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Add static factory methods open / openWithN5 / openWithZarrJava to Pyramidal5DImageData
Lets API consumers open an OME-Zarr image without having to import Pyramidal5DImageDataImpl or the backend classes directly: Pyramidal5DImageData.open(context, path, preferredWidth) Pyramidal5DImageData.openWithN5(context, path, preferredWidth) Pyramidal5DImageData.openWithZarrJava(context, path, preferredWidth) open() reads the configured ZarrReaderBackend from the context's PrefService and delegates to one of the explicit factories, so callers who do not care about backend selection get the user-configured default. The backend-specific factories let callers force a particular library when they need to. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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‎src/main/java/sc/fiji/ome/zarr/pyramid/Pyramidal5DImageData.java‎

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import bdv.viewer.SourceAndConverter;
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import ij.ImagePlus;
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import mpicbg.spim.data.sequence.VoxelDimensions;
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import org.scijava.Context;
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import org.scijava.prefs.PrefService;
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import sc.fiji.ome.zarr.pyramid.exceptions.NoMatchingResolutionException;
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import sc.fiji.ome.zarr.pyramid.backend.zarrjava.ZarrJavaPyramidBackend;
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import sc.fiji.ome.zarr.pyramid.metadata.Omero;
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import sc.fiji.ome.zarr.settings.ZarrDragAndDropOpenSettings;
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import sc.fiji.ome.zarr.settings.ZarrReaderBackend;
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/**
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* 5D multi-resolution array data
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}
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ImagePlus asImagePlus();
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/**
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* Opens an OME-Zarr image using the backend configured in the context's
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* {@link ZarrDragAndDropOpenSettings}, falling back to the N5 backend if no
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* settings service is present.
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*
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* @param preferredWidth maximum width along x for the returned dataset;
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* {@code null} selects the highest available resolution
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* @throws NoMatchingResolutionException if {@code preferredWidth} is smaller
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* than the width of the coarsest resolution level
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*/
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static < T extends NativeType< T > & RealType< T > > Pyramidal5DImageData< T > open(
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final Context context, final String path, final Integer preferredWidth )
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{
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final ZarrReaderBackend backend = ZarrDragAndDropOpenSettings
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.loadSettingsFromPreferences( context.getService( PrefService.class ) )
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.getReaderBackend();
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switch ( backend )
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{
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case ZARR_JAVA:
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return openWithZarrJava( context, path, preferredWidth );
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case N5:
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default:
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return openWithN5( context, path, preferredWidth );
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}
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}
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/**
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* Opens an OME-Zarr image using the N5-universe backend.
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*
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* @param preferredWidth maximum width along x for the returned dataset;
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* {@code null} selects the highest available resolution
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* @throws NoMatchingResolutionException if {@code preferredWidth} is smaller
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* than the width of the coarsest resolution level
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*/
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static < T extends NativeType< T > & RealType< T > > Pyramidal5DImageData< T > openWithN5(
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final Context context, final String path, final Integer preferredWidth )
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{
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return new Pyramidal5DImageDataImpl<>( context, path, preferredWidth );
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}
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/**
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* Opens an OME-Zarr image using the zarr-java backend.
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*
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* @param preferredWidth maximum width along x for the returned dataset;
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* {@code null} selects the highest available resolution
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* @throws NoMatchingResolutionException if {@code preferredWidth} is smaller
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* than the width of the coarsest resolution level
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*/
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@SuppressWarnings( { "rawtypes", "unchecked" } )
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static < T extends NativeType< T > & RealType< T > > Pyramidal5DImageData< T > openWithZarrJava(
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final Context context, final String path, final Integer preferredWidth )
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{
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return new Pyramidal5DImageDataImpl( context, new ZarrJavaPyramidBackend( path, preferredWidth ) );
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}
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}

‎src/test/java/sc/fiji/ome/zarr/pyramid/Pyramidal5DImageDataOpenTest.java‎

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/*-
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* #%L
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* OME-Zarr extras for Fiji
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* %%
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* Copyright (C) 2022 - 2026 SciJava developers
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package sc.fiji.ome.zarr.pyramid;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertNotNull;
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import static org.junit.jupiter.api.Assertions.assertThrows;
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import java.net.URISyntaxException;
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import java.nio.file.Path;
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import org.junit.jupiter.api.Test;
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import org.scijava.Context;
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import org.scijava.prefs.PrefService;
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import sc.fiji.ome.zarr.pyramid.exceptions.NoMatchingResolutionException;
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import sc.fiji.ome.zarr.settings.ZarrDragAndDropOpenSettings;
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import sc.fiji.ome.zarr.settings.ZarrReaderBackend;
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import sc.fiji.ome.zarr.util.ZarrTestUtils;
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/**
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* Unit tests for the three static factory methods on
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* {@link Pyramidal5DImageData}: {@link Pyramidal5DImageData#openWithN5},
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* {@link Pyramidal5DImageData#openWithZarrJava}, and
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* {@link Pyramidal5DImageData#open} (which dispatches based on the user's
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* configured {@link ZarrReaderBackend}).
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* <p>
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* Backend-internal correctness (axis handling, omero metadata, pyramid
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* reading, etc.) is covered by {@link N5BackedPyramidal5DImageDataTest}
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* and {@link ZarrJavaBackedPyramidal5DImageDataTest} via
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* {@link Pyramidal5DImageDataTestBase}; this class only exercises the
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* factory layer.
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*/
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class Pyramidal5DImageDataOpenTest
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{
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private static final String TEST_RESOURCE = "sc/fiji/ome/zarr/util/5d_testing/5d_dataset_v5.ome.zarr";
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@Test
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void testOpenWithN5ReturnsWorkingDataset() throws URISyntaxException
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{
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.openWithN5( context, path.toString(), null );
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assertWorkingDataset( data );
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}
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}
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@Test
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void testOpenWithN5HonorsPreferredWidth() throws URISyntaxException
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{
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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// preferredWidth=50 fits the second pyramid level (32 px), not the
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// full-resolution one (64 px), so the returned dataset is 32x32.
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.openWithN5( context, path.toString(), 50 );
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assertEquals( 32, data.asDataset().getImgPlus().dimension( 0 ) );
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assertEquals( 32, data.asDataset().getImgPlus().dimension( 1 ) );
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}
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}
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@Test
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void testOpenWithN5ThrowsWhenPreferredWidthBelowAllLevels() throws URISyntaxException
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{
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final String pathStr = ZarrTestUtils.resourcePath( TEST_RESOURCE ).toString();
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try (Context context = new Context())
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{
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assertThrows( NoMatchingResolutionException.class,
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() -> Pyramidal5DImageData.openWithN5( context, pathStr, 16 ) );
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}
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}
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@Test
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void testOpenWithZarrJavaReturnsWorkingDataset() throws URISyntaxException
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{
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.openWithZarrJava( context, path.toString(), null );
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assertWorkingDataset( data );
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}
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}
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@Test
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void testOpenWithZarrJavaHonorsPreferredWidth() throws URISyntaxException
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{
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.openWithZarrJava( context, path.toString(), 50 );
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assertEquals( 32, data.asDataset().getImgPlus().dimension( 0 ) );
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assertEquals( 32, data.asDataset().getImgPlus().dimension( 1 ) );
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}
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}
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@Test
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void testOpenWithZarrJavaThrowsWhenPreferredWidthBelowAllLevels() throws URISyntaxException
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{
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final String pathStr = ZarrTestUtils.resourcePath( TEST_RESOURCE ).toString();
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try (Context context = new Context())
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{
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assertThrows( NoMatchingResolutionException.class,
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() -> Pyramidal5DImageData.openWithZarrJava( context, pathStr, 16 ) );
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}
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}
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@Test
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void testOpenDispatchesToN5WhenSettingsSelectN5() throws URISyntaxException
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{
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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persistBackendChoice( context, ZarrReaderBackend.N5 );
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.open( context, path.toString(), null );
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assertWorkingDataset( data );
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}
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}
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@Test
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void testOpenDispatchesToZarrJavaWhenSettingsSelectZarrJava() throws URISyntaxException
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{
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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persistBackendChoice( context, ZarrReaderBackend.ZARR_JAVA );
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.open( context, path.toString(), null );
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assertWorkingDataset( data );
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}
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}
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@Test
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void testOpenWithFreshContextUsesDefaultBackend() throws URISyntaxException
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{
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// No prefs written → loadSettingsFromPreferences falls back to the
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// project's DEFAULT_READER_BACKEND, and open() must succeed.
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final Path path = ZarrTestUtils.resourcePath( TEST_RESOURCE );
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try (Context context = new Context())
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{
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final Pyramidal5DImageData< ? > data = Pyramidal5DImageData.open( context, path.toString(), null );
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assertWorkingDataset( data );
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}
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}
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private static void persistBackendChoice( final Context context, final ZarrReaderBackend backend )
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{
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final PrefService prefs = context.getService( PrefService.class );
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final ZarrDragAndDropOpenSettings settings = ZarrDragAndDropOpenSettings.loadSettingsFromPreferences( prefs );
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settings.setReaderBackend( backend );
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settings.saveSettingsToPreferences( prefs );
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}
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/**
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* Sanity assertions that any of the three open() methods must satisfy
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* for our 5D test dataset (64x64x16, 3 channels, 4 timepoints, 2 levels).
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*/
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private static void assertWorkingDataset( final Pyramidal5DImageData< ? > data )
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{
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assertNotNull( data );
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assertNotNull( data.asDataset() );
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assertNotNull( data.asPyramidalDataset() );
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assertNotNull( data.asSources() );
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assertEquals( 64, data.asDataset().getImgPlus().dimension( 0 ) );
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assertEquals( 64, data.asDataset().getImgPlus().dimension( 1 ) );
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assertEquals( 3, data.numChannels() );
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assertEquals( 4, data.numTimepoints() );
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assertEquals( 2, data.numResolutionLevels() );
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}
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}

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