[ImageJ-devel] 'ops not defined' when running jython script

[Brian Northan]

Regarding the download problem.  The download is 141 MB.  So something must
be wrong with my archive manager set up.  I'll have to figure it out.  It
handles zip fine but not tar.


On Mon, Aug 4, 2014 at 5:14 PM, Brian Northan <bnorthan at gmail.com> wrote:

> Hi Curtis
>
> Thanks, it worked perfectly - btw I doubled posted on the fiji list as I
> figured this question might be of interest to any fiji users trying out the
> new scripting.
>
> Brian
>
>
> On Mon, Aug 4, 2014 at 5:06 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
>> Hi Brian,
>>
>> Thanks for the reports:
>>
>> > 1.  The last couple of days when I try to extract the Fiji Linux 64
>> > continuous release tar file I get an error "truncated gzip input".  I
>> can
>> > work around this by downloading the "all platforms" package instead.
>>
>> Hmm, I did not see this problem when I tried just now. Perhaps the
>> download itself is not completing successfully? It should be ~141MB. If it
>> keeps happening, we could add an MD5 sum for verification if that would be
>> helpful.
>>
>> > 2.  It seems that the ops service is not getting injected into my jython
>> > scripts.  Scripts works fine (ie data and display are injuected) until
>> I try
>> > to call an op.  Then I get "ops is not defined".   This only happens
>> when
>> > using a Fiji release.  If I run imagej2 through a development
>> environment
>> > using maven it works.
>>
>> Yeah, I noticed this same problem the other day, and fixed it on master:
>>
>>
>> https://github.com/scijava/scijava-common/commit/f88984cb587c314c53e06fdce606d4cecf3a4813
>>
>> Using scijava-common-2.28.0 or later will avoid the issue. Or you can
>> work around it by writing:
>>
>>     # @net.imagej.ops.OpService ops
>>
>> Regards,
>> Curtis
>>
>>
>> On Mon, Aug 4, 2014 at 3:32 PM, Brian Northan <bnorthan at gmail.com> wrote:
>>
>>> Hi List
>>>
>>> A couple of things...
>>>
>>> 1.  The last couple of days when I try to extract the Fiji Linux 64
>>> continuous release tar file I get an error "truncated gzip input".  I can
>>> work around this by downloading the "all platforms" package instead.
>>>
>>> 2.  It seems that the ops service is not getting injected into my jython
>>> scripts.  Scripts works fine (ie data and display are injuected) until I
>>> try to call an op.  Then I get "ops is not defined".   This only happens
>>> when using a Fiji release.  If I run imagej2 through a development
>>> environment using maven it works.
>>>
>>> Thanks, an example script is below
>>>
>>> Brian
>>>
>>> # @DatasetService data
>>> # @DisplayService display
>>> # @OpService ops
>>>
>>> # define a local directory to get the images from
>>> directory="/home/bnorthan/Brian2014/Images/TempForEasyAccess/"
>>>
>>> # use 2-channels of the lena image for test image
>>> image1Name="lena_red.tif"
>>> image2Name="lena_green.tif"
>>>
>>> # open first image
>>> image1=data.open(directory+image1Name)
>>> display.createDisplay(image1.getName(), image1);
>>>
>>> # open second image
>>> image2=data.open(directory+image2Name)
>>> display.createDisplay(image2.getName(), image2);
>>>
>>> # add the images
>>> image3 = ops.add(image1,image2)
>>> display.createDisplay(image3.getName(), image3)
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> ImageJ-devel mailing list
>>> ImageJ-devel at imagej.net
>>> http://imagej.net/mailman/listinfo/imagej-devel
>>>
>>>
>>
>
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