[ITK-users] SimpleITK and R wrapping problems (bugs?)

[Mathew Guilfoyle]

Thanks Richard

I’ve built the SWIG branch and used it to recompile SimpleITK with R wrapping - so far working like a charm!

Character vectors as arguments and returns now seems to be working fine; I can access the DICOM image metadata as expected.  The ImageSeriesReader_GetGDCMSeriesFileNames() also now works.  I guess it would be nice to have the static methods available via the $ operator just for consistency with e.g. Python wrapping but it is not a big deal.

Many thanks for the help


> On 5 Apr 2016, at 04:30, Richard Beare <richard.beare at gmail.com> wrote:
> 
> I have a better fix for this now, but it requires building your own swig. I've made a pull request but it will probably take a while to work its way through to the release.
> 
> If you get swig from:
> 
> https://github.com/richardbeare/swig.git <https://github.com/richardbeare/swig.git>
> 
> and use the RCharacterVectorSupport branch then you will end up with a working version (hopefully).
> 
> The issue with static methods seems to vary with language - some bindings allow an instance of a class to access a static method, others don't.
> 
> 
> 
> On Mon, Apr 4, 2016 at 1:18 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com <mailto:mrguilfoyle at gmail.com>> wrote:
> Hi
> 
> I’ve been trying to get to grips with using the R wrapping to SimpleITK.  On OS X 10.11 I’ve successfully built/compiled SimpleITK from source with Python and R wrapping turned on in Cmake.  I can import the SimpleITK package into R 3.2.4 within Studio without any error reports.
> 
> The main difficulties I’m finding are around importing CT image volumes which are stored as a series of image slices within a single directory.   Following the usual workflow I’ve tried in Python I start with:
> 
> reader = ImageSeriesReader()
>  
> this works ok but the ‘GetGDCMSeriesFileNames’ function is not exposed for the reader object via the $ operator.   This is in contrast to the Python wrapping where this function is available as 'reader.GetGDCMSeriesFilenames()'
> 
> In R the ImageSeriesReader_GetGDCMSeriesFileNames() static function is available but does not work when supplied with a directory either as a R character vector or as a SimpleITK ‘VectorString’ object.
> 
> For the moment I have resorted to getting a list of the files with native R code. Passing this list as an argument to reader$SetFileNames() causes the R session to crash.  Instead I’ve created a (SimpleITK) VectorString of appropriate length and then transfer the individual filenames from the R list within a loop, before finally using the reader$SetFileNames(VectorString) method.  When I then run reader$Execute the DICOM image series is correctly read to an image object.
> 
> Next I need to do some initial image transformation based on certain fields of DICOM metadata.  However, I’ve not been able to access this at all.  The image$GetMetaDataKeys() function does not work, reporting the error:
> 
> Error in validObject(.Object) : 
>   invalid class “_p_std__vectorT_std__string_std__allocatorT_std__string_t_t” object: invalid object for slot "ref" in class "_p_std__vectorT_std__string_std__allocatorT_std__string_t_t": got class "character", should be or extend class "externalptr"
> 
> Image$GetMetaData(key) also returns an error whatever key value I use (including DICOM keys that I know are included in the series), whether these are passed as as an R character string or SimpleITK VectorString.
> 
> I know that the metadata is being read, at least to a certain extent, because  basic info like pixel spacing, image direction, origin etc are all present and correct, and accessible via their dedicated Get.. methods.
> 
> If I’m using these functions with incorrect arguments or committing some other error I would be grateful for any pointers.
> 
> Cheers
> Mat
> 
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