int main (int argc, char *argv[]) {
Config mcxconfig;
unsigned int activedev=0;
float *fluence=NULL,totalenergy=0.f;
mcx_initcfg(&mcxconfig);
// parse command line options to initialize the configurations
mcx_parsecmd(argc,argv,&mcxconfig);
// identify gpu number and set one gpu active
if(!mcx_set_gpu(&mcxconfig,&activedev)){
mcx_error(-1,"No compute platform was found\n",__FILE__,__LINE__);
}
if(activedev==0)
return 0;
mcx_createfluence(&fluence,&mcxconfig);
// this launches the MC simulation
mcx_run_simulation(&mcxconfig,fluence,&totalenergy);
// clean up the allocated memory in the config
mcx_clearfluence(&fluence);
mcx_clearcfg(&mcxconfig);
return 0;
}
void mcx_loadvolume(char *filename,Config *cfg){
int datalen,res;
FILE *fp=fopen(filename,"rb");
if(fp==NULL){
mcx_error(-5,"the specified binary volume file does not exist",__FILE__,__LINE__);
}
if(cfg->vol){
free(cfg->vol);
cfg->vol=NULL;
}
datalen=cfg->dim.x*cfg->dim.y*cfg->dim.z;
cfg->vol=(unsigned char*)malloc(sizeof(unsigned char)*datalen);
res=fread(cfg->vol,sizeof(unsigned char),datalen,fp);
fclose(fp);
if(res!=datalen){
mcx_error(-6,"file size does not match specified dimensions",__FILE__,__LINE__);
}
}
void mcx_writeconfig(const char *fname, Config *cfg){
if(fname[0]==0)
mcx_saveconfig(stdout,cfg);
else{
FILE *fp=fopen(fname,"wt");
if(fp==NULL) mcx_error(-2,"can not write to the specified config file",__FILE__,__LINE__);
mcx_saveconfig(fp,cfg);
fclose(fp);
}
}
int main (int argc, char *argv[]) {
/*! structure to store all simulation parameters
*/
Config mcxconfig; /** mcxconfig: structure to store all simulation parameters */
GPUInfo *gpuinfo=NULL; /** gpuinfo: structure to store GPU information */
unsigned int activedev=0; /** activedev: count of total active GPUs to be used */
/**
To start an MCX simulation, we first create a simulation configuration and
set all elements to its default settings.
*/
mcx_initcfg(&mcxconfig);
/**
Then, we parse the full command line parameters and set user specified settings
*/
mcx_parsecmd(argc,argv,&mcxconfig);
/** The next step, we identify gpu number and query all GPU info */
if(!(activedev=mcx_list_gpu(&mcxconfig,&gpuinfo))){
mcx_error(-1,"No GPU device found\n",__FILE__,__LINE__);
}
#ifdef _OPENMP
/**
Now we are ready to launch one thread for each involked GPU to run the simulation
*/
omp_set_num_threads(activedev);
#pragma omp parallel
{
#endif
/**
This line runs the main MCX simulation for each GPU inside each thread
*/
mcx_run_simulation(&mcxconfig,gpuinfo);
#ifdef _OPENMP
}
#endif
/**
Once simulation is complete, we clean up the allocated memory in config and gpuinfo, and exit
*/
mcx_cleargpuinfo(&gpuinfo);
mcx_clearcfg(&mcxconfig);
return 0;
}
int mcx_readarg(int argc, char *argv[], int id, void *output,const char *type){
/*
when a binary option is given without a following number (0~1),
we assume it is 1
*/
if(strcmp(type,"char")==0 && (id>=argc-1||(argv[id+1][0]<'0'||argv[id+1][0]>'9'))){
*((char*)output)=1;
return id;
}
if(id<argc-1){
if(strcmp(type,"char")==0)
*((char*)output)=atoi(argv[id+1]);
else if(strcmp(type,"int")==0)
*((int*)output)=atoi(argv[id+1]);
else if(strcmp(type,"float")==0)
*((float*)output)=atof(argv[id+1]);
else if(strcmp(type,"string")==0)
strcpy((char *)output,argv[id+1]);
else if(strcmp(type,"bytenumlist")==0){
char *nexttok,*numlist=(char *)output;
int len=0,i;
nexttok=strtok(argv[id+1]," ,;");
while(nexttok){
numlist[len++]=(char)(atoi(nexttok)); /*device id<256*/
for(i=0;i<len-1;i++) /* remove duplicaetd ids */
if(numlist[i]==numlist[len-1]){
numlist[--len]='\0';
break;
}
nexttok=strtok(NULL," ,;");
/*if(len>=MAX_DEVICE) break;*/
}
}else if(strcmp(type,"floatlist")==0){
char *nexttok;
float *numlist=(float *)output;
int len=0;
nexttok=strtok(argv[id+1]," ,;");
while(nexttok){
numlist[len++]=atof(nexttok); /*device id<256*/
nexttok=strtok(NULL," ,;");
}
}
}else{
mcx_error(-1,"incomplete input",__FILE__,__LINE__);
}
return id+1;
}
void mcx_readconfig(const char *fname, Config *cfg){
if(fname[0]==0){
mcx_loadconfig(stdin,cfg);
if(cfg->session[0]=='\0'){
strcpy(cfg->session,"default");
}
}
else{
FILE *fp=fopen(fname,"rt");
if(fp==NULL) mcx_error(-2,"can not load the specified config file",__FILE__,__LINE__);
mcx_loadconfig(fp,cfg);
fclose(fp);
if(cfg->session[0]=='\0'){
strcpy(cfg->session,fname);
}
}
}
void mcx_savedata(float *dat, int len, int doappend, const char *suffix, Config *cfg){
FILE *fp;
char name[MAX_PATH_LENGTH];
sprintf(name,"%s.%s",cfg->session,suffix);
if(doappend){
fp=fopen(name,"ab");
}else{
fp=fopen(name,"wb");
}
if(fp==NULL){
mcx_error(-2,"can not save data to disk",__FILE__,__LINE__);
}
if(strcmp(suffix,"mch")==0){
fwrite(&(cfg->his),sizeof(History),1,fp);
}
fwrite(dat,sizeof(float),len,fp);
fclose(fp);
}
int main (int argc, char *argv[]) {
Config mcxconfig;
mcx_initcfg(&mcxconfig);
// parse command line options to initialize the configurations
mcx_parsecmd(argc,argv,&mcxconfig);
// identify gpu number and set one gpu active
if(!mcx_set_gpu(&mcxconfig)){
mcx_error(-1,"No GPU device found\n",__FILE__,__LINE__);
}
// this launches the MC simulation
mcx_run_simulation(&mcxconfig);
// clean up the allocated memory in the config
mcx_clearcfg(&mcxconfig);
return 0;
}
void mcx_parsecmd(int argc, char* argv[], Config *cfg){
int i=1,isinteractive=1,issavelog=0;
char filename[MAX_PATH_LENGTH]={0};
char logfile[MAX_PATH_LENGTH]={0};
float np=0.f;
if(argc<=1){
mcx_usage(argv[0]);
exit(0);
}
while(i<argc){
if(argv[i][0]=='-'){
if(argv[i][1]=='-'){
if(mcx_remap(argv[i])){
mcx_error(-2,"unknown verbose option",__FILE__,__LINE__);
}
}
switch(argv[i][1]){
case 'h':
mcx_usage(argv[0]);
exit(0);
case 'i':
if(filename[0]){
mcx_error(-2,"you can not specify both interactive mode and config file",__FILE__,__LINE__);
}
isinteractive=1;
break;
case 'f':
isinteractive=0;
i=mcx_readarg(argc,argv,i,filename,"string");
break;
case 'm':
mcx_error(-2,"specifying photon move is not supported any more, please use -n",__FILE__,__LINE__);
i=mcx_readarg(argc,argv,i,&(cfg->nphoton),"int");
break;
case 'n':
i=mcx_readarg(argc,argv,i,&(np),"float");
cfg->nphoton=(int)np;
break;
case 't':
i=mcx_readarg(argc,argv,i,&(cfg->nthread),"int");
break;
case 'T':
i=mcx_readarg(argc,argv,i,&(cfg->nblocksize),"int");
break;
case 's':
i=mcx_readarg(argc,argv,i,cfg->session,"string");
break;
case 'a':
i=mcx_readarg(argc,argv,i,&(cfg->isrowmajor),"char");
break;
case 'g':
i=mcx_readarg(argc,argv,i,&(cfg->maxgate),"int");
break;
case 'b':
i=mcx_readarg(argc,argv,i,&(cfg->isreflect),"char");
break;
case 'B':
i=mcx_readarg(argc,argv,i,&(cfg->isref3),"char");
break;
case 'd':
i=mcx_readarg(argc,argv,i,&(cfg->issavedet),"char");
break;
case 'r':
i=mcx_readarg(argc,argv,i,&(cfg->respin),"int");
break;
case 'S':
i=mcx_readarg(argc,argv,i,&(cfg->issave2pt),"char");
break;
case 'p':
i=mcx_readarg(argc,argv,i,&(cfg->printnum),"int");
break;
case 'e':
i=mcx_readarg(argc,argv,i,&(cfg->minenergy),"float");
break;
case 'U':
i=mcx_readarg(argc,argv,i,&(cfg->isnormalized),"char");
break;
case 'R':
i=mcx_readarg(argc,argv,i,&(cfg->sradius),"float");
break;
case 'l':
issavelog=1;
break;
case 'L':
cfg->isgpuinfo=2;
break;
case 'I':
cfg->isgpuinfo=1;
break;
case 'c':
cfg->iscpu=1;
break;
case 'v':
cfg->isverbose=1;
break;
case 'o':
i=mcx_readarg(argc,argv,i,cfg->rootpath,"string");
break;
case 'k':
i=mcx_readarg(argc,argv,i,cfg->kernelfile,"string");
break;
case 'J':
i=mcx_readarg(argc,argv,i,cfg->compileropt,"string");
break;
case 'D':
i=mcx_readarg(argc,argv,i,cfg->deviceid,"bytenumlist");
break;
case 'G':
i=mcx_readarg(argc,argv,i,cfg->deviceid,"string");
break;
case 'W':
i=mcx_readarg(argc,argv,i,cfg->workload,"floatlist");
break;
case 'z':
i=mcx_readarg(argc,argv,i,&(cfg->issrcfrom0),"char");
break;
}
}
i++;
}
if(issavelog && cfg->session){
sprintf(logfile,"%s.log",cfg->session);
cfg->flog=fopen(logfile,"wt");
if(cfg->flog==NULL){
cfg->flog=stdout;
fprintf(cfg->flog,"unable to save to log file, will print from stdout\n");
}
}
if(cfg->clsource==NULL && cfg->isgpuinfo!=2){
FILE *fp=fopen(cfg->kernelfile,"rb");
int srclen;
if(fp==NULL){
mcx_error(-10,"the specified OpenCL kernel file does not exist!",__FILE__,__LINE__);
}
fseek(fp,0,SEEK_END);
srclen=ftell(fp);
cfg->clsource=(char *)malloc(srclen+1);
fseek(fp,0,SEEK_SET);
MCX_ASSERT((fread(cfg->clsource,srclen,1,fp)==1));
cfg->clsource[srclen]='\0';
fclose(fp);
}
if(cfg->isgpuinfo!=2){ /*print gpu info only*/
if(isinteractive){
mcx_readconfig("",cfg);
}else{
mcx_readconfig(filename,cfg);
}
}
}
void mcx_maskdet(Config *cfg){
uint d,dx,dy,dz,idx1d,zi,yi;
float x,y,z,ix,iy,iz;
unsigned char *padvol;
dx=cfg->dim.x+2;
dy=cfg->dim.y+2;
dz=cfg->dim.z+2;
/*handling boundaries in a volume search is tedious, I first pad vol by a layer of zeros,
then I don't need to worry about boundaries any more*/
padvol=(unsigned char*)calloc(dx*dy,dz);
for(zi=1;zi<=cfg->dim.z;zi++)
for(yi=1;yi<=cfg->dim.y;yi++)
memcpy(padvol+zi*dy*dx+yi*dx+1,cfg->vol+(zi-1)*cfg->dim.y*cfg->dim.x+(yi-1)*cfg->dim.x,cfg->dim.x);
for(d=0;d<cfg->detnum;d++) /*loop over each detector*/
for(z=-cfg->detpos[d].w;z<=cfg->detpos[d].w;z++){ /*search in a sphere*/
iz=z+cfg->detpos[d].z; /*1.5=1+0.5, 1 comes from the padding layer, 0.5 move to voxel center*/
for(y=-cfg->detpos[d].w;y<=cfg->detpos[d].w;y++){
iy=y+cfg->detpos[d].y;
for(x=-cfg->detpos[d].w;x<=cfg->detpos[d].w;x++){
ix=x+cfg->detpos[d].x;
if(iz<0||ix<0||iy<0||ix>=cfg->dim.x||iy>=cfg->dim.y||iz>=cfg->dim.z||
x*x+y*y+z*z > (cfg->detpos[d].w+1.f)*(cfg->detpos[d].w+1.f))
continue;
idx1d=(int)((iz+1.f)*dy*dx+(iy+1.f)*dx+(ix+1.f));
if(padvol[idx1d]) /*looking for a voxel on the interface or bounding box*/
if(!(padvol[idx1d+1]&&padvol[idx1d-1]&&padvol[idx1d+dx]&&padvol[idx1d-dx]&&padvol[idx1d+dy*dx]&&padvol[idx1d-dy*dx]&&
padvol[idx1d+dx+1]&&padvol[idx1d+dx-1]&&padvol[idx1d-dx+1]&&padvol[idx1d-dx-1]&&
padvol[idx1d+dy*dx+1]&&padvol[idx1d+dy*dx-1]&&padvol[idx1d-dy*dx+1]&&padvol[idx1d-dy*dx-1]&&
padvol[idx1d+dy*dx+dx]&&padvol[idx1d+dy*dx-dx]&&padvol[idx1d-dy*dx+dx]&&padvol[idx1d-dy*dx-dx]&&
padvol[idx1d+dy*dx+dx+1]&&padvol[idx1d+dy*dx+dx-1]&&padvol[idx1d+dy*dx-dx+1]&&padvol[idx1d+dy*dx-dx-1]&&
padvol[idx1d-dy*dx+dx+1]&&padvol[idx1d-dy*dx+dx-1]&&padvol[idx1d-dy*dx-dx+1]&&padvol[idx1d-dy*dx-dx-1])){
cfg->vol[(int)(iz*cfg->dim.y*cfg->dim.x+iy*cfg->dim.x+ix)]|=(1<<7);/*set the highest bit to 1*/
}
}
}
}
if(cfg->isdumpmask){
char fname[MAX_PATH_LENGTH];
FILE *fp;
sprintf(fname,"%s.mask",cfg->session);
if((fp=fopen(fname,"wb"))==NULL){
mcx_error(-10,"can not save mask file",__FILE__,__LINE__);
}
if(fwrite(cfg->vol,cfg->dim.x*cfg->dim.y,cfg->dim.z,fp)!=cfg->dim.z){
mcx_error(-10,"can not save mask file",__FILE__,__LINE__);
}
fclose(fp);
free(padvol);
exit(0);
}
free(padvol);
}
void mcx_loadconfig(FILE *in, Config *cfg){
int i,idx1d;
unsigned int gates,itmp;
char filename[MAX_PATH_LENGTH]={0}, comment[MAX_PATH_LENGTH],*comm;
if(in==stdin)
fprintf(stdout,"Please specify the total number of photons: [1000000]\n\t");
MCX_ASSERT(fscanf(in,"%d", &(i) )==1);
if(cfg->nphoton==0) cfg->nphoton=i;
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%d\nPlease specify the random number generator seed: [1234567]\n\t",cfg->nphoton);
MCX_ASSERT(fscanf(in,"%d", &(cfg->seed) )==1);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%d\nPlease specify the position of the source: [10 10 5]\n\t",cfg->seed);
MCX_ASSERT(fscanf(in,"%f %f %f", &(cfg->srcpos.x),&(cfg->srcpos.y),&(cfg->srcpos.z) )==3);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(cfg->issrcfrom0==0 && comm!=NULL && sscanf(comm,"%u",&itmp)==1)
cfg->issrcfrom0=itmp;
if(in==stdin)
fprintf(stdout,"%f %f %f\nPlease specify the normal direction of the source fiber: [0 0 1]\n\t",
cfg->srcpos.x,cfg->srcpos.y,cfg->srcpos.z);
if(!cfg->issrcfrom0){
cfg->srcpos.x--;cfg->srcpos.y--;cfg->srcpos.z--; /*convert to C index, grid center*/
}
MCX_ASSERT(fscanf(in,"%f %f %f", &(cfg->srcdir.x),&(cfg->srcdir.y),&(cfg->srcdir.z) )==3);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %f %f\nPlease specify the time gates in seconds (start end and step) [0.0 1e-9 1e-10]\n\t",
cfg->srcdir.x,cfg->srcdir.y,cfg->srcdir.z);
MCX_ASSERT(fscanf(in,"%f %f %f", &(cfg->tstart),&(cfg->tend),&(cfg->tstep) )==3);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %f %f\nPlease specify the path to the volume binary file:\n\t",
cfg->tstart,cfg->tend,cfg->tstep);
if(cfg->tstart>cfg->tend || cfg->tstep==0.f){
mcx_error(-9,"incorrect time gate settings",__FILE__,__LINE__);
}
gates=(unsigned int)((cfg->tend-cfg->tstart)/cfg->tstep+0.5);
if(cfg->maxgate>gates)
cfg->maxgate=gates;
MCX_ASSERT(fscanf(in,"%s", filename)==1);
if(cfg->rootpath[0]){
#ifdef WIN32
sprintf(comment,"%s\\%s",cfg->rootpath,filename);
#else
sprintf(comment,"%s/%s",cfg->rootpath,filename);
#endif
strncpy(filename,comment,MAX_PATH_LENGTH);
}
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%s\nPlease specify the x voxel size (in mm), x dimension, min and max x-index [1.0 100 1 100]:\n\t",filename);
MCX_ASSERT(fscanf(in,"%f %u %u %u", &(cfg->steps.x),&(cfg->dim.x),&(cfg->crop0.x),&(cfg->crop1.x))==4);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %u %u %u\nPlease specify the y voxel size (in mm), y dimension, min and max y-index [1.0 100 1 100]:\n\t",
cfg->steps.x,cfg->dim.x,cfg->crop0.x,cfg->crop1.x);
MCX_ASSERT(fscanf(in,"%f %u %u %u", &(cfg->steps.y),&(cfg->dim.y),&(cfg->crop0.y),&(cfg->crop1.y))==4);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %u %u %u\nPlease specify the z voxel size (in mm), z dimension, min and max z-index [1.0 100 1 100]:\n\t",
cfg->steps.y,cfg->dim.y,cfg->crop0.y,cfg->crop1.y);
MCX_ASSERT(fscanf(in,"%f %u %u %u", &(cfg->steps.z),&(cfg->dim.z),&(cfg->crop0.z),&(cfg->crop1.z))==4);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %u %u %u\nPlease specify the total types of media:\n\t",
cfg->steps.z,cfg->dim.z,cfg->crop0.z,cfg->crop1.z);
MCX_ASSERT(fscanf(in,"%u", &(cfg->medianum))==1);
cfg->medianum++;
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%d\n",cfg->medianum);
cfg->prop=(Medium*)malloc(sizeof(Medium)*cfg->medianum);
cfg->prop[0].mua=0.f; /*property 0 is already air*/
cfg->prop[0].mus=0.f;
cfg->prop[0].g=0.f;
cfg->prop[0].n=1.f;
for(i=1;i<(int)cfg->medianum;i++){
if(in==stdin)
fprintf(stdout,"Please define medium #%d: mus(1/mm), anisotropy, mua(1/mm) and refractive index: [1.01 0.01 0.04 1.37]\n\t",i);
MCX_ASSERT(fscanf(in, "%f %f %f %f", &(cfg->prop[i].mus),&(cfg->prop[i].g),&(cfg->prop[i].mua),&(cfg->prop[i].n))==4);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %f %f %f\n",cfg->prop[i].mus,cfg->prop[i].g,cfg->prop[i].mua,cfg->prop[i].n);
}
if(in==stdin)
fprintf(stdout,"Please specify the total number of detectors and fiber diameter (in mm):\n\t");
MCX_ASSERT(fscanf(in,"%u %f", &(cfg->detnum), &(cfg->detradius))==2);
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%d %f\n",cfg->detnum,cfg->detradius);
cfg->detpos=(float4*)malloc(sizeof(float4)*cfg->detnum);
if(cfg->issavedet && cfg->detnum==0)
cfg->issavedet=0;
for(i=0;i<(int)cfg->detnum;i++){
if(in==stdin)
fprintf(stdout,"Please define detector #%d: x,y,z (in mm): [5 5 5 1]\n\t",i);
MCX_ASSERT(fscanf(in, "%f %f %f", &(cfg->detpos[i].x),&(cfg->detpos[i].y),&(cfg->detpos[i].z))==3);
cfg->detpos[i].w=cfg->detradius*cfg->detradius;
if(!cfg->issrcfrom0){
cfg->detpos[i].x--;cfg->detpos[i].y--;cfg->detpos[i].z--; /*convert to C index*/
}
comm=fgets(comment,MAX_PATH_LENGTH,in);
if(in==stdin)
fprintf(stdout,"%f %f %f\n",cfg->detpos[i].x,cfg->detpos[i].y,cfg->detpos[i].z);
}
if(filename[0]){
mcx_loadvolume(filename,cfg);
if(cfg->isrowmajor){
/*from here on, the array is always col-major*/
mcx_convertrow2col(&(cfg->vol), &(cfg->dim));
cfg->isrowmajor=0;
}
if(cfg->issavedet)
mcx_maskdet(cfg);
if(cfg->srcpos.x<0.f || cfg->srcpos.y<0.f || cfg->srcpos.z<0.f ||
cfg->srcpos.x>=cfg->dim.x || cfg->srcpos.y>=cfg->dim.y || cfg->srcpos.z>=cfg->dim.z)
mcx_error(-4,"source position is outside of the volume",__FILE__,__LINE__);
idx1d=((int)floor(cfg->srcpos.z)*cfg->dim.y*cfg->dim.x+(int)floor(cfg->srcpos.y)*cfg->dim.x+(int)floor(cfg->srcpos.x));
/* if the specified source position is outside the domain, move the source
along the initial vector until it hit the domain */
if(cfg->vol && cfg->vol[idx1d]==0){
printf("source (%f %f %f) is located outside the domain, vol[%d]=%d\n",
cfg->srcpos.x,cfg->srcpos.y,cfg->srcpos.z,idx1d,cfg->vol[idx1d]);
while(cfg->vol[idx1d]==0){
cfg->srcpos.x+=cfg->srcdir.x;
cfg->srcpos.y+=cfg->srcdir.y;
cfg->srcpos.z+=cfg->srcdir.z;
printf("fixing source position to (%f %f %f)\n",cfg->srcpos.x,cfg->srcpos.y,cfg->srcpos.z);
idx1d=cfg->isrowmajor?(int)(floor(cfg->srcpos.x)*cfg->dim.y*cfg->dim.z+floor(cfg->srcpos.y)*cfg->dim.z+floor(cfg->srcpos.z)):\
(int)(floor(cfg->srcpos.z)*cfg->dim.y*cfg->dim.x+floor(cfg->srcpos.y)*cfg->dim.x+floor(cfg->srcpos.x));
}
}
}else{
mcx_error(-4,"one must specify a binary volume file in order to run the simulation",__FILE__,__LINE__);
}
}
void mcx_assess(const int err,const char *msg,const char *file,const int linenum){
if(!err){
mcx_error(err,msg,file,linenum);
}
}
void mcx_validate_config(Config *cfg){
int i,gates,idx1d;
if(!cfg->issrcfrom0){
cfg->srcpos.x--;cfg->srcpos.y--;cfg->srcpos.z--; /*convert to C index, grid center*/
}
if(cfg->tstart>cfg->tend || cfg->tstep==0.f){
mexErrMsgTxt("incorrect time gate settings");
}
if(ABS(cfg->srcdir.x*cfg->srcdir.x+cfg->srcdir.y*cfg->srcdir.y+cfg->srcdir.z*cfg->srcdir.z - 1.f)>1e-5)
mexErrMsgTxt("field 'srcdir' must be a unitary vector");
if(cfg->steps.x==0.f || cfg->steps.y==0.f || cfg->steps.z==0.f)
mexErrMsgTxt("field 'steps' can not have zero elements");
if(cfg->tend<=cfg->tstart)
mexErrMsgTxt("field 'tend' must be greater than field 'tstart'");
gates=(int)((cfg->tend-cfg->tstart)/cfg->tstep+0.5);
if(cfg->maxgate>gates)
cfg->maxgate=gates;
if(cfg->sradius>0.f){
cfg->crop0.x=MAX((int)(cfg->srcpos.x-cfg->sradius),0);
cfg->crop0.y=MAX((int)(cfg->srcpos.y-cfg->sradius),0);
cfg->crop0.z=MAX((int)(cfg->srcpos.z-cfg->sradius),0);
cfg->crop1.x=MIN((int)(cfg->srcpos.x+cfg->sradius),cfg->dim.x-1);
cfg->crop1.y=MIN((int)(cfg->srcpos.y+cfg->sradius),cfg->dim.y-1);
cfg->crop1.z=MIN((int)(cfg->srcpos.z+cfg->sradius),cfg->dim.z-1);
}else if(cfg->sradius==0.f){
memset(&(cfg->crop0),0,sizeof(uint3));
memset(&(cfg->crop1),0,sizeof(uint3));
}
if(cfg->medianum==0)
mexErrMsgTxt("you must define the 'prop' field in the input structure");
if(cfg->dim.x==0||cfg->dim.y==0||cfg->dim.z==0)
mexErrMsgTxt("the 'vol' field in the input structure can not be empty");
if(cfg->steps.x!=1.f && cfg->unitinmm==1.f){
cfg->unitinmm=cfg->steps.x;
cfg->steps.x=1.f;cfg->steps.y=1.f;cfg->steps.z=1.f;
}
if(cfg->unitinmm!=1.f){
for(i=1;i<cfg->medianum;i++){
cfg->prop[i].mus*=cfg->unitinmm;
cfg->prop[i].mua*=cfg->unitinmm;
}
}
if(cfg->issavedet && cfg->detnum==0)
cfg->issavedet=0;
for(i=0;i<cfg->detnum;i++){
if(!cfg->issrcfrom0){
cfg->detpos[i].x--;cfg->detpos[i].y--;cfg->detpos[i].z--; /*convert to C index*/
}
}
if(1){
cfg->isrowmajor=0; /*matlab is always col-major*/
if(cfg->isrowmajor){
/*from here on, the array is always col-major*/
mcx_convertrow2col(&(cfg->vol), &(cfg->dim));
cfg->isrowmajor=0;
}
if(cfg->issavedet)
mcx_maskdet(cfg);
if(cfg->srcpos.x<0.f || cfg->srcpos.y<0.f || cfg->srcpos.z<0.f ||
cfg->srcpos.x>=cfg->dim.x || cfg->srcpos.y>=cfg->dim.y || cfg->srcpos.z>=cfg->dim.z)
mexErrMsgTxt("source position is outside of the volume");
idx1d=(int)(int(cfg->srcpos.z)*cfg->dim.y*cfg->dim.x+int(cfg->srcpos.y)*cfg->dim.x+int(cfg->srcpos.x));
/* if the specified source position is outside the domain, move the source
along the initial vector until it hit the domain */
if(cfg->vol && cfg->vol[idx1d]==0){
printf("source (%f %f %f) is located outside the domain, vol[%d]=%d\n",
cfg->srcpos.x,cfg->srcpos.y,cfg->srcpos.z,idx1d,cfg->vol[idx1d]);
while(cfg->vol[idx1d]==0){
cfg->srcpos.x+=cfg->srcdir.x;
cfg->srcpos.y+=cfg->srcdir.y;
cfg->srcpos.z+=cfg->srcdir.z;
if(cfg->srcpos.x<0.f || cfg->srcpos.y<0.f || cfg->srcpos.z<0.f ||
cfg->srcpos.x>=cfg->dim.x || cfg->srcpos.y>=cfg->dim.y || cfg->srcpos.z>=cfg->dim.z)
mcx_error(-4,"searching non-zero voxel failed along the incident vector",__FILE__,__LINE__);
idx1d=(int)(int(cfg->srcpos.z)*cfg->dim.y*cfg->dim.x+int(cfg->srcpos.y)*cfg->dim.x+int(cfg->srcpos.x));
}
printf("fixing source position to (%f %f %f)\n",cfg->srcpos.x,cfg->srcpos.y,cfg->srcpos.z);
}
}
cfg->his.maxmedia=cfg->medianum-1; /*skip medium 0*/
cfg->his.detnum=cfg->detnum;
cfg->his.colcount=cfg->medianum+1; /*column count=maxmedia+2*/
}
