[Rtk-users] scanner development problems

[Vasiliy Nabokov]

It worked now. The phantom artifact was caused by wrong rotate direction xD
So, when i changed sort of regex result of my tifs from asc to desc phantom
was disappeared!
After scanner geometry calibration by article above, and my self algorithms
i got not bad reconstruction by RTK for me. But there still remain two
problems..
Here is one slice http://i.imgur.com/oVHCodb.png reconstructed from scans
like this http://i.imgur.com/qIYkvY7.png
1). Contrast. Structure reconstructs good, but hard to see. I receive 12
bit per pixel raw data from the detector, convert it to 16 bit just by
(/4095.)*65535. What options i should play in RTK or while tifs generation
at acquisition process in order to make structure more visible ? I tried
different variants of voltage and current of tube, but on the picture is
the best variant of contrast...
2). Also on the slice you can see circles that come from center. As i think
its still geometry problems, i have to do calibration process better, isn't
it ?



On Fri, Mar 18, 2016 at 1:27 PM, Simon Rit <simon.rit at creatis.insa-lyon.fr>
wrote:

> Ok, sorry, I erroneously mixed the size of the reconstructed volume and
> the size of the projections. Then your calculation seems correct and I
> don't know where does your geometry problem come from. For sure, you don't
> have to shift the projections, --proj_iso_x does the same thing directly.
> Regards,
> Simon
>
> On Thu, Mar 17, 2016 at 4:23 AM, Vasiliy Nabokov <nabokajeleboka at gmail.com
> > wrote:
>
>> Dear Simon, as i understand --neworigin is origin for projections. my
>> projection's width 2452 and spacing 0.0148, so 2451/-2*0.0148=-18.137
>>
>> On Wed, Mar 16, 2016 at 6:45 PM, Simon Rit <
>> simon.rit at creatis.insa-lyon.fr> wrote:
>>
>>> Hi,
>>> I think it's a geometry problem. I don't have a solution for you but
>>> just a remark: how did you come up with the neworigin parameter? Changing
>>> this has a similar effect as changing the --proj_iso_x or "offseting" the
>>> projections. And it seems that the value you put (-18.137) makes no sense
>>> to me wrt the total width (800*0.0296=23.68). Typically, I center the
>>> projection which in your case would require as a new origin 799/-2*0.0296.
>>> I hope this helps,
>>> Simon
>>>
>>> On Wed, Mar 16, 2016 at 1:11 PM, Vasiliy Nabokov <
>>> nabokajeleboka at gmail.com> wrote:
>>>
>>>> Hi dear RTK users. Sorry, its offtop post... i just wanna tell you
>>>> about my problems if anyone can help me..
>>>> I develop scanner. Reconstruction of parallelepiped or cube (
>>>> http://i.imgur.com/9YHyfWH.jpg) caused to phantom artifact (
>>>> http://i.imgur.com/yyI184j.png). Don't look at noise, its test scan,
>>>> without averaging and big rotation step.  Yea, it seems that its mainly
>>>> misalignments problems, so i calibrated sourceX, sourceY, detectorX,
>>>> detectorY by the following method
>>>> http://www1.jinr.ru/Pepan_letters/panl_2015_5/10_gongad.pdf, got
>>>> sourceX = -215 mkm, sourceY = 650 mkm, detectorX = 50mkm. i specify this
>>>> information but without success.
>>>>
>>>> I also wrote a little program in this way
>>>>     for (float sourceXOffset_ = sourceXFrom; sourceXOffset_ <
>>>> sourceXTo; sourceXOffset_ += searchStep)
>>>>     for (float sourceYOffset_ = sourceYFrom; sourceYOffset_ <
>>>> sourceYTo; sourceYOffset_ += searchStep)
>>>>     for (float projXOffset = projXFrom; projXOffset < projXTo;
>>>> projXOffset += searchStep)
>>>>     {
>>>>         sprintf(cmd, "./rtksimulatedgeometry -o geometry.xml --n 90
>>>> --arc=360 --sdd=232.241 --sid=170 --source_x=%.6f --source_y=%.6f
>>>> --proj_iso_x=%.6f", sourceXOffset_, sourceYOffset_, projXOffset);
>>>>
>>>>         int r = system(cmd);
>>>>
>>>>         sprintf(cmd, "./rtkfdk --hardware=cuda -p /home/fee/Public/ -r
>>>> [0-9]+.tif$ -o dump/out.mha -g geometry.xml --verbose --dimension 800,1,800
>>>> --spacing 0.0296 --newspacing 0.0148 --neworigin -18.137,-12.128,0
>>>> --subsetsize=1 -l --origin -11.8252,-3.55,-11.8252");
>>>>         r = system(cmd);
>>>> ...
>>>>
>>>> to search scanner alignment but also without success.
>>>>
>>>> I noticed interesting thing: when i specially offset detector
>>>> horizontally to the right by 4.5mm from the center, and specify it by
>>>> --proj_iso_x=4.5 when generating geometry file, phantom disappears! (
>>>> http://i.imgur.com/OOsPsfL.png) I even take scans when the detector on
>>>> the center, reconstruct it, and here is phantom artifact, then i manually
>>>> offset picture to the left on the tifs (from
>>>> http://i.imgur.com/FGxCJUo.png to http://i.imgur.com/brbp5sd.png), and
>>>> it reconstructs without phantom with --proj_iso_x=4.5! So, for this moment
>>>> i work in this way, take scans when detector on the center, manually offset
>>>> picture to the left and specify it by proj_iso_x to avoid phantom artifact,
>>>> but its HUGE WORKAROUND =))
>>>>
>>>>
>>>> What do you think about it ? If its geometry issue, why real or virtual
>>>> offset of detector cleans up the phantom artifact?
>>>>
>>>>
>>>> _______________________________________________
>>>> Rtk-users mailing list
>>>> Rtk-users at public.kitware.com
>>>> http://public.kitware.com/mailman/listinfo/rtk-users
>>>>
>>>>
>>>
>>
>
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