diff --git a/README.md b/README.md index 244ede1e..fc356309 100644 --- a/README.md +++ b/README.md @@ -180,7 +180,7 @@ Supported options for `blosc` are: * `clevel=`, where the default is `clevel=5`. Valid values are integers from 0 to 9 inclusive, where 0 generally indicates no compression and 9 generally indicates most compression. * `blocksize=`, where the default is `blocksize=0`. -* `shuffle=`, where the default is `shuffle=byteshuffle`. Valid values are `noshuffle`, `shuffle`/`byteshuffle`, and `bitshuffle`. +* `shuffle=`, where the default is `shuffle=shuffle`. Valid values are `noshuffle`, `shuffle`, and `bitshuffle`. See also the blosc codec definition in the [Zarr v3 specification](https://zarr-specs.readthedocs.io/en/latest/v3/codecs/blosc/index.html#configuration-parameters). diff --git a/build.gradle b/build.gradle index 935e3ed1..1add4db0 100644 --- a/build.gradle +++ b/build.gradle @@ -45,7 +45,7 @@ dependencies { implementation 'ome:formats-gpl:8.5.0' implementation 'info.picocli:picocli:4.7.5' implementation 'com.univocity:univocity-parsers:2.8.4' - implementation 'dev.zarr:zarr-java:0.1.0' + implementation 'dev.zarr:zarr-java:0.1.3' // implementation 'org.carlspring.cloud.aws:s3fs-nio:1.0-SNAPSHOT' // implementation 'io.nextflow:nxf-s3fs:1.1.0' implementation 'org.lasersonlab:s3fs:2.2.3' diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java index c31b7785..0f284f6c 100644 --- a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java +++ b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java @@ -2561,7 +2561,7 @@ public void saveResolutions(int series) int blocksize = Integer.parseInt( compressionProperties.getOrDefault("blocksize", "0").toString()); String shuffle = compressionProperties.getOrDefault( - "shuffle", "byteshuffle").toString(); + "shuffle", "shuffle").toString(); builder = builder.withBloscCompressor(cname, shuffle, clevel, blocksize); } @@ -3491,7 +3491,7 @@ private CodecBuilder applyCompressionType(CodecBuilder builder) { int blocksize = Integer.parseInt( compressionProperties.getOrDefault("blocksize", "0").toString()); String shuffle = compressionProperties.getOrDefault( - "shuffle", "byteshuffle").toString(); + "shuffle", "shuffle").toString(); return builder.withBlosc(cname, shuffle, clevel, blocksize); }