Posted by
lechristophe on
Oct 03, 2014; 12:16pm
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5009888.html
Hi Mark,
Thanks for the advice; I tried to replace the formats-gpl.jar in the
jars/bioformats directory (daily build) with the version currently on
Jenkins for 5.1. After that I tried to open the big nd2 file I uploaded to
people at Bio-Formats. After half a minute with no big memory usage (around
70 MB), I get a new error:
(Fiji Is Just) ImageJ 2.0.0-rc-14/1.49g; Java 1.6.0_24 [64-bit]; Windows 7
6.1; 61MB of 49071MB (<1%)
java.lang.NoSuchMethodError:
loci.formats.FormatTools.getEmissionWavelength(Ljava/lang/Double;)Lome/xml/model/primitives/PositiveFloat;
at
loci.formats.in.NativeND2Reader.populateMetadataStore(NativeND2Reader.java:1928)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1316)
at loci.formats.FormatReader.setId(FormatReader.java:1317)
at loci.formats.DelegateReader.setId(DelegateReader.java:253)
at loci.formats.ImageReader.setId(ImageReader.java:753)
at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388)
at io.scif.AbstractParser.parse(AbstractParser.java:252)
at io.scif.AbstractParser.parse(AbstractParser.java:335)
at io.scif.AbstractParser.parse(AbstractParser.java:52)
at io.scif.AbstractReader.setSource(AbstractReader.java:270)
at
io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
at
net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
at
net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)
so I guess something else was modified in the new jar that keeps him from
playing nice with the rest of the daily build?
Christophe
2014-10-01 21:21 GMT+02:00 Mark Hiner <
[hidden email]>:
> Hi Christophe,
>
> >As far as I understand, the current dailies are 5.0, not 5.1 yet
>
> You are correct. We will be switching over to 5.1.x, but in the mean time
> it looks like the nd2 fix
> <
https://github.com/openmicroscopy/bioformats/commit/3c857c2e5743e9b23801408bd61de49697716b4d>
> you're looking for only affected the formats-gpl component. You should be
> able to just download that specific jar, and replace the
> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
> version will just be called "formats-gpl.jar" if you still have the
> Bio-Formats update site enabled).
>
> I hope that will hold you over until we migrate to the 5.1.x daily builds,
> but please let us know if there are any problems manually replacing the jar.
>
> Thanks,
> Mark
>
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