/* --------------------------------------------------------------
regio_read_xfm4() - reads a 4x4 transform as the last four
lines of the xfmfile. Blank lines at the end will defeat it.
-------------------------------------------------------------- */
int regio_read_xfm4(char *xfmfile, MATRIX **R)
{
FILE *fp;
char tmpstr[1000];
int r,c,n,nlines;
float val;
memset(tmpstr,'\0',1000);
fp = fopen(xfmfile,"r");
if (fp==NULL)
{
perror("regio_read_xfm4");
fprintf(stderr,"Could read %s\n",xfmfile);
return(1);
}
/* Count the number of lines */
nlines = 0;
while (fgets(tmpstr,1000,fp) != NULL) nlines ++;
rewind(fp);
/* skip all but the last 3 lines */
for (n=0;n<nlines-4;n++) fgets(tmpstr,1000,fp);
*R = MatrixAlloc(4,4,MATRIX_REAL);
if (*R == NULL)
{
fprintf(stderr,"regio_read_xfm4(): could not alloc R\n");
fclose(fp);
return(1);
}
MatrixClear(*R);
/* registration matrix */
for (r=0;r<3;r++)
{ /* note: upper limit = 3 for xfm */
for (c=0;c<4;c++)
{
n = fscanf(fp,"%f",&val);
if (n != 1)
{
perror("regio_read_xfm4()");
fprintf(stderr,"Error reading R[%d][%d] from %s\n",r,c,xfmfile);
fclose(fp);
return(1);
}
(*R)->rptr[r+1][c+1] = val;
/*printf("%7.4f ",val);*/
}
/*printf("\n");*/
}
(*R)->rptr[3+1][3+1] = 1.0;
fclose(fp);
return(0);
}
void MatrixQRDecompColMajor(Matrix*mtR,Matrix*mt){
// gram-schmidt orthonormalization (Lt and Q)
double t, *aT[mt->W];
int W = mt->W;
int i,j;
MatrixClear(mtR);
for (i = 0; i < W;i++) {
aT[i] = Row(mt,i);
for (j = 0; j < i; j++) {
Elem(mtR,j,i) = t = VP(aT[j], aT[i], W);
VSA(aT[i], aT[j], -t, W);
}
Elem(mtR,i,i) = t = sqrt(VP(aT[i],aT[i],W));
VSS(aT[i], 1/t, W);
}
/*
Elem(mtR,0,0) = t = sqrt(VP(aT[0],aT[0],W));
VSS(aT[0], 1/t, W);
Elem(mtR,0,1) = t = VP(aT[0], aT[1], W);
VSA(aT[1], aT[0], -t, W);
Elem(mtR,1,1) = t = sqrt(VP(aT[1],aT[1],W));
VSS(aT[1], 1/t, W);
///////////
Elem(mtR,0,2) = t = VP(aT[0], aT[2], W);
VSA(aT[2], aT[0], -t, W);
Elem(mtR,1,2) = t = VP(aT[1], aT[2], W);
VSA(aT[2], aT[1], -t, W);
Elem(mtR,2,2) = t = sqrt(VP(aT[2],aT[2],W));
VSS(aT[2], 1/t, W);
////// 以下略
*/
}
static int
compute_cluster_statistics(MRI_SURFACE *mris, MRI *mri_profiles, MATRIX **m_covs, VECTOR **v_means, int k) {
int i, vno, cluster, nsamples, num[MAX_CLUSTERS];
int singular, cno_pooled, cno ;
MATRIX *m1, *mpooled, *m_inv_covs[MAX_CLUSTERS] ;
VECTOR *v1 ;
FILE *fp ;
double det, det_pooled ;
memset(num, 0, sizeof(num)) ;
nsamples = mri_profiles->nframes ;
v1 = VectorAlloc(nsamples, MATRIX_REAL) ;
m1 = MatrixAlloc(nsamples, nsamples, MATRIX_REAL) ;
mpooled = MatrixAlloc(nsamples, nsamples, MATRIX_REAL) ;
for (cluster = 0 ; cluster < k ; cluster++) {
VectorClear(v_means[cluster]) ;
MatrixClear(m_covs[cluster]) ;
}
// compute means
// fp = fopen("co.dat", "w") ;
fp = NULL ;
for (vno = 0 ; vno < mris->nvertices ; vno++) {
cluster = mris->vertices[vno].curv ;
for (i = 0 ; i < nsamples ; i++) {
VECTOR_ELT(v1, i+1) = MRIgetVoxVal(mri_profiles, vno, 0, 0, i) ;
if (cluster == 0 && fp)
fprintf(fp, "%f ", VECTOR_ELT(v1, i+1));
}
if (cluster == 0 && fp)
fprintf(fp, "\n") ;
num[cluster]++ ;
VectorAdd(v_means[cluster], v1, v_means[cluster]) ;
}
if (fp)
fclose(fp) ;
for (cluster = 0 ; cluster < k ; cluster++)
if (num[cluster] > 0)
VectorScalarMul(v_means[cluster], 1.0/(double)num[cluster], v_means[cluster]) ;
// compute inverse covariances
for (vno = 0 ; vno < mris->nvertices ; vno++) {
cluster = mris->vertices[vno].curv ;
for (i = 0 ; i < nsamples ; i++)
VECTOR_ELT(v1, i+1) = MRIgetVoxVal(mri_profiles, vno, 0, 0, i) ;
VectorSubtract(v_means[cluster], v1, v1) ;
VectorOuterProduct(v1, v1, m1) ;
MatrixAdd(m_covs[cluster], m1, m_covs[cluster]) ;
MatrixAdd(mpooled, m1, mpooled) ;
}
MatrixScalarMul(mpooled, 1.0/(double)mris->nvertices, mpooled) ;
cno_pooled = MatrixConditionNumber(mpooled) ;
det_pooled = MatrixDeterminant(mpooled) ;
for (cluster = 0 ; cluster < k ; cluster++)
if (num[cluster] > 0)
MatrixScalarMul(m_covs[cluster], 1.0/(double)num[cluster], m_covs[cluster]) ;
// invert all the covariance matrices
MatrixFree(&m1) ;
singular = 0 ;
for (cluster = 0 ; cluster < k ; cluster++) {
m1 = MatrixInverse(m_covs[cluster], NULL) ;
cno = MatrixConditionNumber(m_covs[cluster]) ;
det = MatrixDeterminant(m_covs[cluster]) ;
if (m1 == NULL)
singular++ ;
while (cno > 100*cno_pooled || 100*det < det_pooled) {
if (m1)
MatrixFree(&m1) ;
m1 = MatrixScalarMul(mpooled, 0.1, NULL) ;
MatrixAdd(m_covs[cluster], m1, m_covs[cluster]) ;
MatrixFree(&m1) ;
cno = MatrixConditionNumber(m_covs[cluster]) ;
m1 = MatrixInverse(m_covs[cluster], NULL) ;
det = MatrixDeterminant(m_covs[cluster]) ;
}
m_inv_covs[cluster] = m1 ;
}
for (cluster = 0 ; cluster < k ; cluster++) {
if (m_inv_covs[cluster] == NULL)
DiagBreak() ;
else {
MatrixFree(&m_covs[cluster]) ;
m_covs[cluster] = m_inv_covs[cluster] ;
// MatrixIdentity(m_covs[cluster]->rows, m_covs[cluster]);
}
}
MatrixFree(&mpooled) ;
VectorFree(&v1) ;
return(NO_ERROR) ;
}
/* --------------------------------------------------------------
regio_read_mincxfm() - reads a 3x4 transform as the last three
lines of the xfmfile. Blank lines at the end will defeat it.
If fileinfo != NULL, reads in the "fileinfo". This is the 3rd
line in the minc xfm file. It will contain information about
the center of the transform (-center). This is used by
ltaMNIreadEx() to account for the non-zero center of the MNI
talairach template. If the center infomation is not there,
ltaMNIreadEx() assumes that the center is 0 and will produce
the wrong transform. Thus, if one is going to write out the
xfm, then one needs to keep track of this information when
reading it in. regio_write_mincxfm() takes fileinfo as an
argument. If one is not going to write out the xfm, then
simply set fileinfo to NULL.
-------------------------------------------------------------- */
int regio_read_mincxfm(char *xfmfile, MATRIX **R, char **fileinfo)
{
FILE *fp;
char tmpstr[1000];
int r,c,n,nlines;
float val;
memset(tmpstr,'\0',1000);
fp = fopen(xfmfile,"r");
if (fp==NULL)
{
perror("regio_read_mincxfm");
printf("ERROR: could not read %s\n",xfmfile);
return(1);
}
fgetl(tmpstr, 900, fp) ; /* MNI Transform File */
if (strncmp("MNI Transform File", tmpstr, 18))
{
printf("ERROR: %s does not start as 'MNI Transform File'",xfmfile);
return(1);
}
fgetl(tmpstr, 900, fp) ; /* fileinfo */
if (fileinfo != NULL)
{
*fileinfo = strcpyalloc(tmpstr);
printf("\n%s\n\n",*fileinfo);
}
else printf("Not reading in xfm fileinfo\n");
// Close it and open it up again to rewind it
fclose(fp);
fp = fopen(xfmfile,"r");
/* Count the number of lines */
nlines = 0;
while (fgets(tmpstr,1000,fp) != NULL) nlines ++;
rewind(fp);
/* skip all but the last 3 lines */
for (n=0;n<nlines-3;n++) fgets(tmpstr,1000,fp);
*R = MatrixAlloc(4,4,MATRIX_REAL);
if (*R == NULL)
{
fprintf(stderr,"regio_read_mincxfm(): could not alloc R\n");
fclose(fp);
return(1);
}
MatrixClear(*R);
/* registration matrix */
for (r=0;r<3;r++)
{ /* note: upper limit = 3 for xfm */
for (c=0;c<4;c++)
{
n = fscanf(fp,"%f",&val);
if (n != 1)
{
perror("regio_read_mincxfm()");
fprintf(stderr,"Error reading R[%d][%d] from %s\n",r,c,xfmfile);
fclose(fp);
return(1);
}
(*R)->rptr[r+1][c+1] = val;
/*printf("%7.4f ",val);*/
}
/*printf("\n");*/
}
(*R)->rptr[3+1][3+1] = 1.0;
fclose(fp);
return(0);
}
