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

[Brian Northan]

Ubuntu 14.04 GNU tar 1.27.1.  On second thought I must be having gremlins
while downloading.  I tried again and the download was 148.1 MB this time
and it worked.


On Mon, Aug 4, 2014 at 5:36 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Brian,
>
> > 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.
>
> Which OS? Which program?
>
> On OS X, "tar xf" from the command line works for me.
>
> On Windows, did you try 7-zip?
>
> Regards,
> Curtis
>
>
> On Mon, Aug 4, 2014 at 4:34 PM, Brian Northan <bnorthan at gmail.com> wrote:
>
>> 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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