[Rtk-users] using RTK with python

[Simon Rit]

Please share your ipynb jupyter notebook file because I did the test with a
new conda environment right now and it works for me... Thanks,
Simon

On Tue, Apr 21, 2020 at 10:41 AM 나윤호 <yoonho94.na at gmail.com> wrote:

> Before I run the script, I installed itk and itk-rtk using pip.
> and then I copied and pasted the whole script in FirstReconstruction.py
> in a jupyter notebook cell.
> Do I need any additional installation to use rtk?
>
> Thank you for your answer of second question.
>
> 2020년 4월 21일 (화) 오후 5:27, Aurélien Coussat <
> aurelien.coussat at creatis.insa-lyon.fr>님이 작성:
>
>> On Tue, 2020-04-21 at 17:15 +0900, 나윤호 wrote:
>>
>> Thank you for replying.
>>
>> I'm pretty sure that I haven't changed anything in the example script.
>> What I just did is copy and paste and run it.
>>
>>
>> What process did you follow in order to run it? Are you running it from a
>> shell command line (as in "python FirstReconstruction.py") or from a Python
>> command line (running "python" then copy-pasting everything) ? Could you
>> provide the exact steps you followed in order to reproduce the problem?
>>
>> and could you explain me how to translate(?) does documents into pythonic
>> way?
>> (I don't know much about Clang)
>>
>> for example, in the link you gave me it says
>>
>> *rtk::FDKConeBeamReconstructionFilter< TInputImage, TOutputImage,
>> TFFTPrecision > Class Template Reference  *
>>
>> I empirically know that in python I have to type something like
>>
>> *rtk.FDKConeBeamReconstructionFilter[InputImage, OutputImage,
>> FFTPrecision]*
>>
>> Am I right??
>>
>>
>> Almost, but your intuition is correct! From
>> rtkFDKConeBeamReconstructionFilter header file (
>> http://www.openrtk.org/Doxygen/rtkFDKConeBeamReconstructionFilter_8h_source.html),
>> you can see that default values are already provided for TOutputImage and
>> TFFTPrecision. From Python's point of view only a single argument is
>> therefore required (TInputImage). You can see an example of
>> FDKConeBeamReconstructionFilter starting from the 65th line of
>> FirstReconstruction.py.
>>
>> Good luck!
>>
>> Aurélien.
>>
>>
>> 2020년 4월 21일 (화) 오후 4:58, Aurélien Coussat <
>> aurelien.coussat at creatis.insa-lyon.fr>님이 작성:
>>
>> Hi,
>>
>> Your first error is really strange. The "geometry" variable is supposed
>> to be typed as rtkThreeDCircularProjectionGeometry (defined line 14), while
>> according to your error message it is of type
>> rtkFDKConeBeamReconstructionFilter. Are you sure you haven't somehow
>> altered the example script?
>>
>> About your second question, you can use
>> rtkFDKConeBeamReconstructionFilter and provide it a parallel geometry. See
>> the documentation for more details :
>> http://www.openrtk.org/Doxygen/classrtk_1_1FDKConeBeamReconstructionFilter.html
>> .
>>
>> Don't hesitate if something remains unclear!
>>
>> Aurélien.
>>
>> On Tue, 2020-04-21 at 12:06 +0900, 나윤호 wrote:
>>
>> Hi.
>> I'm a newbie to ITK and RTK.
>> I'm currently using python not C++
>>
>> so I installed ITK package and RTK package using
>>
>> pip install itk
>> pip install itk-rtk
>>
>> using ITK seems OK,  but I'm having difficulties with RTK.
>>
>> When I run the ITK example code, It worked well.
>> but when I tried to run the FirstReconstruction.py in the github,
>> error occurrs.
>>
>> ---------------------------------------------------------------------------AttributeError                            Traceback (most recent call last)<ipython-input-1-be2ee9c70d3d> in <module>     19 for x in range(0,numberOfProjections):     20   angle = firstAngle + x * angularArc / numberOfProjections---> 21   geometry.AddProjection(sid,sdd,angle)     22      23 # Writing the geometry to disk
>> AttributeError: 'rtkFDKConeBeamReconstructionFilterIF3' object has no attribute 'AddProjection'
>>
>>
>>
>> How can I fix this problem?
>>
>> and I have another question.
>> I want the reconstruct the sinogram image to phantom.
>>
>> usually what I did was using skimage.transform.iradon().
>> what should I use in RTK to do Inverse radon transform or Filtered back
>> projection method?
>>
>>
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