correct errors during the interprocessing

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");

src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedBufferToImgLib2.java

 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);
     }
     
     /**

src/main/java/org/bioimageanalysis/icy/deeplearning/tensorflow/v1/tensor/MappedFileBuilder.java

 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;