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improve javadoc
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@carlosuc3m
carlosuc3m committed Oct 1, 2024
1 parent 9e84b85 commit cbc4fe8
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Showing 2 changed files with 21 additions and 127 deletions.
68 changes: 12 additions & 56 deletions src/main/java/io/bioimage/modelrunner/tensorflow/v2/api030/shm/ShmBuilder.java
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Expand Up @@ -28,7 +28,6 @@
import java.nio.ByteBuffer;
import java.util.Arrays;

import org.tensorflow.Tensor;
import org.tensorflow.types.TFloat32;
import org.tensorflow.types.TFloat64;
import org.tensorflow.types.TInt32;
Expand All @@ -43,11 +42,10 @@
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 TType} tensors 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
{
Expand All @@ -58,17 +56,15 @@ 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.
* @return The {@link RandomAccessibleInterval} built from the {@link TType} tensor.
* @throws IllegalArgumentException If the {@link TType} tensor type is not supported.
* @throws IOException
*/
/**
* Create a {@link SharedMemoryArray} from a {@link TType} tensor
* @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(TType tensor, String memoryName) throws IllegalArgumentException, IOException
{
if (tensor instanceof TUint8)
Expand Down Expand Up @@ -97,14 +93,6 @@ else if (tensor instanceof TInt64)
}
}

/**
* 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(TUint8 tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape().asArray();
Expand All @@ -122,14 +110,6 @@ private static void buildFromTensorUByte(TUint8 tensor, String memoryName) throw
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(TInt32 tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape().asArray();
Expand All @@ -148,14 +128,6 @@ private static void buildFromTensorInt(TInt32 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(TFloat32 tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape().asArray();
Expand All @@ -174,14 +146,6 @@ private static void buildFromTensorFloat(TFloat32 tensor, String memoryName) thr
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(TFloat64 tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape().asArray();
Expand All @@ -200,14 +164,6 @@ private static void buildFromTensorDouble(TFloat64 tensor, String memoryName) th
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(TInt64 tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape().asArray();
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80 changes: 9 additions & 71 deletions src/main/java/io/bioimage/modelrunner/tensorflow/v2/api030/shm/TensorBuilder.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
Expand All @@ -55,10 +48,9 @@
import org.tensorflow.types.family.TType;

/**
* A TensorFlow 2 {@link Tensor} builder from {@link Img} and
* {@link io.bioimage.modelrunner.tensor.Tensor} objects.
* Utility class to build Pytorch Bytedeco 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 {

Expand All @@ -68,21 +60,17 @@ public final class TensorBuilder {
private TensorBuilder() {}

/**
* Creates {@link TType} instance with the same size and information as the
* given {@link RandomAccessibleInterval}.
* Creates {@link TType} 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
* the {@link SharedMemoryArray} 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}
* @return the Pytorch {@link TType} as the one stored in the shared memory segment
* @throws IllegalArgumentException if the type of the {@link SharedMemoryArray}
* is not supported
*/
public static TType build(SharedMemoryArray array) throws IllegalArgumentException
{
// Create an Icy sequence of the same type of the tensor
if (array.getOriginalDataType().equals("uint8")) {
return buildUByte(Cast.unchecked(array));
}
Expand All @@ -103,17 +91,7 @@ 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 TUint8 buildUByte(SharedMemoryArray tensor)
private static TUint8 buildUByte(SharedMemoryArray tensor)
throws IllegalArgumentException
{
long[] ogShape = tensor.getOriginalShape();
Expand All @@ -128,17 +106,7 @@ public static TUint8 buildUByte(SharedMemoryArray tensor)
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 TInt32 buildInt(SharedMemoryArray tensor)
private static TInt32 buildInt(SharedMemoryArray tensor)
throws IllegalArgumentException
{
long[] ogShape = tensor.getOriginalShape();
Expand All @@ -157,16 +125,6 @@ public static TInt32 buildInt(SharedMemoryArray tensor)
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 TInt64 buildLong(SharedMemoryArray tensor)
throws IllegalArgumentException
{
Expand All @@ -186,17 +144,7 @@ private static TInt64 buildLong(SharedMemoryArray tensor)
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 TFloat32 buildFloat(SharedMemoryArray tensor)
private static TFloat32 buildFloat(SharedMemoryArray tensor)
throws IllegalArgumentException
{
long[] ogShape = tensor.getOriginalShape();
Expand All @@ -214,16 +162,6 @@ public static TFloat32 buildFloat(SharedMemoryArray tensor)
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 TFloat64 buildDouble(SharedMemoryArray tensor)
throws IllegalArgumentException
{
Expand Down

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