Add Tabs and Use ROI Manager

.github/workflows/maven.yml

@@ -21,71 +21,16 @@ jobs:
 
   build:
     runs-on: ubuntu-latest
-    env:
-      AWS_ACCESS_KEY_ID: jj
-      AWS_SECRET_ACCESS_KEY: jj
-      AWS_DEFAULT_REGION: 'site2-low'
-      AWS_ENDPOINT_URL: "http://127.0.0.1:4000"
-
-
-
-#    https://docs.github.com/en/actions/using-containerized-services/about-service-containers
-    services:
-      s3proxy:
-        image: andrewgaul/s3proxy
-        ports:
-          - 4000:80
-        env:
-          JCLOUDS_FILESYSTEM_BASEDIR: /data
-          JCLOUDS_PROVIDER: filesystem
-          JCLOUDS_REGIONS: site2-low
-          S3PROXY_IDENTITY: jj
-          S3PROXY_CREDENTIAL: jj
-
-          LOG_LEVEL: info
-          S3PROXY_ENDPOINT: http://0.0.0.0:80
-          S3PROXY_AUTHORIZATION: "aws-v2-or-v4"
-          S3PROXY_VIRTUALHOST: ""
-          S3PROXY_KEYSTORE_PATH: keystore.jks
-          S3PROXY_KEYSTORE_PASSWORD: password
-          S3PROXY_CORS_ALLOW_ALL: false
-          S3PROXY_CORS_ALLOW_ORIGINS: ""
-          S3PROXY_CORS_ALLOW_METHODS: ""
-          S3PROXY_CORS_ALLOW_HEADERS: ""
-          S3PROXY_IGNORE_UNKNOWN_HEADERS: false
-          S3PROXY_ENCRYPTED_BLOBSTORE: ""
-          S3PROXY_ENCRYPTED_BLOBSTORE_PASSWORD: ""
-          S3PROXY_ENCRYPTED_BLOBSTORE_SALT: ""
-
-          JCLOUDS_ENDPOINT: ""
-          JCLOUDS_REGION: ""
-          JCLOUDS_IDENTITY: remote-identity
-          JCLOUDS_CREDENTIAL: remote-credential
-          JCLOUDS_KEYSTONE_VERSION: ""
-          JCLOUDS_KEYSTONE_SCOPE: ""
-          JCLOUDS_KEYSTONE_PROJECT_DOMAIN_NAME: ""
-        volumes:
-          - /dockerImage/data:/data
-
     steps:
     - uses: actions/checkout@v3
 
-    - name: Put test resources in S3Proxy Container
-      run: |
-        aws s3 mb s3://nfive
-        aws s3 cp ${{ github.workspace }}/view-simulation-results/src/test/resources/nfive s3://nfive --recursive
-
     - name: Set up JDK 8
       uses: actions/setup-java@v3
       with:
         java-version: '8'
         distribution: 'temurin'
         cache: maven
 
-    #Before building the Repo a docker container needs to intialized such that the test cases can work properly
-#    https://github.com/addnab/docker-run-action
-
-
     - name: Build with Maven
       run: mvn -B package --file pom.xml
 

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

@@ -1,5 +1,6 @@
 package org.vcell.N5;
 
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Stack;
@@ -24,26 +25,28 @@ public FormatExportDataRepresentation(HashMap<String, SimulationExportDataRepres
     }
 
     public static class SimulationExportDataRepresentation {
-        public String exportDate;
-        public String uri;
-        public String jobID;
-        public String dataID;
-        public String simulationName;
-        public String applicationName;
-        public String biomodelName;
-        public String variables;
-        public String startAndEndTime;
-
-        public ArrayList<String> differentParameterValues;
-        public String savedFileName;
+        public final String exportDate;
+        public final String uri;
+        public final String jobID;
+        public final String dataID;
+        public final String simulationName;
+        public final String applicationName;
+        public final String biomodelName;
+        public final String variables;
+        public final String startAndEndTime;
+
+        public final ArrayList<String> differentParameterValues;
+        public final String savedFileName;
+
+        public final ArrayList<URL> imageROIReferences;
 
         public int zSlices;
         public int tSlices;
         public int numVariables;
 
         public SimulationExportDataRepresentation(String exportDate, String uri, String jobID, String dataID, String simulationName,
                                                   String applicationName, String biomodelName, String variables, String startAndEndTime,
-                                                  ArrayList<String> differentParameterValues, String savedFileName){
+                                                  ArrayList<String> differentParameterValues, String savedFileName, ArrayList<URL> imageROIReferences){
             this.exportDate = exportDate;
             this.uri = uri;
             this.jobID = jobID;
@@ -55,6 +58,7 @@ public SimulationExportDataRepresentation(String exportDate, String uri, String
             this.startAndEndTime = startAndEndTime;
             this.differentParameterValues = differentParameterValues;
             this.savedFileName = savedFileName;
+            this.imageROIReferences = imageROIReferences;
         }
     }
 

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

@@ -22,7 +22,6 @@ public class ControlButtonsPanel extends JPanel implements ActionListener {
 //    private final JButton openLocal = new JButton("Open N5 Local");
     private final JButton questionMark;
 
-    public final JCheckBox includeExampleExports;
     public final JCheckBox displayAdvancedFeatures;
 
     private N5ExportTable n5ExportTable;
@@ -31,9 +30,6 @@ public class ControlButtonsPanel extends JPanel implements ActionListener {
     private PanelState panelState = PanelState.NOTHING_OR_LOADING_IMAGE;
 
     public ControlButtonsPanel(){
-        includeExampleExports = new JCheckBox("Show Example Exports");
-        includeExampleExports.setSelected(!N5ImageHandler.exportedDataExists());
-
         displayAdvancedFeatures = new JCheckBox("Advanced Features");
 
         openOrCancel = new JButton("Open Virtual Stack");
@@ -54,7 +50,6 @@ public ControlButtonsPanel(){
 
 
         JPanel bottomRow = new JPanel(new GridBagLayout());
-        bottomRow.add(includeExampleExports);
         gridBagConstraints.gridx = 1;
         bottomRow.add(displayAdvancedFeatures, gridBagConstraints);
         gridBagConstraints.gridx = 2;
@@ -86,7 +81,6 @@ public ControlButtonsPanel(){
         questionMark.addActionListener(this);
         advancedFeatures.useN5Link.addActionListener(this);
 //        openLocal.addActionListener(this);
-        includeExampleExports.addActionListener(this);
         displayAdvancedFeatures.addActionListener(this);
         dataReduction.addActionListener(this);
         advancedFeatures.openInMemory.addActionListener(this);
@@ -130,8 +124,6 @@ public void actionPerformed(ActionEvent e) {
             new HelpExplanation().displayHelpMenu();
         } else if (e.getSource().equals(advancedFeatures.useN5Link)) {
             remoteFileSelection.setVisible(true);
-        } else if (e.getSource().equals(includeExampleExports)){
-            n5ExportTable.updateTableData();
         } else if (e.getSource().equals(displayAdvancedFeatures)) {
             advancedFeatures.setVisible(displayAdvancedFeatures.isSelected());
         }

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

@@ -57,10 +57,6 @@ public TimeFilter(){
     public void actionPerformed(ActionEvent e) {
         if (e.getSource().equals(anyInterval) || e.getSource().equals(todayInterval)
                 || e.getSource().equals(monthInterval) || e.getSource().equals(yearlyInterval)) {
-            if(MainPanel.controlButtonsPanel.includeExampleExports.isSelected()){
-                n5ExportTable.updateTableData();
-                return;
-            }
             n5ExportTable.updateTableData();
         }
     }

view-simulation-results/src/main/java/org/vcell/N5/UI/N5ExportTable.java

@@ -9,8 +9,6 @@
 import org.vcell.N5.retrieving.SimResultsLoader;
 
 import javax.swing.*;
-import javax.swing.border.Border;
-import javax.swing.border.EtchedBorder;
 import javax.swing.event.ListSelectionEvent;
 import javax.swing.event.ListSelectionListener;
 import javax.swing.table.AbstractTableModel;
@@ -24,14 +22,16 @@
 import java.util.*;
 import java.util.concurrent.TimeUnit;
 
-public class N5ExportTable extends JScrollPane implements ListSelectionListener, SimLoadingListener {
-    public N5ExportTableModel n5ExportTableModel;
+public class N5ExportTable extends JTabbedPane implements ListSelectionListener, SimLoadingListener {
+    private N5ExportTableModel n5ExportTableModel;
     private JTable exportListTable;
-
-    private final Border lowerEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
-    private final Border exampleBorder = BorderFactory.createTitledBorder(lowerEtchedBorder, "Example Exports");
+    private JTable exampleExportListTable;
     private final Map<Integer, String> loadingRowsJobID = new HashMap<>();
 
+    private final JScrollPane personalExportsPanel = new JScrollPane();
+    private final JScrollPane exampleExportsPanel = new JScrollPane();
+
+
     private ControlButtonsPanel controlPanel;
     private ExportDetailsPanel exportDetailsPanel;
     private TimeFilter timeFilter;
@@ -49,7 +49,12 @@ public void initialize(ControlButtonsPanel controlButtonsPanel, ExportDetailsPan
         N5ImageHandler.loadingManager.addSimLoadingListener(this);
         n5ExportTableModel = new N5ExportTableModel();
         exportListTable = new JTable(n5ExportTableModel);
-        this.setViewportView(exportListTable);
+        exampleExportListTable = new JTable(n5ExportTableModel);
+        personalExportsPanel.setViewportView(exportListTable);
+        exampleExportsPanel.setViewportView(exampleExportListTable);
+
+        this.addTab("Personal Exports", personalExportsPanel);
+        this.addTab("Example Exports", exampleExportsPanel);
 
 
         DefaultTableCellRenderer cellRenderer = new DefaultTableCellRenderer(){
@@ -70,12 +75,14 @@ public Component getTableCellRendererComponent(JTable table, Object value, boole
         int columns = n5ExportTableModel.getColumnCount();
         for (int i = 0; i < columns; i++){
             exportListTable.getColumnModel().getColumn(i).setCellRenderer(cellRenderer);
+            exampleExportListTable.getColumnModel().getColumn(i).setCellRenderer(cellRenderer);
         }
 
         this.setPreferredSize(new Dimension(500, 400));
-        this.setBorder(BorderFactory.createTitledBorder(lowerEtchedBorder, "Export Table"));
         exportListTable.getSelectionModel().addListSelectionListener(this);
+        exampleExportListTable.getSelectionModel().addListSelectionListener(this);
 
+        this.setSelectedIndex(N5ImageHandler.exportedDataExists() ? 0 : 1);
         updateTableData("");
         automaticRefresh();
     }
@@ -95,13 +102,9 @@ public void updateTableData(String strFilter){
 
     void updateTableData(LocalDateTime oldestTimeAllowed, String strFilter){
         n5ExportTableModel.resetData();
-        if (!controlPanel.includeExampleExports.isSelected()){
-            this.setBorder(BorderFactory.createTitledBorder(lowerEtchedBorder, "Personal Exports"));
-        } else {
-            this.setBorder(exampleBorder);
-        }
         try {
-            ExportDataRepresentation.FormatExportDataRepresentation formatExportData = N5ImageHandler.exportedDataExists() && !controlPanel.includeExampleExports.isSelected() ?
+            boolean hasPersonalExports = N5ImageHandler.exportedDataExists() && this.getSelectedIndex() == 0;
+            ExportDataRepresentation.FormatExportDataRepresentation formatExportData = hasPersonalExports ?
                     N5ImageHandler.getJsonData() : N5ImageHandler.getExampleJSONData();
 
             Stack<String> jobStack = (Stack<String>) formatExportData.formatJobIDs.clone();
@@ -123,7 +126,7 @@ private void automaticRefresh(){
             try {
                 while(true){
                     ExportDataRepresentation.FormatExportDataRepresentation formatExportData = N5ImageHandler.getJsonData();
-                    if (formatExportData != null && !controlPanel.includeExampleExports.isSelected()){
+                    if (formatExportData != null && this.getSelectedIndex() == 0){
                         ExportDataRepresentation.SimulationExportDataRepresentation mostRecentTableEntry = !n5ExportTableModel.tableData.isEmpty() ? n5ExportTableModel.tableData.getFirst() : null;
                         Stack<String> jobStack = formatExportData.formatJobIDs;
                         boolean isUpdated = false;
@@ -156,18 +159,20 @@ private void automaticRefresh(){
 
     public void openSelectedRows(boolean openInMemory, boolean performDataReduction, SimResultsLoader.OpenTag openTag){
         ArrayList<SimResultsLoader> filesToOpen = new ArrayList<>();
-        for(int row: exportListTable.getSelectedRows()){
+        JTable currentTable = getCurrentTable();
+        for(int row: currentTable.getSelectedRows()){
             String uri = n5ExportTableModel.getRowData(row).uri;
             ExportDataRepresentation.SimulationExportDataRepresentation rowData = n5ExportTableModel.getRowData(row);
-            SimResultsLoader simResultsLoader = new SimResultsLoader(uri, rowData.savedFileName, row, rowData.jobID, openTag);
+            SimResultsLoader simResultsLoader = new SimResultsLoader(uri, rowData.savedFileName, row, rowData.jobID, openTag, rowData.imageROIReferences);
             filesToOpen.add(simResultsLoader);
         }
         N5ImageHandler.loadingManager.openN5FileDataset(filesToOpen, openInMemory,
                 performDataReduction);
     }
 
     public void copySelectedRowLink(){
-        ExportDataRepresentation.SimulationExportDataRepresentation selectedRow = n5ExportTableModel.getRowData(exportListTable.getSelectedRow());
+        JTable currentTable = getCurrentTable();
+        ExportDataRepresentation.SimulationExportDataRepresentation selectedRow = n5ExportTableModel.getRowData(currentTable.getSelectedRow());
         Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
         clipboard.setContents(new StringSelection(selectedRow.uri), null);
     }
@@ -192,9 +197,10 @@ else if (n5ExportTableModel.getRowData(currentRow).jobID.equals(expectedJobID) &
 
     @Override
     public void valueChanged(ListSelectionEvent e) {
-        int row = exportListTable.getSelectedRow();
+        JTable currentTable = getCurrentTable();
+        int row = currentTable.getSelectedRow();
         exportDetailsPanel.resetExportDetails();
-        if (row > exportListTable.getRowCount() || row < 0){
+        if (row > currentTable.getRowCount() || row < 0){
             controlPanel.disableAllContextDependentButtons();
             return;
         }
@@ -206,24 +212,33 @@ public void valueChanged(ListSelectionEvent e) {
         controlPanel.updateButtonsToMatchState(loadingRow != -1);
     }
 
+    @Override
+    public void setSelectedIndex(int index) {
+        super.setSelectedIndex(index);
+        updateTableData();
+    }
+
     public void stopSelectedImageFromLoading(){
-        int row = exportListTable.getSelectedRow();
+        JTable currentTable = getCurrentTable();
+        int row = currentTable.getSelectedRow();
         N5ImageHandler.loadingManager.stopLoadingImage(n5ExportTableModel.tableData.get(row).jobID);
         loadingRowsJobID.remove(row);
-        exportListTable.repaint();
+        currentTable.repaint();
     }
 
     public void removeSpecificRowFromLoadingRows(int rowNumber){
+        JTable currentTable = getCurrentTable();
         int realRowNumber = findLoadingRow(rowNumber, rowNumber);
         loadingRowsJobID.remove(realRowNumber);
         controlPanel.updateButtonsToMatchState(false);
-        exportListTable.repaint();
+        currentTable.repaint();
     }
 
     @Override
     public void simIsLoading(int itemRow, String exportID) {
+        JTable currentTable = getCurrentTable();
         loadingRowsJobID.put(itemRow, exportID);
-        exportListTable.repaint();
+        currentTable.repaint();
     }
 
     @Override
@@ -234,6 +249,18 @@ public void simFinishedLoading(SimResultsLoader loadedResults) {
         }
     }
 
+    /**
+     * Required, for there is one table for examples and another for personal exports. The same table
+     * can not be used for both tabs, because a JComponent can have only one parent.
+     */
+    private JTable getCurrentTable(){
+        return this.getSelectedIndex() == 0 ? exportListTable : exampleExportListTable;
+    }
+
+    public N5ExportTableModel getN5ExportTableModel(){
+        return n5ExportTableModel;
+    }
+
     public static class N5ExportTableModel extends AbstractTableModel {
         public final ArrayList<String> headers = new ArrayList<String>(){{
             add("BioModel");

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

@@ -95,7 +95,7 @@ public String getS3URL(){
 
     @Override
     public void actionPerformed(ActionEvent e) {
-        SimResultsLoader simResultsLoader = new SimResultsLoader(getS3URL(), "", -1, "", SimResultsLoader.OpenTag.VIEW);
+        SimResultsLoader simResultsLoader = new SimResultsLoader(getS3URL(), "", -1, "", SimResultsLoader.OpenTag.VIEW, new ArrayList<>());
         N5ImageHandler.loadingManager.openN5FileDataset(new ArrayList<SimResultsLoader>(){{add(simResultsLoader);}},
                 false,
                 false);

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

@@ -141,7 +141,7 @@ public void initializeDataSheets(){
     public void addMetaData(SimResultsLoader loadedResults){
         synchronized (metaDataLock){
             N5ExportTable n5ExportTable = MainPanel.n5ExportTable;
-            ExportDataRepresentation.SimulationExportDataRepresentation data = n5ExportTable.n5ExportTableModel.getRowData(loadedResults.rowNumber);
+            ExportDataRepresentation.SimulationExportDataRepresentation data = n5ExportTable.getN5ExportTableModel().getRowData(loadedResults.rowNumber);
             ArrayList<String> newMetaData = new ArrayList<>();
             newMetaData.add(loadedResults.userSetFileName);
             newMetaData.add(data.biomodelName);