diff --git a/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/Tensorflow1Interface.java b/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/Tensorflow1Interface.java
index 9907ed3de9f85eda71ab1964cc37aec1b1430210..4102d0a1925db0faa36d0054f8814bc70990c99f 100644
--- a/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/Tensorflow1Interface.java
+++ b/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/Tensorflow1Interface.java
@@ -14,6 +14,7 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
+import java.util.stream.Collectors;
import org.bioimageanalysis.icy.deeplearning.engine.DeepLearningEngineInterface;
import org.bioimageanalysis.icy.deeplearning.exceptions.LoadModelException;
@@ -32,6 +33,9 @@ import org.tensorflow.framework.TensorInfo;
import com.google.protobuf.InvalidProtocolBufferException;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+
/**
* This plugin includes the libraries to convert back and forth TensorFlow 1 to Sequences and IcyBufferedImages.
@@ -131,7 +135,7 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
}
}
- public static void main(String[] args) throws LoadModelException {
+ public static void main(String[] args) throws LoadModelException, IOException {
// Unpack the args needed
if (args.length < 4)
throw new IllegalArgumentException("Error exectuting Tensorflow 1, "
@@ -164,17 +168,15 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
HashMap<String, List<String>> map = getInputTensorsFileNames(args);
List<String> inputNames = map.get(INPUTS_MAP_KEY);
+ List<Tensor<?>> inputList = inputNames.stream().map(n -> {
+ try {
+ return tfInterface.retrieveInterprocessingTensorsByName(n);
+ } catch (RunModelException e) {
+ return null;
+ }
+ }).collect(Collectors.toList());
List<String> outputNames = map.get(OUTPUTS_MAP_KEY);
- for
- for (String inName : inputNames) {
- try (RandomAccessFile rd =
- new RandomAccessFile(tfInterface.tmpDir + File.separator + inName, "r");
- FileChannel fc = rd.getChannel();) {
- int initialLenghToRead = inName.length() + DATATYPE_KEY_LENGTH + MAGIC_WORD_LENGTH + TYPICAL_SHAPE_LENTH;
- MappedByteBuffer mem = fc.map(FileChannel.MapMode.READ_WRITE, 0, fc.size());
- }
- }
}
@Override
@@ -308,6 +310,20 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
}
}
+ private < T extends RealType< T > & NativeType< T > > Tensor<T>
+ retrieveInterprocessingTensorsByName(String name) throws RunModelException {
+ try (RandomAccessFile rd =
+ new RandomAccessFile(tmpDir + File.separator + name + FILE_EXTENSION, "r");
+ FileChannel fc = rd.getChannel();) {
+ MappedByteBuffer mem = fc.map(FileChannel.MapMode.READ_WRITE, 0, fc.size());
+ ByteBuffer byteBuffer = mem.duplicate();
+ //tensor.setData(MappedBufferToImgLib2.build(byteBuffer));
+ } catch (IOException e) {
+ throw new RunModelException(e.getCause().toString());
+ }
+ return null;
+ }
+
/**
* Create the arguments needed to execute tensorflow1 in another
* process with the corresponding tensors
diff --git a/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedBufferToImgLib2.java b/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedBufferToImgLib2.java
index 98878c84f9dddddb9f6891c4567309c62ddae703..855195a92c7255d8e6dffc47c3bda7a2ceb3e5b8 100644
--- a/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedBufferToImgLib2.java
+++ b/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedBufferToImgLib2.java
@@ -1,24 +1,20 @@
package org.bioimageanalysis.icy.deeplearning.tensorflow.v1.tensor;
import java.nio.ByteBuffer;
-import java.nio.DoubleBuffer;
-import java.nio.FloatBuffer;
-import java.nio.IntBuffer;
import java.util.Arrays;
import java.util.HashMap;
-import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
-import org.bioimageanalysis.icy.deeplearning.utils.IndexingUtils;
-import org.tensorflow.Tensor;
-import org.tensorflow.types.UInt8;
+import org.bioimageanalysis.icy.deeplearning.tensor.Tensor;
import net.imglib2.Cursor;
import net.imglib2.img.Img;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.cell.CellImgFactory;
+import net.imglib2.type.NativeType;
import net.imglib2.type.Type;
+import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.type.numeric.integer.IntType;
import net.imglib2.type.numeric.real.DoubleType;
@@ -36,7 +32,8 @@ public final class MappedBufferToImgLib2
* and retrieves data type and shape
*/
private static final Pattern HEADER_PATTERN =
- Pattern.compile("\\{'dtype':'([a-zA-Z0-9]+)',shape':'\\[(\\d+(,\\d+)*)\\]'}");
+ Pattern.compile("\\{'dtype':'([a-zA-Z0-9]+)','axes':'([a-zA-Z0-9]+)'"
+ + ",'name':'(.+?)',shape':'\\[(\\d+(,\\d+)*)\\]'}");
/**
* Key for data type info
*/
@@ -45,6 +42,10 @@ public final class MappedBufferToImgLib2
* Key for shape info
*/
private static final String SHAPE_KEY = "shape";
+ /**
+ * Key for axes info
+ */
+ private static final String AXES_KEY = "axes";
/**
* Not used (Utility class).
@@ -53,6 +54,45 @@ public final class MappedBufferToImgLib2
{
}
+ /**
+ * Creates a {@link Img} 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 < T extends RealType< T > & NativeType< T > > Tensor<T> buildTensor(String name, ByteBuffer buff) throws IllegalArgumentException
+ {
+ String infoStr = getTensorInfoFromBuffer(buff);
+ HashMap<String, Object> map = getDataTypeAndShape(infoStr);
+ String dtype = (String) map.get(DATA_TYPE_KEY);
+ String axes = (String) map.get(AXES_KEY);
+ long[] shape = (long[]) map.get(SHAPE_KEY);
+
+ Img<T> data;
+ switch (dtype)
+ {
+ case "byte":
+ data = (Img<T>) buildFromTensorByte(buff, shape);
+ break;
+ case "int32":
+ data = (Img<T>) buildFromTensorInt(buff, shape);
+ break;
+ case "float32":
+ data = (Img<T>) buildFromTensorFloat(buff, shape);
+ break;
+ case "float64":
+ data = (Img<T>) buildFromTensorDouble(buff, shape);
+ break;
+ default:
+ throw new IllegalArgumentException("Unsupported tensor type: " + dtype);
+ }
+ return Tensor.build(name, axes, data);
+ }
+
/**
* Creates a {@link Img} from a given {@link Tensor} and an array with its dimensions order.
*
@@ -204,7 +244,8 @@ public final class MappedBufferToImgLib2
+ "info in file hader: " + infoStr);
}
String typeStr = m.group(1);
- String shapeStr = m.group(2);
+ String axesStr = m.group(2);
+ String shapeStr = m.group(3);
long[] shape = new long[0];
if (!shapeStr.isEmpty()) {
String[] tokens = shapeStr.split(", ?");
@@ -212,7 +253,8 @@ public final class MappedBufferToImgLib2
}
HashMap<String, Object> map = new HashMap<String, Object>();
map.put(DATA_TYPE_KEY, typeStr);
- map.put(SHAPE_KEY, shapeStr);
+ map.put(AXES_KEY, axesStr);
+ map.put(SHAPE_KEY, shape);
return map;
}
}
diff --git a/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedFileBuilder.java b/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedFileBuilder.java
index 183238ea2968e5bd99d0257532d3c52541403c04..af8ade9ad1acade71a582ea82ec0c9f7e5f0e494 100644
--- a/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedFileBuilder.java
+++ b/src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedFileBuilder.java
@@ -188,7 +188,8 @@ public final class MappedFileBuilder
*/
public static < T extends RealType< T > & NativeType< T > > byte[]
createFileHeader(org.bioimageanalysis.icy.deeplearning.tensor.Tensor<T> tensor) {
- String descriptionStr = "{'dtype':'" + tensor.getDataType() + "','shape':'"
+ String descriptionStr = "{'dtype':'" + tensor.getDataType() + "','axes':'"
+ + tensor.getAxesOrderString() + "','name':'" + tensor.getName() + "','shape':'"
+ Arrays.toString(tensor.getData().dimensionsAsLongArray()) + "'}";
byte[] descriptionBytes = descriptionStr.getBytes();