Merge pull request #28 from virtualcell/view-simulation-results-helpe…

…r-menu

View simulation results helper menu

view-simulation-results/pom.xml

@@ -157,6 +157,12 @@
             <artifactId>jsoup</artifactId>
             <version>1.16.1</version>
         </dependency>
+
+        <dependency>
+            <groupId>org.commonmark</groupId>
+            <artifactId>commonmark</artifactId>
+            <version>0.20.0</version>
+        </dependency>
     </dependencies>
 
 </project>

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

@@ -0,0 +1,57 @@
+package org.vcell.N5.UI;
+
+import org.commonmark.node.Node;
+import org.commonmark.parser.Parser;
+import org.commonmark.renderer.html.HtmlRenderer;
+
+import javax.swing.*;
+import java.awt.*;
+import java.io.FileReader;
+import java.io.IOException;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+public class HelpExplanation {
+    private JDialog jDialog;
+
+    public HelpExplanation(){
+        int height = 400;
+        int width = 700;
+
+        JPanel helperPanel = new JPanel();
+        JTextPane textPane = new JTextPane();
+
+        Parser parser = Parser.builder().build();
+        String md;
+        URL mdPath = ClassLoader.getSystemClassLoader().getResource("Help.md");
+        try {
+            md = new String(Files.readAllBytes(Paths.get(mdPath.getPath())));
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+        Node node = parser.parse(md);
+        HtmlRenderer renderer = HtmlRenderer.builder().build();
+        String text = renderer.render(node);
+        textPane.setContentType("text/html");
+        textPane.setSize(width, height);
+        textPane.setPreferredSize(new Dimension(width, height));
+        textPane.setText(text);
+        textPane.setEditable(false);
+
+        JScrollPane scrollPane = new JScrollPane(textPane);
+        scrollPane.setSize(width, height);
+        helperPanel.setSize(width, height);
+        helperPanel.add(scrollPane);
+
+
+        JOptionPane pane = new JOptionPane(helperPanel, JOptionPane.PLAIN_MESSAGE, 0, null, new Object[]{"Close"});
+        jDialog = pane.createDialog("Helper Menu");
+        jDialog.setModal(false);
+        jDialog.setPreferredSize(new Dimension(width, height));
+    }
+
+    public void displayHelpMenu(){
+        jDialog.setVisible(true);
+    }
+}

view-simulation-results/src/main/java/org/vcell/N5/UI/N5ViewerGUI.java

@@ -27,8 +27,10 @@ public class N5ViewerGUI extends JFrame implements ActionListener {
     private N5ExportTable n5ExportTable;
 
     public JButton mostRecentExport;
+    private JButton questionMark;
 
     public RemoteFileSelection remoteFileSelection;
+    private HelpExplanation helpExplanation;
 
     public N5ViewerGUI(N5ImageHandler n5ImageHandler) {
         thisJFrame = this;
@@ -68,14 +70,19 @@ public N5ViewerGUI(N5ImageHandler n5ImageHandler) {
         mainPanelConstraints.gridy = 0;
         mainPanelConstraints.gridx = 4;
         openInMemory = new JLabel();
-        openInMemory.setText("Open Image in Memory");
+        openInMemory.setText("Open in Memory");
         mainPanel.add(openInMemory, mainPanelConstraints);
 
         mainPanelConstraints.gridy = 0;
         mainPanelConstraints.gridx = 5;
         openMemoryCheckBox = new JCheckBox();
         mainPanel.add(openMemoryCheckBox, mainPanelConstraints);
 
+        mainPanelConstraints.gridy = 0;
+        mainPanelConstraints.gridx = 6;
+        questionMark = new JButton("?");
+        mainPanel.add(questionMark, mainPanelConstraints);
+
 
         GridBagConstraints datasetConstraints = new GridBagConstraints();
         datasetConstraints.gridx = 0;
@@ -111,7 +118,7 @@ public N5ViewerGUI(N5ImageHandler n5ImageHandler) {
 
 
         localFiles.addActionListener(this);
-
+        questionMark.addActionListener(this);
         remoteFiles.addActionListener(this);
         exportTableButton.addActionListener(this);
 
@@ -125,6 +132,7 @@ public N5ViewerGUI(N5ImageHandler n5ImageHandler) {
 
 
         n5ExportTable = new N5ExportTable(n5ImageHandler);
+        helpExplanation = new HelpExplanation();
     }
 
     public void updateDatasetList(ArrayList<String> arrayList){
@@ -149,6 +157,8 @@ public void actionPerformed(ActionEvent e) {
             remoteFileSelection.setVisible(true);
         } else if (e.getSource() == exportTableButton) {
             n5ExportTable.displayExportTable();
+        } else if (e.getSource() == questionMark) {
+            helpExplanation.displayHelpMenu();
         }
     }
 

view-simulation-results/src/main/resources/Help.md

@@ -0,0 +1,30 @@
+### Intro
+The VCell (https://vcell.org/) application can export spatial simulation results into multiple formats, with
+.N5 (https://imagej.net/libs/n5) being one of them. N5 exports are 
+stored remotely on VCell servers, allowing applications such as ImageJ
+to directly access the results of these simulations and perform analyses.
+
+### VCell Spatial Simulation
+Simulation solvers generating 2- or 3-dimensional spatial 
+domains can be visualized in ImageJ using this plugin. 
+Spatial dimensions and time directly correspond to fields within an ImageJ 
+image. The image's channels depict different variables within a simulation.
+
+### N5 and Datasets
+Each N5 store is a direct mapping to a VCell simulation, and contains one or more
+datasets. Each dataset holds numerical data and metadata corresponding to an Image in ImageJ.
+Each N5 store is fully identified through its N5 URL which can be shared and opened by other applications
+which support the N5 format.
+
+
+### Accessing Simulation Results
+
+For VCell exports generated from your local VCell installation:
+- Either, Click the recent export button.
+
+- Or, Open the export table and view all past exports with their affiliated metadata.
+
+From N5 URL (VCell Install Not Required):
+- Click the 'Remote Files' button, paste the N5 URL,
+then select dataset from list.
+