Check for ilastik image dimensions

mobie · Mar 15, 2024 · 0da95dc · 0da95dc
1 parent 1ff8296
commit 0da95dc
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Showing 4 changed files with 30 additions and 6 deletions.
diff --git a/pom.xml b/pom.xml
@@ -9,7 +9,7 @@
 
     <groupId>org.embl.mobie</groupId>
     <artifactId>mobie-viewer-fiji</artifactId>
-    <version>4.4.1</version>
+    <version>4.4.2</version>
 
     <!-- force javadoc generation to fetch errors:    -->
     <!-- mvn javadoc:javadoc | grep error -->
@@ -85,7 +85,7 @@
 
         <bigdataviewer-playground.version>0.8.0</bigdataviewer-playground.version>
         <imagej-utils.version>0.6.9</imagej-utils.version>
-        <mobie-io.version>2.2.5</mobie-io.version>
+        <mobie-io.version>2.2.6</mobie-io.version>
         <trove.version>1.0.2</trove.version>
         <annotations.version>16.0.2</annotations.version>
 

diff --git 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
@@ -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
@@ -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();
+    }
+}