[slicer-users] CLP module passed region: can not change coordinate system

Casey Goodlett casey.goodlett at kitware.com
Fri Apr 16 11:17:50 EDT 2010


Jim or Steve,

I looked through the CommandLineMoudleLogic to see if it would be easy to
add support for the coordinate system tag for MRMLROINode, but couldnt find
a good example.

Is this tag for documentation purposes only?  Should I update the
documentation to indicate that changing the tag doesnt change the value of
the coordinates received on the command line for points or regions?

Thanks

Casey

On Thu, Apr 15, 2010 at 10:34 PM, Casey Goodlett <casey.goodlett at kitware.com
> wrote:

> Andriy & Sajendra,
>
> I updated the command line module to accept MRMLROINode as a region to
> support some of the registration modules.  I didn't do anything to support
> different coordinate systems.  I'm using this from ITK in a CLI module but
> just doing the conversion there myself.
>
> I'll update the wiki documentation for CommandLineModule to indicate that
> the coordinate system tag is not supported for this.
>
> Thanks
>
> Casey
>
>
> On Thu, Apr 15, 2010 at 9:15 PM, Andriy Fedorov <fedorov at bwh.harvard.edu>wrote:
>
>> On Thu, Apr 15, 2010 at 18:19, Sajendra <sajendra at gmail.com> wrote:
>> > I saw the earlier thread but it seems some work has been done on this
>> > feature since then (somewhere from 3.4 to 3.5 Alpha). I am able to
>> > define an ROI within slicer and pass those parameters to my CLI
>> > module, but do not seem to be able to modify the coordinate system it
>> > is passed in. If this is a bug I can certainly submit a report if my
>> > understanding of the situation is correct.
>>
>> Ah, you are absolutely correct, and I am out of date! MRMLROINode is
>> indeed supported, and this is great (kudos to Casey!):
>>
>>
>> http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx?rev=12276&view=log
>>
>> However, note that this feature was implemented 6 weeks ago, and the
>> Execution Model documentation was not updated in the corresponding
>> section since last year. I would guess wiki is not up to date.
>>
>> Casey, could you comment?
>>
>> > As an aside, is interfacing with CLI modules an issue that is better
>> > discussed on the users list or the developers list?
>> >
>>
>> Definitely. I am moving this to slicer-devel.
>>
>>
>> > Sajendra
>> >
>> > On Thu, Apr 15, 2010 at 5:39 PM, Andriy Fedorov <
>> fedorov at bwh.harvard.edu> wrote:
>> >> Sajendra,
>> >>
>> >> I do not think this functionality is supported. See earlier thread
>> here:
>> >>
>> >>
>> http://massmail.spl.harvard.edu/public-archives/slicer-devel/2009/003551.html
>> >>
>> >> You can submit a bug report to mantis
>> >> http://www.na-mic.org/Bug/view_all_bug_page.php and describe your
>> >> needs and/or inconsistency of the documentation.
>> >>
>> >> AF
>> >>
>> >>
>> >> On Thu, Apr 15, 2010 at 14:52, Sajendra <sajendra at gmail.com> wrote:
>> >>> Hello,
>> >>>
>> >>> I am trying to create an excecutable plugin with command line options
>> >>> that accepts as input a "region", represented in the slicer GUI as a
>> >>> MRMLROINode. I have tested this with Slicer 3.5 (including the latest
>> >>> Nightly Build: 2010-04-15) and am having a problem with the coordinate
>> >>> system the region is passed in.
>> >>> In my XML file I define the region input variable as follows:
>> >>> <region coordinateSystem="XXX" multiple="false">
>> >>>      <label>Region</label>
>> >>>      <name>region</name>
>> >>>      <longflag>region</longflag>
>> >>>      <description>...</description>
>> >>> </region>
>> >>> where according to the XML schema
>> >>> (
>> http://www.slicer.org/slicerWiki/index.php/Slicer3:Execution_Model_Documentation#XML_Schema
>> )
>> >>> XXX can be set to either "lps","ras", or "ijk". I have found that no
>> >>> matter which of the three I choose, the input passed at the command
>> >>> line to my module is the same. I am assuming that the coordinates are
>> >>> being passed in RAS coordinates as in order to make the region work
>> >>> with ITK code within the command line module I have to negate the x
>> >>> and y coordinates. Similarly, changing multiple to either true or
>> >>> false does not seem to have any effect, but the desired output of that
>> >>> attribute is not clear to me, nor documented, so I can't say what the
>> >>> exact use of it is. Am I missing something regarding reading the
>> >>> region coordinates, or is this a bug where the coordinate system
>> >>> attribue is being ignored?
>> >>>
>> >>> Thank you,
>> >>> Sajendra
>> >>> _______________________________________________
>> >>> slicer-users mailing list
>> >>> slicer-users at bwh.harvard.edu
>> >>> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> >>> To unsubscribe: send email to
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>> subject
>> >>>
>> >>
>> >
>>
>
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