[Gate-users] Gate-users Digest, Vol 94, Issue 15
Tahereh Niknejad
tahereh.nik at gmail.com
Sun Mar 9 03:31:18 CET 2014
Dear Chunhu,
It happened because the amount of yttrium in the Gate materials in very
high.
for example for 10% yttrium you have to make change as below:
LYSO: d=7.105 g/cm3; n=4 ; state=Solid
+el: name=Lutetium ; f=0.714609801
+el: name=Yttrium ; f=0.040381125
+el: name=Silicon; f=0.063520871
+el: name=Oxygen; f=0.181488203
Regards,
Tahereh
On Sun, Mar 9, 2014 at 3:33 AM, <
gate-users-request at lists.opengatecollaboration.org> wrote:
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> Today's Topics:
>
> 1. Re: Unable to use phase space file from IAEA with Gate 6.2
> (Stathis Kamperis)
> 2. Re: Unable to use phase space file from IAEA with Gate 6.2
> (Stathis Kamperis)
> 3. About the performance comparison between LSO ans LYSO (???)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 8 Mar 2014 22:13:46 +0200
> From: Stathis Kamperis <ekamperi at gmail.com>
> To: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Unable to use phase space file from IAEA
> with Gate 6.2
> Message-ID:
> <CACYCkUtbj8p9gE72CC2No7B0n03wXrF=3q9BaQ=
> edMbEfKae1Q at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I'm not sure why Gate can't parse the phase space file. I tried to
> extract the information with Mathematica and it seems that the phase
> space file is ok (not sure about the header though, especially where
> the record contents are declared).
>
> For example I get only 1,2,3 (gammas, e-, e+) for particles:
>
> file =
> BinaryReadList[
> "~/Dropbox/foo",
> Join[
> Flatten@
> {"Byte", PadLeft[{}, 6, ToString at Real32], "Integer32", "Integer32"}],
> ByteOrdering -> -1];
>
> h = HistogramList[file[[All, 1]]]
> {{1, 2, 3, 4}, {1543049, 8306, 161}}
>
> And the ratios seem to be in alignment with what is declared at the header:
>
> First at Last@h/Total at Last@h // N
> 0.994543
>
> 125806703/126491813 // N
> 0.994584
>
> I've only checked 50 MB worth of data but I doubt that there's a wrong
> particle number in the rest (will check though).
>
> So... has anyone ever successfully used the IAEA phase space files
> with Gate 6.2 ?
>
> Best regards,
> Stathis
>
>
>
>
> On Fri, Mar 7, 2014 at 11:40 PM, Stathis Kamperis <ekamperi at gmail.com>
> wrote:
> > Relevant:
> >
> > http://comments.gmane.org/gmane.comp.science.opengate.user/3115
> >
> > Best regards,
> > Stathis
> >
> > On Fri, Mar 7, 2014 at 11:26 PM, Stathis Kamperis <ekamperi at gmail.com>
> wrote:
> >> Greetings everyone,
> >>
> >> I downloaded it from here:
> >> https://www-nds.iaea.org/phsp/photon1/
> >>
> >> ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header
> >> ELEKTA_PRECISE_6mv_part1.IAEAheader
> >>
> >> When I try to use it from within Gate with:
> >>
> >> /gate/source/addSource mybeam phaseSpace
> >> /gate/source/mybeam/addPhaseSpaceFile
> >> /home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp
> >>
> >> I get the following error:
> >>
> /home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc
> >> (l.252): Source phase space: particle not available in IAEA phase
> >> space format.
> >>
> >> I checked the source code:
> >>
> http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231
> >>
> >> and it appears as if Gate can't recognize some particle type that the
> >> header file is including. But,
> >>
> https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader
> >> has only photons, electrons, positrons that Gate should recognize.
> >>
> >> Any thoughts?
> >>
> >> Best regards,
> >> Stathis
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 8 Mar 2014 22:34:36 +0200
> From: Stathis Kamperis <ekamperi at gmail.com>
> To: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Unable to use phase space file from IAEA
> with Gate 6.2
> Message-ID:
> <
> CACYCkUuFkakuzc-WGG9+fpZsjreKK0oaw7MGgfFbwDZkeiB2HA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Sat, Mar 8, 2014 at 10:13 PM, Stathis Kamperis <ekamperi at gmail.com>
> wrote:
> > I'm not sure why Gate can't parse the phase space file. I tried to
> > extract the information with Mathematica and it seems that the phase
> > space file is ok (not sure about the header though, especially where
> > the record contents are declared).
> >
> > For example I get only 1,2,3 (gammas, e-, e+) for particles:
> >
> > file =
> > BinaryReadList[
> > "~/Dropbox/foo",
> > Join[
> > Flatten@
> > {"Byte", PadLeft[{}, 6, ToString at Real32], "Integer32",
> "Integer32"}],
> > ByteOrdering -> -1];
> >
> > h = HistogramList[file[[All, 1]]]
> > {{1, 2, 3, 4}, {1543049, 8306, 161}}
> >
> > And the ratios seem to be in alignment with what is declared at the
> header:
> >
> > First at Last@h/Total at Last@h // N
> > 0.994543
> >
> > 125806703/126491813 // N
> > 0.994584
> >
> > I've only checked 50 MB worth of data but I doubt that there's a wrong
> > particle number in the rest (will check though).
> >
>
> The whole phase space file is ok. I checked it with the following code
> snippet:
>
> [stathis at fedora]~/Downloads% cat read.c
> 22:32:29
> #include <assert.h>
> #include <stdio.h>
>
> struct rec {
> char particle;
> char pad[32];
> } __attribute__((packed));
>
> int
> main(int argc, char *argv[])
> {
> FILE *fp;
> struct rec r;
> int cnt, rv;
>
> fp = fopen(argv[1], "r");
> assert(fp);
>
> cnt = 0;
> do {
> ++cnt;
>
> rv = fread(&r, sizeof(struct rec), 1, fp);
> assert(rv > 0 || (rv == 0 && feof(fp)));
>
> if (r.particle != 1 && r.particle != 2 && r.particle != 3)
> {
> printf("Wrong particle = %d at record = %d\n",
> r.particle, cnt);
> }
> } while(!feof(fp) && !ferror(fp));
>
> fclose(fp);
>
> return 0;
> }
>
> [stathis at fedora]~/Downloads% gcc -Wall -ansi -pedantic read.c
> [stathis at fedora]~/Downloads% ./a.out ELEKTA_PRECISE_6mv_part1.IAEAphsp
> [stathis at fedora]~/Downloads%
> [stathis at fedora]~/Downloads% echo $?
> 0
> [stathis at fedora]~/Downloads%
>
> > So... has anyone ever successfully used the IAEA phase space files
> > with Gate 6.2 ?
> >
> > Best regards,
> > Stathis
> >
> >
> >
> >
> > On Fri, Mar 7, 2014 at 11:40 PM, Stathis Kamperis <ekamperi at gmail.com>
> wrote:
> >> Relevant:
> >>
> >> http://comments.gmane.org/gmane.comp.science.opengate.user/3115
> >>
> >> Best regards,
> >> Stathis
> >>
> >> On Fri, Mar 7, 2014 at 11:26 PM, Stathis Kamperis <ekamperi at gmail.com>
> wrote:
> >>> Greetings everyone,
> >>>
> >>> I downloaded it from here:
> >>> https://www-nds.iaea.org/phsp/photon1/
> >>>
> >>> ELEKTA_PRECISE_6mv_part1.IAEAphsp and its associated header
> >>> ELEKTA_PRECISE_6mv_part1.IAEAheader
> >>>
> >>> When I try to use it from within Gate with:
> >>>
> >>> /gate/source/addSource mybeam phaseSpace
> >>> /gate/source/mybeam/addPhaseSpaceFile
> >>> /home/stathis/Downloads/ELEKTA_PRECISE_6mv_part1.IAEAphsp
> >>>
> >>> I get the following error:
> >>>
> /home/stathis/Downloads/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc
> >>> (l.252): Source phase space: particle not available in IAEA phase
> >>> space format.
> >>>
> >>> I checked the source code:
> >>>
> http://www.opengatecollaboration.org/lxr/source/6.2.0/source/physics/src/GateSourcePhaseSpace.cc#L231
> >>>
> >>> and it appears as if Gate can't recognize some particle type that the
> >>> header file is including. But,
> >>>
> https://www-nds.iaea.org/phsp/photon1/ELEKTA_PRECISE_6mv_part1.IAEAheader
> >>> has only photons, electrons, positrons that Gate should recognize.
> >>>
> >>> Any thoughts?
> >>>
> >>> Best regards,
> >>> Stathis
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 9 Mar 2014 10:07:39 +0800
> From: ??? <arnoxiaolei86 at gmail.com>
> To: "gate-users at lists.opengatecollaboration.org"
> <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] About the performance comparison between LSO ans
> LYSO
> Message-ID:
> <CAGMGNVN=Rx8YpX=
> Qg5Rq+yDbO+1YjY0tM47fDDHMYW1bRgVaFA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello everyone:
> I did two experiments using GateV6.2, The conditions of these
> two experiments are same with each other except the material of the
> crystal (using LSO in first experiment and LYSO in secone one), but
> the Coincidences number recorded in the first experiment is treble as
> many as that recorded in the second experiment. What a bad performance
> of LYSO! Can anyone tell me why? The macros are in the attachment.
> Thanks a lot!--Chunhui Zhang
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> ------------------------------
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> End of Gate-users Digest, Vol 94, Issue 15
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