[ITK-users] (R wrapping/SimpleITK) AddCommand to ImageRegistrationMethod bug

Fri Apr 15 09:15:56 EDT 2016

Thanks Richard.
Followed your advice and found my way. The example script works like a
charm :-)
Are all the itk filters now callable from R, or just a subset ? how can I
know this ?
Thanks for all the great effort.

--
Fethallah

On Thu, Apr 14, 2016 at 11:26 PM, Richard Beare <richard.beare at gmail.com>
wrote:

> You ought to be OK with bison - can you get that?
>
> The latest version of simpleitk on the github site have support for
> building swig from github,so you can avoid the manual build. On all the
> systems I've tested it is bison that appears to be used in the early stages
> of swig building.
>
> On Fri, Apr 15, 2016 at 6:57 AM, Fethallah Benmansour <fethallah at gmail.com
> > wrote:
>
>> Hi there,
>>
>> Any chance to get it to work on a Redhat 6.3 ?
>> The current blocker is yacc, which I couldn't install with yum (EPEL
>> enabled).
>>
>> Thanks,
>>
>> --
>> Fethallah
>>
>> On Mon, Apr 11, 2016 at 5:14 PM, Bradley Lowekamp <brad at lowekamp.net>
>> wrote:
>>
>>> Hello,
>>>
>>> We have R tested with SimpleITK on a number of systems each night. And
>>> this morning we have run the tests on several systems, and it is running
>>> and passing OK, this was with what every old R version was on the systems
>>>
>>> We should focus on getting the tests to pass on your system first. It’s
>>> a good sign that you can run the AddCommand with the sitk::Command class.
>>> Does the rest of the R tests pass when you run ctest?
>>>
>>> I am still suspicious you are not running the latest development
>>> version. What is the git hash you are using?
>>>
>>> As you were digging into the SimpleITK R code you were on the right
>>> track with the ProccessObject::AddCommand and the sitk::Command class. The
>>> other two parts you are missing is the RCommand C++ class [1], and the
>>> overridden ProcessObject::AddCommand method [2]. These were recently added
>>> to SimpleITK since the 0.9 release. You can see that the added procedure
>>> wraps the passed callable, into the RCommand class.
>>>
>>> HTH,
>>> Brad
>>>
>>>
>>> [1]
>>> https://github.com/SimpleITK/SimpleITK/blob/master/Wrapping/R/sitkRCommand.h
>>> [2]
>>> https://github.com/SimpleITK/SimpleITK/blob/2ffffba589b24465a09eed1303bbffd6fe3fe18e/Wrapping/R/R.i#L565-L589
>>>
>>> On Apr 11, 2016, at 3:59 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>> wrote:
>>>
>>> I tried running the code below as suggested - both in RStudio and the
>>> terminal - and get the same abort/segfault error.
>>>
>>> Which version of R are you running? - I can install an older version to
>>> see if it works.
>>>
>>> On 11 Apr 2016, at 01:02, Richard Beare <richard.beare at gmail.com> wrote:
>>>
>>> This is a long shot, but lets try testing whether it is the R garbage
>>> collection causing issues. Modify the test so that every method call result
>>> is assigned to a different variable:
>>>
>>> e.g.
>>>
>>> a1 <- gaussian$SetVariance(2)
>>> a2 <- gaussian$AddCommand( 'sitkStartEvent',  f1 )
>>> a3 <- gaussian$AddCommand( 'sitkEndEvent', f2 )
>>>
>>> I was running in a terminal on my mac, with an older version of R.
>>>
>>>
>>> On Mon, Apr 11, 2016 at 9:56 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com
>>> > wrote:
>>>
>>>> Richard
>>>>
>>>> It seems it must be something specific to my setup.  I ran your example
>>>> and get the same hard abort in Rstudio.  Running the example in R.app I get
>>>> the same error but a  somewhat more graceful crash with the following error
>>>> message:
>>>>
>>>> gaussian$AddCommand( 'sitkStartEvent',  f1 )
>>>>
>>>>  *** caught segfault ***
>>>> address 0x7ff511000080, cause 'memory not mapped'
>>>>
>>>> Traceback:
>>>>  1: .Call("R_swig_ProcessObject_AddCommand", self, event, cmd,
>>>> as.logical(.copy),     PACKAGE = "SimpleITK")
>>>>  2: f(x, ...)
>>>>  3: gaussian$AddCommand("sitkStartEvent", f1)
>>>>
>>>> Possible actions:
>>>> 1: abort (with core dump, if enabled)
>>>> 2: normal R exit
>>>> 3: exit R without saving workspace
>>>> 4: exit R saving workspace
>>>>
>>>> I have tried the version of SimpleITK built without the version of SWIG
>>>> you patched to correct the character argument error, again I get the same
>>>> behaviour.
>>>>
>>>> Bradley - I’m using the latest SimpleITK 0.9 source compiled using the
>>>> super build on OS X 10.11.  I’ve done the build with the supplied SWIG and
>>>> with a version patched by Richard and available here:
>>>> https://github.com/richardbeare/swig.git.  I’m funning R 3.2.4 in
>>>> Rstudio IDE.
>>>>
>>>>
>>>>
>>>> On 10 Apr 2016, at 23:17, Bradley Lowekamp <brad at lowekamp.net> wrote:
>>>>
>>>> Hello,
>>>>
>>>> I would like to know your environment.
>>>>
>>>> What version of SimpleITK?  R? OS? Compiler? Did you use simpleITK's
>>>> super build? If not what version of SWIG?
>>>>
>>>> Thanks
>>>>
>>>> On Apr 10, 2016, at 9:46 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>>> wrote:
>>>>
>>>> Richard
>>>>
>>>> Thanks for the reply.  I hadn't appreciated that function being passed
>>>> in the registration example was a closure.  However, in the
>>>> FiterProgressReporting example it is not a closure.
>>>>
>>>> I have modified my code to be a closure but still get a crash/abort; I
>>>> have also run the code in the examples themselves verbatim and get the same
>>>> problem.
>>>>
>>>> Any further ideas on how to get this working?
>>>>
>>>> Cheers
>>>>
>>>>
>>>> On 10 Apr 2016, at 02:10, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>>> wrote:
>>>>
>>>> There seems to be a problem with using the $AddCommand function to
>>>> ImageRegistrationMethod objects in the R wrapping to SimpleITK.
>>>>
>>>> Using R 3.2.4 on OS X 10.11
>>>>
>>>> Example:
>>>>
>>>> f <- function(x){print(x$GetMetricValue())}
>>>>
>>>> registration = ImageRegistrationMethod()
>>>>
>>>> registration$AddCommand(‘sitkIterationEvent’, f(registration))
>>>>
>>>> This last line causes R to abort/hard crash (no error message).  This
>>>> behaviour is irrespective of which event type I use or the function passed
>>>> as the second argument (e.g. even something simple like print(‘Hello’))
>>>>
>>>> The AddCommand method is inherited from the SimpleITK ProcessObject
>>>> type.  Digging around in the SimpleITK.R file I can see that the
>>>> ProcessObject$AddCommand method expects a second argument of type
>>>> ‘_p_itk__simple__Command’.
>>>>
>>>> There is a ‘Command’ method that generates a new object of type
>>>> ‘_p_itk__simple__Command’.  If I pass this resulting object as the second
>>>> argument to registration$AddCommand then I do not get an error.  However,
>>>> there doesn’t seem to be any way to point the ‘_p_itk__simple__Command’
>>>> object to my function or otherwise convert my function to a
>>>> ‘_p_itk__simple__Command’ type.
>>>>
>>>> The $AddCommand method is used in a couple of example scripts on the
>>>> SimpleITK site (using it for monitoring a registration and a filter e.g.
>>>> https://github.com/SimpleITK/SimpleITK/blob/master/Examples/FilterProgressReporting.R)
>>>> so I don’t know if it was working previously and a bug has been introduced
>>>> more recently? (the example scripts cause the same error when I run them
>>>> now)
>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>>
>>>>
>>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>>
>>> _____________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.kitware.com/opensource/opensource.html
>>>
>>> Kitware offers ITK Training Courses, for more information visit:
>>> http://www.kitware.com/products/protraining.php
>>>
>>> Please keep messages on-topic and check the ITK FAQ at:
>>> http://www.itk.org/Wiki/ITK_FAQ
>>>
>>> Follow this link to subscribe/unsubscribe:
>>> http://public.kitware.com/mailman/listinfo/insight-users
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/insight-users/attachments/20160415/5e9b415b/attachment.html>