Recompress zarr array inplace using n5-zarr. Untested, use at own risk. Does not deal with non-existing blocks. Not multi-threaded. Run with kscript: https://github.com/kscripting/kscript

recompress.kts

@file:Repository("https://maven.scijava.org/content/groups/public")
@file:DependsOn("org.janelia.saalfeldlab:n5-zarr:0.0.8")

import kotlin.math.ceil

import org.janelia.saalfeldlab.n5.zarr.N5ZarrWriter
import org.janelia.saalfeldlab.n5.zarr.ZArrayAttributes
import org.janelia.saalfeldlab.n5.zarr.ZarrCompressor

require(args.size == 2) { "Two arguments required, zarr group and dataset"}
val zarr = N5ZarrWriter(args[0], ".", false)
val dataset = args[1]

require(zarr.datasetExists(dataset)) {"$dataset is not a dataset"}

val attributes = zarr.getZArraryAttributes(dataset)
// hard-coded compressor
val newCompressor = ZarrCompressor.Gzip(5)

val newAttributes = attributes.run {
    ZArrayAttributes(
        zarrFormat,
        shape,
        chunks,
        dType,
        newCompressor,
        fillValue,
        order,
        dimensionSeparator,
        filters // might need to be configured, too
    )
}
val dsAttributes = attributes.datasetAttributes
val newDsAttributes = newAttributes.datasetAttributes

val n = attributes.numDimensions
val shape = attributes.shape
val chunks = attributes.shape
val position = LongArray(n)
val gridSize = (shape zip chunks).map { (s, c) -> s.toDouble() / c.toDouble() }.map { ceil(it).toLong() }

var d = 0
while (d < n) {
    val data = zarr.readBlock(dataset, dsAttributes, *position)
    // zarr.deleteBlock(dataset, *position)
    zarr.writeBlock(dataset, newDsAttributes, data)
    d = 0
    while (d < n) {
        position[d] += 1L
        if (position[d] < gridSize[d])
            break
        else
            position[d] = 0L
        ++d
    }
}

zarr.setZArrayAttributes(dataset, newAttributes)