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

Thu Apr 14 16:57:38 EDT 2016

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)
>>
>>
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