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| 1 | +package sc.fiji.ome.zarr.pyramid; |
| 2 | + |
| 3 | +import dev.zarr.zarrjava.ZarrException; |
| 4 | +import dev.zarr.zarrjava.experimental.ome.MultiscaleImage; |
| 5 | +import dev.zarr.zarrjava.experimental.ome.metadata.OmeroChannel; |
| 6 | +import dev.zarr.zarrjava.experimental.ome.metadata.OmeroMetadata; |
| 7 | +import dev.zarr.zarrjava.experimental.ome.metadata.OmeroRdefs; |
| 8 | +import dev.zarr.zarrjava.experimental.ome.metadata.OmeroWindow; |
| 9 | +import dev.zarr.zarrjava.store.FilesystemStore; |
| 10 | +import dev.zarr.zarrjava.store.StoreHandle; |
| 11 | +import org.junit.jupiter.params.ParameterizedTest; |
| 12 | +import org.junit.jupiter.params.provider.MethodSource; |
| 13 | +import sc.fiji.ome.zarr.util.ZarrTestUtils; |
| 14 | + |
| 15 | +import java.io.IOException; |
| 16 | +import java.net.URISyntaxException; |
| 17 | +import java.nio.file.Path; |
| 18 | +import java.util.List; |
| 19 | +import java.util.stream.Stream; |
| 20 | + |
| 21 | +import static org.junit.jupiter.api.Assertions.*; |
| 22 | + |
| 23 | +class OmeroMetadataAccessTest |
| 24 | +{ |
| 25 | + static Stream< String > omeZarr5dExamples() |
| 26 | + { |
| 27 | + return Stream.of( |
| 28 | + "sc/fiji/ome/zarr/util/5d_testing/5d_dataset_v4.ome.zarr", |
| 29 | + "sc/fiji/ome/zarr/util/5d_testing/5d_dataset_v5.ome.zarr" |
| 30 | + ); |
| 31 | + } |
| 32 | + |
| 33 | + @ParameterizedTest |
| 34 | + @MethodSource( "omeZarr5dExamples" ) |
| 35 | + void testCanAccessOmeroMetadataWithExperimentalOme( final String resource ) throws URISyntaxException, IOException, ZarrException |
| 36 | + { |
| 37 | + final Path path = ZarrTestUtils.resourcePath( resource ); |
| 38 | + final FilesystemStore store = new FilesystemStore( path.toString() ); |
| 39 | + final StoreHandle handle = store.resolve(); |
| 40 | + final MultiscaleImage multiscaleImage = MultiscaleImage.open( handle ); |
| 41 | + |
| 42 | + final OmeroMetadata omero = multiscaleImage.getOmeroMetadata(); |
| 43 | + |
| 44 | + assertNotNull( omero ); |
| 45 | + assertEquals( Integer.valueOf( 1 ), omero.id ); |
| 46 | + assertEquals( "0.4", omero.version ); |
| 47 | + |
| 48 | + final OmeroRdefs rdefs = omero.rdefs; |
| 49 | + assertNotNull( rdefs ); |
| 50 | + assertEquals( Integer.valueOf( 1 ), rdefs.defaultT ); |
| 51 | + assertEquals( Integer.valueOf( 71 ), rdefs.defaultZ ); |
| 52 | + assertEquals( "color", rdefs.model ); |
| 53 | + |
| 54 | + final List< OmeroChannel > channels = omero.channels; |
| 55 | + assertNotNull( channels ); |
| 56 | + assertEquals( 3, channels.size() ); |
| 57 | + |
| 58 | + final OmeroChannel channel0 = channels.get( 0 ); |
| 59 | + assertEquals( "lynEGFP", channel0.label ); |
| 60 | + assertEquals( "00FF00", channel0.color ); |
| 61 | + assertWindow( channel0.window, 0.0, 255.0, 3.0, 246.0 ); |
| 62 | + |
| 63 | + final OmeroChannel channel1 = channels.get( 1 ); |
| 64 | + assertEquals( "NLStdTomato", channel1.label ); |
| 65 | + assertEquals( "FF0000", channel1.color ); |
| 66 | + assertWindow( channel1.window, 0.0, 255.0, 6.0, 133.0 ); |
| 67 | + } |
| 68 | + |
| 69 | + private void assertWindow( final OmeroWindow window, final double min, final double max, final double start, final double end ) |
| 70 | + { |
| 71 | + assertNotNull( window ); |
| 72 | + assertEquals( min, window.min ); |
| 73 | + assertEquals( max, window.max ); |
| 74 | + assertEquals( start, window.start ); |
| 75 | + assertEquals( end, window.end ); |
| 76 | + } |
| 77 | +} |
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