Merge pull request #64 from virtualcell/temporal-analysis

Measurement Script Feature Added to ImageJ Plugin

Author: Ezequiel-Valencia

view-simulation-results/pom.xml

@@ -11,7 +11,7 @@
     </parent>
 
     <artifactId>view-simulation-results</artifactId>
-    <version>1.0-SNAPSHOT</version>
+    <version>2.0</version>
 
     <name>VCell View Simulation Results</name>
     <description>Virtual Cell ImageJ plugin to retrieve VCell simulation results for analysis within ImageJ</description>
@@ -159,39 +159,36 @@
             <version>4.1.1</version>
         </dependency>
 
-
-        <dependency>
-            <groupId>org.jsoup</groupId>
-            <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>
+
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
         </dependency>
-        <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-simple -->
+
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-simple</artifactId>
         </dependency>
 
-        <!-- https://mvnrepository.com/artifact/com.google.code.gson/gson -->
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
-            <version>2.10.1</version>
         </dependency>
+
         <dependency>
             <groupId>software.amazon.awssdk</groupId>
             <artifactId>s3</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>com.opencsv</groupId>
+            <artifactId>opencsv</artifactId>
+        </dependency>
+
 
     </dependencies>
 

view-simulation-results/src/main/java/org/vcell/N5/N5ImageHandler.java

@@ -11,8 +11,7 @@
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.vcell.N5.UI.MainPanel;
-import org.vcell.N5.UI.N5ExportTable;
-import org.vcell.N5.retrieving.LoadingFactory;
+import org.vcell.N5.retrieving.LoadingManager;
 import org.vcell.N5.retrieving.SimResultsLoader;
 
 import java.io.*;
@@ -34,20 +33,23 @@ public class N5ImageHandler implements Command {
     public static MainPanel exportTable;
     public static String exportedMetaDataPath = System.getProperty("user.home") + "/.vcell/exportMetaData.json";
     private static ExportDataRepresentation.FormatExportDataRepresentation exampleJSONData;
-    public static LoadingFactory loadingFactory;
+    public static LoadingManager loadingManager;
 
     @Override
     public void run() {
         initializeLogService();
-        loadingFactory = new LoadingFactory();
+        loadingManager = new LoadingManager();
         exportTable = new MainPanel();
+        MainPanel.controlButtonsPanel.setStateToInitializing(true);
         setExampleJSONData();
 //        N5ImageHandler.logService.setLevel(LogService.DEBUG);
         Thread thread = new Thread(() -> {
             // For some reason getting a standard client takes three seconds.
             // So create one upon initialization, while the user is focused on the GUI
             // and by the time they open an Image it's already loaded.
             SimResultsLoader.s3ClientBuilder = AmazonS3ClientBuilder.standard();
+            MainPanel.controlButtonsPanel.setStateToInitializing(false);
+            MainPanel.n5ExportTable.valueChanged(null);
         });
         thread.start();
     }

view-simulation-results/src/main/java/org/vcell/N5/UI/AdvancedFeatures.java

@@ -0,0 +1,35 @@
+package org.vcell.N5.UI;
+
+import javax.swing.*;
+import javax.swing.border.Border;
+import javax.swing.border.EtchedBorder;
+import java.awt.*;
+
+public class AdvancedFeatures extends JPanel {
+    public final JButton openInMemory;
+    public final JButton copyLink;
+    public final JButton useN5Link;
+
+
+    public AdvancedFeatures(){
+        Border lowerEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
+
+
+        openInMemory = new JButton("Open In Memory");
+        JPanel checkBoxPanel = new JPanel();
+//        checkBoxPanel.add(openInMemory);
+
+        JPanel buttonPanel = new JPanel();
+        copyLink = new JButton("Copy Link");
+        useN5Link = new JButton("Use N5 Link");
+        buttonPanel.add(copyLink);
+        buttonPanel.add(useN5Link);
+        buttonPanel.add(openInMemory);
+
+//        setLayout(new BorderLayout());
+//        add(buttonPanel, BorderLayout.NORTH);
+//        add(checkBoxPanel, BorderLayout.SOUTH);
+        add(buttonPanel);
+        this.setBorder(BorderFactory.createTitledBorder(lowerEtchedBorder, " Advanced Features "));
+    }
+}