@Override
public void extractFeatures(List regions) throws FeatureExtractorException {
for (Region r : (List<Region>) regions) {
if (r.hasAttribute(feature)) {
Contour super_c = (Contour) r.getAttribute(feature);
Contour c;
try {
c = ContourUtils.getSubContour(super_c, r.getStart(), r.getEnd());
} catch (AuToBIException e) {
throw new FeatureExtractorException(e.getMessage());
}
CurveShape falling = smooth(-1, true, c);
CurveShape rising = smooth(c.size(), true, c);
CurveShape best_peak = null;
double min_peak_rmse = Double.MAX_VALUE;
// Sample the curve at at most 20 points to calculate peak and valley likelihoods.
// On long regions calculating at every point gets *very* slow.
int step = Math.max(1, c.size() / 20);
for (int i = 1; i < c.size() - 1; i += step) {
CurveShape peak = smooth(i, true, c);
if (peak.rmse < min_peak_rmse) {
best_peak = peak;
min_peak_rmse = peak.rmse;
}
}
CurveShape best_valley = null;
double min_valley_rmse = Double.MAX_VALUE;
for (int i = 1; i < c.size() - 1; i += step) {
CurveShape valley = smooth(i, false, c);
if (valley.rmse < min_valley_rmse) {
best_valley = valley;
min_valley_rmse = valley.rmse;
}
}
r.setAttribute("risingCurve[" + feature + "]", rising);
r.setAttribute("fallingCurve[" + feature + "]", falling);
r.setAttribute("peakCurve[" + feature + "]", best_peak);
r.setAttribute("valleyCurve[" + feature + "]", best_valley);
}
}
}
private CurveShape smooth(int p, boolean isPeak, Contour c) {
CurveShape curve = new CurveShape(p, isPeak);
if (p > 0 && p < c.size() && c.isEmpty(p)) {
curve.rmse = Double.MAX_VALUE;
return curve;
}
// reflect values around the peak
double[] v = new double[c.size()];
for (int i = 0; i < c.size(); ++i) {
if (!c.isEmpty(i)) {
if (i >= p) {
if (p < 0) {
v[i] = -c.get(i);
} else {
v[i] = 2 * c.get(p) - c.get(i);
}
} else {
v[i] = c.get(i);
}
if (!isPeak) {
v[i] = -v[i];
}
} else {
v[i] = Double.NaN;
}
}
ArrayList<Block> pava_blocks = new ArrayList<Block>();
// initialize blocks
for (int i = 0; i < c.size(); ++i) {
if (!Double.isNaN(v[i])) {
pava_blocks.add(new Block(i, i, v[i]));
}
}
// Merge blocks using PAVA
boolean done = false;
boolean increasing = true;
int idx = 1;
int start_merge = -1, end_merge = -1;
while (!done) {
while (idx < pava_blocks.size()) {
// monotonically increasing.
if (pava_blocks.get(idx - 1).x < pava_blocks.get(idx).x) {
if (!increasing) {
// merge
break;
}
} else if (pava_blocks.get(idx - 1).x > pava_blocks.get(idx).x) {
if (increasing) {
start_merge = idx - 1;
}
end_merge = idx;
increasing = false;
}
idx++;
}
done = true;
if (start_merge != end_merge) {
// merge blocks
double value = 0.0;
for (int i = start_merge; i <= end_merge; ++i) {
value +=
pava_blocks.get(i).x * (pava_blocks.get(i).high_idx - pava_blocks.get(i).low_idx + 1);
}
value /= (pava_blocks.get(end_merge).high_idx - pava_blocks.get(start_merge).low_idx + 1);
Block new_block =
new Block(
pava_blocks.get(start_merge).low_idx, pava_blocks.get(end_merge).high_idx, value);
// remove the old blocks
while (start_merge <= end_merge) {
pava_blocks.remove(start_merge);
end_merge--;
}
// replace with the new, merged block
pava_blocks.add(start_merge, new_block);
done = false;
// Reset
idx = 1;
start_merge = -1;
end_merge = -1;
increasing = true;
}
}
// Generate a smooth contour from block representation
double[] smoothed = new double[c.size()];
for (Block b : pava_blocks) {
for (int i = b.low_idx; i <= b.high_idx; ++i) {
if (!c.isEmpty(i)) {
if (i >= p) {
if (p < 0) {
smoothed[i] = -b.x;
} else {
if (!isPeak) {
smoothed[i] = 2 * -c.get(p) - b.x;
} else {
smoothed[i] = 2 * c.get(p) - b.x;
}
}
} else {
smoothed[i] = b.x;
}
}
if (!isPeak) {
smoothed[i] = -smoothed[i];
}
}
}
// Calculate RMSE
double rmse = 0.0;
for (int i = 0; i < c.size(); ++i) {
if (!c.isEmpty(i)) {
rmse += (c.get(i) - smoothed[i]) * (c.get(i) - smoothed[i]);
}
}
rmse /= c.contentSize();
rmse = Math.sqrt(rmse);
curve.rmse = rmse;
curve.smoothed_curve = smoothed;
return curve;
}