[ITK] How to get to get image similarity metrics under .NET ?

[Oleg Subachev]

Thank you, Ziv:
Now merics are calculated successfully.
But where to get information about meaning of various kinds of
supported metrics.
E.g. this code for the same image
using ( ImageRegistrationMethod method = new ImageRegistrationMethod() )
{
method.SetMetricAsMattesMutualInformation();
method.SetInitialTransform( new Euler2DTransform() );
double metric = method.MetricEvaluate(
SimpleITK.ReadImage( "1.png", PixelIDValueEnum.sitkFloat32 ),
SimpleITK.ReadImage( "1.png", PixelIDValueEnum.sitkFloat32 ) );
}
yields -0,984914070939179
Whereas:
SetMetricAsANTSNeighborhoodCorrelation( 2 ) yields -1
SetMetricAsCorrelation() yields -1
SetMetricAsJointHistogramMutualInformation() yields -0,601327526729281
SetMetricAsMeanSquares() yields 0

How to normalize all metrics to the same range ?
-- 
Best regards,
Oleg Subachev

On Thu, Nov 19, 2015 at 7:49 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
<zivrafael.yaniv at nih.gov> wrote:
> Hello Oleg,
>
> It is necessary to set the initial transform as the MetricEvaluate method
> will use that transformation to evaluate your similarity metric, the same
> way it is done during registration. There is always a transformation
> between the two images, even if it is the identity. Something like
> method.SetInitialTransform(new Euler3DTransform()) if your images are 3D
> or Euler2DTransform() if they are 2D. In your case the you can use any of
> the transformation types Translation,AffineŠ as you are creating the
> identity transform.
>
>    Ziv
>
>
>
> On 11/19/15, 6:57 AM, "Oleg Subachev" <osubachev at gmail.com> wrote:
>
>>Since error message says something about "initial transform" may be it
>>is necessary to set up initial transform ?
>>As you see from code I do not call SetInitialTransform method at all.
>>I hope that no initial transform or default initial transform (if any)
>>will be enough.
>>I simply want to get similarity metric value for two image files
>>without any transform.
>>
>>--
>>Best regards,
>>Oleg Subachev
>>
>>On Thu, Nov 19, 2015 at 12:01 PM, Oleg Subachev <osubachev at gmail.com>
>>wrote:
>>> Thanks all of you.
>>> But now the code:
>>> using ( ImageRegistrationMethod method = new ImageRegistrationMethod() )
>>> {
>>> method.SetMetricAsMattesMutualInformation();
>>> double metric = method.MetricEvaluate(
>>> SimpleITK.ReadImage( "1.png", PixelIDValueEnum.sitkFloat32
>>> ),SimpleITK.ReadImage( "2.png", PixelIDValueEnum.sitkFloat32 ));
>>> }
>>>
>>> throws new exception:
>>> {"Exception thrown in SimpleITK
>>> ImageRegistrationMethod_MetricEvaluate:
>>>
>>>..\\..\\..\\..\\..\\SimpleITK\\Code\\Registration\\src\\sitkImageRegistra
>>>tionMethod.cxx:922:\nsitk::ERROR:
>>> Unexpected error converting initial transform! Possible miss matching
>>> dimensions!"}
>>>
>>> --
>>> Best regards,
>>> Oleg Subachev
>>>
>>>
>>> On Wed, Nov 18, 2015 at 8:14 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
>>> <zivrafael.yaniv at nih.gov> wrote:
>>>> Hello Oleg,
>>>>
>>>> The ImageRegistrationMethod only supports images with pixel type
>>>> sitkFloat32 and sitkFloat64. You can either specify the pixel type when
>>>> reading the image
>>>>
>>>>(http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#a0
>>>>2ff
>>>> c30c3c55dd9eeff3f76ba19f35e7) or read the image with its native pixel
>>>>type
>>>> and then
>>>> use the SimpleITK Cast function
>>>>
>>>>(http://www.itk.org/SimpleITKDoxygen/html/namespaceitk_1_1simple.html#af
>>>>8c9
>>>> d7cc96a299a05890e9c3db911885), casting it to either of these two types.
>>>>
>>>>    Ziv
>>>>
>>>>
>>>>
>>>> On 11/18/15, 9:51 AM, "Oleg Subachev" <osubachev at gmail.com> wrote:
>>>>
>>>>>Thanks, Brad.
>>>>>
>>>>>But when I try this code:
>>>>>using ( ImageRegistrationMethod method = new ImageRegistrationMethod()
>>>>>)
>>>>>{
>>>>>method.SetMetricAsMattesMutualInformation( 50 );
>>>>>double metric = method.MetricEvaluate( SimpleITK.ReadImage( "1.png" ),
>>>>>SimpleITK.ReadImage( "2.png" ) );
>>>>>}
>>>>>
>>>>>I get the exception:
>>>>>{"Exception thrown in SimpleITK
>>>>>ImageRegistrationMethod_MetricEvaluate:
>>>>>..\\..\\..\\..\\..\\SimpleITK\\Code\\Registration\\src\\sitkImageRegist
>>>>>rat
>>>>>ionMethod.cxx:862:\nsitk::ERROR:
>>>>>Filter does not support fixed image type: vector of 8-bit unsigned
>>>>>integer"}
>>>>>
>>>>>What's wrong ?
>>>>>What is the simplest way to get similarity value of two image files ?
>>>>>
>>>>>--
>>>>>Best regards,
>>>>>Oleg Subachev
>>>>>
>>>>>On Tue, Nov 17, 2015 at 6:41 PM, Bradley Lowekamp
>>>>><blowekamp at mail.nih.gov> wrote:
>>>>>> Hello,
>>>>>>
>>>>>> You should look into SimpleITK's
>>>>>>ImageRegistrationMethod::MetricEvaluate( Image, Image ) member
>>>>>>function.
>>>>>>
>>>>>> Here is a Python example of using the method, C# should be similar:
>>>>>>
>>>>>>
>>>>>>http://insightsoftwareconsortium.github.io/SimpleITK-Notebooks/63_Regi
>>>>>>str
>>>>>>ation_Initialization.html
>>>>>>
>>>>>> HTH,
>>>>>> Brad
>>>>>>
>>>>>> On Nov 17, 2015, at 8:24 AM, Oleg Subachev <osubachev at gmail.com>
>>>>>>wrote:
>>>>>>
>>>>>>> I need to get similarity metrics for 2D images under .NET.
>>>>>>> According to ITK documentation
>>>>>>> (http://www.itk.org/Doxygen/html/ImageSimilarityMetricsPage.html)
>>>>>>> there are several Image To Image metrics available.
>>>>>>> ITK itself contains corresponding methods.
>>>>>>> But I cannot find those methods in SimpleITK :-(
>>>>>>> There is SimpleITK.NormalizedCorrelation(Image, Image, Image)
>>>>>>>method,
>>>>>>> but it seems to have nothing with similarity metrics.
>>>>>>>
>>>>>>> How to get to get image similarity metrics under .NET ?
>>>>>>>
>>>>>>> --
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Oleg Subachev
>>>>>>> _______________________________________________
>>>>>>> Community mailing list
>>>>>>> Community at itk.org
>>>>>>> http://public.kitware.com/mailman/listinfo/community
>>>>>>
>>>>>_______________________________________________
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