Specify the saved file name

Instead of using the dataset name within the URL, it utilizes a property of the JSON file for it's saved file name.
virtualcell · Mar 28, 2024 · 9f9db4c · 9f9db4c
1 parent b2d56b8
commit 9f9db4c
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Showing 3 changed files with 13 additions and 18 deletions.
diff --git a/view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java b/view-simulation-results/src/main/java/org/vcell/N5/SimResultsLoader.java
@@ -7,25 +7,20 @@
 import com.amazonaws.services.s3.AmazonS3;
 import com.amazonaws.services.s3.AmazonS3ClientBuilder;
 import com.amazonaws.services.s3.AmazonS3URI;
-import com.google.gson.GsonBuilder;
 import ij.ImagePlus;
 import net.imglib2.cache.img.CachedCellImg;
 import net.imglib2.img.display.imagej.ImageJFunctions;
 import net.imglib2.type.numeric.real.DoubleType;
 import org.janelia.saalfeldlab.n5.N5FSReader;
-import org.janelia.saalfeldlab.n5.N5KeyValueReader;
 import org.janelia.saalfeldlab.n5.N5Reader;
-import org.janelia.saalfeldlab.n5.ij.N5IJUtils;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
-import org.janelia.saalfeldlab.n5.s3.AmazonS3KeyValueAccess;
 import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
 
 import java.io.File;
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.URI;
 import java.net.URLDecoder;
-import java.net.URLEncoder;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -37,14 +32,15 @@ public class SimResultsLoader {
     private String s3ObjectKey;
     private URI uri;
     private String dataSetChosen;
-    private String uriSafeDataSetChosen;
+    private String userSetFileName;
 
     public SimResultsLoader(){
 
     }
 
-    public SimResultsLoader(String stringURI){
+    public SimResultsLoader(String stringURI, String userSetFileName){
         uri = URI.create(stringURI);
+        this.userSetFileName = userSetFileName;
         setURI(uri);
     }
 
@@ -124,30 +120,29 @@ public void setSelectedLocalFile(File selectedLocalFile){
 
     public ImagePlus getImgPlusFromLocalN5File() throws IOException {
         N5Reader n5Reader = new N5FSReader(selectedLocalFile.getPath());
-        return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5Reader, dataSetChosen), dataSetChosen);
+        return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5Reader, dataSetChosen), userSetFileName);
     }
 
     public ImagePlus getImgPlusFromN5File() throws IOException {
 //        AmazonS3KeyValueAccess amazonS3KeyValueAccess = new AmazonS3KeyValueAccess(s3Client, bucketName, false);
 //        N5KeyValueReader n5KeyValueReader = new N5KeyValueReader(amazonS3KeyValueAccess, s3ObjectKey, new GsonBuilder(), true);
         N5AmazonS3Reader n5AmazonS3Reader = new N5AmazonS3Reader(s3Client, bucketName, "/" + s3ObjectKey);
-        return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5AmazonS3Reader, dataSetChosen), dataSetChosen);
+        return ImageJFunctions.wrap((CachedCellImg<DoubleType, ?>) N5Utils.open(n5AmazonS3Reader, dataSetChosen), userSetFileName);
     }
 
     public void setURI(URI uri){
         this.uri = uri;
         if(!(uri.getQuery() == null)){
-            uriSafeDataSetChosen = uri.getQuery().split("=")[1]; // query should be "dataSetName=name", thus splitting it by = and getting the second entry gives the name
+            dataSetChosen = uri.getQuery().split("=")[1]; // query should be "dataSetName=name", thus splitting it by = and getting the second entry gives the name
             try {
-                dataSetChosen = URLDecoder.decode(uriSafeDataSetChosen, "UTF-8");
+                dataSetChosen = URLDecoder.decode(dataSetChosen, "UTF-8");
             } catch (UnsupportedEncodingException e) {
                 throw new RuntimeException(e);
             }
         }
     }
 
-    public void setDataSetChosen(String dataSetChosen) throws UnsupportedEncodingException {
+    public void setDataSetChosen(String dataSetChosen) {
         this.dataSetChosen = dataSetChosen;
-        uriSafeDataSetChosen = URLEncoder.encode(dataSetChosen, "UTF-8");
     }
 }
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
@@ -274,7 +274,7 @@ public void actionPerformed(ActionEvent e) {
             ArrayList<SimResultsLoader> filesToOpen = new ArrayList<>();
             for(int row: exportListTable.getSelectedRows()){
                 String uri = n5ExportTableModel.getRowData(row).uri;
-                SimResultsLoader simResultsLoader = new SimResultsLoader(uri);
+                SimResultsLoader simResultsLoader = new SimResultsLoader(uri, n5ExportTableModel.getRowData(row).savedFileName);
                 filesToOpen.add(simResultsLoader);
             }
             openN5FileDataset(filesToOpen, openInMemory.isSelected());
@@ -289,7 +289,7 @@ public void actionPerformed(ActionEvent e) {
         } else if (e.getSource().equals(useN5Link)) {
             remoteFileSelection.setVisible(true);
         } else if (e.getSource().equals(remoteFileSelection.submitS3Info)) {
-            SimResultsLoader simResultsLoader = new SimResultsLoader(remoteFileSelection.getS3URL());
+            SimResultsLoader simResultsLoader = new SimResultsLoader(remoteFileSelection.getS3URL(), "");
             openN5FileDataset(new ArrayList<SimResultsLoader>(){{add(simResultsLoader);}}, openInMemory.isSelected());
             remoteFileSelection.setVisible(false);
         }

diff --git a/view-simulation-results/src/test/java/org/vcell/N5/N5ImageHandlerTest.java b/view-simulation-results/src/test/java/org/vcell/N5/N5ImageHandlerTest.java
@@ -74,7 +74,7 @@ public void testS3Client() throws IOException {
 
         final String s3ProxyURI = "http://localhost:4000/" + this.n5FileName + "?datasetName=" + datasetName;
 
-        SimResultsLoader simResultsLoader = new SimResultsLoader(s3ProxyURI);
+        SimResultsLoader simResultsLoader = new SimResultsLoader(s3ProxyURI, "");
 
         // Environment variables are set in github actions VM
 
@@ -95,7 +95,7 @@ public void testS3Client() 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.createS3Client();
             ImagePlus imagePlus = simResultsLoader.getImgPlusFromN5File();
 
@@ -110,7 +110,7 @@ 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.createS3Client();
             ImagePlus imagePlus = simResultsLoader.getImgPlusFromN5File();
             alphaStatsTest(new Duplicator().run(imagePlus), n5DataSetFile, stats.HISTMAX);