fix: writing transform metadata

* add transform write/parse tests

src/main/java/org/janelia/saalfeldlab/n5/metadata/transforms/AbstractLinearSpatialTransform.java

@@ -1,7 +1,6 @@
 package org.janelia.saalfeldlab.n5.metadata.transforms;
 
 import java.io.IOException;
-import java.util.Arrays;
 
 import org.janelia.saalfeldlab.n5.N5Reader;
 import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
@@ -55,11 +54,8 @@ protected static <T extends RealType<T> & NativeType<T>> double[] getDoubleArray
 				while (c.hasNext())
 					params[i++] = c.next().getRealDouble();
 
-				System.out.println("got params: " + Arrays.toString(params));
 				return params;
-
-			} catch (IOException e) {
-			}
+			} catch (IOException e) { }
 		}
 		return null;
 	}

src/main/java/org/janelia/saalfeldlab/n5/metadata/transforms/AffineSpatialTransform.java

@@ -9,7 +9,7 @@
 
 public class AffineSpatialTransform extends AbstractLinearSpatialTransform {
 
-	public final double[] affine;
+	public double[] affine;
 
 	public transient AffineGet transform;
 
@@ -25,8 +25,14 @@ public AffineSpatialTransform( final N5Reader n5, final String path ) {
 		buildTransform( affine );
 	}
 
+	public AffineSpatialTransform( final String path ) {
+		super("affine", path );
+		this.affine = null;
+	}
+
 	@Override
 	public AffineGet buildTransform( double[] parameters ) {
+		this.affine = parameters;
 		if( parameters.length == 6 ) {
 			AffineTransform2D tmp = new AffineTransform2D();
 			tmp.set( parameters );

src/main/java/org/janelia/saalfeldlab/n5/metadata/transforms/ScaleSpatialTransform.java

@@ -9,7 +9,7 @@
 
 public class ScaleSpatialTransform extends AbstractLinearSpatialTransform {
 
-	public final double[] scale;
+	public double[] scale;
 
 	public transient AffineGet transform;
 
@@ -20,14 +20,20 @@ public ScaleSpatialTransform( final double[] scale ) {
 	}
 
 	public ScaleSpatialTransform( final N5Reader n5, final String path ) {
-		super("scale");
+		super("scale", path );
 		this.scale = getParameters(n5);
 		buildTransform( scale );
 	}
 
+	public ScaleSpatialTransform( final String path ) {
+		super("scale", path );
+		this.scale = null;
+	}
+
 	@Override
 	public AffineGet buildTransform( double[] parameters )
 	{
+		this.scale = parameters;
 		if( parameters.length == 2 )
 			transform = new Scale2D(parameters);
 		else if( parameters.length == 3 )

src/main/java/org/janelia/saalfeldlab/n5/metadata/transforms/SpatialTransformAdapter.java

@@ -63,7 +63,6 @@ public SpatialTransform deserialize(JsonElement json, Type typeOfT, JsonDeserial
 	private final SpatialTransform readTransformParameters( final SpatialTransform transform ) {
 
 		if( transform instanceof ParametrizedTransform ) {
-			System.out.println( "reading transform params" );
 			ParametrizedTransform pt = (ParametrizedTransform)transform;
 			if( pt.getParameterPath() != null ) {
 				pt.buildTransform( pt.getParameters(n5));

src/main/java/org/janelia/saalfeldlab/n5/metadata/transforms/TranslationSpatialTransform.java

@@ -9,7 +9,7 @@
 
 public class TranslationSpatialTransform extends AbstractLinearSpatialTransform {
 
-	public final double[] translation;
+	public double[] translation;
 
 	public transient AffineGet transform;
 
@@ -25,9 +25,15 @@ public TranslationSpatialTransform( final N5Reader n5, final String path ) {
 		buildTransform( translation );
 	}
 
+	public TranslationSpatialTransform( final String path ) {
+		super("translation", path );
+		this.translation = null;
+	}
+
 	@Override
 	public AffineGet buildTransform( double[] parameters )
 	{
+		this.translation = parameters;
 		if( parameters.length == 2 )
 			transform = new Translation2D(parameters);
 		else if( parameters.length == 3 )

src/test/java/org/janelia/saalfeldlab/n5/metadata/TransformTests.java

@@ -0,0 +1,155 @@
+package org.janelia.saalfeldlab.n5.metadata;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.Optional;
+
+import org.janelia.saalfeldlab.n5.GzipCompression;
+import org.janelia.saalfeldlab.n5.N5FSWriter;
+import org.janelia.saalfeldlab.n5.N5Writer;
+import org.janelia.saalfeldlab.n5.RunImportExportTest;
+import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
+import org.janelia.saalfeldlab.n5.metadata.canonical.CanonicalMetadata;
+import org.janelia.saalfeldlab.n5.metadata.canonical.SpatialMetadataCanonical;
+import org.janelia.saalfeldlab.n5.metadata.canonical.TranslatedTreeMetadataParser;
+import org.janelia.saalfeldlab.n5.metadata.transforms.AffineSpatialTransform;
+import org.janelia.saalfeldlab.n5.metadata.transforms.ScaleSpatialTransform;
+import org.janelia.saalfeldlab.n5.metadata.transforms.SequenceSpatialTransform;
+import org.janelia.saalfeldlab.n5.metadata.transforms.SpatialTransform;
+import org.janelia.saalfeldlab.n5.metadata.transforms.TranslationSpatialTransform;
+import org.junit.After;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.Test;
+
+import net.imglib2.img.array.ArrayCursor;
+import net.imglib2.img.array.ArrayImg;
+import net.imglib2.img.array.ArrayImgs;
+import net.imglib2.img.basictypeaccess.array.ByteArray;
+import net.imglib2.img.basictypeaccess.array.DoubleArray;
+import net.imglib2.type.numeric.integer.UnsignedByteType;
+import net.imglib2.type.numeric.real.DoubleType;
+
+
+public class TransformTests {
+
+	private File containerDir;
+
+	private N5Writer n5;
+
+	private ArrayImg<UnsignedByteType, ByteArray> img;
+
+	private double[] translation = new double[] { 100, 200, 300 };
+
+	private double[] scale = new double[] { 1.1, 2.2, 3.3 };
+
+	private double[] affine = new double[] { 
+			1.1, 0.1, 0.2, -10,
+			0.3, 2.2, 0.4, -20,
+			0.5, 0.6, 3.3, -30 };
+
+	@Before
+	public void before()
+	{
+		URL configUrl = RunImportExportTest.class.getResource( "/plugins.config" );
+		File baseDir = new File( configUrl.getFile() ).getParentFile();
+		containerDir = new File( baseDir, "transforms.n5" );
+
+		try {
+			n5 = new N5FSWriter( containerDir.getCanonicalPath() );
+
+			int v = 0;
+			img = ArrayImgs.unsignedBytes( 3, 4, 5);
+			ArrayCursor<UnsignedByteType> c = img.cursor();
+			while( c.hasNext())
+				c.next().set( v++ );
+
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+	}
+
+	@After
+	public void after()
+	{
+		try {
+			n5.remove();
+		} catch (IOException e) { }
+	}
+
+	@Test
+	public void testParametrizedTransforms() throws IOException {
+
+		// translation
+		ArrayImg<DoubleType, DoubleArray> translationParams = ArrayImgs.doubles( translation, 3 );
+		N5Utils.save( translationParams, n5, "translation", new int[]{3}, new GzipCompression());
+
+		// scale
+		ArrayImg<DoubleType, DoubleArray> scaleParams = ArrayImgs.doubles( scale, 3 );
+		N5Utils.save( scaleParams, n5, "scale", new int[]{3}, new GzipCompression());
+
+		// affine
+		ArrayImg<DoubleType, DoubleArray> affineParams = ArrayImgs.doubles( affine, 12 );
+		N5Utils.save( affineParams, n5, "affine", new int[]{12}, new GzipCompression());
+
+		final ScaleSpatialTransform scaleTransform = new ScaleSpatialTransform( "scale" );
+		final TranslationSpatialTransform translationTransform = new TranslationSpatialTransform( "translation" );
+		final AffineSpatialTransform affineTransform = new AffineSpatialTransform( "affine" );
+		final SequenceSpatialTransform seq = new SequenceSpatialTransform( 
+				new SpatialTransform[]{ affineTransform, scaleTransform, translationTransform });
+
+		// make an image
+		N5Utils.save( img, n5, "imgParam", new int[] {5, 5, 5}, new GzipCompression());
+
+		// set the transform metadata
+		SpatialMetadataCanonical transform = new SpatialMetadataCanonical(null, seq, "pixel", null);
+		n5.setAttribute("imgParam", "spatialTransform", transform);
+
+		testParsedTransformSeq("/imgParam");
+	}
+
+	@Test
+	public void testTransforms() throws IOException {
+
+		final ScaleSpatialTransform scaleTransform = new ScaleSpatialTransform( scale );
+		final TranslationSpatialTransform translationTransform = new TranslationSpatialTransform( translation );
+		final AffineSpatialTransform affineTransform = new AffineSpatialTransform( affine );
+		final SequenceSpatialTransform seq = new SequenceSpatialTransform( 
+				new SpatialTransform[]{ affineTransform, scaleTransform, translationTransform });
+
+		// make an image
+		N5Utils.save( img, n5, "img", new int[] {5, 5, 5}, new GzipCompression());
+
+		// set the transform metadata
+		SpatialMetadataCanonical transform = new SpatialMetadataCanonical(null, seq, "pixel", null);
+		n5.setAttribute("img", "spatialTransform", transform);
+
+		testParsedTransformSeq("img");
+	}
+
+	private void testParsedTransformSeq( String dataset )
+	{
+		// canonical parser
+		final TranslatedTreeMetadataParser parser = new TranslatedTreeMetadataParser( n5, "." );
+		Optional<CanonicalMetadata> metaOpt = parser.parseMetadata(n5, dataset);
+		CanonicalMetadata meta = metaOpt.get();
+		SpatialMetadataCanonical parsedXfm = meta.getSpatialTransform();
+
+		Assert.assertTrue("parsed as sequence", parsedXfm.transform() instanceof SequenceSpatialTransform);
+		SequenceSpatialTransform parsedSeq = (SequenceSpatialTransform)parsedXfm.transform();
+		SpatialTransform transform0 = parsedSeq.getTransformations()[0];
+		SpatialTransform transform1 = parsedSeq.getTransformations()[1];
+		SpatialTransform transform2 = parsedSeq.getTransformations()[2];
+
+		Assert.assertTrue("transform0 is affine", transform0 instanceof AffineSpatialTransform);
+		Assert.assertArrayEquals( "parsed affine parameters", affine, ((AffineSpatialTransform)transform0).affine, 1e-9 );
+
+		Assert.assertTrue("transform1 is scale", transform1 instanceof ScaleSpatialTransform);
+		Assert.assertArrayEquals( "parsed scale parameters", scale, ((ScaleSpatialTransform)transform1).scale, 1e-9 );
+
+		Assert.assertTrue("transform2 is translation", transform2 instanceof TranslationSpatialTransform);
+		Assert.assertArrayEquals( "parsed translation parameters", translation, ((TranslationSpatialTransform)transform2).translation, 1e-9 );
+	}
+
+}