Add Image Open Tagging

Tag the images which are being opened to distinguish between "Viewing" and "Data Reduction".
virtualcell · Nov 12, 2024 · 42ef820 · 42ef820
1 parent 5777315
commit 42ef820
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Showing 7 changed files with 36 additions and 22 deletions.
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/ControlButtonsPanel.java b/view-simulation-results/src/main/java/org/vcell/N5/UI/ControlButtonsPanel.java
@@ -1,6 +1,7 @@
 package org.vcell.N5.UI;
 
 import org.vcell.N5.N5ImageHandler;
+import org.vcell.N5.retrieving.SimResultsLoader;
 
 import javax.swing.*;
 import javax.swing.border.Border;
@@ -108,7 +109,8 @@ public void actionPerformed(ActionEvent e) {
             if (openOrCancel.getText().equals("Cancel")){
                 n5ExportTable.removeFromLoadingRows();
             } else {
-                n5ExportTable.openSelectedRows(inMemory, performDataReduction);
+                SimResultsLoader.OpenTag openTag = performDataReduction ? SimResultsLoader.OpenTag.DATA_REDUCTION : SimResultsLoader.OpenTag.VIEW;
+                n5ExportTable.openSelectedRows(inMemory, performDataReduction, openTag);
             }
         } else if (e.getSource().equals(advancedFeatures.copyLink)) {
             n5ExportTable.copySelectedRowLink();

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
@@ -155,12 +155,12 @@ private void automaticRefresh(){
         refreshTableThread.start();
     }
 
-    public void openSelectedRows(boolean openInMemory, boolean performDataReduction){
+    public void openSelectedRows(boolean openInMemory, boolean performDataReduction, SimResultsLoader.OpenTag openTag){
         ArrayList<SimResultsLoader> filesToOpen = new ArrayList<>();
         for(int row: exportListTable.getSelectedRows()){
             String uri = n5ExportTableModel.getRowData(row).uri;
             ExportDataRepresentation.SimulationExportDataRepresentation rowData = n5ExportTableModel.getRowData(row);
-            SimResultsLoader simResultsLoader = new SimResultsLoader(uri, rowData.savedFileName, row, rowData.jobID);
+            SimResultsLoader simResultsLoader = new SimResultsLoader(uri, rowData.savedFileName, row, rowData.jobID, openTag);
             filesToOpen.add(simResultsLoader);
         }
         N5ImageHandler.loadingManager.openN5FileDataset(filesToOpen, openInMemory,
@@ -226,7 +226,9 @@ public void simFinishedLoading(SimResultsLoader loadedResults) {
         loadingRowsJobID.remove(loadedResults.rowNumber);
         exportListTable.repaint();
         controlPanel.allowCancel(false);
-        loadedResults.getImagePlus().show();
+        if (loadedResults.openTag == SimResultsLoader.OpenTag.VIEW){
+            loadedResults.getImagePlus().show();
+        }
     }
 
     public static class N5ExportTableModel extends AbstractTableModel {

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/UI/RemoteFileSelection.java b/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 simResultsLoader = new SimResultsLoader(getS3URL(), "", -1, "", SimResultsLoader.OpenTag.VIEW);
         N5ImageHandler.loadingManager.openN5FileDataset(new ArrayList<SimResultsLoader>(){{add(simResultsLoader);}},
                 false,
                 false);

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/reduction/DataReductionWriter.java b/view-simulation-results/src/main/java/org/vcell/N5/reduction/DataReductionWriter.java
@@ -261,14 +261,16 @@ public void simIsLoading(int itemRow, String exportID) {
 
     @Override
     public void simFinishedLoading(SimResultsLoader loadedResults) {
-        Thread imageProcessingThread = new Thread(() -> {
-            ImagePlus imagePlus = loadedResults.getImagePlus();
-            imagePlus.show();
-            addMetaData(loadedResults);
-            calculateAndAddResults(imagePlus, submission.simNormRange, submission.simImageRange,
-                    submission.arrayOfSimRois, loadedResults.getChannelInfo());
-        }, "Processing Image: " + loadedResults.userSetFileName);
-        imageProcessingThread.start();
+        if (loadedResults.openTag == SimResultsLoader.OpenTag.DATA_REDUCTION){
+            Thread imageProcessingThread = new Thread(() -> {
+                ImagePlus imagePlus = loadedResults.getImagePlus();
+                imagePlus.show();
+                addMetaData(loadedResults);
+                calculateAndAddResults(imagePlus, submission.simNormRange, submission.simImageRange,
+                        submission.arrayOfSimRois, loadedResults.getChannelInfo());
+            }, "Processing Image: " + loadedResults.userSetFileName);
+            imageProcessingThread.start();
+        }
     }
 
 }

diff --git a/view-simulation-results/src/main/java/org/vcell/N5/retrieving/SimResultsLoader.java b/view-simulation-results/src/main/java/org/vcell/N5/retrieving/SimResultsLoader.java
@@ -53,21 +53,22 @@ public class SimResultsLoader {
     private static final Logger logger = N5ImageHandler.getLogger(SimResultsLoader.class);
     public static AmazonS3ClientBuilder s3ClientBuilder;
     private ImagePlus imagePlus = null;
+    public final OpenTag openTag;
 
 
     public String userSetFileName = null;
     public int rowNumber;
     public String exportID;
 
     public SimResultsLoader(){
-
+        openTag = OpenTag.NONE;
     }
-    public SimResultsLoader(String stringURI, String userSetFileName, int rowNumber, String exportID){
-        this(stringURI, userSetFileName);
+    public SimResultsLoader(String stringURI, String userSetFileName, int rowNumber, String exportID, OpenTag openTag){
+        this(stringURI, userSetFileName, openTag);
         this.rowNumber = rowNumber;
         this.exportID = exportID;
     }
-    public SimResultsLoader(String stringURI, String userSetFileName){
+    public SimResultsLoader(String stringURI, String userSetFileName, OpenTag openTag){
         uri = URI.create(stringURI);
         this.userSetFileName = userSetFileName;
         if(!(uri.getQuery() == null)){
@@ -78,6 +79,7 @@ public SimResultsLoader(String stringURI, String userSetFileName){
                 throw new RuntimeException(e);
             }
         }
+        this.openTag = openTag;
     }
 
     /////////////////////////////////
@@ -225,4 +227,10 @@ ImagePlus getImgPlusFromLocalN5File() throws IOException {
         N5Reader n5Reader = new N5FSReader(selectedLocalFile.getPath());
         return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5Reader, dataSetChosen), userSetFileName);
     }
+
+    public enum OpenTag{
+        VIEW,
+        DATA_REDUCTION,
+        NONE
+    }
 }
diff --git a/view-simulation-results/src/test/java/org/vcell/N5/reduction/ReductionCalculationsTest.java b/view-simulation-results/src/test/java/org/vcell/N5/reduction/ReductionCalculationsTest.java
@@ -66,7 +66,7 @@ private void compareExpectedCalculations(ImagePlus imagePlus, ArrayList<Roi> roi
     @Test
     public void testMean2DCalculation(){
         // Ensure the mean calculated for each ROI, and each time point is what's to be expected
-        SimResultsLoader simResultsLoader = new SimResultsLoader("https://vcell.cam.uchc.edu/n5Data/ezequiel23/ddf7f4f0c77dffd.n5?dataSetName=4864003788", "test1");
+        SimResultsLoader simResultsLoader = new SimResultsLoader("https://vcell.cam.uchc.edu/n5Data/ezequiel23/ddf7f4f0c77dffd.n5?dataSetName=4864003788", "test1", SimResultsLoader.OpenTag.NONE);
         ImagePlus labResultImage2D = simResultsLoader.getImagePlus();
 
         Roi labRoi = RoiDecoder.open(getTestResourceFiles("ROIs/Lab ROI.roi").getAbsolutePath());
@@ -85,7 +85,7 @@ public void testMean3DCalculation(){
 
     @Test
     public void testMeanAndNormalization2DCalculation(){
-        SimResultsLoader simResultsLoader = new SimResultsLoader("https://vcell.cam.uchc.edu/n5Data/ezequiel23/ddf7f4f0c77dffd.n5?dataSetName=4864003788", "test1");
+        SimResultsLoader simResultsLoader = new SimResultsLoader("https://vcell.cam.uchc.edu/n5Data/ezequiel23/ddf7f4f0c77dffd.n5?dataSetName=4864003788", "test1", SimResultsLoader.OpenTag.NONE);
         ImagePlus labResultImage2D = simResultsLoader.getImagePlus();
         Roi labRoi = RoiDecoder.open(getTestResourceFiles("ROIs/Lab ROI.roi").getAbsolutePath());
         Roi simROI = RoiDecoder.open(getTestResourceFiles("ROIs/Sim ROI.roi").getAbsolutePath());

diff --git a/view-simulation-results/src/test/java/org/vcell/N5/retrieving/N5ImageHandlerTest.java b/view-simulation-results/src/test/java/org/vcell/N5/retrieving/N5ImageHandlerTest.java
@@ -75,7 +75,7 @@ public void testGettingImgPlus() throws IOException {
     public void testS3AlphaInstance() throws IOException{
         N5DataSetFile[] n5DataSetFiles = N5DataSetFile.alphaTestFiles();
         for(N5DataSetFile n5DataSetFile : n5DataSetFiles) {
-            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "");
+            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "", SimResultsLoader.OpenTag.NONE);
             simResultsLoader.createS3ClientAndReader();
             simResultsLoader.loadImageFromN5File();
             ImagePlus imagePlus = simResultsLoader.getImagePlus();
@@ -91,7 +91,7 @@ public void testS3AlphaInstance() throws IOException{
     public void testS3AlphaInstanceLoadedIntoMemory() throws IOException {
         N5DataSetFile[] n5DataSetFiles = N5DataSetFile.alphaTestFiles();
         for(N5DataSetFile n5DataSetFile : n5DataSetFiles) {
-            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "");
+            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "", SimResultsLoader.OpenTag.NONE);
             simResultsLoader.createS3ClientAndReader();
             simResultsLoader.loadImageFromN5File();
             ImagePlus imagePlus = simResultsLoader.getImagePlus();
@@ -113,7 +113,7 @@ interface PixelCalculations {
     public void testUnits() throws IOException {
         N5DataSetFile[] n5DataSetFiles = N5DataSetFile.alphaTestFiles();
         for (N5DataSetFile n5DataSetFile: n5DataSetFiles){
-            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "");
+            SimResultsLoader simResultsLoader = new SimResultsLoader(n5DataSetFile.uri, "", SimResultsLoader.OpenTag.NONE);
             simResultsLoader.createS3ClientAndReader();
             simResultsLoader.loadImageFromN5File();
             ImagePlus imagePlus = simResultsLoader.getImagePlus();