[Insight-users] Wrapping R with SimpleITK

Brandon Whitcher bwhitcher at gmail.com
Wed Jan 4 10:07:53 EST 2012 

Wes, thanks for your input here.  That would be great.  Do your methods
depend upon any ITK/SimpleITK routines?  I'm wondering if it would be
better to keep SimpleITK (the R wrapper version) as a separate R package
and then develop additional packages that add features, or just put
everything in one package (hmm).

For me, I've developed (with others) a lot of mathematical modelling and
statistical inference methods in R that operate on multidimensional arrays
(usually coming from one of the medical imaging data formats); e.g., for
functional MRI, DTI, HARDI or DCE-MRI.  What we lack is the so-called
pre-processing techniques needed in medical image analysis: segmentation,
filtering, registration, etc.  Hence, SimpleITK (the R wrapper version)
would be a great way to access the techniques listed previously on data
that have been read it via R, and stored as multidimensional arrays, then
take the output back into R for further analysis and visualization.

I'm looking for the best way to incorporate the impressive variety of ITK
routines into my R-based data analysis pipeline.

cheers...

Brandon
On 3 January 2012 18:28, Wes Turner <wes.turner at kitware.com> wrote:

>
>
> On Tue, Jan 3, 2012 at 10:37 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
>
>> Hello,
>>
>> It is great to hear that you are approaching ITK for the first time with
>> SimpleITK. Your feed back is very much appreciated so that we can improve
>> the documentations and the compilation procedures for a easier experience.
>>
>>
>> I have added the source of your Data problem to the FAQ here:
>>
>>
>> http://www.itk.org/Wiki/ITK/Release_4/SimpleITK/FAQ#Where_is_the_Input_Data.3F_or_Why_is_my_Testing.2FData_directory_empty.3F
>>
>> The output you have attached looks great! I hope you have had success
>> trying additional filters by now.
>>
>> You said that you want to read Nifti and ANALYZE data with R. ITK  and
>> SimpleITK also have good support for these image formats, so you may be
>> able to read directly with SimpleITK's ReadImage method or the
>> ImageFileReader object.
>>
>> There is currently no optimized method for exporting a SimpleITK image
>> into an R array. So you are likely must use the slow SetPixel and GetPixel
>> methods.
>>
>
> There are methods currently in VTK for conversion between VTK and R
> structures for some subset of formats.  I would be willing to provide some
> help and guidance.  It is only two classes and should be a short putt.
>
> - Wes
>
>
>> For visualization in SimpleITK we have a primitive sitk.Show method. This
>> method currently just writes the image out to disk and then loads is up in
>> ImageJ. To use the, you need a recent version of ImageJ. We hope to make
>> this methods more configurable in the future, and take advantage built in
>> language specific visualization tools. However, with SimpleITK supporting
>> 2D, 3D image, along with all the vector pixel types, and complex pixel
>> types etc... many existing tools don't have the needs support for all these
>> possibilities.
>>
>> Enjoy,
>>
>> Brad
>>
>>
>> ========================================================
>> Bradley Lowekamp
>> Medical Science and Computing for
>> Office of High Performance Computing and Communications
>> National Library of Medicine
>> blowekamp at mail.nih.gov
>>
>> On Jan 2, 2012, at 3:46 AM, Brandon Whitcher wrote:
>>
>> Following up on my previous message I found a copy of cthead1.png at
>>
>>
>> http://itk.org/gitweb?p=SimpleITKData.git;a=commitdiff;h=f7d86582b91a35e5c8d30f1b58320bc47cc658fa
>>
>> ...and downloaded it.  I have attached it and the "out.png" file from
>> your example code.
>>
>> > source("load.R")
>>
>> Creating a generic function for ‘print’ from package ‘base’ in the global
>> environment
>> > img <- ReadImage( "Input/cthead1.png" )
>> > (pid <- Image_GetPixelIDValue( img ))
>> [1] 1
>>
>> > simg <- SmoothingRecursiveGaussian( img, 4 )
>> > cimg <- Cast( simg, pid )
>> > WriteImage( cimg, "out.png" )
>>
>> Success!
>>
>> Now I need to read up on ITK functions and how to take an array in R
>> (containing ANALYZE or NIfTI data) and pass it into ITK, process it and
>> bring it back in order to visualize/manipulate in R.  I have a package that
>> performs basic I/O for ANALYZE and NIfTI using S4 objects in R (called
>> oro.nifti) and it would be great to pass these arrays (along with the
>> metadata) back-and-forth with SimpleITK.
>>
>> cheers...
>>
>> Brandon
>>
>>
>>
>> On 2 January 2012 08:37, Brandon Whitcher <bwhitcher at gmail.com> wrote:
>>
>>> Brad, as you can tell I'm completely new to ITK... thank-you for your
>>> patience.  My SimpleITK (source) Testing/Data directory is empty from my
>>> "clone-ing" via Git (I am also a Git novice, sorry).  Looking at the
>>> version control tree at
>>>
>>>
>>> http://itk.org/gitweb?p=SimpleITK.git;a=tree;f=Testing;h=eb50d756edee129fc26beb6d4c00f288ea49309a;hb=HEAD
>>>
>>> ...I get...
>>>
>>> m--------- - Data history
>>>
>>> ...which doesn't look too promising from my knowledge of file
>>> permissions.  How can I overcome this?  May I ask for "cthead1.png" via
>>> email to try this example ASAP?
>>>
>>> cheers...
>>>
>>> Brandon
>>>
>>>
>>> On 2 January 2012 04:21, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
>>>
>>>> Hello Brandon,
>>>>
>>>> As is frequently the case the first exception is the cause of the
>>>> remainder. To understand the first error message some explanation of the
>>>> how SimpleITK manages image types is needed.
>>>>
>>>> There may be some relevant information in the SimpleITK presentation
>>>> from MICCAI 2011:
>>>>
>>>> https://github.com/SimpleITK/SimpleITK-MICCAI-2011-Tutorial/blob/master/Presentation/SimpleITK-MICCAI-2011.pdf?raw=true
>>>>
>>>>
>>>> The sitk::Image class is a typeless image class which wraps numerous
>>>> ITK image types. Externally the sitk::Image class presents the same
>>>> interface for all images, wether it is a scalar itk::Image, a
>>>> multicomponent itk::VectorImage, or even a run-line compressed
>>>> itk::LabelMap. And then each of these ITK image types are templated over
>>>> the dimension and the pixel type. So SimpleITK presents dozens of itk
>>>> images types through a single sitk::Image object.
>>>>
>>>> So SimpelITK is not strongly typed on these individual image types, but
>>>> it is type aware.
>>>>
>>>> ITK  filters are also templated on the input, and output image types.
>>>> But SimpleITK again type not expose the details of all the templated types,
>>>> and instead just exposes a generic interface to the image filter, and
>>>> internally is instantiates the image filter with all the plausible input
>>>> image types, and the sensible corresponding output image types.
>>>>
>>>> There are a few methods which can be used to interrogate the image
>>>> after it's loaded:
>>>>
>>>> First there is the ToString member function which just dumps out  bunch
>>>> of information about the internal ITK object:
>>>>
>>>> >cat( Image_ToString( myimage ) )
>>>>
>>>> And more specific methods:
>>>>
>>>> > Image_GetDimension( myimage )
>>>> > Image_GetPixelIDTypeAsString( myimage )
>>>> > Image_GetPixelIDValue( myimage )
>>>>
>>>> So lets look at what happens with the image you have chosen to run this
>>>> script with
>>>>
>>>> On Jan 1, 2012, at 9:03 AM, Brandon Whitcher wrote:
>>>>
>>>> Brad,
>>>>
>>>> I have attempted to run SimpleGaussian.R in an interactive R session by
>>>> executing
>>>>
>>>>
>>>> using the "spine1.png" image (attached, along with load.R).
>>>>
>>>>
>>>> The data used for the tests can be found in the
>>>> {SIMPLEITK_SOURCE}/Testing/Data.
>>>>
>>>>
>>>> The code fails to produce a smoothed image, here is the output
>>>>
>>>> > source("load.R") # library(SimpleITK)
>>>> >
>>>> > args <- c("spine1.png", 5, "spine1_smooth.png") # commandArgs(TRUE)
>>>> >
>>>> > myreader <- ImageFileReader()
>>>> > myreader <- ImageFileReader_SetFileName(myreader, args[[1]])
>>>> > myimage <- ImageFileReader_Execute(myreader)
>>>> >
>>>>
>>>>
>>>> if you run:
>>>> >cat( Image_ToString( myimage ) )
>>>>
>>>> You should see the following line:
>>>>
>>>> RTTI typeinfo:   itk::VectorImage< unsigned char, 2u>
>>>>
>>>> Or if you run:
>>>>
>>>> > Image_GetPixelIDTypeAsString( myimage )
>>>> [1] "vector of 8-bit unsigned integer"
>>>>
>>>> So with either of these methods you see that this file is not a black
>>>> and white image that it first appears, but actually a RGB image loaded into
>>>> an Itk::VectorImage
>>>>
>>>> > pixeltype <- Image_GetPixelIDValue(myimage)
>>>> >
>>>> > myfilter <- SmoothingRecursiveGaussianImageFilter()
>>>> > myfilter <- SmoothingRecursiveGaussianImageFilter_SetSigma(myfilter,
>>>> as.double(args[2]))
>>>> > smoothedimage <-
>>>> SmoothingRecursiveGaussianImageFilter_Execute(myfilter, myimage)
>>>> Warning message:
>>>> In f(...) :
>>>>   Exception thrown in SimpleITK
>>>> SmoothingRecursiveGaussianImageFilter_Execute:
>>>> /srv/SimpleITK/Code/Common/include/sitkMemberFunctionFactory.txx:173:
>>>> sitk::ERROR: Pixel type: vector of 8-bit unsigned integer is not
>>>> supported in 2D byN3itk6simple37SmoothingRecursiveGaussianImageFilterE
>>>>
>>>>
>>>> While this error message could use improvement  ( and will be improved
>>>> ). It basically says that this filter doesn't work with this particular
>>>> image type  ( it should also list the types of images it does work with ).
>>>> This particular filter currently only works with scalar image type. So this
>>>> image with sitkVectorUInt8 pixels is not going to work.
>>>>
>>>>
>>>>
>>>> >
>>>> > mycaster <- CastImageFilter()
>>>> > mycaster <- CastImageFilter_SetOutputPixelType(mycaster, pixeltype)
>>>> > castedimage <- CastImageFilter_Execute(mycaster, soothedimage)
>>>> Error in CastImageFilter_Execute(mycaster, soothedimage) :
>>>>   object 'soothedimage' not found
>>>>
>>>>
>>>> There appears to be a typeo "soothedimage" should be "smoothedimage".
>>>> However, I think the same error message should be generated because the
>>>> smoothedimage was not assigned due to the previous exception.
>>>>
>>>> >
>>>> > mywriter <- ImageFileWriter()
>>>> > mywriter <- ImageFileWriter_SetFileName(mywriter, args[[3]])
>>>> > mywriter <- ImageFileWriter_Execute(mywriter, castedimage)
>>>> Error in ImageFileWriter_Execute(mywriter, castedimage) :
>>>>   object 'castedimage' not found
>>>>
>>>> I am not sure what to make of the warnings or errors (sorry).  Any
>>>> advice or modifications would be helpful.  I am using spine1.png since I
>>>> cannot locate STAPLE1.png in either the ITK or SimpleITK directories.
>>>>
>>>>
>>>> Using the functional interface the following may be simpler:
>>>>
>>>> img <- ReadImage( "/src/SimpleITK/Testing/Data/Input/cthead1.png" )
>>>> pid <- Image_GetPixelIDValue( img )
>>>> simg <- SmoothingRecursiveGaussian( img, 4 )
>>>> cimg <- Cast( simg, pid )
>>>> WriteImage( cimg, "out.png" )
>>>>
>>>> Good luck,
>>>> Brad
>>>>
>>>>  thanks,
>>>>
>>>> Brandon
>>>>
>>>>
>>>> On 31 December 2011 18:34, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
>>>>
>>>>> Hello again,
>>>>>
>>>>> I was not able to get the R packaging to work as described in the link
>>>>> provided. I did find a manual way to load the SimpleITK R library.
>>>>>
>>>>> Copy the SimpleITK.R file and the libSimpleITK.so ( renamed to
>>>>> SimpleITK.so ) into your current path, such as with the following commands:
>>>>>
>>>>> cp SimpleITK/SimpleITK-build/Wrapping/SimpleITK.R
>>>>> cp SimpleITK/SimpleITK-build/Wrapping/SimpleITK.R ./
>>>>>
>>>>>
>>>>> The fire up R and type:
>>>>>
>>>>> $ R
>>>>>
>>>>> R version 2.14.0 (2011-10-31)
>>>>> ...
>>>>>
>>>>> > dyn.load( paste("SimpleITK", .Platform$dynlib.ext, sep="" ))
>>>>> > source ( "SimpleITK.R" )
>>>>> Creating a generic function for ‘print’ from package ‘base’ in the
>>>>> global environment
>>>>> > cacheMetaData( 1 )
>>>>>
>>>>> Here is an example that was working at one point:
>>>>>
>>>>> http://www.itk.org/SimpleITKDoxygen/html/SimpleGaussian_8R-example.html
>>>>>
>>>>> However the "library( SimpleITK )" call is used for when SimpleITK is
>>>>> installed as a package not the adhoc approach used above.
>>>>>
>>>>> Good Luck,
>>>>> Brad
>>>>>
>>>>> On Dec 31, 2011, at 1:11 PM, Lowekamp, Bradley (NIH/NLM/LHC) [C] wrote:
>>>>>
>>>>> Hello Brandon,
>>>>>
>>>>> The particular files you looking for are in the SimpleITK source
>>>>> directory not the build. You will need both the DESCRIPTION and the zzz.R
>>>>> files from the {SIMPLEITK_SOURCE}/Wrapping/R_Package directory.
>>>>>
>>>>> We have been calling R a Tier 2 or Tier 3 language in SimpleITK
>>>>> because is not as well supported as the other wrapped languages such as
>>>>> Python, Java, CSharp or even Ruby, or TCL. The primary reason for this is
>>>>> that we have not gotten the automatic testing working for R, so that it
>>>>> will show up on the nightly dashboard. Additionally, we also are hoping for
>>>>> contribution from the community to get the R language specific features
>>>>> polished and up to the expected R standard conventions.
>>>>>
>>>>> I hope this helps you with getting SimpleITK working R,
>>>>>
>>>>> Brad
>>>>>
>>>>> ========================================================
>>>>> Bradley Lowekamp
>>>>> Medical Science and Computing for
>>>>> Office of High Performance Computing and Communications
>>>>> National Library of Medicine
>>>>> blowekamp at mail.nih.gov
>>>>>
>>>>> On Dec 31, 2011, at 9:28 AM, Brandon Whitcher wrote:
>>>>>
>>>>> Dear ITK/SimpleITK experts,
>>>>>
>>>>> I have installed SimpleITK by turning off all wrapping facilities
>>>>> except WRAP_R.  I am now following the instructions in
>>>>>
>>>>> http://www.itk.org/SimpleITKDoxygen/html/Wrapping.html
>>>>>
>>>>> Specifically,
>>>>>
>>>>>
>>>>>    - 6) Copy the file
>>>>>
>>>>>        SimpleITK/Wrapping/R_Package/DESCRIPTION
>>>>>
>>>>> into the current
>>>>>
>>>>>        SimpleITK/DESCRIPTION
>>>>>
>>>>> ...but I cannot find the file Wrapping/R_package/DESCRIPTION in my
>>>>> SimpleITK-binary installation.  Where is this file?
>>>>>
>>>>> thank-you,
>>>>>
>>>>> Brandon
>>>>>
>>>>>
>>
>>
>>
>>
>>
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>>
>
>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> Technical Leader
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4920
>
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