Emphasis different parts

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

@@ -0,0 +1,42 @@
+package org.vcell.N5.reduction.DTO;
+
+import ij.ImagePlus;
+import ij.gui.Roi;
+import org.vcell.N5.reduction.GUI.conclusion.SelectMeasurements;
+
+import java.io.File;
+import java.util.ArrayList;
+
+public class DataReductionSubmission {
+    public final boolean normalizeMeasurementsBool;
+    public final ArrayList<Roi> arrayOfSimRois;
+    public final ArrayList<Roi> arrayOfLabRois;
+    public final ImagePlus labResults;
+    public final int numOfSimImages;
+    public final File fileToSaveResultsTo;
+    public final RangeOfImage experiementNormRange;
+    public final RangeOfImage simNormRange;
+    public final RangeOfImage experimentImageRange;
+    public final RangeOfImage simImageRange;
+    public final ArrayList<SelectMeasurements.AvailableMeasurements> selectedMeasurements;
+    public final boolean wideTable;
+
+    public DataReductionSubmission(boolean normalizeMeasurementsBool, ArrayList<Roi> arrayOfSimRois, ArrayList<Roi> arrayOfLabRois,
+                                   ImagePlus labResults, int simStartPointNorm, int simEndPointNorm, int imageStartPointNorm,
+                                   int imageEndPointNorm, int numOfSimImages, File fileToSaveResultsTo,
+                                   RangeOfImage simRange, ArrayList<SelectMeasurements.AvailableMeasurements> selectedMeasurements, boolean wideTable) {
+        this.normalizeMeasurementsBool = normalizeMeasurementsBool;
+        this.arrayOfSimRois = arrayOfSimRois;
+        this.arrayOfLabRois = arrayOfLabRois;
+        this.labResults = labResults;
+        this.numOfSimImages = numOfSimImages;
+        this.fileToSaveResultsTo = fileToSaveResultsTo;
+        this.experiementNormRange = new RangeOfImage(imageStartPointNorm, imageEndPointNorm);
+        this.simNormRange = new RangeOfImage(simStartPointNorm, simEndPointNorm);
+        this.experimentImageRange = new RangeOfImage(1, labResults.getNFrames(),
+                1, labResults.getNSlices(), 1, labResults.getNChannels());
+        this.simImageRange = simRange;
+        this.selectedMeasurements = selectedMeasurements;
+        this.wideTable = wideTable;
+    }
+}

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

@@ -1,6 +1,6 @@
 package org.vcell.N5.reduction.DTO;
 
-import org.vcell.N5.reduction.GUI.SelectMeasurements;
+import org.vcell.N5.reduction.GUI.conclusion.SelectMeasurements;
 
 import java.util.ArrayList;
 import java.util.HashMap;

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

@@ -10,7 +10,7 @@
 import org.vcell.N5.UI.MainPanel;
 import org.vcell.N5.reduction.DTO.RangeOfImage;
 import org.vcell.N5.reduction.DTO.ReducedData;
-import org.vcell.N5.reduction.GUI.DataReductionGUI;
+import org.vcell.N5.reduction.DTO.DataReductionSubmission;
 import org.vcell.N5.retrieving.SimLoadingListener;
 import org.vcell.N5.retrieving.SimResultsLoader;
 
@@ -27,14 +27,14 @@ public class DataReductionManager implements SimLoadingListener {
     private int numOfImagesToOpen;
     private final ReductionCalculations calculations;
 
-    public final DataReductionGUI.DataReductionSubmission submission;
+    public final DataReductionSubmission submission;
 
     private final ConcurrentHashMap<String, ThreadStruct> threadPool = new ConcurrentHashMap<>();
     private final Object threadPoolLock = new Object();
 
     private DataReductionWriter dataReductionWriter;
 
-    public DataReductionManager(DataReductionGUI.DataReductionSubmission submission){
+    public DataReductionManager(DataReductionSubmission submission){
         N5ImageHandler.loadingManager.addSimLoadingListener(this);
         this.submission = submission;
 

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

@@ -6,8 +6,8 @@
 import org.vcell.N5.UI.N5ExportTable;
 import org.vcell.N5.reduction.DTO.RangeOfImage;
 import org.vcell.N5.reduction.DTO.ReducedData;
-import org.vcell.N5.reduction.GUI.DataReductionGUI;
-import org.vcell.N5.reduction.GUI.SelectMeasurements;
+import org.vcell.N5.reduction.DTO.DataReductionSubmission;
+import org.vcell.N5.reduction.GUI.conclusion.SelectMeasurements;
 import org.vcell.N5.retrieving.SimResultsLoader;
 
 import java.io.File;
@@ -21,7 +21,7 @@ public class DataReductionWriter{
     private final Object metaDataLock = new Object();
     private final File file;
 
-    public final DataReductionGUI.DataReductionSubmission submission;
+    public final DataReductionSubmission submission;
 
     private final ArrayList<ArrayList<String>> averageMatrix = new ArrayList<>();
     private final ArrayList<ArrayList<String>> standardDivMatrix = new ArrayList<>();
@@ -52,7 +52,7 @@ public class DataReductionWriter{
     // Initialize Sheet and Lab results //
     /////////////////////////////////////
 
-    public DataReductionWriter(DataReductionGUI.DataReductionSubmission submission, int maxT, int maxZ){
+    public DataReductionWriter(DataReductionSubmission submission, int maxT, int maxZ){
         this.submission = submission;
         this.selectedMeasurements = submission.selectedMeasurements;
         this.file = submission.fileToSaveResultsTo;

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

@@ -1,82 +1,60 @@
 package org.vcell.N5.reduction.GUI;
 
-import ij.ImagePlus;
-import ij.WindowManager;
-import ij.gui.Roi;
 import org.vcell.N5.UI.ControlButtonsPanel;
 import org.vcell.N5.UI.MainPanel;
-import org.vcell.N5.reduction.DTO.RangeOfImage;
+import org.vcell.N5.reduction.DTO.DataReductionSubmission;
+import org.vcell.N5.reduction.GUI.ROIs.RoiSelection;
+import org.vcell.N5.reduction.GUI.conclusion.Conclusion;
+import org.vcell.N5.reduction.GUI.images.ImagesToMeasure;
 import org.vcell.N5.retrieving.SimResultsLoader;
 
 import javax.swing.*;
-import javax.swing.border.Border;
 import javax.swing.border.EmptyBorder;
-import javax.swing.border.EtchedBorder;
 import java.awt.*;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.File;
 import java.util.ArrayList;
 
 public class DataReductionGUI extends JPanel implements ActionListener {
-    private JComboBox<String> chosenImage;
-    private final JCheckBox selectRangeOfMeasurement = new JCheckBox("Select Measurement Range: ");
-    private final JCheckBox normalizeMeasurement = new JCheckBox("Normalize Measurement: ");
-    private final JCheckBox choseCSVTableFormat = new JCheckBox("Choose CSV Format: ");
-
     private final JDialog jDialog = new JDialog(MainPanel.exportTableDialog, true);
     private final JButton okayButton = new JButton("Okay");
     private final JButton cancelButton = new JButton("Cancel");
-    private File chosenFile;
 
-    private final ArrayList<SimResultsLoader> filesToOpen;
+    private File resultSaveFile;
+
+    private final ArrayList<SimResultsLoader> simsToOpen;
+    private final ArrayList<JPanel> panels = new ArrayList<>();
 
     public int fileChooserReturnValue;
 
-    private final SelectSimRange selectSimRange;
     private final RoiSelection roiSelection;
+    private final ImagesToMeasure imagesToMeasurePanel;
     private final NormalizeGUI normalizeGUI;
-    private final SelectMeasurements selectMeasurements;
-    private final SelectTableFormat selectTableFormat;
+    private final Conclusion conclusion;
 
     private boolean continueWithProcess = false;
 
-    private final Border lowerEtchedBorder = BorderFactory.createEtchedBorder(EtchedBorder.LOWERED);
 
-    public DataReductionGUI(ArrayList<SimResultsLoader> filesToOpen, double simCSize, double simZSize, double simTSize){
-        this.filesToOpen = filesToOpen;
+    public DataReductionGUI(ArrayList<SimResultsLoader> simsToOpen, double simCSize, double simZSize, double simTSize){
+        this.simsToOpen = simsToOpen;
         setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
         okayButton.setEnabled(false);
 
-
-        selectSimRange = new SelectSimRange(jDialog, simCSize, simZSize, simTSize);
         roiSelection = new RoiSelection(this);
         normalizeGUI = new NormalizeGUI(jDialog, simTSize);
-        selectMeasurements = new SelectMeasurements(this);
-        selectTableFormat = new SelectTableFormat();
-
-        JPanel imagesToMeasurePanel = new JPanel();
-        imagesToMeasurePanel.setLayout(new BoxLayout(imagesToMeasurePanel, BoxLayout.Y_AXIS));
-        imagesToMeasurePanel.setBorder(BorderFactory.createTitledBorder(lowerEtchedBorder, "Images To Measure"));
-        imagesToMeasurePanel.add(imageSelectionPanel());
-        imagesToMeasurePanel.add(selectedImagesToOpenPanel());
+        conclusion = new Conclusion(this, simCSize, simZSize, simTSize);
+        imagesToMeasurePanel = new ImagesToMeasure(simsToOpen);
 
         add(imagesToMeasurePanel);
         add(roiSelection);
-        add(selectMeasurements);
-        add(displayOptionsPanel());
-        add(selectTableFormat);
-//        add(normalizeGUI);
-        add(selectSimRange);
+        add(conclusion);
         add(okayCancelPanel());
-
         setVisible(true);
 
         okayButton.addActionListener(this);
         cancelButton.addActionListener(this);
-        normalizeMeasurement.addActionListener(this);
-        selectRangeOfMeasurement.addActionListener(this);
-        choseCSVTableFormat.addActionListener(this);
+
 
         this.setBorder(new EmptyBorder(15, 12, 15, 12));
 
@@ -91,11 +69,11 @@ public DataReductionGUI(ArrayList<SimResultsLoader> filesToOpen, double simCSize
     public DataReductionSubmission createSubmission(){
         int[] simRange = normalizeGUI.getSimTimRange();
         int[] labRange = normalizeGUI.getImageTimeRange();
-        return new DataReductionSubmission(normalizeMeasurement.isSelected(),
+        return new DataReductionSubmission(false,
                 roiSelection.getSimROIList(), roiSelection.getImageROIList(),
-                WindowManager.getImage((String) chosenImage.getSelectedItem()),
-                simRange[0], simRange[1], labRange[0], labRange[1], filesToOpen.size(), chosenFile,
-                selectSimRange.getRangeOfSim(), selectMeasurements.getChosenMeasurements(), selectTableFormat.isWideTableSelected());
+                imagesToMeasurePanel.getChosenExpImage(),
+                simRange[0], simRange[1], labRange[0], labRange[1], simsToOpen.size(), resultSaveFile,
+                conclusion.selectSimRange.getRangeOfSim(), conclusion.selectMeasurements.getChosenMeasurements(), conclusion.selectTableFormat.isWideTableSelected());
     }
 
     private JPanel okayCancelPanel(){
@@ -105,65 +83,26 @@ private JPanel okayCancelPanel(){
         return jPanel;
     }
 
-    private JPanel imageSelectionPanel(){
-        JPanel jPanel = new JPanel(new GridLayout(1, 2));
-        jPanel.add(new JLabel("Experimental"));
-        chosenImage = new JComboBox<>(WindowManager.getImageTitles());
-        jPanel.add(chosenImage);
-        return jPanel;
-    }
-
-    private JPanel selectedImagesToOpenPanel(){
-        JPanel jPanel = new JPanel();
-        String[] namesOfImagesToOpen = new String[filesToOpen.size()];
-        for (int i = 0; i < filesToOpen.size(); i++){
-            namesOfImagesToOpen[i] = filesToOpen.get(i).userSetFileName;
-        }
-        JList<String> selectedImagesToOpen = new JList<>(namesOfImagesToOpen);
-        selectedImagesToOpen.setEnabled(false);
-        selectedImagesToOpen.setVisibleRowCount(4);
-        JScrollPane jScrollPane = new JScrollPane(selectedImagesToOpen);
-        jPanel.add(new JLabel("Selected Simulations"));
-        jPanel.add(jScrollPane);
-        jPanel.setLayout(new GridLayout(1, 2));
-        return jPanel;
-    }
-
-    private JPanel displayOptionsPanel(){
-        JPanel jPanel = new JPanel();
-        jPanel.setLayout(new BoxLayout(jPanel, BoxLayout.X_AXIS));
-//        jPanel.add(normalizeMeasurement);
-        jPanel.add(selectRangeOfMeasurement);
-        jPanel.add(choseCSVTableFormat);
-        return jPanel;
-    }
-
     public void activateOkayButton(){
-        boolean selectedAMeasurement = !selectMeasurements.getChosenMeasurements().isEmpty();
-        boolean chosenExperimentImage = chosenImage.getSelectedItem() != null;
-//        boolean roisIsSelected = !roiSelection.getImageROIList().isEmpty() && !roiSelection.getSimROIList().isEmpty();
+        boolean selectedAMeasurement = !conclusion.selectMeasurements.getChosenMeasurements().isEmpty();
+        boolean chosenExperimentImage = imagesToMeasurePanel.getChosenExpImage() != null;
         okayButton.setEnabled(selectedAMeasurement && chosenExperimentImage);
     }
 
+    public void updateDisplay(){
+        jDialog.revalidate();
+        jDialog.repaint();
+        jDialog.pack();
+    }
+
     @Override
     public void actionPerformed(ActionEvent e) {
-        if (e.getSource().equals(normalizeMeasurement)) {
-            normalizeGUI.setVisible(normalizeMeasurement.isSelected());
-        } else if (e.getSource().equals(selectRangeOfMeasurement)){
-            selectSimRange.setVisible(selectRangeOfMeasurement.isSelected());
-        } else if (e.getSource().equals(choseCSVTableFormat)) {
-            selectTableFormat.setVisible(choseCSVTableFormat.isSelected());
-            selectTableFormat.revalidate();
-            selectTableFormat.repaint();
-            jDialog.revalidate();
-            jDialog.repaint();
-            jDialog.pack();
-        } else if (e.getSource().equals(okayButton)) {
+        if (e.getSource().equals(okayButton)) {
             JFileChooser saveToFile = new JFileChooser();
             saveToFile.setFileSelectionMode(JFileChooser.FILES_ONLY);
             fileChooserReturnValue = saveToFile.showDialog(this, "Save Results To File");
             if (fileChooserReturnValue == JFileChooser.APPROVE_OPTION){
-                chosenFile = saveToFile.getSelectedFile();
+                resultSaveFile = saveToFile.getSelectedFile();
                 MainPanel.controlButtonsPanel.updateButtonsToMatchState();
                 continueWithProcess = true;
                 jDialog.dispose();
@@ -178,45 +117,6 @@ public boolean shouldContinueWithProcess() {
         return continueWithProcess;
     }
 
-    public static class DataReductionSubmission{
-        public final boolean normalizeMeasurementsBool;
-        public final ArrayList<Roi> arrayOfSimRois;
-        public final ArrayList<Roi> arrayOfLabRois;
-        public final ImagePlus labResults;
-        public final int numOfSimImages;
-        public final File fileToSaveResultsTo;
-
-        public final RangeOfImage experiementNormRange;
-        public final RangeOfImage simNormRange;
-
-        public final RangeOfImage experimentImageRange;
-        public final RangeOfImage simImageRange;
-        public final ArrayList<SelectMeasurements.AvailableMeasurements> selectedMeasurements;
-
-        public final boolean wideTable;
-
-        public DataReductionSubmission(boolean normalizeMeasurementsBool, ArrayList<Roi> arrayOfSimRois, ArrayList<Roi> arrayOfLabRois,
-                                       ImagePlus labResults, int simStartPointNorm, int simEndPointNorm, int imageStartPointNorm,
-                                       int imageEndPointNorm, int numOfSimImages, File fileToSaveResultsTo,
-                                       RangeOfImage simRange, ArrayList<SelectMeasurements.AvailableMeasurements> selectedMeasurements, boolean wideTable){
-            this.normalizeMeasurementsBool = normalizeMeasurementsBool;
-            this.arrayOfLabRois = arrayOfLabRois;
-            this.arrayOfSimRois = arrayOfSimRois;
-            this.labResults = labResults;
-            this.numOfSimImages = numOfSimImages;
-            this.fileToSaveResultsTo = fileToSaveResultsTo;
-
-            this.experiementNormRange = new RangeOfImage(imageStartPointNorm, imageEndPointNorm);
-            this.simNormRange = new RangeOfImage(simStartPointNorm, simEndPointNorm);
-
-            this.experimentImageRange = new RangeOfImage(1, labResults.getNFrames(),
-                    1, labResults.getNSlices(), 1, labResults.getNChannels());
-            this.simImageRange = simRange;
-            this.selectedMeasurements = selectedMeasurements;
-            this.wideTable = wideTable;
-        }
-    }
-
     public static void main(String[] args) {
         DataReductionGUI dataReductionGUI = new DataReductionGUI(new ArrayList<>(), 0, 0, 0);
     }