[ImageJ-devel] KNIME and ops

Christian Dietz christian.dietz at uni-konstanz.de
Tue Aug 25 02:57:43 CDT 2015


Hi Brian,

The ImageJ2 Extension of KNIME is not part of the "Trusted Community
Nodes", and therefore not visible directly in the "Trusted Community
Contributions" Update-Site, as some testing workflows are missing and
there will be some refactoring before it's considered as "trusted".
However, you can install it via the "Stable" or "Nightly" update-sites
of the KNIME Community Contributions (see "Step 2.2" in
https://tech.knime.org/wiki/install-knime-image-processing and
https://tech.knime.org/wiki/knime-image-processing-nightly-build ).

Let me know if you need further help.

Christian




On Mo, 2015-08-24 at 17:04 -0400, Brian Northan wrote: 
> Hi Christian
> 
> 
> I hope you had a nice holiday.  Are you back now??
> 
> 
> I found some example KNIME workflows for imagej/imagej2 integration
> here https://tech.knime.org/community/imagej
> .
> 
> The problem is that I cannot find the 'ImageJ Macro' or the 'Image2
> integration' nodes.  I searched for 'imagej' in the node repository
> and explored the community nodes.  I also looked for them using
> "Install KNIME extensions...", but couldn't find anything imagej
> related. 
> 
> 
> Any suggestions??
> 
> 
> Thanks
> 
> 
> Brian 
> 
> 
> On Thu, Aug 20, 2015 at 10:50 AM, JAY W WARRICK <warrick at wisc.edu>
> wrote:
>         It happens that I just put that in my calendar to try and
>         attend (at least what I can fit in). Cool.
>         
>         J 
>         
>         On Aug 20, 2015, at 9:47 AM, Curtis Rueden <ctrueden at wisc.edu>
>         wrote:
>         
>         
>         > Hi Jay,
>         > 
>         > Christian will not be at the IJ conference (conflict with
>         > another conference), but will be at the hackathon afterward.
>         > 
>         > Regards,
>         > Curtis
>         > 
>         > On Aug 20, 2015 9:42 AM, "JAY W WARRICK" <warrick at wisc.edu>
>         > wrote: 
>         >         I'd be interested in keeping up with this
>         >         conversation. We do the same thing in JEX to expose
>         >         ImageJ commands (that are headless and have a menu
>         >         path) as functions. Exposing some Ops would be great
>         >         too. Will you be at the imagej conference that I
>         >         could pick your brain on related questions? 
>         >         
>         >         
>         >         Cheers, 
>         >         
>         >         
>         >         Jay 
>         >         
>         >         > On Aug 19, 2015, at 2:19 PM, Christian Dietz
>         >         > <Christian.Dietz at uni-konstanz.de> wrote: 
>         >         > 
>         >         > Sorry, I was not really precise: all Commands
>         >         > which are declared as headless and have a menu
>         >         > path.
>         >         > 
>         >         > And yes: like this we could select the ops which
>         >         > are exposed as nodes.
>         >         > 
>         >         > Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden
>         >         > <ctrueden at wisc.edu>: 
>         >         >         Hi Christian, 
>         >         >         
>         >         >         
>         >         >         > currently, we can automatically create
>         >         >         nodes from Commands and not 
>         >         >         > from ops. 
>         >         >         
>         >         >         
>         >         >         But all Ops are Commands...? 
>         >         >         
>         >         >         
>         >         >         > From a technical point of view it would
>         >         >         be easy to adapt this 
>         >         >         > mechanism to Ops, but I am not sure if
>         >         >         we want that (as you dont want 
>         >         >         > to create a node for each and every
>         >         >         atomar op). I hope we will 
>         >         >         > find a nice strategy when to expose an
>         >         >         Op as a KNIME node. 
>         >         >         
>         >         >         
>         >         >         Possible solutions: 
>         >         >         * Expose all Commands (including Ops) that
>         >         >         declare a menu path. 
>         >         >         * Expose Commands which have (or do not
>         >         >         have) a particular attribute key. We use
>         >         >         this for ImageJ1, adding a "no-legacy"
>         >         >         attribute for commands which should not be
>         >         >         exposed from the legacy ImageJ1 user
>         >         >         interface. 
>         >         >         
>         >         >         
>         >         >         Regards, 
>         >         >         Curtis 
>         >         >         
>         >         >         On Wed, Aug 19, 2015 at 12:36 PM,
>         >         >         Christian Dietz
>         >         >         <christian.dietz at uni-konstanz.de> wrote:
>         >         >                 Hi Brian,
>         >         >                 
>         >         >                 currently, we can automatically
>         >         >                 create nodes from Commands and not
>         >         >                 from ops. From a technical point
>         >         >                 of view it would be easy to adapt
>         >         >                 this mechanism to Ops, but I am
>         >         >                 not sure if we want that (as you
>         >         >                 dont want to create a node for
>         >         >                 each and every atomar op). I hope
>         >         >                 we will find a nice strategy when
>         >         >                 to expose an Op as a KNIME node.
>         >         >                 
>         >         >                 Anyway, Commands can be installed
>         >         >                 if the imagej2 extension is also
>         >         >                 installed within KNIME. I can send
>         >         >                 you more details next Monday, when
>         >         >                 I'm back from vacation.
>         >         >                 
>         >         >                 Hope this helps,
>         >         >                 
>         >         >                 Christian 
>         >         >                 
>         >         >                 Am 19.08.2015 5:58 nachm. schrieb
>         >         >                 Brian Northan
>         >         >                 <bnorthan at gmail.com>:
>         >         >                 >
>         >         >                 > Hi
>         >         >                 >
>         >         >                 > I have a question for the KNIME
>         >         >                 folks. 
>         >         >                 >
>         >         >                 > My understanding is that KNIME
>         >         >                 can auto-generate a node for every
>         >         >                 class that implements an op.  Is
>         >         >                 this correct??  And if so does the
>         >         >                 current release of KNIME recognize
>         >         >                 ops??  Or do I need a development
>         >         >                 version??
>         >         >                 >
>         >         >                 > How does one install an op to
>         >         >                 KNIME??  Do you just place
>         >         >                 the .jar file in a certain
>         >         >                 directory??  Or do you have to go
>         >         >                 through the 'install KNIME
>         >         >                 extensions' option??  Or something
>         >         >                 else??
>         >         >                 >
>         >         >                 > Thanks
>         >         >                 >
>         >         >                 > Brian
>         >         >                 
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