[Insight-users] Loading a CT Volume in C# - SimpleITK or ITK
Dan Mueller
dan.muel at gmail.com
Mon Sep 16 16:17:30 EDT 2013
Hi Jason,
Good to hear your issue is resolved. Happy SimpleITKing!
Cheers, Dan
On 17 September 2013 05:40, Jason Gibbs <jdgibbs at gmail.com> wrote:
> Dan -
>
> I was using 0.5.1. Sure enough those methods are there 0.6.2.256. Thank
> you for cluing me in to that!
>
> Jason
>
>
> On Mon, Sep 16, 2013 at 3:33 PM, Dan Mueller <dan.muel at gmail.com> wrote:
>>
>> Hi Jason,
>>
>> What version of SimpleITK are you using? These methods have been
>> available since at least 0.6.2... There is nothing special you need to
>> do to access these functions.
>>
>> How are you viewing/searching the assembly? Visual Studio object
>> browser? MonoDevelop assembly browswer?
>>
>> Cheers, Dan
>>
>> On 17 September 2013 00:38, Jason Gibbs <jdgibbs at gmail.com> wrote:
>> > Hi Dan,
>> >
>> > Thanks for the reply! I've hacked my way around this for now but for the
>> > future I'd like to see if I can figure this out the right way. My
>> > problem
>> > was that ImageSeriesReader.GetGDCMSeriesFileNames wasn't showing up in
>> > the
>> > assembly as an option. The assembly metadata is listed as below, which
>> > isn't including that method. Is there something special about static
>> > methods with swig and C#? I'm very new to swig and how it should be
>> > configured with CMake.
>> >
>> > #region Assembly SimpleITKCSharpManaged.dll, v2.0.50727 //
>> > C:\Users\jgibbs\Documents\Visual Studio
>> > 2010\Projects\DisplayDICOM\DisplayDICOM\SimpleITKCSharpManaged.dll
>> > #endregion using System; namespace itk.simple { public class
>> > ImageSeriesReader : IDisposable { protected bool swigCMemOwn; public
>> > ImageSeriesReader(); public virtual void Dispose(); public Image
>> > Execute();
>> > public VectorString GetFileNames(); public ImageSeriesReader
>> > SetFileNames(VectorString fns); } }
>> >
>> > Thanks again for your help!
>> > Jason
>> >
>> >
>> > On Mon, Sep 16, 2013 at 7:14 AM, Dan Mueller <dan.muel at gmail.com> wrote:
>> >>
>> >> Hi Jason,
>> >>
>> >> Sorry for the delayed response — I've been away the last few days.
>> >>
>> >> You should be able to use the following code to obtain the file names:
>> >>
>> >> var reader = new ImageSeriesReader();
>> >> var names = ImageSeriesReader.GetGDCMSeriesFileNames("C:/Temp");
>> >> reader.SetFileNames(names);
>> >> var image = reader.Execute();
>> >>
>> >> BTW: If you are not already using it, the new SimpleITK 0.7.0rc1 has
>> >> added C# operators which are really nice e.g.
>> >>
>> >> var threshold = image >= 128;
>> >>
>> >> HTH
>> >>
>> >> Cheers, Dan
>> >>
>> >> On 7 September 2013 02:04, Jason Gibbs <jdgibbs at gmail.com> wrote:
>> >> > Brad,
>> >> >
>> >> > Thank you for the response! I'm pretty sure that global functions
>> >> > aren't
>> >> > allowed in C# so it would have to be shoved into some class
>> >> > somewhere,
>> >> > with
>> >> > the natural one being ImageSeriesReader.
>> >> >
>> >> > I did search through the assembly for any "GDCM" substring in the
>> >> > object
>> >> > browser; no luck. For now I've wrapped the function on my own and it
>> >> > works
>> >> > fine. However I'd be interested if anyone has a more elegant
>> >> > solution
>> >> > moving forward.
>> >> >
>> >> > Thanks again!
>> >> > Jason
>> >> >
>> >> >
>> >> > On Fri, Sep 6, 2013 at 12:16 PM, Bradley Lowekamp
>> >> > <blowekamp at mail.nih.gov>
>> >> > wrote:
>> >> >>
>> >> >> Hello Jason,
>> >> >>
>> >> >> You are correct that you need a method like
>> >> >> ImageSeriesReader::GetGDCMSeriesFilenames()[1] which is a static
>> >> >> member
>> >> >> function in C++.
>> >> >>
>> >> >> I am not certain, but I believe SWIG translate these static member
>> >> >> methods
>> >> >> to global functions with names such as
>> >> >> ImageSeriesReader_GetGDCMSeriesFilenames. But hopefully you can
>> >> >> search
>> >> >> for
>> >> >> that function name and find it in the assembly.
>> >> >>
>> >> >> Please let up know if you figure it out,
>> >> >> Brad
>> >> >>
>> >> >> [1]
>> >> >>
>> >> >>
>> >> >> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageSeriesReader.html#a26da9041bf5efd3db05524258de15dc2
>> >> >>
>> >> >> On Sep 5, 2013, at 6:11 PM, Jason Gibbs <jdgibbs at gmail.com> wrote:
>> >> >>
>> >> >> Hello,
>> >> >>
>> >> >> I am writing a pure C# based application and first started out using
>> >> >> the
>> >> >> SimpleITKCSharpManaged assembly. I'm attempting to load a DICOM
>> >> >> image
>> >> >> from a
>> >> >> folder. It is known the folder contains only one series. However,
>> >> >> I'm
>> >> >> having trouble ordering the files correctly.
>> >> >>
>> >> >> Doing this loads an image, but the slices are all out of order:
>> >> >> var FilesInFolder = Directory.EnumerateFiles(m_folder).ToList();
>> >> >>
>> >> >> itk.simple.ImageSeriesReader reader = new
>> >> >> itk.simple.ImageSeriesReader();
>> >> >> itk.simple.VectorString vs = new
>> >> >> itk.simple.VectorString();
>> >> >>
>> >> >> foreach (var file in FilesInFolder)
>> >> >> vs.Add(file);
>> >> >> reader.SetFileNames(vs);
>> >> >>
>> >> >> m_ITKImg = reader.Execute();
>> >> >>
>> >> >> I realize that I need something along the lines of
>> >> >> GetGDCMSeriesFileNames
>> >> >> to order the files correctly. It seems this is a public static
>> >> >> member
>> >> >> of
>> >> >> itk.simple.ImageSeriesReader. However this does not seem to appear
>> >> >> in
>> >> >> the
>> >> >> assembly metadata (below). Is there something I'm missing or a
>> >> >> different
>> >> >> route to achieve the same end result of loading the image in C#? I'm
>> >> >> assuming that others have loaded CT volumes in the C# wrapper before
>> >> >> so
>> >> >> I'm
>> >> >> guessing it's something I'm doing incorrectly. Thank you for any
>> >> >> help!
>> >> >>
>> >> >> Jason Gibbs
>> >> >>
>> >> >>
>> >> >> #region Assembly SimpleITKCSharpManaged.dll, v2.0.50727 //
>> >> >> C:\Users\jgibbs\Documents\Visual Studio
>> >> >> 2010\Projects\DisplayDICOM\DisplayDICOM\SimpleITKCSharpManaged.dll
>> >> >> #endregion using System; namespace itk.simple { public class
>> >> >> ImageSeriesReader : IDisposable { protected bool swigCMemOwn; public
>> >> >> ImageSeriesReader(); public virtual void Dispose(); public Image
>> >> >> Execute();
>> >> >> public VectorString GetFileNames(); public ImageSeriesReader
>> >> >> SetFileNames(VectorString fns); } }
>> >> >>
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>> >> >>
>> >> >
>> >> >
>> >> > _____________________________________
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>> >> >
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>> >> >
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