[Insight-developers] How simple is SimpleITK

Thu Jan 27 04:56:06 EST 2011

Hi all,

the current syntax in ITK is very cumbersome. At least 3-4 lines of code are
needed (typedef, instantiate, set parameters, and perhaps update) to use any
filter. I support the attempts to simplify it - I like Bill's first post
very much.

Regards,
Dženan

On Wed, Jan 26, 2011 at 16:53, Daniel Blezek <Blezek.Daniel at mayo.edu> wrote:

> Hi Gaëtan,
>
>  I haven't forgotten about our conversation. 8)
>
>  Here is where I got to today:
>
> Python 2.6.4 (r264:75706, Nov 17 2009, 11:52:40)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from SimpleITK import *
> >>> image = ReadImage ( '../SimpleITK/Testing/Data/Input/RA-Float.nrrd' )
> >>> out = GrayscaleErode ( image )
> >>> WriteImage ( out, '/tmp/Garf.nrrd' )
>
> The RecursiveGaussian has many parameters and isn't a simple example:
>
>    Image::Pointer RecursiveGaussian ( Image::Pointer image, double Sigma,
> bool NormalizeAcrossScale, RecursiveGaussianImageFilter::OrderEnumType
> Order, unsigned int Direction );
>
> The code is just about ready to be pushed to SimpleITK.
>
> Cheers,
> -dan
>
> On 1/25/11 1:29 PM, "Gaëtan Lehmann" <gaetan.lehmann at jouy.inra.fr> wrote:
>
> >
> > Dan,
> >
> > During the last SimpleITK tcon, I think we've talked about trying to
> > generate a set of functions to make the coding style more procedural.
> > IIRC, they would
> > * hide the filter creation and use of Set and Execute methods
> > * be in an sitk name space
> > * remove the Filter suffix
> >
> > That would give something very close to what Bill would like:
> >
> >    sitk::Image::Pointer image  = sitk::readImage(inputfilename);
> >    image = sitk::recursiveGaussian(image, sigma);
> >    sitk::writeImage(outputfilename);
> >
> > In c++, there is still the Pointer though, but not in python:
> >
> >    import sitk
> >    image = sitk.readImage(inputfilename)
> >    image = sitk.recursiveGaussian(image, sigma)
> >    sitk.writeImage(outputfilename)
> >
> > this kind of syntax is OK for a python developer, really.
> > There is a lot of code in python libs in procedural style and even
> > some functional style.
> >
> > Gaëtan
> >
> >
> > Le 25 janv. 11 à 19:03, Bill Lorensen a écrit :
> >
> >> Dan,
> >>
> >> My example was extreme and meant to be provocative.
> >>
> >> I like your first approach (without the Pointer)
> >> using namespace itk::simple;
> >> Image image;
> >> image = ImageFileReader ( "Foo" );
> >> image = RecursiveGaussian ( image, 2.0 )
> >> ImageFileWriter ( image, "Bar" );
> >>
> >> or even
> >> itk::simple::Image image;
> >> image = itk::simple::ImageFileReader ( "Foo" );
> >> image = itk::simple::RecursiveGaussian ( image, 2.0 )
> >> itk::simple::ImageFileWriter ( image, "Bar" );
> >>
> >> I think the OO pattern is not as simple. Who is the audience, Python
> >> and Java developers or biomedical researchers?
> >>
> >> Sorry I was not in Iowa and won't be in Boston. I hope you have a
> >> lively and procutive meeting.
> >>
> >> Bill
> >>
> >> On Tue, Jan 25, 2011 at 12:50 PM, Blezek, Daniel J.
> >> <Blezek.Daniel at mayo.edu> wrote:
> >>> Hi Bill,
> >>>
> >>>  For some reason everyone thinks that SimpleITK is going to look like
> >>> Matlab...  The plan has been to _enable_ Matlab-like syntax, not
> >>> demand
> >>> it.  We will continue the object oriented pattern, but augment with a
> >>> set of procedural calls.  So your example code would end up looking
> >>> something like this:
> >>>
> >>>
> >>> using namespace itk::simple;
> >>> Image::Pointer image;
> >>> image = ImageFileReader ( "Foo" );
> >>> image = RecursiveGaussian ( image, 2.0 )
> >>> ImageFileWriter ( image, "Bar" );
> >>>
> >>> Or, if you like, this can be all done on one line...
> >>>
> >>> ImageFileWriter ( RecursiveGaussian ( ImageFileReader ( "Foo" ),
> >>> 2.0 ),
> >>> "Bar" );
> >>>
> >>> In the OO pattern:
> >>>
> >>> image = ImageFileReader().SetFilename ( "Foo" ).Execute()
> >>> image = RecursiveGaussion().SetSigma ( 2.0 ).Execute ( image )
> >>> ImageFileWriter().SetFilename ( "Bar" ).Execute ( image )
> >>>
> >>> We are investigating making Execute a static method, so the code
> >>> would
> >>> look like:
> >>>
> >>> image = ImageFileReader::Execute ( "Foo" )
> >>> image = RecursiveGaussian::Execute ( image, 2.0 )
> >>> ImageFileWriter::Execute ( image, "Bar" )
> >>>
> >>> This has not been checked in, because SWIG does not wrap it
> >>> properly.  I
> >>> am working on this.
> >>>
> >>> At the Iowa meeting, we decided to take the OO approach, as it was
> >>> more
> >>> broadly approachable to Python and Java developers.
> >>>
> >>> -dan
> >>>
> >>> -----Original Message-----
> >>> From: insight-developers-bounces at itk.org
> >>> [mailto:insight-developers-bounces at itk.org] On Behalf Of Bill
> >>> Lorensen
> >>> Sent: Tuesday, January 25, 2011 11:28 AM
> >>> To: Insight Developers
> >>> Subject: [Insight-developers] How simple is SimpleITK
> >>>
> >>> Folks,
> >>>
> >>> I just took a look at the current SimpleITK repo.
> >>>
> >>> To me it looks like itk without templates and without pipelines.
> >>> Simpler indeed. And probably simpler to wrap.
> >>>
> >>> However, it still is object-oriented, has namespaces, has Pointer's,
> >>> still uses set/get methods and still has an Execute method. It is
> >>> still
> >>> quite ITK-like.
> >>>
> >>> I thought it would be a bit more procedural and more acceptable to
> >>> non-itk(e.g. Matlab) users.
> >>>
> >>> itksImage image  = itksReadImage(inputfilename);
> >>> image=itksRecursiveGaussian(image, sigma);
> >>> itksWriteImage(outputfilename);
> >>>
> >>> versus
> >>>
> >>>  itk::simple::Image::Pointer image;
> >>>  itk::simple::ImageFileReader reader;
> >>>  reader.SetFileName ( inputFilename);
> >>>  image = reader.Execute();
> >>>
> >>>  itk::simple::RecursiveGaussianImageFilter gaussian;
> >>>  gaussian.SetSigma ( gaussian );
> >>>  image = gaussian.Execute ( image );
> >>>
> >>>  itk::simple::ImageFileWriter writer;
> >>>  writer.SetFileName ( outputFilename );
> >>>  writer.Execute ( image );
> >>>
> >>> Bill
> >>> _______________________________________________
> >>> Powered by www.kitware.com
> >>>
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> >>> http://www.kitware.com/opensource/opensource.html
> >>>
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> >>> http://kitware.com/products/protraining.html
> >>>
> >>> Please keep messages on-topic and check the ITK FAQ at:
> >>> http://www.itk.org/Wiki/ITK_FAQ
> >>>
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> >>> http://www.itk.org/mailman/listinfo/insight-developers
> >>>
> >> _______________________________________________
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> >>
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> >>
> >> Kitware offers ITK Training Courses, for more information visit:
> >> http://kitware.com/products/protraining.html
> >>
> >> Please keep messages on-topic and check the ITK FAQ at:
> >> http://www.itk.org/Wiki/ITK_FAQ
> >>
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> >> http://www.itk.org/mailman/listinfo/insight-developers
>
> --
> Daniel Blezek, PhD
> Medical Imaging Informatics Innovation Center
>
> P 127 or (77) 8 8886
> T 507 538 8886
> E blezek.daniel at mayo.edu
>
> Mayo Clinic
> 200 First St. S.W.
> Harwick SL-44
> Rochester, MN 55905
> mayoclinic.org
> "It is more complicated than you think." -- RFC 1925
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
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