feat: open transform graph without explicit coord systems

* create coordinate systems implied by transformations
saalfeldlab · Jan 8, 2024 · a53357d · a53357d
1 parent 91e9049
commit a53357d
Show file tree

Hide file tree

Showing 2 changed files with 50 additions and 11 deletions.
diff --git a/src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v05/Common.java b/src/main/java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v05/Common.java
@@ -17,7 +17,9 @@
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
 import org.janelia.saalfeldlab.n5.universe.N5Factory;
 import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
+import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
 import org.janelia.saalfeldlab.n5.universe.metadata.axes.CoordinateSystem;
+import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.CoordinateSystems;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.graph.TransformGraph;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransformAdapter;
 import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v05.transformations.AffineCoordinateTransform;
@@ -242,32 +244,64 @@ public static <T extends NumericType<T> & NativeType<T>> RealRandomAccessible<T>
 //		return null;
 	}
 
+	public static TransformGraph openGraph( final String uri ) {
+
+		try {
+
+			final N5URI n5uri = new N5URI(uri);
+			final N5Reader n5 = new N5Factory().gsonBuilder(gsonBuilder()).openReader(n5uri.getContainerPath());
+			return openGraph(n5, n5uri.getGroupPath());
+
+		} catch (URISyntaxException e) {}
+		return null;
+	}
+
 	public static TransformGraph openGraph( final N5Reader n5 )
 	{
 		return openGraph( n5, "/" );
 	}
 
-	public static TransformGraph openGraph( final N5Reader n5, final String dataset )
+	public static TransformGraph openGraph( final N5Reader n5, final String group )
 	{
 		int nd = 5;
-		if( n5.datasetExists( dataset ))
-			nd = n5.getDatasetAttributes( dataset ).getNumDimensions();
+		if( n5.datasetExists( group ))
+			nd = n5.getDatasetAttributes( group ).getNumDimensions();
 
-		return openGraph( n5, dataset, nd );
+		return openGraph( n5, group, nd );
 	}
 
-	public static TransformGraph openGraph( final N5Reader n5, final String dataset, final int nd )
+	public static TransformGraph openGraph( final N5Reader n5, final String group, final int nd )
 	{
-		CoordinateSystem[] spaces = n5.getAttribute(dataset, "spaces", CoordinateSystem[].class);
+		CoordinateSystem[] spaces = n5.getAttribute(group, "coordinateSystems", CoordinateSystem[].class);
 		if( spaces == null )
-			spaces = n5.getAttribute(dataset, "coordinateSystems", CoordinateSystem[].class);
+			spaces = n5.getAttribute(group, "coordinateSystems", CoordinateSystem[].class);
 
-		CoordinateTransform<?>[] transforms = n5.getAttribute(dataset, "transformations", CoordinateTransform[].class);
+		if( spaces == null )
+			return openGraphImpliedSpaces( n5, group, nd );
+
+		CoordinateTransform<?>[] transforms = n5.getAttribute(group, "coordinateTransformations", CoordinateTransform[].class);
 		if( transforms == null )
-			transforms = n5.getAttribute(dataset, "coordinateTransformations", CoordinateTransform[].class);
+			transforms = n5.getAttribute(group, "transformations", CoordinateTransform[].class);
 
 //		return new TransformGraph( Arrays.asList( transforms ), Arrays.asList(spaces));
-		return new SpacesTransforms( spaces, transforms ).buildTransformGraph(dataset, nd);
+		return new SpacesTransforms( spaces, transforms ).buildTransformGraph(group, nd);
+	}
+
+	protected static TransformGraph openGraphImpliedSpaces(final N5Reader n5, final String dataset, final int nd) {
+
+		CoordinateTransform<?>[] transforms = n5.getAttribute(dataset, "coordinateTransformations", CoordinateTransform[].class);
+		if (transforms == null)
+			transforms = n5.getAttribute(dataset, "transformations", CoordinateTransform[].class);
+
+		final CoordinateSystem[] coordinateSystems = Arrays.stream(transforms).flatMap(x -> {
+			return Stream.of(
+					new CoordinateSystem(x.getInput(), nd),
+					new CoordinateSystem(x.getOutput(), nd));
+		}).toArray(N -> {
+			return new CoordinateSystem[N];
+		});
+
+		return new SpacesTransforms(coordinateSystems, transforms).buildTransformGraph(dataset, nd);
 	}
 
 	public static TransformGraph openGraph( final N5Reader n5, final String... datasets ) throws IOException

diff --git a/.../java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v05/graph/TransformGraph.java b/.../java/org/janelia/saalfeldlab/n5/universe/metadata/ome/ngff/v05/graph/TransformGraph.java
@@ -99,7 +99,12 @@ public void addTransform( final CoordinateTransform<?> t ) {
 	}
 
 	private void addTransform( final CoordinateTransform<?> t, final boolean addInverse ) {
-		if( transforms.stream().anyMatch( x -> x.getName().equals(t.getName())) )
+		if( transforms.stream().anyMatch( x -> {
+			if( x != null && x.getName() != null )
+				return x.getName().equals(t.getName());
+			else
+				return false;
+		}))
 			return;
 
 		if( spaces.hasSpace(t.getInput()) && spaces.hasSpace(t.getOutput()))