Progress towards attributes

jamesmudd · May 23, 2024 · 26a8b21 · 26a8b21
1 parent a29bce5
commit 26a8b21
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Showing 8 changed files with 116 additions and 3 deletions.
diff --git a/jhdf/src/main/java/io/jhdf/AttributeImpl.java b/jhdf/src/main/java/io/jhdf/AttributeImpl.java
@@ -14,6 +14,7 @@
 import io.jhdf.dataset.DatasetReader;
 import io.jhdf.object.datatype.DataType;
 import io.jhdf.object.message.AttributeMessage;
+import io.jhdf.object.message.DataSpace;
 import io.jhdf.storage.HdfBackingStorage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -101,4 +102,14 @@ public Class<?> getJavaType() {
 	public ByteBuffer getBuffer() {
 		return message.getDataBuffer();
 	}
+
+	@Override
+	public DataSpace getDataSpace() {
+		return message.getDataSpace();
+	}
+
+	@Override
+    public DataType getDataType() {
+        return message.getDataType();
+    }
 }
diff --git a/jhdf/src/main/java/io/jhdf/WritableGroupImpl.java b/jhdf/src/main/java/io/jhdf/WritableGroupImpl.java
@@ -10,6 +10,7 @@
 
 package io.jhdf;
 
+import io.jhdf.api.Attribute;
 import io.jhdf.api.Dataset;
 import io.jhdf.api.Group;
 import io.jhdf.api.Node;
@@ -18,6 +19,7 @@
 import io.jhdf.api.WritableNode;
 import io.jhdf.api.WritiableDataset;
 import io.jhdf.exceptions.UnsupportedHdfException;
+import io.jhdf.object.message.AttributeMessage;
 import io.jhdf.object.message.GroupInfoMessage;
 import io.jhdf.object.message.LinkInfoMessage;
 import io.jhdf.object.message.LinkMessage;
@@ -131,6 +133,12 @@ public long write(HdfFileChannel hdfFileChannel, long position) {
 			messages.add(linkMessage);
 		}
 
+		for (Map.Entry<String, Attribute> attribute : getAttributes().entrySet()) {
+			logger.info("Writing attribute [{}]", attribute.getKey());
+			AttributeMessage attributeMessage = AttributeMessage.create(attribute.getKey(), attribute.getValue());
+			messages.add(attributeMessage);
+		}
+
 		ObjectHeader.ObjectHeaderV2 objectHeader = new ObjectHeader.ObjectHeaderV2(position, messages);
 
 		ByteBuffer tempBuffer = objectHeader.toBuffer();

diff --git a/jhdf/src/main/java/io/jhdf/api/Attribute.java b/jhdf/src/main/java/io/jhdf/api/Attribute.java
@@ -18,6 +18,9 @@
  */
 package io.jhdf.api;
 
+import io.jhdf.object.datatype.DataType;
+import io.jhdf.object.message.DataSpace;
+
 import java.nio.ByteBuffer;
 
 /**
@@ -109,4 +112,7 @@ public interface Attribute {
 	ByteBuffer getBuffer();
 
 
+	DataSpace getDataSpace();
+
+	DataType getDataType();
 }
diff --git a/jhdf/src/main/java/io/jhdf/api/WritableAttributeImpl.java b/jhdf/src/main/java/io/jhdf/api/WritableAttributeImpl.java
@@ -76,7 +76,16 @@ public boolean isEmpty() {
 
 	@Override
 	public ByteBuffer getBuffer() {
-		// TODO
-		return null;
+		return dataType.encodeData(data);
+	}
+
+	@Override
+	public DataSpace getDataSpace() {
+		return dataSpace;
+	}
+
+	@Override
+	public DataType getDataType() {
+		return dataType;
 	}
 }
diff --git a/jhdf/src/main/java/io/jhdf/object/datatype/DataType.java b/jhdf/src/main/java/io/jhdf/object/datatype/DataType.java
@@ -144,6 +144,11 @@ public int getSize() {
 	 */
 	public abstract Object fillData(ByteBuffer buffer, int[] dimensions, HdfBackingStorage hdfBackingStorage);
 
+	// TODO could be abstract when there are more impls
+	public ByteBuffer encodeData(Object data){
+		throw new UnsupportedHdfException("Data type [" + getClass().getSimpleName() + "] does not support writing");
+	}
+
 	// TODO could be abstract when there are more impls
 	public ByteBuffer toBuffer() {
 		throw new UnsupportedHdfException("Data type [" + getClass().getSimpleName() + "] does not support writing");

diff --git a/jhdf/src/main/java/io/jhdf/object/datatype/FixedPoint.java b/jhdf/src/main/java/io/jhdf/object/datatype/FixedPoint.java
@@ -9,8 +9,11 @@
  */
 package io.jhdf.object.datatype;
 
+import io.jhdf.Utils;
 import io.jhdf.exceptions.HdfTypeException;
+import io.jhdf.exceptions.UnsupportedHdfException;
 import io.jhdf.storage.HdfBackingStorage;
+import org.apache.commons.lang3.ArrayUtils;
 
 import java.lang.reflect.Array;
 import java.math.BigInteger;
@@ -19,7 +22,9 @@
 import java.nio.IntBuffer;
 import java.nio.LongBuffer;
 import java.nio.ShortBuffer;
+import java.util.Arrays;
 
+import static io.jhdf.Utils.flatten;
 import static io.jhdf.Utils.stripLeadingIndex;
 
 public class FixedPoint extends DataType implements OrderedDataType, WritableDataType {
@@ -163,7 +168,20 @@ public Object fillData(ByteBuffer buffer, int[] dimensions, HdfBackingStorage hd
 		return data;
 	}
 
-	// Signed Fixed Point
+    @Override
+    public ByteBuffer encodeData(Object data) {
+		Class<?> type = Utils.getArrayType(data);
+		// TODO multi dimensional and scalar and empty
+		if(type == int.class) {
+			Object[] flattened = flatten(data);
+			ByteBuffer buffer = ByteBuffer.allocate(flattened.length * 4);
+			buffer.asIntBuffer().put((int[]) data);
+			return buffer;
+		}
+		throw new UnsupportedHdfException("Cant write type");
+	}
+
+    // Signed Fixed Point
 
 	private static void fillData(Object data, int[] dims, ByteBuffer buffer) {
 		if (dims.length > 1) {

diff --git a/jhdf/src/main/java/io/jhdf/object/message/AttributeMessage.java b/jhdf/src/main/java/io/jhdf/object/message/AttributeMessage.java
@@ -9,8 +9,10 @@
  */
 package io.jhdf.object.message;
 
+import io.jhdf.BufferBuilder;
 import io.jhdf.ObjectHeader;
 import io.jhdf.Utils;
+import io.jhdf.api.Attribute;
 import io.jhdf.exceptions.UnsupportedHdfException;
 import io.jhdf.object.datatype.DataType;
 import io.jhdf.storage.HdfBackingStorage;
@@ -164,4 +166,36 @@ public int getMessageType() {
 		return MESSAGE_TYPE;
 	}
 
+	public static AttributeMessage create(String name, Attribute attribute) {
+		return new AttributeMessage(name, attribute.getDataSpace(), attribute.getDataType(), attribute.getData());
+	}
+
+	private AttributeMessage(String name, DataSpace dataSpace, DataType dataType, Object data) {
+		this.name = name;
+		this.version = 3;
+		this.dataSpace = dataSpace;
+		this.dataType = dataType;
+		this.data = dataType.encodeData(data);
+	}
+
+	@Override
+	public ByteBuffer toBuffer() {
+
+		byte[] nameBytes = name.getBytes(StandardCharsets.UTF_8);
+		ByteBuffer dataTypeBytes = dataType.toBuffer();
+		ByteBuffer dataSpaceBytes = dataSpace.toBuffer();
+
+		return new BufferBuilder()
+			.writeByte(3) // version
+			.writeByte(0) // flags
+			.writeShort(nameBytes.length)
+			.writeShort(dataTypeBytes.capacity())
+			.writeShort(dataSpaceBytes.capacity())
+			.writeByte(1) // name charset
+			.writeBytes(nameBytes)
+			.writeBuffer(dataTypeBytes)
+			.writeBuffer(dataSpaceBytes)
+			.writeBuffer(data)
+			.build();
+	}
 }
diff --git a/jhdf/src/test/java/io/jhdf/SimpleWritingTest.java b/jhdf/src/test/java/io/jhdf/SimpleWritingTest.java
@@ -10,6 +10,7 @@
 
 package io.jhdf;
 
+import io.jhdf.api.Attribute;
 import io.jhdf.api.Dataset;
 import io.jhdf.api.Node;
 import io.jhdf.api.WritableGroup;
@@ -145,4 +146,25 @@ void readSimpleFileWithDatasetsWithH5Dump() throws Exception {
 			H5Dump.assetXmlAndHdfFileMatch(hdf5FileXml, hdfFile);
 		}
 	}
+
+	@Test
+	@Order(5)
+	void writeAttributes() throws Exception {
+		WritableHdfFile writableHdfFile = HdfFile.write(tempFile);
+
+		WritableGroup intGroup = writableHdfFile.putGroup("intGroup");
+		int[] intData1 = new int[]{-5, -4, -3, -2, -1, 0, 1,2,3,4,5 };
+		intGroup.putDataset("intData1", intData1);
+
+		writableHdfFile.putAttribute("rootAttribute", new int[] {1,2,3});
+
+		// Actually flush and write everything
+		writableHdfFile.close();
+
+		// Now read it back
+		try(HdfFile hdfFile = new HdfFile(tempFile)) {
+			Map<String, Attribute> attributes = hdfFile.getAttributes();
+			assertThat(attributes).containsKeys("rootAttribute");
+		}
+	}
 }