diff --git a/pom.xml b/pom.xml
index 89e4bab9..47416f63 100644
--- a/pom.xml
+++ b/pom.xml
@@ -9,7 +9,7 @@
org.embl.mobie
mobie-viewer-fiji
- 4.4.1
+ 4.4.2
@@ -85,7 +85,7 @@
0.8.0
0.6.9
- 2.2.5
+ 2.2.6
1.0.2
16.0.2
diff --git a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java b/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
index d5a085d5..fe46dc73 100644
--- a/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
+++ b/src/main/java/org/embl/mobie/lib/MoBIEHelper.java
@@ -35,7 +35,9 @@
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.AbstractSpimData;
import net.imglib2.Dimensions;
+import net.imglib2.RandomAccessibleInterval;
import org.embl.mobie.DataStore;
+import org.embl.mobie.io.CachedCellImgOpener;
import org.embl.mobie.io.ImageDataFormat;
import org.embl.mobie.io.SpimDataOpener;
import org.embl.mobie.io.github.GitHubUtils;
@@ -211,6 +213,7 @@ public static Metadata getMetadataFromImageFile( String path, int channelIndex )
throw new RuntimeException( "Path does not exist: " + path );
}
+
if ( path.contains( ".zarr" ) )
{
try
@@ -230,9 +233,14 @@ public static Metadata getMetadataFromImageFile( String path, int channelIndex )
}
else if ( path.endsWith( ".h5" ) )
{
- return new Metadata();
+ CachedCellImgOpener< ? > opener = new CachedCellImgOpener<>( path, ImageDataFormat.IlastikHDF5, ThreadHelper.sharedQueue );
+ RandomAccessibleInterval< ? > rai = opener.getRAI( 0 );
+ Metadata metadata = new Metadata();
+ metadata.numZSlices = (int) rai.dimension( 2 );
+
+ return metadata;
}
- else if ( path.endsWith( ".toml" ) )
+ if ( path.endsWith( ".toml" ) )
{
final ImagePlus imagePlus = new TOMLOpener( path ).asImagePlus();
return new Metadata( imagePlus );
diff --git a/src/main/java/org/embl/mobie/lib/source/Metadata.java b/src/main/java/org/embl/mobie/lib/source/Metadata.java
index a583c062..ed7c46bb 100644
--- a/src/main/java/org/embl/mobie/lib/source/Metadata.java
+++ b/src/main/java/org/embl/mobie/lib/source/Metadata.java
@@ -28,7 +28,6 @@
*/
package org.embl.mobie.lib.source;
-import IceInternal.Ex;
import ij.IJ;
import ij.ImagePlus;
import ij.plugin.ContrastEnhancer;
@@ -43,7 +42,7 @@ public class Metadata
public double[] contrastLimits = null;
public Integer numTimePoints = null;
public Integer numZSlices = 1;
- public Integer numChannelsContainer = 1; // in MoBIE each image has jsut one channel, but the container could have multiple
+ public Integer numChannelsContainer = 1; // in MoBIE each image has just one channel, but the container could have multiple
private static boolean logBFError = true;
public Metadata()
diff --git a/src/test/java/debug/DebugOpen3DIlastikImage.java b/src/test/java/debug/DebugOpen3DIlastikImage.java
new file mode 100644
index 00000000..b53c6054
--- /dev/null
+++ b/src/test/java/debug/DebugOpen3DIlastikImage.java
@@ -0,0 +1,17 @@
+package debug;
+
+import net.imagej.ImageJ;
+import org.embl.mobie.command.open.OpenImageAndLabelsCommand;
+
+import java.io.File;
+
+public class DebugOpen3DIlastikImage
+{
+ public static void main( String[] args )
+ {
+ new ImageJ().ui().showUI();
+ OpenImageAndLabelsCommand command = new OpenImageAndLabelsCommand();
+ command.image = new File("/Users/tischer/Downloads/export.h5");
+ command.run();
+ }
+}