add logback logging

pom.xml

@@ -126,6 +126,15 @@
 			<artifactId>imagej-utils</artifactId>
 			<version>${imagej-utils.version}</version>
 		</dependency>
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+		</dependency>
+		<dependency>
+			<groupId>ch.qos.logback</groupId>
+			<artifactId>logback-classic</artifactId>
+			<scope>test</scope>
+		</dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter</artifactId>

src/main/java/de/embl/schwab/crosshair/io/STLResourceLoader.java

@@ -2,8 +2,9 @@
 
 import customnode.CustomMesh;
 import customnode.CustomTriangleMesh;
-import ij.IJ;
 import org.scijava.vecmath.Point3f;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.*;
 import java.util.ArrayList;
@@ -17,6 +18,9 @@
  * input stream, and load from resource name
  */
 public class STLResourceLoader {
+
+    private static final Logger logger = LoggerFactory.getLogger(STLResourceLoader.class);
+
     private HashMap<String, CustomMesh> meshes;
     private ArrayList<Point3f> vertices = new ArrayList();
     private String name = null;
@@ -35,7 +39,7 @@ public static Map<String, CustomMesh> loadSTL(String name) {
         try {
             return STLResourceLoader.load(name);
         } catch (Exception var2) {
-            var2.printStackTrace();
+            logger.error("Error loading STL file", var2);
             return null;
         }
     }
@@ -52,7 +56,7 @@ public static Map<String, CustomMesh> load(String name) throws IOException {
         try {
             sl.parse(name);
         } catch (RuntimeException var3) {
-            IJ.log("error reading " + sl.name);
+            logger.error("error reading " + sl.name);
             throw var3;
         }
 
@@ -101,8 +105,7 @@ private void parseBinary() {
 
             inputStream.close();
         } catch (IOException var10) {
-            var10.printStackTrace();
-
+            logger.error("Error parsing binary", var10);
         }
 
         CustomMesh cm = this.createCustomMesh();

src/main/java/de/embl/schwab/crosshair/legacy/OldFormatSettingsReader.java

@@ -1,6 +1,8 @@
 package de.embl.schwab.crosshair.legacy;
 
 import com.google.gson.Gson;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 import java.io.FileReader;
@@ -11,6 +13,8 @@
  */
 public class OldFormatSettingsReader {
 
+    private static final Logger logger = LoggerFactory.getLogger(OldFormatSettingsReader.class);
+
     /**
      * Create a settings reader
      */
@@ -26,7 +30,7 @@ public OldFormatSettings readSettings( String filePath ) {
         try ( FileReader fileReader = new FileReader(filePath) ) {
             return gson.fromJson(fileReader, OldFormatSettings.class);
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error("Error reading settings", e);
         }
 
         return null;

src/main/java/de/embl/schwab/crosshair/settings/SettingsReader.java

@@ -12,6 +12,8 @@
 import de.embl.schwab.crosshair.ui.swing.OtherPanel;
 import ij.IJ;
 import ij3d.Content;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.FileReader;
 import java.io.IOException;
@@ -20,6 +22,8 @@
 
 public class SettingsReader {
 
+    private static final Logger logger = LoggerFactory.getLogger(SettingsReader.class);
+
     public SettingsReader() {}
 
     public Settings readSettings(String filePath ) {
@@ -30,7 +34,7 @@ public Settings readSettings(String filePath ) {
         try ( FileReader fileReader = new FileReader(filePath) ) {
             return gson.fromJson(fileReader, Settings.class);
         } catch (IOException e1) {
-            e1.printStackTrace();
+            logger.error("Error reading settings file", e1);
         }
 
         return null;

src/main/java/de/embl/schwab/crosshair/settings/SettingsWriter.java

@@ -5,6 +5,8 @@
 import de.embl.schwab.crosshair.plane.Plane;
 import de.embl.schwab.crosshair.plane.PlaneManager;
 import ij3d.Content;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.FileWriter;
 import java.io.IOException;
@@ -13,6 +15,8 @@
 
 public class SettingsWriter {
 
+    private static final Logger logger = LoggerFactory.getLogger(SettingsWriter.class);
+
     public SettingsWriter() { }
 
     public Settings createSettings(PlaneManager planeManager, Map<String, Content> imageNameToContent ) {
@@ -58,7 +62,7 @@ public void writeSettings( Settings settings, String filePath ) {
             fileWriter.flush();
             fileWriter.close();
         } catch (IOException e1) {
-            e1.printStackTrace();
+            logger.error("Error writing settings", e1);
         }
     }
 }

src/main/java/de/embl/schwab/crosshair/solution/SolutionReader.java

@@ -5,11 +5,16 @@
 import com.google.gson.reflect.TypeToken;
 import de.embl.schwab.crosshair.io.serialise.VertexPointAdapter;
 import de.embl.schwab.crosshair.points.VertexPoint;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.FileReader;
 import java.io.IOException;
 
 public class SolutionReader {
+
+    private static final Logger logger = LoggerFactory.getLogger(SolutionReader.class);
+
     public SolutionReader() {}
 
     public Solution readSolution( String filePath ) {
@@ -19,7 +24,7 @@ public Solution readSolution( String filePath ) {
         try ( FileReader fileReader = new FileReader(filePath) ) {
             return gson.fromJson(fileReader, Solution.class);
         } catch (IOException e) {
-            e.printStackTrace();
+            logger.error("Error reading solutions file", e);
         }
 
         return  null;

src/main/java/de/embl/schwab/crosshair/solution/SolutionWriter.java

@@ -5,13 +5,16 @@
 import com.google.gson.reflect.TypeToken;
 import de.embl.schwab.crosshair.io.serialise.VertexPointAdapter;
 import de.embl.schwab.crosshair.points.VertexPoint;
-import de.embl.schwab.crosshair.solution.Solution;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.FileWriter;
 import java.io.IOException;
 
 public class SolutionWriter {
 
+    private static final Logger logger = LoggerFactory.getLogger(SolutionWriter.class);
+
     private Solution solution;
     private String filePath;
 
@@ -29,7 +32,7 @@ public void writeSolution() {
             fileWriter.flush();
             fileWriter.close();
         } catch (IOException e1) {
-            e1.printStackTrace();
+            logger.error("Error writing solution", e1);
         }
     }
 

src/main/java/de/embl/schwab/crosshair/targetingaccuracy/AccuracyCalculator.java

@@ -8,6 +8,8 @@
 import de.embl.schwab.crosshair.utils.GeometryUtils;
 import net.imglib2.RealPoint;
 import org.scijava.vecmath.Vector3d;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.FileWriter;
 import java.io.IOException;
@@ -18,6 +20,8 @@
 
 public class AccuracyCalculator {
 
+    private static final Logger logger = LoggerFactory.getLogger(AccuracyCalculator.class);
+
     private transient BlockPlane beforeBlock;
     private transient BlockPlane beforeTarget;
     private transient Plane afterBlock;
@@ -97,7 +101,7 @@ public void saveAccuracy( String jsonPath ) {
             fileWriter.flush();
             fileWriter.close();
         } catch (IOException e1) {
-            e1.printStackTrace();
+            logger.error("Error saving accuracy measures", e1);
         }
     }
 

src/main/java/de/embl/schwab/crosshair/ui/command/MeasureTargetingAccuracyCommand.java

@@ -6,6 +6,8 @@
 import org.scijava.command.Command;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import java.io.File;
 
@@ -14,6 +16,8 @@
 @Plugin(type = Command.class, menuPath = "Plugins>Crosshair>Analysis>Measure Targeting Accuracy" )
 public class MeasureTargetingAccuracyCommand implements Command {
 
+    private static final Logger logger = LoggerFactory.getLogger(MeasureTargetingAccuracyCommand.class);
+
     @Parameter(label="Before targeting image xml")
     public File beforeTargetingXml;
 
@@ -41,7 +45,7 @@ public void run() {
                 new TargetingAccuracy( beforeTargetingXml, registeredAfterTargetingXml,
                         crosshairSettingsJson, crosshairSolutionJson );
             } catch (SpimDataException e) {
-                e.printStackTrace();
+                logger.error("Error opening targeting accuracy", e);
             }
         }
     }

src/main/java/de/embl/schwab/crosshair/ui/swing/SliderPanelDouble.java

@@ -47,6 +47,8 @@
 
 import bdv.util.BoundedValue;
 import bdv.util.BoundedValueDouble;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  * A {@link JSlider} with a {@link JSpinner} next to it, both modifying the same
@@ -55,6 +57,8 @@
  */
 public class SliderPanelDouble extends JPanel implements BoundedValueDouble.UpdateListener
 {
+    private static final Logger logger = LoggerFactory.getLogger(SliderPanelDouble.class);
+
     private static final long serialVersionUID = 6444334522127424416L;
 
     private static final int sliderLength = 10000;
@@ -168,7 +172,7 @@ public void commitSpinnerEdits() {
         try {
             spinner.commitEdit();
         } catch (ParseException e) {
-            e.printStackTrace();
+            logger.error("Error committing spinner edits", e);
         }
     }
 

src/main/java/de/embl/schwab/crosshair/utils/Utils.java

@@ -4,6 +4,8 @@
 import ij3d.Content;
 import ij3d.Image3DUniverse;
 import org.scijava.vecmath.Point3d;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.swing.*;
 import java.awt.*;
@@ -12,6 +14,8 @@
 
 public class Utils {
 
+    private static final Logger logger = LoggerFactory.getLogger(Utils.class);
+
     public static void printImageMinMax (Content imageContent) {
         Point3d min = new Point3d();
         Point3d max = new Point3d();
@@ -78,7 +82,7 @@ public static void resetCrossPlatformSwingLookAndFeel() {
         try {
             UIManager.setLookAndFeel( UIManager.getCrossPlatformLookAndFeelClassName() );
         } catch (Exception e) {
-            e.printStackTrace();
+            logger.error("Error setting look and feel", e);
         }
     }
 }

src/test/java/de/embl/schwab/crosshair/io/STLResourceLoaderTest.java

@@ -1,9 +1,12 @@
 package de.embl.schwab.crosshair.io;
 
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
 import customnode.CustomMesh;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.ValueSource;
+import org.slf4j.LoggerFactory;
 
 import java.util.Map;
 
@@ -20,6 +23,10 @@ void loadSTL(String modelName) {
 
     @Test
     void loadInvalidSTL() {
+        // Disable logging to keep the test logs clean (we're expecting an error here)
+        Logger logger = (Logger) LoggerFactory.getLogger(STLResourceLoader.class);
+        logger.setLevel(Level.OFF);
+
         Map<String, CustomMesh> currentStl = STLResourceLoader.loadSTL("invalid.stl");
         assertNull(currentStl);
     }

src/test/java/de/embl/schwab/crosshair/legacy/OldFormatSettingsReaderTest.java

@@ -1,8 +1,11 @@
 package de.embl.schwab.crosshair.legacy;
 
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
+import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.nio.file.Path;
@@ -32,6 +35,10 @@ void readSettings() {
 
     @Test
     void readInvalidSettings( @TempDir Path tempDir ) {
+        // Disable logging to keep the test logs clean (we're expecting an error here)
+        Logger logger = (Logger) LoggerFactory.getLogger(OldFormatSettingsReader.class);
+        logger.setLevel(Level.OFF);
+
         File invalidJsonPath = tempDir.resolve( "invalid.json" ).toFile();
         OldFormatSettings settings = oldFormatSettingsReader.readSettings( invalidJsonPath.getAbsolutePath() );
 

src/test/java/de/embl/schwab/crosshair/settings/SettingsReaderTest.java

@@ -1,8 +1,11 @@
 package de.embl.schwab.crosshair.settings;
 
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
+import org.slf4j.LoggerFactory;
 
 import java.io.File;
 import java.nio.file.Path;
@@ -39,6 +42,10 @@ void readSettings() {
 
     @Test
     void readInvalidSettings( @TempDir Path tempDir ) {
+        // Disable logging to keep the test logs clean (we're expecting an error here)
+        Logger logger = (Logger) LoggerFactory.getLogger(SettingsReader.class);
+        logger.setLevel(Level.OFF);
+
         File invalidJsonPath = tempDir.resolve( "invalid.json" ).toFile();
         Settings settings = settingsReader.readSettings( invalidJsonPath.getAbsolutePath() );
 

src/test/java/de/embl/schwab/crosshair/solution/SolutionReaderTest.java

@@ -4,6 +4,9 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.io.TempDir;
+import org.slf4j.LoggerFactory;
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
 
 import java.io.File;
 import java.nio.file.Path;
@@ -36,6 +39,10 @@ void readSolution() {
 
     @Test
     void readInvalidSolution( @TempDir Path tempDir ) {
+        // Disable logging to keep the test logs clean (we're expecting an error here)
+        Logger logger = (Logger) LoggerFactory.getLogger(SolutionReader.class);
+        logger.setLevel(Level.OFF);
+
         File invalidJsonPath = tempDir.resolve( "invalid.json" ).toFile();
         Solution solution = solutionReader.readSolution( invalidJsonPath.getAbsolutePath() );