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 4531f54d3fbd559da0af277f95937d0a17669def..6ed3e29ab43039ae17baf232bc0bf9155bf62bf4 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
@@ -103,7 +103,7 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
private static SavedModelBundle model;
private static SignatureDef sig;
- private boolean interprocessing = false;
+ private boolean interprocessing = true;
private String tmpDir;
@@ -111,6 +111,8 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
public Tensorflow1Interface() throws IOException
{
+ // TODO remove tmpDIr
+ tmpDir = getTemporaryDir();
boolean isMac = PlatformDetection.isMacOS();
boolean isIntel = new PlatformDetection().getArch().equals(PlatformDetection.ARCH_X86_64);
if (isMac && isIntel) {
@@ -122,6 +124,8 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
public Tensorflow1Interface(boolean doInterprocessing) throws IOException
{
+ // TODO remove tmpDIr
+ tmpDir = getTemporaryDir();
if (!doInterprocessing) {
interprocessing = false;
} else {
@@ -139,7 +143,7 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
// Unpack the args needed
if (args.length < 4)
throw new IllegalArgumentException("Error exectuting Tensorflow 1, "
- + "at least arguments are required:" + System.lineSeparator()
+ + "at least 5 arguments are required:" + System.lineSeparator()
+ " - Folder where the model is located" + System.lineSeparator()
+ " - Temporary dir where the memory mapped files are located" + System.lineSeparator()
+ " - Name of the model input followed by the String + '_model_input'" + System.lineSeparator()
@@ -152,14 +156,14 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
+ " - Name of the nth model output (if it exists) followed by the String + '_model_output'" + System.lineSeparator()
);
String modelFolder = args[0];
- if (new File(modelFolder).isDirectory()) {
+ if (!(new File(modelFolder).isDirectory())) {
throw new IllegalArgumentException("Argument 0 of the main method, '" + modelFolder + "' "
+ "should be an existing directory containing a Tensorflow 1 model.");
}
- Tensorflow1Interface tfInterface = new Tensorflow1Interface();
+ Tensorflow1Interface tfInterface = new Tensorflow1Interface(false);
tfInterface.tmpDir = args[1];
- if (new File(args[1]).isDirectory()) {
+ if (!(new File(args[1]).isDirectory())) {
throw new IllegalArgumentException("Argument 1 of the main method, '" + args[1] + "' "
+ "should be an existing directory.");
}
@@ -241,6 +245,18 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
args.add(this.tmpDir);
for (Tensor tensor : inputTensors) {args.add(tensor.getName() + INPUT_FILE_TERMINATION);}
for (Tensor tensor : outputTensors) {args.add(tensor.getName() + OUTPUT_FILE_TERMINATION);}
+ try {
+ main(new String[] {args.get(4), args.get(5), args.get(6), args.get(7)});
+ } catch (LoadModelException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ } catch (RunModelException e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
ProcessBuilder builder = new ProcessBuilder(args);
Process process;
@@ -323,13 +339,12 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
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());
+ MappedByteBuffer mem = fc.map(FileChannel.MapMode.READ_ONLY, 0, fc.size());
ByteBuffer byteBuffer = mem.duplicate();
- //tensor.setData(MappedBufferToImgLib2.build(byteBuffer));
+ return MappedBufferToImgLib2.buildTensor(byteBuffer);
} catch (IOException e) {
throw new RunModelException(e.getCause().toString());
}
- return null;
}
/**
@@ -338,7 +353,6 @@ public class Tensorflow1Interface implements DeepLearningEngineInterface
* @return
*/
private List<String> getProcessCommandsWithoutArgs(){
- System.out.println(System.getProperty("java.library.path"));
String javaHome = System.getProperty("java.home");
String javaBin = javaHome + File.separator + "bin" + File.separator + "java";
String classpath = System.getProperty("java.class.path");
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 f5d63adbee9e1e4848d709b4b9923f042af2573b..143358d0a9c50e0a49e3aec92ee853e725a6ea04 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
@@ -1,6 +1,7 @@
package org.bioimageanalysis.icy.deeplearning.tensorflow.v1.tensor;
import java.nio.ByteBuffer;
+import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import java.util.HashMap;
import java.util.regex.Matcher;
@@ -237,7 +238,7 @@ public final class MappedBufferToImgLib2
int lenInfo = ByteBuffer.wrap(lenInfoInBytes).getInt();
byte[] stringInfoBytes = new byte[lenInfo];
buff.get(stringInfoBytes);
- return new String(stringInfoBytes);
+ return new String(stringInfoBytes, StandardCharsets.UTF_8);
}
/**
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 a941153bd503ffc28010c11ca1829bf70bf5bee3..6819629d305865721528276806fa8df48dbe94b2 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
@@ -1,6 +1,7 @@
package org.bioimageanalysis.icy.deeplearning.tensorflow.v1.tensor;
import java.nio.ByteBuffer;
+import java.nio.charset.StandardCharsets;
import java.util.Arrays;
import org.tensorflow.Tensor;
@@ -189,17 +190,17 @@ public final class MappedFileBuilder
+ tensor.getAxesOrderString() + "','name':'" + tensor.getName() + "','shape':'"
+ dimsStr + "'}";
- byte[] descriptionBytes = descriptionStr.getBytes();
+ byte[] descriptionBytes = descriptionStr.getBytes(StandardCharsets.UTF_8);
int lenDescriptionBytes = descriptionBytes.length;
- byte[] inAsBytes = ByteBuffer.allocate(4).putInt(lenDescriptionBytes).array();
- int totalHeaderLen = MODEL_RUNNER_HEADER.length + inAsBytes.length + lenDescriptionBytes;
+ byte[] intAsBytes = ByteBuffer.allocate(4).putInt(lenDescriptionBytes).array();
+ int totalHeaderLen = MODEL_RUNNER_HEADER.length + intAsBytes.length + lenDescriptionBytes;
byte[] byteHeader = new byte[totalHeaderLen];
for (int i = 0; i < MODEL_RUNNER_HEADER.length; i ++)
byteHeader[i] = MODEL_RUNNER_HEADER[i];
- for (int i = MODEL_RUNNER_HEADER.length; i < MODEL_RUNNER_HEADER.length + inAsBytes.length; i ++)
- byteHeader[i] = MODEL_RUNNER_HEADER[i - MODEL_RUNNER_HEADER.length];
- for (int i = MODEL_RUNNER_HEADER.length + inAsBytes.length; i < totalHeaderLen; i ++)
- byteHeader[i] = MODEL_RUNNER_HEADER[i - MODEL_RUNNER_HEADER.length - inAsBytes.length];
+ for (int i = MODEL_RUNNER_HEADER.length; i < MODEL_RUNNER_HEADER.length + intAsBytes.length; i ++)
+ byteHeader[i] = intAsBytes[i - MODEL_RUNNER_HEADER.length];
+ for (int i = MODEL_RUNNER_HEADER.length + intAsBytes.length; i < totalHeaderLen; i ++)
+ byteHeader[i] = descriptionBytes[i - MODEL_RUNNER_HEADER.length - intAsBytes.length];
return byteHeader;
}
@@ -214,7 +215,9 @@ public final class MappedFileBuilder
public static < T extends RealType< T > & NativeType< T > > long
findTotalLengthFile(org.bioimageanalysis.icy.deeplearning.tensor.Tensor<T> tensor) {
long startLen = createFileHeader(tensor).length;
- long[] dimsArr = tensor.getData().dimensionsAsLongArray();
+ long[] dimsArr = tensor.getData() != null ? tensor.getData().dimensionsAsLongArray() : null;
+ if (dimsArr == null)
+ return startLen;
long totSizeFlat = 1;
for (long i : dimsArr) {totSizeFlat *= i;}
long nBytesDt = 1;