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correct javadoc
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@carlosuc3m
carlosuc3m committed Oct 1, 2024
1 parent 4eb89ff commit dc6b0e2
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Showing 3 changed files with 29 additions and 127 deletions.
8 changes: 7 additions & 1 deletion src/main/java/io/bioimage/modelrunner/tensorflow/v1/JavaWorker.java
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Expand Up @@ -21,7 +21,13 @@ public class JavaWorker {
private final Tensorflow1Interface ti;

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)){
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67 changes: 12 additions & 55 deletions src/main/java/io/bioimage/modelrunner/tensorflow/v1/shm/ShmBuilder.java
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Expand Up @@ -31,19 +31,17 @@
import org.tensorflow.Tensor;
import org.tensorflow.types.UInt8;

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 Tensor} 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 @@ -54,16 +52,15 @@ 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
*/
/**
* Create a {@link SharedMemoryArray} from a {@link Tensor} 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
*/
@SuppressWarnings("unchecked")
public static void build(Tensor<?> tensor, String memoryName) throws IllegalArgumentException, IOException
{
Expand All @@ -84,14 +81,6 @@ public static void build(Tensor<?> tensor, String memoryName) throws IllegalArgu
}
}

/**
* 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(Tensor<UInt8> tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape();
Expand All @@ -104,14 +93,6 @@ private static void buildFromTensorUByte(Tensor<UInt8> tensor, String memoryName
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(Tensor<Integer> tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape();
Expand All @@ -125,14 +106,6 @@ private static void buildFromTensorInt(Tensor<Integer> tensor, String memoryName
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(Tensor<Float> tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape();
Expand All @@ -146,14 +119,6 @@ private static void buildFromTensorFloat(Tensor<Float> tensor, String memoryName
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(Tensor<Double> tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape();
Expand All @@ -167,14 +132,6 @@ private static void buildFromTensorDouble(Tensor<Double> tensor, String memoryNa
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(Tensor<Long> tensor, String memoryName) throws IOException
{
long[] arrayShape = tensor.shape();
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81 changes: 10 additions & 71 deletions src/main/java/io/bioimage/modelrunner/tensorflow/v1/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 @@ -43,10 +36,9 @@
import org.tensorflow.types.UInt8;

/**
* A TensorFlow 2 {@link Tensor} builder from {@link Img} and
* {@link io.bioimage.modelrunner.tensor.Tensor} objects.
* Utility class to build Tensorflow 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 @@ -56,16 +48,13 @@ public final class TensorBuilder {
private TensorBuilder() {}

/**
* Creates {@link TType} instance with the same size and information as the
* given {@link RandomAccessibleInterval}.
* Creates {@link Tensor} 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 Tensor} tensor
* @return the Tensorflow {@link Tensor} as the one stored in the shared memory segment
* @throws IllegalArgumentException if the type of the {@link SharedMemoryArray}
* is not supported
*/
public static Tensor<?> build(SharedMemoryArray array) throws IllegalArgumentException
Expand All @@ -91,17 +80,7 @@ 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 Tensor<UInt8> buildUByte(SharedMemoryArray tensor)
private static Tensor<UInt8> buildUByte(SharedMemoryArray tensor)
throws IllegalArgumentException
{
long[] ogShape = tensor.getOriginalShape();
Expand All @@ -115,17 +94,7 @@ public static Tensor<UInt8> 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 Tensor<Integer> buildInt(SharedMemoryArray tensor)
private static Tensor<Integer> buildInt(SharedMemoryArray tensor)
throws IllegalArgumentException
{
long[] ogShape = tensor.getOriginalShape();
Expand All @@ -142,16 +111,6 @@ public static Tensor<Integer> 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 Tensor<Long> buildLong(SharedMemoryArray tensor)
throws IllegalArgumentException
{
Expand All @@ -169,17 +128,7 @@ private static Tensor<Long> 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 Tensor<Float> buildFloat(SharedMemoryArray tensor)
private static Tensor<Float> buildFloat(SharedMemoryArray tensor)
throws IllegalArgumentException
{
long[] ogShape = tensor.getOriginalShape();
Expand All @@ -196,16 +145,6 @@ public static Tensor<Float> 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 Tensor<Double> buildDouble(SharedMemoryArray tensor)
throws IllegalArgumentException
{
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