Move logging configuration to beginning of call() method

[melissalinkert]

This ensures that the correct log level is set before OpenCV is loaded.

Compare using --log-level ERROR with and without this PR.

[melissalinkert]

75cc25a adds one more potential fix to address the illegal access warning logged to stderr, as noted by @erindiel :

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.esotericsoftware.reflectasm.AccessClassLoader (file:/home/melissa/bioformats2raw/build/distributions/bioformats2raw-0.9.0-SNAPSHOT/lib/reflectasm-1.11.9.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.esotericsoftware.reflectasm.AccessClassLoader
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

The full stack trace, which results from setting JAVA_OPTS="--illegal-access=debug":

WARNING: Illegal reflective access by com.esotericsoftware.reflectasm.AccessClassLoader (file:/home/melissa/bioformats2raw/build/distributions/bioformats2raw-0.9.0-SNAPSHOT/lib/reflectasm-1.11.9.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
    at com.esotericsoftware.reflectasm.AccessClassLoader.getDefineClassMethod(AccessClassLoader.java:111)
    at com.esotericsoftware.reflectasm.AccessClassLoader.defineClass(AccessClassLoader.java:73)
    at com.esotericsoftware.reflectasm.AccessClassLoader.defineAccessClass(AccessClassLoader.java:57)
    at com.esotericsoftware.reflectasm.ConstructorAccess.get(ConstructorAccess.java:99)
    at com.esotericsoftware.kryo.util.DefaultInstantiatorStrategy.newInstantiatorOf(DefaultInstantiatorStrategy.java:59)
    at com.esotericsoftware.kryo.Kryo.newInstantiator(Kryo.java:1190)
    at com.esotericsoftware.kryo.Kryo.newInstance(Kryo.java:1199)
    at com.esotericsoftware.kryo.serializers.FieldSerializer.create(FieldSerializer.java:163)
    at com.esotericsoftware.kryo.serializers.FieldSerializer.read(FieldSerializer.java:122)
    at com.esotericsoftware.kryo.Kryo.readObject(Kryo.java:774)
    at loci.formats.Memoizer$KryoDeser.loadReader(Memoizer.java:169)
    at loci.formats.Memoizer.loadMemo(Memoizer.java:924)
    at loci.formats.Memoizer.setId(Memoizer.java:702)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
    at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)
    at com.glencoesoftware.bioformats2raw.Converter.convert(Converter.java:1241)
    at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:1176)
    at com.glencoesoftware.bioformats2raw.Converter.call(Converter.java:104)
    at picocli.CommandLine.executeUserObject(CommandLine.java:2041)
    at picocli.CommandLine.access$1500(CommandLine.java:148)
    at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2461)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2453)
    at picocli.CommandLine$RunLast.handle(CommandLine.java:2415)
    at picocli.CommandLine$AbstractParseResultHandler.handleParseResult(CommandLine.java:2264)
    at picocli.CommandLine.parseWithHandlers(CommandLine.java:2664)
    at picocli.CommandLine.parseWithHandler(CommandLine.java:2599)
    at picocli.CommandLine.call(CommandLine.java:2875)
    at com.glencoesoftware.bioformats2raw.Converter.main(Converter.java:2946)

This warning only shows up when a memo file is loaded, so either the memo file must exist prior to conversion or multiple workers need to be used in order to see the warning.

https://github.com/EsotericSoftware/reflectasm/issues/64 and https://github.com/EsotericSoftware/kryo/issues/692 are relevant upstream issues.

From what I can tell (based on this documentation in particular), --add-opens java.base/java.lang=ALL-UNNAMED (as used in 75cc25a) is the next best option if the problematic library cannot be updated. Definitely happy to hear better ideas though.

[sbesson]

Unfortunately, 75cc25a seems to have caused regression on JDK 8 runtime environments when using the 0.9.0 distribution bundle - see #237

Reproduced locally

sbesson@Sebastiens-MacBook-Pro-3 Downloads % jenv local 1.8   
sbesson@Sebastiens-MacBook-Pro-3 Downloads % ./bioformats2raw-0.9.0/bin/bioformats2raw test.fake test.zarr
Unrecognized option: --add-opens
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
sbesson@Sebastiens-MacBook-Pro-3 Downloads % jenv local 11.0
sbesson@Sebastiens-MacBook-Pro-3 Downloads % ./bioformats2raw-0.9.0/bin/bioformats2raw test.fake test.zarr
sbesson@Sebastiens-MacBook-Pro-3 Downloads % rm -rf test.zarr 
sbesson@Sebastiens-MacBook-Pro-3 Downloads % jenv local 17.0
sbesson@Sebastiens-MacBook-Pro-3 Downloads % ./bioformats2raw-0.9.0/bin/bioformats2raw test.fake test.zarr