Fixes #163

mobie · Mar 15, 2024 · 33e5d25 · 33e5d25
1 parent 0216a25
commit 33e5d25
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Showing 2 changed files with 25 additions and 13 deletions.
diff --git a/src/main/java/org/embl/mobie/io/CachedCellImgOpener.java b/src/main/java/org/embl/mobie/io/CachedCellImgOpener.java
@@ -46,6 +46,7 @@
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
@@ -92,9 +93,11 @@ private void openIlastikHDF5() throws IOException
 	{
 		final N5HDF5Reader n5 = new N5HDF5Reader( path );
 
-		final String dataset = "exported_data";
+		String dataset = "exported_data";
+		if ( ! n5.datasetExists( dataset ) )
+			dataset = "data";
 
-		ArrayList< String > axes = getIlastikAxesLabels( n5, dataset );
+		List< String > axes = fetchAxesLabels( n5, dataset );
 
 		final CachedCellImg< T, ? > cachedCellImg = N5Utils.openVolatile( n5, dataset );
 		channelRAIs = Axes.getChannels( cachedCellImg, axes );
@@ -115,19 +118,28 @@ private RandomAccessibleInterval< Volatile< T > > getVolatileRAI( CachedCellImg<
 		}
 	}
 
-	private ArrayList< String > getIlastikAxesLabels( N5HDF5Reader n5, String dataset ) throws IOException
+	private static List< String > fetchAxesLabels( N5HDF5Reader n5, String dataset ) throws IOException
 	{
-		ArrayList< String > axes = new ArrayList<>();
-		final JsonObject axistags = n5.getAttribute( dataset,"axistags", JsonObject.class );
-		final JsonArray jsonArray = axistags.get( "axes" ).getAsJsonArray();
-		for ( JsonElement jsonElement : jsonArray )
+		try
+		{
+			ArrayList< String > axes = new ArrayList<>();
+			final JsonObject axisTags = n5.getAttribute( dataset, "axistags", JsonObject.class );
+			final JsonArray jsonArray = axisTags.get( "axes" ).getAsJsonArray();
+			for ( JsonElement jsonElement : jsonArray )
+			{
+				final JsonObject jsonObject = jsonElement.getAsJsonObject();
+				final String axisLabel = jsonObject.get( "key" ).getAsString();
+				axes.add( axisLabel );
+			}
+			Collections.reverse( axes );
+			return axes;
+		}
+		catch ( Exception e )
 		{
-			final JsonObject jsonObject = jsonElement.getAsJsonObject();
-			final String axisLabel = jsonObject.get( "key" ).getAsString();
-			axes.add( axisLabel );
+			List< String > axes = Arrays.asList( "t", "z", "c", "x", "y" );
+			Collections.reverse( axes );
+			return axes;
 		}
-		Collections.reverse( axes );
-		return axes;
 	}
 
 	public RandomAccessibleInterval< T > getRAI( int c )

diff --git a/src/test/java/develop/OpenIlastikHDF5.java b/src/test/java/develop/OpenIlastikHDF5.java
@@ -53,7 +53,7 @@ public class OpenIlastikHDF5
 {
 	public static void main( String[] args ) throws IOException
 	{
-		final CachedCellImgOpener< ? > opener = new CachedCellImgOpener( "/Users/tischer/Desktop/mobie-data/ilastik/A1_2022-07-06-093303-0000--0.4.0-0-1.4.0--tracking-oids.h5", ImageDataFormat.IlastikHDF5, null );
+		final CachedCellImgOpener< ? > opener = new CachedCellImgOpener( "/Users/tischer/Downloads/export.h5", ImageDataFormat.IlastikHDF5, null );
 		final RandomAccessibleInterval< ? > rai = opener.getRAI( 0 );
 		final RandomAccessibleInterval< ? > vRAI = opener.getVolatileRAI( 0 );
 	}