From e8def844cae3dbb0e0a93f5b08074fb55e51b4d6 Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Tue, 30 Apr 2024 17:18:16 +0200
Subject: [PATCH] Add test for TrackMateWrapper

---
 pom.xml                                       |   6 +-
 .../java/ch/fmi/TrackMateWrapperTest.java     | 100 ++++++++++++++++++
 2 files changed, 105 insertions(+), 1 deletion(-)
 create mode 100644 src/test/java/ch/fmi/TrackMateWrapperTest.java

diff --git a/pom.xml b/pom.xml
index f9f936a..fa5986b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 
 	<parent>
@@ -108,6 +108,10 @@
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-roi</artifactId>
 		</dependency>
+		<dependency>
+			<groupId>net.imglib2</groupId>
+			<artifactId>imglib2-ij</artifactId>
+		</dependency>
 		<dependency>
 			<groupId>sc.fiji</groupId>
 			<artifactId>AnalyzeSkeleton_</artifactId>
diff --git a/src/test/java/ch/fmi/TrackMateWrapperTest.java b/src/test/java/ch/fmi/TrackMateWrapperTest.java
new file mode 100644
index 0000000..84f0f9d
--- /dev/null
+++ b/src/test/java/ch/fmi/TrackMateWrapperTest.java
@@ -0,0 +1,100 @@
+
+package ch.fmi;
+
+import static org.junit.Assert.assertArrayEquals;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.concurrent.ExecutionException;
+
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.array.ArrayImgs;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.scijava.Context;
+import org.scijava.command.CommandModule;
+import org.scijava.command.CommandService;
+
+import ij.ImagePlus;
+
+public class TrackMateWrapperTest {
+
+	private Context context;
+
+	@Before
+	public void initialize() {
+		context = new Context();
+	}
+
+	@After
+	public void disposeContext() {
+		if (context != null) {
+			context.dispose();
+			context = null;
+		}
+	}
+
+	@Test
+	public void testTrackMate() throws InterruptedException, ExecutionException {
+		CommandService commandService = context.getService(CommandService.class);
+
+		// Prepare
+		RandomAccessibleInterval<UnsignedByteType> img = ArrayImgs.unsignedBytes(16,
+			16, 1, 1, 5);
+		img.getAt(5, 7, 0, 0, 0).setReal(192);
+		img.getAt(5, 6, 0, 0, 1).setReal(186);
+		img.getAt(6, 6, 0, 0, 2).setReal(180);
+		img.getAt(6, 7, 0, 0, 3).setReal(174);
+		img.getAt(5, 7, 0, 0, 4).setReal(168);
+		ImagePlus imp = ImageJFunctions.wrapUnsignedByte(img, "Test Image");
+		assertNotNull(imp);
+		Map<String, Object> inputMap = new HashMap<>();
+		inputMap.put("imp", imp);
+		inputMap.put("frameInterval", 0.5);
+
+		// Run TrackMateWrapper
+		CommandModule module = commandService.run(TrackMateWrapper.class, false,
+			inputMap).get();
+
+		// Compare
+		int nSpotsFound = (int) module.getOutput("nSpotsFound");
+		int nTracksFound = (int) module.getOutput("nTracksFound");
+		double[] x = (double[]) module.getOutput("x");
+		double[] y = (double[]) module.getOutput("y");
+		double[] z = (double[]) module.getOutput("z");
+		double[] t = (double[]) module.getOutput("t");
+		double[] frame = (double[]) module.getOutput("frame");
+
+		assertEquals(5, nSpotsFound);
+		assertEquals(1, nTracksFound);
+
+		System.out.println(Arrays.toString(x));
+		System.out.println(Arrays.toString(y));
+		System.out.println(Arrays.toString(z));
+		System.out.println(Arrays.toString(t));
+
+		Arrays.sort(x);
+		Arrays.sort(y);
+		Arrays.sort(t);
+		Arrays.sort(frame);
+
+		double[] x1 = { 5, 5, 5, 6, 6 };
+		double[] y1 = { 6, 6, 7, 7, 7 };
+		double[] z1 = { 0, 0, 0, 0, 0 };
+		double[] t1 = { 0, 0.5, 1.0, 1.5, 2.0 };
+		double[] frame1 = { 0, 1, 2, 3, 4 };
+
+		assertArrayEquals(x1, x, 0.2);
+		assertArrayEquals(y1, y, 0.2);
+		assertArrayEquals(z1, z, 0.0001);
+		assertArrayEquals(t1, t, 0.01);
+		assertArrayEquals(frame1, frame, 0.01);
+	}
+}