Posted by
Aryeh Weiss on
Nov 27, 2014; 7:45am
URL: http://imagej.273.s1.nabble.com/Latest-Bio-Formats-in-Fiji-tp5009834p5010654.html
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]>
>>> 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
>>>>
>>>>
>>>>
>
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
--
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