Merge branch...

Merge branch '115-make-logging-into-the-outputwindow-available-from-low-level-modules' into 'master'

Resolve "Make logging into the OutputWindow available from low-level modules"

Closes #115

See merge request grp-fidentis/analyst2!127

Comparison/src/main/java/cz/fidentis/analyst/icp/RandomStrategy.java

@@ -18,7 +18,7 @@ public class RandomStrategy extends UndersamplingStrategy {
     /**
      * Constructor for PERCENTAGE undersampling type.
      * 
-     * @param perc Percentage - a value in (0.0, 1.0&gtl
+     * @param perc Percentage - a value in (0.0, 1.0>
      * @throws IllegalArgumentException if the input parameter is wrong
      */
     public RandomStrategy(double perc) {

GUI/src/main/java/cz/fidentis/analyst/core/OutputWindow.java

 package cz.fidentis.analyst.core;
 
+import cz.fidentis.analyst.Logger;
 import java.awt.BorderLayout;
-import java.text.SimpleDateFormat;
-import java.time.Duration;
+import java.util.List;
 import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
+import javax.swing.SwingWorker;
 import org.openide.windows.TopComponent;
 import org.openide.windows.WindowManager;
 
 /**
- * Wrapper for default output window of the Java Netbeans Platform application.
- * It enables to write debug messages into the window.
+ * Wrapper of the default Java Netbeans Platform output window.
+ * This wrapper runs in the worker thread, reads messages logged through 
+ * the {@link cz.fidentis.analyst.Logger} and displays them in the output window.
+ * 
+ * The {@code OutputWindow} is currently executed from 
+ * the {@link cz.fidentis.analyst.core.ProjectTopComp}, which is always presented.
  * 
  * @author Radek Oslejsek
  */
-public class OutputWindow {
+public class OutputWindow extends SwingWorker<String, String> {
 
     private static JTextArea textArea; 
     
-    private long lastTime = System.currentTimeMillis();
-    
-    protected OutputWindow() {
-        initTextArea();
-    }
-    
     /**
-     * Prints the message.
-     * 
-     * @param msg Message to be printed
+     * Constructor.
      */
-    public static void print(String msg) {
-        JTextArea ta = initTextArea();
-        ta.setText(ta.getText() 
-                + new SimpleDateFormat("HH:mm:ss").format(System.currentTimeMillis())
-                + " [duration unknown]: "
-                + msg.trim() 
-                + System.lineSeparator()
-        );
+    public OutputWindow() {
+        TopComponent outputWin = WindowManager.getDefault().findTopComponent("output");
+        textArea = new JTextArea();
+        JScrollPane sp = new JScrollPane(textArea);
+        outputWin.add(sp, BorderLayout.CENTER);
     }
 
     /**
-     * Starts measuring of some operation. 
-     * Call {@link #printDuration(java.lang.String)} on returned OutputWindow
-     * to print the measured duration.
+     * Reads messages of the {@code Logger} in the background and re-sends them
+     * the {@link #process(java.util.List)} method.
      * 
-     * @return An object used to print measured duration and message
+     * @return Complete text displayed in the output window.
+     * @throws Exception 
      */
-    public static OutputWindow measureTime() {
-        OutputWindow ret = new OutputWindow();
-        ret.lastTime = System.currentTimeMillis();
-        return ret;
+    @Override
+    protected String doInBackground() throws Exception {
+        String line = Logger.reader().readLine();
+        while (line != null) {
+            publish(line);
+            line = Logger.reader().readLine();
+        }
+        return textArea.getText();
     }
     
     /**
-     * Prints the message about an operation and the duration of the operation. 
-     * The duration is computed as the difference between current system time and 
-     * the time of calling {@link #measureTime()}. The time difference is measured in 
-     * milliseconds and printed as [+mm:ss.SSS] where mm=minutes, ss=seconds, 
-     * and SSS=milliseconds.
+     * Takes text lines process by the {@link #doInBackground()} method and
+     * adds them to the output window.
      * 
-     * @param msg Message to be printed
+     * @param chunks process lines
      */
-    public void printDuration(String msg) {
-        Duration duration = Duration.ofMillis(System.currentTimeMillis() - lastTime);
-        textArea.setText(textArea.getText() 
-                + new SimpleDateFormat("HH:mm:ss").format(System.currentTimeMillis())
-                + " [duration "
-                + String.format(
-                        "%02d:%02d.%03d", 
-                        duration.toMinutes(), 
-                        duration.toSecondsPart(),
-                        duration.toMillisPart())
-                + "]: "
-                + msg.trim() 
-                + System.lineSeparator()
-        );
-    }
-    
-    protected static JTextArea initTextArea() {
-        if (textArea == null) {
-            TopComponent outputWin = WindowManager.getDefault().findTopComponent("output");
-            textArea = new JTextArea();
-            JScrollPane sp = new JScrollPane(textArea);
-            outputWin.add(sp, BorderLayout.CENTER);
-        }
-        return textArea;
+    @Override
+    protected void process(List<String> chunks) {
+        StringBuilder sb = new StringBuilder();
+        sb.append(textArea.getText());
+        chunks.forEach(str -> {
+            sb.append(str + System.lineSeparator());
+        });
+        textArea.setText(sb.toString());
     }
+        
 }

GUI/src/main/java/cz/fidentis/analyst/core/ProjectTopComp.java

-/*
- * To change this license header, choose License Headers in Project Properties.
- * To change this template file, choose Tools | Templates
- * and open the template in the editor.
- */
 package cz.fidentis.analyst.core;
 
+import cz.fidentis.analyst.Logger;
 import org.netbeans.api.settings.ConvertAsProperties;
 import org.openide.awt.ActionID;
 import org.openide.awt.ActionReference;
@@ -84,6 +80,10 @@ public final class ProjectTopComp extends TopComponent {
         putClientProperty(TopComponent.PROP_CLOSING_DISABLED, Boolean.TRUE);
         putClientProperty(TopComponent.PROP_DRAGGING_DISABLED, Boolean.TRUE);
         putClientProperty(TopComponent.PROP_UNDOCKING_DISABLED, Boolean.TRUE);
+        
+        // Execute OutputWindow in the worker thread so that messages
+        // logged via Logger are displayed in the output window
+        (new OutputWindow()).execute();
     }
 
     /**
@@ -671,7 +671,7 @@ public final class ProjectTopComp extends TopComponent {
         if (files == null) {
             System.out.print("No file chosen.");
         } else {
-            OutputWindow out = OutputWindow.measureTime();
+            Logger out = Logger.measureTime();
             for (File file : files) {
                 String faceId = HumanFaceFactory.instance().loadFace(file);
                 HumanFace face = HumanFaceFactory.instance().getFace(faceId);

GUI/src/main/java/cz/fidentis/analyst/curvature/CurvatureAction.java

 package cz.fidentis.analyst.curvature;
 
+import cz.fidentis.analyst.Logger;
 import cz.fidentis.analyst.canvas.Canvas;
 import cz.fidentis.analyst.core.ControlPanelAction;
-import cz.fidentis.analyst.core.OutputWindow;
 import cz.fidentis.analyst.visitors.mesh.Curvature;
 import java.awt.event.ActionEvent;
 import javax.swing.JComboBox;
@@ -77,7 +77,7 @@ public class CurvatureAction extends ControlPanelAction {
     
     protected void setHeatmap() {
         if (visitor == null) { // compute missing curvature
-            OutputWindow out = OutputWindow.measureTime();
+            Logger out = Logger.measureTime();
             this.visitor = new Curvature();
             getPrimaryDrawableFace().getModel().compute(visitor);
             out.printDuration("Computation of curvature for a model with " 

GUI/src/main/java/cz/fidentis/analyst/distance/DistanceAction.java

 package cz.fidentis.analyst.distance;
 
 import com.jogamp.opengl.GL2;
+import cz.fidentis.analyst.Logger;
 import cz.fidentis.analyst.canvas.Canvas;
 import cz.fidentis.analyst.core.LoadedActionEvent;
 import cz.fidentis.analyst.core.ControlPanelAction;
 import cz.fidentis.analyst.core.ControlPanelBuilder;
-import cz.fidentis.analyst.core.OutputWindow;
 import cz.fidentis.analyst.feature.FeaturePoint;
 import cz.fidentis.analyst.feature.FeaturePointType;
 import cz.fidentis.analyst.mesh.core.MeshFacet;
@@ -267,7 +267,7 @@ public class DistanceAction extends ControlPanelAction {
                 throw new UnsupportedOperationException(strategy);
         }
         
-        OutputWindow out = OutputWindow.measureTime();
+        Logger out = Logger.measureTime();
         this.visitor = new HausdorffDistancePrioritized(getPrimaryDrawableFace().getModel(),
                 featurePoints,
                 useStrategy,

GUI/src/main/java/cz/fidentis/analyst/registration/RegistrationAction.java

 package cz.fidentis.analyst.registration;
 
+import cz.fidentis.analyst.Logger;
 import cz.fidentis.analyst.canvas.Canvas;
 import cz.fidentis.analyst.core.ControlPanelAction;
-import cz.fidentis.analyst.core.OutputWindow;
 import cz.fidentis.analyst.face.HumanFace;
 import cz.fidentis.analyst.feature.FeaturePoint;
 import cz.fidentis.analyst.icp.IcpTransformation;
@@ -258,7 +258,7 @@ public class RegistrationAction extends ControlPanelAction {
     }
     
     protected void applyICP() {
-        OutputWindow out = OutputWindow.measureTime();
+        Logger out = Logger.measureTime();
         
         IcpTransformer visitor = new IcpTransformer(getPrimaryDrawableFace().getModel(), maxIterations, scale, error, undersampling);
         getSecondaryDrawableFace().getModel().compute(visitor); // NOTE: the secondary face is physically transformed
@@ -306,7 +306,7 @@ public class RegistrationAction extends ControlPanelAction {
      * otherwise set color to default
      */
     private void calculateFeaturePoints() {
-        OutputWindow.print("Calculation of feature points");
+        Logger.print("Calculation of feature points");
         
         if (getPrimaryDrawableFace() == null) { // scene not yet initiated
             return;
@@ -346,7 +346,7 @@ public class RegistrationAction extends ControlPanelAction {
     }
     
     private void calculateHausdorffDistance() {
-        OutputWindow out = OutputWindow.measureTime();
+        Logger out = Logger.measureTime();
         
         HumanFace primFace = getScene().getHumanFace(0);
         primFace.computeKdTree(false);
@@ -467,7 +467,7 @@ public class RegistrationAction extends ControlPanelAction {
         }
         
         if (hdVisitor == null) { 
-            OutputWindow out = OutputWindow.measureTime();
+            Logger out = Logger.measureTime();
             
             this.hdVisitor = new HausdorffDistance(getPrimaryDrawableFace().getModel(), useStrategy, relativeDist, true);
             getSecondaryDrawableFace().getModel().compute(hdVisitor);

MeshModel/pom.xml

@@ -17,6 +17,7 @@
                 <configuration>
                     <useOSGiDependencies>true</useOSGiDependencies>
                     <publicPackages> <!-- expose API/packages to other modules -->
+                       <publicPackage>cz.fidentis.analyst.*</publicPackage>
                        <publicPackage>cz.fidentis.analyst.mesh.core.*</publicPackage>
                        <publicPackage>cz.fidentis.analyst.mesh.io.*</publicPackage>
                        <publicPackage>cz.fidentis.analyst.mesh.*</publicPackage>

MeshModel/src/main/java/cz/fidentis/analyst/Logger.java

+package cz.fidentis.analyst;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PipedInputStream;
+import java.io.PipedOutputStream;
+import java.io.PrintStream;
+import java.text.SimpleDateFormat;
+import java.time.Duration;
+import java.util.logging.Level;
+
+/**
+ * A logging class that can be used from anywhere to display debugging or other
+ * messages.
+ * <p>
+ * Messages are printed into the standard output unless the {@link #reader()} 
+ * method is called. Then the messages are redirected to the returned {@code BufferedReader}.
+ * </p>
+ * <p>
+ * The implementation supposes that the caller of the {@link #reader()} method 
+ * (or other object} will read the messages from the {@code BufferedReader} forever. 
+ * Otherwise, the program can freeze due to the full buffer.
+ * </p>
+ * <p>
+ * FIDENTIS application automatically redirects logged messages to the output window.
+ * </p>
+ * <p>
+ * <b>Usage:</b>
+ * <ul>
+ *    <li>To print a message, use {@code Logger.print("message")}. A timestamp is added automatically.</li>
+ *    <li>To print message together with duration, call {@code Logger log = Logger.measureTime();}, 
+ *        then call the measured operations and finally call {@code log.printDuration("message")}. 
+ *        a timestamp and measured duration are added to the log message automatically.</li>
+ * </ul>
+ * </p>
+ * 
+ * @author Radek Oslejsek
+ */
+public final class Logger {
+    
+    private static PrintStream out = System.out;
+    private static BufferedReader in;
+    
+    private long lastTime = System.currentTimeMillis();
+    
+    private Logger() {
+    }
+    
+    /**
+     * Redirects logs from standard output to the {@code BufferedReader}.
+     * 
+     * @return {@code BufferedReader} to which the logs are redirected.
+     */
+    public static BufferedReader reader() {
+        if (in == null) {
+            PipedOutputStream pOut = new PipedOutputStream();
+            out = new PrintStream(pOut);
+            try {
+                in = new BufferedReader(new InputStreamReader(new PipedInputStream(pOut)));
+            } catch (IOException ex) {
+                java.util.logging.Logger.getLogger(Logger.class.getName()).log(Level.SEVERE, null, ex);
+            }
+        }
+        return in;
+    }
+    
+    /**
+     * Prints a message. The log time added automatically.
+     * 
+     * @param msg Message to be logged
+     */
+    public static void print(String msg) {
+        String outMsg = 
+                new SimpleDateFormat("HH:mm:ss").format(System.currentTimeMillis())
+                + " [duration unknown]: "
+                + msg.trim();
+        out.println(outMsg);
+    }
+
+    /**
+     * Starts measuring of some operation. 
+     * Call {@link #printDuration(java.lang.String)} on returned object
+     * to print the measured duration.
+     * 
+     * @return An object used to print measured duration and message
+     */
+    public static Logger measureTime() {
+        Logger ret = new Logger();
+        ret.lastTime = System.currentTimeMillis();
+        return ret;
+    }
+    
+    /**
+     * Prints the message about an operation and the duration of the operation. 
+     * The duration is computed as the difference between current system time and 
+     * the time of calling {@link #measureTime()}. The time difference is measured in 
+     * milliseconds and printed as [+mm:ss.SSS] where mm=minutes, ss=seconds, 
+     * and SSS=milliseconds.
+     * 
+     * @param msg Message to be printed
+     */
+    public void printDuration(String msg) {
+        Duration duration = Duration.ofMillis(System.currentTimeMillis() - lastTime);
+        String outMsg = 
+                new SimpleDateFormat("HH:mm:ss").format(System.currentTimeMillis())
+                + " [duration "
+                + String.format(
+                        "%02d:%02d.%03d", 
+                        duration.toMinutes(), 
+                        duration.toSecondsPart(),
+                        duration.toMillisPart())
+                + "]: "
+                + msg.trim();
+        
+        out.println(outMsg);
+    }
+    
+}

MeshModel/src/main/java/cz/fidentis/analyst/feature/services/FeaturePointCsvExporter.java

@@ -19,7 +19,7 @@ public class FeaturePointCsvExporter {
 
     /**
      * Exports a file to set location in csv format <br>
-     * File is located and named as {@param objectName}_landmarks.csv
+     * File is located and named as {@code objectName}_landmarks.csv
      *
      * @param featurePointList
      * @param objectName