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ome / ZarrReader

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Unidata dependency unification #15

Closed sbesson closed 2 years ago

sbesson commented 2 years ago

From the testing in https://github.com/ome/ZarrReader/pull/8

Using the latest Bio-Formats command-line tools bundle (6.9.1), extracting the OMEZarr artifact and executing it against sample data leads to java.lang.NoSuchMethodError when running openBytes:

(java_dev) sbesson@Sebastiens-MacBook-Pro bftools % BF_CP=~/Downloads/bftools/OMEZarrReader-0.1.0-SNAPSHOT.jar ./showinf ~/Desktop/embl/cyx.ome.zarr/.zattrs -noflat -autoscale
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/Users/sbesson/Downloads/bftools/bioformats_package.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/Users/sbesson/Downloads/bftools/OMEZarrReader-0.1.0-SNAPSHOT.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
No native library available for this platform.
Checking file format [Zarr]
Initializing reader
ZarrReader initializing /Users/sbesson/Desktop/embl/cyx.ome.zarr/.zattrs
Initialization took 0.162s

Reading core metadata
filename = /Users/sbesson/Desktop/embl/cyx.ome.zarr/.zattrs
Used files:
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s2/.zarray
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s2/.zattrs
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s2/0/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s2/1/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s2/3/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s2/2/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/.zattrs
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/.zgroup
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/.zarray
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/.zattrs
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/0/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/0/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/0/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/0/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/1/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/1/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/1/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/1/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/3/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/3/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/3/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/3/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/2/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/2/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/2/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s1/2/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/.zarray
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/.zattrs
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/0/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/0/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/1/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/1/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/3/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/3/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/3/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/3/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/2/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/2/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/2/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/0/2/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/0/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/0/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/1/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/1/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/3/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/3/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/3/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/3/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/2/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/2/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/2/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/1/2/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/0/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/0/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/1/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/1/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/3/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/3/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/3/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/3/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/2/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/2/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/2/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/3/2/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/0/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/0/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/0/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/0/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/1/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/1/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/1/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/1/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/3/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/3/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/3/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/3/2
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/2/0
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/2/1
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/2/3
    /Users/sbesson/Desktop/embl/cyx.ome.zarr/s0/2/2/2
Series count = 1
Series #0 :
    Resolutions = 3
        sizeX[0] = 1024
        sizeX[1] = 512
        sizeX[2] = 256
    Image count = 4
    RGB = false (1) 
    Interleaved = false
    Indexed = false (false color)
    Width = 1024
    Height = 930
    SizeZ = 4
    SizeT = 1
    SizeC = 1
    Tile size = 1 x 256
    Thumbnail size = 128 x 116
    Endianness = intel (little)
    Dimension order = XYCZT (uncertain)
    Pixel type = uint16
    Valid bits per pixel = 16
    Metadata complete = false
    Thumbnail series = false
    -----
    Plane #0 <=> Z 0, C 0, T 0
    Plane #2 <=> Z 2, C 0, T 0
    Plane #3 <=> Z 3, C 0, T 0

Reading pixel data (0-3)
Exception in thread "main" java.lang.NoSuchMethodError: 'ucar.ma2.DataType ucar.ma2.DataType.getType(java.lang.Class, boolean)'
    at com.bc.zarr.ucar.NetCDF_Util.createArrayWithGivenStorage(NetCDF_Util.java:46)
    at com.bc.zarr.ZarrArray.read(ZarrArray.java:326)
    at com.bc.zarr.ZarrArray.read(ZarrArray.java:298)
    at loci.formats.services.JZarrServiceImpl.readBytes(JZarrServiceImpl.java:239)
    at loci.formats.in.ZarrReader.openBytes(ZarrReader.java:405)
    at loci.formats.ImageReader.openBytes(ImageReader.java:465)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
    at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:269)
    at loci.formats.MinMaxCalculator.openBytes(MinMaxCalculator.java:260)
    at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:334)
    at loci.formats.tools.ImageInfo.readPixels(ImageInfo.java:825)
    at loci.formats.tools.ImageInfo.testRead(ImageInfo.java:1055)
    at loci.formats.tools.ImageInfo.main(ImageInfo.java:1121)

Using the latest Bio-Formats 6.9.1-SNAPSHOT, including https://github.com/ome/bioformats/pull/3788 suffices to fix the error and display the data.

The alternative is to update https://github.com/ome/bioformats/blob/ef26436c2d079f05c1047816e564ffcc63bb0b04/tools/bf.sh#L60 and prepend the JAR to the classpath rather than appending it so that the latest cdm-core dependency is loaded first. In general though this is probably an incentive to moving towards a Bio-Formats (patch?) release with the cdm upgrade to make our tools less dependent on the classpath

sbesson commented 2 years ago

This should be solved with the Bio-Formats 6.9.1 release which bumps cdm-core to same version as the one used in jzarr. This question of compatility matrix between the upstream Bio-Formats JARs and ZarrReader still remains but I think this is another component of the larger discussion in #32 so I am closing this issue in favor of the more recent one.