Re: Cannot use TurboReg plugin by using matlab

Posted by Mario Emmenlauer-3 on Dec 02, 2016; 12:55pm
URL: http://imagej.273.s1.nabble.com/Cannot-use-TurboReg-plugin-by-using-matlab-tp5017668p5017675.html

Hi,

On 02.12.2016 13:16, Curtis Rueden wrote:
> Alternately, as Mario said, you can try updating MATLAB to use Java 8.

I tried to rather discourage this path :-) :-) :-) Whenever I tried
to change Matlab Java (even minor changes in the same major version)
I got into a hell lot of problems. Java is integral to Matlab, and
Matlab brings a whole lot of dependencies (that are not meant to be
modified), so its likely to create a huge mess :-)

Just my two cents! Cheers,

    Mario

> Hopefully Mathworks will update MATLAB to support Java 8 in the future.
>
> 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 Thu, Dec 1, 2016 at 7:28 PM, LCY <[hidden email]> wrote:
>
>> Hi, Mario,
>>
>> Thank you very much for your help! Maybe I can try other plugins that have
>> the same function with TurboReg.
>>
>> All the best,
>>
>> Chunyue
>>
>>
>>
>> 2016-12-01 22:14 GMT+08:00 Mario Emmenlauer-3 [via ImageJ] <
>> [hidden email]>:
>>
>>> Hi Chunyue,
>>>
>>> On 01.12.2016 14:43, LCY wrote:
>>>
>>>> Dear all,
>>>>
>>>> I try to align a tiff stack to a tiff template image.  The tiff stack
>>>> contains more than 900 images, so I write a  Matlab code to use
>> TurboReg
>>> to
>>>> finish this step. The code is as follow:
>>>>
>>>> MIJ.run('TurboReg ', ['-align ', '-file ',fileNames{1,1},' ','0 0 ',
>>>> num2str(width),' ',num2str(height),' ',
>>>>     '-file ',fileNames{2,1},' ','0 0 ',num2str(width),' ',
>>> num2str(height)
>>>> ,' ','-rigidBody ',num2str(width/2),' ',num2str(height/2),'
>>>> ',num2str(width/2),' ',num2str(height/2),' ','0',num2str(height/2),'
>>> ','0
>>>> ',num2str(height/2),' ',num2str(width-1),' ',num2str(height/2),'
>>>> ',num2str(width-1),' ',num2str(height/2),' ','-showOutput']);
>>>>
>>>> However, ImageJ Exception showed as follow:
>>>> " ImageJ 1.51h; Java 1.7.0_60 [64-bit]; Windows 8 6.2; 422MB of 3725MB
>>> (11%)
>>>>
>>>> java.lang.UnsupportedClassVersionError: HandleExtraFileTypes :
>>> Unsupported
>>>> major.minor version 52.0
>>>>
>>>> This plugin requires Java 1.8 or later."
>>>>
>>>> Fiji outside Matlab showed java' version is 1.8.0_112. But when I
>>> launched
>>>> ImageJ from Matlab, the java version changed to  1.7.0_60.
>>>
>>> Matlab brings its own version of Java. Its an integral part of
>>> Matlab. I can not recommend running Matlab with a different version
>>> of Java, and certainly not going from 1.7 to 1.8 (unless somebody
>>> has by chance good experience with this). I tried it in the past and
>>> got many problems.
>>>
>>> It might be a lot easier to compile your Fiji dependencies with
>>> Java 1.7 and use this in Matlab.
>>>
>>> Hope this helps...
>>>
>>> Viele Grüße,
>>>
>>>     Mario Emmenlauer
>>>
>>>
>>> --
>>> BioDataAnalysis GmbH, Mario Emmenlauer      Tel. Buero: [phone]
>>> <+49%2089%2074677203>
>>> Balanstr. 43                   mailto: memmenlauer * biodataanalysis.de
>>> D-81669 München                          http://www.biodataanalysis.de/
>>>
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>>>
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Viele Gruesse,

    Mario Emmenlauer


--
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