[Gate-users] phase space error

[Stathis Kamperis]

On Fri, Apr 18, 2014 at 11:04 PM, Stathis Kamperis <ekamperi at gmail.com> wrote:
> 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.
Actually, the safest way to go is to fix the definition of IAEA_I32,
like for instance:

typedef int32_t IAEA_I32;

(and also include stdint.h)

>
> 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
Missing reference here:
[4] http://www.opengatecollaboration.org/lxr/source/6.2.0/source/general/include/GateIAEAConfig.h#L28

>
>
> /*
>  * 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
>>
>> Doctorante en Charge d'Enseignement
>>
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