[Rtk-users] Question about the geometry

Fri Oct 16 08:33:38 EDT 2015

Hi Chao Wu

Thank you very much! This is definitely something I can use in order
to move forward. I'm not trying to make the best possible
reconstruction out of this dataset, but just have something that works
so I can start playing around and get familiar with RTK. Which I do
have now.

And to Simon: Thanks for the link.

bets

Arvid

On Fri, Oct 16, 2015 at 2:15 PM, Simon Rit
<simon.rit at creatis.insa-lyon.fr> wrote:
> 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 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
>>> >>
>>> >
>>
>>
>>
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