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

Mathew Guilfoyle mrguilfoyle at gmail.com
Mon Apr 11 03:59:44 EDT 2016 

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$AddCommand( 'sitkEndEvent', f2 )
> 
> I was running in a terminal on my mac, with an older version of R.
> 
> 
> On Mon, Apr 11, 2016 at 9:56 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com <mailto:mrguilfoyle at gmail.com>> wrote:
> Richard
> 
> It seems it must be something specific to my setup.  I ran your example and get the same hard abort in Rstudio.  Running the example in R.app I get the same error but a  somewhat more graceful crash with the following error message:
> 
> gaussian$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)
>>> 
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