[Insight-developers] How simple is SimpleITK

Wed Jan 26 10:53:01 EST 2011

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
>>> _______________________________________________
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>> _______________________________________________
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>> 
>> Visit other Kitware open-source projects at
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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:
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>> 
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-- 
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
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Harwick SL-44
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