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Merged
sbesson merged 1 commit into from
Jun 30, 2026
Merged

Upgrade to zarr-java 0.1.3 #327

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -180,7 +180,7 @@ Supported options for `blosc` are:
* `clevel=<level>`, 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=<blocksize>`, where the default is `blocksize=0`.
* `shuffle=<shuffle type>`, where the default is `shuffle=byteshuffle`. Valid values are `noshuffle`, `shuffle`/`byteshuffle`, and `bitshuffle`.
* `shuffle=<shuffle type>`, 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).

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2 changes: 1 addition & 1 deletion build.gradle
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Expand Up @@ -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'
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4 changes: 2 additions & 2 deletions src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Expand Up @@ -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);
}
Expand Down Expand Up @@ -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);
}
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