void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg){
const char *name=mxGetFieldNameByNumber(root,idx);
const int *arraydim;
char *jsonshapes=NULL;
int i,j;
cfg->flog=stderr;
GET_1ST_FIELD(cfg,nphoton)
GET_ONE_FIELD(cfg,nblocksize)
GET_ONE_FIELD(cfg,nthread)
GET_ONE_FIELD(cfg,seed)
GET_ONE_FIELD(cfg,tstart)
GET_ONE_FIELD(cfg,tstep)
GET_ONE_FIELD(cfg,tend)
GET_ONE_FIELD(cfg,maxdetphoton)
GET_ONE_FIELD(cfg,sradius)
GET_ONE_FIELD(cfg,maxgate)
GET_ONE_FIELD(cfg,respin)
GET_ONE_FIELD(cfg,gpuid)
GET_ONE_FIELD(cfg,isreflect)
GET_ONE_FIELD(cfg,isref3)
GET_ONE_FIELD(cfg,isrefint)
GET_ONE_FIELD(cfg,isnormalized)
GET_ONE_FIELD(cfg,issavedet)
GET_ONE_FIELD(cfg,issave2pt)
GET_ONE_FIELD(cfg,isgpuinfo)
GET_ONE_FIELD(cfg,issrcfrom0)
GET_ONE_FIELD(cfg,autopilot)
GET_ONE_FIELD(cfg,minenergy)
GET_ONE_FIELD(cfg,unitinmm)
GET_VEC3_FIELD(cfg,srcpos)
GET_VEC3_FIELD(cfg,srcdir)
GET_VEC3_FIELD(cfg,steps)
GET_VEC3_FIELD(cfg,crop0)
GET_VEC3_FIELD(cfg,crop1)
else if(strcmp(name,"vol")==0){
if(!mxIsUint8(item) || mxGetNumberOfDimensions(item)!=3 )
mexErrMsgTxt("the 'vol' field must be a 3D uint8 array");
arraydim=mxGetDimensions(item);
for(i=0;i<3;i++) ((unsigned int *)(&cfg->dim))[i]=arraydim[i];
if(cfg->vol) free(cfg->vol);
cfg->vol=(unsigned char *)malloc(cfg->dim.x*cfg->dim.y*cfg->dim.z);
memcpy(cfg->vol,mxGetData(item),cfg->dim.x*cfg->dim.y*cfg->dim.z);
printf("mcx.dim=[%d %d %d];\n",cfg->dim.x,cfg->dim.y,cfg->dim.z);
}else if(strcmp(name,"detpos")==0){
arraydim=mxGetDimensions(item);
if(arraydim[0]>0 && arraydim[1]!=4)
mexErrMsgTxt("the 'detpos' field must have 4 columns (x,y,z,radius)");
double *val=mxGetPr(item);
cfg->detnum=arraydim[0];
if(cfg->detpos) free(cfg->detpos);
cfg->detpos=(float4 *)malloc(cfg->detnum*sizeof(float4));
for(j=0;j<4;j++)
for(i=0;i<cfg->detnum;i++)
((float *)(&cfg->detpos[i]))[j]=val[j*cfg->detnum+i];
printf("mcx.detnum=%d;\n",cfg->detnum);
}else if(strcmp(name,"prop")==0){
arraydim=mxGetDimensions(item);
if(arraydim[0]>0 && arraydim[1]!=4)
mexErrMsgTxt("the 'prop' field must have 4 columns (mua,mus,g,n)");
double *val=mxGetPr(item);
cfg->medianum=arraydim[0];
if(cfg->prop) free(cfg->prop);
cfg->prop=(Medium *)malloc(cfg->medianum*sizeof(Medium));
for(j=0;j<4;j++)
for(i=0;i<cfg->medianum;i++)
((float *)(&cfg->prop[i]))[j]=val[j*cfg->medianum+i];
printf("mcx.medianum=%d;\n",cfg->medianum);
}else if(strcmp(name,"session")==0){
int len=mxGetNumberOfElements(item);
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'session' field must be a non-empty string");
if(len>MAX_SESSION_LENGTH)
mexErrMsgTxt("the 'session' field is too long");
int status = mxGetString(item, cfg->session, MAX_SESSION_LENGTH);
if (status != 0)
mexWarnMsgTxt("not enough space. string is truncated.");
printf("mcx.session='%s';\n",cfg->session);
}else if(strcmp(name,"shapes")==0){
int len=mxGetNumberOfElements(item);
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'shapes' field must be a non-empty string");
jsonshapes=new char[len+1];
mxGetString(item, jsonshapes, len+1);
jsonshapes[len]='\0';
}else{
printf("WARNING: redundant field '%s'\n",name);
}
if(jsonshapes){
Grid3D grid={&(cfg->vol),&(cfg->dim),{1.f,1.f,1.f},0};
if(cfg->issrcfrom0) memset(&(grid.orig.x),0,sizeof(float3));
int status=mcx_parse_shapestring(&grid,jsonshapes);
delete [] jsonshapes;
if(status){
mexErrMsgTxt(mcx_last_shapeerror());
}
}
}
void mcx_set_field(const mxArray *root,const mxArray *item,int idx, Config *cfg){
const char *name=mxGetFieldNameByNumber(root,idx);
const int *arraydim;
char *jsonshapes=NULL;
int i,j;
if(strcmp(name,"nphoton")==0 && cfg->replay.seed!=NULL)
return;
cfg->flog=stderr;
GET_1ST_FIELD(cfg,nphoton)
GET_ONE_FIELD(cfg,nblocksize)
GET_ONE_FIELD(cfg,nthread)
GET_ONE_FIELD(cfg,tstart)
GET_ONE_FIELD(cfg,tstep)
GET_ONE_FIELD(cfg,tend)
GET_ONE_FIELD(cfg,maxdetphoton)
GET_ONE_FIELD(cfg,sradius)
GET_ONE_FIELD(cfg,maxgate)
GET_ONE_FIELD(cfg,respin)
GET_ONE_FIELD(cfg,isreflect)
GET_ONE_FIELD(cfg,isref3)
GET_ONE_FIELD(cfg,isrefint)
GET_ONE_FIELD(cfg,isnormalized)
GET_ONE_FIELD(cfg,isgpuinfo)
GET_ONE_FIELD(cfg,issrcfrom0)
GET_ONE_FIELD(cfg,autopilot)
GET_ONE_FIELD(cfg,minenergy)
GET_ONE_FIELD(cfg,unitinmm)
GET_ONE_FIELD(cfg,reseedlimit)
GET_ONE_FIELD(cfg,printnum)
GET_ONE_FIELD(cfg,voidtime)
GET_ONE_FIELD(cfg,issaveseed)
GET_ONE_FIELD(cfg,replaydet)
GET_ONE_FIELD(cfg,faststep)
GET_ONE_FIELD(cfg,maxvoidstep)
GET_ONE_FIELD(cfg,maxjumpdebug)
GET_VEC3_FIELD(cfg,srcpos)
GET_VEC3_FIELD(cfg,srcdir)
GET_VEC3_FIELD(cfg,steps)
GET_VEC3_FIELD(cfg,crop0)
GET_VEC3_FIELD(cfg,crop1)
GET_VEC4_FIELD(cfg,srcparam1)
GET_VEC4_FIELD(cfg,srcparam2)
else if(strcmp(name,"vol")==0){
if(!mxIsUint8(item) || mxGetNumberOfDimensions(item)!=3 )
mexErrMsgTxt("the 'vol' field must be a 3D uint8 array");
arraydim=mxGetDimensions(item);
for(i=0;i<3;i++) ((unsigned int *)(&cfg->dim))[i]=arraydim[i];
if(cfg->vol) free(cfg->vol);
cfg->vol=(unsigned char *)malloc(cfg->dim.x*cfg->dim.y*cfg->dim.z);
memcpy(cfg->vol,mxGetData(item),cfg->dim.x*cfg->dim.y*cfg->dim.z);
printf("mcx.dim=[%d %d %d];\n",cfg->dim.x,cfg->dim.y,cfg->dim.z);
}else if(strcmp(name,"detpos")==0){
arraydim=mxGetDimensions(item);
if(arraydim[0]>0 && arraydim[1]!=4)
mexErrMsgTxt("the 'detpos' field must have 4 columns (x,y,z,radius)");
double *val=mxGetPr(item);
cfg->detnum=arraydim[0];
if(cfg->detpos) free(cfg->detpos);
cfg->detpos=(float4 *)malloc(cfg->detnum*sizeof(float4));
for(j=0;j<4;j++)
for(i=0;i<cfg->detnum;i++)
((float *)(&cfg->detpos[i]))[j]=val[j*cfg->detnum+i];
printf("mcx.detnum=%d;\n",cfg->detnum);
}else if(strcmp(name,"prop")==0){
arraydim=mxGetDimensions(item);
if(arraydim[0]>0 && arraydim[1]!=4)
mexErrMsgTxt("the 'prop' field must have 4 columns (mua,mus,g,n)");
double *val=mxGetPr(item);
cfg->medianum=arraydim[0];
if(cfg->prop) free(cfg->prop);
cfg->prop=(Medium *)malloc(cfg->medianum*sizeof(Medium));
for(j=0;j<4;j++)
for(i=0;i<cfg->medianum;i++)
((float *)(&cfg->prop[i]))[j]=val[j*cfg->medianum+i];
printf("mcx.medianum=%d;\n",cfg->medianum);
}else if(strcmp(name,"session")==0){
int len=mxGetNumberOfElements(item);
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'session' field must be a non-empty string");
if(len>MAX_SESSION_LENGTH)
mexErrMsgTxt("the 'session' field is too long");
int status = mxGetString(item, cfg->session, MAX_SESSION_LENGTH);
if (status != 0)
mexWarnMsgTxt("not enough space. string is truncated.");
printf("mcx.session='%s';\n",cfg->session);
}else if(strcmp(name,"srctype")==0){
int len=mxGetNumberOfElements(item);
const char *srctypeid[]={"pencil","isotropic","cone","gaussian","planar","pattern","fourier","arcsine","disk","fourierx","fourierx2d","zgaussian","line","slit", "rectangular",""};
char strtypestr[MAX_SESSION_LENGTH]={'\0'};
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'srctype' field must be a non-empty string");
if(len>MAX_SESSION_LENGTH)
mexErrMsgTxt("the 'srctype' field is too long");
int status = mxGetString(item, strtypestr, MAX_SESSION_LENGTH);
if (status != 0)
mexWarnMsgTxt("not enough space. string is truncated.");
cfg->srctype=mcx_keylookup(strtypestr,srctypeid);
if(cfg->srctype==-1)
mexErrMsgTxt("the specified source type is not supported");
printf("mcx.srctype='%s';\n",strtypestr);
}else if(strcmp(name,"outputtype")==0){
int len=mxGetNumberOfElements(item);
const char *outputtype[]={"flux","fluence","energy","jacobian",""};
char outputstr[MAX_SESSION_LENGTH]={'\0'};
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'outputtype' field must be a non-empty string");
if(len>MAX_SESSION_LENGTH)
mexErrMsgTxt("the 'outputtype' field is too long");
int status = mxGetString(item, outputstr, MAX_SESSION_LENGTH);
if (status != 0)
mexWarnMsgTxt("not enough space. string is truncated.");
cfg->outputtype=mcx_keylookup(outputstr,outputtype);
if(cfg->outputtype==-1)
mexErrMsgTxt("the specified output type is not supported");
printf("mcx.outputtype='%s';\n",outputstr);
}else if(strcmp(name,"debuglevel")==0){
int len=mxGetNumberOfElements(item);
const char debugflag[]={'R','M','P','\0'};
char debuglevel[MAX_SESSION_LENGTH]={'\0'};
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'debuglevel' field must be a non-empty string");
if(len>MAX_SESSION_LENGTH)
mexErrMsgTxt("the 'debuglevel' field is too long");
int status = mxGetString(item, debuglevel, MAX_SESSION_LENGTH);
if (status != 0)
mexWarnMsgTxt("not enough space. string is truncated.");
cfg->debuglevel=mcx_parsedebugopt(debuglevel,debugflag);
if(cfg->debuglevel==0)
mexWarnMsgTxt("the specified debuglevel is not supported");
printf("mcx.debuglevel='%d';\n",cfg->debuglevel);
}else if(strcmp(name,"srcpattern")==0){
arraydim=mxGetDimensions(item);
double *val=mxGetPr(item);
if(cfg->srcpattern) free(cfg->srcpattern);
cfg->srcpattern=(float*)malloc(arraydim[0]*arraydim[1]*sizeof(float));
for(i=0;i<arraydim[0]*arraydim[1];i++)
cfg->srcpattern[i]=val[i];
printf("mcx.srcpattern=[%d %d];\n",arraydim[0],arraydim[1]);
}else if(strcmp(name,"shapes")==0){
int len=mxGetNumberOfElements(item);
if(!mxIsChar(item) || len==0)
mexErrMsgTxt("the 'shapes' field must be a non-empty string");
jsonshapes=new char[len+1];
mxGetString(item, jsonshapes, len+1);
jsonshapes[len]='\0';
}else if(strcmp(name,"detphotons")==0){
arraydim=mxGetDimensions(item);
dimdetps[0]=arraydim[0];
dimdetps[1]=arraydim[1];
detps=(float *)malloc(arraydim[0]*arraydim[1]*sizeof(float));
memcpy(detps,mxGetData(item),arraydim[0]*arraydim[1]*sizeof(float));
printf("mcx.detphotons=[%d %d];\n",arraydim[0],arraydim[1]);
}else if(strcmp(name,"seed")==0){
arraydim=mxGetDimensions(item);
if(MAX(arraydim[0],arraydim[1])==0)
mexErrMsgTxt("the 'seed' field can not be empty");
if(!mxIsUint8(item)){
double *val=mxGetPr(item);
cfg->seed=val[0];
printf("mcx.seed=%d;\n",cfg->seed);
}else{
seedbyte=arraydim[0];
cfg->replay.seed=malloc(arraydim[0]*arraydim[1]);
if(arraydim[0]!=sizeof(float)*RAND_BUF_LEN)
mexErrMsgTxt("the row number of cfg.seed does not match RNG seed byte-length");
memcpy(cfg->replay.seed,mxGetData(item),arraydim[0]*arraydim[1]);
cfg->seed=SEED_FROM_FILE;
cfg->nphoton=arraydim[1];
printf("mcx.nphoton=%d;\n",cfg->nphoton);
}
}else if(strcmp(name,"gpuid")==0){
int len=mxGetNumberOfElements(item);
if(mxIsChar(item)){
if(len==0)
mexErrMsgTxt("the 'gpuid' field must be an integer or non-empty string");
if(len>MAX_DEVICE)
mexErrMsgTxt("the 'gpuid' field is too long");
int status = mxGetString(item, cfg->deviceid, MAX_DEVICE);
if (status != 0)
mexWarnMsgTxt("not enough space. string is truncated.");
printf("mcx.gpuid='%s';\n",cfg->deviceid);
}else{
double *val=mxGetPr(item);
cfg->gpuid=val[0];
memset(cfg->deviceid,0,MAX_DEVICE);
if(cfg->gpuid<MAX_DEVICE){
memset(cfg->deviceid,'0',cfg->gpuid-1);
cfg->deviceid[cfg->gpuid-1]='1';
}else
mexErrMsgTxt("GPU id can not be more than 256");
printf("mcx.gpuid=%d;\n",cfg->gpuid);
}
for(int i=0;i<MAX_DEVICE;i++)
if(cfg->deviceid[i]=='0')
cfg->deviceid[i]='\0';
}else if(strcmp(name,"workload")==0){
double *val=mxGetPr(item);
arraydim=mxGetDimensions(item);
if(arraydim[0]*arraydim[1]>MAX_DEVICE)
mexErrMsgTxt("the workload list can not be longer than 256");
for(i=0;i<arraydim[0]*arraydim[1];i++)
cfg->workload[i]=val[i];
printf("mcx.workload=<<%d>>;\n",arraydim[0]*arraydim[1]);
}else{
printf("WARNING: redundant field '%s'\n",name);
}
if(jsonshapes){
Grid3D grid={&(cfg->vol),&(cfg->dim),{1.f,1.f,1.f},0};
if(cfg->issrcfrom0) memset(&(grid.orig.x),0,sizeof(float3));
int status=mcx_parse_shapestring(&grid,jsonshapes);
delete [] jsonshapes;
if(status){
mexErrMsgTxt(mcx_last_shapeerror());
}
}
}