void PoissonSubstitutionProcess::AddMeanSuffStat(double*** down, double*** up, double*** at, double branchlength, double* meanratecount, double* meanratebeta, double& meanlengthcount, double& meanlengthbeta, double** meanprofilecount, int* nonmissing, double* weight) {
for (int i=GetSiteMin(); i<GetSiteMax(); i++) {
if (ActiveSite(i)) {
double extw = 1.0;
if (weight) {
extw = weight[i];
}
if (nonmissing[i] == 2) {
if (branchlength) {
cerr << "error: non root for missing 2\n";
exit(1);
}
int nstate = GetNstate(i);
int j = ratealloc[i];
double* a = at[i][j];
double totz[nstate];
double tot = 0;
for (int k=0; k<nstate; k++) {
totz[k] = a[k];
tot += totz[k];
}
for (int k=0; k<nstate; k++) {
totz[k] /= tot;
}
AddZipToTrueMeanProfileSuffStat(i,totz,meanprofilecount[i],extw);
}
else if (nonmissing[i] == 1) {
if (! down) {
cerr << "error in PoissonSubstitutionProcess::AddMeanSuffStat: non root calculation called on root\n";
exit(1);
}
if (! branchlength) {
cerr << "error: root for missing 1\n";
exit(1);
}
int nstate = GetNstate(i);
const double* stat = GetStationary(i);
double rate = GetRate(i);
double length = rate * branchlength;
double e = exp(-length);
int j = ratealloc[i];
double* d = down[i][j];
double* u = up[i][j];
double totw = 0;
double totn = 0;
double totz[nstate];
for (int k=0; k<nstate; k++) {
totz[k] = 0;
}
double hidden = 0;
for (int k=0; k<nstate; k++) {
for (int l=0; l<nstate; l++) {
if (k == l) {
double w = stat[k] * d[k] * u[l] * (e + (1-e)*stat[l]);
totw += w;
double n = length * stat[k] / (e + (1-e)*stat[k]);
double z = (1-e) * stat[k] / (e + (1-e)*stat[k]);
totn += w * n;
totz[l] += w * z;
hidden += w * (n-z);
}
else {
double w = stat[k] * d[k] * u[l] * (1-e) * stat[l];
totw += w;
double n = 0;
if (length < 1e-8) {
n = 1;
}
else {
n = length / (1-e);
}
double z = 1;
totn += w * n;
totz[l] += w * z;
hidden += w * (n-z);
}
}
}
if (totw) {
totn /= totw;
}
else {
totn = 0;
}
if (isnan(totn)) {
cerr << "totn is nan\n";
cerr << totw << '\n';
exit(1);
}
double total = 0;
for (int k=0; k<nstate; k++) {
totz[k] += hidden * stat[k];
if (totw) {
totz[k] /= totw;
}
else {
totz[k] = 0;
}
total += totz[k];
}
if (fabs(total - totn) > 1e-6) {
cerr << "error in total count in PoissonSubstitutionProcess::AddMeanSuffStat\n";
exit(1);
}
AddZipToTrueMeanProfileSuffStat(i,totz,meanprofilecount[i],extw);
meanratecount[i] += extw * totn;
meanratebeta[i] += extw * branchlength;
meanlengthcount += extw * totn;
meanlengthbeta += extw * rate;
}
}
}
}
STDMETHODIMP CStreamSwitcherPassThru::GetRate(double* pdRate)
{
CallPeerSeeking(GetRate(pdRate));
}
void TranscriptionToolBar::OnAutomateSelection(wxCommandEvent & WXUNUSED(event))
{
//If IO is busy, abort immediately
if (gAudioIO->IsBusy())
{
SetButton(false,mButtons[TTB_EndOff]);
return;
}
wxBusyCursor busy;
mVk->AdjustThreshold(GetSensitivity());
AudacityProject *p = GetActiveProject();
TrackList *tl = p->GetTracks();
TrackListOfKindIterator iter(Track::Wave, tl);
Track *t = iter.First(); //Make a track
if(t)
{
auto wt = static_cast<const WaveTrack*>(t);
sampleCount start, len;
GetSamples(wt, &start, &len);
//Adjust length to end if selection is null
if(len == 0)
{
len = start;
start = 0;
}
sampleCount lastlen = 0;
double newStartPos, newEndPos;
//This is the minumum word size in samples (.05 is 50 ms)
int minWordSize = (int)(wt->GetRate() * .05);
//Continue until we have processed the entire
//region, or we are making no progress.
while(len > 0 && lastlen != len)
{
lastlen = len;
auto newStart = mVk->OnForward(*wt, start, len);
//JKC: If no start found then don't add any labels.
if( newStart==start)
break;
//Adjust len by the NEW start position
len -= (newStart - start);
//Adjust len by the minimum word size
len -= minWordSize;
//OK, now we have found a NEW starting point. A 'word' should be at least
//50 ms long, so jump ahead minWordSize
auto newEnd =
mVk->OffForward(*wt, newStart + minWordSize, len);
//If newEnd didn't move, we should give up, because
// there isn't another end before the end of the selection.
if(newEnd == (newStart + minWordSize))
break;
//Adjust len by the NEW word end
len -= (newEnd - newStart);
//Calculate the start and end of the words, in seconds
newStartPos = newStart.as_double() / wt->GetRate();
newEndPos = newEnd.as_double() / wt->GetRate();
//Increment
start = newEnd;
p->DoAddLabel(SelectedRegion(newStartPos, newEndPos));
p->RedrawProject();
}
SetButton(false, mButtons[TTB_AutomateSelection]);
}
}
