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Support for uint8 #23

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krokicki opened this issue Jul 16, 2021 · 0 comments
Open

Support for uint8 #23

krokicki opened this issue Jul 16, 2021 · 0 comments

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@krokicki
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I'm trying to create a MIP for a uint8 data set, a large binary mask. Here's my attributes.json file:

{
    "blockSize": [
        512,
        512,
        512
    ],
    "compression": {
        "level": 1,
        "type": "gzip",
        "useZlib": false
    },
    "dataType": "uint8",
    "dimensions": [
        10325,
        6150,
        2560
    ]
}```

It looks like this datatype isn't supported:

Exception in thread "main" com.esotericsoftware.kryo.KryoException: java.lang.RuntimeException: Could not ser
ialize lambda
Serialization trace:
createLinkedType (net.imglib2.type.NativeTypeFactory)
typeFactory (net.imglib2.type.numeric.integer.UnsignedByteType)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:101)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObjectOrNull(Kryo.java:629)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:86)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at org.apache.spark.serializer.KryoSerializationStream.writeObject(KryoSerializer.scala:259)
at org.apache.spark.broadcast.TorrentBroadcast$.$anonfun$blockifyObject$4(TorrentBroadcast.scala:311)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:313)
at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:137)
at org.apache.spark.broadcast.TorrentBroadcast.(TorrentBroadcast.scala:91)
at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:35)
at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:77)
at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1479)
at org.apache.spark.api.java.JavaSparkContext.broadcast(JavaSparkContext.scala:546)
at org.janelia.saalfeldlab.n5.spark.N5MaxIntensityProjectionSpark.createMaxIntensityProjection(N5MaxI
ntensityProjectionSpark.java:243)
at org.janelia.saalfeldlab.n5.spark.N5MaxIntensityProjectionSpark.createMaxIntensityProjection(N5MaxI
ntensityProjectionSpark.java:179)
at org.janelia.saalfeldlab.n5.spark.N5MaxIntensityProjectionSpark.main(N5MaxIntensityProjectionSpark.
java:377)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.JavaMainApplication.start(SparkApplication.scala:52)
at org.apache.spark.deploy.SparkSubmit.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala
:928)
at org.apache.spark.deploy.SparkSubmit.doRunMain$1(SparkSubmit.scala:180)
at org.apache.spark.deploy.SparkSubmit.submit(SparkSubmit.scala:203)
at org.apache.spark.deploy.SparkSubmit.doSubmit(SparkSubmit.scala:90)
at org.apache.spark.deploy.SparkSubmit$$anon$2.doSubmit(SparkSubmit.scala:1007)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:1016)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.RuntimeException: Could not serialize lambda
at com.esotericsoftware.kryo.serializers.ClosureSerializer.write(ClosureSerializer.java:69)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
... 30 more
Caused by: java.lang.NoSuchMethodException: net.imglib2.type.numeric.integer.UnsignedByteType$$Lambda$718/922
871524.writeReplace()
at java.lang.Class.getDeclaredMethod(Class.java:2130)
at com.esotericsoftware.kryo.serializers.ClosureSerializer.write(ClosureSerializer.java:60)
... 32 more

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