Merge pull request #593 from jamesmudd/scalar-attributes

Filling out attribute support
jamesmudd · Jul 20, 2024 · bf85a6f · bf85a6f
2 parents 29384a1 + c28b354
commit bf85a6f
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Showing 47 changed files with 1,229 additions and 244 deletions.
diff --git a/jhdf/src/main/java/io/jhdf/AbstractWritableNode.java b/jhdf/src/main/java/io/jhdf/AbstractWritableNode.java
@@ -14,11 +14,13 @@
 import io.jhdf.api.Group;
 import io.jhdf.api.WritableAttributeImpl;
 import io.jhdf.api.WritableNode;
+import org.apache.commons.lang3.StringUtils;
 
 import java.io.File;
 import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.Objects;
 
 public abstract class AbstractWritableNode implements WritableNode {
 	private final Group parent;
@@ -77,6 +79,10 @@ public HdfFile getHdfFile() {
 
 	@Override
 	public Attribute putAttribute(String name, Object data) {
+		if(StringUtils.isBlank(name)) {
+			throw new IllegalArgumentException("name cannot be null or blank");
+		}
+		Objects.requireNonNull(data, "Cannot write null attributes");
 		WritableAttributeImpl attribute = new WritableAttributeImpl(name, this, data);
 		return attributes.put(name, attribute);
 	}

diff --git a/jhdf/src/main/java/io/jhdf/FractalHeap.java b/jhdf/src/main/java/io/jhdf/FractalHeap.java
@@ -9,6 +9,8 @@
  */
 package io.jhdf;
 
+import io.jhdf.btree.BTreeV2;
+import io.jhdf.btree.record.HugeFractalHeapObjectUnfilteredRecord;
 import io.jhdf.checksum.ChecksumUtils;
 import io.jhdf.exceptions.HdfException;
 import io.jhdf.exceptions.UnsupportedHdfException;
@@ -35,9 +37,6 @@
 import static io.jhdf.Utils.readBytesAsUnsignedLong;
 import static java.nio.ByteOrder.LITTLE_ENDIAN;
 
-import io.jhdf.btree.BTreeV2;
-import io.jhdf.btree.record.HugeFractalHeapObjectUnfilteredRecord;
-
 /**
  * Fractal heap implementation. Used for storing data which can be looked up via
  * an ID.

diff --git a/jhdf/src/main/java/io/jhdf/HdfFile.java b/jhdf/src/main/java/io/jhdf/HdfFile.java
@@ -35,8 +35,8 @@
 import java.net.URI;
 import java.nio.ByteBuffer;
 import java.nio.channels.FileChannel;
-import java.nio.file.Files;
 import java.nio.file.FileSystems;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.nio.file.StandardCopyOption;

diff --git a/jhdf/src/main/java/io/jhdf/Utils.java b/jhdf/src/main/java/io/jhdf/Utils.java
@@ -379,9 +379,9 @@ public static void setBit(byte[] bytes, int bit, boolean value) {
 		final int byteIndex = bit / 8;
 		final int bitInByte = bit % 8;
 		if(value) {
-			bytes[byteIndex] |= 1 << bitInByte;
+			bytes[byteIndex] |= (byte) (1 << bitInByte);
 		} else {
-			bytes[byteIndex] &= ~(1 << bitInByte);
+			bytes[byteIndex] &= (byte) ~(1 << bitInByte);
 		}
 	}
 
@@ -403,6 +403,16 @@ public static int[] getDimensions(Object data) {
 		return ArrayUtils.toPrimitive(dims.toArray(new Integer[0]));
 	}
 
+	public static Class<?> getType(Object obj) {
+		final Class<?> type;
+		if(obj.getClass().isArray()) {
+			type = getArrayType(obj);
+		} else {
+			type = obj.getClass();
+		}
+		return type;
+	}
+
 	public static Class<?> getArrayType(Object array) {
 		Object element = Array.get(array, 0);
 		if (element.getClass().isArray()) {
@@ -432,14 +442,18 @@ public static Object[] flatten(Object data) {
     }
 
 	private static void flattenInternal(Object data, List<Object> flat) {
-		int length = Array.getLength(data);
-		for (int i = 0; i < length; i++) {
-			Object element = Array.get(data, i);
-			if (element.getClass().isArray()) {
-				flattenInternal(element, flat);
-			} else {
-				flat.add(element);
+		if (data.getClass().isArray()) {
+			int length = Array.getLength(data);
+			for (int i = 0; i < length; i++) {
+				Object element = Array.get(data, i);
+				if (element.getClass().isArray()) {
+					flattenInternal(element, flat);
+				} else {
+					flat.add(element);
+				}
 			}
+		} else {
+			flat.add(data);
 		}
 	}
 }
diff --git a/jhdf/src/main/java/io/jhdf/WritableDatasetImpl.java b/jhdf/src/main/java/io/jhdf/WritableDatasetImpl.java
@@ -15,7 +15,6 @@
 import io.jhdf.api.NodeType;
 import io.jhdf.api.WritiableDataset;
 import io.jhdf.exceptions.HdfWritingException;
-import io.jhdf.exceptions.UnsupportedHdfException;
 import io.jhdf.filter.PipelineFilterWithData;
 import io.jhdf.object.datatype.DataType;
 import io.jhdf.object.message.AttributeInfoMessage;
@@ -34,7 +33,6 @@
 import java.io.File;
 import java.lang.reflect.Array;
 import java.nio.ByteBuffer;
-import java.nio.ByteOrder;
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collections;
@@ -78,7 +76,7 @@ public long getStorageInBytes() {
 
 	@Override
 	public int[] getDimensions() {
-		return Utils.getDimensions(data);
+		return dataSpace.getDimensions();
 	}
 
 	@Override
@@ -232,52 +230,15 @@ public long write(HdfFileChannel hdfFileChannel, long position) {
 
 	private long writeData(HdfFileChannel hdfFileChannel, long dataAddress) {
 		logger.info("Writing data for dataset [{}] at position [{}]", getPath(), dataAddress);
-		Class<?> arrayType = Utils.getArrayType(this.data);
-		long totalBytes = dataSpace.getTotalLength() * dataType.getSize();
 
-		int[] dimensions = dataSpace.getDimensions();
-		int fastDimSize = dimensions[dimensions.length - 1];
-		ByteBuffer buffer = ByteBuffer.allocate(fastDimSize * dataType.getSize()).order(ByteOrder.nativeOrder());
 		hdfFileChannel.position(dataAddress);
 
-		// TODO move out into data types?
-		if(arrayType.equals(byte.class)) {
-			writeByteData(data, dimensions, buffer, hdfFileChannel);
-		} else if(arrayType.equals(int.class)) {
-			writeIntData(data, dimensions, buffer, hdfFileChannel);
-		} else if (arrayType.equals(double.class)) {
-			writeDoubleData(data, dimensions, buffer, hdfFileChannel);
-		} else {
-			throw new UnsupportedHdfException("Writing [" + arrayType.getSimpleName() + "] is not supported");
-		}
-		return totalBytes;
-	}
+		dataType.writeData(data, getDimensions(), hdfFileChannel);
 
-	private static void writeByteData(Object data, int[] dims, ByteBuffer buffer, HdfFileChannel hdfFileChannel) {
-		if (dims.length > 1) {
-			for (int i = 0; i < dims[0]; i++) {
-				Object newArray = Array.get(data, i);
-				writeByteData(newArray, stripLeadingIndex(dims), buffer, hdfFileChannel);
-			}
-		} else {
-			buffer.put((byte[]) data);
-			buffer.rewind();
-			hdfFileChannel.write(buffer);
-			buffer.clear();
-		}
-	}
-	private static void writeIntData(Object data, int[] dims, ByteBuffer buffer, HdfFileChannel hdfFileChannel) {
-		if (dims.length > 1) {
-			for (int i = 0; i < dims[0]; i++) {
-				Object newArray = Array.get(data, i);
-				writeIntData(newArray, stripLeadingIndex(dims), buffer, hdfFileChannel);
-			}
-		} else {
-			buffer.asIntBuffer().put((int[]) data);
-			hdfFileChannel.write(buffer);
-			buffer.clear();
-		}
+		return  dataSpace.getTotalLength() * dataType.getSize();
 	}
+
+
 	private static void writeDoubleData(Object data, int[] dims, ByteBuffer buffer, HdfFileChannel hdfFileChannel) {
 		if (dims.length > 1) {
 			for (int i = 0; i < dims[0]; i++) {

diff --git a/jhdf/src/main/java/io/jhdf/WritableGroupImpl.java b/jhdf/src/main/java/io/jhdf/WritableGroupImpl.java
@@ -26,6 +26,7 @@
 import io.jhdf.object.message.LinkMessage;
 import io.jhdf.object.message.Message;
 import io.jhdf.storage.HdfFileChannel;
+import org.apache.commons.lang3.StringUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -100,6 +101,9 @@ public boolean isAttributeCreationOrderTracked() {
 
 	@Override
 	public WritiableDataset putDataset(String name, Object data) {
+		if(StringUtils.isBlank(name)) {
+			throw new IllegalArgumentException("name cannot be null or blank");
+		}
 		WritableDatasetImpl writableDataset = new WritableDatasetImpl(data, name, this);
 		children.put(name, writableDataset);
 		logger.info("Added dataset [{}] to group [{}]", name, getPath());
@@ -108,6 +112,9 @@ public WritiableDataset putDataset(String name, Object data) {
 
 	@Override
 	public WritableGroup putGroup(String name) {
+		if(StringUtils.isBlank(name)) {
+			throw new IllegalArgumentException("name cannot be null or blank");
+		}
 		WritableGroupImpl newGroup = new WritableGroupImpl(this, name);
 		children.put(name, newGroup);
 		logger.info("Added group [{}] to group [{}]", name, getPath());
@@ -139,7 +146,7 @@ public long write(HdfFileChannel hdfFileChannel, long position) {
 			AttributeInfoMessage attributeInfoMessage = AttributeInfoMessage.create();
 			messages.add(attributeInfoMessage);
 			for (Map.Entry<String, Attribute> attribute : getAttributes().entrySet()) {
-				logger.info("Writing attribute [{}]", attribute.getKey());
+				logger.info("Writing attribute [{}] in group [{}]", attribute.getKey(), getName());
 				AttributeMessage attributeMessage = AttributeMessage.create(attribute.getKey(), attribute.getValue());
 				messages.add(attributeMessage);
 			}

diff --git a/jhdf/src/main/java/io/jhdf/dataset/DatasetReader.java b/jhdf/src/main/java/io/jhdf/dataset/DatasetReader.java
@@ -11,6 +11,7 @@
 
 import io.jhdf.object.datatype.DataType;
 import io.jhdf.storage.HdfBackingStorage;
+
 import java.lang.reflect.Array;
 import java.nio.ByteBuffer;
 

diff --git a/jhdf/src/main/java/io/jhdf/object/datatype/ArrayDataType.java b/jhdf/src/main/java/io/jhdf/object/datatype/ArrayDataType.java
@@ -9,12 +9,14 @@
  */
 package io.jhdf.object.datatype;
 
-import static io.jhdf.Utils.readBytesAsUnsignedInt;
 import io.jhdf.dataset.DatasetReader;
 import io.jhdf.storage.HdfBackingStorage;
+import org.apache.commons.lang3.ArrayUtils;
+
 import java.lang.reflect.Array;
 import java.nio.ByteBuffer;
-import org.apache.commons.lang3.ArrayUtils;
+
+import static io.jhdf.Utils.readBytesAsUnsignedInt;
 
 /**
  * Class for reading array data type messages.

diff --git a/jhdf/src/main/java/io/jhdf/object/datatype/DataType.java b/jhdf/src/main/java/io/jhdf/object/datatype/DataType.java
@@ -14,6 +14,7 @@
 import io.jhdf.exceptions.HdfException;
 import io.jhdf.exceptions.UnsupportedHdfException;
 import io.jhdf.storage.HdfBackingStorage;
+import io.jhdf.storage.HdfFileChannel;
 
 import java.nio.ByteBuffer;
 import java.util.BitSet;
@@ -94,25 +95,22 @@ protected DataType(ByteBuffer bb) {
 	}
 
 	public static DataType fromObject(Object data) {
-		if (data.getClass().isArray()) {
-			Class<?> type = Utils.getArrayType(data);
-			if(type.equals(byte.class)) {
-				return new FixedPoint(1);
-			} else if (type.equals(short.class)) {
-				return new FixedPoint(2);
-			} else if (type.equals(int.class)) {
-				return new FixedPoint(4);
-			} else if (type.equals(long.class)) {
-				return new FixedPoint(8);
-			} else if (type.equals(float.class)) {
-				return FloatingPoint.FLOAT;
-			} else if (type.equals(double.class)) {
-				return FloatingPoint.DOUBLE;
-			}
-			throw new HdfException("Could not create DataType for: " + type);
-
+		final Class<?> type = Utils.getType(data);
+
+		if (type == byte.class || type == Byte.class) {
+			return new FixedPoint(1);
+		} else if (type == short.class || type == Short.class) {
+			return new FixedPoint(2);
+		} else if (type == int.class || type == Integer.class) {
+			return new FixedPoint(4);
+		} else if (type == long.class || type == Long.class) {
+			return new FixedPoint(8);
+		} else if (type == float.class || type == Float.class) {
+			return FloatingPoint.FLOAT;
+		} else if (type == double.class || type == Double.class) {
+			return FloatingPoint.DOUBLE;
 		} else {
-			throw new UnsupportedHdfException("Only arrays can be written at the moment");
+			throw new HdfException("Could not create DataType for: " + type);
 		}
 	}
 
@@ -170,4 +168,8 @@ protected BufferBuilder toBufferBuilder() {
 			.writeBitSet(classBits, 3)
 			.writeInt(getSize());
 	}
+
+	public void writeData(Object data, int[] dimensions, HdfFileChannel hdfFileChannel) {
+		throw new UnsupportedHdfException("Data type [" + getClass().getSimpleName() + "] does not support writing");
+	}
 }