// Returns the log probability of a reconciled gene tree ('tree', 'recon')
// from the coalescent model given a species tree 'stree' and
// population sizes 'n'
double prob_multicoal_recon_topology2(intnode *itree, int nnodes, int *recon,
int *pstree, int nsnodes,
double *stimes, double *popsizes)
{
LineageCounts counts(nsnodes);
count_lineages_per_branch(&counts, nnodes, recon, pstree, nsnodes);
TopStats top_stats(nnodes, nsnodes);
get_topology_stats2(&top_stats, itree, nnodes, recon, pstree, nsnodes);
// iterate through species tree branches
double lnp = 0.0; // log probability
for (int snode=0; snode<nsnodes-1; snode++) {
const int a = counts.starts[snode];
const int b = counts.ends[snode];
if (a == 1)
continue;
const int n = top_stats.nodes_per_species[snode];
double fact = 1.0; for (int i=2; i<=n; i++) fact *= i; // fact(n)
const double t = stimes[pstree[snode]] - stimes[snode];
lnp += log(prob_coal_counts(a, b, t, popsizes[snode])
* fact / num_labeled_histories(a, b));
}
// root branch
const int snode = nsnodes - 1;
const int a = counts.starts[snode];
const int n = top_stats.nodes_per_species[snode];
double fact = 1.0; for (int i=2; i<=n; i++) fact *= i; // fact(n)
lnp += log(fact / num_labeled_histories(a, 1));
const int nleaves = (nnodes + 1) / 2;
for (int node=nleaves; node<nnodes; node++)
lnp -= log(top_stats.descend_nodes[node]);
return lnp;
}
// Returns a new x-height maximally compatible with the result in word_res.
// See comment above for overall algorithm.
float Tesseract::ComputeCompatibleXheight(WERD_RES *word_res) {
STATS top_stats(0, MAX_UINT8);
TBLOB* blob = word_res->rebuild_word->blobs;
int blob_id = 0;
for (; blob != NULL; blob = blob->next, ++blob_id) {
UNICHAR_ID class_id = word_res->best_choice->unichar_id(blob_id);
if (unicharset.get_isalpha(class_id) || unicharset.get_isdigit(class_id)) {
int top = blob->bounding_box().top();
// Clip the top to the limit of normalized feature space.
if (top >= INT_FEAT_RANGE)
top = INT_FEAT_RANGE - 1;
int bottom = blob->bounding_box().bottom();
int min_bottom, max_bottom, min_top, max_top;
unicharset.get_top_bottom(class_id, &min_bottom, &max_bottom,
&min_top, &max_top);
// Chars with a wild top range would mess up the result so ignore them.
if (max_top - min_top > kMaxCharTopRange)
continue;
int misfit_dist = MAX((min_top - x_ht_acceptance_tolerance) - top,
top - (max_top + x_ht_acceptance_tolerance));
int height = top - kBlnBaselineOffset;
if (debug_x_ht_level >= 20) {
tprintf("Class %s: height=%d, bottom=%d,%d top=%d,%d, actual=%d,%d : ",
unicharset.id_to_unichar(class_id),
height, min_bottom, max_bottom, min_top, max_top,
bottom, top);
}
// Use only chars that fit in the expected bottom range, and where
// the range of tops is sensibly near the xheight.
if (min_bottom <= bottom + x_ht_acceptance_tolerance &&
bottom - x_ht_acceptance_tolerance <= max_bottom &&
min_top > kBlnBaselineOffset &&
max_top - kBlnBaselineOffset >= kBlnXHeight &&
misfit_dist > 0) {
// Compute the x-height position using proportionality between the
// actual height and expected height.
int min_xht = DivRounded(height * kBlnXHeight,
max_top - kBlnBaselineOffset);
int max_xht = DivRounded(height * kBlnXHeight,
min_top - kBlnBaselineOffset);
if (debug_x_ht_level >= 20) {
tprintf(" xht range min=%d, max=%d\n",
min_xht, max_xht);
}
// The range of expected heights gets a vote equal to the distance
// of the actual top from the expected top.
for (int y = min_xht; y <= max_xht; ++y)
top_stats.add(y, misfit_dist);
} else if (debug_x_ht_level >= 20) {
tprintf(" already OK\n");
}
}
}
if (top_stats.get_total() == 0)
return 0.0f;
// The new xheight is just the median vote, which is then scaled out
// of BLN space back to pixel space to get the x-height in pixel space.
float new_xht = top_stats.median();
if (debug_x_ht_level >= 20) {
tprintf("Median xht=%f\n", new_xht);
tprintf("Mode20:A: New x-height = %f (norm), %f (orig)\n",
new_xht, new_xht / word_res->denorm.y_scale());
}
// The xheight must change by at least x_ht_min_change to be used.
if (fabs(new_xht - kBlnXHeight) >= x_ht_min_change)
return new_xht / word_res->denorm.y_scale();
else
return 0.0f;
}
// Returns a new x-height maximally compatible with the result in word_res.
// See comment above for overall algorithm.
float Tesseract::ComputeCompatibleXheight(WERD_RES *word_res,
float* baseline_shift) {
STATS top_stats(0, MAX_UINT8);
STATS shift_stats(-MAX_UINT8, MAX_UINT8);
int bottom_shift = 0;
int num_blobs = word_res->rebuild_word->NumBlobs();
do {
top_stats.clear();
shift_stats.clear();
for (int blob_id = 0; blob_id < num_blobs; ++blob_id) {
TBLOB* blob = word_res->rebuild_word->blobs[blob_id];
UNICHAR_ID class_id = word_res->best_choice->unichar_id(blob_id);
if (unicharset.get_isalpha(class_id) ||
unicharset.get_isdigit(class_id)) {
int top = blob->bounding_box().top() + bottom_shift;
// Clip the top to the limit of normalized feature space.
if (top >= INT_FEAT_RANGE)
top = INT_FEAT_RANGE - 1;
int bottom = blob->bounding_box().bottom() + bottom_shift;
int min_bottom, max_bottom, min_top, max_top;
unicharset.get_top_bottom(class_id, &min_bottom, &max_bottom,
&min_top, &max_top);
// Chars with a wild top range would mess up the result so ignore them.
if (max_top - min_top > kMaxCharTopRange)
continue;
int misfit_dist = MAX((min_top - x_ht_acceptance_tolerance) - top,
top - (max_top + x_ht_acceptance_tolerance));
int height = top - kBlnBaselineOffset;
if (debug_x_ht_level >= 2) {
tprintf("Class %s: height=%d, bottom=%d,%d top=%d,%d, actual=%d,%d: ",
unicharset.id_to_unichar(class_id),
height, min_bottom, max_bottom, min_top, max_top,
bottom, top);
}
// Use only chars that fit in the expected bottom range, and where
// the range of tops is sensibly near the xheight.
if (min_bottom <= bottom + x_ht_acceptance_tolerance &&
bottom - x_ht_acceptance_tolerance <= max_bottom &&
min_top > kBlnBaselineOffset &&
max_top - kBlnBaselineOffset >= kBlnXHeight &&
misfit_dist > 0) {
// Compute the x-height position using proportionality between the
// actual height and expected height.
int min_xht = DivRounded(height * kBlnXHeight,
max_top - kBlnBaselineOffset);
int max_xht = DivRounded(height * kBlnXHeight,
min_top - kBlnBaselineOffset);
if (debug_x_ht_level >= 2) {
tprintf(" xht range min=%d, max=%d\n", min_xht, max_xht);
}
// The range of expected heights gets a vote equal to the distance
// of the actual top from the expected top.
for (int y = min_xht; y <= max_xht; ++y)
top_stats.add(y, misfit_dist);
} else if ((min_bottom > bottom + x_ht_acceptance_tolerance ||
bottom - x_ht_acceptance_tolerance > max_bottom) &&
bottom_shift == 0) {
// Get the range of required bottom shift.
int min_shift = min_bottom - bottom;
int max_shift = max_bottom - bottom;
if (debug_x_ht_level >= 2) {
tprintf(" bottom shift min=%d, max=%d\n", min_shift, max_shift);
}
// The range of expected shifts gets a vote equal to the min distance
// of the actual bottom from the expected bottom, spread over the
// range of its acceptance.
int misfit_weight = abs(min_shift);
if (max_shift > min_shift)
misfit_weight /= max_shift - min_shift;
for (int y = min_shift; y <= max_shift; ++y)
shift_stats.add(y, misfit_weight);
} else {
if (bottom_shift == 0) {
// Things with bottoms that are already ok need to say so, on the
// 1st iteration only.
shift_stats.add(0, kBlnBaselineOffset);
}
if (debug_x_ht_level >= 2) {
tprintf(" already OK\n");
}
}
}
}
if (shift_stats.get_total() > top_stats.get_total()) {
bottom_shift = IntCastRounded(shift_stats.median());
if (debug_x_ht_level >= 2) {
tprintf("Applying bottom shift=%d\n", bottom_shift);
}
}
} while (bottom_shift != 0 &&
top_stats.get_total() < shift_stats.get_total());
// Baseline shift is opposite sign to the bottom shift.
*baseline_shift = -bottom_shift / word_res->denorm.y_scale();
if (debug_x_ht_level >= 2) {
tprintf("baseline shift=%g\n", *baseline_shift);
}
if (top_stats.get_total() == 0)
return bottom_shift != 0 ? word_res->x_height : 0.0f;
// The new xheight is just the median vote, which is then scaled out
// of BLN space back to pixel space to get the x-height in pixel space.
float new_xht = top_stats.median();
if (debug_x_ht_level >= 2) {
tprintf("Median xht=%f\n", new_xht);
tprintf("Mode20:A: New x-height = %f (norm), %f (orig)\n",
new_xht, new_xht / word_res->denorm.y_scale());
}
// The xheight must change by at least x_ht_min_change to be used.
if (fabs(new_xht - kBlnXHeight) >= x_ht_min_change)
return new_xht / word_res->denorm.y_scale();
else
return bottom_shift != 0 ? word_res->x_height : 0.0f;
}
