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cgoinacgoina
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getting the package to compile
1 parent 272fb08 commit 7daab28

8 files changed

Lines changed: 83 additions & 52 deletions

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‎pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -103,7 +103,7 @@
103103
<bigdataviewer-n5.version>1.0.2</bigdataviewer-n5.version>
104104

105105
<spim_data.version>2.3.5</spim_data.version>
106-
<multiview-reconstruction.version>8.0.1-SNAPSHOT</multiview-reconstruction.version>
106+
<multiview-reconstruction.version>8.1.2-SNAPSHOT</multiview-reconstruction.version>
107107
<BigStitcher.version>2.5.0</BigStitcher.version>
108108

109109
<n5-universe.version>2.3.0</n5-universe.version>

‎src/main/java/net/preibisch/bigstitcher/spark/Compressions.java‎

Lines changed: 5 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,5 @@
1+
package net.preibisch.bigstitcher.spark;
2+
3+
public enum Compressions {
4+
Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw
5+
}

‎src/main/java/net/preibisch/bigstitcher/spark/CreateFusionContainer.java‎

Lines changed: 48 additions & 27 deletions
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,18 @@
77
import java.util.Arrays;
88
import java.util.Collection;
99
import java.util.HashMap;
10+
import java.util.HashSet;
1011
import java.util.List;
1112
import java.util.Map;
13+
import java.util.Set;
1214
import java.util.concurrent.Callable;
1315
import java.util.function.Function;
1416

17+
import mpicbg.spim.data.generic.base.Entity;
18+
import mpicbg.spim.data.registration.ViewRegistrations;
19+
import net.imglib2.util.Pair;
20+
import net.imglib2.util.ValuePair;
21+
import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
1522
import org.janelia.saalfeldlab.n5.Compression;
1623
import org.janelia.saalfeldlab.n5.DataType;
1724
import org.janelia.saalfeldlab.n5.N5Writer;
@@ -59,8 +66,6 @@ public class CreateFusionContainer extends AbstractBasic implements Callable<Voi
5966
{
6067
private static final long serialVersionUID = -9140450542904228386L;
6168

62-
public enum Compressions { Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw };
63-
6469
@Option(names = { "-o", "--outputPath" }, required = true, description = "OME-ZARR/N5/HDF5 path for saving, e.g. -o /home/fused.zarr, file:/home/fused.n5 or e.g. s3://myBucket/data.zarr")
6570
private String outputPathURIString = null;
6671

@@ -70,7 +75,7 @@ public enum Compressions { Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw };
7075

7176
@Option(names = {"-c", "--compression"}, defaultValue = "Zstandard", showDefaultValue = CommandLine.Help.Visibility.ALWAYS,
7277
description = "Dataset compression")
73-
private Compressions compression = null;
78+
private Compressions compressionType = null;
7479

7580
@Option(names = {"-cl", "--compressionLevel" }, description = "compression level, if supported by the codec (default: gzip 1, Zstandard 3, xz 6)")
7681
private Integer compressionLevel = null;
@@ -116,7 +121,10 @@ public enum Compressions { Lz4, Gzip, Zstandard, Blosc, Bzip2, Xz, Raw };
116121
@Option(names = { "--anisotropyFactor" }, description = "define the anisotropy factor if preserveAnisotropy is set to true (default: compute from data)")
117122
private double anisotropyFactor = Double.NaN;
118123

119-
URI outPathURI = null, xmlOutURI = null;
124+
private URI outPathURI = null, xmlOutURI = null;
125+
private double[] cal = new double[] { 1, 1, 1 };
126+
private String calUnit = "micrometer";
127+
private double avgAnisotropy = Double.NaN;
120128

121129
@Override
122130
public Void call() throws Exception
@@ -215,9 +223,9 @@ else if ( numTimepoints > numTimepointsXML )
215223
System.out.println( "Fusion target: " + boundingBox.getTitle() + ": " + Util.printInterval( boundingBox ) + " with blocksize " + Util.printCoordinates( blockSize ) );
216224

217225
// compression and data type
218-
final Compression compression = N5Util.getCompression( this.compression, this.compressionLevel );
226+
final Compression compression = N5Util.getCompression( this.compressionType, this.compressionLevel );
219227

220-
System.out.println( "Compression: " + this.compression );
228+
System.out.println( "Compression: " + this.compressionType );
221229
System.out.println( "Compression level: " + ( compressionLevel == null ? "default" : compressionLevel ) );
222230

223231
final DataType dt;
@@ -362,29 +370,23 @@ else if ( storageType == StorageFormat.N5 || storageType == StorageFormat.ZARR )
362370
final Function<Integer, AffineTransform3D> levelToMipmapTransform =
363371
(level) -> MipmapTransforms.getMipmapTransformDefault( mrInfo[level].absoluteDownsamplingDouble() );
364372

373+
updateAnisotropyAndCalibration(dataGlobal, viewIdsGlobal);
365374
// extract the resolution of the s0 export
366-
// TODO: this is inaccurate, we should actually estimate it from the final transformn that is applied
367-
// TODO: this is a hack (returns 1,1,1) so the export downsampling pyramid is working
368-
final VoxelDimensions vx = dataGlobal.getSequenceDescription().getViewSetupsOrdered().iterator().next().getVoxelSize();
369-
final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx );
375+
final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( cal, avgAnisotropy, Double.NaN );
370376

371-
System.out.println( "Resolution of level 0: " + Util.printCoordinates( resolutionS0 ) + " " + "micrometer" ); //vx.unit() might not be OME-ZARR compatiblevx.unit() );
377+
System.out.println( "Resolution of level 0: " + Util.printCoordinates( resolutionS0 ) + " " + calUnit );
372378

373379
// create metadata
374380
final OmeNgffMultiScaleMetadata[] meta = OMEZarrAttibutes.createOMEZarrMetadata(
375381
5, // int n
376382
"/", // String name, I also saw "/"
377383
resolutionS0, // double[] resolutionS0,
378-
"micrometer", //vx.unit() might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
384+
calUnit, //vx.unit() might not be OME-ZARR compatible // String unitXYZ, // e.g micrometer
379385
mrInfos[ 0 ].length, // int numResolutionLevels,
380386
levelToName,
381387
levelToMipmapTransform );
382388

383389
// save metadata
384-
385-
//org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadata
386-
// for this to work you need to register an adapter in the N5Factory class
387-
// final GsonBuilder builder = new GsonBuilder().registerTypeAdapter( CoordinateTransformation.class, new CoordinateTransformationAdapter() );
388390
driverVolumeWriter.setAttribute( "/", "multiscales", meta );
389391
}
390392

@@ -410,12 +412,12 @@ else if ( storageType == StorageFormat.ZARR )
410412
tps.add( new TimePoint( t ) );
411413

412414
// extract the resolution of the s0 export
413-
final VoxelDimensions vx = dataGlobal.getSequenceDescription().getViewSetupsOrdered().iterator().next().getVoxelSize();
414-
final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( vx );
415+
416+
final double[] resolutionS0 = OMEZarrAttibutes.getResolutionS0( cal, avgAnisotropy, Double.NaN );
415417

416418
System.out.println( "Resolution of level 0: " + Util.printCoordinates( resolutionS0 ) + " " + "m" ); //vx.unit() might not be OME-ZARR compatiblevx.unit() );
417419

418-
final VoxelDimensions vxNew = new FinalVoxelDimensions( "micrometer", resolutionS0 );
420+
final VoxelDimensions vxNew = new FinalVoxelDimensions( calUnit, resolutionS0 );
419421

420422
for ( int c = 0; c < numChannels; ++c )
421423
{
@@ -441,7 +443,7 @@ else if ( storageType == StorageFormat.ZARR )
441443
for ( int t = 0; t < numTimepoints; ++t )
442444
{
443445
final OMEZARREntry omeZarrEntry = new OMEZARREntry(
444-
mrInfos[ 0 ][ 0 ].dataset.substring(0, mrInfos[ 0 ][ 0 ].dataset.lastIndexOf( "/" ) ),
446+
mrInfos[ t ][ c ].dataset.substring(0, mrInfos[ t ][ c ].dataset.lastIndexOf( "/" ) ),
445447
new int[] { c, t } );
446448

447449
viewIdToPath.put( new ViewId( t, c ), omeZarrEntry );
@@ -521,16 +523,35 @@ else if ( storageType == StorageFormat.N5 || storageType == StorageFormat.HDF5 )
521523
return null;
522524
}
523525

524-
public static void main(final String... args) throws SpimDataException
526+
private void updateAnisotropyAndCalibration( SpimData2 dataGlobal, List<ViewId> viewIdsGlobal )
525527
{
528+
ViewRegistrations registrations = dataGlobal.getViewRegistrations();
529+
// get all view descriptions
530+
List<ViewDescription> vds = SpimData2.getAllViewDescriptionsSorted(dataGlobal, viewIdsGlobal);
531+
// group by timepoint and channel
532+
Set<Class<? extends Entity>> groupingFactors = new HashSet<>(Arrays.asList(TimePoint.class, Channel.class));
533+
List<Group<ViewDescription>> fusionGroups = Group.splitBy( vds, groupingFactors );
534+
Pair<double[], String> calAndUnit = fusionGroups.stream().findFirst()
535+
.map(group -> TransformationTools.computeAverageCalibration(group, registrations))
536+
.orElse(new ValuePair<>(new double[]{ 1, 1, 1 }, "micrometer"));
537+
cal = calAndUnit.getA();
538+
calUnit = calAndUnit.getB();
539+
540+
if (preserveAnisotropy) {
541+
if (!Double.isNaN(this.anisotropyFactor)) {
542+
avgAnisotropy = this.anisotropyFactor;
543+
} else {
544+
avgAnisotropy = TransformationTools.getAverageAnisotropyFactor(dataGlobal, viewIdsGlobal);
545+
}
546+
} else {
547+
avgAnisotropy = Double.NaN;
548+
}
549+
}
526550

527-
//final XmlIoSpimData io = new XmlIoSpimData();
528-
//final SpimData spimData = io.load( "/Users/preibischs/Documents/Microscopy/Stitching/Truman/standard/output/dataset.xml" );
529-
//BdvFunctions.show( spimData );
530-
//SimpleMultiThreading.threadHaltUnClean();
531-
551+
public static void main(final String... args) throws SpimDataException
552+
{
532553
System.out.println(Arrays.toString(args));
533554

534555
System.exit(new CommandLine(new CreateFusionContainer()).execute(args));
535556
}
536-
}
557+
}

‎src/main/java/net/preibisch/bigstitcher/spark/Solver.java‎

Lines changed: 12 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -289,7 +289,7 @@ public Void call() throws Exception
289289
return null;
290290
}
291291

292-
final GlobalOptimizationParameters globalOptParameters = new GlobalOptimizationParameters(relativeThreshold, absoluteThreshold, globalOptType, false );
292+
final GlobalOptimizationParameters globalOptParameters = new GlobalOptimizationParameters(relativeThreshold, absoluteThreshold, globalOptType, false, false );
293293
final Collection< Pair< Group< ViewId >, Group< ViewId > > > removedInconsistentPairs = new ArrayList<>();
294294
final HashMap<ViewId, Tile > models;
295295
final Model<?> model = createModelInstance(transformationModel, regularizationModel, regularizationLambda);
@@ -299,7 +299,8 @@ public Void call() throws Exception
299299
final ConvergenceStrategy cs = new ConvergenceStrategy( maxError, maxIterations, maxPlateauwidth );
300300

301301
models = (HashMap)GlobalOpt.computeTiles(
302-
(Model)(Object)model,
302+
(Model)model,
303+
globalOptParameters.preAlign,
303304
pmc,
304305
cs,
305306
fixedViewIds,
@@ -308,7 +309,8 @@ public Void call() throws Exception
308309
else if ( globalOptParameters.method == GlobalOptType.ONE_ROUND_ITERATIVE )
309310
{
310311
models = (HashMap)GlobalOptIterative.computeTiles(
311-
(Model)(Object)model,
312+
(Model)model,
313+
globalOptParameters.preAlign,
312314
pmc,
313315
new SimpleIterativeConvergenceStrategy( Double.MAX_VALUE, maxIterations, maxPlateauwidth, globalOptParameters.relativeThreshold, globalOptParameters.absoluteThreshold ),
314316
new MaxErrorLinkRemoval(),
@@ -322,7 +324,8 @@ else if ( globalOptParameters.method == GlobalOptType.ONE_ROUND_ITERATIVE )
322324
globalOptParameters.relativeThreshold = globalOptParameters.absoluteThreshold = Double.MAX_VALUE;
323325

324326
models = (HashMap)GlobalOptTwoRound.computeTiles(
325-
(Model & Affine3D)(Object)model,
327+
(Model & Affine3D)model,
328+
globalOptParameters.preAlign,
326329
pmc,
327330
new SimpleIterativeConvergenceStrategy( Double.MAX_VALUE, maxIterations, maxPlateauwidth, globalOptParameters.relativeThreshold, globalOptParameters.absoluteThreshold ), // if it's simple, both will be Double.MAX
328331
new MaxErrorLinkRemoval(),
@@ -512,18 +515,18 @@ public static InterestPointMatchCreator setupPointMatchesFromInterestPoints(
512515
pairResult.setLabelA( labelA );
513516
pairResult.setLabelB( labelB );
514517

515-
final List<CorrespondingInterestPoints> cpA = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vA ).getInterestPointList( labelA ).getCorrespondingInterestPointsCopy();
518+
final Collection<CorrespondingInterestPoints> cpA = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vA ).getInterestPointList( labelA ).getCorrespondingInterestPointsCopy();
516519
//List<CorrespondingInterestPoints> cpB = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vB ).getInterestPointList( label ).getCorrespondingInterestPointsCopy();
517520

518-
final List<InterestPoint> ipListA = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vA ).getInterestPointList( labelA ).getInterestPointsCopy();
519-
final List<InterestPoint> ipListB = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vB ).getInterestPointList( labelB ).getInterestPointsCopy();
521+
final Map<Integer, InterestPoint> ipMapA = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vA ).getInterestPointList( labelA ).getInterestPointsCopy();
522+
final Map<Integer, InterestPoint> ipMapB = dataGlobal.getViewInterestPoints().getViewInterestPointLists( vB ).getInterestPointList( labelB ).getInterestPointsCopy();
520523

521524
for ( final CorrespondingInterestPoints p : cpA )
522525
{
523526
if ( p.getCorrespodingLabel().equals( labelB ) && p.getCorrespondingViewId().equals( vB ) )
524527
{
525-
InterestPoint ipA = ipListA.get( p.getDetectionId() );
526-
InterestPoint ipB = ipListB.get( p.getCorrespondingDetectionId() );
528+
InterestPoint ipA = ipMapA.get( p.getDetectionId() );
529+
InterestPoint ipB = ipMapB.get( p.getCorrespondingDetectionId() );
527530

528531
// we need to copy the array because it might not be bijective
529532
// (some points in one list might correspond with the same point in the other list)

‎src/main/java/net/preibisch/bigstitcher/spark/SparkGeometricDescriptorMatching.java‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
2424
import java.net.URI;
2525
import java.util.ArrayList;
2626
import java.util.Arrays;
27+
import java.util.Collection;
2728
import java.util.HashMap;
2829
import java.util.HashSet;
2930
import java.util.List;
@@ -283,7 +284,7 @@ else if ( ransacIterations == null )
283284
} );
284285

285286
// load & transform all interest points
286-
final Map< ViewId, HashMap< String, List< InterestPoint > > > interestpoints =
287+
final Map< ViewId, HashMap< String, Collection< InterestPoint > > > interestpoints =
287288
TransformationTools.getAllTransformedInterestPoints(
288289
views,
289290
data.getViewRegistrations().getViewRegistrations(),
@@ -299,8 +300,8 @@ else if ( ransacIterations == null )
299300
interestpoints, groups, data.getViewRegistrations().getViewRegistrations(), data.getSequenceDescription().getViewDescriptions() );
300301

301302
System.out.println( Group.pvid( task.vA ) + " (" + task.labelA + ") <=> " + Group.pvid( task.vB ) + " (" + task.labelB + "): Remaining interest points for alignment: " );
302-
for ( final Entry< ViewId, HashMap< String, List< InterestPoint > > > element: interestpoints.entrySet() )
303-
for ( final Entry< String, List< InterestPoint > > subElement : element.getValue().entrySet() )
303+
for ( final Entry< ViewId, HashMap< String, Collection< InterestPoint > > > element: interestpoints.entrySet() )
304+
for ( final Entry< String, Collection< InterestPoint > > subElement : element.getValue().entrySet() )
304305
System.out.println( Group.pvid( element.getKey() ) + ", '" + subElement.getKey() + "' : " + subElement.getValue().size() );
305306
}
306307

@@ -390,7 +391,7 @@ else if ( ransacIterations == null )
390391
} );
391392

392393
// load & transform all interest points
393-
final Map< ViewId, HashMap< String, List< InterestPoint > > > interestpoints =
394+
final Map< ViewId, HashMap< String, Collection< InterestPoint >> > interestpoints =
394395
TransformationTools.getAllTransformedInterestPoints(
395396
views,
396397
data.getViewRegistrations().getViewRegistrations(),
@@ -410,12 +411,12 @@ else if ( ransacIterations == null )
410411
TransformationTools.filterForOverlappingInterestPoints( interestpoints, groups, data.getViewRegistrations().getViewRegistrations(), data.getSequenceDescription().getViewDescriptions() );
411412

412413
System.out.println( task.vA + " (" + task.labelA + ") <=> " + task.vB + " (" + task.labelB + "): Remaining interest points for alignment: " );
413-
for ( final Entry< ViewId, HashMap< String, List< InterestPoint > > > element: interestpoints.entrySet() )
414-
for ( final Entry< String, List< InterestPoint > > subElement : element.getValue().entrySet() )
414+
for ( final Entry< ViewId, HashMap< String, Collection< InterestPoint > > > element: interestpoints.entrySet() )
415+
for ( final Entry< String, Collection< InterestPoint > > subElement : element.getValue().entrySet() )
415416
System.out.println( Group.pvid( element.getKey() ) + ", '" + subElement.getKey() + "' : " + subElement.getValue().size() );
416417
}
417418

418-
final Map< Group< ViewId >, HashMap< String, List< GroupedInterestPoint< ViewId > > > > groupedInterestpoints = new HashMap<>();
419+
final Map< Group< ViewId >, HashMap< String, Collection< GroupedInterestPoint< ViewId > > > > groupedInterestpoints = new HashMap<>();
419420

420421
final InterestPointGroupingMinDistance< ViewId > ipGrouping
421422
= new InterestPointGroupingMinDistance<>( interestPointMergeDistance, interestpoints );

‎src/main/java/net/preibisch/bigstitcher/spark/SparkResaveN5.java‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -43,9 +43,9 @@
4343

4444
import bdv.img.n5.N5ImageLoader;
4545
import mpicbg.spim.data.sequence.ViewId;
46+
import mpicbg.spim.data.sequence.VoxelDimensions;
4647
import net.imglib2.util.Util;
4748
import net.imglib2.util.ValuePair;
48-
import net.preibisch.bigstitcher.spark.CreateFusionContainer.Compressions;
4949
import net.preibisch.bigstitcher.spark.abstractcmdline.AbstractBasic;
5050
import net.preibisch.bigstitcher.spark.util.Import;
5151
import net.preibisch.bigstitcher.spark.util.N5Util;
@@ -96,7 +96,7 @@ public class SparkResaveN5 extends AbstractBasic implements Callable<Void>, Seri
9696

9797
@Option(names = {"-c", "--compression"}, defaultValue = "Zstandard", showDefaultValue = CommandLine.Help.Visibility.ALWAYS,
9898
description = "Dataset compression")
99-
private Compressions compression = null;
99+
private Compressions compressionType = null;
100100

101101
@Option(names = {"-cl", "--compressionLevel" }, description = "compression level, if supported by the codec (default: gzip 1, Zstandard 3, xz 6)")
102102
private Integer compressionLevel = null;
@@ -164,7 +164,7 @@ public Void call() throws Exception
164164
}
165165

166166
final URI n5PathURI = URITools.toURI( this.n5PathURIString == null ? URITools.appendName( URITools.getParentURI( xmlOutURI ), (useN5 ? "dataset.n5" : "dataset.ome.zarr") ) : n5PathURIString );
167-
final Compression compression = N5Util.getCompression( this.compression, this.compressionLevel );
167+
final Compression compression = N5Util.getCompression( this.compressionType, this.compressionLevel );
168168

169169
final int[] blockSize = Import.csvStringToIntArray(blockSizeString);
170170
final int[] blockScale = Import.csvStringToIntArray(blockScaleString);
@@ -177,7 +177,7 @@ public Void call() throws Exception
177177
//final N5Writer n5 = new N5FSWriter(n5Path);
178178
final N5Writer n5Writer = URITools.instantiateN5Writer( useN5 ? StorageFormat.N5 : StorageFormat.ZARR, n5PathURI );
179179

180-
System.out.println( "Compression: " + this.compression );
180+
System.out.println( "Compression: " + this.compressionType );
181181
System.out.println( "Compression level: " + ( compressionLevel == null ? "default" : compressionLevel ) );
182182
System.out.println( "N5 block size=" + Util.printCoordinates( blockSize ) );
183183
System.out.println( "Compute block size=" + Util.printCoordinates( computeBlockSize ) );
@@ -242,13 +242,14 @@ public Void call() throws Exception
242242
else
243243
{
244244
System.out.println( Arrays.toString( blockSize ) );
245-
245+
VoxelDimensions vx = dataGlobal.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize();
246246
mrInfo = N5ApiTools.setupBdvDatasetsOMEZARR(
247247
n5Writer,
248248
viewId,
249249
dataTypes.get( viewId.getViewSetupId() ),
250250
dimensions.get( viewId.getViewSetupId() ),
251-
dataGlobal.getSequenceDescription().getViewDescription( viewId ).getViewSetup().getVoxelSize().dimensionsAsDoubleArray(),
251+
vx.dimensionsAsDoubleArray(),
252+
vx.unit(),
252253
compression,
253254
blockSize,
254255
downsamplings);

‎src/main/java/net/preibisch/bigstitcher/spark/SplitDatasets.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -41,7 +41,7 @@ public class SplitDatasets extends AbstractBasic
4141
private boolean disableOptimization = false;
4242

4343
@Option(names = { "-fip", "--fakeInterestPoints" }, description = "add fake interest points to overlapping regions of split images/views")
44-
private boolean fakeInterestPoints = false;
44+
private Split_Views.InterestPointAdding fakeInterestPoints = Split_Views.InterestPointAdding.NONE;
4545

4646
@Option(names = { "--fipDensity" }, description = "density of fake interest points; number of points per 100x100x100 px volume (default: 100.0)")
4747
private double fipDensity = 100.0;

‎src/main/java/net/preibisch/bigstitcher/spark/util/N5Util.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
import org.janelia.saalfeldlab.n5.universe.StorageFormat;
3737
import org.janelia.scicomp.n5.zstandard.ZstandardCompression;
3838

39-
import net.preibisch.bigstitcher.spark.CreateFusionContainer.Compressions;
39+
import net.preibisch.bigstitcher.spark.Compressions;
4040
import net.preibisch.legacy.io.IOFunctions;
4141
import util.URITools;
4242

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