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

Mon Apr 11 11:14:23 EDT 2016

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 <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 <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 <mailto: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 <mailto: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$AddCommand( 'sitkEndEvent', f2 )
>> 
>> I was running in a terminal on my mac, with an older version of R.
>> 
>> 
>> On Mon, Apr 11, 2016 at 9:56 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com <mailto:mrguilfoyle at gmail.com>> wrote:
>> Richard
>> 
>> It seems it must be something specific to my setup.  I ran your example and get the same hard abort in Rstudio.  Running the example in R.app I get the same error but a  somewhat more graceful crash with the following error message:
>> 
>> gaussian$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 <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 <mailto: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 <mailto: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 <mailto: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 <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 <http://www.kitware.com/>
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html <http://www.kitware.com/opensource/opensource.html>
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php <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 <http://www.itk.org/Wiki/ITK_FAQ>
>>>> 
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://public.kitware.com/mailman/listinfo/insight-users <http://public.kitware.com/mailman/listinfo/insight-users>
>> 
>> 
> 
> _____________________________________
> Powered by www.kitware.com <http://www.kitware.com/>
> 
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html <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/20160411/7dfc5d42/attachment.html>