[ITK-users] [ITK] SimpleITK, read MHD volume and convert it into a numpy array respecting its transformation

[Paolo Zaffino]

Hi Fausto,
if you want to accomplish all the stuff entirely from the scipy/scikit 
side, I think you could use [1] and [2] (check the matching between 
documentation version and library version).

HTH.
Best.

Paolo

[1] 
http://docs.scipy.org/doc/scipy-0.16.0/reference/generated/scipy.ndimage.interpolation.rotate.html
[2] 
http://scikit-image.org/docs/dev/api/skimage.transform.html#skimage.transform.rotate



On 04/05/2016 20:40, fausto milletarì wrote:
> Hello,
>
> I thank you for you fast and accurate answer. This was exactly what I 
> was looking for. Actually I don’t need to visualise the data but 
> further process it in a common reference frame. I think that your 
> answer solves the problem. I will look into the ResampleImageFilter 
> (that so far I was using only to adjust the resolution of different 
> volumes acquired with different scanners to a common one).
>
>
> Thanks a lot!
>
> Fausto Milletari
>> On 04 May 2016, at 20:36, Lowekamp, Bradley (NIH/NLM/LHC) [C] 
>> <blowekamp at mail.nih.gov <mailto:blowekamp at mail.nih.gov>> wrote:
>>
>> Hello,
>>
>> If I understand you correctly you want to rotate the image and pad it 
>> for visualization before exporting to numpy.
>>
>> Have you looked into the ResampleImageFilter? It accepts a transform, 
>> along with output image geometry so that you can readily manipulate 
>> the image for display. You also may want to scale the image’s 
>> intensity with a WindowLevelImageFilter for better visualization of 
>> the range of interest.
>>
>> HTH,
>> Brad
>>
>>> On May 4, 2016, at 1:14 PM, fausto milletarì 
>>> <fausto.milletari at gmail.com <mailto:fausto.milletari at gmail.com>> wrote:
>>>
>>> Hello everyone,
>>>
>>> I have a probably naive question about simpleITK. I find simpleITK 
>>> extremely useful to process medical data such as MRI scans but I 
>>> would like also to enjoy being able to convert my images in numpy 
>>> format while respecting the transformation of the volume.
>>>
>>> In other words I would like to get the MRI image in numpy rotated by 
>>> the correct amount around each axis with zero padding for example.
>>>
>>> when i do simply sitk.GetArrayFromImage(imgResampledCropped)I get 
>>> back the raw data itself, but what I would like to do is to have a 
>>> numpy array that contains the data “ready to visualise” by simple 
>>> slicing of the array itself.
>>>
>>> Do you think this is doable? Is there a standard way of doing it?
>>>
>>>
>>>
>>> Kind regards,
>>>
>>> Fausto
>>>
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>
>
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