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Hi Simon,</div>
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Sorry to bother you again. Just want to check if I have used itkChangeInformationImageFilter correctly in the snippet of code below:</div>
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<span style="font-family: "Courier New", monospace;">using FilterType = itk::ChangeInformationImageFilter<ImageType>;</span>
<div><span style="font-family: "Courier New", monospace;">FilterType::Pointer filter = FilterType::New();</span></div>
<div><span style="font-family: "Courier New", monospace;">ImageType::ConstPointer inputImage = reader->GetOutput();</span></div>
<div><span style="font-family: "Courier New", monospace;">ImageType::PointType firstOrigin = inputImage->GetOrigin();</span></div>
<div><span style="font-family: "Courier New", monospace;">ImageType::SpacingType firstSpacing = inputImage->GetSpacing();</span></div>
<div><span style="font-family: "Courier New", monospace;"></span></div>
<div><span style="font-family: "Courier New", monospace;">for (unsigned int i= 0; i < Dimension;i++) {</span></div>
<div><span style="font-family: "Courier New", monospace;">firstSpacing[i]*=0.2;</span></div>
<div><span style="font-family: "Courier New", monospace;">}</span></div>
<div><span style="font-family: "Courier New", monospace;">filter->SetOutputSpacing(firstSpacing);</span></div>
<div><span style="font-family: "Courier New", monospace;">filter->ChangeSpacingOn();</span></div>
<div><span style="font-family: "Courier New", monospace;"></span></div>
<div><span style="font-family: "Courier New", monospace;">ImageType::PointType::VectorType translation;</span></div>
<div><br>
</div>
<div><span style="font-family: "Courier New", monospace;">translation[0] = -0.5*1951*0.2;</span></div>
<div><span style="font-family: "Courier New", monospace;">translation[1] = -0.5*1951*0.2;</span></div>
<div><span style="font-family: "Courier New", monospace;">translation[2] = -0.5*1951*0.2;</span></div>
<div><br>
</div>
<div><span style="font-family: "Courier New", monospace;">firstOrigin += translation;</span></div>
<div><span style="font-family: "Courier New", monospace;"></span></div>
<div><span style="font-family: "Courier New", monospace;">filter->SetOutputOrigin(firstOrigin);</span></div>
<div><span style="font-family: "Courier New", monospace;">filter->ChangeOriginOn();</span></div>
<div><br>
</div>
<span style="font-family: "Courier New", monospace;">filter->SetInput(reader->GetOutput());</span><br>
</div>
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<span style="font-family: "Courier New", monospace;">...</span></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: "Courier New", monospace;">feldkamp->SetInput(0, constantImageSource->GetOutput());
</span></div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="font-family: "Courier New", monospace;">feldkamp->SetInput(1, filter->GetOutput());<br>
</span></div>
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<span style="font-family: "Courier New", monospace;"><br>
</span></div>
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<span style="font-family: Calibri, Helvetica, sans-serif;">Also, I would like to ask if there are any difference to the </span><span style="font-family: "Courier New", monospace;">PixelType </span><span style="font-family: Calibri, Helvetica, sans-serif;">being </span><span style="font-family: "Courier New", monospace;">unsigned
short</span><span style="font-family: Calibri, Helvetica, sans-serif;"> or </span><span style="font-family: "Courier New", monospace;">unsigned char</span><span style="font-family: Calibri, Helvetica, sans-serif;">? This is because the source code fail to
compile when I used unsigned short on one computer but it works on the other computer.</span><br>
</div>
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<span style="font-family: Calibri, Helvetica, sans-serif;"><br>
</span></div>
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Looking forward to your reply and answers! Much thanks in advance!</div>
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<br>
</div>
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Regards,</div>
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
lyh</div>
<div id="appendonsend"></div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Simon Rit <simon.rit@creatis.insa-lyon.fr><br>
<b>Sent:</b> Wednesday, January 13, 2021 5:07 PM<br>
<b>To:</b> Lai Yao Hao <yao_hao777@hotmail.com><br>
<b>Cc:</b> rtk-users@public.kitware.com <rtk-users@public.kitware.com><br>
<b>Subject:</b> Re: [Rtk-users] FirstReconstruction questions</font>
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<div>Hi,</div>
<div>For the first line (rtksimulatedgeometry), it's already there I believe. For the second line, as I said, you need to use itkChangeInformationImageFilter and set the origin and spacing of the projections equal to those given by newspacing and neworigin.<br>
</div>
<div>Simon<br>
</div>
</div>
<br>
<div class="x_gmail_quote">
<div dir="ltr" class="x_gmail_attr">On Wed, Jan 13, 2021 at 9:51 AM Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com">yao_hao777@hotmail.com</a>> wrote:<br>
</div>
<blockquote class="x_gmail_quote" style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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Hi Simon</div>
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<br>
</div>
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Thank you so much for your help; the reconstructed image is almost similar to the image you sent (see attached file). In the previous email, for the command lines</div>
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<div><span style="font-family:monospace">rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo 278.044+372.528 | bc -l) -f 6.3</span></div>
<div><span style="font-family:monospace">rtkfdk -p images -r p_[0-9]*.tif -o fdk.mha -g g --newspacing 0.2 --neworigin $(echo -0.5*1951*0.2 | bc -l) --spacing 0.25 --dimension 512</span></div>
how do I get this line into the test.cxx file? If there is no way to get these lines into the test.cxx file, then do I run these lines in the terminal?</div>
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<br>
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Look forward for your favourable reply.</div>
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With thanks</div>
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lyh<br>
</div>
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<br>
</div>
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<br>
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<div id="x_gmail-m_2010060914223583565appendonsend"></div>
<hr style="display:inline-block; width:98%">
<div id="x_gmail-m_2010060914223583565divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> Tuesday, January 12, 2021 4:22 AM<br>
<b>To:</b> Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a> <<a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a>><br>
<b>Subject:</b> Re: [Rtk-users] FirstReconstruction questions</font>
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<div>Hi lyh,</div>
<div>I had a look at what you've sent. I obtain a first result with the following command lines:</div>
<div><span style="font-family:monospace">rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo 278.044+372.528 | bc -l) -f 6.3</span></div>
<div><span style="font-family:monospace">rtkfdk -p images -r p_[0-9]*.tif -o fdk.mha -g g --newspacing 0.2 --neworigin $(echo -0.5*1951*0.2 | bc -l) --spacing 0.25 --dimension 512<br>
</span></div>
<div>The newspacing and neworigin options set the projections spacing and origin with the ChangeInformationImageFilter. The result is not perfect, I believe the geometry is not right yet. Maybe there is a detector offset you're not aware of? But your text file
indicate no offset so I don't know what's wrong. Attached is a snapshot. There are also some dead pixels which you could try to prefilter.<br>
</div>
<div>I hope this helps. Cheers,</div>
<div>Simon<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Tue, Jan 5, 2021 at 5:35 PM Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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Hi,</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
I cannot send the projections via email as the projections are too big in size. Instead, I am sharing the files on Drive, with the hyperlink as below. In the folder, there is a subset of 100 projections out of the 800 projections, with the angle between each
projection being 3.6 degrees. There are other details on the projects as listed in report.txt file in the folder.</div>
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<br>
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Google drive share link:</div>
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<a href="https://drive.google.com/drive/folders/1wMRo3Rmr6HszUVil0vEsLPtLSLftFyfQ?usp=sharing" id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945LPlnk116246" target="_blank">https://drive.google.com/drive/folders/1wMRo3Rmr6HszUVil0vEsLPtLSLftFyfQ?usp=sharing</a></div>
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<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Regards</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
lyh<br>
</div>
<div id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945appendonsend">
</div>
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<div id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> Tuesday, January 5, 2021 5:21 PM<br>
<b>To:</b> Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a> <<a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a>><br>
<b>Subject:</b> Re: [Rtk-users] FirstReconstruction questions</font>
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<div>Hi,</div>
<div>I think the issue is that your projection images are given in the TIFF file format which does not contain important meta information such as the origin and the spacing of the projections. You should use
<a href="https://itk.org/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html" target="_blank">
ChangeInformationFilter</a> to set these. I'm guessing that the origin is currently (0,0) and since you do not set any offsets when using AddProjection, it comes down to having the corner of your projection aligned with the central ray (line defined by the
source and the center of rotation).</div>
<div>You can share projections or a subset of them if you'd like us to give it a try with your code.</div>
<div>Good luck!</div>
<div>Simon<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Mon, Jan 4, 2021 at 4:35 PM Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Hi,</div>
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<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
The code is as attached. Just for further reference, I am given images as attached, and there are 800 of them, with 0.45 degrees separating each frame. The naming of the screenshots depicts the frame that it is in.
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<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Thanks in advance for the advice and help!! I really appreciate this community <span id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945x_gmail-m_-9043481848435839607gmail-m_4926400425546106679🙂">
🙂</span><br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Regards</div>
<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
lyh<br>
</div>
<div id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945x_gmail-m_-9043481848435839607gmail-m_4926400425546106679appendonsend">
</div>
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<div id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945x_gmail-m_-9043481848435839607gmail-m_4926400425546106679divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> Wednesday, December 30, 2020 9:35 PM<br>
<b>To:</b> Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a> <<a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a>><br>
<b>Subject:</b> Re: [Rtk-users] FirstReconstruction questions</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi,</div>
<div>RTK cone beam reconstruction filters expect line integrals but the projection that you are showing seems to have the highest value in air. RTK automatically processes such projections with log and normalization if the pixels are unsigned short. Otherwise,
you need to do it yourself.<br>
</div>
<div>It is not clear if the geometry is correct from the reconstruction screen shot. The best would be to share your code if you want us to have a look.</div>
<div>Simon<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Mon, Dec 28, 2020 at 8:34 AM Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
<div style="margin:0px; font-size:12pt; color:black; background-color:white">Dear Simon and the RTK community</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white"><br>
</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white">Really thank you for the answer, and really sorry for the late reply. I am trying to reconstruct a 3d model using 800 images, rotating an object 360 degrees using rtk::ThreeDCircularProjectionGeometry,
rtk::ConstantImageSource and rtk:: FDKConeBeamReconstructionFilter from the FirstReconstruction example as well as itk::ImageSeriesReader.</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white"><br>
</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white">However, the reconstruction created is shown above in the screenshot and after checking all the parameters, I have no idea on how to move forward from here. From reading the forums,
I think that I should do one more image filter before applying the cone beam reconstruction? However, I am not too sure. Please advise on the next steps that can enable me to get the 3d reconstruction.</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white"><br>
</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white">Thanks so much in advance and look forward to everyone's reply!!</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white"><br>
</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white">PS: the tif file is just 1 of the 800 images I am given to reconstruct the object</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white"><br>
</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white">Regards</div>
<div style="margin:0px; font-size:12pt; color:black; background-color:white">lyh</div>
<br>
</div>
<div id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945x_gmail-m_-9043481848435839607gmail-m_4926400425546106679x_gmail-m_-2603944410746494337appendonsend">
</div>
<hr style="display:inline-block; width:98%">
<div id="x_gmail-m_2010060914223583565x_gmail-m_4994640668561699945x_gmail-m_-9043481848435839607gmail-m_4926400425546106679x_gmail-m_-2603944410746494337divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Simon Rit <<a href="mailto:simon.rit@creatis.insa-lyon.fr" target="_blank">simon.rit@creatis.insa-lyon.fr</a>><br>
<b>Sent:</b> Wednesday, December 9, 2020 4:23 PM<br>
<b>To:</b> Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>><br>
<b>Cc:</b> <a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a> <<a href="mailto:rtk-users@public.kitware.com" target="_blank">rtk-users@public.kitware.com</a>><br>
<b>Subject:</b> Re: [Rtk-users] FirstReconstruction questions</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi,</div>
<div>constantImageSource creates a constant volume. In the example, one is used as input of the simulation of projections of an ellipsoid (rei) and one as input of the reconstruction algorithm (feldkamp). fieldofview masks out (i.e., set to 0) voxels which
are not in the field of view.</div>
<div>I don't understand your screenshot either but if you use the tiff format, make sure you use a viewer capable of dealing with 3D tiff images (e.g.,
<a href="http://vv.creatis.insa-lyon.fr" target="_blank">vv</a> or ImageJ).</div>
<div>Simon<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Dec 9, 2020 at 8:59 AM Lai Yao Hao <<a href="mailto:yao_hao777@hotmail.com" target="_blank">yao_hao777@hotmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0px 0px 0px 0.8ex; border-left:1px solid rgb(204,204,204); padding-left:1ex">
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<div style="font-family:Calibri,Helvetica,sans-serif; font-size:12pt; color:rgb(0,0,0)">
Hi to all the rtk-users</div>
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<br>
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I am a new user of rtk, and I have some questions regarding the FirstReconstruction example given in github. I have generated an image as attached, with 4 tiny ball-like drawing hanging from the top. Can anyone explain to me why do I get such image and what
are the implications of constantImageSource, rei, constantImageSource2, feldkamp and fieldofview?</div>
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Your explanation will be much appreciated. Thanks in advance!</div>
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Regards</div>
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lyh<br>
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