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java.lang.ClassNotFoundException: loci.formats.in.SlideBook6

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Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

java.lang.ClassNotFoundException: loci.formats.in.SlideBook6

Postby darwinjob » Sun Oct 29, 2017 11:37 am

Hi
I get this error no matter what file I'm trying to read

[main] DEBUG loci.formats.ClassList - Could not find loci.formats.in.SlideBook6Reader
java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader
at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[na:1.8.0_45]
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[na:1.8.0_45]
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) ~[na:1.8.0_45]
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_45]
at java.lang.Class.forName0(Native Method) ~[na:1.8.0_45]
at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_45]
at loci.formats.ClassList.parseLine(ClassList.java:196) [bioformats_package_5_7_1.jar:5.7.1]
at loci.formats.ClassList.parseFile(ClassList.java:258) [bioformats_package_5_7_1.jar:5.7.1]
at loci.formats.ClassList.<init>(ClassList.java:138) [bioformats_package_5_7_1.jar:5.7.1]
at loci.formats.ClassList.<init>(ClassList.java:122) [bioformats_package_5_7_1.jar:5.7.1]
at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:79) [bioformats_package_5_7_1.jar:5.7.1]
at loci.formats.ImageReader.<init>(ImageReader.java:116) [bioformats_package_5_7_1.jar:5.7.1]

Version 5.7.1, W764
Bug?
darwinjob
 
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Re: java.lang.ClassNotFoundException: loci.formats.in.SlideB

Postby sbesson » Mon Oct 30, 2017 11:04 am

Hi,

this is not a bug but rather a consequence of the externalization of the 3i Slidebook reader from the Bio-Formats codebase.

Following this externalization, the 3i Slidebook JAR is now maintained in its own JAR, optional and detected at runtime when creating a new ImageReader instance. If the JAR is not found on the classpath, an exception is logged at the DEBUG level as shown by your stack trace.

How do you configure your logging? To reduce the noise, it is possible to set either the root logger level or the level of the `loci.formats.ClassList` logger at the INFO level or higher.

Best
Sebastien
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sbesson
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Re: java.lang.ClassNotFoundException: loci.formats.in.SlideB

Postby darwinjob » Mon Oct 30, 2017 1:11 pm

OK, thanks. So this java.lang.ClassNotFoundException will not affect general functionality as far as I don't (and I don't) touch this SlideBook6 file format?
darwinjob
 
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Re: java.lang.ClassNotFoundException: loci.formats.in.SlideB

Postby sbesson » Mon Oct 30, 2017 2:09 pm

The only impact would be that if you were to open Slidebook files, Bio-Formats would select the SlidebookReader in the main codebase rather than the native 3i Slidebook6 reader.

For any other usage of the library, the general functionality should be unaffected.

Best,
Sebastien
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sbesson
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Re: java.lang.ClassNotFoundException: loci.formats.in.SlideB

Postby darwinjob » Mon Oct 30, 2017 11:25 pm

sbesson wrote:How do you configure your logging?

I don't. This is a minimalistic main() method running in Eclipse with the sole bioformats_package.jar referenced in the build path. This is the default output.
darwinjob
 
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Re: java.lang.ClassNotFoundException: loci.formats.in.SlideB

Postby sbesson » Tue Oct 31, 2017 10:45 am

Understood,

if you are using bioformats_package.jar and want to reduce the logging as mentioned above, you should be able to configure logback by putting a configuration file in the class path - see the logback.xml file shipped with the command-line tools as an example.

Best,
Sebastien
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