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stefanhahmannstefanhahmann
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Rename PyramidalBdvDataset to PyramidalBdv across the codebase.
1 parent 58c118f commit 9d88ea1

8 files changed

Lines changed: 43 additions & 40 deletions

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‎src/main/java/sc/fiji/ome/zarr/open/ZarrOpenActions.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@
5656

5757
import ij.IJ;
5858
import sc.fiji.ome.zarr.pyramid.Pyramidal5DImageDataImpl;
59-
import sc.fiji.ome.zarr.pyramid.PyramidalBdvDataset;
59+
import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
6060
import sc.fiji.ome.zarr.pyramid.exceptions.MultiImageDatasetException;
6161
import sc.fiji.ome.zarr.pyramid.exceptions.NoMatchingResolutionException;
6262
import sc.fiji.ome.zarr.pyramid.exceptions.NonExistingResolutionLevelException;
@@ -228,7 +228,7 @@ public Object openBDVWithImage()
228228
{
229229
return openPyramidImage(
230230
() -> {
231-
final PyramidalBdvDataset< ? > dataset = new PyramidalBdvDataset<>( getPyramid() );
231+
final PyramidalBdv< ? > dataset = new PyramidalBdv<>( getPyramid() );
232232
final PyramidalService pyramidalService = context.getService( PyramidalService.class );
233233
final Object result = BdvUtils.showBdvAndRegisterDataset( dataset, pyramidalService );
234234
logger.info( "Opened dataset in BigDataViewer: {}", inputUri );

‎src/main/java/sc/fiji/ome/zarr/plugins/OpenInBDVCommand.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -39,7 +39,7 @@
3939
import org.slf4j.LoggerFactory;
4040

4141
import sc.fiji.ome.zarr.pyramid.Pyramidal;
42-
import sc.fiji.ome.zarr.pyramid.PyramidalBdvDataset;
42+
import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
4343
import sc.fiji.ome.zarr.util.PyramidalService;
4444
import sc.fiji.ome.zarr.util.BdvUtils;
4545

@@ -66,7 +66,7 @@ public void run()
6666
uiService.showDialog( "The active image is not an OME-Zarr dataset.", "Open in BigDataViewer" );
6767
return;
6868
}
69-
final PyramidalBdvDataset< ? > bdvDataset = new PyramidalBdvDataset<>( pyramidal.getPyramidal5DImageData() );
69+
final PyramidalBdv< ? > bdvDataset = new PyramidalBdv<>( pyramidal.getPyramidal5DImageData() );
7070
BdvUtils.showBdvAndRegisterDataset( bdvDataset, pyramidalService );
7171
}
7272
}

src/main/java/sc/fiji/ome/zarr/pyramid/PyramidalBdvDataset.java renamed to src/main/java/sc/fiji/ome/zarr/pyramid/PyramidalBdv.java

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -26,7 +26,7 @@
2626
import sc.fiji.ome.zarr.pyramid.backend.PyramidContents;
2727
import sc.fiji.ome.zarr.pyramid.metadata.Omero;
2828

29-
public class PyramidalBdvDataset< T extends NativeType< T > & RealType< T > > extends AbstractContextual implements Pyramidal
29+
public class PyramidalBdv< T extends NativeType< T > & RealType< T > > extends AbstractContextual implements Pyramidal
3030
{
3131

3232
private static final Logger logger = LoggerFactory.getLogger( MethodHandles.lookup().lookupClass() );
@@ -35,7 +35,7 @@ public class PyramidalBdvDataset< T extends NativeType< T > & RealType< T > > ex
3535

3636
private final List< SourceAndConverter< T > > sources;
3737

38-
public PyramidalBdvDataset( final Pyramidal5DImageData< T > data )
38+
public PyramidalBdv( final Pyramidal5DImageData< T > data )
3939
{
4040
this.data = data;
4141
sources = initSourceAndConverters( data.getPyramidContents() );

‎src/main/java/sc/fiji/ome/zarr/util/BdvUtils.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@
4848
import bdv.util.BdvHandle;
4949
import bdv.util.BdvOptions;
5050
import bdv.viewer.SourceAndConverter;
51-
import sc.fiji.ome.zarr.pyramid.PyramidalBdvDataset;
51+
import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
5252
import sc.fiji.ome.zarr.pyramid.metadata.Omero;
5353

5454
public class BdvUtils
@@ -69,7 +69,7 @@ private BdvUtils()
6969
* contains multi-resolution image data along with associated metadata.
7070
* @return a {@code BdvHandle} instance representing the BDV window.
7171
*/
72-
public static BdvHandle showBdvAndRegisterDataset( final PyramidalBdvDataset< ? > pyramidalDataset )
72+
public static BdvHandle showBdvAndRegisterDataset( final PyramidalBdv< ? > pyramidalDataset )
7373
{
7474
return showBdvAndRegisterDataset( pyramidalDataset, null );
7575
}
@@ -86,7 +86,7 @@ public static BdvHandle showBdvAndRegisterDataset( final PyramidalBdvDataset< ?
8686
* @return a {@code BdvHandle} instance representing the BDV window
8787
*/
8888
public static < T extends NativeType< T > & RealType< T > > BdvHandle showBdvAndRegisterDataset(
89-
final PyramidalBdvDataset< ? > pyramidalDataset,
89+
final PyramidalBdv< ? > pyramidalDataset,
9090
final PyramidalService pyramidalService
9191
)
9292
{
@@ -114,7 +114,7 @@ public static < T extends NativeType< T > & RealType< T > > BdvHandle showBdvAnd
114114
* Focus switches themselves are observed centrally by {@link PyramidalService} via the AWT
115115
* {@link java.awt.KeyboardFocusManager}, so no per-window focus listener is needed here.
116116
*/
117-
private static void registerDatasetLifecycle( final PyramidalBdvDataset< ? > pyramidalDataset, final Window window,
117+
private static void registerDatasetLifecycle( final PyramidalBdv< ? > pyramidalDataset, final Window window,
118118
final PyramidalService pyramidalService
119119
)
120120
{
@@ -133,7 +133,7 @@ public void windowClosed( final WindowEvent e )
133133
} );
134134
}
135135

136-
private static void setChannelProperties( final PyramidalBdvDataset< ? > pyramidalDataset, final BdvHandle bdvHandle )
136+
private static void setChannelProperties( final PyramidalBdv< ? > pyramidalDataset, final BdvHandle bdvHandle )
137137
{
138138
Omero omero = pyramidalDataset.getOmeroProperties();
139139
if ( omero == null || omero.channels == null || omero.channels.isEmpty() )

‎src/test/java/sc/fiji/ome/zarr/open/ZarrOpenActionsTest.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -93,7 +93,7 @@
9393
import sc.fiji.ome.zarr.plugins.settings.UserScriptSettings;
9494
import sc.fiji.ome.zarr.pyramid.Pyramidal;
9595
import sc.fiji.ome.zarr.pyramid.Pyramidal5DImageData;
96-
import sc.fiji.ome.zarr.pyramid.PyramidalBdvDataset;
96+
import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
9797
import sc.fiji.ome.zarr.pyramid.PyramidalDataset;
9898
import sc.fiji.ome.zarr.open.options.ZarrOpeningSettings;
9999
import sc.fiji.ome.zarr.open.options.ZarrOpenBehavior;
@@ -750,7 +750,7 @@ void openEachResolutionLevelInIJThenBDVTwice()
750750
PyramidalDataset ijLevel0 = Cast.unchecked( pyramidalService.getPyramidals().get( 0 ) );
751751
PyramidalDataset ijLevel1 = Cast.unchecked( pyramidalService.getPyramidals().get( 1 ) );
752752

753-
PyramidalBdvDataset< ? > bdv1 = Cast.unchecked( pyramidalService.getPyramidals().get( 2 ) );
753+
PyramidalBdv< ? > bdv1 = Cast.unchecked( pyramidalService.getPyramidals().get( 2 ) );
754754

755755
// All 4 datasets (2 IJ + 2 BDV) must be backed by the exact same Pyramidal5DImageData object
756756
Pyramidal5DImageData< ? > sharedPyramid = ijLevel0.getPyramidal5DImageData();
@@ -824,7 +824,7 @@ void openInBDVThenOpenSpecificResolutionInIJ()
824824
assertEquals( 2, pyramidalService.getPyramidals().size() );
825825
assertEquals( 1, datasetService.getDatasets().size() );
826826

827-
PyramidalBdvDataset< ? > bdvDataset = Cast.unchecked( pyramidalService.getPyramidals().get( 0 ) );
827+
PyramidalBdv< ? > bdvDataset = Cast.unchecked( pyramidalService.getPyramidals().get( 0 ) );
828828
PyramidalDataset ijDataset = Cast.unchecked( pyramidalService.getPyramidals().get( 1 ) );
829829
assertSame( bdvDataset.getPyramidal5DImageData(), ijDataset.getPyramidal5DImageData(),
830830
"BDV and IJ datasets must share the same Pyramidal5DImageData instance" );
@@ -875,7 +875,7 @@ void sharedCachedCellImgAcrossDatasetsAtSameResolutionLevel()
875875
PyramidalService pyramidalService = context.getService( PyramidalService.class );
876876
PyramidalDataset ijLevel0First = Cast.unchecked( pyramidalService.getPyramidals().get( 0 ) );
877877
PyramidalDataset ijLevel0Second = Cast.unchecked( pyramidalService.getPyramidals().get( 1 ) );
878-
PyramidalBdvDataset< ? > bdv = Cast.unchecked( pyramidalService.getPyramidals().get( 2 ) );
878+
PyramidalBdv< ? > bdv = Cast.unchecked( pyramidalService.getPyramidals().get( 2 ) );
879879
PyramidalDataset ijLevel1 = Cast.unchecked( pyramidalService.getPyramidals().get( 3 ) );
880880

881881
Img< ? > cellImgIj0First = ijLevel0First.getImgPlus().getImg();

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -65,7 +65,8 @@ class Pyramidal5DImageDataOpenTest
6565
{
6666
private static final String TEST_RESOURCE = "sc/fiji/ome/zarr/util/5d_testing/5d_dataset_v5.ome.zarr";
6767

68-
private static final String SINGLE_LEVEL_RESOURCE = "sc/fiji/ome/zarr/util/single_resolution_testing/single_resolution_dataset_v5.ome.zarr";
68+
private static final String SINGLE_LEVEL_RESOURCE =
69+
"sc/fiji/ome/zarr/util/single_resolution_testing/single_resolution_dataset_v5.ome.zarr";
6970

7071
@Test
7172
void testOpenWithN5ReturnsWorkingDataset() throws URISyntaxException
@@ -228,7 +229,7 @@ private static void persistBackendChoice( final Context context, final ZarrReade
228229
private static void assertWorkingDataset( final Pyramidal5DImageData< ? > data )
229230
{
230231
assertNotNull( data );
231-
assertNotNull( new PyramidalBdvDataset<>( data ).asSources() );
232+
assertNotNull( new PyramidalBdv<>( data ).asSources() );
232233
final PyramidalDataset dataset = new PyramidalDataset( data );
233234
assertNotNull( dataset.getImgPlus() );
234235
assertEquals( 64, dataset.getImgPlus().dimension( 0 ) );

‎src/test/java/sc/fiji/ome/zarr/pyramid/Pyramidal5DImageDataTestBase.java‎

Lines changed: 20 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -148,9 +148,9 @@ default void testAsSources( String resource ) throws URISyntaxException
148148
try (Context context = new Context())
149149
{
150150
Pyramidal5DImageData< ? > pyramidal5DImageData = load( resource, context );
151-
PyramidalBdvDataset< ? > pyramidalBdvDataset = new PyramidalBdvDataset<>( pyramidal5DImageData );
152-
assertNotNull( pyramidalBdvDataset.asSources() );
153-
Source< ? > channel0 = pyramidalBdvDataset.asSources().get( 0 ).getSpimSource();
151+
PyramidalBdv< ? > pyramidalBdv = new PyramidalBdv<>( pyramidal5DImageData );
152+
assertNotNull( pyramidalBdv.asSources() );
153+
Source< ? > channel0 = pyramidalBdv.asSources().get( 0 ).getSpimSource();
154154
VoxelDimensions voxelDimensions = channel0.getVoxelDimensions();
155155
assertEquals( 2, channel0.getNumMipmapLevels() ); // 2 resolution levels
156156
assertInstanceOf( UnsignedByteType.class, channel0.getType() );
@@ -163,9 +163,9 @@ default void testAsSources( String resource ) throws URISyntaxException
163163
assertNotNull( channel0.getSource( 1, 1 ) ); // timepoint 1, resolution level 1
164164
long[] dimensions = channel0.getSource( 0, 0 ).dimensionsAsLongArray();
165165
assertArrayEquals( new long[] { 64, 64, 16 }, dimensions );
166-
assertEquals( 3, pyramidalBdvDataset.asSources().size() ); // 3 channels
167-
assertEquals( "lynEGFP", pyramidalBdvDataset.asSources().get( 0 ).getSpimSource().getName() );
168-
assertEquals( "NLStdTomato", pyramidalBdvDataset.asSources().get( 1 ).getSpimSource().getName() );
166+
assertEquals( 3, pyramidalBdv.asSources().size() ); // 3 channels
167+
assertEquals( "lynEGFP", pyramidalBdv.asSources().get( 0 ).getSpimSource().getName() );
168+
assertEquals( "NLStdTomato", pyramidalBdv.asSources().get( 1 ).getSpimSource().getName() );
169169
assertEquals( 1, pyramidal5DImageData.getOmeroProperties().rdefs.defaultT );
170170
}
171171
if ( resource.contains( "4d_testing" ) )
@@ -185,9 +185,9 @@ default void testAsSources( String resource ) throws URISyntaxException
185185
if ( resource.contains( "xyzc" ) || resource.contains( "xyzt" ) )
186186
assertArrayEquals( new long[] { 64, 64, 16 }, dimensions );
187187
if ( resource.contains( "xyct" ) || resource.contains( "xyzc" ) )
188-
assertEquals( 3, pyramidalBdvDataset.asSources().size() ); // 3 channels
188+
assertEquals( 3, pyramidalBdv.asSources().size() ); // 3 channels
189189
if ( resource.contains( "xyzt" ) )
190-
assertEquals( 1, pyramidalBdvDataset.asSources().size() ); // 1 channel
190+
assertEquals( 1, pyramidalBdv.asSources().size() ); // 1 channel
191191
}
192192
if ( resource.contains( "3d_testing" ) )
193193
{
@@ -206,18 +206,18 @@ default void testAsSources( String resource ) throws URISyntaxException
206206
if ( resource.contains( "xyz" ) )
207207
assertArrayEquals( new long[] { 64, 64, 16 }, dimensions );
208208
if ( resource.contains( "xyc" ) )
209-
assertEquals( 3, pyramidalBdvDataset.asSources().size() ); // 3 channels
209+
assertEquals( 3, pyramidalBdv.asSources().size() ); // 3 channels
210210
if ( resource.contains( "xyt" ) || resource.contains( "xyz" ) )
211-
assertEquals( 1, pyramidalBdvDataset.asSources().size() ); // 1 channel
211+
assertEquals( 1, pyramidalBdv.asSources().size() ); // 1 channel
212212
}
213213
if ( resource.contains( "2d_testing" ) )
214214
{
215-
assertEquals( 1, pyramidalBdvDataset.asSources().size() ); // 1 channel
215+
assertEquals( 1, pyramidalBdv.asSources().size() ); // 1 channel
216216

217217
long[] dimensions = channel0.getSource( 0, 0 ).dimensionsAsLongArray();
218218
assertArrayEquals( new long[] { 64, 64, 1 }, dimensions );
219-
assertEquals( 1, pyramidalBdvDataset.asSources().size() ); // 1 channel
220-
assertEquals( ZarrTestUtils.IMAGE_NAME, pyramidalBdvDataset.asSources().get( 0 ).getSpimSource().getName() );
219+
assertEquals( 1, pyramidalBdv.asSources().size() ); // 1 channel
220+
assertEquals( ZarrTestUtils.IMAGE_NAME, pyramidalBdv.asSources().get( 0 ).getSpimSource().getName() );
221221
}
222222
}
223223
}
@@ -306,8 +306,8 @@ default void testNumResolutionLevels( String resource ) throws URISyntaxExceptio
306306
{
307307
Pyramidal5DImageData< ? > pyramidal5DImageData = load( resource, context );
308308
assertEquals( 2, pyramidal5DImageData.numResolutionLevels() );
309-
PyramidalBdvDataset< ? > pyramidalBdvDataset = new PyramidalBdvDataset<>( pyramidal5DImageData );
310-
assertEquals( 2, pyramidalBdvDataset.asSources().get( 0 ).getSpimSource().getNumMipmapLevels() );
309+
PyramidalBdv< ? > pyramidalBdv = new PyramidalBdv<>( pyramidal5DImageData );
310+
assertEquals( 2, pyramidalBdv.asSources().get( 0 ).getSpimSource().getNumMipmapLevels() );
311311
}
312312
}
313313

@@ -391,8 +391,8 @@ default void testGetPyramidLevels( String resource ) throws URISyntaxException
391391
try (Context context = new Context())
392392
{
393393
Pyramidal5DImageData< ? > pyramidal5DImageData = load( resource, context );
394-
PyramidalBdvDataset< ? > pyramidalBdvDataset = new PyramidalBdvDataset<>( pyramidal5DImageData );
395-
Source< ? > spimSource = pyramidalBdvDataset.asSources().get( 0 ).getSpimSource();
394+
PyramidalBdv< ? > pyramidalBdv = new PyramidalBdv<>( pyramidal5DImageData );
395+
Source< ? > spimSource = pyramidalBdv.asSources().get( 0 ).getSpimSource();
396396

397397
RandomAccessibleInterval< ? > resolutionLevel0 = spimSource.getSource( 0, 0 );
398398
RandomAccess< ? > randomAccessLevel0 = resolutionLevel0.randomAccess();
@@ -464,10 +464,10 @@ default void testConverterSetup( final String resource ) throws URISyntaxExcepti
464464
try (Context context = new Context())
465465
{
466466
Pyramidal5DImageData< ? > pyramidal5DImageData = load( resource, context );
467-
PyramidalBdvDataset< ? > pyramidalBdvDataset = new PyramidalBdvDataset<>( pyramidal5DImageData );
468-
BdvHandle bdvHandle = BdvUtils.showBdvAndRegisterDataset( pyramidalBdvDataset );
467+
PyramidalBdv< ? > pyramidalBdv = new PyramidalBdv<>( pyramidal5DImageData );
468+
BdvHandle bdvHandle = BdvUtils.showBdvAndRegisterDataset( pyramidalBdv );
469469
List< ConverterSetup > converterSetups =
470-
bdvHandle.getConverterSetups().getConverterSetups( pyramidalBdvDataset.asSources() );
470+
bdvHandle.getConverterSetups().getConverterSetups( pyramidalBdv.asSources() );
471471
assertNotNull( converterSetups );
472472
if ( resource.contains( "2d_testing" ) ) // dataset without omero properties
473473
{

‎src/test/java/sc/fiji/ome/zarr/pyramid/backend/BackendBenchmark.java‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -51,7 +51,7 @@
5151
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.OmeNgffMetadata;
5252

5353
import sc.fiji.ome.zarr.pyramid.Pyramidal5DImageDataImpl;
54-
import sc.fiji.ome.zarr.pyramid.PyramidalBdvDataset;
54+
import sc.fiji.ome.zarr.pyramid.PyramidalBdv;
5555
import sc.fiji.ome.zarr.pyramid.backend.zarrjava.ZarrJavaPyramidBackend;
5656
import sc.fiji.ome.zarr.util.ZarrTestUtils;
5757

@@ -213,13 +213,15 @@ private static OpenedReadContexts openReadContexts( final String dataset ) throw
213213
{
214214
final Context n5Context = new Context();
215215
final Pyramidal5DImageDataImpl< ?, ? > n5Wrapped = new Pyramidal5DImageDataImpl<>( n5Context, Paths.get( dataset ).toUri() );
216-
final RandomAccessibleInterval< ? > n5WrappedLevel0 = new PyramidalBdvDataset<>( n5Wrapped ).asSources().get( 0 ).getSpimSource().getSource( 0, 0 );
216+
final RandomAccessibleInterval< ? > n5WrappedLevel0 =
217+
new PyramidalBdv<>( n5Wrapped ).asSources().get( 0 ).getSpimSource().getSource( 0, 0 );
217218

218219
final Context zjContext = new Context();
219220
@SuppressWarnings( { "rawtypes", "unchecked" } )
220221
final Pyramidal5DImageDataImpl< ?, ? > zjWrapped =
221222
new Pyramidal5DImageDataImpl( zjContext, new ZarrJavaPyramidBackend( Paths.get( dataset ).toUri() ) );
222-
final RandomAccessibleInterval< ? > zjWrappedLevel0 = new PyramidalBdvDataset<>(zjWrapped ).asSources().get( 0 ).getSpimSource().getSource( 0, 0 );
223+
final RandomAccessibleInterval< ? > zjWrappedLevel0 =
224+
new PyramidalBdv<>( zjWrapped ).asSources().get( 0 ).getSpimSource().getSource( 0, 0 );
223225

224226
final N5OpenContext n5Pure = openN5Context( Paths.get( dataset ) );
225227
final String level0Path = resolveN5Level0Path( n5Pure );

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