Features/kshape (#25)

avilchess · web-flow · commit 7c9c4545ec13 · 2019-03-06T21:07:20.000+01:00
* Adding Khiva and updating copyright year to 2019

* Adding Clustering module.

* Add tests for Clustering

* Fix tests.

* Testing CI
diff --git a/.CI/travis/build-and-test.sh b/.CI/travis/build-and-test.sh
@@ -1,9 +1,9 @@
 #!/bin/bash
-# Copyright (c) 2018 Shapelets.io
+# Copyright (c) 2019 Shapelets.io
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
 # file, You can obtain one at http://mozilla.org/MPL/2.0/.
 
 mvn javadoc:javadoc
-mvn test
+mvn test
diff --git a/.CI/travis/install-arrayfire.sh b/.CI/travis/install-arrayfire.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Copyright (c) 2018 Shapelets.io
+# Copyright (c) 2019 Shapelets.io
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/.CI/travis/install-java.sh b/.CI/travis/install-java.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Copyright (c) 2018 Shapelets.io
+# Copyright (c) 2019 Shapelets.io
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/.CI/travis/install-khiva.sh b/.CI/travis/install-khiva.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Copyright (c) 2018 Shapelets.io
+# Copyright (c) 2019 Shapelets.io
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/.appveyor.yml b/.appveyor.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2018 Shapelets.io
+# Copyright (c) 2019 Shapelets.io
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md
@@ -90,4 +90,4 @@ If some members of staff were angered by the incident, it is best to apologise t
 
 ## Attribution
 
-This Code of Conduct was adapted from both [Golang](https://golang.org/conduct) an the [Golang UK Conference](http://golanguk.com/conduct/).
+This Code of Conduct was adapted from both [Golang](https://golang.org/conduct) an the [Golang UK Conference](http://golanguk.com/conduct/).
diff --git a/.travis.yml b/.travis.yml
@@ -1,4 +1,4 @@
-# Copyright (c) 2018 Shapelets.io
+# Copyright (c) 2019 Shapelets.io
 #
 # This Source Code Form is subject to the terms of the Mozilla Public
 # License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -80,4 +80,4 @@ Start a new docker container.
 ```
 # Start docker
 docker run --rm -ti shapelets/khiva-java
-```
+```
diff --git a/README.md b/README.md
@@ -44,4 +44,4 @@ mvn javadoc:javadoc
 ## Contributing
 The rules to contribute to this project are described [here](CONTRIBUTING.md)
 
-[![Powered by Shapelets](https://img.shields.io/badge/powered%20by-Shapelets-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://shapelets.io)
+[![Powered by Shapelets](https://img.shields.io/badge/powered%20by-Shapelets-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://shapelets.io)
diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
     </properties>
     <groupId>io.shapelets</groupId>
     <artifactId>khiva</artifactId>
-    <version>0.1.1</version>
+    <version>0.2.0</version>
 
     <name>khiva-java</name>
     <url>https://github.com/shapelets/khiva-java</url>
diff --git a/src/main/java/io/shapelets/khiva/Array.java b/src/main/java/io/shapelets/khiva/Array.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Clustering.java b/src/main/java/io/shapelets/khiva/Clustering.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright (c) 2019 Shapelets.io
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ */
+
+package io.shapelets.khiva;
+
+/**
+ * Khiva Clustering class containing several clustering methods.
+ */
+public class Clustering extends Library{
+
+    private native static long[] kMeans(long tss, int k, float tolerance, int maxIterations);
+
+    private native static long[] kShape(long tss, int k, float tolerance, int maxIterations);
+
+    /**
+     * Calculates the KMeans algorithm.
+     *
+     * [1] S. Lloyd. 1982. Least squares quantization in PCM. IEEE Transactions on Information Theory, 28, 2,
+     * Pages 129-137.
+     *
+     * @param tss               The set of time series to be clusterized.
+     * @param k                 The number of centroids.
+     * @param tolerance         The maximum error tolerance.
+     * @param maxIterations     The maximum number of iterations.
+     * @return An Array of arrays with the resulting centroids and labels.
+     */
+    public static Array[] kMeans(Array tss, int k, float tolerance, int maxIterations) {
+        long[] refs = kMeans(tss.getReference(), k, tolerance, maxIterations);
+        tss.setReference(refs[0]);
+        Array[] result = {new Array(refs[1]), new Array(refs[2])};
+        return result;
+    }
+
+    /**
+     * Calculates the KShape algorithm.
+     *
+     * [1] John Paparrizos and Luis Gravano. 2016. k-Shape: Efficient and Accurate Clustering of Time Series.
+     * SIGMOD Rec. 45, 1 (June 2016), 69-76.
+     *
+     * @param tss               The set of time series to be clusterized.
+     * @param k                 The number of centroids.
+     * @param tolerance         The maximum error tolerance.
+     * @param maxIterations     The maximum number of iterations.
+     * @return An Array of arrays with the resulting centroids and labels.
+     */
+    public static Array[] kShape(Array tss, int k, float tolerance, int maxIterations) {
+        long[] refs = kShape(tss.getReference(), k, tolerance, maxIterations);
+        tss.setReference(refs[0]);
+        Array[] result = {new Array(refs[1]), new Array(refs[2])};
+        return result;
+    }
+}
diff --git a/src/main/java/io/shapelets/khiva/Dimensionality.java b/src/main/java/io/shapelets/khiva/Dimensionality.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Distances.java b/src/main/java/io/shapelets/khiva/Distances.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/DoubleComplex.java b/src/main/java/io/shapelets/khiva/DoubleComplex.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -100,4 +100,4 @@ public boolean equals(Object obj) {
         }
         return dc != null && this.real == dc.real && this.imag == dc.imag;
     }
-}
+}
diff --git a/src/main/java/io/shapelets/khiva/Features.java b/src/main/java/io/shapelets/khiva/Features.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/FloatComplex.java b/src/main/java/io/shapelets/khiva/FloatComplex.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -100,4 +100,4 @@ public boolean equals(Object obj) {
         }
         return fc != null && this.real == fc.real && this.imag == fc.imag;
     }
-}
+}
diff --git a/src/main/java/io/shapelets/khiva/Library.java b/src/main/java/io/shapelets/khiva/Library.java
@@ -1,6 +1,6 @@
 
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -178,4 +178,4 @@ public static int getKhivaDeviceCount() {
      * @return A string with the khiva version.
      */
     public static String getKhivaVersion() { return version(); }
-}
+}
diff --git a/src/main/java/io/shapelets/khiva/Linalg.java b/src/main/java/io/shapelets/khiva/Linalg.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Matrix.java b/src/main/java/io/shapelets/khiva/Matrix.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Normalization.java b/src/main/java/io/shapelets/khiva/Normalization.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Polynomial.java b/src/main/java/io/shapelets/khiva/Polynomial.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Regression.java b/src/main/java/io/shapelets/khiva/Regression.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Regularization.java b/src/main/java/io/shapelets/khiva/Regularization.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/main/java/io/shapelets/khiva/Statistics.java b/src/main/java/io/shapelets/khiva/Statistics.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/test/java/io/shapelets/khiva/ArrayTest.java b/src/test/java/io/shapelets/khiva/ArrayTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
diff --git a/src/test/java/io/shapelets/khiva/ClusteringTest.java b/src/test/java/io/shapelets/khiva/ClusteringTest.java
@@ -0,0 +1,76 @@
+/*
+ * Copyright (c) 2019 Shapelets.io
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ */
+
+package io.shapelets.khiva;
+
+import org.junit.Assert;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+public class ClusteringTest {
+
+    @BeforeClass
+    public static void setUp() {
+        Library.setKhivaBackend(Library.Backend.KHIVA_BACKEND_CPU);
+    }
+
+    @Test
+    public void testKMeans() throws Exception {
+        float[] tss = {0.0f, 1.0f, 2.0f, 3.0f, 6.0f, 7.0f,  8.0f, 9.0f, 2.0f, -2.0f, 4.0f, -4.0f,
+                8.0f, 5.0f,  3.0f, 1.0f, 15.0f, 10.0f, 5.0f, 0.0f, 7.0f, -7.0f,  1.0f, -1.0f};
+        long[] dims = {4, 6, 1, 1};
+
+        float[] expected = {0.0f, 0.1667f, 0.3333f, 0.5f,
+                            1.5f, -1.5f, 0.8333f, -0.8333f,
+                            4.8333f, 3.6667f, 2.6667f, 1.6667f};
+
+        float tolerance = 1e-10f;
+        int maxIterations = 100;
+        int k = 3;
+        try (
+                Array a = new Array(tss, dims)
+        ){
+            Array[] result = Clustering.kMeans(a, k, tolerance, maxIterations);
+            float[] centroids = result[0].getData();
+
+            for (int i = 0; i < 4; i++){
+                Assert.assertEquals(expected[i] + expected[i + 4] + expected[i + 8],
+                        centroids[i] + centroids[i + 4] + centroids[i + 8], 1e-4f);
+            }
+        }
+    }
+
+    @Test
+    public void testKShape() throws Exception {
+        float[] tss = {1.0f,  2.0f,  3.0f,  4.0f,  5.0f,   6.0f,  7.0f,  0.0f, 10.0f, 4.0f, 5.0f, 7.0f,
+                -3.0f, 0.0f,  -1.0f, 15.0f, -12.0f, 8.0f,  9.0f,  4.0f, 5.0f,  2.0f, 8.0f, 7.0f,
+                -6.0f, -1.0f, 2.0f,  9.0f,  -5.0f,  -5.0f, -6.0f, 7.0f, 9.0f,  9.0f, 0.0f};
+        long[] dims = {7, 5, 1, 1};
+
+        float[] expected_c = {-0.5234f, 0.1560f, -0.3627f, -1.2764f, -0.7781f,  0.9135f,  1.8711f,
+                -0.7825f, 1.5990f,  0.1701f,  0.4082f,  0.8845f, -1.4969f, -0.7825f,
+                -0.6278f, 1.3812f, -2.0090f,  0.5022f,  0.6278f, -0.0000f,  0.1256f};
+
+
+        float tolerance = 1e-10f;
+        int maxIterations = 100;
+        int k = 3;
+        try (
+                Array a = new Array(tss, dims)
+        ){
+            Array[] result = Clustering.kShape(a, k, tolerance, maxIterations);
+            float[] centroids = result[0].getData();
+
+            for (int i = 0; i < centroids.length; i++){
+                Assert.assertEquals(expected_c[i], centroids[i],1e-4f);
+            }
+        }
+
+    }
+}
diff --git a/src/test/java/io/shapelets/khiva/DimensionalityTest.java b/src/test/java/io/shapelets/khiva/DimensionalityTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -37,15 +37,15 @@ public void testRamerDouglasPeucker() throws Exception {
 
     @Test
     public void testVisvalingam() throws Exception {
-        float[] tss = {0f, 1f, 2f, 3f, 4f, 5f, 6f, 7f, 8f, 9f, 0f, 0.1f,
-                -0.1f, 5.0f, 6.0f, 7.0f, 8.1f, 9.0f, 9.0f, 9.0f};
+        float[] tss = {0f, 1f, 2f, 3f, 4f, 5f, 6f, 7f, 8f, 9f,
+                       0f, 0.1f,-0.1f, 5.0f, 6.0f, 7.0f, 8.1f, 9.0f, 9.0f, 9.0f};
         long[] dims = {10, 2, 1, 1};
         try (
                 Array a = new Array(tss, dims);
                 Array b = Dimensionality.visvalingam(a, 5)
         ) {
             float[] result = b.getData();
-            float[] expected = {0f, 2f, 5f, 7f, 9f, 0f, -0.1f, 7.0f, 9.0f, 9.0f};
+            float[] expected = {0f, 2f, 3f, 7f, 9f, 0f, -0.1f, 5.0f, 9.0f, 9.0f};
             Assert.assertArrayEquals(result, expected, 1e-6f);
         }
 
@@ -68,15 +68,15 @@ public void testPaa() throws Exception {
 
     @Test
     public void testSax() throws Exception {
-        float[] tss = {0.05f, 2.45f, 6.5f, 8.55f, 9.0f, 0.05f, 2.45f, 6.5f, 8.55f, 9.0f};
+        float[] tss = {0.0f, 0.1f, -0.1f, 5.0f, 6.0f, 7.0f, 8.1f, 9.0f, 9.0f, 9.0f};
         long[] dims = {5, 2, 1, 1};
         try (
                 Array a = new Array(tss, dims);
                 Array b = Dimensionality.sax(a, 3)
         ) {
-            int[] result = b.getData();
-            int[] expected = {0, 0, 1, 2, 2, 0, 0, 1, 2, 2};
-            Assert.assertArrayEquals(result, expected);
+            float[] result = b.getData();
+            float[] expected = {0.0f, 0.1f, -0.1f, 5.0f, 6.0f, 0.0f, 1.0f, 2.0f, 2.0f, 2.0f};
+            Assert.assertArrayEquals(result, expected, 1e-4f);
         }
     }
 
diff --git a/src/test/java/io/shapelets/khiva/DistancesTest.java b/src/test/java/io/shapelets/khiva/DistancesTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2018 Shapelets.io
+ * Copyright (c) 2019 Shapelets.io
  *
  * This Source Code Form is subject to the terms of the Mozilla Public
  * License, v. 2.0. If a copy of the MPL was not distributed with this
@@ -131,4 +131,4 @@ public void testSquaredEuclidean() throws Exception {
             Assert.assertEquals(result[8], 0, DELTA);
         }
     }
-}
+}
diff --git a/src/test/java/io/shapelets/khiva/DoubleComplexTest.java b/src/test/java/io/shapelets/khiva/DoubleComplexTest.java
diff --git a/src/test/java/io/shapelets/khiva/FeaturesTest.java b/src/test/java/io/shapelets/khiva/FeaturesTest.java
diff --git a/src/test/java/io/shapelets/khiva/FloatComplexTest.java b/src/test/java/io/shapelets/khiva/FloatComplexTest.java
diff --git a/src/test/java/io/shapelets/khiva/LibraryTest.java b/src/test/java/io/shapelets/khiva/LibraryTest.java
diff --git a/src/test/java/io/shapelets/khiva/LinalgTest.java b/src/test/java/io/shapelets/khiva/LinalgTest.java
diff --git a/src/test/java/io/shapelets/khiva/MatrixTest.java b/src/test/java/io/shapelets/khiva/MatrixTest.java
diff --git a/src/test/java/io/shapelets/khiva/NormalizationTest.java b/src/test/java/io/shapelets/khiva/NormalizationTest.java
diff --git a/src/test/java/io/shapelets/khiva/PolynomialTest.java b/src/test/java/io/shapelets/khiva/PolynomialTest.java
diff --git a/src/test/java/io/shapelets/khiva/RegressionTest.java b/src/test/java/io/shapelets/khiva/RegressionTest.java
diff --git a/src/test/java/io/shapelets/khiva/RegularizationTest.java b/src/test/java/io/shapelets/khiva/RegularizationTest.java
diff --git a/src/test/java/io/shapelets/khiva/StatisticsTest.java b/src/test/java/io/shapelets/khiva/StatisticsTest.java

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`#!/bin/bash`
`2`		`-# Copyright (c) 2018 Shapelets.io`
	`2`	`+# Copyright (c) 2019 Shapelets.io`
`3`	`3`	`#`
`4`	`4`	`# This Source Code Form is subject to the terms of the Mozilla Public`
`5`	`5`	`# License, v. 2.0. If a copy of the MPL was not distributed with this`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# Copyright (c) 2018 Shapelets.io`
	`1`	`+# Copyright (c) 2019 Shapelets.io`
`2`	`2`	`#`
`3`	`3`	`# This Source Code Form is subject to the terms of the Mozilla Public`
`4`	`4`	`# License, v. 2.0. If a copy of the MPL was not distributed with this`
Original file line number	Diff line number	Diff line change
`@@ -90,4 +90,4 @@ If some members of staff were angered by the incident, it is best to apologise t`
`90`	`90`
`91`	`91`	`## Attribution`
`92`	`92`
`93`		`-This Code of Conduct was adapted from both [Golang](https://golang.org/conduct) an the [Golang UK Conference](http://golanguk.com/conduct/).`
	`93`	`+This Code of Conduct was adapted from both [Golang](https://golang.org/conduct) an the [Golang UK Conference](http://golanguk.com/conduct/).`