Fixes and updates

pom.xml

@@ -93,7 +93,7 @@
 
         <!-- Java 8	Update Site	-->
         <imglib2-cache.version>1.0.0-beta-16</imglib2-cache.version>
-        <bigdataviewer-core.version>10.2.1</bigdataviewer-core.version>
+        <bigdataviewer-core.version>10.2.2</bigdataviewer-core.version>
         <bigdataviewer-vistools.version>1.0.0-beta-28</bigdataviewer-vistools.version>
 
         <!-- spim_data.version required for writing tests to run properly -->

src/main/java/org/embl/mobie/io/SpimDataOpener.java

@@ -4,9 +4,11 @@
 import bdv.spimdata.SpimDataMinimal;
 import bdv.util.volatiles.SharedQueue;
 import ij.IJ;
+import lombok.extern.slf4j.Slf4j;
 import mpicbg.spim.data.SpimData;
 import mpicbg.spim.data.SpimDataException;
 import mpicbg.spim.data.generic.AbstractSpimData;
+import net.imglib2.util.Cast;
 import org.embl.mobie.io.n5.openers.N5Opener;
 import org.embl.mobie.io.n5.openers.N5S3Opener;
 import org.embl.mobie.io.ome.zarr.loaders.N5S3OMEZarrImageLoader;
@@ -32,6 +34,7 @@
 import static mpicbg.spim.data.XmlKeys.IMGLOADER_TAG;
 import static mpicbg.spim.data.XmlKeys.SEQUENCEDESCRIPTION_TAG;
 
+@Slf4j
 public class SpimDataOpener {
 
     public static final String ERROR_WHILE_TRYING_TO_READ_SPIM_DATA = "Error while trying to read spimData";
@@ -156,18 +159,39 @@ private SpimData openOpenOrganelleS3(String path) throws SpimDataException {
         }
     }
 
-    private SpimData openBdvOmeZarrS3(String path, SharedQueue queue) throws SpimDataException {
+    private SpimData openBdvOmeZarrS3(String path, SharedQueue queue) {
+        //Todo: finish bug fixing
         try {
-            N5S3OMEZarrImageLoader imageLoader = createN5S3OmeZarrImageLoader(path, queue);
-            SpimData spimData = openBdvXml(path);
-            if (spimData != null) {
-                spimData.getSequenceDescription().setImgLoader(imageLoader);
-                return spimData;
+            SAXBuilder sax = new SAXBuilder();
+            InputStream stream = FileAndUrlUtils.getInputStream(path);
+            Document doc = sax.build(stream);
+            Element imgLoaderElem = doc.getRootElement().getChild("SequenceDescription").getChild("ImageLoader");
+            String bucketAndObject = imgLoaderElem.getChild("BucketName").getText() + "/" + imgLoaderElem.getChild("Key").getText();
+            String[] split = bucketAndObject.split("/");
+            String bucket = split[0];
+            String object = Arrays.stream(split).skip(1L).collect(Collectors.joining("/"));
+            N5S3OMEZarrImageLoader imageLoader;
+            if (queue != null) {
+                imageLoader = new N5S3OMEZarrImageLoader(imgLoaderElem.getChild("ServiceEndpoint").getText(), imgLoaderElem.getChild("SigningRegion").getText(), bucket, object, ".", queue);
             } else {
-                throw new SpimDataException("Error while trying to read spimData. SpimData is null");
+               imageLoader = new N5S3OMEZarrImageLoader(imgLoaderElem.getChild("ServiceEndpoint").getText(), imgLoaderElem.getChild("SigningRegion").getText(), bucket, object, ".");
             }
-        } catch (IOException | JDOMException e) {
-            throw new SpimDataException(ERROR_WHILE_TRYING_TO_READ_SPIM_DATA + e.getMessage());
+            SpimData spim = new SpimData(null, Cast.unchecked(imageLoader.getSequenceDescription()), imageLoader.getViewRegistrations());
+            SpimData sp1;
+            try {
+                InputStream st = FileAndUrlUtils.getInputStream(path);
+                sp1 = (new CustomXmlIoSpimData()).loadFromStream(st, path);
+            } catch (SpimDataException exception) {
+                log.debug("Failed to load stream from {}", path, exception);
+                return null;
+            }
+            sp1.setBasePath(null);
+            sp1.getSequenceDescription().setImgLoader(spim.getSequenceDescription().getImgLoader());
+            sp1.getSequenceDescription().getAllChannels().putAll(spim.getSequenceDescription().getAllChannels());
+            return sp1;
+        } catch (JDOMException | IOException var13) {
+            var13.printStackTrace();
+            return null;
         }
     }
 
@@ -207,12 +231,15 @@ private SpimData getSpimDataWithImageLoader(String path, @Nullable SharedQueue s
             final Document doc = sax.build(stream);
             final Element imgLoaderElem = doc.getRootElement().getChild(SEQUENCEDESCRIPTION_TAG).getChild(IMGLOADER_TAG);
             String imagesFile = XmlN5OmeZarrImageLoader.getDatasetsPathFromXml(imgLoaderElem, path);
-            if (imagesFile != null && new File(imagesFile).exists()) {
-                if (sharedQueue != null) {
-                    return OMEZarrOpener.openFile(path, sharedQueue);
+            if (imagesFile != null) {
+                    if (new File(imagesFile).exists()) {
+                        return sharedQueue != null ? OMEZarrOpener.openFile(imagesFile, sharedQueue)
+                                : OMEZarrOpener.openFile(imagesFile);
+                    } else {
+                        return sharedQueue != null ? OMEZarrS3Opener.readURL(imagesFile, sharedQueue)
+                        : OMEZarrS3Opener.readURL(imagesFile);
+                    }
                 }
-                return OMEZarrOpener.openFile(imagesFile);
-            }
         } catch (JDOMException | IOException e) {
             IJ.log(e.getMessage());
         }

src/main/java/org/embl/mobie/io/n5/loaders/N5ImageLoader.java

@@ -277,7 +277,7 @@ private static class N5CacheArrayLoader<A> implements SimpleCacheArrayLoader<A>
         }
 
         @Override
-        public A loadArray(final long[] gridPosition) throws IOException {
+        public A loadArray(final long[] gridPosition, final int[] cellDimensions) throws IOException {
             DataBlock<?> block = null;
 
             try {

src/main/java/org/embl/mobie/io/n5/util/N5CacheArrayLoader.java

@@ -22,7 +22,7 @@ public N5CacheArrayLoader(final N5Reader n5, final String pathName, final Datase
     }
 
     @Override
-    public A loadArray(final long[] gridPosition) {
+    public A loadArray(final long[] gridPosition, final int[] cellDimensions) {
         DataBlock<?> block = null;
 
         try {

src/main/java/org/embl/mobie/io/n5/writers/WriteSequenceToN5.java

@@ -325,7 +325,7 @@ public RandomAccessibleInterval<T> getImage(final int level) throws IOException
                         final long[] cellGridPosition = new long[n];
                         grid.getCellDimensions(key, cellMin, cellDims);
                         grid.getCellGridPositionFlat(key, cellGridPosition);
-                        return new Cell<>(cellDims, cellMin, cacheArrayLoader.loadArray(cellGridPosition));
+                        return new Cell<>(cellDims, cellMin, cacheArrayLoader.loadArray(cellGridPosition, cellDims));
                     },
                     options().cellDimensions(cellDimensions));
         }

src/main/java/org/embl/mobie/io/ome/zarr/loaders/N5OMEZarrImageLoader.java

@@ -275,6 +275,8 @@ private OmeZarrMultiscales[] getMultiscale(String pathName) throws IOException {
                 location += "; container path: " + s3ZarrReader.getContainerPath();
                 location += "; path: " + pathName;
                 location += "; attribute: " + MULTI_SCALE_KEY;
+            } else {
+                location += " path: " + pathName;
             }
             throw new UnsupportedOperationException("Could not find multiscales at " + location);
         }

src/main/java/org/embl/mobie/io/ome/zarr/readers/N5S3OmeZarrReader.java

@@ -25,6 +25,7 @@
  */
 package org.embl.mobie.io.ome.zarr.readers;
 
+import com.amazonaws.SdkClientException;
 import com.amazonaws.services.s3.AmazonS3;
 import com.amazonaws.services.s3.model.AmazonS3Exception;
 import com.google.gson.GsonBuilder;
@@ -266,18 +267,15 @@ public DataBlock<?> readBlock(
      *
      * @param objectPath
      * @return null if the object does not exist, otherwise the loaded attributes.
-     * @throws IOException
      */
-    public HashMap<String, JsonElement> readJson(String objectPath) throws IOException {
-        if (!this.s3.doesObjectExist(this.bucketName, objectPath)) {
-            return null;
-        } else {
+    public HashMap<String, JsonElement> readJson(String objectPath) {
+        try {
             InputStream in = this.readS3Object(objectPath);
             Throwable var4 = null;
 
-            HashMap<String, JsonElement> var5;
+            HashMap<String, JsonElement> hashMap;
             try {
-                var5 = GsonAttributesParser.readAttributes(new InputStreamReader(in), this.gson);
+                hashMap = GsonAttributesParser.readAttributes(new InputStreamReader(in), this.gson);
             } catch (Throwable var14) {
                 var4 = var14;
                 throw var14;
@@ -295,8 +293,10 @@ public HashMap<String, JsonElement> readJson(String objectPath) throws IOExcepti
                 }
 
             }
-
-            return var5;
+            return hashMap;
+        } catch (SdkClientException | IOException e) {
+            log.debug("Failed to readJson: object {} does not exist in bucket {}", objectPath, this.bucketName);
+            return null;
         }
     }
 

src/main/java/org/embl/mobie/io/ome/zarr/util/N5OMEZarrCacheArrayLoader.java

@@ -35,7 +35,7 @@ public N5OMEZarrCacheArrayLoader(final N5Reader n5, final String pathName, final
     }
 
     @Override
-    public A loadArray(final long[] gridPosition) throws IOException {
+    public A loadArray(final long[] gridPosition, int[] cellDimensions) throws IOException {
         DataBlock<?> block = null;
 
         long[] dataBlockIndices = toDataBlockIndices(gridPosition);

src/main/java/org/embl/mobie/io/ome/zarr/writers/imageplus/WriteSequenceToN5OmeZarr.java

@@ -408,7 +408,7 @@ public RandomAccessibleInterval<T> getImage(final int level) throws IOException
                         final long[] cellGridPosition = new long[n];
                         grid.getCellDimensions(key, cellMin, cellDims);
                         grid.getCellGridPositionFlat(key, cellGridPosition);
-                        return new Cell<>(cellDims, cellMin, cacheArrayLoader.loadArray(cellGridPosition));
+                        return new Cell<>(cellDims, cellMin, cacheArrayLoader.loadArray(cellGridPosition, cellDims));
                     },
                     options().cellDimensions(cellDimensions));
         }

src/main/java/org/embl/mobie/io/openorganelle/N5CacheArrayLoader.java

@@ -24,7 +24,7 @@ public class N5CacheArrayLoader<A> implements SimpleCacheArrayLoader<A> {
     }
 
     @Override
-    public A loadArray(final long[] gridPosition) {
+    public A loadArray(final long[] gridPosition, final int[] cellDimensions) {
         DataBlock<?> block = null;
 
         try {

src/main/java/org/embl/mobie/io/util/CustomXmlIoSpimData.java

@@ -41,28 +41,26 @@
 
 import java.io.File;
 import java.io.InputStream;
+import java.util.Objects;
 
 import static mpicbg.spim.data.XmlKeys.SPIMDATA_TAG;
 
-
 public class CustomXmlIoSpimData extends XmlIoAbstractSpimData<SequenceDescription, SpimData> {
     public CustomXmlIoSpimData() {
         super(SpimData.class, new XmlIoSequenceDescription(), new XmlIoViewRegistrations());
     }
 
-    // NOTE we still need to pass the xml filename here, so that bdv can determine the relative
-    // paths for local files.
     public SpimData loadFromStream(InputStream in, String xmlFilename) throws SpimDataException {
-        final SAXBuilder sax = new SAXBuilder();
+        SAXBuilder sax = new SAXBuilder();
+
         Document doc;
         try {
             doc = sax.build(in);
-        } catch (final Exception e) {
-            throw new SpimDataIOException(e);
+        } catch (Exception exception) {
+            throw new SpimDataIOException(exception);
         }
         final Element root = doc.getRootElement();
-
-        if (root.getName() != SPIMDATA_TAG)
+        if (!root.getName().equals(SPIMDATA_TAG))
             throw new RuntimeException("expected <" + SPIMDATA_TAG + "> root element. wrong file?");
 
         return fromXml(root, new File(xmlFilename));

src/test/java/ui/BdvOmeZarrOpener.java

@@ -0,0 +1,29 @@
+package ui;
+
+import bdv.util.BdvFunctions;
+import bdv.util.volatiles.SharedQueue;
+import mpicbg.spim.data.SpimData;
+import mpicbg.spim.data.SpimDataException;
+import org.embl.mobie.io.ImageDataFormat;
+import org.embl.mobie.io.SpimDataOpener;
+
+public class BdvOmeZarrOpener {
+    public static void main(String[] args) {
+        showProject();
+    }
+    public static void showProject() {
+        SharedQueue sharedQueue = new SharedQueue( 7 );
+        SpimDataOpener spimDataOpener = new SpimDataOpener();
+        SpimData image = null;
+        try {
+//            image =(SpimData) spimDataOpener.openSpimData("https://raw.githubusercontent.com/mobie/clem-example-project//more-views/data/hela/images/bdv-n5-s3/fluorescence-a2-FMR-c2.xml",
+//                    ImageDataFormat.BdvN5S3, sharedQueue);
+            image = (SpimData) spimDataOpener.openSpimData("https://s3.embl.de/i2k-2020/project-bdv-ome-zarr/Covid19-S4-Area2/images/bdv.ome.zarr.s3/raw.xml",
+                    ImageDataFormat.BdvOmeZarrS3, sharedQueue);
+        } catch (SpimDataException e) {
+            e.printStackTrace();
+        }
+        assert image != null;
+        BdvFunctions.show(image);
+    }
+}