http://imagej.273.s1.nabble.com/Phansalkar-threshold-bug-tp5016717p5016802.html
Perhaps I missed it (if so, I apologize) - but, since I’ve just finished processing some 1500 images with a plugin that
depends on Phansalkar…can someone please give me a gloss on what the bug is and how it manifests itself?
The good/bad news is that the Phansalkar thresholding is a preliminary step - followed immediately by manual editing.
On the one hand, my collaborator would *not* be pleased with the prospect of re-processing all 1500 images again.
On the other hand, whatever errors were introduced were probably fixed in the manual editing.
> On Jul 1, 2016, at 08:54, Curtis Rueden <
[hidden email]> wrote:
>
> Hi Gabriel,
>
>> Be warned that when I switched to the Java8 update site, an old
>> install (using Java 1.6) stopped working and had to download a new
>> install of Fiji again, which includes the Java 8 jdk.
>>
>> So, in resume, it is probably best to install Fiji again (which now
>> includes Java 1.8) to make sure that you have the latest fix.
>
> Yes, downloading a new Fiji bundle is the simplest solution.
>
> However, you certainly can update an existing Fiji installation if you
> prefer. But you need to make sure it is running Java 8 _before_ you enable
> the Java-8 update site. For more details, see:
>
>
http://imagej.net/2016-05-10_-_ImageJ_HOWTO_-_Java_8,_Java_6,_Java_3D#Upgrading_an_old_installation>
>> In Fiji the version number is handled automatically and is currently
>> 1.16.3 (elsewhere it is 1.7 as stated in the source code).
>
> You could unify this: remove the hardcoded version in the source code, in
> favor of calling org.scijava.util.VersionUtils.getVersion(Class) to
> retrieve the version from the JAR manifest or POM.
>
> Regards,
> Curtis
>
> --
> Curtis Rueden
> LOCI software architect -
http://loci.wisc.edu/software> ImageJ2 lead, Fiji maintainer -
http://imagej.net/User:Rueden> Did you know ImageJ has a forum?
http://forum.imagej.net/>
>
> On Fri, Jul 1, 2016 at 5:21 AM, Gabriel Landini <
[hidden email]>
> wrote:
>
>> On Thursday 23 Jun 2016 09:24:55 I wrote:
>>> There was a bug fixed in the computation of the Phansalkar local
>> threshold
>>> method. This affected the file I provide in my page, the one installed by
>>> default in plain IJ and the one in Fiji. It does not affect the
>> ImageJ-ops
>>> version.
>>>
>>> Wayne updated the class in the download package he provides, it was also
>>> pushed into the Fiji repository (so it should appear as an update soon)
>> and
>>> it was also updated in my page.
>>>
>>
http://www.mecourse.com/landinig/software/autothreshold/autothreshold.html>>
>> Hi, Just to update on this subject for those using Fiji.
>> The fix for Fiji is now available as an update, but note the the plugin is
>> now
>> available from the Java8 update site (so you need to subscribe to it to
>> receive the fix).
>> If you stay with 1.6 it appears that it is not possible to receive the
>> update.
>>
>> Be warned that when I switched to the Java8 update site, an old install
>> (using
>> Java 1.6) stopped working and had to download a new install of Fiji again,
>> which includes the Java 8 jdk.
>>
>> So, in resume, it is probably best to install Fiji again (which now
>> includes
>> Java 1.8) to make sure that you have the latest fix.
>>
>> In Fiji the version number is handled automatically and is currently 1.16.3
>> (elsewhere it is 1.7 as stated in the source code).
>>
>> Cheers
>>
>> Gabriel
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html