http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5011398.html
files correctly. The problem still appears to be in formats-gpl.jar.
ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
and tried those. The same problem occurs, except that
On the OME tracking system, this bug is said to be resolved. If so, then
> On 12/6/14, 12:16 AM, Curtis Rueden wrote:
>> Hi Aryeh,
>>
>> > About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
>> > updater to update formats-gpl. The updated version correctly read my
>> > multifield ND2, so I thought that this bug was resolved. However,
>> > yesterday, following an update, the problem reappeared. Again,the
>> > workaround was to use the 5.0.2 version of formats-gpl.
>>
>> That is very odd. It would be great if you could somehow isolate the
>> difference between the working version of Fiji vs. the non-working
>> one—especially if they both used Bio-Formats 5.0.6.
>>
> I checked my backups, and I have been unable to find a working updated
> bioformats-gpl in my recent backups. This most likely means that I was
> mistaken about the problem being temporarily fixed.
>> What happens if you enable the Bio-Formats update site? Still non-working?
>>
> It fails both ways.
> Here is the info form teh advanced mode of the updater for the two
> bioformats-gpl files:
>
> bioformats from fiji site
> bioformats-gpl-5.0.6
> Modified 11 Nov 2014
>
> bioformats from bioformats site
> bioformats-gpl
> Modified 04 Nov 2014
>
> Both fail the same way.
>> If you get a chance, you could also test with the "showinf" command
>> line tool [1], which would rule out any Fiji-specific installation
>> issues. And of course testing from multiple different machines might
>> also shed some light on things.
>>
> The showinf output has the same error -- it is not Fiji specific.
> I can also tell you that the same problem occurs on a Windows 7-64bit
> OS, and the workaroudn is identical (fall back to gpl-5.0.2
>
> As long as the workaround works, it is ok. However, that seems like
> living on borrowed time...
>> Regards,
>> Curtis
>>
> Thank you for your attention to this.
>
> Best regards,
> --aryeh
>
>> [1]
>>
http://openmicroscopy.org/site/support/bio-formats5/users/comlinetools/>>
>> On Thu, Nov 27, 2014 at 1:45 AM, Aryeh Weiss <
[hidden email]
>> <mailto:
[hidden email]>> wrote:
>>
>> On 10/6/14, 11:17 PM, Aryeh Weiss wrote:
>>
>> Hi Melissa
>>
>> On 10/6/14, 4:27 PM, Melissa Linkert wrote:
>>
>> Hi Aryeh,
>>
>> 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).
>>
>> How can I turn this into the formats-gpl.jar file?
>> If I can do that, I will replace my version 5.0.2
>> file, and see if it
>> works properly
>>
>> Instead of compiling from source, you can also download
>> the latest 5.1
>> builds from:
>>
>>
http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>>
>>
>> For anyone trying this though, please do note that mixing
>> 5.1 and 5.0
>> files is not supported and very unlikely to work, so you
>> will need to
>> update all files to 5.1. Be aware that this can cause
>> problems with
>> other plugins that use Bio-Formats, as there are API
>> differences between
>> the two versions (though we have not yet released 5.1.0).
>>
>>
>> Thank you (and also Mark) for your replies.
>> I downloaded the 5.1 builds for all of the jar files in the
>> jars/bio-formats directory of my Fiji distribution.
>> When I dragged one of my nd2 files into Fiji, bio-formats
>> opened, but had the same bug as reported previously.
>> When I restored the old bio-formats directory with the 5.0.2
>> version of gpl, it worked properly.
>> I did not try the 5.0.2 gpl with the 5.1 release, because of
>> Melissa warning concerning mixing the two versions.
>>
>>
>> Best regards
>> --aryeh
>>
>>
>> We are also considering this fix for a 5.0.6 release of
>> Bio-Formats, which
>> would eliminate the need to manually update files.
>>
>> Regards,
>> -Melissa
>>
>>
>> About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
>> updater to update formats-gpl.
>> The updated version correctly read my multifield ND2, so I thought
>> that this bug was resolved.
>> However, yesterday, following an update, the problem reappeared.
>> Again,the workaround was to use the 5.0.2 version of
>> formats-gpl.
>>
>> I have not had a chance to search my recent backups for this file
>> to see if I can determine exactly when it broke again -- I will
>> try to do that.
>>
>>
>> Best regards,
>> --aryeh
>>
>>
>>
>> On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
>>
>> Hi Aryeh,
>>
>> How can I turn this into the formats-gpl.jar file?
>>
>> Great question! I'm cc'ing the list because I think
>> this information is of
>> general interest.
>>
>> The Bio-Formats site has a page with instructions for
>> downloading and
>> building the jars from source:
>>
https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html>>
>>
>> After cloning the Bio-Formats repository
>> <
http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
>>
>> you can either:
>> * Check out a specific tag
>> <
http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
>>
>> or
>> * Check out a specific commit
>> <
http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>>
>>
>> Or it should be fine to just build the "develop"
>> branch, since the patch in
>> question was merged.
>>
>> After building Bio-Formats, all the output .jars will
>> be in the /artifacts
>> sub-directory of your Bio-Formats checkout.
>>
>> Let me know if you have any more questions, and thank
>> you for taking the
>> time to test this!
>>
>> Regards,
>> Mark
>>
>>
>> On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss
>> <
[hidden email] <mailto:
[hidden email]>> wrote:
>>
>> Hi Mark
>>
>> On 10/1/14, 10:21 PM, Mark Hiner wrote:
>>
>> 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).
>>
>> How can I turn this into the formats-gpl.jar file?
>> If I can do that, I will replace my version 5.0.2
>> file, and see if it
>> works properly
>>
>> thanks and best regards
>> --aryeh
>>
>>
>>
>>
>>
>>