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Perfect, thanks<br>
Johnson<br>
<br>
<div class="moz-cite-prefix">On 3/18/2016 9:31 AM, Cyril Mory wrote:<br>
</div>
<blockquote cite="mid:56EC0335.50109@uclouvain.be" type="cite">
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Hi again,<br>
<br>
You got the SART filter right. As for the conjugate gradient, the
filter is actually ConjugateGradientConeBeamReconstructionFilter
(for the 3D non-regularized reconstruction) and
RegularizedConjugateGradientConeBeamReconstructionFilter (its
regularized counterpart). <br>
<br>
The filter you found,
FourDConjugateGradientConeBeamReconstructionFilter, is used for 4D
reconstruction (you need a cardiac or respiratory phase signal).
Its regularized counterpart is
FourDROOSTERConeBeamReconstructionFilter.<br>
<br>
In addition to those, RTK also has
ADMMTotalVariationConeBeamReconstructionFilter and
ADMMWaveletsConeBeamReconstructionFilter, which implement the
Alternating Direction Method of Multiplier algorithm. <br>
<br>
You can find a description of these algorithms in <a
moz-do-not-send="true" class="moz-txt-link-freetext"
href="https://hal.inria.fr/tel-00985728/document"><a class="moz-txt-link-freetext" href="https://hal.inria.fr/tel-00985728/document">https://hal.inria.fr/tel-00985728/document</a></a><br>
<br>
Note that the SART filter has a m_NumberOfProjectionsPerSubset
member. Setting it to 1 (default) gives you SART, setting it to n
with 1 < n < TotalNumberOfProjections gives you OS-SART, and
setting it to n=TotalNumberOfProjections gives you SIRT.<br>
<br>
That's pretty much all there is in RTK at the moment.<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 03/18/2016 02:11 PM, Johnson
Keiriz wrote:<br>
</div>
<blockquote cite="mid:56EBFE6A.2070606@theobjects.com" type="cite">
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Hello,<br>
Can you please confirm that the following classes are the ones
used for the iterative reconstruction:<br>
1 - SART: SARTConeBeamReconstructionFilter<br>
2- Conjugate gradient:
FourDConjugateGradientConeBeamReconstructionFilter<br>
<br>
Is there a 3D conjugate gradient?<br>
Are these the only classes for iterative reconstruction?<br>
<br>
Thanks,<br>
Johnson<br>
<br>
<div class="moz-cite-prefix">On 3/18/2016 4:12 AM, Cyril Mory
wrote:<br>
</div>
<blockquote cite="mid:56EBB86E.80409@uclouvain.be" type="cite">
Hi Johnson,<br>
<br>
Regarding the iterative methods:<br>
- In SART, you can use the CUDA forward and back projectors,
but the rest of the calculation is performed on CPU. We do not
use SART a lot, so we have not fully optimized it. <br>
- Conjugate gradient, on the other hand, is entirely performed
on the GPU. Note that a regularized conjugate gradient
reconstruction filter is also available (with total variation
denoising, wavelets denoising, and positivity enforcement)<br>
<br>
I hope you will find what you need,<br>
Regards,<br>
Cyril<br>
<br>
<div class="moz-cite-prefix">On 03/17/2016 08:54 PM, Johnson
Keiriz wrote:<br>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hello,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I
did rebuild and now things are working. I tested
reconstruction with and without the filtering and
there were differences. Though, I am not sure that
filtering have provided a better reconstruction.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I
want to experiment the iterative methods. Can you
please confirm for me which iterative method are fully
implemented in CUDA: is it the conjugate gradient or
SART ?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I
have noticed that they are not wrapped at all, any
guide on how to introduce new filters?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Once
I have tested my wrapping, I will submit a github
pull-request. <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Johnson<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:simon.rit@gmail.com">simon.rit@gmail.com</a>
[<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="mailto:simon.rit@gmail.com">mailto:simon.rit@gmail.com</a>]
<b>On Behalf Of </b>Simon Rit<br>
<b>Sent:</b> Thursday, March 17, 2016 1:54 PM<br>
<b>To:</b> Johnson Keiriz<br>
<b>Cc:</b> <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:rtk-users@public.kitware.com">rtk-users@public.kitware.com</a><br>
<b>Subject:</b> Re: [Rtk-users] Python Wrapping<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Hi,<o:p></o:p></p>
</div>
<p class="MsoNormal">Good! Indeed, many things are
not wrapped. There is a trick regarding
modifications of the wrappings. You need to either
start from scratch the compilation or delete the
file
SimpleRTK-prefix/src/SimpleRTK-stamp/SimpleRTK-configure.
This will trigger a reconfiguration of the
SimpleRTK and, hopefully, account for your
modifications.<o:p></o:p></p>
</div>
<p class="MsoNormal">Don't hesitate to submit a github
pull-request when you have something working.<o:p></o:p></p>
</div>
<p class="MsoNormal">Simon<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Thu, Mar 17, 2016 at 4:33 PM,
Johnson Keiriz <<a moz-do-not-send="true"
href="mailto:jkeiriz@theobjects.com"
target="_blank">jkeiriz@theobjects.com</a>>
wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Hello again,</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">I found out about the
json wrapping files. I added the wrapping for
all the filters, but I haven’t noticed any
effect from setting the filters !!! </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Any hints ?</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Regards,</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Johnson</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<div>
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1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
Rtk-users [mailto:<a
moz-do-not-send="true"
href="mailto:rtk-users-bounces@public.kitware.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:rtk-users-bounces@public.kitware.com">rtk-users-bounces@public.kitware.com</a></a>]
<b>On Behalf Of </b>Johnson Keiriz<br>
<b>Sent:</b> Thursday, March 17, 2016 9:23
AM<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:rtk-users@public.kitware.com"
target="_blank">rtk-users@public.kitware.com</a>;
Simon Rit<br>
<b>Subject:</b> [Rtk-users] Python
Wrapping</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,
<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
am using the Python wrapped version of RTK.
I have a question regarding the wrapping:<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">It
seems that not all functionality is
available, for example: for the <b>CudaFDKConeBeamReconstructionFilter,
</b>I was not able to set the cut frequency
of the any of the filters<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">(RamLaK,
Cosine, ShepLogan) except for the Hann . Are
the methods not wrapped ?<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks,<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Johnson<o:p></o:p></p>
<p class="MsoNormal"
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<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:10.0pt;color:#1F497D" lang="EN-CA">Johnson Keiriz, PhD<br>
Senior Software Engineer</span></b><o:p></o:p></p>
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