[mcxtrace-users] EI mcxtrace

Fri Sep 30 12:49:08 CEST 2016

I noticed there may be an interest in simulating the EI phase contrast method using mcxtrace. I have in the past written a number of components to do this. If these may be useful then do feel free to email me and I'll see if I can help.

Cheers,

Tom

t.millard at ucl.ac.uk

On 30 Sep 2016 11:00 a.m., mcxtrace-users-request at mcxtrace.org wrote:

>

> >

> Send mcxtrace-users mailing list submissions to
>         mcxtrace-users at mcxtrace.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://mailman.mcxtrace.org/cgi-bin/mailman/listinfo/mcxtrace-users
> or, via email, send a message with subject or body 'help' to
>         mcxtrace-users-request at mcxtrace.org
>
> You can reach the person managing the list at
>         mcxtrace-users-owner at mcxtrace.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of mcxtrace-users digest..."
>
>
> Today's Topics:
>
>    1. Re: some questions about McXtrace (Erik B Knudsen)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 29 Sep 2016 22:38:45 +0200
> From: Erik B Knudsen <erkn at fysik.dtu.dk>
> To: <mcxtrace-users at mcxtrace.org>
> Subject: Re: [mcxtrace-users] some questions about McXtrace
> Message-ID: <5a46ad96-b9bb-1dee-108a-5431d963f25c at fysik.dtu.dk>
> Content-Type: text/plain; charset="utf-8"; format=flowed
>
> 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
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > mcxtrace-users mailing list
> > mcxtrace-users at mcxtrace.org
> > http://mailman.mcxtrace.org/cgi-bin/mailman/listinfo/mcxtrace-users
> >
>
> --
> Erik Bergbäck Knudsen, Research Engineer         | DTU | morituri
> NEXMAP, DTU Fysik, DK-2800 Kgs. Lyngby, Denmark  |<>-<>|    te
> phone: (+45) 2132 6655                           |<>-<>| salutant
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> mcxtrace-users mailing list
> mcxtrace-users at mcxtrace.org
> http://mailman.mcxtrace.org/cgi-bin/mailman/listinfo/mcxtrace-users<http://mailman.mcxtrace.org/cgi-bin/mailman/listinfo/mcxtrace-users>
>
>
> ------------------------------
>
> End of mcxtrace-users Digest, Vol 19, Issue 4
> *********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mcstasmailman.esss.dk/pipermail/mcxtrace-users/attachments/20160930/19920de1/attachment.html>