[Rtk-users] using RTK with python

Tue Apr 21 22:33:44 EDT 2020

Here's my jupyter file.

I just found something strange.

I'll send you two files.

they both have same script in it but having different error.

FirstReconstruction.ipynb is exactly same as the one in the github example.

and the other one is same except for the plotting of sinogram data for
practicing itk.

I have no idea why they have different error

2020년 4월 21일 (화) 오후 10:22, Simon Rit <simon.rit at creatis.insa-lyon.fr>님이 작성:

> 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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