[Insight-users] Parellel Beam Reconstruction
Oleksandr Dzyubak
adzyubak at gmail.com
Wed Aug 4 18:29:58 EDT 2010
Hi Naresh,
Let's say you have a file with sinograms.
Usage :
./DirectFourierReconstruct input output r_dir z_dir alpha_dir nz ng
fc nb alpha_range x y z sx sy sz sigma
"input" is your 3D sinogram file.
"output" will be your reconstructed image.
Pay attention that this contribution works with 3D, that is, you
experimental setup
have to be a 2D detector array (X-Y) "rotating" about your sample (Alpha).
Depending on how you organized readout system, you have to map
"directions" accordingly.
For example, you acquire data from the detector array and then step
through alpha.
In this case row detectors give you X-dimension, column detectors->Z,
and
"slices"-->Angular. Thus you have to "map" directions as below.
r_dir = 0(x)
z_dir = 1(y)
alpha_dir = 2(z)
For the sake of reducing aliasing artifacts in the reconstructed images,
leave these three as below.
nz = 2 SetZeroPadding order (usually 2)
ng = 2 SetOverSampling order (usually 2)
fc = 1 SetCutoff friquency f= (0; 1] usually 1
If you have enough memory, keep nb = 3 (however can be up to 5).
nb = 3 SetRadialSplineOrder nb=3 gives quite good results
Finally, the angular range covered by the projections has to be specified
according to your acquisition setup.
(Lets say you have 180 degree with step size 1).
alpha_range = 180
The rest is even easier.
x = 0 origin X
y = 0 origin Y
z = 0 origin Z
sx = 512 size x (cropped or zero-padded row detectors)
sy = 512 size y (cropped or zero-padded row detectors)
sz = 2 size z (size your column detectors)
sigma = 0 kernel size from itk::RecursiveGaussianImageFilter
Smoothing in radial direction. If sigma=0, no smoothing involved at all.
Pay attention that "sx" and "sy" should be power of 2 though.
You might want either to crop you sinograms down or zero-pad it.
And again do it ONLY in radial direction!!! Well, if you follow this recipe,
it should work and produce very nice results.
You you want just to play with the example from the contribution,
command line is below.
./DirectFourierReconstruct sinogram.hdr recon.hdr 1 2 0 2 2 1 3 180 0 0
0 512 512 2 0
Good luck,
Alex
naresh wrote:
> Dear Wes
>
> Yes i tried to run with test include with submission . Can you tell
> me the value of argument used in sample test suite ?
>
> r_dir
> z_dir
> alpha_dir
> nz
> ng
> fc
> nb
> alpha_range
> x
> y
> z
> sx
> sy
> sz
> sigma
>
> That will help me find my problem if you have values memorized.
>
>
> Naresh
>
>
> ----- Original Message -----
> *From:* Wes Turner <mailto:wes.turner at kitware.com>
> *To:* naresh <mailto:naresh at winner.co.in>
> *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
> *Sent:* Thursday, May 20, 2010 6:21 PM
> *Subject:* Re: [Insight-users] Parellel Beam Reconstruction
>
> I have not used it in my own application, but I was able to
> compile and run the Insight Journal submission successfully
> without threadlock. Have you tried running the test included with
> the submission. I think I had some small issue with it. You
> might want to read my review for some very small pointers.
>
> - Wes
>
> On Thu, May 20, 2010 at 1:11 AM, naresh <naresh at winner.co.in
> <mailto:naresh at winner.co.in>> wrote:
>
> Dear Wes
>
> Did you already used this programe ? I tried to use it but i
> got nothing as output. It just going in some thread lock
> situations.
>
> Also how can i use it with my own image projection that i
> still donot know. ?
>
> Naresh
>
>
>
> ----- Original Message -----
> *From:* Wes Turner <mailto:wes.turner at kitware.com>
> *To:* naresh <mailto:naresh at winner.co.in>
> *Cc:* insight-users at itk.org <mailto:insight-users at itk.org>
> *Sent:* Wednesday, May 19, 2010 6:59 PM
> *Subject:* Re: [Insight-users] Parellel Beam Reconstruction
>
> Naresh,
>
> Check out the following Insight Journal article.
>
> http://hdl.handle.net/1926/585
>
> - Wes
>
> On Wed, May 19, 2010 at 3:46 AM, naresh
> <naresh at winner.co.in <mailto:naresh at winner.co.in>> wrote:
>
> Hi
>
> I am learning Parellel Beam Reconstruction for X-ray
> CT. I want to implement it with ITK . So anyone done
> previously with ITK ?
>
> Please post if you have any has any good starting
> document or some example codes .
>
>
> Naresh
>
>
> _____________________________________
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>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> Technical Leader
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4920
>
>
>
>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> Technical Leader
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4920
>
> ------------------------------------------------------------------------
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
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