Merge branch 'develop' of

https://gitlab.pasteur.fr/bia/tensorflow-1-interface.git into develop

src/main/java/org/bioimageanalysis/icy/tensorflow/v1/tensor/ImgLib2Builder.java

+package org.bioimageanalysis.icy.tensorflow.v1.tensor;
+
+import java.nio.ByteBuffer;
+import java.nio.DoubleBuffer;
+import java.nio.FloatBuffer;
+import java.nio.IntBuffer;
+
+import org.nd4j.linalg.api.buffer.DataType;
+import org.nd4j.linalg.api.ndarray.INDArray;
+import org.nd4j.linalg.factory.Nd4j;
+import org.tensorflow.Tensor;
+import org.tensorflow.types.UInt8;
+
+/**
+ * A {@link INDArray} builder for TensorFlow {@link Tensor} objects.
+ * 
+ * @author Carlos Garcia Lopez de Haro
+ */
+public final class ImgLib2Builder
+{
+
+    /**
+     * Not used (Utility class).
+     */
+    private ImgLib2Builder()
+    {
+    }
+
+    /**
+     * Creates a {@link INDArray} from a given {@link Tensor} and an array with its dimensions order.
+     * 
+     * @param tensor
+     *        The tensor data is read from.
+     * @return The INDArray built from the tensor.
+     * @throws IllegalArgumentException
+     *         If the tensor type is not supported.
+     */
+    @SuppressWarnings("unchecked")
+    public static INDArray build(Tensor<?> tensor) throws IllegalArgumentException
+    {
+        // Create an INDArray of the same type of the tensor
+        switch (tensor.dataType())
+        {
+            case UINT8:
+                return buildFromTensorByte((Tensor<UInt8>) tensor);
+            case INT32:
+                return buildFromTensorInt((Tensor<Integer>) tensor);
+            case FLOAT:
+                return buildFromTensorFloat((Tensor<Float>) tensor);
+            case DOUBLE:
+                return buildFromTensorDouble((Tensor<Double>) tensor);
+            default:
+                throw new IllegalArgumentException("Unsupported tensor type: " + tensor.dataType());
+        }
+    }
+
+    /**
+     * Builds a {@link INDArray} from a unsigned byte-typed {@link Tensor}.
+     * 
+     * @param tensor
+     *        The tensor data is read from.
+     * @return The INDArray built from the tensor of type {@link DataType#UBYTE}.
+     */
+    private static INDArray buildFromTensorByte(Tensor<UInt8> tensor)
+    {
+    	long[] tensorShape = tensor.shape();
+		int totalSize = 1;
+		for (long i : tensorShape) {totalSize *= i;}
+        byte[] flatImageArray = new byte[totalSize];
+		ByteBuffer outBuff = ByteBuffer.wrap(flatImageArray);
+	 	tensor.writeTo(outBuff);
+	 	outBuff = null;
+	 	return Nd4j.create(flatImageArray, tensorShape, DataType.INT8);
+	}
+
+    /**
+     * Builds a {@link INDArray} from a unsigned integer-typed {@link Tensor}.
+     * 
+     * @param tensor
+     *        The tensor data is read from.
+     * @return The sequence built from the tensor of type {@link DataType#INT}.
+     */
+    private static INDArray buildFromTensorInt(Tensor<Integer> tensor)
+    {
+		long[] tensorShape = tensor.shape();
+		int totalSize = 1;
+		for (long i : tensorShape) {totalSize *= i;}
+    	int[] flatImageArray = new int[totalSize];
+    	IntBuffer outBuff = IntBuffer.wrap(flatImageArray);
+	 	tensor.writeTo(outBuff);
+	 	outBuff = null;
+	 	return Nd4j.create(flatImageArray, tensorShape, DataType.INT32);
+    }
+
+    /**
+     * Builds a {@link INDArray} from a unsigned float-typed {@link Tensor}.
+     * 
+     * @param tensor
+     *        The tensor data is read from.
+     * @return The INDArray built from the tensor of type {@link DataType#FLOAT}.
+     */
+    private static INDArray buildFromTensorFloat(Tensor<Float> tensor)
+    {
+		long[] tensorShape = tensor.shape();
+		int totalSize = 1;
+		for (long i : tensorShape) {totalSize *= i;}
+		float[] flatImageArray = new float[totalSize];
+		FloatBuffer outBuff = FloatBuffer.wrap(flatImageArray);
+	 	tensor.writeTo(outBuff);
+	 	outBuff = null;
+	 	return Nd4j.create(flatImageArray, tensorShape, DataType.FLOAT);
+    }
+
+    /**
+     * Builds a {@link INDArray} from a unsigned double-typed {@link Tensor}.
+     * 
+     * @param tensor
+     *        The tensor data is read from.
+     * @return The INDArray built from the tensor of type {@link DataType#DOUBLE}.
+     */
+    private static INDArray buildFromTensorDouble(Tensor<Double> tensor)
+    {
+		long[] tensorShape = tensor.shape();
+		int totalSize = 1;
+		for (long i : tensorShape) {totalSize *= i;}
+		double[] flatImageArray = new double[totalSize];
+		DoubleBuffer outBuff = DoubleBuffer.wrap(flatImageArray);
+	 	tensor.writeTo(outBuff);
+	 	outBuff = null;
+	 	return Nd4j.create(flatImageArray, tensorShape, DataType.DOUBLE);
+    }
+}

src/main/java/org/bioimageanalysis/icy/tensorflow/v1/tensor/TensorBuilder.java

 package org.bioimageanalysis.icy.tensorflow.v1.tensor;
 
-import org.nd4j.linalg.api.buffer.DataType;
-import org.nd4j.linalg.api.ndarray.INDArray;
 import org.tensorflow.Tensor;
 import org.tensorflow.types.UInt8;
 
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.type.Type;
+
 /**
  * A TensorFlow {@link Tensor} builder for {@link INDArray} and {@link org.bioimageanalysis.icy.deeplearning.tensor.Tensor} objects.
  * 
@@ -35,7 +36,7 @@ public final class TensorBuilder
     }
 
     /**
-     * Creates a {@link Tensor} based on the provided {@link INDArray} and the desired dimension order for the resulting tensor.
+     * Creates a {@link Tensor} based on the provided {@link RandomAccessibleInterval} and the desired dimension order for the resulting tensor.
      * 
      * @param ndarray
      *        The NDArray to be converted.
@@ -43,7 +44,7 @@ public final class TensorBuilder
      * @throws IllegalArgumentException
      *         If the ndarray type is not supported.
      */
-    public static Tensor<?> build(INDArray ndarray)
+    public static <T extends Type<T>> Tensor<?> build(RandomAccessibleInterval<T> ndarray)
     {
     	if (ndarray.dataType() == DataType.INT8 || ndarray.dataType() == DataType.UINT8) {
     		return buildByte(ndarray);