From 0eed6442421f841d2bbb483dafc9f6f8c4437073 Mon Sep 17 00:00:00 2001
From: Sergey Lisitsyn <lisitsyn@hey.com>
Date: Mon, 6 May 2024 17:22:01 +0100
Subject: [PATCH] Add empty implementation for UMAP

---
 include/tapkee/defines/methods.hpp |  3 +++
 include/tapkee/methods.hpp         |  1 +
 include/tapkee/methods/all.hpp     |  1 +
 include/tapkee/methods/umap.hpp    | 25 +++++++++++++++++++++++++
 src/cli/main.cpp                   |  2 +-
 src/cli/util.hpp                   |  2 ++
 test/unit/methods.cpp              |  5 +++++
 7 files changed, 38 insertions(+), 1 deletion(-)
 create mode 100644 include/tapkee/methods/umap.hpp

diff --git a/include/tapkee/defines/methods.hpp b/include/tapkee/defines/methods.hpp
index 90382cc..04feeab 100644
--- a/include/tapkee/defines/methods.hpp
+++ b/include/tapkee/defines/methods.hpp
@@ -136,6 +136,9 @@ static const DimensionReductionMethod tDistributedStochasticNeighborEmbedding("t
  * @cite Gashler2007 */
 static const DimensionReductionMethod ManifoldSculpting("Manifold Sculpting", RequiresFeatures);
 
+/** Uniform Manifold Approximation and Projection (UMAP) */
+static const DimensionReductionMethod UniformManifoldApproximationAndProjection("Uniform Manifold Approximation and Projection", RequiresFeatures);
+
 /** Passing through (doing nothing just passes the
  * data through) */
 static const DimensionReductionMethod PassThru("Pass-through", RequiresFeatures);
diff --git a/include/tapkee/methods.hpp b/include/tapkee/methods.hpp
index 4d2cd93..c150d78 100644
--- a/include/tapkee/methods.hpp
+++ b/include/tapkee/methods.hpp
@@ -70,6 +70,7 @@ class DynamicImplementation : public ImplementationBase<RandomAccessIterator, Ke
         tapkee_method_handle(FactorAnalysis);
         tapkee_method_handle(tDistributedStochasticNeighborEmbedding);
         tapkee_method_handle(ManifoldSculpting);
+        tapkee_method_handle(UniformManifoldApproximationAndProjection);
 #undef tapkee_method_handle
         return TapkeeOutput();
     }
diff --git a/include/tapkee/methods/all.hpp b/include/tapkee/methods/all.hpp
index c19bc25..dcbbc57 100644
--- a/include/tapkee/methods/all.hpp
+++ b/include/tapkee/methods/all.hpp
@@ -25,6 +25,7 @@
 #include <tapkee/methods/factor_analysis.hpp>
 #include <tapkee/methods/manifold_sculpting.hpp>
 #include <tapkee/methods/tsne.hpp>
+#include <tapkee/methods/umap.hpp>
 /* End of Tapkee includes */
 
 namespace tapkee
diff --git a/include/tapkee/methods/umap.hpp b/include/tapkee/methods/umap.hpp
new file mode 100644
index 0000000..78c1379
--- /dev/null
+++ b/include/tapkee/methods/umap.hpp
@@ -0,0 +1,25 @@
+/* This software is distributed under BSD 3-clause license (see LICENSE file).
+ *
+ * Copyright (c) 2024 Sergey Lisitsyn, Fernando Iglesias
+ */
+#pragma once
+
+/* Tapkee includes */
+#include <tapkee/methods/base.hpp>
+/* End of Tapkee includes */
+
+namespace tapkee
+{
+namespace tapkee_internal
+{
+
+__TAPKEE_IMPLEMENTATION(UniformManifoldApproximationAndProjection)
+    TapkeeOutput embed()
+    {
+        DenseMatrix feature_matrix{this->end - this->begin, static_cast<IndexType>(this->parameters[target_dimension])};
+        return TapkeeOutput(feature_matrix, unimplementedProjectingFunction());
+    }
+__TAPKEE_END_IMPLEMENTATION()
+
+} // End of namespace tapkee_internal
+} // End of namespace tapkee
diff --git a/src/cli/main.cpp b/src/cli/main.cpp
index b22919d..a6cbe7e 100644
--- a/src/cli/main.cpp
+++ b/src/cli/main.cpp
@@ -146,7 +146,7 @@ int run(int argc, const char **argv)
      "diffusion_map (dm), isomap, landmark_isomap (l-isomap), multidimensional_scaling (mds), \n"
      "landmark_multidimensional_scaling (l-mds), stochastic_proximity_embedding (spe), \n"
      "kernel_pca (kpca), pca, random_projection (ra), factor_analysis (fa), \n"
-     "t-stochastic_neighborhood_embedding (t-sne), manifold_sculpting (ms).",
+     "t-stochastic_neighborhood_embedding (t-sne), manifold_sculpting (ms), umap.",
      with_default("locally_linear_embedding"s)
     )
     (
diff --git a/src/cli/util.hpp b/src/cli/util.hpp
index 43e70d1..ec1c300 100644
--- a/src/cli/util.hpp
+++ b/src/cli/util.hpp
@@ -137,6 +137,8 @@ tapkee::DimensionReductionMethod parse_reduction_method(const char* str)
         return tapkee::tDistributedStochasticNeighborEmbedding;
     if (!strcmp(str, "manifold_sculpting") || !strcmp(str, "ms"))
         return tapkee::ManifoldSculpting;
+    if (!strcmp(str, "umap"))
+        return tapkee::UniformManifoldApproximationAndProjection;
 
     throw std::exception();
     return tapkee::PassThru;
diff --git a/test/unit/methods.cpp b/test/unit/methods.cpp
index a7e5af2..fa390d9 100644
--- a/test/unit/methods.cpp
+++ b/test/unit/methods.cpp
@@ -120,3 +120,8 @@ TEST(Methods, tDistributedStochasticNeighborEmbeddingSmokeTest)
 {
     smoketest(tDistributedStochasticNeighborEmbedding);
 }
+
+TEST(Methods, UniformManifoldApproximationAndProjection)
+{
+    smoketest(UniformManifoldApproximationAndProjection);
+}