[Rtk-users] Question about the geometry

[Simon Rit]

Thanks a lot Chao, I'm so glad that someone else than me did this!
Just as a side note, Arvid, if you don't understand what is the origin and
the spacing, look at the ITK software guide
<http://www.itk.org/ItkSoftwareGuide.pdf> section 4.1.4, this is VERY
important.
Simon

On Fri, Oct 16, 2015 at 2:03 PM, Chao Wu <wuchao04 at gmail.com> wrote:

> Hi Arvid,
>
> Since you know how important a correct geometry is, you should understand
> why you need projection origin and spacing.
> CT geometry has more parameters than sid and sdd. How big the detector
> pixel size (spacing) and how the detector is places w.r.t. the central ray
> (origin) also play a role in the geometry. And in-plane/out-of-plane
> rotations etc.
> In your dataset the correct spacing and origin information is not stored
> correctly in the projection data, so the total geometry is wrong.
>
> I have tested your data with the following command line and it gives
> meaningful image. The newspacing and neworigin arguments force rtkfdk to
> accept spacing and origin information of projections from command line
> instead of from the data. Also I change the spacing of the volume from 2 to
> 0.2 because your object is small.
>
> rtkfdk -p c:\Work\out_dir\ -r cylinder-a.mha -o
> c:\Work\out_dir\cylinder_a_recon.mha
> -g c:\Work\out_dir\geometry_real.xml --spacing=0.2 --dimension=256
>  --newspacing=0.2 --neworigin=-20,-20
>
> Apparently there is still some misalignment between this guessed geometry
> and the real geometry, which you need to figure out with your own hardware.
>
> Regards,
> Chao
>
>
> 2015-10-16 13:15 GMT+02:00 Arvid Piehl Lauritsen Böttiger <
> bottiger at gmail.com>:
>
>> Hi Chao.
>>
>> Thank you for the reply. However, I'm not quite sure what you mean by
>> origin and spacing.
>> A pixel on the detector is ~200 microns, and the sample is magnified
>> around 1.3 times.
>>
>> I do understand that having a correct geometry is important to get an
>> output image with correct dimensions, but I do not understand it's so
>> difficult for me to make a single successful reconstruction (possibly
>> with a dummy geometry).
>>
>> best
>>
>> Arvid
>>
>> PS: Just to validate the data I'm testing on I installed Octave and
>> created a sinogram I then ran through its iradon implementation. It
>> seemed to work quite nicely (see attachments).
>>
>> On Fri, Oct 16, 2015 at 12:09 PM, Chao Wu <wuchao04 at gmail.com> wrote:
>> > Hi Arvid,
>> >
>> > Is the origin and spacing of your projection data correct? What is your
>> > projection pixel size?
>> >
>> > Regards, Chao
>> >
>> > 2015-10-16 9:12 GMT+02:00 Arvid Piehl Lauritsen Böttiger
>> > <bottiger at gmail.com>:
>> >>
>> >> Dear all. Hello again.
>> >>
>> >> I writing to you again because I need some help to understand how to
>> >> declare the geometry of the system.
>> >>
>> >> Cyril redirected me towards this document (
>> >> http://www.creatis.insa-lyon.fr/~srit/geometry.pdf ) which helped a
>> >> lot, but unfortunately it has not been enough to make me reconstruct a
>> >> tomogram.
>> >>
>> >> I have attached a drawing of my setup (setup.jpg). The
>> >> source-to-detector distance is around 1600 mm. I just rotate the
>> >> sample instead of the source, and the sample-detector distance is 15
>> >> cm which makes the isocenter distance 1450. The field of view is
>> >> around 2 cm.
>> >>
>> >> The aligned projections are located here:
>> >> https://www.dropbox.com/s/ycg41qkeym61kec/cylinder-a.mha?dl=0
>> >> and the raw tiffs are here:
>> >> https://www.dropbox.com/s/hb67pkueyb3zcc3/tiffs.zip?dl=0
>> >>
>> >> I would say the input data looks as nice, but when reconstructing I'm
>> >> still just getting noise:
>> >>
>> >> This is how I perform my "reconstruction"
>> >>
>> >> # 361 projections from 0 to 360 degrees. The source-detector distance
>> >> is 1.6 m and the
>> >> # sample-detector distance is 15 cm
>> >> # I have tried with many variations of --ssd and --sid but I think
>> >> they all look the same
>> >> rtksimulatedgeometry.exe -f 0 -n 361 -a 360 --sdd 1600 --sid 1450 -o
>> >> c:\Work\out_dir\geometry_real.xml
>> >>
>> >> # make a mha file out of the tiff files
>> >> rtkprojections.exe --path c:\Work\tomography_data\tiffs\ --output
>> >> c:\Work\out_dir\cylinder-a.mha --regexp .tif
>> >>
>> >> # "Reconstruct" the data.
>> >> rtkfdk.exe -p c:\Work\out_dir\ -r cylinder-a.mha -o
>> >> c:\Work\out_dir\cylinder_a_recon.mha -g
>> >> c:\Work\out_dir\geometry_real.xml --spacing 2 --dimension 256
>> >>
>> >> The result can be viewed in the recon_result.PNG attachment.
>> >> The reconstrcution can be found here:
>> >> https://www.dropbox.com/s/cbwwnbbzvhqiyvy/cylinder_a_recon.mha?dl=0
>> >>
>> >> Can someone please help me what I am doing wrong?
>> >>
>> >> best
>> >>
>> >> Arvid
>> >>
>> >> _______________________________________________
>> >> Rtk-users mailing list
>> >> Rtk-users at public.kitware.com
>> >> http://public.kitware.com/mailman/listinfo/rtk-users
>> >>
>> >
>>
>
>
> _______________________________________________
> Rtk-users mailing list
> Rtk-users at public.kitware.com
> http://public.kitware.com/mailman/listinfo/rtk-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/rtk-users/attachments/20151016/818ed166/attachment-0010.html>