double local_GCAcomputeLogSampleProbability( GCA *gca,
GCA_SAMPLE *gcas,
MRI *mri,
MATRIX *m_L,
int nsamples,
int exvivo,
double clamp)
{
static TRANSFORM *transform = NULL ;
if (!transform)
{
transform = TransformAlloc(LINEAR_VOX_TO_VOX, NULL) ;
}
((LTA *)transform->xform)->xforms[0].m_L = m_L ;
if (exvivo)
{
double gm, wm, fluid ;
compute_tissue_modes(mri, gca, gcas, transform, nsamples,
&wm, &gm, &fluid ) ;
return( (SQR(gm - wm) +
SQR(gm-fluid) +
SQR(fluid - wm) +
SQR(gm) -
SQR(fluid))) ;
}
double result;
if (robust)
{
// Defined 0 at the top of the file
result = GCAcomputeNumberOfGoodFittingSamples( gca, gcas, mri,
transform, nsamples );
}
else
{
result = GCAcomputeLogSampleProbability( gca, gcas, mri,
transform, nsamples, clamp );
}
return( result );
}
static GCA_SAMPLE *
find_control_points(GCA *gca, GCA_SAMPLE *gcas_total,
int total_samples, int *pnorm_samples, int nregions, int label,
MRI *mri_in, TRANSFORM *transform, double min_prior, double ctl_point_pct)
{
int i, j, *ordered_indices, nsamples,
xmin, ymin, zmin, xmax, ymax, zmax, xv,yv,zv,
x, y, z, xi, yi, zi, region_samples,
used_in_region, prior_wsize=5, image_wsize=3, histo_peak, n,
nbins ;
GCA_SAMPLE *gcas, *gcas_region, *gcas_norm ;
double means[MAX_GCA_INPUTS], vars[MAX_GCA_INPUTS], val, nsigma ;
HISTOGRAM *histo, *hsmooth ;
GC1D *gc ;
float fmin, fmax ;
MRI *mri_T1 = NULL ;
if (label == Gdiag_no)
DiagBreak() ;
MRIvalRange(mri_in, &fmin, &fmax) ;
nbins = (int)(fmax-fmin+1);
histo = HISTOalloc(nbins) ; hsmooth = HISTOalloc(nbins) ;
for (nsamples = i = 0 ; i < total_samples ; i++)
{
if (gcas_total[i].label != label)
continue ;
nsamples++ ;
}
*pnorm_samples = 0 ;
printf("found %d control points for structure...\n", nsamples) ;
if (nsamples == 0)
{
DiagBreak() ;
return(NO_ERROR) ;
}
gcas = (GCA_SAMPLE *)calloc(nsamples, sizeof(GCA_SAMPLE)) ;
gcas_region = (GCA_SAMPLE *)calloc(nsamples, sizeof(GCA_SAMPLE)) ;
gcas_norm = (GCA_SAMPLE *)calloc(nsamples, sizeof(GCA_SAMPLE)) ;
if (!gcas || !gcas_region || !gcas_norm)
ErrorExit
(ERROR_NOMEMORY,
"find_control_points: could not allocate %d samples\n",nsamples);
for (j = i = 0 ; i < total_samples ; i++)
{
if (gcas_total[i].label != label)
continue ;
memmove(&gcas[j], &gcas_total[i], sizeof(GCA_SAMPLE)) ;
j++ ;
}
ordered_indices = (int *)calloc(nsamples, sizeof(int)) ;
gcas_bounding_box(gcas, nsamples, &xmin, &ymin, &zmin, &xmax, &ymax, &zmax, label) ;
printf("bounding box (%d, %d, %d) --> (%d, %d, %d)\n",
xmin, ymin, zmin, xmax, ymax, zmax) ;
for (x = 0 ; x < nregions ; x++)
{
for (y = 0 ; y < nregions ; y++)
{
for (z = 0 ; z < nregions ; z++)
{
/* only process samples in this region */
nsigma = 1.0 ;
do
{
for (region_samples = i = 0 ; i < nsamples ; i++)
{
xi = (int)(nregions*(gcas[i].x - xmin) / (xmax-xmin+1)) ;
yi = (int)(nregions*(gcas[i].y - ymin) / (ymax-ymin+1)) ;
zi = (int)(nregions*(gcas[i].z - zmin) / (zmax-zmin+1)) ;
if ((xi < 0 || xi >= nregions) ||
(yi < 0 || yi >= nregions) ||
(zi < 0 || zi >= nregions))
DiagBreak() ;
xv = gcas[i].x ; yv = gcas[i].y ; zv = gcas[i].z ;
if (xi != x || yi != y || zi != z
|| gcas[i].prior < min_prior)
continue ;
if (xv == Gx && yv == Gy && zv == Gz)
DiagBreak() ;
if (sqrt(SQR(xv-Gx)+SQR(yv-Gy)+SQR(zv-Gz)) < 2)
DiagBreak() ;
if (min_region_prior(gca, gcas[i].xp, gcas[i].yp, gcas[i].zp,prior_wsize, label) < min_prior)
continue ;
if (uniform_region(gca, mri_in, transform,
xv, yv, zv,
image_wsize, &gcas[i], nsigma) == 0)
continue ;
memmove(&gcas_region[region_samples],
&gcas[i],
sizeof(GCA_SAMPLE)) ;
region_samples++ ;
if (gcas[i].x == Gx &&
gcas[i].y == Gy &&
gcas[i].z == Gz)
DiagBreak() ;
}
nsigma *= 1.1 ;
} while (region_samples < 8 && nsigma < 3) ;
if (region_samples < 8)/* can't reliably estimate statistics */
continue ;
if (DIAG_VERBOSE_ON)
printf("\t%d total samples found in region (%d, %d, %d)\n",
region_samples,x, y,z) ;
/* compute mean and variance of label within this region */
for (n = 0 ; n < mri_in->nframes ; n++)
{
HISTOclear(histo, histo) ;
histo->bin_size = 1 ;
for (means[n] = vars[n] = 0.0, i = 0 ;
i < region_samples ;
i++)
{
MRIsampleVolumeFrame
(mri_in,
gcas_region[i].x,gcas_region[i].y,gcas_region[i].z,
n, &val) ;
if (FZERO(val))
{
if (i < (region_samples-1))
memmove(&gcas_region[i],
&gcas_region[i+1],
(region_samples-(i+1))*sizeof(GCA_SAMPLE));
i-- ;
region_samples-- ;
continue ;
}
histo->counts[(int)val]++ ;
means[n] += val ;
vars[n] += (val*val) ;
}
HISTOsmooth(histo, hsmooth, 2) ;
histo_peak =
HISTOfindHighestPeakInRegion(hsmooth, 1, hsmooth->nbins) ;
if (histo_peak < 0) /* couldn't find a valid peak? */
break ;
for (means[n] = vars[n] = 0.0, i = 0 ;
i < region_samples ;
i++)
{
if (gcas_region[i].label < 0)
continue ;
MRIsampleVolumeFrame
(mri_in,
gcas_region[i].x,
gcas_region[i].y,
gcas_region[i].z,
n, &val) ;
means[n] += val ;
vars[n] += (val*val) ;
}
means[n] /= (double)region_samples ;
vars[n] = vars[n] / (double)region_samples - means[n]*means[n] ;
means[n] = histo_peak ;
if (DIAG_VERBOSE_ON)
printf("\tlabel %s[%d]: %2.1f +- %2.1f\n",
cma_label_to_name(label),
n, means[n], sqrt(vars[n])) ;
}
/* ignore GCA mean and variance -
use image instead (otherwise bias field will mess us up) */
for (i = 0 ; i < region_samples ; i++)
{
int r ;
for (r = 0 ; r < gca->ninputs ; r++)
gcas_region[i].means[r] = means[r] ;
/* gcas_region[i].var = var ;*/
}
GCAcomputeLogSampleProbability
(gca, gcas_region, mri_in, transform, region_samples) ;
GCArankSamples
(gca, gcas_region, region_samples, ordered_indices) ;
GCAremoveOutlyingSamples
(gca, gcas_region, mri_in, transform, region_samples, 2.0) ;
for (used_in_region = i = 0 ; i < region_samples ; i++)
{
j = ordered_indices[i] ;
if (gcas_region[j].label != label) /* it was an outlier */
continue ;
memmove
(&gcas_norm[*pnorm_samples],
&gcas_region[j],
sizeof(GCA_SAMPLE)) ;
(*pnorm_samples)++ ; used_in_region++ ;
}
if ((used_in_region <= 0) && region_samples>0)
{
j = ordered_indices[0] ;
/* gcas_region[j].label = label ;*/
printf("forcing use of sample %d @ (%d, %d, %d)\n", j,
gcas_region[j].x,
gcas_region[j].y,
gcas_region[j].z) ;
memmove(&gcas_norm[*pnorm_samples],
&gcas_region[j],
sizeof(GCA_SAMPLE)) ;
(*pnorm_samples)++ ; used_in_region++ ;
}
if (DIAG_VERBOSE_ON)
printf("\t%d samples used in region\n", used_in_region) ;
}
}
}
/* put gca means back into samples */
for (i = 0 ; i < *pnorm_samples ; i++)
{
gc = GCAfindPriorGC(gca,
gcas_norm[i].xp,
gcas_norm[i].yp,
gcas_norm[i].zp,
gcas_norm[i].label) ;
if (gc)
{
int r, c, v ;
for (v = r = 0 ; r < gca->ninputs ; r++)
{
for (c = r ; c < gca->ninputs ; c++, v++)
{
gcas_norm[i].means[v] = gc->means[v] ;
gcas_norm[i].covars[v] = gc->covars[v] ;
}
}
}
}
HISTOfree(&histo) ; HISTOfree(&hsmooth) ;
free(gcas_region) ;
free(gcas) ;
if (mri_T1)
MRIfree(&mri_T1) ;
return(gcas_norm) ;
}
