improve javadoc

Author: carlosuc3m

src/main/java/io/bioimage/modelrunner/pytorch/JavaWorker.java

@@ -21,7 +21,13 @@ public class JavaWorker {
 	private final PytorchInterface pi;
 
 	private boolean cancelRequested = false;
-	
+
+	/**
+	 * Method in the child process that is in charge of keeping the process open and calling the model load,
+	 * model inference and model closing
+	 * @param args
+	 * 	args of the parent process
+	 */
 	public static void main(String[] args) {
 
     	try(Scanner scanner = new Scanner(System.in)){

src/main/java/io/bioimage/modelrunner/pytorch/shm/ShmBuilder.java

@@ -29,20 +29,17 @@
 import java.util.Arrays;
 
 import ai.djl.ndarray.NDArray;
-import ai.djl.ndarray.types.DataType;
-import net.imglib2.RandomAccessibleInterval;
 import net.imglib2.type.numeric.integer.IntType;
 import net.imglib2.type.numeric.integer.LongType;
 import net.imglib2.type.numeric.integer.UnsignedByteType;
 import net.imglib2.type.numeric.real.DoubleType;
 import net.imglib2.type.numeric.real.FloatType;
 
 /**
- * A {@link RandomAccessibleInterval} builder for TensorFlow {@link Tensor} objects.
- * Build ImgLib2 objects (backend of {@link io.bioimage.modelrunner.tensor.Tensor})
- * from Tensorflow 2 {@link Tensor}
+ * A utility class that converts {@link NDArray}s into {@link SharedMemoryArray}s for
+ * interprocessing communication
  * 
- * @author Carlos Garcia Lopez de Haro and Daniel Felipe Gonzalez Obando
+ * @author Carlos Garcia Lopez de Haro
  */
 public final class ShmBuilder
 {
@@ -53,17 +50,15 @@ private ShmBuilder()
     {
     }
 
-	/**
-	 * Creates a {@link RandomAccessibleInterval} from a given {@link TType} tensor
-	 * 
-	 * @param <T> 
-	 * 	the possible ImgLib2 datatypes of the image
-	 * @param tensor 
-	 * 	The {@link TType} tensor data is read from.
-	 * @throws IllegalArgumentException If the {@link TType} tensor type is not supported.
-	 * @throws IOException 
-	 */
-    @SuppressWarnings("unchecked")
+    /**
+     * Create a {@link SharedMemoryArray} from a {@link NDArray}
+     * @param tensor
+     * 	the tensor to be passed into the other process through the shared memory
+     * @param memoryName
+     * 	the name of the memory region where the tensor is going to be copied
+     * @throws IllegalArgumentException if the data type of the tensor is not supported
+     * @throws IOException if there is any error creating the shared memory array
+     */
 	public static void build(NDArray  tensor, String memoryName) throws IllegalArgumentException, IOException
     {
 		switch (tensor.getDataType())
@@ -83,14 +78,6 @@ public static void build(NDArray  tensor, String memoryName) throws IllegalArgum
         }
     }
 
-	/**
-	 * Builds a {@link RandomAccessibleInterval} from a unsigned byte-typed {@link TUint8} tensor.
-	 * 
-	 * @param tensor 
-	 * 	The {@link TUint8} tensor data is read from.
-	 * @return The {@link RandomAccessibleInterval} built from the tensor, of type {@link UnsignedByteType}.
-	 * @throws IOException 
-	 */
     private static void buildFromTensorUByte(NDArray tensor, String memoryName) throws IOException
     {
     	long[] arrayShape = tensor.getShape().getShape();
@@ -102,14 +89,6 @@ private static void buildFromTensorUByte(NDArray tensor, String memoryName) thro
         if (PlatformDetection.isWindows()) shma.close();
     }
 
-	/**
-	 * Builds a {@link RandomAccessibleInterval} from a unsigned int32-typed {@link TInt32} tensor.
-	 * 
-	 * @param tensor 
-	 * 	The {@link TInt32} tensor data is read from.
-	 * @return The {@link RandomAccessibleInterval} built from the tensor, of type {@link IntType}.
-	 * @throws IOException 
-	 */
     private static void buildFromTensorInt(NDArray tensor, String memoryName) throws IOException
     {
     	long[] arrayShape = tensor.getShape().getShape();
@@ -122,14 +101,6 @@ private static void buildFromTensorInt(NDArray tensor, String memoryName) throws
         if (PlatformDetection.isWindows()) shma.close();
     }
 
-	/**
-	 * Builds a {@link RandomAccessibleInterval} from a unsigned float32-typed {@link TFloat32} tensor.
-	 * 
-	 * @param tensor 
-	 * 	The {@link TFloat32} tensor data is read from.
-	 * @return The {@link RandomAccessibleInterval} built from the tensor, of type {@link FloatType}.
-	 * @throws IOException 
-	 */
     private static void buildFromTensorFloat(NDArray tensor, String memoryName) throws IOException
     {
     	long[] arrayShape = tensor.getShape().getShape();
@@ -142,14 +113,6 @@ private static void buildFromTensorFloat(NDArray tensor, String memoryName) thro
         if (PlatformDetection.isWindows()) shma.close();
     }
 
-	/**
-	 * Builds a {@link RandomAccessibleInterval} from a unsigned float64-typed {@link TFloat64} tensor.
-	 * 
-	 * @param tensor 
-	 * 	The {@link TFloat64} tensor data is read from.
-	 * @return The {@link RandomAccessibleInterval} built from the tensor, of type {@link DoubleType}.
-	 * @throws IOException 
-	 */
     private static void buildFromTensorDouble(NDArray tensor, String memoryName) throws IOException
     {
     	long[] arrayShape = tensor.getShape().getShape();
@@ -162,14 +125,6 @@ private static void buildFromTensorDouble(NDArray tensor, String memoryName) thr
         if (PlatformDetection.isWindows()) shma.close();
     }
 
-	/**
-	 * Builds a {@link RandomAccessibleInterval} from a unsigned int64-typed {@link TInt64} tensor.
-	 * 
-	 * @param tensor 
-	 * 	The {@link TInt64} tensor data is read from.
-	 * @return The {@link RandomAccessibleInterval} built from the tensor, of type {@link LongType}.
-	 * @throws IOException 
-	 */
     private static void buildFromTensorLong(NDArray tensor, String memoryName) throws IOException
     {
     	long[] arrayShape = tensor.getShape().getShape();

src/main/java/io/bioimage/modelrunner/pytorch/shm/TensorBuilder.java

@@ -23,13 +23,6 @@
 
 import io.bioimage.modelrunner.tensor.shm.SharedMemoryArray;
 import io.bioimage.modelrunner.utils.CommonUtils;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.img.Img;
-import net.imglib2.type.numeric.integer.IntType;
-import net.imglib2.type.numeric.integer.LongType;
-import net.imglib2.type.numeric.integer.UnsignedByteType;
-import net.imglib2.type.numeric.real.DoubleType;
-import net.imglib2.type.numeric.real.FloatType;
 import net.imglib2.util.Cast;
 
 import java.nio.ByteBuffer;
@@ -44,10 +37,9 @@
 import ai.djl.ndarray.types.Shape;
 
 /**
- * A TensorFlow 2 {@link Tensor} builder from {@link Img} and
- * {@link io.bioimage.modelrunner.tensor.Tensor} objects.
+ * Utility class to build Pytorch tensors from shm segments using {@link SharedMemoryArray}
  * 
- * @author Carlos Garcia Lopez de Haro and Daniel Felipe Gonzalez Obando
+ * @author Carlos Garcia Lopez de Haro
  */
 public final class TensorBuilder {
 
@@ -57,16 +49,15 @@ public final class TensorBuilder {
 	private TensorBuilder() {}
 
 	/**
-	 * Creates {@link TType} instance with the same size and information as the
-	 * given {@link RandomAccessibleInterval}.
+	 * Creates {@link NDArray} instance from a {@link SharedMemoryArray}
 	 * 
-	 * @param <T>
-	 * 	the ImgLib2 data types the {@link RandomAccessibleInterval} can be
 	 * @param array
-	 * 	the {@link RandomAccessibleInterval} that is going to be converted into
-	 *  a {@link TType} tensor
-	 * @return a {@link TType} tensor
-	 * @throws IllegalArgumentException if the type of the {@link RandomAccessibleInterval}
+	 * 	the {@link SharedMemoryArray} that is going to be converted into
+	 *  a {@link NDArray} tensor
+	 * @param manager
+	 * 	DJL manager that controls the creation and destruction of {@link NDArrays}
+	 * @return the Pytorch {@link NDArray} as the one stored in the shared memory segment
+	 * @throws IllegalArgumentException if the type of the {@link SharedMemoryArray}
 	 *  is not supported
 	 */
 	public static NDArray build(SharedMemoryArray array, NDManager manager) throws IllegalArgumentException
@@ -92,17 +83,7 @@ else if (array.getOriginalDataType().equals("int64")) {
 		}
 	}
 
-	/**
-	 * Creates a {@link TType} tensor of type {@link TUint8} from an
-	 * {@link RandomAccessibleInterval} of type {@link UnsignedByteType}
-	 * 
-	 * @param tensor 
-	 * 	The {@link RandomAccessibleInterval} to fill the tensor with.
-	 * @return The {@link TType} tensor filled with the {@link RandomAccessibleInterval} data.
-	 * @throws IllegalArgumentException if the input {@link RandomAccessibleInterval} type is
-	 * not compatible
-	 */
-	public static NDArray buildUByte(SharedMemoryArray tensor, NDManager manager)
+	private static NDArray buildUByte(SharedMemoryArray tensor, NDManager manager)
 		throws IllegalArgumentException
 	{
 		long[] ogShape = tensor.getOriginalShape();
@@ -116,17 +97,7 @@ public static NDArray buildUByte(SharedMemoryArray tensor, NDManager manager)
 		return ndarray;
 	}
 
-	/**
-	 * Creates a {@link TInt32} tensor of type {@link TInt32} from an
-	 * {@link RandomAccessibleInterval} of type {@link IntType}
-	 * 
-	 * @param tensor 
-	 * 	The {@link RandomAccessibleInterval} to fill the tensor with.
-	 * @return The {@link TInt32} tensor filled with the {@link RandomAccessibleInterval} data.
-	 * @throws IllegalArgumentException if the input {@link RandomAccessibleInterval} type is
-	 * not compatible
-	 */
-	public static NDArray buildInt(SharedMemoryArray tensor, NDManager manager)
+	private static NDArray buildInt(SharedMemoryArray tensor, NDManager manager)
 		throws IllegalArgumentException
 	{
 		long[] ogShape = tensor.getOriginalShape();
@@ -143,16 +114,6 @@ public static NDArray buildInt(SharedMemoryArray tensor, NDManager manager)
 		return ndarray;
 	}
 
-	/**
-	 * Creates a {@link TInt64} tensor of type {@link TInt64} from an
-	 * {@link RandomAccessibleInterval} of type {@link LongType}
-	 * 
-	 * @param tensor 
-	 * 	The {@link RandomAccessibleInterval} to fill the tensor with.
-	 * @return The {@link TInt64} tensor filled with the {@link RandomAccessibleInterval} data.
-	 * @throws IllegalArgumentException if the input {@link RandomAccessibleInterval} type is
-	 * not compatible
-	 */
 	private static NDArray buildLong(SharedMemoryArray tensor, NDManager manager)
 		throws IllegalArgumentException
 	{
@@ -170,17 +131,7 @@ private static NDArray buildLong(SharedMemoryArray tensor, NDManager manager)
 		return ndarray;
 	}
 
-	/**
-	 * Creates a {@link TFloat32} tensor of type {@link TFloat32} from an
-	 * {@link RandomAccessibleInterval} of type {@link FloatType}
-	 * 
-	 * @param tensor 
-	 * 	The {@link RandomAccessibleInterval} to fill the tensor with.
-	 * @return The {@link TFloat32} tensor filled with the {@link RandomAccessibleInterval} data.
-	 * @throws IllegalArgumentException if the input {@link RandomAccessibleInterval} type is
-	 * not compatible
-	 */
-	public static NDArray buildFloat(SharedMemoryArray tensor, NDManager manager)
+	private static NDArray buildFloat(SharedMemoryArray tensor, NDManager manager)
 		throws IllegalArgumentException
 	{
 		long[] ogShape = tensor.getOriginalShape();
@@ -197,16 +148,6 @@ public static NDArray buildFloat(SharedMemoryArray tensor, NDManager manager)
 		return ndarray;
 	}
 
-	/**
-	 * Creates a {@link TFloat64} tensor of type {@link TFloat64} from an
-	 * {@link RandomAccessibleInterval} of type {@link DoubleType}
-	 * 
-	 * @param tensor 
-	 * 	The {@link RandomAccessibleInterval} to fill the tensor with.
-	 * @return The {@link TFloat64} tensor filled with the {@link RandomAccessibleInterval} data.
-	 * @throws IllegalArgumentException if the input {@link RandomAccessibleInterval} type is
-	 * not compatible
-	 */
 	private static NDArray buildDouble(SharedMemoryArray tensor, NDManager manager)
 		throws IllegalArgumentException
 	{