void cppar(char *par1,struct pars *p1,char *par2,struct pars *p2)
{
int i;
int ix;
struct pars p3;
/* Find the index of par1 in the p1 set otherwise return */
ix=parindex(par1,p1);
if (ix<0) return;
/* Search for par2 in the p2 set to modify an exisiting parameter */
for (i=0;i<p2->npars;i++) {
if (!strcmp(p2->name[i],par2)) { /* There is a match */
/* Free existing values */
switch(p2->type[i]) {
case 0:
free(p2->i[i]);
break;
case 1:
free(p2->d[i]);
break;
case 2:
free(p2->s[i]);
break;
} /* end p->type switch */
/* Copy values from p1 to p2 */
copyvalues(p1,ix,p2,i);
return;
}
}
/* If we have not already returned then add the parameter */
/* Copy the current p2 set to p3 */
p3.npars = p2->npars;
if (p3.npars > 0) mallocnpars(&p3);
for (i=0;i<p3.npars;i++) {
if ((p3.name[i] = (char *)malloc((strlen(p2->name[i])+1)*sizeof(char))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
strcpy(p3.name[i],p2->name[i]);
/* Copy values from p2 to p3 */
copyvalues(p2,i,&p3,i);
}
/* Clear the current p2 set */
clearpars(p2);
/* Restore the p2 set but allocate for an extra parameter */
p2->npars = p3.npars+1;
mallocnpars(p2);
for (i=0;i<p3.npars;i++) {
if ((p2->name[i] = (char *)malloc((strlen(p3.name[i])+1)*sizeof(char))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
strcpy(p2->name[i],p3.name[i]);
/* Copy values back from p3 to p2 */
copyvalues(&p3,i,p2,i);
}
/* Clear the p3 set */
clearpars(&p3);
/* Now add the parameter */
if ((p2->name[i] = (char *)malloc((strlen(par2)+1)*sizeof(char))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
strcpy(p2->name[i],par2);
/* Copy values from p1 to p2 */
copyvalues(p1,ix,p2,i);
}
void sliceorder2D(struct data *d)
{
int index;
int ns,nr;
double *pss;
fftw_complex ***slice;
int i,j,k;
#ifdef DEBUG
struct timeval tp;
double t1,t2;
char function[20];
strcpy(function,"sliceorder2D"); /* Set function name */
fprintf(stdout,"\n%s: %s()\n",SOURCEFILE,function);
gettimeofday(&tp, NULL);
t1=(double)tp.tv_sec+(1.e-6)*tp.tv_usec;
fflush(stdout);
#endif
/* Index of pss in pars struct, return if pss is not found */
index=parindex("pss",&d->p);
if (index < 0) return;
/* Number of slices and receivers */
ns=d->ns; nr=d->nr;
/* Take a copy of the starting slice order */
if ((pss = (double *)malloc(ns*sizeof(double))) == NULL) nomem();
for (i=0;i<ns;i++) pss[i]=d->p.d[index][i];
/* Sort slice positions into ascending order */
qsort(d->p.d[index],ns,sizeof(d->p.d[index][0]),doublecmp);
/* Allocate memory for some data pointers to the slices */
if ((slice = (fftw_complex ***)fftw_malloc(nr*sizeof(fftw_complex **))) == NULL) nomem();
for (i=0;i<nr;i++) { /* loop over receiver blocks */
if ((slice[i] = (fftw_complex **)fftw_malloc(ns*sizeof(fftw_complex *))) == NULL) nomem();
for (j=0;j<ns;j++) /* loop over slices */
if ((slice[i][j] = (fftw_complex *)fftw_malloc(sizeof(fftw_complex))) == NULL) nomem();
}
/* Set new pointers to slices in ascending order */
for (i=0;i<ns;i++) {
for (j=0;j<ns;j++) {
if (d->p.d[index][i] == pss[j]) {
for (k=0;k<nr;k++)
slice[k][i]=d->data[k][j];
break;
}
}
}
/* Reset original data pointers in ascending order */
for (i=0;i<nr;i++)
for (j=0;j<ns;j++)
d->data[i][j]=slice[i][j];
fftw_free(slice);
#ifdef DEBUG
gettimeofday(&tp, NULL);
t2=(double)tp.tv_sec+(1.e-6)*tp.tv_usec;
fprintf(stdout," Took %f secs\n",t2-t1);
fprintf(stdout," pss\n");
fprintf(stdout," original\tnew\n");
for (i=0;i<ns;i++)
fprintf(stdout," %f\t%f\n",pss[i],d->p.d[index][i]);
fflush(stdout);
#endif
free(pss);
}
void settep(struct data *d, int mode)
{
int dim1,dim2,dim3,nr;
int **max;
int i,j,k,l,n;
int ix;
int nseg,nnav,etl,altread,echo,oddcount,evencount;
int steadyStates,flipLine;
double re,im,M2,maxM,oddmax,evenmax,sw,tepadjust;
char tepfile[MAXPATHLEN];
FILE *f_out;
#ifdef DEBUG
struct timeval tp;
double t1,t2;
int rtn;
fprintf(stdout,"\n%s: %s()\n",__FILE__,__FUNCTION__);
fprintf(stdout," Attempting to calculate correction for tep ...\n");
rtn=gettimeofday(&tp, NULL);
t1=(double)tp.tv_sec+(1.e-6)*tp.tv_usec;
fflush(stdout);
#endif
/* Set data dimensions */
dim1=d->np/2; dim2=d->nv; dim3=d->endpos-d->startpos; nr=d->nr;
/* Allow for arbitrary number of acquired steady state echoes (default 1) */
steadyStates = (int)*val("acquiredSteadyStates",&d->p);
if (parindex("acquiredSteadyStates",&d->p) < 0) steadyStates = 1;
/* Allow for sequences with readout polarity set constant for the first acquired EPI echo,
i.e. the set polarity depends on # navigators and # acquired steady states */
flipLine = (int)*val("flipLine",&d->p);
if (flipLine != 1) flipLine = 0;
switch(mode) {
case STD: /* Use maximum magnitude */
/* If noise data does not exist set it to zero */
if (!d->noise.data) zeronoise(d);
/* If noise data is zero sample the noise */
if (d->noise.zero) getnoise(d,STD);
/* Set some defaults */
zeromax(d);
if ((max = (int **)malloc(nr*sizeof(int *))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
for (i=0;i<nr;i++)
if ((max[i] = (int *)malloc(dim2*sizeof(int))) == NULL) nomem(__FILE__,__FUNCTION__,__LINE__);
/* Get coordinates of maxima for odd and even echoes */
for (i=0;i<nr;i++) {
for (j=0;j<dim3;j++) {
for (k=0;k<dim2;k++) {
max[i][k]=-1;
maxM=0.0;
for (l=0;l<dim1;l++) {
re=fabs(d->data[i][j][k*dim1+l][0]);
im=fabs(d->data[i][j][k*dim1+l][1]);
M2=re*re+im*im;
if ((M2 > maxM) && (M2 > 4*d->noise.M2[i])) {
maxM=M2;
max[i][k]=l;
}
}
}
}
}
oddcount=0; oddmax=0.0;
evencount=0; evenmax=0.0;
nseg=(int)*val("nseg",&d->p);
nnav=(int)*val("nnav",&d->p);
etl=(int)*val("etl",&d->p);
altread=spar(d,"altread","y"); /* alternating read gradient for alternate segments ... */
if (nseg<2) altread=FALSE; /* ... only if nseg>1 ... */
if (nseg%2==0) altread=FALSE; /* ... and only if nseg is odd */
for (n=0;n<nseg;n++) {
ix=n*(nnav+etl);
for (i=0;i<nr;i++) {
echo=0;
if (altread && n%2) echo=1;
for (k=0;k<nnav;k++) {
if (max[i][k] > -1) {
if (echo%2==flipLine) {
oddmax += max[i][ix+k];
oddcount++;
} else {
evenmax += max[i][ix+k];
evencount++;
}
}
echo++;
}
/* Skip the steady state readout gradients */
echo += steadyStates;
for (k=nnav;k<etl;k++) {
if (max[i][k] > -1) {
if (echo%2==flipLine) {
oddmax += max[i][ix+k];
oddcount++;
} else {
evenmax += max[i][ix+k];
evencount++;
}
}
echo++;
}
}
} /* end nseg loop */
oddmax /=oddcount;
evenmax /=evencount;
for (i=0;i<nr;i++) free(max[i]);
free(max);
sw=*val("sw",&d->p);
tepadjust=0.5e6*(oddmax-evenmax)/sw;
strcpy(tepfile,vnmrj_path);
strcat(tepfile,"tepadjust");
if ((f_out = fopen(tepfile, "w")) == NULL) {
fprintf(stderr,"\n%s: %s()\n",__FILE__,__FUNCTION__);
fprintf(stderr," Unable to write to %s\n",tepfile);
fflush(stderr);
return;
}
fprintf(f_out,"tepadjust %f",tepadjust);
fclose(f_out);
#ifdef DEBUG
rtn=gettimeofday(&tp, NULL);
t2=(double)tp.tv_sec+(1.e-6)*tp.tv_usec;
fprintf(stdout,"\n%s: %s()\n",__FILE__,__FUNCTION__);
fprintf(stdout," Magnitude data suggests add %f us to value of tep\n",tepadjust);
fprintf(stdout," Result written to file %s\n",tepfile);
fflush(stdout);
#endif
break;
default:
break;
}
}
