Unit tests: add class TestResources for querying paths of resource files

juglab · Jan 11, 2024 · a31d5a8 · a31d5a8
1 parent 214ff98
commit a31d5a8
Show file tree

Hide file tree

Showing 11 changed files with 59 additions and 82 deletions.
diff --git a/src/test/java/demo/LabelingComponentHdf5Demo.java b/src/test/java/demo/LabelingComponentHdf5Demo.java
@@ -34,6 +34,7 @@
 import sc.fiji.labkit.ui.LabelingComponent;
 import sc.fiji.labkit.ui.inputimage.SpimDataInputImage;
 import sc.fiji.labkit.ui.models.ImageLabelingModel;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 import javax.swing.*;
 import java.awt.event.WindowAdapter;
@@ -46,7 +47,7 @@ public class LabelingComponentHdf5Demo {
 
 	public static void main(String... args) throws SpimDataException {
 		JFrame frame = initFrame();
-		final String fn = LabelingComponentHdf5Demo.class.getResource("/export.xml").getPath();
+		final String fn = TestResources.fullPath("/export.xml");
 		frame.add(initLabelingComponent(frame, fn));
 		frame.setVisible(true);
 	}

diff --git a/src/test/java/sc/fiji/labkit/ui/inputimage/SpimDataToImgPlusTest.java b/src/test/java/sc/fiji/labkit/ui/inputimage/SpimDataToImgPlusTest.java
@@ -40,6 +40,7 @@
 import net.imglib2.type.numeric.integer.UnsignedShortType;
 import net.imglib2.util.Cast;
 import org.junit.Test;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 import java.util.Arrays;
 import java.util.stream.IntStream;
@@ -50,7 +51,7 @@ public class SpimDataToImgPlusTest {
 
 	@Test
 	public void testOpen() {
-		String filename = SpimDataToImgPlusTest.class.getResource("/export.xml").getPath();
+		String filename = TestResources.fullPath("/export.xml");
 		ImgPlus<UnsignedShortType> result = Cast.unchecked(SpimDataToImgPlus.open(filename, 0));
 		assertEquals(Arrays.asList(Axes.X, Axes.Y, Axes.Z, Axes.CHANNEL, Axes.TIME), ImgPlusViewsOld
 			.getAxes(result));
@@ -60,14 +61,13 @@ public void testOpen() {
 
 	@Test(expected = SpimDataInputException.class)
 	public void testExceptionForMultipleAngles() {
-		String filename = SpimDataToImgPlusTest.class.getResource("/multi-angle-dataset.xml").getPath();
+		String filename = TestResources.fullPath("/multi-angle-dataset.xml");
 		SpimDataToImgPlus.open(filename, 0);
 	}
 
 	@Test(expected = SpimDataInputException.class)
 	public void testExceptionForSizeMismatch() {
-		String filename = SpimDataToImgPlusTest.class.getResource("/size-mismatch-dataset.xml")
-			.getPath();
+		String filename = TestResources.fullPath("/size-mismatch-dataset.xml");
 		SpimDataToImgPlus.open(filename, 0);
 	}
 

diff --git a/src/test/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitIJ1PluginTest.java b/src/test/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitIJ1PluginTest.java
@@ -12,15 +12,16 @@
 import net.imglib2.test.ImgLib2Assert;
 import org.junit.Test;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 public class CalculateProbabilityMapWithLabkitIJ1PluginTest {
 
 	@Test
 	public void test() throws IOException {
 		SingletonContext.getInstance();
-		String inputImage = fullPath("/blobs.tif");
-		String blobsModel = fullPath("/blobs.classifier");
-		String source = fullPath("/blobs_probability_map.tif");
+		String inputImage = TestResources.fullPath("/blobs.tif");
+		String blobsModel = TestResources.fullPath("/blobs.classifier");
+		String source = TestResources.fullPath("/blobs_probability_map.tif");
 		File outputImage = File.createTempFile("labkit-segmentation-test", ".tif");
 		String macroTemplate = "close('*');\n" +
 			"open('INPUT_TIF');\n" +
@@ -37,11 +38,7 @@ public void test() throws IOException {
 		assertTrue(outputImage.exists());
 		ImagePlus expected = IJ.openImage(source);
 		ImagePlus result = IJ.openImage(outputImage.getAbsolutePath());
-		ImgLib2Assert.assertImageEquals(VirtualStackAdapter.wrap(expected), VirtualStackAdapter.wrap(result), Object::equals);
-	}
-
-	private String fullPath(String name) {
-		return SegmentImageWithLabkitPluginTest.class.getResource(
-			name).getFile();
+		ImgLib2Assert.assertImageEquals(VirtualStackAdapter.wrap(expected),
+			VirtualStackAdapter.wrap(result), Object::equals);
 	}
 }
diff --git a/src/test/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitPluginTest.java b/src/test/java/sc/fiji/labkit/ui/plugin/CalculateProbabilityMapWithLabkitPluginTest.java
@@ -34,16 +34,17 @@
 import net.imglib2.test.ImgLib2Assert;
 import org.junit.Test;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 public class CalculateProbabilityMapWithLabkitPluginTest {
 
 	@Test
 	public void test() throws Exception {
 		// setup
 		ImageJ imageJ = new ImageJ(SingletonContext.getInstance());
-		Dataset image = imageJ.scifio().datasetIO().open(fullPath("/blobs.tif"));
-		String blobsModel = fullPath("/blobs.classifier");
-		Dataset expectedImage = imageJ.scifio().datasetIO().open(fullPath(
+		Dataset image = imageJ.scifio().datasetIO().open(TestResources.fullPath("/blobs.tif"));
+		String blobsModel = TestResources.fullPath("/blobs.classifier");
+		Dataset expectedImage = imageJ.scifio().datasetIO().open(TestResources.fullPath(
 			"/blobs_probability_map.tif"));
 		// process
 		Dataset output = (Dataset) imageJ.command().run(CalculateProbabilityMapWithLabkitPlugin.class,
@@ -55,9 +56,4 @@ public void test() throws Exception {
 		// test
 		ImgLib2Assert.assertImageEqualsRealType(expectedImage, output, 0.0);
 	}
-
-	private String fullPath(String name) {
-		return CalculateProbabilityMapWithLabkitPluginTest.class.getResource(
-			name).getFile();
-	}
 }
diff --git a/...est/java/sc/fiji/labkit/ui/plugin/LabkitProbabilityMapForImagesInDirectoryPluginTest.java b/...est/java/sc/fiji/labkit/ui/plugin/LabkitProbabilityMapForImagesInDirectoryPluginTest.java
@@ -43,6 +43,7 @@
 import org.scijava.io.location.FileLocation;
 import org.scijava.plugin.Parameter;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 import java.io.File;
 import java.io.IOException;
@@ -81,15 +82,15 @@ public void test()
 			"file_filter", "*.tif",
 			"output_directory", outputDirectory,
 			"output_file_suffix", "_probability_map.tif",
-			"segmenter_file", fullPath("/leaf.classifier"),
+			"segmenter_file", TestResources.fullPath("/leaf.classifier"),
 			"use_gpu", false).get();
 		testOutputDirectory(outputDirectory);
 	}
 
 	private File createTestInputDirectory() throws IOException {
 		File folder = Files.createTempDirectory("labkit-test-input").toFile();
 		RandomAccessibleInterval<UnsignedByteType> image =
-			Cast.unchecked(io.open(fullPath("/leaf.tif")));
+			Cast.unchecked(io.open(TestResources.fullPath("/leaf.tif")));
 		for (int i = 0; i < 4; i++) {
 			File file = new File(folder, "image" + i + ".tif");
 			saveImage(image, file);
@@ -99,8 +100,8 @@ private File createTestInputDirectory() throws IOException {
 	}
 
 	private void testOutputDirectory(File folder) throws IOException {
-		RandomAccessibleInterval<? extends RealType<?>> expected = io.open(fullPath(
-			"/leaf_probability_map.tif"));
+		RandomAccessibleInterval<? extends RealType<?>> expected = io.open(
+			TestResources.fullPath("/leaf_probability_map.tif"));
 		for (int i = 0; i < 4; i++) {
 			File file = new File(folder, "image" + i + "_probability_map.tif");
 			assertTrue("Expected output file is missing: " + file, file.exists());
@@ -121,9 +122,4 @@ private void saveImage(RandomAccessibleInterval<UnsignedByteType> image, File fi
 		dataset.axis(2).setType(Axes.CHANNEL);
 		io.save(dataset, new FileLocation(file));
 	}
-
-	private String fullPath(String name) {
-		return this.getClass().getResource(name).getFile();
-	}
-
 }
diff --git a/src/test/java/sc/fiji/labkit/ui/plugin/LabkitSegmentImagesInDirectoryPluginTest.java b/src/test/java/sc/fiji/labkit/ui/plugin/LabkitSegmentImagesInDirectoryPluginTest.java
@@ -46,6 +46,7 @@
 import org.scijava.io.location.FileLocation;
 import org.scijava.plugin.Parameter;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 import java.io.File;
 import java.io.IOException;
@@ -83,15 +84,15 @@ public void test()
 			"file_filter", "*.tif",
 			"output_directory", outputDirectory,
 			"output_file_suffix", "_segmentation.tif",
-			"segmenter_file", fullPath("/leaf.classifier"),
+			"segmenter_file", TestResources.fullPath("/leaf.classifier"),
 			"use_gpu", false).get();
 		testOutputDirectory(outputDirectory);
 	}
 
 	private File createTestInputDirectory() throws IOException {
 		File folder = Files.createTempDirectory("labkit-test-input").toFile();
 		RandomAccessibleInterval<UnsignedByteType> image =
-			Cast.unchecked(io.open(fullPath("/leaf.tif")));
+			Cast.unchecked(io.open(TestResources.fullPath("/leaf.tif")));
 		for (int i = 0; i < 4; i++) {
 			File file = new File(folder, "image" + i + ".tif");
 			saveImage(image, file);
@@ -101,7 +102,7 @@ private File createTestInputDirectory() throws IOException {
 	}
 
 	private void testOutputDirectory(File folder) throws IOException {
-		RandomAccessibleInterval<? extends RealType<?>> expected = io.open(fullPath(
+		RandomAccessibleInterval<? extends RealType<?>> expected = io.open(TestResources.fullPath(
 			"/leaf_segmentation.tif"));
 		for (int i = 0; i < 4; i++) {
 			File file = new File(folder, "image" + i + "_segmentation.tif");
@@ -134,9 +135,4 @@ private void assertAlmostIdentical(RandomAccessibleInterval<? extends RealType<?
 		});
 		assertTrue(count[0] < 10);
 	}
-
-	private String fullPath(String name) {
-		return this.getClass().getResource(name).getFile();
-	}
-
 }
diff --git a/src/test/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitIJ1PluginTest.java b/src/test/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitIJ1PluginTest.java
@@ -12,15 +12,16 @@
 import net.imglib2.test.ImgLib2Assert;
 import org.junit.Test;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 public class SegmentImageWithLabkitIJ1PluginTest {
 
 	@Test
 	public void test() throws IOException {
 		SingletonContext.getInstance();
-		String inputImage = fullPath("/blobs.tif");
-		String blobsModel = fullPath("/blobs.classifier");
-		String source = fullPath("/blobs_segmentation.tif");
+		String inputImage = TestResources.fullPath("/blobs.tif");
+		String blobsModel = TestResources.fullPath("/blobs.classifier");
+		String source = TestResources.fullPath("/blobs_segmentation.tif");
 		File outputImage = File.createTempFile("labkit-segmentation-test", ".tif");
 		String macroTemplate = "close('*');\n" +
 			"open('INPUT_TIF');\n" +
@@ -37,11 +38,7 @@ public void test() throws IOException {
 		assertTrue(outputImage.exists());
 		ImagePlus expected = IJ.openImage(source);
 		ImagePlus result = IJ.openImage(outputImage.getAbsolutePath());
-		ImgLib2Assert.assertImageEquals(VirtualStackAdapter.wrap(expected), VirtualStackAdapter.wrap(result), Object::equals);
-	}
-
-	private String fullPath(String name) {
-		return SegmentImageWithLabkitPluginTest.class.getResource(
-			name).getFile();
+		ImgLib2Assert.assertImageEquals(VirtualStackAdapter.wrap(expected),
+			VirtualStackAdapter.wrap(result), Object::equals);
 	}
 }
diff --git a/src/test/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitPluginTest.java b/src/test/java/sc/fiji/labkit/ui/plugin/SegmentImageWithLabkitPluginTest.java
@@ -34,16 +34,17 @@
 import net.imglib2.test.ImgLib2Assert;
 import org.junit.Test;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 public class SegmentImageWithLabkitPluginTest {
 
 	@Test
 	public void test() throws Exception {
 		// setup
 		ImageJ imageJ = new ImageJ(SingletonContext.getInstance());
-		Dataset image = imageJ.scifio().datasetIO().open(fullPath("/blobs.tif"));
-		String blobsModel = fullPath("/blobs.classifier");
-		Dataset expectedImage = imageJ.scifio().datasetIO().open(fullPath("/blobs_segmentation.tif"));
+		Dataset image = imageJ.scifio().datasetIO().open(TestResources.fullPath("/blobs.tif"));
+		String blobsModel = TestResources.fullPath("/blobs.classifier");
+		Dataset expectedImage = imageJ.scifio().datasetIO().open(TestResources.fullPath("/blobs_segmentation.tif"));
 		// process
 		Dataset output = (Dataset) imageJ.command().run(SegmentImageWithLabkitPlugin.class, true,
 			"input", image,
@@ -53,9 +54,4 @@ public void test() throws Exception {
 		// test
 		ImgLib2Assert.assertImageEqualsRealType(expectedImage, output, 0.0);
 	}
-
-	private String fullPath(String name) {
-		return SegmentImageWithLabkitPluginTest.class.getResource(
-			name).getFile();
-	}
 }
diff --git a/src/test/java/sc/fiji/labkit/ui/plugin/SegmentRGBImageTest.java b/src/test/java/sc/fiji/labkit/ui/plugin/SegmentRGBImageTest.java
@@ -31,17 +31,11 @@
 
 import net.imagej.Dataset;
 import net.imagej.ImageJ;
-import net.imagej.ImgPlus;
 import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.array.ArrayImgs;
 import net.imglib2.test.ImgLib2Assert;
-import net.imglib2.type.numeric.integer.ShortType;
-import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.ValuePair;
-import net.imglib2.view.Views;
 import org.junit.Test;
-import org.scijava.Context;
 import sc.fiji.labkit.pixel_classification.utils.SingletonContext;
 import sc.fiji.labkit.ui.inputimage.DatasetInputImage;
 import sc.fiji.labkit.ui.inputimage.InputImage;
@@ -52,6 +46,7 @@
 import sc.fiji.labkit.ui.models.SegmentationModel;
 import sc.fiji.labkit.ui.segmentation.SegmentationPlugin;
 import sc.fiji.labkit.ui.segmentation.weka.PixelClassificationPlugin;
+import sc.fiji.labkit.ui.utils.TestResources;
 
 import java.io.IOException;
 import java.util.Collections;
@@ -64,8 +59,8 @@ public void testSegmentation()
 		throws IOException, ExecutionException, InterruptedException
 	{
 		ImageJ imageJ = new ImageJ(SingletonContext.getInstance());
-		Dataset image = imageJ.scifio().datasetIO().open(fullPath("/leaf.tif"));
-		String blobsModel = fullPath("/leaf.classifier");
+		Dataset image = imageJ.scifio().datasetIO().open(TestResources.fullPath("/leaf.tif"));
+		String blobsModel = TestResources.fullPath("/leaf.classifier");
 		// process
 		Dataset output = (Dataset) imageJ.command().run(CalculateProbabilityMapWithLabkitPlugin.class,
 			true,
@@ -74,19 +69,20 @@ public void testSegmentation()
 			"use_gpu", false)
 			.get().getOutput("output");
 		// test
-		Dataset expectedImage = imageJ.scifio().datasetIO().open(fullPath("/leaf_probability_map.tif"));
+		Dataset expectedImage = imageJ.scifio().datasetIO().open(
+			TestResources.fullPath("/leaf_probability_map.tif"));
 		ImgLib2Assert.assertImageEqualsRealType(expectedImage, output, 0.0);
 	}
 
 	@Test
 	public void testTraining() throws IOException {
 		ImageJ imageJ = new ImageJ(SingletonContext.getInstance());
-		Dataset image = imageJ.scifio().datasetIO().open(fullPath("/leaf.tif"));
+		Dataset image = imageJ.scifio().datasetIO().open(TestResources.fullPath("/leaf.tif"));
 		InputImage inputImage = new DatasetInputImage(image);
 		SegmentationModel segmentationModel = new DefaultSegmentationModel(imageJ.context(),
 			inputImage);
-		Labeling labeling = new LabelingSerializer(SingletonContext.getInstance()).open(fullPath(
-			"/leaf.tif.labeling"));
+		Labeling labeling = new LabelingSerializer(SingletonContext.getInstance()).open(
+			TestResources.fullPath("/leaf.tif.labeling"));
 		segmentationModel.imageLabelingModel().labeling().set(labeling);
 		SegmentationPlugin plugin = PixelClassificationPlugin.create();
 		SegmentationItem segmenter = segmentationModel.segmenterList().addSegmenter(plugin);
@@ -98,11 +94,8 @@ public void testTraining() throws IOException {
 			.imageLabelingModel()).prediction();
 
 		// output
-		Dataset expectedImage = imageJ.scifio().datasetIO().open(fullPath("/leaf_probability_map.tif"));
+		Dataset expectedImage = imageJ.scifio().datasetIO().open(
+			TestResources.fullPath("/leaf_probability_map.tif"));
 		ImgLib2Assert.assertImageEqualsRealType(expectedImage, prediction, 0.0);
 	}
-
-	private String fullPath(String name) {
-		return this.getClass().getResource(name).getFile();
-	}
 }