void Trajectory::shiftIntoBox(Positions &p) {
if (p.getBox().empty()) return;
const vector<Vector3D> &box = p.getBox();
if (offsets.size() < p.size()) offsets.resize(p.size());
// NOTE: This method was stolen from:
// gromacs-4.5.4/src/gmxlib/rmpbc.c:rm_gropbc()
// With the difference that we are accumulating offsets over the whole
// trajectory.
for (unsigned n = 1; n < p.size(); n++) {
Vector3D orig = p[n];
p[n] += offsets[n];
for (int m = 2; 0 <= m; m--) {
double dist;
while (0.75 * box[m][m] < fabs(dist = p[n][m] - p[n - 1][m])) {
if (10 * box[m][m] < fabs(dist)) break; // Ignore unreasonable
if (0 < dist) for (int d = 0; d <= m; d++) p[n][d] -= box[m][d];
else for (int d = 0; d <= m; d++) p[n][d] += box[m][d];
}
}
offsets[n] = p[n] - orig;
LOG_DEBUG(5, "SHIFT: " << n << ' ' << p[n] << ' ' << offsets[n]);
}
}
static double alignment(const Positions &p1, const Positions &p2) {
// Computes a metric of how aligned the two sets of positions are
double d = 0;
// Only consider every 8th position for better performance
for (unsigned i = 1; i < p1.size(); i += 8)
d += p1[i].distanceSquared(p2[i]);
return sqrt(d) * 8 / p1.size();
}
void DoubleTapDetector::initGesture(const Positions& positions)
{
if (!_canBeDoubleTap)
{
// adding initial points
if (positions.size() > _touchStartPos.size())
{
if (_touchStartPos.empty())
_startGesture(positions);
else
_touchStartPos = positions;
return;
}
// all points released, decide if potential double tap or abort
if (positions.empty())
{
_canBeDoubleTap = _doubleTapTimer.isActive();
if (!_canBeDoubleTap)
cancelGesture();
}
return;
}
// points pressed again, check for double tap
if (positions.size() == _touchStartPos.size() &&
!MathUtils::hasMoved(positions, _touchStartPos, _doubleTapThresholdPx))
{
emit doubleTap(MathUtils::computeCenter(_touchStartPos),
_touchStartPos.size());
_doubleTapTimer.stop();
}
// all points released, reset everything for next detection
if (positions.empty())
cancelGesture();
}
void Trajectory::alignToLast(Positions &p) {
// This function uses a random search, similar to simulated annealing, to
// find a rotation of the current positions which is close to the previous.
// This helps stabilize the view of the protein and improve interpolation
// between frames.
if (empty() || p.empty()) return;
const Positions &last = *back();
double align = alignment(p, last);
double start = align;
double angle = 2 * M_PI;
unsigned rounds = 64;
const double magicStoppingPoint = 0.3;
double rate = pow(4.0 / 360.0, 1.0 / rounds); // Within 4 degrees
for (unsigned j = 0; magicStoppingPoint < align && j < rounds; j++) {
for (unsigned l = 0; l < 2; l++) {
uint8_t r = Random::instance().rand<uint8_t>();
Vector3D v(!(r & 1), !(r & 2), !(r & 4));
AxisAngleD a(angle * l ? -1 : 1, v.normalize());
// Rotate
Positions tmp(p);
for (unsigned i = 0; i < p.size(); i++)
tmp[i] = a.rotate(tmp[i]);
// Recheck
double newAlign = alignment(tmp, last);
if (newAlign < align) {
// Accept
align = newAlign;
p = tmp;
}
}
angle *= rate;
}
if (magicStoppingPoint <= start)
LOG_DEBUG(3, "Alignment start=" << start << " end=" << align << " improved "
<< String::printf("%0.2f%%", (1.0 - align / start) * 100));
}