[Rtk-users] Question about the geometry

[Arvid Piehl Lauritsen Böttiger]

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
>>
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>>
>
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