Merge pull request #49 from clEsperanto/create-tests

Create tests

.github/workflows/build.yaml

@@ -75,7 +75,7 @@ jobs:
       run: sudo apt install ocl-icd-opencl-dev
 
     - name: Build with Maven
-      run:  mvn clean install
+      run:  mvn clean install -DskipTests
       shell: bash
 
     - name: Run Java class (only possible on MacOS)

.github/workflows/test.yaml

@@ -0,0 +1,20 @@
+name: ClesperantoJ tests
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: macos-13
+    strategy:
+      matrix:
+        java: [8, 11, 17, 21]
+    name: Test with Java ${{ matrix.java }}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Setup java
+        uses: actions/setup-java@v2
+        with:
+          java-version: ${{ matrix.java }}
+          distribution: 'zulu'
+      - name: Execute the tests
+        run: mvn clean test -X

pom.xml

@@ -127,6 +127,18 @@
 			<groupId>net.imagej</groupId>
 			<artifactId>ij</artifactId>
 		</dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.7.0</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-engine</artifactId>
+            <version>5.7.0</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <repositories>
@@ -294,14 +306,16 @@
 			</plugin>
 
 			<!-- Test plugin -->
-	        <plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.4.1</version>
-				<configuration>
-					<argLine>-Xmx2G</argLine>
-				</configuration>
-			</plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.22.2</version>
+			    <configuration>
+			        <redirectTestOutputToFile>true</redirectTestOutputToFile>
+	                <forkCount>1</forkCount>
+	                <reuseForks>false</reuseForks>
+			    </configuration>
+            </plugin>
 
 		</plugins>
 	</build>

src/main/java/net/clesperanto/ImagePlusClesperantoJExample.java

@@ -33,9 +33,9 @@ public static void main(String[] args) {
         IJ.run(input_imp, "32-bit", "");
         input_imp.show();
 
-        ArrayJ input = ImageJConverters.copyImgLib2ToArrayJ(input_imp, currentDevice, "buffer");
+        ArrayJ input = ImageJConverters.copyImagePlus2ToArrayJ(input_imp, currentDevice, "buffer");
         ArrayJ output = Tier1.absolute(currentDevice, input, null);
-        ImagePlus output_imp = ImageJConverters.copyArrayJToImgLib2(output);
+        ImagePlus output_imp = ImageJConverters.copyArrayJToImagePlus(output);
 
         output_imp.show();
     }

src/main/java/net/clesperanto/icy/IcyConverters.java

@@ -3,13 +3,17 @@
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.nio.FloatBuffer;
+import java.nio.IntBuffer;
 import java.nio.ShortBuffer;
 import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
 
 import icy.image.IcyBufferedImage;
+import icy.preferences.ApplicationPreferences;
+import icy.preferences.GeneralPreferences;
+import icy.preferences.IcyPreferences;
 import icy.sequence.Sequence;
 import icy.sequence.SequenceCursor;
 import net.clesperanto.core.ArrayJ;
@@ -25,6 +29,12 @@
  */
 public class IcyConverters {
 
+	// Icy requires that the preferences are initialized if they have not bee initialized before.
+	// TODO check if htey have been initialized before
+	static {
+		initIcyPreferences();
+	}
+
 	/** TODO extend to RandomAccessibleInterval
 	 * Conert an {@link ArrayJ} into an ImgLib2 {@link ArrayImg} of the same dimensions and data type.
 	 * Creates a copy of the ArrayJ in the GPU into an ArrayImg in the CPU
@@ -33,7 +43,7 @@ public class IcyConverters {
 	 * 	array that is located in the GPU for clesperanto to do some operations
 	 * @return and ImgLib2 {@link ArrayImg} on the CPU copied from the {@link ArrayJ} on the GPU
 	 */
-	public static Sequence copyArrayJToImgLib2( ArrayJ arrayj )
+	public static Sequence copyArrayJToSequence( ArrayJ arrayj )
 	{
 		long flatDims = arrayj.getHeight() * arrayj.getDepth() * arrayj.getWidth();
 		IcyDataType dataType = IcyDataType.fromString(arrayj.getDataType());
@@ -62,9 +72,9 @@ public static Sequence copyArrayJToImgLib2( ArrayJ arrayj )
 	 * 	String "image", for buffer use "buffer"
 	 * @return an {@link ArrayJ} copied from the {@link RandomAccessibleInterval} of the CPU
 	 */
-	public static ArrayJ copyImgLib2ToArrayJ(Sequence rai, DeviceJ device, String memoryType) {
-		Map<String, Integer> sizeMap = checkSize(rai);
+	public static ArrayJ copySequenceToArrayJ(Sequence rai, DeviceJ device, String memoryType) {
 		IcyDataType dataType = IcyDataType.fromIcyDataType(rai.getDataType_());
+		Map<String, Integer> sizeMap = checkSize(rai, dataType.getByteSize());
 		long totalSize = sizeMap.values().stream().reduce((int) 1L, (a, b) -> a * b);
 
 		long[] dims = sizeMap.values().stream().mapToLong(i -> (long) i).toArray();
@@ -98,13 +108,28 @@ private static Sequence fromBuffer(ByteBuffer byteBuffer, IcyDataType type, long
 	            FloatBuffer floatBuff = byteBuffer.asFloatBuffer();
 	            fillImage(im, dimensions, floatBuff::get);
 	            break;
+	        case INT8:
+	            fillImage(im, dimensions, byteBuffer::get);
+	            break;
 	        case UINT8:
 	            fillImage(im, dimensions, byteBuffer::get);
 	            break;
 	        case UINT16:
+	            ShortBuffer uShortBuff = byteBuffer.asShortBuffer();
+	            fillImage(im, dimensions, uShortBuff::get);
+	            break;
+	        case INT16:
 	            ShortBuffer shortBuff = byteBuffer.asShortBuffer();
 	            fillImage(im, dimensions, shortBuff::get);
 	            break;
+	        case INT32:
+	            IntBuffer intBuff = byteBuffer.asIntBuffer();
+	            fillImage(im, dimensions, intBuff::get);
+	            break;
+	        case UINT32:
+	            IntBuffer uIntBuff = byteBuffer.asIntBuffer();
+	            fillImage(im, dimensions, uIntBuff::get);
+	            break;
 	        default:
 	            throw new IllegalArgumentException("Data type not supported.");
 	    }
@@ -124,28 +149,15 @@ private static void fillImage(Sequence im, long[] dimensions, Supplier<Number> g
 	    cursor.commitChanges();
 	}
 
-	private static Map<String, Integer> checkSize(Sequence imp) {
+	private static Map<String, Integer> checkSize(Sequence imp, long byteSize) {
 		Map<String, Integer> sizeMap = new LinkedHashMap<String, Integer>();
-		sizeMap.put("x", imp.getWidth());
-		sizeMap.put("y", imp.getHeight());
-		sizeMap.put("c", imp.getSizeC());
-		sizeMap.put("z", imp.getSizeZ());
-		sizeMap.put("t", imp.getSizeT());
-		sizeMap = sizeMap.entrySet().stream()
-				.filter(ee -> ee.getValue() == 1).collect(Collectors.toMap(ee -> ee.getKey(), ee -> ee.getValue()));
-		while (sizeMap.entrySet().size() > 3) {
-			if (sizeMap.get("t") != null)
-				sizeMap.remove("t");
-			else if (sizeMap.get("c") != null)
-				sizeMap.remove("c");
-			else if (sizeMap.get("z") != null)
-				sizeMap.remove("z");
-		}
-		int tot = 1;
+		sizeMap.put("x", imp.getWidth() == 0 ? 1 : imp.getWidth());
+		sizeMap.put("y", imp.getHeight() == 0 ? 1 : imp.getHeight());
+		sizeMap.put("z", imp.getSizeZ() == 0 ? 1 : imp.getSizeZ());
 		for (Integer vv : sizeMap.values()) {
-			tot *= vv;
+			byteSize *= (long) vv;
 		}
-		if (tot > Integer.MAX_VALUE)
+		if (byteSize > Integer.MAX_VALUE)
 			throw new IllegalArgumentException();
 		return sizeMap;
 	}
@@ -158,7 +170,7 @@ else if (sizeMap.get("z") != null)
      * 	type of the sequence
      * @return empty Icy sequence of the wanted type and dimensions
      */
-    private static Sequence createSequence(long[] dims, icy.type.DataType type)
+    public static Sequence createSequence(long[] dims, icy.type.DataType type)
     {
     	while (dims.length < 3) {
     		long[] newArray = new long[dims.length + 1];
@@ -174,4 +186,20 @@ private static Sequence createSequence(long[] dims, icy.type.DataType type)
         }
         return seq;
     }
+
+    /**
+     * Initialize the Icy meta data that is required to use Icy Sequences.
+     * Only initializes it if it has not been done before.
+     */
+    public static void initIcyPreferences() {
+    	if (ApplicationPreferences.getPreferences() == null
+    			|| GeneralPreferences.getPreferences() == null) {
+            IcyPreferences.init();
+    	}
+    }
+
+    public static void main(String[] args) {
+
+    	createSequence(new long[] {5, 5, 5}, icy.type.DataType.FLOAT);
+    }
 }

src/main/java/net/clesperanto/icy/IcyDataType.java

@@ -20,6 +20,18 @@ public enum IcyDataType {
     private final icy.type.DataType icyDT;
     private final Class<?> arrayClass;
 
+	public final static long MAX_UINT32 = (long) Math.pow(2, 32);
+
+	public final static int MAX_INT32 = Integer.MAX_VALUE;
+
+	public final static int MAX_UINT16 = 65536;
+
+	public final static int MAX_INT16 = 65536 /  2 - 1;
+
+	public final static int MAX_UINT8 = 256;
+
+	public final static int MAX_INT8 = 256 / 2 - 1;
+
     IcyDataType(DataType dt, icy.type.DataType icyDT, Class<?> arrayClass) {
     	this.dt = dt;
         this.icyDT = icyDT;
@@ -84,15 +96,22 @@ public void putValInArray(Object arr, int pos, Number value) {
             case FLOAT32:
                 ((float[]) arr)[pos] = value.floatValue();
                 break;
+            case UINT32:
+                ((int[]) arr)[pos] = (int) (value.doubleValue() > Integer.MAX_VALUE ? value.doubleValue() - MAX_UINT32 : value.doubleValue());
+                break;
             case INT32:
                 ((int[]) arr)[pos] = value.intValue();
                 break;
-            case INT16:
             case UINT16:
+                ((short[]) arr)[pos] = (short) (value.doubleValue() > Short.MAX_VALUE ? value.doubleValue() - MAX_UINT16 : value.doubleValue());
+                break;
+            case INT16:
                 ((short[]) arr)[pos] = value.shortValue();
                 break;
-            case INT8:
             case UINT8:
+                ((byte[]) arr)[pos] = (byte) (value.doubleValue() > Byte.MAX_VALUE ? value.doubleValue() - MAX_UINT8 : value.doubleValue());
+                break;
+            case INT8:
                 ((byte[]) arr)[pos] = value.byteValue();
                 break;
             default:

src/main/java/net/clesperanto/imagej/ImageJConverters.java

@@ -7,7 +7,6 @@
 import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.function.Supplier;
-import java.util.stream.Collectors;
 
 import ij.IJ;
 import ij.ImagePlus;
@@ -35,7 +34,7 @@ public class ImageJConverters {
 	 * 	array that is located in the GPU for clesperanto to do some operations
 	 * @return and ImgLib2 {@link ArrayImg} on the CPU copied from the {@link ArrayJ} on the GPU
 	 */
-	public static ImagePlus copyArrayJToImgLib2( ArrayJ arrayj )
+	public static ImagePlus copyArrayJToImagePlus( ArrayJ arrayj )
 	{
 		long flatDims = arrayj.getHeight() * arrayj.getDepth() * arrayj.getWidth();
 		ImageJDataType dataType = ImageJDataType.fromString(arrayj.getDataType());
@@ -64,8 +63,9 @@ public static ImagePlus copyArrayJToImgLib2( ArrayJ arrayj )
 	 * 	String "image", for buffer use "buffer"
 	 * @return an {@link ArrayJ} copied from the {@link RandomAccessibleInterval} of the CPU
 	 */
-	public static ArrayJ copyImgLib2ToArrayJ(ImagePlus rai, DeviceJ device, String memoryType) {
+	public static ArrayJ copyImagePlus2ToArrayJ(ImagePlus rai, DeviceJ device, String memoryType) {
 		Map<String, Integer> sizeMap = checkSize(rai, rai.getBytesPerPixel());
+
 		ImageJDataType dataType = ImageJDataType.fromImgPlusDataType(rai.getType());
 		long totalSize = sizeMap.values().stream().reduce((int) 1L, (a, b) -> a * b);
 
@@ -96,7 +96,7 @@ public static ArrayJ copyImgLib2ToArrayJ(ImagePlus rai, DeviceJ device, String m
 	}
 
 	private static ImagePlus fromBuffer(ByteBuffer byteBuffer, ImageJDataType type, long[] dimensions) {
-	    ImagePlus im = IJ.createImage("image", (int) dimensions[0], (int) dimensions[1], (int) dimensions[2], type.createType());
+	    ImagePlus im = IJ.createImage("image", (int) dimensions[0], (int) dimensions[1], (int) dimensions[2], type.getBitDepth());
 
 	    switch (type) {
 	        case FLOAT32:

src/main/java/net/clesperanto/imagej/ImageJDataType.java

@@ -9,18 +9,20 @@
 
 // TODO add all types ImagePlus.GRAY8, ImagePlus.GRAY16, ImagePlus.GRAY32, ImagePlus.COLOR_256 or ImagePlus.COLOR_RGB)
 public enum ImageJDataType {
-    FLOAT32(DataType.fromString("float"), ImagePlus.GRAY32, float[].class),
-    UINT16(DataType.fromString("ushort"), ImagePlus.GRAY16, short[].class),
-    UINT8(DataType.fromString("uchar"), ImagePlus.GRAY8, byte[].class);
+    FLOAT32(DataType.fromString("float"), ImagePlus.GRAY32, float[].class, 32),
+    UINT16(DataType.fromString("ushort"), ImagePlus.GRAY16, short[].class, 16),
+    UINT8(DataType.fromString("uchar"), ImagePlus.GRAY8, byte[].class, 8);
 
 	private final DataType dt;
     private final int imgDtype;
+    private final int bitDepth;
     private final Class<?> arrayClass;
 
-    ImageJDataType(DataType dt, int imgDtype, Class<?> arrayClass) {
+    ImageJDataType(DataType dt, int imgDtype, Class<?> arrayClass, int bitDepth) {
         this.dt = dt;
         this.imgDtype = imgDtype;
         this.arrayClass = arrayClass;
+        this.bitDepth = bitDepth;
     }
 
     public static ImageJDataType fromString(String dType) {
@@ -53,6 +55,10 @@ public int getByteSize() {
     	return dt.getByteSize();
     }
 
+    public int getBitDepth() {
+    	return this.bitDepth;
+    }
+
     public void readToBuffer(ArrayJ arrayj, ByteBuffer buffer) {
     	this.dt.readToBuffer(arrayj, buffer);
     }

src/test/java/TestAbsolute.java

@@ -0,0 +1,49 @@
+import org.junit.jupiter.api.Test;
+
+import net.clesperanto.kernels.Tier1;
+import net.clesperanto.core.MemoryJ;
+import net.clesperanto.core.ArrayJ;
+import net.clesperanto.core.DeviceJ;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+import java.nio.IntBuffer;
+import java.util.Arrays;
+
+public class TestAbsolute {
+
+    @Test
+    public void testAbsolute() {
+    	DeviceJ device = DeviceJ.getDefaultDevice();
+    	ArrayJ in = MemoryJ.makeIntBuffer(device, 2, 2, 0, 2, "buffer");
+    	in.fillMemory(-1);
+    	ArrayJ out = MemoryJ.makeIntBuffer(device, 2, 2, 0, 2, "buffer");
+    	out.fillMemory(-1);
+        Tier1.absolute(device, in, out);
+
+        int[] result = new int[4];
+        IntBuffer resultBuff = IntBuffer.wrap(result);
+        MemoryJ.readIntBuffer(out, resultBuff, 4);
+
+        assertEquals(1, Arrays.stream(result).min().getAsInt());
+        assertEquals(1, Arrays.stream(result).max().getAsInt());
+        assertEquals(1, Arrays.stream(result).average().getAsDouble());
+    }
+
+    @Test
+    public void testAbsolute1() {
+    	DeviceJ device = DeviceJ.getDefaultDevice();
+    	ArrayJ in = MemoryJ.makeIntBuffer(device, 2, 2, 0, 2, "buffer");
+    	in.fillMemory(-1);
+        ArrayJ out = Tier1.absolute(device, in, null);
+
+        int[] result = new int[4];
+        IntBuffer resultBuff = IntBuffer.wrap(result);
+        MemoryJ.readIntBuffer(out, resultBuff, 4);
+
+        for (int val : result)
+        	assertEquals(1, val);
+		in = null;
+		out = null;
+    }
+}