[ITK-users] [ITK] ImageToImageMetric in Python
Matt McCormick
matt.mccormick at kitware.com
Tue Apr 15 23:19:29 EDT 2014
Hi Sven,
Glad to hear it worked out well.
What exception is created and why is it occurring?
Thanks,
Matt
On Tue, Apr 15, 2014 at 7:18 AM, Prevrhal, Sven
<Sven.Prevrhal at philips.com> wrote:
> Yes it did, great! Thanks a lot! I went by the examples I found on the web, and they never called Initialize(). So, for documentation, below is what worked for me.
>
> One question remains, and that is how to wrap this in a loop in which the moving image changes. I tried only repeating the SetMovingImage call, but the result did not change. Then I tried adding the Initialize call to the loop after SetMovingImage, which caused an Exception. The only way I got it to work was to place all New()'s etc inside the loop as well. Is there a better way?
>
> Kind regards,
> Sven
>
> # ------ Python code that works for me to compute NCC between two images, both of type itk.Image.F3
> metricType = itk.NormalizedCorrelationImageToImageMetric.IF3IF3
> transformType = itk.IdentityTransform.D3
> interpolatorType = itk.NearestNeighborInterpolateImageFunction.IF3D
>
> metric = metricType.New()
> tr = transformType.New()
> ip = interpolatorType.New()
>
> metric.SetTransform(tr)
> metric.SetInterpolator(ip)
> metric.SetFixedImage(fixedImage)
> metric.SetFixedImageRegion( fixedImage.GetBufferedRegion() )
> metric.SetMovingImage(movingImage)
> metric.Initialize()
>
> zeroDisplacement = tr.GetParameters() # could also set to itk.OptimizerParameters.D(3)
> zeroDisplacement.Fill(0)
>
> v = metric.GetValue(zeroDisplacement)
> print 'NCC = %f' % v
>
> -----Original Message-----
> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
> Sent: Montag, 14. April 2014 22:32
> To: Prevrhal, Sven
> Cc: Jagjeet Nain; insight-users at itk.org
> Subject: Re: [ITK] [ITK-users] ImageToImageMetric in Python
>
> Hi Sven,
>
> Does calling Initialize() [1] help?
>
> Thanks,
> Matt
>
> [1] http://www.itk.org/Doxygen/html/classitk_1_1ImageToImageMetric.html#a2bd5955a3bedf31e701aed3ee1d4e473
>
>
> On Mon, Apr 14, 2014 at 12:25 PM, Prevrhal, Sven <Sven.Prevrhal at philips.com> wrote:
>> Thanks Matt and Jagjeet,
>> It's better but still not working correctly. Here's what I have now:
>>
>>
>>
>> metricType = itk.NormalizedCorrelationImageToImageMetric.IF3IF3
>> transformType = itk.TranslationTransform.D3
>> interpolatorType = itk.LinearInterpolateImageFunction.IF3D
>> fixedImage = files['T2']['itkImage'] # I checked, data are
>> fine
>>
>> metric = metricType.New()
>> tr = transformType.New()
>> ip = interpolatorType.New()
>>
>> metric.SetTransform(tr)
>> tr.SetIdentity()
>> metric.SetInterpolator(ip)
>> metric.SetFixedImage(fixedImage)
>>
>> # metric.GetFixedImageRegion() is [0,0,0], [0,0,0] without a line like:
>> #metric.SetFixedImageRegion( fixedImage.GetBufferedRegion() )
>> metric.SetFixedImageRegion(
>> itk.ImageRegion._3([0,0,0],[10,10,10]) )
>>
>> zeroDisplacement = itk.OptimizerParameters.D(3)
>> for i,v in enumerate([0,0,0]):
>> zeroDisplacement.SetElement(i,v)
>>
>> movingImage = files[typ]['itkImage'] # data are fine and different from fixedImage
>> metric.SetMovingImage(movingImage)
>> v = metric.GetValue(zeroDisplacement)
>> print 'NCC T2 - %s: %f' % (typ, v)
>>
>>
>>
>> The code crashes without error message at the GetValue call. If I drop the SetFixedImageRegion, it does run but produces v=0.0 no matter what. Any more insight would be greatly appreciated.
>>
>> Kind regards,
>> Sven
>>
>> -----Original Message-----
>> From: Matt McCormick [mailto:matt.mccormick at kitware.com]
>> Sent: Dienstag, 8. April 2014 20:10
>> To: Prevrhal, Sven
>> Cc: insight-users at itk.org
>> Subject: Re: [ITK] [ITK-users] ImageToImageMetric in Python
>>
>> Hi Sven,
>>
>> To find the type of MetricType::TransformParametersType, look at the Doxygen documentation for NormalizedCorrelationImageToImageMetric [1].
>> Following the typedef trail [2], the type is OptimizerParameters [3],
>> which can be created with
>>
>> displacement = itk.OptimizerParameters.F( Dimension )
>>
>> Hope this helps,
>> Matt
>>
>> [1]
>> http://www.itk.org/Doxygen/html/classitk_1_1NormalizedCorrelationImage
>> ToImageMetric.html
>>
>> [2]
>> http://www.itk.org/Doxygen/html/classitk_1_1TransformBaseTemplate.html
>>
>> [3]
>> http://www.itk.org/Doxygen/html/classitk_1_1OptimizerParameters.html
>>
>> On Tue, Apr 8, 2014 at 1:34 PM, Prevrhal, Sven <Sven.Prevrhal at philips.com> wrote:
>>> I am looking at the itk Software Guide to figure out how to implement
>>> this in Python. I have:
>>>
>>>
>>>
>>> nccMetric =
>>> itk.NormalizedCorrelationImageToImageMetric.IF3IF3.New()
>>>
>>> nccMetric.SetTransform(itk.IdentityTransform.D3.New())
>>>
>>>
>>> nccMetric.SetInterpolator(itk.NearestNeighborInterpolateImageFunction.
>>> IF3D.New())
>>>
>>> nccMetric.SetFixedImage(fixedImage)
>>>
>>> nccMetric.SetMovingImage(movingImage)
>>>
>>>
>>>
>>> which I believe works fine. I am getting stumped by the translation
>>> of this to Python:
>>>
>>>
>>>
>>> # ITK software guide page 390
>>>
>>> # C++ code: MetricType::TransformParametersType displacement(
>>> Dimension );
>>>
>>> displacement = nccMetric.??
>>>
>>>
>>>
>>> After which
>>>
>>>
>>>
>>> value = nccMetric.GetValue( displacement )
>>>
>>>
>>>
>>> should work fine. Anybody knows this?
>>>
>>>
>>>
>>> Regards,
>>>
>>> Sven
>>>
>>>
>>>
>>> Sven Prevrhal
>>>
>>> Philips Research
>>>
>>>
>>>
>>>
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