<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hello, <br>
I am trying to do the wrapping for the
RegularizedConjugateGradientConeBeamReconstructionFilter, do I need
to wrap all the filters that it uses ?<br>
Is there any guiding document for the wrapping method?<br>
<br>
Regards,<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">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
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">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
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>
</div>
<blockquote cite="mid:002701d18086$c174df10$445e9d30$@com"
type="cite">
<meta name="Generator" content="Microsoft Word 12 (filtered
medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]-->
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-priority:99;
mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-priority:99;
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
span.EmailStyle19
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<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>
<div style="border:none;border-top:solid #B5C4DF
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"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<table class="MsoNormalTable"
style="width:347.55pt" border="0"
cellpadding="0" cellspacing="0" width="463">
<tbody>
<tr style="height:83.25pt">
<td style="width:212.9pt;padding:0in 0in
0in 0in;height:83.25pt" width="284">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:16.0pt;color:#1F497D"><img id="_x0000_i1025"
src="cid:part8.02020108.01040800@theobjects.com"
alt="Description:
cid:image002.jpg@01CB5984.4EABACE0"
border="0" height="74"
width="206"></span></b><o:p></o:p></p>
</td>
<td style="width:78.0pt;padding:0in 0in
0in 0in;height:83.25pt" width="104">
<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>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:7.5pt;color:#1F497D" lang="EN-CA">760 St-Paul W, #101<br>
Montreal, QC<br>
Canada H3C 1M4<br>
tel: <a moz-do-not-send="true"
href="tel:%28514%29%20843-3861"
target="_blank">(514) 843-3861</a><br>
ext 217</span><o:p></o:p></p>
</td>
<td style="width:56.65pt;padding:0in 0in
0in 0in;height:83.25pt" width="76">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D" lang="EN-CA"> </span><o:p></o:p></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:9.0pt;color:#0F243E"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Rtk-users mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Rtk-users@public.kitware.com">Rtk-users@public.kitware.com</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://public.kitware.com/mailman/listinfo/rtk-users">http://public.kitware.com/mailman/listinfo/rtk-users</a>
</pre>
</blockquote>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<meta name="Generator" content="Microsoft Word 12 (filtered)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin-top:0in;
margin-right:0in;
margin-bottom:10.0pt;
margin-left:0in;
line-height:115%;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
.MsoPapDefault
{margin-bottom:10.0pt;
line-height:115%;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<div class="WordSection1">
<p class="MsoNormal" style="line-height:normal"><b><span
style="font-size:10.0pt;font-family:"Times New
Roman","serif";color:#1F497D"
lang="EN-CA">Johnson Keiriz, PhD<br>
Senior Software Engineer</span></b></p>
<p class="MsoNormal"><span
style="font-size:7.5pt;line-height:115%;
font-family:"Times New
Roman","serif";color:#1F497D"
lang="EN-CA">760 St-Paul W, #101<br>
Montreal, QC<br>
Canada H3C 1M4<br>
tel: (514) 843-3861<br>
ext 217</span></p>
</div>
</div>
</blockquote>
<br>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<meta name="Generator" content="Microsoft Word 12 (filtered)">
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin-top:0in;
margin-right:0in;
margin-bottom:10.0pt;
margin-left:0in;
line-height:115%;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
p.MsoAcetate, li.MsoAcetate, div.MsoAcetate
{mso-style-link:"Balloon Text Char";
margin:0in;
margin-bottom:.0001pt;
font-size:8.0pt;
font-family:"Tahoma","sans-serif";}
span.BalloonTextChar
{mso-style-name:"Balloon Text Char";
mso-style-link:"Balloon Text";
font-family:"Tahoma","sans-serif";}
.MsoPapDefault
{margin-bottom:10.0pt;
line-height:115%;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
-->
</style>
<div class="WordSection1">
<p class="MsoNormal" style="line-height:normal"><b><span
style="font-size:10.0pt;font-family:"Times New
Roman","serif";color:#1F497D" lang="EN-CA">Johnson
Keiriz,
PhD<br>
Senior Software Engineer</span></b></p>
<p class="MsoNormal"><span
style="font-size:7.5pt;line-height:115%;
font-family:"Times New
Roman","serif";color:#1F497D" lang="EN-CA">760
St-Paul W, #101<br>
Montreal, QC<br>
Canada H3C 1M4<br>
tel: (514) 843-3861<br>
ext 217</span></p>
</div>
</div>
</body>
</html>