virtual void run(Voxel& voxel, VoxelData& data)
{
gradient_fun g(b_vec,data.space);
fun f(b_vec,data.space);
std::map<float,image::vector<3,float>,std::greater<float> > result;
for (unsigned int index = 0;index < voxel.max_fiber_number;++index)
{
if (data.fa[index] <= 0.0)
break;
image::vector<3,float> initial_dir(voxel.ti.vertices[data.dir_index[index]]);
image::optimization::gradient_descent(initial_dir,f,g,(double)0.01);
double fa = -data.min_odf-f(initial_dir);
initial_dir.normalize();
if (std::abs(image::vector<3,float>(voxel.ti.vertices[data.dir_index[index]]) * initial_dir) < 0.939692623) // the angle greater than 20 degrees
result[data.fa[index]] = image::vector<3,float>(voxel.ti.vertices[data.dir_index[index]]);
else
result[fa] = initial_dir;
}
std::map<float,image::vector<3,float>,std::greater<float> >::const_iterator iter = result.begin();
std::map<float,image::vector<3,float>,std::greater<float> >::const_iterator end = result.end();
for (unsigned int index = 0;iter != end;++index,++iter)
{
data.fa[index] = iter->first;
data.dir[index] = iter->second;
}
}
int align_traceback(aligndatap data,
char *aln1,
char *aln2,
int bufferlen,
int (*stop)(aligndatap,int,int)) {
int i,j,k,identity,dir,oi,oj;
int alnpos,alnlen;
alignmentp aobj;
/*
if (stop == &align_stop_partialfree) {
fprintf(stdout,"OK asp");
} else if (stop == &align_stop_endsfree) {
fprintf(stdout,"OK ase");
} else if (stop == &align_stop_global) {
fprintf(stdout,"OK asg");
} else if (stop == &align_stop_local) {
fprintf(stdout,"OK asl");
} else {
fprintf(stdout,"Lost value for stop: %x",stop);
}
fflush(stdout);
*/
/* fprintf(stdout,"start traceback: str1=%s str2=%s\n",data->s1,data->s2); */
/* fprintf(stdout,"3.1..."); fflush(stdout); */
aobj = data->alignment;
identity = 0;
i = aobj->end1+1;
j = aobj->end2+1;
/* fprintf(stdout," end1=%d end2=%d\n",i,j); fflush(stdout); */
/* fprintf(stdout,"3.2 (e1=%d, e2=%d)...",i,j); fflush(stdout); */
alnpos = bufferlen-1;
dir = initial_dir(data,i,j);
while (!(*stop)(data,i,j)) {
if (alnpos < 0) {
fprintf(stderr,"traceback: alignment buffers too small, aborting\n");
return -1;
}
oi = i; oj = j;
switch (dir) {
case UP:
aln1[alnpos] = data->s1[--i];
aln2[alnpos--] = '-';
break;
case DIAG:
if (data->s1[--i] == data->s2[--j]) { identity++; }
aln1[alnpos] = data->s1[i];
aln2[alnpos--] = data->s2[j];
break;
case LEFT:
aln1[alnpos] = '-';
aln2[alnpos--] = data->s2[--j];
break;
default:
fprintf(stderr,"dir(%d,%d) = %d\n",i,j,dir);
exit(-1);
}
/* fprintf(stdout,"<%d,%d,%d",i,j,dir); fflush(stdout); */
dir = direction(data,oi,oj,dir);
/* fprintf(stdout,">"); fflush(stdout); */
/* fprintf(stderr,"aln1[%d]: %c aln2[%d]: %c\n",alnpos+1,aln1[alnpos+1],alnpos+1,aln2[alnpos+1]); */
}
aobj->start1 = i;
aobj->start2 = j;
/* fprintf(stdout,"3.3..."); fflush(stdout); */
alnlen = bufferlen - alnpos - 1;
for (k=0;k<alnlen;k++) {
aln1[k] = aln1[k+alnpos+1];
aln2[k] = aln2[k+alnpos+1];
}
/* fprintf(stdout,"3.4..."); fflush(stdout); */
aln1[alnlen] = '\0';
aln2[alnlen] = '\0';
/* fprintf(stderr,"alnlen: %d\naln1: %s\naln2: %s\n",alnlen,aln1,aln2); */
aobj->aln1 = aln1;
aobj->aln2 = aln2;
aobj->alignlen = alnlen;
aobj->identity = identity;
return alnlen;
}
