[Gate-users] phase space error

[Stathis Kamperis]

Greetings,

the usage of IAEA phase space files is problematic in many levels.

Most of the times, in my experience, the actual record length of the
space file is not interpreted correctly. E.g., record length is 53
bytes but GATE assumes some other length (for reasons I am going to
list later).

This is a typical case of a framing error (similar to genetics where a
mutation occurs that inserts or deletes a *single* nucleotide from a
DNA sequence and all the triplets past that mutation are translated
incorrectly). The end result is that soon (i.e., after a few particles
are read) some particle ends up with a particle number other than
those that are supported (1-5) and GATE fails with:

"GateSourcePhaseSpace.cc (l.252): Source phase space: particle not
available in IAEA phase space format."

So, an error like the above is indicative that GATE and phase space
files don't agree on the actual record length.

In Sara's case, the header file looks like this:

$RECORD_CONTENTS:
    1     // X is stored ?
    1     // Y is stored ?
    1     // Z is stored ?
    1     // U is stored ?
    1     // V is stored ?
    1     // W is stored ?
    1     // Weight is stored ?
    0     // Extra floats stored ?
    6     // Extra longs stored ?
    1     // Incremental history number stored in the extralong array [ 0]
    0     // Generic integer variable stored in the extralong array [ 1]
    0     // Generic integer variable stored in the extralong array [ 2]
    0     // Generic integer variable stored in the extralong array [ 3]
    0     // Generic integer variable stored in the extralong array [ 4]
    3     // ILB PENELOPE variable stored in the extralong array [ 5]

So:
1 byte for particle type +
4 bytes for energy +
6*4 bytes for (x,y,z,u,v,w) +
4 bytes for weight factor +
6*4bytes for the extra longs
sum = 57 bytes

But the header file says:

$RECORD_LENGTH:
53

If you recall my previous analysis that can be found here[1] GATE
doesn't check for 'W' no matter the value of it in the header file. So
'W' is as if it doesn't exist. I don't understand though why the
header says '1' and doesn't count it later on in the record length. I
would expect that the header file, at least, would be self-consistent,
i.e., the sum of record contents would always equal record length.

So:
1 byte for particle type +
4 bytes for energy +
5*4 bytes for (x,y,z,u,v) +
4 bytes for weight factor +
6*4bytes for the extra longs
sum = 53 bytes

But the header file says:

$RECORD_LENGTH:
53

So, we are good! But why GATE can't read a record ?

Well, it seems that GATE doesn't read the value of longs or floats
from the header file, but instead uses some defaults[2]. So, if one
uses a phase space with extra longs or floats either s/he needs to
stop using them or inject the correct value of 'iextralong' or
'iextrafloat' in GATE and rebuild. Sara is using 6 extra longs so
'iextralong' needs to be 6. Right ? Well, not exactly :)

If you take a look here[3], you see that the long array which holds
the extra longs is declared as IAEA_I32. Considering the name one
would expect that this is a variable 32 bits long (=4bytes), no matter
your CPU architecture (32 or 64bits). But, if you look at the
definition of it here[4], you realize that it is typedef'd to 'long'.
But sizeof(long) might be 4 bytes on 32 bit CPUs or 8 bytes like mine
or whatever. So, for me, 'iextralong' needs to be '3' and not '6',
since 3*8 = 6*4.

If I do this Sara, the phase space files that you sent me are
interpreted fine and the simulation continues uninterrupted.

Best regards,
Stathis

_____
[1] http://permalink.gmane.org/gmane.comp.science.opengate.user/3701
[2] http://www.opengatecollaboration.org/lxr/source/6.2.0/source/general/src/GateIAEARecord.cc#L68
[3] http://www.opengatecollaboration.org/lxr/source/6.2.0/source/general/src/GateIAEARecord.cc#L159


/*
 * A debugging ONLY program that checks a phase space file for unknown particles
 * and replaces them with photons. If you still get an unknown particle error
 * after you run this on you phase space file (take a backup first), then you
 * have a frameshift error.
 */

#include <assert.h>
#include <stdio.h>

#define ABS(x) ((x)<0 ? -(x) : (x))

struct rec {
        char particle;
        char pad[52];    /* 1 + 52 = 53 bytes which is the record
length as found in the header file */
} __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)));
                /* Particle number maybe negative, that's OK. */
                char part = ABS(r.particle);
                if (part != 1 && part != 2 && part != 3 && part !=4 &&
part != 5) {
                        printf("Wrong particle=%d at record=%d byte=%ld",
                               r.particle, cnt, ftell(fp));
                        /* Override unknown particle with a photon */
                        r.particle = 1;
                        assert(fseek(fp, -sizeof(struct rec), SEEK_CUR) != -1);
                        assert(fwrite(&r, sizeof(struct rec), 1, fp) == 1);
                        printf(" [Fixed]\n");
                }
        } while(!feof(fp) && !ferror(fp));

        assert(fclose(fp) != -1);

        return 0;
}

On Mon, Apr 14, 2014 at 11:43 AM, Sara Beilla <beilla.sara1 at gmail.com> wrote:
> Dear Gaters,
>
> I used a phase space created by PRIMO ( Software allowing to create a phase
> space) but when i lauched my simulation i have an error message:
>
> /home/beilla/Software/gate_v6.2/source/physics/src/GateSourcePhaseSpace.cc
> (l.252): Source phase space: particle not available in IAEA phase space
> format.
>
> i didn't find solution to this problem in messages already posted.
>
> I have already check in GateSourcePhaseSpace.cc and my phase space, my
> particles are indentified (gamma, e-, e+)
>
> Thank you in advance.
>
> Best regards,
>
> Beilla Sara
>
> ________________________________________________
>
> Beilla Sara
>
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>
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