improve javadoc

bioimage-io · Dec 12, 2023 · 26e15ab · 26e15ab
1 parent d5b7910
commit 26e15ab
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Showing 5 changed files with 325 additions and 356 deletions.
diff --git a/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java b/src/main/java/io/bioimage/modelrunner/bioimageio/description/TensorSpec.java
@@ -362,6 +362,8 @@ public void validate(int[] tileSize) throws Exception {
      * please use {@link #setTileSizeForTensorAndImageSize(int[], int[])}
      * @param tileSize
      * 	the patch array size to validate, it has to be in the axes order of the tensor
+     * @param tileAxesOrder
+     * 	the axes order of the 'tileSize' argument
      * @throws Exception if the patch does not comply with the constraints specified
      */
     public void validate(int[] tileSize, String tileAxesOrder) throws Exception {
@@ -414,6 +416,8 @@ public void setTileSizeForTensorAndImageSize(int[] tileSize, int[] tensorImageSi
      * 	axes order of the tile provided
      * @param tensorImageSize
      * 	size of the image that is used for the tensor.
+     * @param imageAxesOrder
+     * 	the axes order of the image size provided
      * @throws Exception if the patch size is not able to 
      * 	fulfill the requirements of the tensor
      */

diff --git a/src/main/java/io/bioimage/modelrunner/tensor/ImgLib2ToArray.java b/src/main/java/io/bioimage/modelrunner/tensor/ImgLib2ToArray.java
@@ -20,8 +20,6 @@
  */
 package io.bioimage.modelrunner.tensor;
 
-import java.nio.ByteBuffer;
-
 import net.imglib2.Cursor;
 import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.NativeType;
@@ -40,9 +38,7 @@
 import net.imglib2.view.Views;
 
 /**
- * Class that maps {@link Tensor} objects to {@link ByteBuffer} objects.
- * This is done to modify the files that are used to communicate between process
- * to avoid the TF2-TF1/Pytorch incompatibility that happens in these systems
+ * Class that maps {@link Tensor} objects to an array of the corresponding primitive type.
  * 
  * @author Carlos Garcia Lopez de Haro
  */
@@ -76,18 +72,18 @@ public static < T extends RealType< T > & NativeType< T > > Object build(Tensor<
     }
 
     /**
-     * Adds the {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link RandomAccessibleInterval} data into a Java flat array of the corresponding 
+     * primitive type with C-ordering
      * 
      * @param <T> 
      * 	the type of the {@link RandomAccessibleInterval}
      * @param rai 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat array of the corresponding primitive type that contains the data of the {@link RandomAccessibleInterval}
+     * 	in C-order
      * @throws IllegalArgumentException If the {@link RandomAccessibleInterval} type is not supported.
      */
-    public static <T extends Type<T>> Object build(RandomAccessibleInterval<T> rai)
+    public static < T extends RealType< T > & NativeType< T > > Object build(RandomAccessibleInterval<T> rai)
     {
     	if (Util.getTypeFromInterval(rai) instanceof ByteType) {
     		return buildInt8((RandomAccessibleInterval<ByteType>) rai);
@@ -113,13 +109,11 @@ public static <T extends Type<T>> Object build(RandomAccessibleInterval<T> rai)
     }
 
     /**
-     * Adds the ByteType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link ByteType} {@link RandomAccessibleInterval} data into a Java flat byte array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat byte array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static byte[] buildInt8(RandomAccessibleInterval<ByteType> tensor)
     {
@@ -142,13 +136,11 @@ private static byte[] buildInt8(RandomAccessibleInterval<ByteType> tensor)
     }
 
     /**
-     * Adds the ByteType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link UnsignedByteType} {@link RandomAccessibleInterval} data into a Java flat byte array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat byte array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static byte[] buildUint8(RandomAccessibleInterval<UnsignedByteType> tensor)
     {
@@ -171,13 +163,11 @@ private static byte[] buildUint8(RandomAccessibleInterval<UnsignedByteType> tens
     }
 
     /**
-     * Adds the ByteType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link ShortType} {@link RandomAccessibleInterval} data into a Java flat short array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat short array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static short[] buildInt16(RandomAccessibleInterval<ShortType> tensor)
     {
@@ -200,13 +190,11 @@ private static short[] buildInt16(RandomAccessibleInterval<ShortType> tensor)
     }
 
     /**
-     * Adds the ByteType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link UnsignedShortType} {@link RandomAccessibleInterval} data into a Java flat short array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat short array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static short[] buildUint16(RandomAccessibleInterval<UnsignedShortType> tensor)
     {
@@ -229,13 +217,11 @@ private static short[] buildUint16(RandomAccessibleInterval<UnsignedShortType> t
     }
 
     /**
-     * Adds the IntType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link IntType} {@link RandomAccessibleInterval} data into a Java flat int array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat int array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static int[] buildInt32(RandomAccessibleInterval<IntType> tensor)
     {
@@ -258,13 +244,11 @@ private static int[] buildInt32(RandomAccessibleInterval<IntType> tensor)
     }
 
     /**
-     * Adds the IntType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link UnsignedIntType} {@link RandomAccessibleInterval} data into a Java flat int array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat int array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static int[] buildUint32(RandomAccessibleInterval<UnsignedIntType> tensor)
     {
@@ -287,13 +271,11 @@ private static int[] buildUint32(RandomAccessibleInterval<UnsignedIntType> tenso
     }
 
     /**
-     * Adds the IntType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link LongType} {@link RandomAccessibleInterval} data into a Java flat long array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat long array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static long[] buildInt64(RandomAccessibleInterval<LongType> tensor)
     {
@@ -316,13 +298,11 @@ private static long[] buildInt64(RandomAccessibleInterval<LongType> tensor)
     }
 
     /**
-     * Adds the FloatType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link FloatType} {@link RandomAccessibleInterval} data into a Java flat float array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat float array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static float[] buildFloat32(RandomAccessibleInterval<FloatType> tensor)
     {
@@ -345,13 +325,11 @@ private static float[] buildFloat32(RandomAccessibleInterval<FloatType> tensor)
     }
 
     /**
-     * Adds the DoubleType {@link RandomAccessibleInterval} data to the {@link ByteBuffer} provided.
-     * The position of the ByteBuffer is kept in the same place as it was received.
+     * Gets the {@link DoubleType} {@link RandomAccessibleInterval} data into a Java flat double array with C-ordering
      * 
      * @param tensor 
-     * 	{@link RandomAccessibleInterval} to be mapped into byte buffer
-     * @param byteBuffer 
-     * 	target bytebuffer
+     * 	{@link RandomAccessibleInterval} to be flattened into a Java array
+     * @return a Java flat double array that contains the data of the {@link RandomAccessibleInterval} in C-order
      */
     private static double[] buildFloat64(RandomAccessibleInterval<DoubleType> tensor)
     {