Add Java bindings

.gitignore

@@ -13,6 +13,7 @@ build-emscripten
 build-wasi
 src/io/internal/ImageIOIndex.ts
 src/io/internal/MeshIOIndex.ts
+wasi-build/
 
 dist/*
 !dist/dicom

packages/core/java/.gitignore

@@ -0,0 +1,4 @@
+/.classpath
+/.project
+/.settings/
+/target/

packages/core/java/pom.xml

@@ -0,0 +1,111 @@
+<?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 https://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <parent>
+    <groupId>org.scijava</groupId>
+    <artifactId>pom-scijava</artifactId>
+    <version>35.1.1</version>
+  </parent>
+
+  <groupId>org.itk.wasm</groupId>
+  <artifactId>itk-wasm</artifactId>
+  <version>0.1.0-SNAPSHOT</version>
+
+  <name>itk-wasm for Java</name>
+  <description>Java interface to itk-wasm WebAssembly modules.</description>
+  <url>https://github.com/InsightSoftwareConsortium/itk-wasm</url>
+  <inceptionYear>2023</inceptionYear>
+  <organization>
+    <name>ITK</name>
+    <url>https://itk.org/</url>
+  </organization>
+  <licenses>
+    <license>
+      <name>The Apache License, Version 2.0</name>
+      <url>https://www.apache.org/licenses/LICENSE-2.0</url>
+    </license>
+  </licenses>
+
+  <developers>
+    <developer>
+      <name>Matt McCormick</name>
+      <url>https://github.com/thewtex</url>
+      <id>thewtex</id>
+    </developer>
+  </developers>
+  <contributors>
+    <contributor>
+      <name>Curtis Rueden</name>
+      <url>https://github.com/ctrueden</url>
+      <properties><id>ctrueden</id></properties>
+    </contributor>
+  </contributors>
+
+  <mailingLists>
+    <mailingList>
+      <name>ITK Forum</name>
+      <archive>https://discourse.itk.org/</archive>
+    </mailingList>
+  </mailingLists>
+
+  <scm>
+    <connection>scm:https://github.com/InsightSoftwareConsortium/itk-wasm</connection>
+    <developerConnection>scm:[email protected]:InsightSoftwareConsortium/itk-wasm</developerConnection>
+    <url>https://github.com/InsightSoftwareConsortium/itk-wasm</url>
+  </scm>
+  <issueManagement>
+    <system>GitHub Issues</system>
+    <url>https://github.com/InsightSoftwareConsortium/itk-wasm/issues</url>
+  </issueManagement>
+  <ciManagement>
+    <system>GitHub Actions</system>
+    <url>https://github.com/InsightSoftwareConsortium/itk-wasm/actions</url>
+  </ciManagement>
+
+  <properties>
+    <main-class>org.itk.wasm.Main</main-class>
+
+    <license.licenseName>apache_v2</license.licenseName>
+    <license.copyrightOwners>ITK developers.</license.copyrightOwners>
+    <license.projectName>Java bindings for itk-wasm.</license.projectName>
+
+    <wasmtime-java.version>0.14.0</wasmtime-java.version>
+  </properties>
+
+  <dependencies>
+    <dependency>
+      <groupId>io.github.kawamuray.wasmtime</groupId>
+      <artifactId>wasmtime-java</artifactId>
+      <version>${wasmtime-java.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>net.imglib2</groupId>
+      <artifactId>imglib2</artifactId>
+    </dependency>
+		<dependency>
+			<groupId>net.java.dev.jna</groupId>
+			<artifactId>jna</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>net.java.dev.jna</groupId>
+			<artifactId>jna-platform</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>com.google.code.gson</groupId>
+			<artifactId>gson</artifactId>
+		</dependency>
+
+		<!-- Test scope dependencies -->
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-api</artifactId>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter-engine</artifactId>
+			<scope>test</scope>
+		</dependency>
+  </dependencies>
+</project>

packages/core/java/src/main/java/org/itk/wasm/BinaryFile.java

@@ -0,0 +1,15 @@
+package org.itk.wasm;
+
+import java.nio.file.Path;
+
+public class BinaryFile {
+	public PurePosixPath path;
+
+	public BinaryFile(PurePosixPath path) {
+		this.path = path;
+	}
+
+	public BinaryFile(Path path) {
+		this(new PurePosixPath(path));
+	}
+}

packages/core/java/src/main/java/org/itk/wasm/BinaryStream.java

@@ -0,0 +1,28 @@
+/*-
+ * #%L
+ * Java bindings for itk-wasm.
+ * %%
+ * Copyright (C) 2023 ITK developers.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package org.itk.wasm;
+
+public class BinaryStream {
+  public byte[] data;
+
+  public BinaryStream(byte[] data) {
+    this.data = data;
+  }
+}

packages/core/java/src/main/java/org/itk/wasm/FloatTypes.java

@@ -0,0 +1,18 @@
+package org.itk.wasm;
+
+public enum FloatTypes {
+    Float32("float32"),
+    Float64("float64"),
+    SpacePrecisionType("float64");
+
+    private final String value;
+
+    FloatTypes(String value) {
+        this.value = value;
+    }
+
+    @Override
+    public String toString() {
+        return value;
+    }
+}

packages/core/java/src/main/java/org/itk/wasm/IO.java

@@ -0,0 +1,29 @@
+package org.itk.wasm;
+
+import java.io.ByteArrayOutputStream;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+public final class IO {
+
+	public IO() { }
+
+  public static byte[] readBytes(String path) throws IOException {
+    //try (InputStream is = Main.class.getResourceAsStream(filename)) {
+    try (InputStream is = new FileInputStream(path)) {
+      ByteArrayOutputStream buffer = new ByteArrayOutputStream();
+      int nRead;
+      byte[] buf = new byte[16384];
+      while ((nRead = is.read(buf, 0, buf.length)) != -1) {
+        buffer.write(buf, 0, nRead);
+      }
+      return buffer.toByteArray();
+    }
+  }
+
+  public static String readString(String path) throws IOException {
+  	return new String(readBytes(path), StandardCharsets.UTF_8);
+  }
+}

packages/core/java/src/main/java/org/itk/wasm/Image.java

@@ -0,0 +1,69 @@
+package org.itk.wasm;
+
+import java.util.*;
+
+public class Image {
+	public ImageType imageType;
+	public String name;
+	public List<Double> origin;
+	public List<Double> spacing;
+	public double[][] direction;
+	public List<Integer> size;
+	public Map<String, Object> metadata;
+	public double[] data;
+
+	public Image() {
+		this.imageType = new ImageType();
+		this.name = "Image";
+		this.origin = new ArrayList<>();
+		this.spacing = new ArrayList<>();
+		this.direction = new double[0][0];
+		this.size = new ArrayList<>();
+		this.metadata = new HashMap<>();
+		this.data = null;
+	}
+
+	public void postInit() {
+		if (imageType instanceof Map) {
+			imageType = new ImageType();
+			Map<String, Object> imageTypeMap = asdict(imageType);
+			// Set values from the map to the corresponding fields in ImageType
+			// Example: imageType.setDimension((int) imageTypeMap.get("dimension"));
+			// Add similar code for other fields
+		}
+
+		int dimension = imageType.dimension;
+		if (origin.isEmpty()) {
+			for (int i = 0; i < dimension; i++) {
+				origin.add(0.0);
+			}
+		}
+
+		if (spacing.isEmpty()) {
+			for (int i = 0; i < dimension; i++) {
+				spacing.add(1.0);
+			}
+		}
+
+		if (direction.length == 0) {
+			direction = new double[dimension][dimension];
+			for (int i = 0; i < dimension; i++) {
+				for (int j = 0; j < dimension; j++) {
+					if (i == j) {
+						direction[i][j] = 1.0;
+					} else {
+						direction[i][j] = 0.0;
+					}
+				}
+			}
+		}
+
+		if (size.isEmpty()) {
+			for (int i = 0; i < dimension; i++) {
+				size.add(1);
+			}
+		}
+	}
+
+	// Add getters and setters for the fields
+}

packages/core/java/src/main/java/org/itk/wasm/ImageType.java

@@ -0,0 +1,17 @@
+package org.itk.wasm;
+
+public class ImageType {
+	public int dimension;
+	public IntTypes componentType;
+	public PixelType pixelType;
+	public int components;
+
+	public ImageType() {
+		this.dimension = 2;
+		this.componentType = IntTypes.UInt8;
+		this.pixelType = PixelType.Scalar;
+		this.components = 1;
+	}
+
+	// Add getters and setters for the fields
+}

packages/core/java/src/main/java/org/itk/wasm/IntTypes.java

@@ -0,0 +1,27 @@
+package org.itk.wasm;
+
+public enum IntTypes {
+    Int8("int8"),
+    UInt8("uint8"),
+    Int16("int16"),
+    UInt16("uint16"),
+    Int32("int32"),
+    UInt32("uint32"),
+    Int64("int64"),
+    UInt64("uint64"),
+    SizeValueType("uint64"),
+    IdentifierType("uint64"),
+    IndexValueType("int64"),
+    OffsetValueType("int64");
+
+    private final String value;
+
+    IntTypes(String value) {
+        this.value = value;
+    }
+
+    @Override
+    public String toString() {
+        return value;
+    }
+}

packages/core/java/src/main/java/org/itk/wasm/InterfaceType.java

@@ -0,0 +1,31 @@
+/*-
+ * #%L
+ * Java bindings for itk-wasm.
+ * %%
+ * Copyright (C) 2023 ITK developers.
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+package org.itk.wasm;
+
+public enum InterfaceType {
+  TextFile,
+  BinaryFile,
+  TextStream,
+  BinaryStream,
+  Image,
+  Mesh,
+  PolyData,
+  JsonObject
+}

packages/core/java/src/main/java/org/itk/wasm/JsonObject.java

@@ -0,0 +1,19 @@
+package org.itk.wasm;
+
+import java.util.Map;
+
+public class JsonObject {
+    private Map<String, Object> data;
+
+    public JsonObject(Map<String, Object> data) {
+        this.data = data;
+    }
+
+    public Map<String, Object> getData() {
+        return data;
+    }
+
+    public void setData(Map<String, Object> data) {
+        this.data = data;
+    }
+}