[ome-devel] JAI

Tue Jun 16 23:40:19 BST 2015

Hi Douglas and Curtis,

> > I'm just trying to use the BFS3 Handler and I'm running into a problem
> > with Java Advanced Imaging.
> >
> > 11:04:14.008 [main] INFO  loci.formats.FormatHandler - Checking for JAI
> > Exception in thread "main" loci.formats.MissingLibraryException: Java
> > Advanced Imaging (JAI) is required to read some TIFF files. Please install
> > JAI from https://jai.dev.java.net/
> > at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:111)
> > at loci.formats.FormatReader.setId(FormatReader.java:1426)
> > at loci.formats.DelegateReader.setId(DelegateReader.java:298)
> > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
> > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
> > at loci.plugins.BF.openImagePlus(BF.java:92)
> > at loci.plugins.BF.openImagePlus(BF.java:77)
> > at edu.harvard.hms.bfs3.Main.main(Main.java:54)
> > Caused by: loci.common.ReflectException: No such class:
> > javax.media.jai.NullOpImage
> > at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:161)
> > at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:104)
> > ... 7 more
> > Caused by: java.lang.ClassNotFoundException: javax.media.jai.NullOpImage
> > at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> > at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> > at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> > at java.lang.Class.forName0(Native Method)
> > at java.lang.Class.forName(Class.java:348)
> > at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:153)
> > ... 8 more

This error always implies that something went wrong with Bio-Formats'
own TIFF reader - the vast majority of the time, it's something simple,
and does not indicate that JAI is or should be required.

Is there a stack trace prior to this in the log?  Can you upload the
file?

> IIRC, the reason JAI is not available from a Maven repo is due to licensing
> issues: Java Advanced Imaging is not open source! [1] So redistributing it
> from a Maven repo has legal problems.
> 
> Actually though, it looks like there _is_ a fork in Maven Central now,
> slightly stripped down to avoid said legal issues:
> * https://github.com/jai-imageio/jai-imageio-core
> *
> http://search.maven.org/#search%7Cgav%7C1%7Cg%3A%22com.github.jai-imageio%22%20AND%20a%3A%22jai-imageio-core%22
> 
> So maybe we could update Bio-Formats to use that! The package names are
> different so it would require some code changes, though.
> 
> Melissa: any ideas on how you'd prefer to address this issue in Bio-Formats
> proper?

We've considered jai-imageio-core in the past; we haven't used it so far
because it's not actively maintained, and the value added is minimal compared to
the time required to add/test/maintain support for it.  As far as I can see, it only
buys us support for a couple of very uncommon TIFF codecs.

If Douglas' file does indeed require support for one of those codecs,
then we can certainly take a closer look at depending on
jai-imageio-core, but I'd like to rule out an easier solution first.

Regards,
-Melissa

On Tue, Jun 16, 2015 at 11:37:01AM -0500, Curtis Rueden wrote:
> Hi Douglas,
> 
> CCing ome-devel, as this may interest others.
> 
> > I'm just trying to use the BFS3 Handler and I'm running into a problem
> > with Java Advanced Imaging.
> 
> Yeah, unfortunately, JAI is not just a library -- it's a Java platform
> extension. This means it installs into the lib/ext folder of your JRE.
> Usually this is done because native libraries are installed, too. (The
> whole "Java platform extension" thing is so last decade, though... ;-)
> 
> Anyway, the reason it works on OS X out of the box is that Apple Java 6
> ships with Java 3D and JAI installed in /Library/Java/Extensions. They are
> really old versions, but in this case I guess it did the job.
> 
> IIRC, the reason JAI is not available from a Maven repo is due to licensing
> issues: Java Advanced Imaging is not open source! [1] So redistributing it
> from a Maven repo has legal problems.
> 
> Actually though, it looks like there _is_ a fork in Maven Central now,
> slightly stripped down to avoid said legal issues:
> * https://github.com/jai-imageio/jai-imageio-core
> *
> http://search.maven.org/#search%7Cgav%7C1%7Cg%3A%22com.github.jai-imageio%22%20AND%20a%3A%22jai-imageio-core%22
> 
> So maybe we could update Bio-Formats to use that! The package names are
> different so it would require some code changes, though.
> 
> Melissa: any ideas on how you'd prefer to address this issue in Bio-Formats
> proper?
> 
> Regards,
> Curtis
> 
> [1] https://en.wikipedia.org/wiki/Java_Advanced_Imaging
> 
> On Tue, Jun 16, 2015 at 10:21 AM, Douglas Russell <root at dpwrussell.com>
> wrote:
> 
> > Hi Curtis,
> >
> > I'm just trying to use the BFS3 Handler and I'm running into a problem
> > with Java Advanced Imaging.
> >
> > 11:04:14.008 [main] INFO  loci.formats.FormatHandler - Checking for JAI
> > Exception in thread "main" loci.formats.MissingLibraryException: Java
> > Advanced Imaging (JAI) is required to read some TIFF files. Please install
> > JAI from https://jai.dev.java.net/
> > at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:111)
> > at loci.formats.FormatReader.setId(FormatReader.java:1426)
> > at loci.formats.DelegateReader.setId(DelegateReader.java:298)
> > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
> > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
> > at loci.plugins.BF.openImagePlus(BF.java:92)
> > at loci.plugins.BF.openImagePlus(BF.java:77)
> > at edu.harvard.hms.bfs3.Main.main(Main.java:54)
> > Caused by: loci.common.ReflectException: No such class:
> > javax.media.jai.NullOpImage
> > at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:161)
> > at loci.formats.in.TiffJAIReader.initFile(TiffJAIReader.java:104)
> > ... 7 more
> > Caused by: java.lang.ClassNotFoundException: javax.media.jai.NullOpImage
> > at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> > at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
> > at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> > at java.lang.Class.forName0(Native Method)
> > at java.lang.Class.forName(Class.java:348)
> > at loci.common.ReflectedUniverse.exec(ReflectedUniverse.java:153)
> > ... 8 more
> >
> > I tried adding a maven dependency for JAI, but it looks like that is not
> > in the imagej maven repository. Obviously it worked on your laptop in Paris
> > so it must have been there somehow. What do you think the best resolution
> > is? My knowledge of Maven is extremely limited as I stopped using Java
> > around the time it was really taking off, but I would have thought that
> > this could be fixed by adding another maven repository to the pom... but
> > it's odd that it worked for you on your laptop without any of that.
> >
> > Cheers,
> >
> > Douglas
> >

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