Add MutualInformationAffine Python example file #251
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tbirdso
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| # small steps along scale parameters | ||
| optimizer.SetScales([100, 0.5, 0.5, 100, 0.001, 0.001]) | ||
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| registrar = itk.ImageRegistrationMethod[type(fixed_image), type(moving_image)].New() |
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Can we used the functional Python interface here? e.g.
result_transform = itk.image_registration_method(fixed_image=fixed_image, moving_image=moving_image, transform=transform, [...]
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The functional Python interface appears to be expecting images of type signed short and fails when unsigned char images are provided. I've checked that ITK is wrapped for both types. Is there a way to explicitly set the image type? Is this a wrapping that needs to be added to ITK?
Error:
Traceback (most recent call last):
File "Code.py", line 73, in
result_object = itk.image_registration_method(
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkHelpers.py", line 211, in image_filter_wrapper
return image_filter(*args, **kwargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\itkImageRegistrationMethodPython.py", line 581, in image_registration_method
instance = itk.ImageRegistrationMethod.New(*args, **kwargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkTemplate.py", line 726, in New
return self[list(keys)[0]].New(*args, **kwargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\itkImageRegistrationMethodPython.py", line 339, in New
itkTemplate.New(obj, *args, **kargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkTemplate.py", line 792, in New
itk.set_inputs(self, args, kargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkExtras.py", line 928, in set_inputs
attrib(itk.output(value))
TypeError: in method 'itkImageRegistrationMethodISS2ISS2_SetFixedImage', argument 2 of type 'itkImageSS2 const *'
Verified input types:
> print(type(fixed_image))
<class 'itk.itkImagePython.itkImageUC2'>
> print(type(moving_image))
<class 'itk.itkImagePython.itkImageUC2'>
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Also note that itk.image_registration_method returns an object of type 'itk.itkTransformBasePython.itkDataObjectDecoratorTD22' which cannot be passed directly to resample_image_filter as an itk.transform. Not a big deal given that the registration transform is updated in-place and can be passed on, but I'm not sure what this object contains. Where can I find documentation for the functional interface?
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We can be explicit with the types we want with the ttype keyword argument.
However, we could have the filter select the proper default template type by looking at the first positional argument / template argument. This corresponds to the first indexed input to the filter, the primary input. While itk::ImageRegistrationMethod does not identify the FixedImage as its primary input, itk::ImageRegistrationMethodv4 does:
So, we should update this examples to use the v4 registration method.
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This example currently relies on the Viola-Wells mutual information metric but it seems that only the Mattes mutual information metric has a v4 counterpart. Given that a v4 metric is required for the v4 registration method, is it suitable to explicitly set ttype in this example for the v3 metric and open an issue to add a new example using the Mattes mutual information v4 metric? It doesn't look like we currently have an example making use of MattesMutualInformationImageToImageMetricv4.
| DefaultPixelValue=100, | ||
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| resample.Update() |
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Let's use the simpler, functional interface:
resampled = itk.resample_image_filter(moving_image, output_origin=fixed_image.GetOrigin(), [...]
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Same type issue as noted above. Functional interface seems to expect images of type itk.SS.
Traceback (most recent call last):
File "Code.py", line 93, in
resampled = itk.resample_image_filter(
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkHelpers.py", line 211, in image_filter_wrapper
return image_filter(*args, **kwargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\itkResampleImageFilterPython.py", line 1927, in resample_image_filter
instance = itk.ResampleImageFilter.New(*args, **kwargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkTemplate.py", line 726, in New
return self[list(keys)[0]].New(*args, **kwargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\itkResampleImageFilterPython.py", line 680, in New
itkTemplate.New(obj, *args, **kargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkTemplate.py", line 792, in New
itk.set_inputs(self, args, kargs)
File "C:\repos\ITK-builds-2\Wrapping\Generators\Python\itk\support\itkExtras.py", line 928, in set_inputs
attrib(itk.output(value))
TypeError: Expecting argument of type itkImageSS2 or itkImageSourceISS2.
Additional information:
Wrong number or type of arguments for overloaded function 'itkImageToImageFilterISS2ISS2_SetInput'.
Possible C/C++ prototypes are:
itkImageToImageFilterISS2ISS2::SetInput(itkImageSS2 const *)
itkImageToImageFilterISS2ISS2::SetInput(unsigned int,itkImageSS2 const *)
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> print(type(moving_image))
<class 'itk.itkImagePython.itkImageUC2'>
Note that no error is thrown when reading in images of type itk.SS but itk.imwrite does not support writing itk.SS PNG output images by default.
Per above, this may be resolved by updating to the v4 metric.
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