http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5009889.html
of your FormatTools class it has access to. This means that it needs the
a) download all the 5.1.x jars from Jenkins and switch to these. I assume
the same process you did with formats-gpl. FormatTools is in the
"formats-api" jar. If you keep getting "NoSuchMethodError"s, you can look
>. For example, I
Hope this helps. Please let me know if you have any other problems or
> 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
>>
>
>