance=1.0e-6)
+
+
+f <- 2
+a <- new(AnnoyDotProduct, f)
+a$addItem(0, c(1, 0))
+a$addItem(1, c(0, 0))
+checkEqual(a$getDistance(0, 1), 0, msg="distance 4", tolerance=1.0e-6)
+
+
+## Generate pairs of random points where the pair is super close
+f <- 10
+a <- new(AnnoyDotProduct, f)
+set.seed(123)
+for (j in seq(0, 10000, by=2)) {
+    p <- rnorm(f)
+    f1 <- runif(1) + 1
+    f2 <- runif(1) + 1
+    x <- f1 * p + rnorm(f, 0, 1.0e-2)
+    y <- f2 * p + rnorm(f, 0, 1.0e-2)
+    a$addItem(j, x / norm(x, "2"))
+    a$addItem(j+1, y/norm(y, "2"))
+}
+a$build(10)
+res <- TRUE
+for (j in seq(0, 10000, by=2)) {
+    #expect_equal(a$getNNsByItem(j,   2), c(j,   j+1), msg="getNNsByItem check1")
+    #expect_equal(a$getNNsByItem(j+1, 2), c(j+1, j),   msg="getNNsByItem check1")
+    res <- res &&
+        all.equal(a$getNNsByItem(j,   2), c(j,   j+1)) &&
+        all.equal(a$getNNsByItem(j+1, 2), c(j+1, j))
+}
+checkTrue(res)

src/annoy.cpp

@@ -121,11 +121,42 @@ class Annoy
 
 }
 
+typedef Annoy::Annoy<int32_t, float,    Annoy::DotProduct,Kiss64Random, RcppAnnoyIndexThreadPolicy> AnnoyDotProduct;
 typedef Annoy::Annoy<int32_t, float,    Annoy::Angular,   Kiss64Random, RcppAnnoyIndexThreadPolicy> AnnoyAngular;
 typedef Annoy::Annoy<int32_t, float,    Annoy::Euclidean, Kiss64Random, RcppAnnoyIndexThreadPolicy> AnnoyEuclidean;
 typedef Annoy::Annoy<int32_t, float,    Annoy::Manhattan, Kiss64Random, RcppAnnoyIndexThreadPolicy> AnnoyManhattan;
 typedef Annoy::Annoy<int32_t, uint64_t, Annoy::Hamming,   Kiss64Random, RcppAnnoyIndexThreadPolicy> AnnoyHamming;
 
+RCPP_EXPOSED_CLASS_NODECL(AnnoyDotProduct)
+RCPP_MODULE(AnnoyDotProduct) {
+    Rcpp::class_<AnnoyDotProduct>("AnnoyDotProduct")
+
+        .constructor<int32_t>("constructor with integer count")
+
+        .method("addItem",        &AnnoyDotProduct::addItem,         "add item")
+        .method("build",          &AnnoyDotProduct::callBuild,       "build an index")
+        .method("unbuild",        &AnnoyDotProduct::callUnbuild,     "unbuild an index")
+        .method("save",           &AnnoyDotProduct::callSave,        "save index to file")
+        .method("load",           &AnnoyDotProduct::callLoad,        "load index from file")
+        .method("unload",         &AnnoyDotProduct::callUnload,      "unload index")
+        .method("getDistance",    &AnnoyDotProduct::getDistance,     "get distance between i and j")
+        .method("getNNsByItem",   &AnnoyDotProduct::getNNsByItem,
+                "retrieve Nearest Neigbours given item")
+        .method("getNNsByItemList",  &AnnoyDotProduct::getNNsByItemList,
+                "retrieve Nearest Neigbours given item")
+        .method("getNNsByVector", &AnnoyDotProduct::getNNsByVector,
+                "retrieve Nearest Neigbours given vector")
+        .method("getNNsByVectorList",  &AnnoyDotProduct::getNNsByVectorList,
+                "retrieve Nearest Neigbours given vector")
+        .method("getItemsVector", &AnnoyDotProduct::getItemsVector,  "retrieve item vector")
+        .method("getNItems",      &AnnoyDotProduct::getNItems,       "get number of items")
+        .method("getNTrees",      &AnnoyDotProduct::getNTrees,       "get number of trees")
+        .method("setVerbose",     &AnnoyDotProduct::verbose,         "set verbose")
+        .method("setSeed",        &AnnoyDotProduct::setSeed,         "set seed")
+        .method("onDiskBuild",    &AnnoyDotProduct::onDiskBuild,     "build in given file")
+        ;
+}
+
 RCPP_EXPOSED_CLASS_NODECL(AnnoyAngular)
 RCPP_MODULE(AnnoyAngular) {
     Rcpp::class_<AnnoyAngular>("AnnoyAngular")

src/init.c

@@ -8,6 +8,7 @@
 */
 
 /* .Call calls */
+extern SEXP _rcpp_module_boot_AnnoyDotProduct(void);
 extern SEXP _rcpp_module_boot_AnnoyAngular(void);
 extern SEXP _rcpp_module_boot_AnnoyEuclidean(void);
 extern SEXP _rcpp_module_boot_AnnoyManhattan(void);
@@ -16,6 +17,7 @@ extern SEXP _RcppAnnoy_getArchictectureStatus(void);
 extern SEXP _RcppAnnoy_annoy_version(void);
 
 static const R_CallMethodDef CallEntries[] = {
+    {"_rcpp_module_boot_AnnoyDotProduct",(DL_FUNC) &_rcpp_module_boot_AnnoyDotProduct,0},
     {"_rcpp_module_boot_AnnoyAngular",   (DL_FUNC) &_rcpp_module_boot_AnnoyAngular,   0},
     {"_rcpp_module_boot_AnnoyEuclidean", (DL_FUNC) &_rcpp_module_boot_AnnoyEuclidean, 0},
     {"_rcpp_module_boot_AnnoyManhattan", (DL_FUNC) &_rcpp_module_boot_AnnoyManhattan, 0},