Unify logging (#21)

* Unify logging Unifies logging to remove the dependency on com.neuronrobotics.sdk.common.Log and to use the console and file logger as default. * Removed ThreadUtil dependency
NAMI-THU · Sep 11, 2023 · c225a62 · c225a62
1 parent 38b0375
commit c225a62
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Showing 19 changed files with 142 additions and 113 deletions.
diff --git a/src/main/java/inputOutput/OpenIGTLinkConnection.java b/src/main/java/inputOutput/OpenIGTLinkConnection.java
@@ -1,7 +1,6 @@
 package inputOutput;
 
 import com.neuronrobotics.sdk.addons.kinematics.math.TransformNR;
-import com.neuronrobotics.sdk.common.Log;
 
 import Jama.Matrix;
 
@@ -45,10 +44,7 @@ public class OpenIGTLinkConnection implements IOpenIgtPacketListener {
      */
     public OpenIGTLinkConnection() {
         try {
-            Log.enableDebugPrint(false);
-            Log.enableSystemPrint(false);
-
-            Log.debug("Starting client");
+            logger.log(Level.INFO, "Starting OIGTL client");
             this.client = new GenericIGTLinkClient(this.ip, this.port);
 
             this.client.addIOpenIgtOnPacket(this);
@@ -70,10 +66,7 @@ public OpenIGTLinkConnection(String ip, int port) {
         this.setPort(port);
 
         try {
-            Log.enableDebugPrint(false);
-            Log.enableSystemPrint(false);
-
-            Log.debug("Starting client");
+            logger.log(Level.INFO, "Starting OIGTL client");
             this.client = new GenericIGTLinkClient(this.ip, this.port);
 
             client.addIOpenIgtOnPacket(this);
@@ -166,7 +159,7 @@ public boolean isConnected() {
     // from networkconnection
     @Override
     public void onRxTransform(String name, TransformNR t) {
-        Log.debug("Received Transform: " + t);
+        logger.log(Level.FINE, "Received Transform: " + t);
 
         if (this.exit && this.stop) {
 
@@ -195,19 +188,19 @@ public void onRxTransform(String name, TransformNR t) {
 
         if (name.equals("RegistrationTransform") || name.equals("CALIBRATION")) {
             // System.err.println("Received Registration Transform");
-            Log.debug("Setting fiducial registration matrix: " + t);
+            logger.log(Level.FINE, "Setting fiducial registration matrix: " + t);
             return;
         } else if (name.equals("TARGET")) {
             // System.err.println("Received RAS Transform: TARGET");
-            Log.debug("Setting task space pose: " + t);
+            logger.log(Level.FINE, "Setting task space pose: " + t);
 
         } else if (name.equals("myTransform")) {
             // System.err.println("Received Transformation Matrix: myTransform");
-            Log.debug("Setting task space pose: " + t);
+            logger.log(Level.FINE, "Setting task space pose: " + t);
 
         } else {
             // System.err.println("Received unidentified transform matrix");
-            Log.debug("Setting task space pose: " + t);
+            logger.log(Level.FINE, "Setting task space pose: " + t);
         }
     }
 

diff --git a/src/main/java/mainMethod/App.java b/src/main/java/mainMethod/App.java
@@ -2,6 +2,10 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.logging.ConsoleHandler;
+import java.util.logging.FileHandler;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 import javafx.application.Application;
 import javafx.fxml.FXMLLoader;
@@ -12,7 +16,7 @@
 import util.CustomLogger;
 
 public class App extends Application {
-
+    static Logger logger = Logger.getLogger(Application.class.getName());
 
     @Override
     public void start(Stage primaryStage) throws IOException {
@@ -23,6 +27,10 @@ public void start(Stage primaryStage) throws IOException {
             e.printStackTrace();
         }
 
+        Thread.setDefaultUncaughtExceptionHandler((thread, throwable) -> {
+            logger.log(Level.SEVERE, "Uncaught exception in thread " + thread.getName(), throwable);
+        });
+
         String path = "/view/MainView.fxml";
         FXMLLoader loader = new FXMLLoader();
         loader.setLocation(getClass().getResource(path));

diff --git a/src/main/java/org/medcare/igtl/messages/ImageMessage.java b/src/main/java/org/medcare/igtl/messages/ImageMessage.java
@@ -16,11 +16,12 @@
 
 package org.medcare.igtl.messages;
 
-import com.neuronrobotics.sdk.common.Log;
 import org.medcare.igtl.util.BytesArray;
 import org.medcare.igtl.util.Header;
 
 import java.util.Arrays;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 /**
  * ** This class create an Image object from bytes received or help to generate
@@ -29,6 +30,7 @@
  * @author Andre Charles Legendre
  */
 public class ImageMessage extends OpenIGTMessage {
+    static Logger logger = Logger.getLogger(ImageMessage.class.getName());
 
     public static final int TYPE_INT8 = 2;
     public static final int TYPE_UINT8 = 3;
@@ -595,7 +597,7 @@ public double[][] getMatrix() {
     public void setMatrix(double[][] matrix) {
         this.matrix = matrix;
 
-        Log.debug(Arrays.toString(matrix));
+        logger.log(Level.FINE, "Matrix: " + Arrays.toString(matrix));
         norm_i = new double[3];
         norm_j = new double[3];
         norm_k = new double[3];

diff --git a/src/main/java/org/medcare/igtl/messages/OpenIGTMessage.java b/src/main/java/org/medcare/igtl/messages/OpenIGTMessage.java
@@ -16,10 +16,12 @@
 
 package org.medcare.igtl.messages;
 
-import com.neuronrobotics.sdk.common.Log;
 import org.medcare.igtl.util.BytesArray;
 import org.medcare.igtl.util.Header;
 
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 //import org.medcare.igtl.util.CrcException;
 
 //import com.neuronrobotics.sdk.common.ByteList;
@@ -31,6 +33,7 @@
  **/
 
 public abstract class OpenIGTMessage {
+    static Logger logger = Logger.getLogger(OpenIGTMessage.class.getName());
     // ------------------------------------------------------------------------
     public String deviceName;
     private byte[] body;
@@ -77,7 +80,7 @@ public boolean Unpack() throws Exception {
         if (getBody().length > 0
             //&& !isBodyUnpacked
         ) {
-            Log.debug("Unpacking message...");
+            logger.log(Level.FINE, "Unpacking message...");
             //if (header.getCrc() == bytesArray.crc64(body, body.length, 0L)) {
             isBodyUnpacked = unpackBody();
             return isBodyUnpacked;

diff --git a/src/main/java/org/medcare/igtl/messages/TransformMessage.java b/src/main/java/org/medcare/igtl/messages/TransformMessage.java
@@ -16,10 +16,12 @@
 
 package org.medcare.igtl.messages;
 
-import com.neuronrobotics.sdk.common.Log;
 import org.medcare.igtl.util.BytesArray;
 import org.medcare.igtl.util.Header;
 
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 //import com.neuronrobotics.sdk.common.ByteList;
 
 /**
@@ -29,6 +31,7 @@
  * @author Andre Charles Legendre
  */
 public class TransformMessage extends OpenIGTMessage {
+    static Logger logger = Logger.getLogger(TransformMessage.class.getName());
 
     public static int IGTL_TRANSFORM_SIZE = 48;
 
@@ -97,7 +100,8 @@ public TransformMessage(String deviceName, double[] positionAray, double[][] rot
     public boolean unpackBody() throws Exception {
         //Log.debug("Unpacking Transform Body..");
         transformData = new byte[IGTL_TRANSFORM_SIZE];
-        Log.debug("Body size: " + getBody().length + " date size: " + transformData.length);
+
+        logger.log(Level.FINE,"Body size: " + getBody().length + " date size: " + transformData.length);
         System.arraycopy(getBody(), 0, transformData, 0, IGTL_TRANSFORM_SIZE);
         setTransformData(transformData);
 
@@ -425,7 +429,6 @@ public void printDoubleDataArray(double[][] matrixArray) {
             for (int j = 0; j < matrixArray[0].length; j++) {
                 System.out.print(matrixArray[i][j] + " ");
             }
-            Log.debug("\n");
         }
     }
 }

diff --git a/src/main/java/org/medcare/igtl/network/GenericIGTLinkClient.java b/src/main/java/org/medcare/igtl/network/GenericIGTLinkClient.java
@@ -11,9 +11,12 @@
 import java.util.ArrayList;
 import java.util.LinkedList;
 import java.util.Queue;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 
 public class GenericIGTLinkClient extends OpenIGTClient implements IOpenIgtPacketListener {
+    static Logger logger = Logger.getLogger(GenericIGTLinkClient.class.getName());
     ArrayList<IOpenIgtPacketListener> listeners = new ArrayList<IOpenIgtPacketListener>();
     Sender s = new Sender();
 
@@ -25,7 +28,7 @@ public void error(String message, Exception exception, int errorCode) {
                 System.err.println(message);
             }
         });
-        Log.debug("GenericIGTLinkClient started");
+        logger.log(Level.FINE, "Starting GenericIGTLinkClient");
         s.start();
 
     }
@@ -158,7 +161,7 @@ public void stopClient() {
         interrupt();
         while (isConnected()) ;
 
-        Log.debug("Stopped IGTLink client");
+        logger.log(Level.FINE, "Stopped GenericIGTLinkClient");
     }
 
 
@@ -251,7 +254,7 @@ public void run() {
                 //take out a message from Queue and send it
                 try {
                     if (messageQueue.size() > 0) {
-                        Log.debug("Number of messages in Queue = " + messageQueue.size());
+                        logger.log(Level.FINE, "Number of messages in Queue = " + messageQueue.size());
                     }
                     OpenIGTMessage msg = messageQueue.poll();
                     if (msg != null) {
@@ -263,14 +266,13 @@ public void run() {
                 } catch (Exception e) {
                     if (!messageQueue.isEmpty()) {
                         messageQueue.clear(); //clear message queue if ws not able to send as that is a connection problem
-                        Log.debug("Clearing Message Sender Queue ; Number of messages in Queue = " + messageQueue.size());
+                        logger.log(Level.FINE, "Clearing Message Sender Queue ; Number of messages in Queue = " + messageQueue.size());
                     }
                     // TODO Auto-generated catch block
                     e.printStackTrace();
                 }
             }
-            Log.debug("Stopped IGTLink client Sender");
-
+            logger.log(Level.FINE, "Stopped IGTLink client Sender");
         }
     }
 }

diff --git a/src/main/java/org/medcare/igtl/network/GenericIGTLinkServer.java b/src/main/java/org/medcare/igtl/network/GenericIGTLinkServer.java
@@ -10,9 +10,12 @@
 import java.util.ArrayList;
 import java.util.LinkedList;
 import java.util.Queue;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 public class GenericIGTLinkServer extends OpenIGTServer implements IOpenIgtPacketListener {
 
+    static Logger logger = Logger.getLogger(GenericIGTLinkServer.class.getName());
     public Sender s = new Sender();
     ArrayList<IOpenIgtPacketListener> listeners = new ArrayList<IOpenIgtPacketListener>();
 
@@ -236,7 +239,7 @@ public void run() {
                 while (getServerThread() == null || getServerThread().isAlive() == false) {
                     if (!messageQueue.isEmpty()) {
                         messageQueue.clear(); //keep cleaning the message Queue till Clinet connects
-                        Log.debug("Clearing Message Sender Queue ; Number of messages in Queue = " + messageQueue.size());
+                        logger.log(Level.FINE, "Clearing Message Sender Queue ; Number of messages in Queue = " + messageQueue.size());
                     }
                     try {
                         Thread.sleep(200);
@@ -255,7 +258,7 @@ public void run() {
                     //take out a message from Queue and send it
                     try {
                         if (messageQueue.size() > 0) {
-                            Log.debug("Number of messages in Queue = " + messageQueue.size());
+                            logger.log(Level.FINE, "Number of messages in Queue = " + messageQueue.size());
                         }
                         OpenIGTMessage msg = messageQueue.poll();
                         if (msg != null) {
@@ -267,7 +270,7 @@ public void run() {
                     } catch (Exception e) {
                         if (!messageQueue.isEmpty()) {
                             messageQueue.clear(); //clear message queue if ws not able to send as that is a connection problem
-                            Log.debug("Clearing Message Sender Queue ; Number of messages in Queue = " + messageQueue.size());
+                            logger.log(Level.FINE, "Clearing Message Sender Queue ; Number of messages in Queue = " + messageQueue.size());
                         }
                         // TODO Auto-generated catch block
                         e.printStackTrace();

diff --git a/src/main/java/org/medcare/igtl/network/GenericMessageNodeHandler.java b/src/main/java/org/medcare/igtl/network/GenericMessageNodeHandler.java
@@ -2,12 +2,14 @@
 
 import com.neuronrobotics.sdk.addons.kinematics.math.RotationNR;
 import com.neuronrobotics.sdk.addons.kinematics.math.TransformNR;
-import com.neuronrobotics.sdk.common.Log;
 import org.medcare.igtl.messages.*;
 import org.medcare.igtl.util.Header;
 
-public class GenericMessageNodeHandler {
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
+public class GenericMessageNodeHandler {
+    static Logger logger = Logger.getLogger(GenericMessageNodeHandler.class.getName());
     public OpenIGTMessage openIGTMessage;
 
     public OpenIGTMessage perform(String messageType, Header head, byte[] body, IOpenIgtPacketListener node) throws Exception {
@@ -16,7 +18,7 @@ public OpenIGTMessage perform(String messageType, Header head, byte[] body, IOpe
         //TODO - GSF: Need to add complete set of new IGTLInk commands for BRP robot
         //http://wiki.ncigt.org/index.php/P41:Prostate:BRP:MRI_New_BRP_OpenIGTLink_Protocol_2012_Mar
         //Should support both TRANSFORM and QTRANSFORM packets
-        Log.debug("Perform messageType : " + messageType);
+        logger.log(java.util.logging.Level.FINE, "perform messageType : " + messageType);
         if (messageType.equals("TRANSFORM")) {
             openIGTMessage = new TransformMessage(head, body);
             TransformMessage transform = (TransformMessage) openIGTMessage;
@@ -33,7 +35,7 @@ public OpenIGTMessage perform(String messageType, Header head, byte[] body, IOpe
             // Position vector and rotation matrix from the received transform
             node.getTxTransform(openIGTMessage.getDeviceName());
         } else if (messageType.equals("POSITION") || messageType.equals("MOVE_TO")) {
-            Log.debug("perform POSITION");
+            logger.log(java.util.logging.Level.FINE, "perform POSITION");
             openIGTMessage = new PositionMessage(head, body);
             PositionMessage transform = (PositionMessage) openIGTMessage;
             transform.Unpack();
@@ -50,7 +52,7 @@ public OpenIGTMessage perform(String messageType, Header head, byte[] body, IOpe
             node.onRxImage(openIGTMessage.getDeviceName(), imgMesg);
 
         } else if (messageType.equals("ARRAY")) {
-            Log.error("This method is not complete");
+            logger.log(Level.SEVERE, "This method is not complete");
             DataArrayMessage datMesg = new DataArrayMessage(head, body);
             openIGTMessage = datMesg;
             node.onRxDataArray(openIGTMessage.getDeviceName(), datMesg.getDataMatrix());// this is a non functional stub
@@ -82,7 +84,7 @@ public OpenIGTMessage perform(String messageType, Header head, byte[] body, IOpe
             node.onRxNDArray(openIGTMessage.getDeviceName(), ndArrayMsg.get1DFloatData());// this is a non functional stub
         } else {
 
-            Log.debug("Message Type : " + messageType + " not implemented");
+            logger.log(Level.WARNING, "Message Type : " + messageType + " not implemented");
             return null;
         }
         return openIGTMessage;

diff --git a/src/main/java/org/medcare/igtl/network/MessageQueueManager.java b/src/main/java/org/medcare/igtl/network/MessageQueueManager.java
@@ -16,11 +16,12 @@
 
 package org.medcare.igtl.network;
 
-import com.neuronrobotics.sdk.common.Log;
 import org.medcare.igtl.util.CrcException;
 import org.medcare.igtl.util.ErrorManager;
 
 import java.util.concurrent.ConcurrentLinkedQueue;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
 /**
  * One MessageQueueManager is created by each ServerThread to add MessageHandler
@@ -31,6 +32,7 @@
  * @author Andre Charles Legendre
  */
 public class MessageQueueManager extends Thread {
+    static Logger logger = Logger.getLogger(MessageQueueManager.class.getName());
     private static String VERSION = "0.1a";
 
     private long sleep;
@@ -74,7 +76,7 @@ public void run() {
                             e.printStackTrace();
                             errorManager.error("PB messageHandler ", e, ErrorManager.MESSAGE_EXCEPTION);
                         } finally {
-                            Log.debug("MessageQueueManager messageHandler.performRequest OK");
+                            logger.log(Level.FINE, "MessageQueueManager messageHandler.performRequest OK");
                         }
 
                     } else {