[Rtk-users] FirstReconstruction questions

[Simon Rit]

Hi,
rtkfdk is a full pipeline which also allows to do short scans (
https://doi.org/10.1118/1.595078) or displaced detector (
https://doi.org/10.1118/1.1489043).
The first yellow mark disables or enables the displaced detector filter
depending on a parameter on the command line.
The second yellow park sets how large should the gap be to be a short scan
(in the Parker algorithm).
The last mark uses streaming to compute the final image by parts.
args_info.divisions_arg is the number of parts.
If you have a regular full revolution with a centered detector and a
computer with enough RAM, you won't need any of this, no.
Simon

On Thu, Jan 28, 2021 at 11:18 AM Lai Yao Hao <yao_hao777 at hotmail.com> wrote:

> Hi Simon
>
> Thanks for the clarification. In the rtkfdk.cxx file, there are these
> following lines:
> using DDFCPUType = rtk::DisplacedDetectorImageFilter<OutputImageType>;
> ...
> ddf->SetDisable(args_info.nodisplaced_flag);
>
> ...
>
> using PSSFCPUType = rtk::ParkerShortScanImageFilter<OutputImageType>;
> PSSFCPUType::Pointer pssf;
> ...
> pssf->SetAngularGapThreshold(args_info.short_arg * itk::Math::pi / 180.);
>
> ...
>
> using StreamerType = itk::StreamingImageFilter<CPUOutputImageType,
> CPUOutputImageType>;
> ...
> streamerBP->SetNumberOfStreamDivisions(args_info.divisions_arg);
> ...
>
>
> Can I ask what are purpose do these 3 sections serve and do you think I
> need to include these 3 sections in my code? If so, what values should I
> include in the highlighted inputs?
>
> Appreciate your advice and look forward for your reply!
>
> Regards
> lyh
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, January 27, 2021 6:21 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> itk::ChangeInformationImageFilter is encapsulated in
> rtk::ProjectionsReader, see
> https://github.com/SimonRit/RTK/blob/master/include/rtkProjectionsReader.hxx#L481-L510.
> Option (3) is the correct one below. SetSpacing should be set according to
> your knowledge of the pixel spacing on the projections (the third dimension
> is ignored). SetOrigin should be set such that coordinate (0,0) on the
> detector corresponds to the line defined by the source and the center of
> rotation. If you have centered your detector, that should be
> -0.5*spacing*(size-1).
> Simon
>
> On Wed, Jan 27, 2021 at 8:28 AM Lai Yao Hao <yao_hao777 at hotmail.com>
> wrote:
>
> Hi
>
> I am confused when following rtkfdk.cxx for the implementation, because in
> that file, there is no usage of itk::ChangeInformationFilter. Can I confirm
> if the usage of itkChangeInformationFilter should be according to one of
> the following steps?
>
> (1) Read in the projections using itk::ImageSeriesReader and
> itk::NumericSeriesFileNames -> use itk::ChangeInformationFilter to change
> spacing and origin -> use rtk::ProjectionsReader to read the images with
> new spacing and origin
>
>
> (2) Read in the projections using rtk::ProjectionsReader and
> itk::NumericSeriesFileNames -> use itk::ChangeInformationFilter to change
> spacing and origin
>
> (3) Read in the projections using rtk::ProjectionsReader and
> itk::NumericSeriesFileNames and change the spacing and origin using
> rtk::ProjectionsReader::SetSpacing and rtk::ProjectionsReader::SetOrigin.
>
> If (3) is the correct method, what input should be in the
> rtk::ProjectionsReader::SetSpacing and SetOrigin method and how do I get
> these inputs?
>
> If the above steps for reading the input projections are not correct, is
> it possible to suggest steps which I can read the projections correctly
> with the correct spacing and origin?
>
> Thanks in advance for the advice and I look forward towards your reply!
>
> Regards
> lyh
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Thursday, January 21, 2021 10:52 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> Instead of
> firstSpacing[i]*=0.2;
> I would have written
> firstSpacing[i]=0.2;
> Sorry I did not look closely at the original code but you should modify
> it. The input images should be read with rtk::ProjectionsReader for being
> converted to line integrals (using the Beer-Lambert law). The output pixel
> type should be float or double, it won't work with integer values. I
> suggest to follow rtkfdk.cxx for implementing this.
> Simon
>
> On Tue, Jan 19, 2021 at 4:59 AM Lai Yao Hao <yao_hao777 at hotmail.com>
> wrote:
>
> Hi Simon,
>
> Sorry to bother you again. Just want to check if I have used
> itkChangeInformationImageFilter correctly in the snippet of code below:
>
> using FilterType = itk::ChangeInformationImageFilter<ImageType>;
> FilterType::Pointer filter = FilterType::New();
> ImageType::ConstPointer inputImage = reader->GetOutput();
> ImageType::PointType firstOrigin = inputImage->GetOrigin();
> ImageType::SpacingType firstSpacing = inputImage->GetSpacing();
> for (unsigned int i= 0; i < Dimension;i++) {
> firstSpacing[i]*=0.2;
> }
> filter->SetOutputSpacing(firstSpacing);
> filter->ChangeSpacingOn();
> ImageType::PointType::VectorType translation;
>
> translation[0] = -0.5*1951*0.2;
> translation[1] = -0.5*1951*0.2;
> translation[2] = -0.5*1951*0.2;
>
> firstOrigin += translation;
> filter->SetOutputOrigin(firstOrigin);
> filter->ChangeOriginOn();
>
> filter->SetInput(reader->GetOutput());
> ...
> feldkamp->SetInput(0, constantImageSource->GetOutput());
> feldkamp->SetInput(1, filter->GetOutput());
>
> Also, I would like to ask if there are any difference to the PixelType
> being unsigned short or unsigned char? This is because the source code
> fail to compile when I used unsigned short on one computer but it works on
> the other computer.
>
> Looking forward to your reply and answers! Much thanks in advance!
>
> Regards,
> lyh
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, January 13, 2021 5:07 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> 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.
> Simon
>
> On Wed, Jan 13, 2021 at 9:51 AM Lai Yao Hao <yao_hao777 at hotmail.com>
> wrote:
>
> Hi Simon
>
> 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
> rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo
> 278.044+372.528 | bc -l) -f 6.3
> 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
> 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?
>
> Look forward for your favourable reply.
>
> With thanks
> lyh
>
>
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Tuesday, January 12, 2021 4:22 AM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi lyh,
> I had a look at what you've sent. I obtain a first result with the
> following command lines:
> rtksimulatedgeometry -n 100 -o g --sid 278.044 --sdd $(echo
> 278.044+372.528 | bc -l) -f 6.3
> 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
> 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.
> I hope this helps. Cheers,
> Simon
>
> On Tue, Jan 5, 2021 at 5:35 PM Lai Yao Hao <yao_hao777 at hotmail.com> wrote:
>
> Hi,
> 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.
>
> Google drive share link:
>
> https://drive.google.com/drive/folders/1wMRo3Rmr6HszUVil0vEsLPtLSLftFyfQ?usp=sharing
>
> Regards
> lyh
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Tuesday, January 5, 2021 5:21 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> 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
> ChangeInformationFilter
> <https://itk.org/Doxygen/html/classitk_1_1ChangeInformationImageFilter.html>
> 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).
> You can share projections or a subset of them if you'd like us to give it
> a try with your code.
> Good luck!
> Simon
>
> On Mon, Jan 4, 2021 at 4:35 PM Lai Yao Hao <yao_hao777 at hotmail.com> wrote:
>
> Hi,
>
> 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.
>
> Thanks in advance for the advice and help!! I really appreciate this
> community 🙂
>
> Regards
> lyh
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, December 30, 2020 9:35 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> 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.
> 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.
> Simon
>
> On Mon, Dec 28, 2020 at 8:34 AM Lai Yao Hao <yao_hao777 at hotmail.com>
> wrote:
>
> Dear Simon and the RTK community
>
> 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.
>
> 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.
>
> Thanks so much in advance and look forward to everyone's reply!!
>
> PS: the tif file is just 1 of the 800 images I am given to reconstruct the
> object
>
> Regards
> lyh
>
> ------------------------------
> *From:* Simon Rit <simon.rit at creatis.insa-lyon.fr>
> *Sent:* Wednesday, December 9, 2020 4:23 PM
> *To:* Lai Yao Hao <yao_hao777 at hotmail.com>
> *Cc:* rtk-users at public.kitware.com <rtk-users at public.kitware.com>
> *Subject:* Re: [Rtk-users] FirstReconstruction questions
>
> Hi,
> 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.
> 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.,
> vv <http://vv.creatis.insa-lyon.fr> or ImageJ).
> Simon
>
> On Wed, Dec 9, 2020 at 8:59 AM Lai Yao Hao <yao_hao777 at hotmail.com> wrote:
>
> Hi to all the rtk-users
>
> 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?
>
> Your explanation will be much appreciated. Thanks in advance!
>
> Regards
> lyh
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