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Merged
StephanPreibisch merged 25 commits into from
Aug 21, 2025
+8 −12
Merged

Upgrade n5 zarr #48

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ed958d6
docker recipe
cgoina Apr 8, 2025
509b68a
Merge branch 'main' of github.com:PreibischLab/BigStitcher-Spark
cgoina Apr 9, 2025
e2dea1a
Merge branch 'main' of github.com:PreibischLab/BigStitcher-Spark
cgoina Apr 10, 2025
526021d
a simple Dockerfile for testing uncommited BigStitcher code
cgoina Apr 10, 2025
90b9913
Merge branch 'main' of github.com:PreibischLab/BigStitcher-Spark
cgoina Apr 11, 2025
a1c6c47
Merge branch 'main' of github.com:PreibischLab/BigStitcher-Spark
cgoina Apr 11, 2025
555b6af
added hdf5 library
cgoina Apr 14, 2025
bc8575a
Merge branch 'main' of github.com:JaneliaSciComp/BigStitcher-Spark
cgoina Jun 4, 2025
46451ed
upgrade scijava and n5-zarr
cgoina Jul 8, 2025
639ecf3
option to create the container under a specific group
cgoina Jul 17, 2025
fe213cc
group option for affine fusion too
cgoina Jul 17, 2025
dcbf4e7
remove redundant static modifier for enum
cgoina Jul 17, 2025
a70db27
paths in OME attributes is not set correctly
cgoina Jul 18, 2025
33e69fe
in NGFF metadata the path is set relative to current group
cgoina Jul 18, 2025
01426d1
update Dockerfile
cgoina Jul 19, 2025
90f2c17
Merge branch 'main' of github.com:JaneliaSciComp/BigStitcher-Spark
cgoina Jul 19, 2025
c95e54b
merges from main
cgoina Jul 19, 2025
baa05f4
Merge branch 'main' of github.com:JaneliaSciComp/BigStitcher-Spark
cgoina Aug 18, 2025
b4420c2
Merge branch 'main' into upgrade-n5-zarr
cgoina Aug 18, 2025
cdec895
reverted the scijava upgrade
cgoina Aug 21, 2025
0a80152
Merge branch 'main' of github.com:JaneliaSciComp/BigStitcher-Spark
cgoina Aug 21, 2025
1dbba81
Merge branch 'main' into upgrade-n5-zarr
cgoina Aug 21, 2025
3b632e9
removed group arg
cgoina Aug 21, 2025
8f7d869
Dockerfile not wanted
cgoina Aug 21, 2025
82c2241
removed whitespace
cgoina Aug 21, 2025
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9 changes: 3 additions & 6 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -96,18 +96,16 @@
<bigdataviewer-core.version>10.6.1</bigdataviewer-core.version>
<bigdataviewer-vistools.version>1.0.0-beta-36</bigdataviewer-vistools.version>
-->
<!-- <n5-zarr.version>1.3.5</n5-zarr.version> -->

<imglib2.version>7.1.4</imglib2.version>
<imglib2-algorithm.version>0.18.0</imglib2-algorithm.version>
<bigdataviewer-core.version>10.6.4</bigdataviewer-core.version>
<spim_data.version>2.3.5</spim_data.version>
<multiview-reconstruction.version>7.0.2</multiview-reconstruction.version>
<BigStitcher.version>2.5.0</BigStitcher.version>

<n5-universe.version>2.1.0</n5-universe.version>
<n5-version>3.4.1</n5-version>
<n5-zarr-version>1.5.0</n5-zarr-version>
<n5-universe.version>2.3.0</n5-universe.version>
<n5.version>3.5.0</n5.version>
<n5-zarr.version>1.5.1</n5-zarr.version>

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@cgoina cgoina Jul 8, 2025

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the correct property is n5-zarr.version not n5-zarr-version

<mpicbg.mpicbg.version>1.6.5</mpicbg.mpicbg.version>

Expand Down Expand Up @@ -305,7 +303,6 @@
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
<artifactId>n5-hdf5</artifactId>
<!-- <version>2.0.0</version> -->
</dependency>
<dependency>
<groupId>org.janelia.saalfeldlab</groupId>
Expand Down
9 changes: 4 additions & 5 deletions src/main/java/net/preibisch/bigstitcher/spark/CreateFusionContainer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -297,7 +297,6 @@ else if ( storageType == StorageFormat.N5 || storageType == StorageFormat.ZARR )
{
System.out.println( "Unsupported format: " + storageType );
return null;

}

driverVolumeWriter.setAttribute( "/", "Bigstitcher-Spark/InputXML", xmlURI );
Expand Down Expand Up @@ -463,20 +462,20 @@ else if ( storageType == StorageFormat.ZARR )
if ( storageType != StorageFormat.ZARR )
{
final Collection<ViewDescription> vds = dataFusion.getSequenceDescription().getViewDescriptions().values();

mrInfos = new MultiResolutionLevelInfo[ vds.size() ][];
final MultiResolutionLevelInfo myMrInfo[][] = mrInfos;

vds.stream().parallel().forEach( vd ->
{
final int c = vd.getViewSetup().getChannel().getId();
final int t = vd.getTimePointId();

if ( storageType == StorageFormat.N5 )
{
myMrInfo[ c + t*c ] = N5ApiTools.setupBdvDatasetsN5(
driverVolumeWriter, vd, dt, bb, compression, blockSize, downsamplings);

driverVolumeWriter.setAttribute( "/", "Bigstitcher-Spark/FusionFormat", "BDV/N5" );
}
else // HDF5
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/net/preibisch/bigstitcher/spark/SparkAffineFusion.java
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Expand Up @@ -91,7 +91,7 @@

public class SparkAffineFusion extends AbstractInfrastructure implements Callable<Void>, Serializable
{
public static enum DataTypeFusion
public enum DataTypeFusion
{
UINT8, UINT16, FLOAT32
}
Expand Down