[ITK] [ITK-users] Python Bindings, Templates, and ConfidenceConnectedImageFilter

Michka Popoff michkapopoff at gmail.com
Fri Jun 12 12:53:18 EDT 2015 

The types that are wrapped are defined in the .wrap file I linked to before. You may change the WRAP_ITK_INT to WRAP_ITK_SCALAR in this file.

In fact we do not wrap all types out of the box because this increases compilation time.

A patch is welcome of course. I'll be off the internet during the weekend, maybe others will help you if you have further questions. 

Cheers 

Michka


Envoyé de mon iPhone

> Le 12 juin 2015 à 18:37, Porter, Justin <porterj at wusm.wustl.edu> a écrit :
> 
> Thanks for your quick and helpful response!
> 
> Whatever version of ITK I am running has the GetTypes method, and it looks like ConfidenceConnectedImageFilter allows 2 and 3 dimensional doubles, floats, SS, and UC on the input end, but only 2 and 3 dimensional UC and SS as output types.
> 
> The output from ConfidenceConnectedImageFilter.GetTypes():
> 
>> <itkTemplate itk::ConfidenceConnectedImageFilter>
>> Options:
>>   [<class 'itkImagePython.itkImageD2'>, <class 'itkImagePython.itkImageSS2'>]
>>   [<class 'itkImagePython.itkImageD2'>, <class 'itkImagePython.itkImageUC2'>]
>>   [<class 'itkImagePython.itkImageD3'>, <class 'itkImagePython.itkImageSS3'>]
>>   [<class 'itkImagePython.itkImageD3'>, <class 'itkImagePython.itkImageUC3'>]
>>   [<class 'itkImagePython.itkImageF2'>, <class 'itkImagePython.itkImageSS2'>]
>>   [<class 'itkImagePython.itkImageF2'>, <class 'itkImagePython.itkImageUC2'>]
>>   [<class 'itkImagePython.itkImageF3'>, <class 'itkImagePython.itkImageSS3'>]
>>   [<class 'itkImagePython.itkImageF3'>, <class 'itkImagePython.itkImageUC3'>]
>>   [<class 'itkImagePython.itkImageSS2'>, <class 'itkImagePython.itkImageSS2'>]
>>   [<class 'itkImagePython.itkImageSS2'>, <class 'itkImagePython.itkImageUC2'>]
>>   [<class 'itkImagePython.itkImageSS3'>, <class 'itkImagePython.itkImageSS3'>]
>>   [<class 'itkImagePython.itkImageSS3'>, <class 'itkImagePython.itkImageUC3'>]
>>   [<class 'itkImagePython.itkImageUC2'>, <class 'itkImagePython.itkImageSS2'>]
>>   [<class 'itkImagePython.itkImageUC2'>, <class 'itkImagePython.itkImageUC2'>]
>>   [<class 'itkImagePython.itkImageUC3'>, <class 'itkImagePython.itkImageSS3'>]
>>   [<class 'itkImagePython.itkImageUC3'>, <class 'itkImagePython.itkImageUC3'>]
> 
> Is this by design? In the example script, both the input and the output for ConfidenceConnectedImageFilter are 3d floats…
> 
> If not, I would be happy to try to fix the issue and commit a fix if there are guidelines somewhere for doing so.
> 
> Cheers,
> Justin
> 
>> On Jun 12, 2015, at 10:26 AM, Michka Popoff <michkapopoff at gmail.com> wrote:
>> 
>> Hi
>> 
>> one good way to know which types are available is to use the GetTypes method on your template (before calling New). This method way introduced in 4.7 or after, I don't remember. But it is definitively available in 4.8 rc 1.
>> 
>> I am not in front on a computer so please check this out yourself. Looking at the code we wrap float combinations here:
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Segmentation/RegionGrowing/wrapping/itkConfidenceConnectedImageFilter.wrap
>> 
>> Michka
>> 
>> 
>> 
>> Envoyé de mon iPhone
>> 
>> Le 12 juin 2015 à 17:03, Porter, Justin <porterj at wusm.wustl.edu> a écrit :
>> 
>>> Hey all,
>>> 
>>> I’m just getting started with ITK, and I’m using the python bindings, which are really awesome. It looks like it was a fair bit of work to get such a heavily templated library to work in Python, but it’s really nice to be able to build scripts in python!
>>> 
>>> I set out to reimplement Slicer’s “Simple Region Growing Segmentation” using ITK-Python, but I keep getting an error when I try to define a ConfidenceConnectedImageFilter template on a 3d float (and double, too). IMG_F == itk.Image[itk.F, 3] elsewhere in the script.
>>> 
>>>> Traceback (most recent call last):
>>>>   File "simple_region_growing_segmentation.py", line 169, in <module>
>>>>     sys.exit(main(sys.argv))
>>>>   File "simple_region_growing_segmentation.py", line 154, in main
>>>>     args.seed)
>>>>   File "simple_region_growing_segmentation.py", line 98, in attach_connect
>>>>     ccif = ConfidenceConnectedImageFilter[IMG_F, IMG_F].New()
>>>>   File "/home/jporter/usr/local/ITK/bin/Wrapping/Generators/Python/itkTemplate.py", line 263, in __getitem__
>>>>     (str(parameters), self.__name__))
>>>> KeyError: "itkTemplate : No template (<class 'itkImagePython.itkImageF3'>, <class 'itkImagePython.itkImageF3'>) for the itk::ConfidenceConnectedImageFilter class"
>>> 
>>> I’m pretty sure I built the bindings appropriately to get float support:
>>> 
>>>> cmake -DITK_USE_REVIEW=ON -DITK_WRAP_PYTHON=ON -DBUILD_SHARED_LIBS=ON -DITK_LEGACY_SILENT=ON -DITK_WRAP_float=ON -DITK_WRAP_rgb_unsigned_char=ON -DITK_WRAP_vector_double=ON -DITK_WRAP_complex_double=ON -DITK_WRAP_double=ON 
>>> 
>>> Interestingly, I can build a CurvatureFlowImageFilter or a CastImageFilter templated against 3d floats. I can also instantiate a ConfidenceConnectedImageFilter templated against itk.UC (presumably unsigned char?). That made me think that it’s not possible to build a ConfidenceConnectedImageFilter templated on floats, but the ConfidenceConnected example segmentation script does just that.
>>> 
>>> I’d love to hear thought/suggestions as to how I can proceed!
>>> 
>>> Cheers,
>>> Justin
>>> 
>>>  
>>> 
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>  
> 
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