Instantiate Log Service

virtualcell · Apr 23, 2024 · 1b69322 · 1b69322
1 parent f7dd10e
commit 1b69322
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Showing 5 changed files with 35 additions and 32 deletions.
diff --git a/view-simulation-results/pom.xml b/view-simulation-results/pom.xml
@@ -176,6 +176,13 @@
             <artifactId>jsoup</artifactId>
             <version>1.16.1</version>
         </dependency>
+        <!-- https://mvnrepository.com/artifact/org.scijava/scijava-log-slf4j -->
+        <dependency>
+            <groupId>org.scijava</groupId>
+            <artifactId>scijava-log-slf4j</artifactId>
+            <version>1.0.6</version>
+        </dependency>
+
     </dependencies>
 
 </project>
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/N5ImageHandler.java b/view-simulation-results/src/main/java/org/vcell/N5/N5ImageHandler.java
@@ -1,44 +1,22 @@
 package org.vcell.N5;
 
 
-import org.scijava.service.Service;
+import org.scijava.log.slf4j.SLF4JLogService;
 import org.vcell.N5.UI.N5ExportTable;
 import org.vcell.N5.UI.N5ViewerGUI;
-import com.amazonaws.auth.AWSStaticCredentialsProvider;
-import com.amazonaws.auth.AnonymousAWSCredentials;
-import com.amazonaws.auth.BasicAWSCredentials;
-import com.amazonaws.client.builder.AwsClientBuilder;
-import com.amazonaws.services.s3.AmazonS3;
-import com.amazonaws.services.s3.AmazonS3ClientBuilder;
-import com.amazonaws.services.s3.AmazonS3URI;
-import com.google.gson.Gson;
-import com.google.gson.GsonBuilder;
 import ij.ImagePlus;
 import ij.plugin.Duplicator;
-import net.imglib2.cache.img.CachedCellImg;
-import net.imglib2.img.display.imagej.ImageJFunctions;
-import net.imglib2.type.numeric.integer.*;
-import net.imglib2.type.numeric.real.DoubleType;
-import net.imglib2.type.numeric.real.FloatType;
-import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
-import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
 import org.scijava.command.Command;
 import org.scijava.log.LogService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
-import org.janelia.saalfeldlab.n5.*;
 
 import javax.swing.*;
 import java.awt.*;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
-import java.lang.reflect.Type;
 import java.net.URI;
-import java.util.*;
 
 
 /*
@@ -120,6 +98,10 @@ public void enableCriticalButtons(boolean enable) {
         logService.error("Test Error");
     }
 
+    static {
+
+    }
+
     @Override
     public void run() {
 //        this.vGui = new N5ViewerGUI(this);
@@ -130,6 +112,9 @@ public void run() {
 //        this.vGui.remoteFileSelection.submitS3Info.addActionListener(this);
 //        this.vGui.mostRecentExport.addActionListener(this);
         N5ExportTable exportTable = new N5ExportTable(this);
+        if(N5ImageHandler.logService == null){
+            N5ImageHandler.logService = new SLF4JLogService();
+        }
         N5ImageHandler.logService.setLevel(LogService.DEBUG);
         exportTable.displayExportTable();
     }
@@ -144,6 +129,13 @@ public void displayN5Dataset(ImagePlus imagePlus) throws IOException {
         }
     }
 
+    public static LogService getLogger(){
+        if (logService == null){
+            logService = new SLF4JLogService();
+        }
+        return logService;
+    }
+
     public static void main(String[] args) {
         N5ImageHandler n5ImageHandler = new N5ImageHandler();
         n5ImageHandler.run();

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java b/view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java
@@ -8,7 +8,6 @@
 import com.amazonaws.services.s3.AmazonS3ClientBuilder;
 import com.amazonaws.services.s3.AmazonS3URI;
 import ij.ImagePlus;
-import loci.common.DebugTools;
 import net.imglib2.cache.img.CachedCellImg;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.numeric.real.DoubleType;
@@ -17,7 +16,6 @@
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
 import org.scijava.log.LogService;
-import org.scijava.plugin.Parameter;
 
 import java.io.File;
 import java.io.IOException;
@@ -28,8 +26,6 @@
 import java.util.Arrays;
 import java.util.HashMap;
 
-import static org.vcell.N5.N5ImageHandler.logService;
-
 public class SimResultsLoader {
     private File selectedLocalFile;
     private AmazonS3 s3Client;
@@ -39,6 +35,8 @@ public class SimResultsLoader {
     private String dataSetChosen;
     private String userSetFileName;
 
+    private final LogService logService = N5ImageHandler.getLogger();
+
     public SimResultsLoader(){
 
     }

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java
@@ -5,7 +5,6 @@
 import ij.ImagePlus;
 import ij.plugin.Duplicator;
 import org.scijava.log.LogService;
-import org.scijava.plugin.Parameter;
 import org.vcell.N5.ExportDataRepresentation;
 import org.vcell.N5.N5ImageHandler;
 import org.vcell.N5.SimResultsLoader;
@@ -54,6 +53,8 @@ public class N5ExportTable implements ActionListener, ListSelectionListener {
     private RemoteFileSelection remoteFileSelection;
     private final int paneWidth = 800;
 
+    private final LogService logService = N5ImageHandler.getLogger();
+
     public N5ExportTable(N5ImageHandler n5ImageHandler){
         remoteFileSelection = new RemoteFileSelection();
     }
@@ -244,14 +245,14 @@ public void openN5FileDataset(ArrayList<SimResultsLoader> filesToOpen, boolean o
             enableCriticalButtons(false);
             try{
                 for(SimResultsLoader simResultsLoader: filesToOpen){
-                    N5ImageHandler.logService.debug("Creating S3 Client from Table");
+                    logService.debug("Creating S3 Client from Table");
                     simResultsLoader.createS3Client();
                     ImagePlus imagePlus = simResultsLoader.getImgPlusFromN5File();
-                    N5ImageHandler.logService.debug("Got ImagePlus in Table");
+                    logService.debug("Got ImagePlus in Table");
                     if(openInMemory){
-                        N5ImageHandler.logService.debug("Loading Image Into Memory");
+                        logService.debug("Loading Image Into Memory");
                         imagePlus = new Duplicator().run(imagePlus);
-                        N5ImageHandler.logService.debug("Loaded Image Into Memory");
+                        logService.debug("Loaded Image Into Memory");
                     }
                     imagePlus.show();
                 }

diff --git a/view-simulation-results/src/test/java/org/vcell/N5/N5ImageHandlerTest.java b/view-simulation-results/src/test/java/org/vcell/N5/N5ImageHandlerTest.java
@@ -41,6 +41,11 @@ private File getTestResourceFiles(String filePath){
         }
     }
 
+    @Before
+    public void run(){
+        N5ImageHandler.getLogger();
+    }
+
     @Test
     public void testN5DatasetList() throws IOException {
         SimResultsLoader simResultsLoader = new SimResultsLoader();