diff --git a/pom.xml b/pom.xml
index eee839b9..104abfb4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -93,7 +93,7 @@
1.0.0-beta-16
- 10.2.1
+ 10.2.2
1.0.0-beta-28
diff --git a/src/main/java/org/embl/mobie/io/SpimDataOpener.java b/src/main/java/org/embl/mobie/io/SpimDataOpener.java
index 42e0b3d1..04cf8b02 100644
--- a/src/main/java/org/embl/mobie/io/SpimDataOpener.java
+++ b/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 spimData;
+ try {
+ InputStream st = FileAndUrlUtils.getInputStream(path);
+ spimData = (new CustomXmlIoSpimData()).loadFromStream(st, path);
+ } catch (SpimDataException exception) {
+ log.debug("Failed to load stream from {}", path, exception);
+ return null;
+ }
+ spimData.setBasePath(null);
+ spimData.getSequenceDescription().setImgLoader(spim.getSequenceDescription().getImgLoader());
+ spimData.getSequenceDescription().getAllChannels().putAll(spim.getSequenceDescription().getAllChannels());
+ return spimData;
+ } catch (JDOMException | IOException e) {
+ log.debug("Failed to open openBdvOmeZarrS3", e);
+ 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());
}
diff --git a/src/main/java/org/embl/mobie/io/n5/loaders/N5ImageLoader.java b/src/main/java/org/embl/mobie/io/n5/loaders/N5ImageLoader.java
index 371f2530..06e857ba 100644
--- a/src/main/java/org/embl/mobie/io/n5/loaders/N5ImageLoader.java
+++ b/src/main/java/org/embl/mobie/io/n5/loaders/N5ImageLoader.java
@@ -277,7 +277,7 @@ private static class N5CacheArrayLoader implements SimpleCacheArrayLoader
}
@Override
- public A loadArray(final long[] gridPosition) throws IOException {
+ public A loadArray(final long[] gridPosition, final int[] cellDimensions) throws IOException {
DataBlock block = null;
try {
diff --git a/src/main/java/org/embl/mobie/io/n5/util/N5CacheArrayLoader.java b/src/main/java/org/embl/mobie/io/n5/util/N5CacheArrayLoader.java
index d51cfbea..ca61c6c0 100644
--- a/src/main/java/org/embl/mobie/io/n5/util/N5CacheArrayLoader.java
+++ b/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 {
diff --git a/src/main/java/org/embl/mobie/io/n5/writers/WriteSequenceToN5.java b/src/main/java/org/embl/mobie/io/n5/writers/WriteSequenceToN5.java
index 0586775f..f67f4378 100644
--- a/src/main/java/org/embl/mobie/io/n5/writers/WriteSequenceToN5.java
+++ b/src/main/java/org/embl/mobie/io/n5/writers/WriteSequenceToN5.java
@@ -325,7 +325,7 @@ public RandomAccessibleInterval 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));
}
diff --git a/src/main/java/org/embl/mobie/io/ome/zarr/loaders/N5OMEZarrImageLoader.java b/src/main/java/org/embl/mobie/io/ome/zarr/loaders/N5OMEZarrImageLoader.java
index cdc9196f..91c1adaf 100644
--- a/src/main/java/org/embl/mobie/io/ome/zarr/loaders/N5OMEZarrImageLoader.java
+++ b/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);
}
diff --git a/src/main/java/org/embl/mobie/io/ome/zarr/readers/N5S3OmeZarrReader.java b/src/main/java/org/embl/mobie/io/ome/zarr/readers/N5S3OmeZarrReader.java
index a3c844f2..3c942b0f 100644
--- a/src/main/java/org/embl/mobie/io/ome/zarr/readers/N5S3OmeZarrReader.java
+++ b/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;
@@ -266,28 +267,25 @@ public DataBlock readBlock(
*
* @param objectPath
* @return null if the object does not exist, otherwise the loaded attributes.
- * @throws IOException
*/
- public HashMap readJson(String objectPath) throws IOException {
- if (!this.s3.doesObjectExist(this.bucketName, objectPath)) {
- return null;
- } else {
+ public HashMap readJson(String objectPath) {
+ try {
InputStream in = this.readS3Object(objectPath);
- Throwable var4 = null;
+ Throwable throwable = null;
- HashMap var5;
+ HashMap hashMap;
try {
- var5 = GsonAttributesParser.readAttributes(new InputStreamReader(in), this.gson);
- } catch (Throwable var14) {
- var4 = var14;
- throw var14;
+ hashMap = GsonAttributesParser.readAttributes(new InputStreamReader(in), this.gson);
+ } catch (Throwable error) {
+ throwable = error;
+ throw error;
} finally {
if (in != null) {
- if (var4 != null) {
+ if (throwable != null) {
try {
in.close();
- } catch (Throwable var13) {
- var4.addSuppressed(var13);
+ } catch (Throwable exception) {
+ throwable.addSuppressed(exception);
}
} else {
in.close();
@@ -295,8 +293,10 @@ public HashMap 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;
}
}
diff --git a/src/main/java/org/embl/mobie/io/ome/zarr/util/N5OMEZarrCacheArrayLoader.java b/src/main/java/org/embl/mobie/io/ome/zarr/util/N5OMEZarrCacheArrayLoader.java
index 4405578f..b020bf27 100644
--- a/src/main/java/org/embl/mobie/io/ome/zarr/util/N5OMEZarrCacheArrayLoader.java
+++ b/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);
diff --git a/src/main/java/org/embl/mobie/io/ome/zarr/writers/imageplus/WriteSequenceToN5OmeZarr.java b/src/main/java/org/embl/mobie/io/ome/zarr/writers/imageplus/WriteSequenceToN5OmeZarr.java
index 571f1147..269ac3b1 100644
--- a/src/main/java/org/embl/mobie/io/ome/zarr/writers/imageplus/WriteSequenceToN5OmeZarr.java
+++ b/src/main/java/org/embl/mobie/io/ome/zarr/writers/imageplus/WriteSequenceToN5OmeZarr.java
@@ -408,7 +408,7 @@ public RandomAccessibleInterval 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));
}
diff --git a/src/main/java/org/embl/mobie/io/openorganelle/N5CacheArrayLoader.java b/src/main/java/org/embl/mobie/io/openorganelle/N5CacheArrayLoader.java
index 9fb07654..0603ccc7 100644
--- a/src/main/java/org/embl/mobie/io/openorganelle/N5CacheArrayLoader.java
+++ b/src/main/java/org/embl/mobie/io/openorganelle/N5CacheArrayLoader.java
@@ -24,7 +24,7 @@ public class N5CacheArrayLoader implements SimpleCacheArrayLoader {
}
@Override
- public A loadArray(final long[] gridPosition) {
+ public A loadArray(final long[] gridPosition, final int[] cellDimensions) {
DataBlock block = null;
try {
diff --git a/src/main/java/org/embl/mobie/io/util/CustomXmlIoSpimData.java b/src/main/java/org/embl/mobie/io/util/CustomXmlIoSpimData.java
index bdc4c57f..35f3858c 100644
--- a/src/main/java/org/embl/mobie/io/util/CustomXmlIoSpimData.java
+++ b/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 {
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));
diff --git a/src/test/java/ui/BdvOmeZarrOpener.java b/src/test/java/ui/BdvOmeZarrOpener.java
new file mode 100644
index 00000000..69283b8b
--- /dev/null
+++ b/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);
+ }
+}