[ITK Community] Fwd: Problems with slice extraction from a 3D image for directions different from z

[Luis Ibanez]

Simon,

I'm looking at the code of the filter and there are
not many ways for it to generate unit spacing.

Output image spacing is computed in line 195:
https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkExtractImageFilter.hxx#L195

Something else is going on with your code...

Could you reduce it to a minimal .cxx that displays
this behavior, and share it in the list ?

In that way we will able to attempt to replicate the problem


    Thanks


       Luis



On Sat, Mar 8, 2014 at 8:42 PM, Simon Wimmer <wimmersimon at gmail.com> wrote:

> Hi all,
>
> as a follow up, I just checked the spacings in the original image and the
> extracted slice.
>
> reader->GetOutput()->GetSpacing()
> gives
> [0.747159, 0.747159, 6].
>
> But
> filter->GetOutput()->GetSpacing()
> gives
> [1, 1],
> which explains the "loss of spacing information" I observed.
> I guess if the spacing was preserved the filter->
> SetDirectionCollapseToIndentity() setting would give me the desired slice
> images.
> Any tips on how I could track down the problem here?
>
>
> Simon
>
>
> 2014-03-08 22:10 GMT+01:00 Luis Ibanez <luis.ibanez at kitware.com>:
>
> Hi Simon,
>>
>> On Sat, Mar 8, 2014 at 3:56 PM, Simon Wimmer <wimmersimon at gmail.com>wrote:
>>
>>>
>>> My direction matrix is simply the identity.
>>> So I would guess that in this case filter->
>>> SetDirectionCollapseToIndentity() and filter->
>>> SetDirectionCollapseToSubmatrix() should do the same?
>>>
>>>
>> It should...yes... I think.
>>
>> mm, maybe we need to take a closer look at the way the Submatrix is being
>> composed:
>>
>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkExtractImageFilter.hxx#L223
>>
>>
>> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/Core/Common/include/itkExtractImageFilter.hxx#L188
>>
>>
>>
>>
>>>  Taking out  InPlaceOn() sounds reasonable.
>>>
>>
>> OK
>>
>>
>>>  Regarding the spacing issue my intuition would have been that the
>>> extraction of course destroys the information for the projection direction,
>>>  but should preserve it for the other ones. Is that correct?
>>>
>>
>> Yes, that's correct.
>>
>> So, if the initial 3D image had spacing values
>>
>>         1.7,  2.9,   3.1
>>
>> in X, Y, Z respectively,
>>
>>
>> and you collapse Z,
>> you should end up with a 2D image with spacing values
>>
>>          1.7,   2.9
>>
>> in X and Y respectively.
>>
>>
>>   HTH
>>
>>
>>       Luis
>>
>>
>
>
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