[Insight-developers] SimpleITK - Image::GetPixel methods

Wed Apr 27 11:54:01 EDT 2011

Great! 

I'll give a shot at the __iter__ implementation as well.

Do you think there are any other intrinsic python operators which should be implemented for SimpleITK, or have we covered most of them now?

Brad

On Apr 27, 2011, at 5:11 AM, Gaëtan Lehmann wrote:

> 
> Le 27 avr. 11 à 03:41, Bradley Lowekamp a écrit :
> 
>> Great!
>> 
>> I know I was doing things not quite right there!
>> 
>> 
>> On Apr 26, 2011, at 5:36 AM, Gaëtan Lehmann wrote:
>>> 
>>> 
>>> It would be interesting to look at the GetPixel() performance - if it is a lot slower than the specialized versions, then it may be better to not hide the specialized versions, for the users who wants to write faster code.
>> 
>> Is your concern that the cost of all the if statements will be too great?
> 
> Yes.
> I'm not sure it will have much effect on performance, but it would be nice to look at it.
> 
> I've made a very simple timing test for WrapITK/Python when I moved to a pure swig implementation, and it was quite informative:
> 
>  Wrapping/WrapITK/Languages/Python/Tests/timing.py
> 
>> I have seen switch like statements implemented with dictionaries. This should reduce the switch statement from cost of N to logN or perhaps they are implemented with a hash... either way N is only 8, and it should be an interesting comparison.
> 
> Yes, would be nice to compare.
> 
>> 
>> The current implementation in sitkImage is  that the correct set/get methods is required to be call or else and exception will be thrown. For strongly typed languages like C++ or Java this will be a pain, for for the implementation we have discussed here in python or other scripting languages, should be pretty easy to use.
>> 
> 
> I think it should be possible to use overloaded methods to avoid that pain with the Set methods.
> For the Get method, I don't see what else could be done...
> 
>> 
>> On another note, what do you think of implementing the iteration hidden function in python for the simpleITK Image?
> 
> looks like a very good idea. There could be 2 versions:
> 
> * the standard __iter__ would return only the pixel value
> * another one which would also return the index
> 
> Could be something like:
> 
> def __iter__(self):
>  for idx, value in self.IterateWithIndex():
>     yield value
> 
> def IterateWithIndex(self):
>  if self.GetDimension() == 2:
>    for x in range(self.GetWidth()):
>      for y in range(self.GetHeight()):
>        idx = (x, y)
>        value = self.GetPixel(*idx)
>        yield idx, value
>  elif self.GetDimension() == 3:
>    for x in range(self.GetWidth()):
>      for y in range(self.GetHeight()):
>        for z in range(self.GetDepth()):
>          idx = (x, y, z)
>          value = self.GetPixel(*idx)
>          yield idx, value
> 
> 
> that can be used that way
> 
>  # compute the mean pixel value in the image
>  mean = sum(img) / len(img)
> 
> or
> 
>  # compute the square value pixel wise
>  for idx, value in img.IterateWithIndex():
>    img[idx] = value**2
> 
> Gaëtan
> 
> 
>> 
>> Brad
>> 
>>> 
>>> Gaëtan
>>> 
>>> 
>>> 
>>> 
>>> Le 22 avr. 11 à 22:25, Bradley Lowekamp a écrit :
>>> 
>>>> Gaetan,
>>>> 
>>>> You have provided valuable feedback with several other python related issues and was looking for comments on the current.
>>>> 
>>>> Despite it sounding easy, implementing the sitk::Image::GetPixel method is rather challenging due to the numerous types of images underneath. I have a branch in my SimpleITK github, which will add this much needed feature.
>>>> 
>>>> The sitk::Image class will be customized for each language to provide a natural interface. This is what I have done for python:
>>>> 
>>>> https://github.com/blowekamp/SimpleITK/commit/b821617f013ee18c7cc2ae727eec3d20ad2b5875
>>>> 
>>>> I realize now it needs some comments....
>>>> 
>>>> It is not clear to me if the index argument should be multiple arguments or an array, or both. As arguments are not strongly typed, I am not certain of how to do methods overloading, based on the arguments. In another methods I used isinstance(), but some frown about that. Do you have a suggestion on how I should overload methods in python? What do you think of this current interface?
>>>> 
>>>> Brad
>>>> 
>>>> ========================================================
>>>> Bradley Lowekamp
>>>> Lockheed Martin Contractor for
>>>> Office of High Performance Computing and Communications
>>>> National Library of Medicine
>>>> blowekamp at mail.nih.gov
>>>> 
>>>> 
>>> 
>>> -- 
>>> Gaëtan Lehmann
>>> Biologie du Développement et de la Reproduction
>>> INRA de Jouy-en-Josas (France)
>>> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
>>> http://voxel.jouy.inra.fr  http://www.itk.org
>>> http://www.mandriva.org  http://www.bepo.fr
>>> 
>> 
> 
> -- 
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
> 

========================================================
Bradley Lowekamp  
Lockheed Martin Contractor for
Office of High Performance Computing and Communications
National Library of Medicine 
blowekamp at mail.nih.gov

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