Conversion of image with uneven dimensions fails
Closed this issue · 18 comments
korseby commented
Hi,
I am trying to convert a single image to ome.tiff. I tried tiff and jpeg formats but the conversion constantly fails. The image has the following properties:
Colour Model: RGB
Depth: 8
DPI Height: 300
DPI Width: 300
Orientation: 1 (Normal)
Pixel Height: 4.160
Pixel Width: 5.547
Profile Name: sRGB IEC61966-2.1
I am on a Mac and this is what I am doing:
i="riccia_glauca_thallus_epidermis_cross_section1.jpeg"
k="$(echo $i | perl -pe 's/(^\.\/|\.jpeg)//g')"
/opt/src/bioformats2raw-0.4.0/bin/bioformats2raw "${k}.pattern" "${k}.zarr"
/opt/src/raw2ometiff-0.3.0/bin/raw2ometiff "${k}.zarr" "${k}.ome.tiff"
rm -rf "$k.zarr"
rm "$k.pattern"
This causes the following error:
[..]
2022-03-12 11:00:16,959 [main] ERROR c.g.bioformats2raw.Converter - Error while writing series 0
java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:332)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1527)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.allOf(CompletableFuture.java:2419)
at com.glencoesoftware.bioformats2raw.Converter.saveResolutions(Converter.java:1314)
at com.glencoesoftware.bioformats2raw.Converter.write(Converter.java:691)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:646)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Exception in thread "main" picocli.CommandLine$ExecutionException: Error while calling command (com.glencoesoftware.bioformats2raw.Converter@3427b02d): java.lang.RuntimeException: java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at picocli.CommandLine.executeUserObject(CommandLine.java:1962)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.RuntimeException: java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at com.glencoesoftware.bioformats2raw.Converter.unwrapException(Converter.java:1548)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:650)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
... 9 more
Caused by: java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:332)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1527)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1517)
at java.base/java.util.concurrent.CompletableFuture.allOf(CompletableFuture.java:2419)
at com.glencoesoftware.bioformats2raw.Converter.saveResolutions(Converter.java:1314)
at com.glencoesoftware.bioformats2raw.Converter.write(Converter.java:691)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:646)
... 12 more
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
I am using this java version:
java --version
openjdk 17.0.1 2021-10-19
OpenJDK Runtime Environment Temurin-17.0.1+12 (build 17.0.1+12)
OpenJDK 64-Bit Server VM Temurin-17.0.1+12 (build 17.0.1+12, mixed mode, sharing)
The conversion also fails for other images with similar uneven dimensions. As I am preparing a large upload to IDR, I can send you the files for testing.
Is the error in my side or is this a bug?
melissalinkert commented
Thanks for reporting this, @korseby. The error messages you are seeing mean that blosc is either not installed or not found.
#101 (comment) and the Requirements section of the readme have instructions for using blosc on a Mac. If you still see an error message after following those instructions, let us know.
korseby commented
Hi @melissalinkert ,
blosc is installed and bioformats2raw is working as expected for other files. This time I used a tiff-file. Below is the full error message:
2022-03-14 20:52:29,347 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:101)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:29,537 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:29,916 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:30,243 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:30,504 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:30,693 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:30,909 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:32,422 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:32,655 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:32,959 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:33,143 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:33,383 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:33,619 [main] WARN loci.formats.Memoizer - failed to save memo file: /Volumes/micromoss_04/micromoss_riccia_upload/IDR/processed/.riccia_sorocarpa_voucher_specimen1.pattern.bfmemo
com.esotericsoftware.kryo.KryoException: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
Serialization trace:
cellomicsPattern (loci.formats.in.CellomicsReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
reader (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
readers (loci.formats.ImageReader)
reader (loci.formats.DimensionSwapper)
readers (loci.formats.FileStitcher$ExternalSeries)
externals (loci.formats.FileStitcher)
helper (loci.formats.in.FilePatternReader)
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.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeClassAndObject(Kryo.java:651)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:361)
at com.esotericsoftware.kryo.serializers.DefaultArraySerializers$ObjectArraySerializer.write(DefaultArraySerializers.java:302)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:575)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:79)
at com.esotericsoftware.kryo.serializers.FieldSerializer.write(FieldSerializer.java:508)
at com.esotericsoftware.kryo.Kryo.writeObject(Kryo.java:557)
at loci.formats.Memoizer$KryoDeser.saveReader(Memoizer.java:206)
at loci.formats.Memoizer.saveMemo(Memoizer.java:968)
at loci.formats.Memoizer.setId(Memoizer.java:697)
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:547)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.IllegalArgumentException: Unable to create serializer "com.esotericsoftware.kryo.serializers.FieldSerializer" for class: java.util.regex.Pattern
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:65)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:43)
at com.esotericsoftware.kryo.Kryo.newDefaultSerializer(Kryo.java:396)
at com.esotericsoftware.kryo.Kryo.getDefaultSerializer(Kryo.java:380)
at com.esotericsoftware.kryo.util.DefaultClassResolver.registerImplicit(DefaultClassResolver.java:74)
at com.esotericsoftware.kryo.Kryo.getRegistration(Kryo.java:508)
at com.esotericsoftware.kryo.Kryo.getSerializer(Kryo.java:528)
at com.esotericsoftware.kryo.serializers.ObjectField.write(ObjectField.java:82)
... 59 common frames omitted
Caused by: java.lang.reflect.InvocationTargetException: null
at jdk.internal.reflect.GeneratedConstructorAccessor3.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
at com.esotericsoftware.kryo.factories.ReflectionSerializerFactory.makeSerializer(ReflectionSerializerFactory.java:51)
... 66 common frames omitted
Caused by: java.lang.reflect.InaccessibleObjectException: Unable to make field private java.lang.String java.util.regex.Pattern.pattern accessible: module java.base does not "opens java.util.regex" to unnamed module @1ca7bef1
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354)
at java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297)
at java.base/java.lang.reflect.Field.checkCanSetAccessible(Field.java:178)
at java.base/java.lang.reflect.Field.setAccessible(Field.java:172)
at com.esotericsoftware.kryo.serializers.FieldSerializer.buildValidFields(FieldSerializer.java:283)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:216)
at com.esotericsoftware.kryo.serializers.FieldSerializer.rebuildCachedFields(FieldSerializer.java:157)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:150)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:134)
at com.esotericsoftware.kryo.serializers.FieldSerializer.<init>(FieldSerializer.java:130)
... 71 common frames omitted
2022-03-14 20:52:40,467 [pool-1-thread-14] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=1024 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=1024, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,466 [pool-1-thread-24] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=1024 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=1024, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,468 [pool-1-thread-22] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=0 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=0, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,470 [pool-1-thread-20] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=4096 yy=1024 zz=1 width=62 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=4096, y=1024, w=62, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,470 [pool-1-thread-30] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=4096 yy=2048 zz=1 width=62 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=4096, y=2048, w=62, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,470 [pool-1-thread-12] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=0 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=0, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,471 [pool-1-thread-28] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=3072 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=3072, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,471 [pool-1-thread-18] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=3072 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=3072, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,472 [pool-1-thread-10] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=4096 yy=0 zz=1 width=62 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=4096, y=0, w=62, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,472 [pool-1-thread-26] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=2048 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=2048, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,472 [pool-1-thread-8] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=3072 yy=0 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=3072, y=0, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,472 [pool-1-thread-16] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=2048 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=2048, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-3] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=1024 yy=0 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-5] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=2048 yy=0 zz=0 width=1024 height=1024 depth=1
java.lang.UnsatisfiedLinkError: Unable to load library 'blosc': Native library (darwin/libblosc.dylib) not found in resource path (/opt/src/bioformats2raw-0.4.0/lib/bioformats2raw-0.4.0.jar:/opt/src/bioformats2raw-0.4.0/lib/formats-gpl-6.8.0.jar:/opt/src/bioformats2raw-0.4.0/lib/picocli-4.6.1.jar:/opt/src/bioformats2raw-0.4.0/lib/univocity-parsers-2.8.4.jar:/opt/src/bioformats2raw-0.4.0/lib/jzarr-0.3.3-gs-SNAPSHOT.jar:/opt/src/bioformats2raw-0.4.0/lib/s3fs-2.2.3.jar:/opt/src/bioformats2raw-0.4.0/lib/jaxb-api-2.3.0.jar:/opt/src/bioformats2raw-0.4.0/lib/opencv-3.4.2-1.jar:/opt/src/bioformats2raw-0.4.0/lib/progressbar-0.9.0.jar:/opt/src/bioformats2raw-0.4.0/lib/formats-bsd-6.8.0.jar:/opt/src/bioformats2raw-0.4.0/lib/formats-api-6.8.0.jar:/opt/src/bioformats2raw-0.4.0/lib/ome-xml-6.2.3.jar:/opt/src/bioformats2raw-0.4.0/lib/metakit-5.3.3.jar:/opt/src/bioformats2raw-0.4.0/lib/ome-poi-5.3.4.jar:/opt/src/bioformats2raw-0.4.0/lib/ome-codecs-0.3.1.jar:/opt/src/bioformats2raw-0.4.0/lib/ome-common-6.0.7.jar:/opt/src/bioformats2raw-0.4.0/lib/ome-mdbtools-5.3.2.jar:/opt/src/bioformats2raw-0.4.0/lib/cdm-core-5.3.3.jar:/opt/src/bioformats2raw-0.4.0/lib/jcl-over-slf4j-1.7.5.jar:/opt/src/bioformats2raw-0.4.0/lib/logback-classic-1.2.0.jar:/opt/src/bioformats2raw-0.4.0/lib/jxrlib-all-0.2.4.jar:/opt/src/bioformats2raw-0.4.0/lib/native-lib-loader-2.1.4.jar:/opt/src/bioformats2raw-0.4.0/lib/udunits-5.3.3.jar:/opt/src/bioformats2raw-0.4.0/lib/httpservices-5.3.3.jar:/opt/src/bioformats2raw-0.4.0/lib/slf4j-api-1.7.28.jar:/opt/src/bioformats2raw-0.4.0/lib/JWlz-1.4.0.jar:/opt/src/bioformats2raw-0.4.0/lib/minio-5.0.2.jar:/opt/src/bioformats2raw-0.4.0/lib/aws-java-sdk-s3-1.11.232.jar:/opt/src/bioformats2raw-0.4.0/lib/aws-java-sdk-kms-1.11.232.jar:/opt/src/bioformats2raw-0.4.0/lib/aws-java-sdk-core-1.11.232.jar:/opt/src/bioformats2raw-0.4.0/lib/joda-time-2.10.3.jar:/opt/src/bioformats2raw-0.4.0/lib/kryo-4.0.2.jar:/opt/src/bioformats2raw-0.4.0/lib/aircompressor-0.18.jar:/opt/src/bioformats2raw-0.4.0/lib/json-20090211.jar:/opt/src/bioformats2raw-0.4.0/lib/sqlite-jdbc-3.28.0.jar:/opt/src/bioformats2raw-0.4.0/lib/jmespath-java-1.11.232.jar:/opt/src/bioformats2raw-0.4.0/lib/jackson-databind-2.10.3.jar:/opt/src/bioformats2raw-0.4.0/lib/jblosc-1.0.1.jar:/opt/src/bioformats2raw-0.4.0/lib/guava-29.0-jre.jar:/opt/src/bioformats2raw-0.4.0/lib/tika-core-1.5.jar:/opt/src/bioformats2raw-0.4.0/lib/jsr305-3.0.2.jar:/opt/src/bioformats2raw-0.4.0/lib/jline-3.16.0.jar:/opt/src/bioformats2raw-0.4.0/lib/logback-core-1.2.0.jar:/opt/src/bioformats2raw-0.4.0/lib/xalan-2.7.2.jar:/opt/src/bioformats2raw-0.4.0/lib/serializer-2.7.2.jar:/opt/src/bioformats2raw-0.4.0/lib/specification-6.2.3.jar:/opt/src/bioformats2raw-0.4.0/lib/turbojpeg-6.8.0.jar:/opt/src/bioformats2raw-0.4.0/lib/jgoodies-forms-1.7.2.jar:/opt/src/bioformats2raw-0.4.0/lib/commons-lang-2.6.jar:/opt/src/bioformats2raw-0.4.0/lib/perf4j-0.9.16.jar:/opt/src/bioformats2raw-0.4.0/lib/jhdf5-19.04.0.jar:/opt/src/bioformats2raw-0.4.0/lib/metadata-extractor-2.11.0.jar:/opt/src/bioformats2raw-0.4.0/lib/xercesImpl-2.8.1.jar:/opt/src/bioformats2raw-0.4.0/lib/httpmime-4.5.9.jar:/opt/src/bioformats2raw-0.4.0/lib/google-http-client-xml-1.20.0.jar:/opt/src/bioformats2raw-0.4.0/lib/google-http-client-1.20.0.jar:/opt/src/bioformats2raw-0.4.0/lib/httpclient-4.5.9.jar:/opt/src/bioformats2raw-0.4.0/lib/commons-logging-1.2.jar:/opt/src/bioformats2raw-0.4.0/lib/reflectasm-1.11.3.jar:/opt/src/bioformats2raw-0.4.0/lib/minlog-1.3.0.jar:/opt/src/bioformats2raw-0.4.0/lib/objenesis-2.5.1.jar:/opt/src/bioformats2raw-0.4.0/lib/jdom2-2.0.6.jar:/opt/src/bioformats2raw-0.4.0/lib/protobuf-java-3.9.1.jar:/opt/src/bioformats2raw-0.4.0/lib/jcommander-1.78.jar:/opt/src/bioformats2raw-0.4.0/lib/httpcore-4.4.11.jar:/opt/src/bioformats2raw-0.4.0/lib/re2j-1.3.jar:/opt/src/bioformats2raw-0.4.0/lib/jackson-annotations-2.10.3.jar:/opt/src/bioformats2raw-0.4.0/lib/jackson-dataformat-cbor-2.6.7.jar:/opt/src/bioformats2raw-0.4.0/lib/jackson-core-2.10.3.jar:/opt/src/bioformats2raw-0.4.0/lib/junit-4.12.jar:/opt/src/bioformats2raw-0.4.0/lib/jna-4.2.2.jar:/opt/src/bioformats2raw-0.4.0/lib/failureaccess-1.0.1.jar:/opt/src/bioformats2raw-0.4.0/lib/listenablefuture-9999.0-empty-to-avoid-conflict-with-guava.jar:/opt/src/bioformats2raw-0.4.0/lib/checker-qual-2.11.1.jar:/opt/src/bioformats2raw-0.4.0/lib/error_prone_annotations-2.3.4.jar:/opt/src/bioformats2raw-0.4.0/lib/j2objc-annotations-1.3.jar:/opt/src/bioformats2raw-0.4.0/lib/okhttp-3.7.0.jar:/opt/src/bioformats2raw-0.4.0/lib/okio-1.12.0.jar:/opt/src/bioformats2raw-0.4.0/lib/xml-apis-1.3.04.jar:/opt/src/bioformats2raw-0.4.0/lib/ome-jai-0.1.0.jar:/opt/src/bioformats2raw-0.4.0/lib/jgoodies-common-1.7.0.jar:/opt/src/bioformats2raw-0.4.0/lib/base-18.09.0.jar:/opt/src/bioformats2raw-0.4.0/lib/commons-io-2.7.jar:/opt/src/bioformats2raw-0.4.0/lib/commons-lang3-3.10.jar:/opt/src/bioformats2raw-0.4.0/lib/xmpcore-5.1.3.jar:/opt/src/bioformats2raw-0.4.0/lib/asm-5.0.4.jar:/opt/src/bioformats2raw-0.4.0/lib/hamcrest-core-1.3.jar:/opt/src/bioformats2raw-0.4.0/lib/ion-java-1.0.2.jar:/opt/src/bioformats2raw-0.4.0/lib/xpp3-1.1.4c.jar:/opt/src/bioformats2raw-0.4.0/lib/commons-codec-1.11.jar)
at com.sun.jna.NativeLibrary.loadLibrary(NativeLibrary.java:277)
at com.sun.jna.NativeLibrary.getInstance(NativeLibrary.java:403)
at com.sun.jna.Native.register(Native.java:1529)
at com.sun.jna.Native.register(Native.java:1252)
at org.blosc.IBloscDll.<clinit>(IBloscDll.java:15)
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-7] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=3072 yy=0 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-6] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=2048 yy=0 zz=1 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-29] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=4096 yy=2048 zz=0 width=62 height=125 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-4] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=1024 yy=0 zz=1 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-2] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=0 yy=0 zz=1 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-1] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=0 yy=0 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-13] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=1024 yy=1024 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-15] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=2048 yy=1024 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-17] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=3072 yy=1024 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,555 [pool-1-thread-11] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=0 yy=1024 zz=0 width=1024 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,559 [pool-1-thread-9] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=4096 yy=0 zz=0 width=62 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,559 [pool-1-thread-19] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=4096 yy=1024 zz=0 width=62 height=1024 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,580 [pool-1-thread-21] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=0 yy=2048 zz=0 width=1024 height=125 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,580 [pool-1-thread-23] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=1024 yy=2048 zz=0 width=1024 height=125 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,580 [pool-1-thread-27] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=3072 yy=2048 zz=0 width=1024 height=125 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,580 [pool-1-thread-25] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=0 xx=2048 yy=2048 zz=0 width=1024 height=125 depth=1
java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:282)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
2022-03-14 20:52:40,581 [main] ERROR c.g.bioformats2raw.Converter - Error while writing series 0
java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:332)
at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:347)
at java.base/java.util.concurrent.CompletableFuture$BiRelay.tryFire(CompletableFuture.java:1498)
at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
at java.base/java.util.concurrent.CompletableFuture.completeExceptionally(CompletableFuture.java:2162)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1294)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
... 3 common frames omitted
Exception in thread "main" picocli.CommandLine$ExecutionException: Error while calling command (com.glencoesoftware.bioformats2raw.Converter@3427b02d): java.lang.RuntimeException: java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at picocli.CommandLine.executeUserObject(CommandLine.java:1962)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: java.lang.RuntimeException: java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at com.glencoesoftware.bioformats2raw.Converter.unwrapException(Converter.java:1548)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:650)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
... 9 more
Caused by: java.util.concurrent.CompletionException: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:332)
at java.base/java.util.concurrent.CompletableFuture.completeThrowable(CompletableFuture.java:347)
at java.base/java.util.concurrent.CompletableFuture$BiRelay.tryFire(CompletableFuture.java:1498)
at java.base/java.util.concurrent.CompletableFuture.postComplete(CompletableFuture.java:510)
at java.base/java.util.concurrent.CompletableFuture.completeExceptionally(CompletableFuture.java:2162)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1294)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:833)
Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.blosc.IBloscDll
at org.blosc.JBlosc.compressCtx(JBlosc.java:213)
at com.bc.zarr.CompressorFactory$BloscCompressor.compress(CompressorFactory.java:327)
at com.bc.zarr.chunk.ChunkReaderWriterImpl_Byte.write(ChunkReaderWriterImpl_Byte.java:67)
at com.bc.zarr.ZarrArray.write(ZarrArray.java:278)
at com.glencoesoftware.bioformats2raw.Converter.writeBytes(Converter.java:852)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1090)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
... 3 more
melissalinkert commented
The latest output shows several different things going wrong.
I can reproduce the Unable to create serializer/Unable to make field private issues with Java 17 and any pattern file. google/gson#1898 explains the underlying issue pretty well. This is something we'll need to fix in Bio-Formats itself, but it shouldn't cause the conversion to fail.
The various Failure processing chunk errors indicate that the image width and height (in pixels) is not the same for every TIFF file referenced by riccia_sorocarpa_voucher_specimen1.pattern. It is important that the dimensions are the same for every file referenced by a pattern file. Bio-Formats' showinf command line tool can give the dimensions for each TIFF file.
The blosc errors may be a result of the Failure processing chunk errors, but I would suggest making sure that you can convert a single TIFF referenced by riccia_sorocarpa_voucher_specimen1.pattern without error just to be sure.
korseby commented
I am using the default recommended setting for blosc:
export JAVA_OPTS='-Djna.library.path=/usr/local/Cellar/c-blosc/1.21.1/lib'
The riccia_sorocarpa_voucher_specimen1.pattern only contains one line riccia_sorocarpa_voucher_specimen1.tif referencing just one file. It makes no difference with JPEG or TIFF or 64-bit TIFF (with ImageMagick's convert). I can send you the file.
Would it make a difference in using a different Java version? What version would you recommend?
melissalinkert commented
At this point, if you can send the TIFF file that would be helpful. If I understand correctly, it was converted from the JPEG referenced in #138? If so, it would also help to have the original JPEG and the exact command used to convert from JPEG to TIFF. If you need somewhere to upload files, we suggest Zenodo.
ome/bioformats#3796 proposes a fix for the Unable to create serializer/Unable to make field private errors. Downgrading to Java 11 would be a work-around for now, but it's not strictly necessary to make the conversion succeed.
korseby commented
Can you try this file? It is "just" a photo of the voucher of the specimen. The data will be uploaded on IDR soon.
https://www.korseby.net/riccia_sorocarpa_voucher_specimen1.zip
melissalinkert commented
Thanks for sending the files, @korseby. I am able to convert both of these files, as well as a pattern file that only references riccia_sorocarpa_voucher_specimen1.tiff:
On Linux, with Java 11 and blosc installed according to the readme, bioformats2raw 0.4.0 "just works" with no errors or warnings.
Since you're using a Mac, please check whether you have an M1 or not. The arch command will show arm64 for an M1, otherwise x86_64.
If you don't have an M1, I would just double-check that /usr/local/Cellar/c-blosc/1.21.1/lib/libblosc.dylib exists, and that lipo -info /usr/local/Cellar/c-blosc/1.21.1/lib/libblosc.dylib shows the same architecture as arch.
On an M1 Mac, I was able to reproduce the errors in #139 (comment), and these steps seemed to solve it:
- Check that the architecture of the installed blosc library is
arm64usinglipo -info /opt/homebrew/Cellar/c-blosc/1.21.1/lib/libblosc.dylib - Make sure the installed JDK has the correct architecture (
aarch64). I tested with https://github.com/adoptium/temurin17-binaries/releases/download/jdk-17.0.2%2B8/OpenJDK17U-jdk_aarch64_mac_hotspot_17.0.2_8.pkg. - Set
JAVA_OPTSto the blosc directory as you have already done. For me, this wasexport JAVA_OPTS='-Djna.library.path=/opt/homebrew/Cellar/c-blosc/1.21.1/lib' - Download and unpack the build of #141 from https://github.com/glencoesoftware/bioformats2raw/suites/5674543795/artifacts/186269362.
- Run
bioformats2raw -p riccia_sorocarpa_voucher_specimen1.tiff test-tiffor similar. I would expect some warnings that OpenCV cannot be found (due to openpnp/opencv#81), but this won't stop the conversion.
I'm still confused how you were able to convert other files without seeing blosc errors, assuming all conversions were done on the same machine. Can you clarify what kind of Mac you have, and whether the working conversions were done somewhere else?
korseby commented
Hi,
I really hope that the 14 TB I just finished uploading for almost 3 months to IDR were not pointless. We checked a few generated ome.tiff files and they were fine even with all the blosc errors. ;)
Let's take this step by step. I am still on a Mac Pro. I installed Java 11 and with that version I am unable to convert any file. See below. With the patch(es) you have applied, do I need to recompile the entire bioformats2raw to test those out?
$ export JAVA_HOME="/Library/Java/JavaVirtualMachines/openjdk11-temurin/Contents/Home"
$ export JAVA_OPTS='-Djna.library.path=/usr/local/Cellar/c-blosc/1.21.1/lib'
$ uname -a
Darwin adlib.localnet 20.6.0 Darwin Kernel Version 20.6.0: Wed Nov 10 22:23:07 PST 2021; root:xnu-7195.141.14~1/RELEASE_X86_64 x86_64
$ lipo -info /usr/local/Cellar/c-blosc/1.21.1/lib/libblosc.dylib
Non-fat file: /usr/local/Cellar/c-blosc/1.21.1/lib/libblosc.dylib is architecture: x86_64
$ java -version
openjdk version "11.0.14.1" 2022-02-08
OpenJDK Runtime Environment Temurin-11.0.14.1+1 (build 11.0.14.1+1)
OpenJDK 64-Bit Server VM Temurin-11.0.14.1+1 (build 11.0.14.1+1, mixed mode)
$ opt/src/bioformats2raw-0.4.0/bin/bioformats2raw riccia_sorocarpa.pattern riccia_sorocarpa.zarr
WARNING: Illegal reflective access by com.esotericsoftware.kryo.util.UnsafeUtil (file:/opt/src/bioformats2raw-0.4.0/lib/kryo-4.0.2.jar) to constructor java.nio.DirectByteBuffer(long,int,java.lang.Object)
WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.kryo.util.UnsafeUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
melissalinkert commented
Thanks for the additional info, you can ignore everything I said above about M1 Macs.
$ opt/src/bioformats2raw-0.4.0/bin/bioformats2raw riccia_sorocarpa.pattern riccia_sorocarpa.zarr
WARNING: Illegal reflective access by com.esotericsoftware.kryo.util.UnsafeUtil (file:/opt/src/bioformats2raw-0.4.0/lib/kryo-4.0.2.jar) to constructor java.nio.DirectByteBuffer(long,int,java.lang.Object)
WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.kryo.util.UnsafeUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
This warning does not mean that the conversion failed. It is expected, and can be ignored. Is that the complete output?
korseby commented
I upgraded to the latest macOS and upgraded brew and macports. Sadly, same errors.
Using openjdk11 the messages are gone for files that are successfully converted except for the message above.
When trying to process the "problematic" tiff file, same errors appear. Should I try a development version?
$ /opt/share/bioformats2raw-0.4.0/bin/bioformats2raw riccia_sorocarpa_voucher_specimen1.pattern riccia_sorocarpa_voucher_specimen1.zarr
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.esotericsoftware.kryo.util.UnsafeUtil (file:/opt/local/share/bioformats2raw-0.4.0/lib/kryo-4.0.2.jar) to constructor java.nio.DirectByteBuffer(long,int,java.lang.Object)
WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.kryo.util.UnsafeUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2022-03-17 08:59:55,061 [pool-1-thread-4] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=3072 yy=0 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=3072, y=0, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,106 [pool-1-thread-3] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=0 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=0, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,124 [pool-1-thread-1] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=4096 yy=0 zz=1 width=62 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=4096, y=0, w=62, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,152 [pool-1-thread-1] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=1024 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=1024, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,154 [pool-1-thread-1] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=3072 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=3072, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,168 [pool-1-thread-3] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=2048 yy=1024 zz=1 width=1024 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=2048, y=1024, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,171 [pool-1-thread-3] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=4096 yy=1024 zz=1 width=62 height=1024 depth=1
loci.formats.FormatException: Invalid tile size: x=4096, y=1024, w=62, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,175 [pool-1-thread-2] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=0 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=0, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,187 [pool-1-thread-4] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=1024 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=1024, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,199 [pool-1-thread-1] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=2048 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=2048, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,213 [pool-1-thread-3] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=3072 yy=2048 zz=1 width=1024 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=3072, y=2048, w=1024, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,215 [pool-1-thread-3] ERROR c.g.bioformats2raw.Converter - Failure processing chunk; resolution=0 plane=1 xx=4096 yy=2048 zz=1 width=62 height=125 depth=1
loci.formats.FormatException: Invalid tile size: x=4096, y=2048, w=62, h=125
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
2022-03-17 08:59:55,234 [main] ERROR c.g.bioformats2raw.Converter - Error while writing series 0
java.util.concurrent.CompletionException: loci.formats.FormatException: Invalid tile size: x=3072, y=0, w=1024, h=1024
at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:331)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1452)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1444)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1444)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1442)
at java.base/java.util.concurrent.CompletableFuture.andTree(CompletableFuture.java:1442)
at java.base/java.util.concurrent.CompletableFuture.allOf(CompletableFuture.java:2337)
at com.glencoesoftware.bioformats2raw.Converter.saveResolutions(Converter.java:1314)
at com.glencoesoftware.bioformats2raw.Converter.write(Converter.java:691)
at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:646)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:477)
at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:92)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: loci.formats.FormatException: Invalid tile size: x=3072, y=0, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
Exception in thread "main" picocli.CommandLine$ExecutionException: Error while calling command (com.glencoesoftware.bioformats2raw.Converter@f0c8a99): loci.formats.FormatException: Invalid tile size: x=3072, y=0, w=1024, h=1024
at picocli.CommandLine.executeUserObject(CommandLine.java:1962)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2172)
at picocli.CommandLine.parseWithHandlers(CommandLine.java:2550)
at picocli.CommandLine.parseWithHandler(CommandLine.java:2485)
at picocli.CommandLine.call(CommandLine.java:2761)
at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:1808)
Caused by: loci.formats.FormatException: Invalid tile size: x=3072, y=0, w=1024, h=1024
at loci.formats.FormatTools.checkTileSize(FormatTools.java:1026)
at loci.formats.FormatTools.checkPlaneParameters(FormatTools.java:1002)
at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:289)
at loci.formats.in.TiffDelegateReader.openBytes(TiffDelegateReader.java:71)
at loci.formats.ImageReader.openBytes(ImageReader.java:465)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:249)
at loci.formats.FileStitcher.openBytes(FileStitcher.java:482)
at loci.formats.WrappedReader.openBytes(WrappedReader.java:247)
at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:348)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:229)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:161)
at com.glencoesoftware.bioformats2raw.Converter.getTile(Converter.java:961)
at com.glencoesoftware.bioformats2raw.Converter.processChunk(Converter.java:1072)
at com.glencoesoftware.bioformats2raw.Converter.lambda$saveResolutions$4(Converter.java:1286)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:829)
melissalinkert commented
Does removing all .*.bfmemo files in the same directory as riccia_sorocarpa_voucher_specimen1.pattern make any difference? That's the only other thing I can think of to try at this point, as converting the TIFF file you have sent still works for me:
$ java -version
openjdk version "11.0.14" 2022-01-18
OpenJDK Runtime Environment (build 11.0.14+9-Ubuntu-0ubuntu2.18.04)
OpenJDK 64-Bit Server VM (build 11.0.14+9-Ubuntu-0ubuntu2.18.04, mixed mode, sharing)
$ cat ~/data/koresby/riccia_sorocarpa_voucher_specimen1.pattern
riccia_sorocarpa_voucher_specimen1.tiff
$ md5sum ~/data/koresby/riccia_sorocarpa_voucher_specimen1.tiff
21bbfb7bdedec4487cef101696c00c84 /home/melissa/data/koresby/riccia_sorocarpa_voucher_specimen1.tiff
$ bin/bioformats2raw ~/data/koresby/riccia_sorocarpa_voucher_specimen1.pattern pattern-test
OpenJDK 64-Bit Server VM warning: You have loaded library /tmp/opencv_openpnp5604269015671581165/nu/pattern/opencv/linux/x86_64/libopencv_java342.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c <libfile>', or link it with '-z noexecstack'.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.esotericsoftware.kryo.util.UnsafeUtil (file:/home/melissa/bioformats2raw/build/distributions/bioformats2raw-0.4.0/lib/kryo-4.0.2.jar) to constructor java.nio.DirectByteBuffer(long,int,java.lang.Object)
WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.kryo.util.UnsafeUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
$ du -hs pattern-test/
11M pattern-test/
korseby commented
Hi @melissalinkert ,
I got it to work but ONLY when putting the TIFF and the pattern files together in a separate subdirectory and saving the zarr structure in the parent directory. Here is an example, the subdir is called test.
$ /opt/share/bioformats2raw-0.4.0/bin/bioformats2raw test/riccia_sorocarpa_voucher_specimen1.pattern riccia_sorocarpa_voucher_specimen1.zarr
$ /opt/share/raw2ometiff-0.3.0/bin/raw2ometiff riccia_sorocarpa_voucher_specimen1.zarr riccia_sorocarpa_voucher_specimen1.ome.tiff
If that is not the case, or I put the zarr in the subdirectory alone, then it will fail again.
Strange thing is, why does it work for the other tiff files?
melissalinkert commented
Can you paste the output of ls -ahl on the directory that contains the TIFF and pattern file, in the case where they are not in a separate subdirectory (i.e. the conversion fails)?
korseby commented
Hi,
the directory looks like this:
drwxr-xr-x@ 16 kristian staff 544 Mar 22 09:59 .
drwxr-xr-x 11 kristian staff 374 Mar 15 16:52 ..
-rw-r--r--@ 1 kristian staff 6148 Mar 22 09:59 .DS_Store
-rwxr-xr-x@ 1 kristian staff 715 Mar 17 10:20 _generate_single_ome_tiff_targeted.sh
-rw-r--r-- 1 kristian staff 113940793 Mar 14 20:32 riccia_sorocarpa.tiff
-rw-r--r-- 1 kristian staff 69233678 Mar 14 20:32 riccia_sorocarpa_spores.tiff
-rw-r--r-- 1 kristian staff 193149827 Mar 14 20:32 riccia_sorocarpa_stature.tiff
-rw-r--r-- 1 kristian staff 107960467 Mar 14 20:32 riccia_sorocarpa_stature_dorsal_side.tiff
-rw-r--r-- 1 kristian staff 126660028 Mar 14 20:32 riccia_sorocarpa_stature_ventral_side.tiff
-rw-r--r-- 1 kristian staff 69235870 Mar 14 20:32 riccia_sorocarpa_thallus_archegonium_cross_section.tiff
-rw-r--r-- 1 kristian staff 318496012 Mar 14 20:32 riccia_sorocarpa_thallus_cross_section.tiff
-rw-r--r-- 1 kristian staff 69236848 Mar 14 20:32 riccia_sorocarpa_thallus_epidermis_anterior_view.tiff
-rw-r--r-- 1 kristian staff 69246502 Mar 14 20:32 riccia_sorocarpa_thallus_epidermis_cross_section.tiff
-rw-r--r--@ 1 kristian staff 39 Mar 17 08:51 riccia_sorocarpa_voucher_specimen1.pattern
-rw-r--r--@ 1 kristian staff 9055666 Mar 14 20:32 riccia_sorocarpa_voucher_specimen1.tiff
-rw-r--r-- 1 kristian staff 6919246 Mar 14 20:32 riccia_sorocarpa_voucher_specimen2.tiff
melissalinkert commented
OK, I think I see the problem, but just to be sure: if you copy just riccia_sorocarpa_voucher_specimen1.pattern, riccia_sorocarpa_voucher_specimen1.tiff, and riccia_sorocarpa_voucher_specimen2.tiff to a subdirectory, does the conversion now fail? And by removing riccia_sorocarpa_voucher_specimen2.tiff from the subdirectory, does the conversion succeed again?
korseby commented
Yes. That is exactly the case. Any other tiff file in that same subdirectory will also result in the error.
melissalinkert commented
Great, that's what I would have expected. We have a proposed fix for this problem in ome/bioformats#3801, but that won't help you immediately.
Three ways to work around the problem now:
- Don't use a pattern file for a single file, just convert the TIFF directly.
- If you do use a pattern file for a single file, enclose the file name in
<>, e.g.<riccia_sorocarpa_voucher_specimen1.tiff> - Organize each dataset (pattern file and its referenced files only) into a separate subdirectory.
The first option is what I would suggest. There is no advantage to using a pattern file that references a single file, as pattern files are meant for grouping multiple files together.
korseby commented
Okay. I can confirm that conversion works for using the TIFF files directly. I close this issue now. Thanks. :)