[mcxtrace-users] some questions about McXtrace

[Erik B Knudsen]

Hi Ali,

Answers to your questions below:

cheers
Erik

On 29/09/16 20:27, Ali Kazemi wrote:
> Hi
>
>
> 1)There is a “phase” parameter in the source components. I know the
> meaning of phase for waves but I don’t understand the determination of
> phase with a number. For example, for the source _Pt the default phase
> is -1. What does it mean?
The concept is simply to consider the ray as a plane wave travelling in 
the direction of the wavevector. Then the number reflects the phase of 
the particular ray at the point where the particle is (x,y,z). '

The -1 in source_pt simply reflects a known default of something. It 
could basically be anything. Sure enough -1 could be considered an odd 
choice.
>
>
> 2) The goal of putting a target for sources is to restrict our radiation
> to a solid angle. Isn’t it?
Yes - this is correct.

>
>
> 3) Do the x-rays get traced beyond this virtual target (figure 1) or not
> (figure 2)?
Actually neither. Photon rays are generated as the source with a 
wavevector such that they will hit the target. Unless some object in 
between blocks or reflects them of course. The rays do not leave the source.
>
>
> 4) when the “random phase” is set to 1 it means that the source is
> spatially incoherent and when set to 0 it means that the source is
> spatially coherent?
Well - it really means just that _random_. It randomphase != 0 the the 
phase is chosen at random. If randomphase is 0 then the phase of all 
photon rays is set to whatever the phase parameter happens to be.
>
>
> 5) It is mentioned in the component manual that “photons within the slit
> opening are unaffected, while all other photons are discarded”. I want
> to simulate a gold mask with some parallel slits (masks used in EI
> method in phase contrast x-ray imaging). If I put some slits and filters
> (with material data file gold) alternatively in y direction, do the x
> rays which hit the masks get discarded or attenuated? If discarded, what
> is the solution?
To do this you'd have to use a GROUP. If you don't the rays that miss 
the first slit opening will all be discarded. Remember in McXtrace the 
order is important.

>
>
>
> 6) I am windows user and I couldn’t download data files from NIST FFAST
> as it was described in the component manual. (figure 3)
get_xray_db_data is a bash shell script, but you really don't need it. 
Yuo can just as easily log on the NIST website - navigate to the FFAST 
database and generate whatever dat you need from there. In the end what 
you need is a simply an ascii datafile along the lines of the ones 
shipped with McXtrace. What kind of data do you need?

>
>
> 7) I couldn’t find the contrib directory where components that were
> submitted by users is there.
It's beacuse at that point in time when McXtrace 1.2 packages were 
generated contrib was empty and some systems installations delete empty 
directories. If you need it (I'm not sure why) you can just create the 
folde inside the library directory (alongside sources, monitors, optics, 
etc.)

>
>
> 8)
>
> COMPONENT transfocator1=Lens_simple(
>
>       xwidth=2e-1,yheight=2e-1,N=T1_N, material_datafile="Be.txt")
>
> WHEN(1) AT(0,0,31.5) RELATIVE Origin
>
> ROTATED (0,ANGLE,0) RELATIVE PREVIOUS
>
>
> What is the meaning of the condition WHEN(1) and when it get satisfied?
A 1 is always satisfied - the WHEN clause is a remnant of functionality 
which was removed.

>
>
>
> 9) I didn’t understand what “restore x ray” means in monitors?
In order to measure the photon ray, a monitor transports the photon to 
its surface. If restore_xray!=0 the monitor will nicely put the photon 
back where it came from. This way a monitor can safely overlap a 
subsequent component
>
>
> 10) in the instrument file of “Test sources” example, the first source
> is set to E0 = 5, dE = 1. But what energy monitor shows is dE = 0.5.
> (figure 4)
There was some inconsistency among the source models as to whether dE 
mean half spread or full spread - this has been homogenized in the 
development tree.
>
>
> 11) what is the “I_err” in the PSD monitors and why are its value the
> same as intensity values?
I should certainly hope they're not the same as the intensity values. 
This would mean you have only one single ray hitting each of the pixels. 
The I_err values are uncertainty estimates on the corresponding 
intensity value of that pixel.

>
>
>
> 12) It is mentioned in the component manual that the output of monitors
> are intensity, counts and M(x,y). what is M?


>
>
>
> 13) Are the monitors considered virtual components and we can put some
> monitors in a same position?
That depends on the geometry of the monitor, but if you set restore_xray 
- then yes.

>
>
> 14) Is the distance that x rays travel till hitting a component
> considered vacuum?
Yes
>
>
> 15) when we want to simulate x-ray imaging, should we use “Absorption
> sample” as a sample? Don’t you think the geometry of a sample is so
> limited in McXtrace?
You should use whatever sample that best describes your experiment.
Absorption_sample is of course limited to sphere, cylinder, or box 
inside a box or cylinder. This however was more than sufficient for the 
experiment we were dealing with at the time it was written. If you need 
something more sophisticated you could extend Absorption_sample.
Did you have something particular in mind?

>
>
> 16) Does refraction happen in “Absorption sample” apart from attenuation?
At present no. Filter can do that.

>
>
> 17) sorry for large number of questions!
No problem - it is what the mailing list is for - after all.

>
>
> Thanks
>
>
>
>
>
>
>
>
>
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-- 
Erik Bergbäck Knudsen, Research Engineer         | DTU | morituri
NEXMAP, DTU Fysik, DK-2800 Kgs. Lyngby, Denmark  |<>-<>|    te
phone: (+45) 2132 6655                           |<>-<>| salutant