/**
* Transforms the specified array of times and marks. Known samples are those for which times are
* zero, and times and marks for these known samples are used to compute times and marks for
* unknown samples.
*
* @param times input/output array of times.
* @param marks input/output array of marks.
*/
public void apply(float[][][] times, int[][][] marks) {
// Measure elapsed time in seconds.
Stopwatch sw = new Stopwatch();
sw.start();
log.fine("TimeMarker3.apply: begin time=" + (int) sw.time());
// Initialize all unknown times to infinity.
for (int i3 = 0; i3 < _n3; ++i3) {
for (int i2 = 0; i2 < _n2; ++i2) {
for (int i1 = 0; i1 < _n1; ++i1) {
if (times[i3][i2][i1] != 0.0f) times[i3][i2][i1] = INFINITY;
}
}
}
// Indices of known samples in random order.
short[][] kk = indexKnownSamples(times);
short[] k1 = kk[0];
short[] k2 = kk[1];
short[] k3 = kk[2];
shuffle(k1, k2, k3);
int nk = k1.length;
// Array for the eikonal solution times.
float[][][] t = new float[_n3][_n2][_n1];
// Active list of samples used to compute times.
ActiveList al = new ActiveList();
// For all known samples, ...
for (int ik = 0; ik < nk; ++ik) {
if (ik % (1 + (nk - 1) / 100) == 0)
log.fine(" apply: ik/nk=" + ik + "/" + nk + " time=" + (int) sw.time());
int i1 = k1[ik];
int i2 = k2[ik];
int i3 = k3[ik];
// Clear activated flags so we can tell which samples become activated.
clearActivated();
// Put the known sample with time zero into the active list.
t[i3][i2][i1] = 0.0f;
al.append(_s[i3][i2][i1]);
// The mark for the known sample.
int m = marks[i3][i2][i1];
// Process the active list until empty.
solve(al, t, m, times, marks);
}
// Log elapsed time.
sw.stop();
log.fine("TimeMarker3.apply: end time=" + (int) sw.time());
}
/*
* Solves for times by processing samples in the active list in parallel.
*/
private void solveParallel(
final ActiveList al,
final float[][][] t,
final int m,
final float[][][] times,
final int[][][] marks) {
int mbmin = 64; // target minimum number of samples per block
int nbmax = 256; // maximum number of blocks
final float[][] dtask = new float[nbmax][];
final ActiveList[] bltask = new ActiveList[nbmax];
while (!al.isEmpty()) {
final int n = al.size(); // number of samples in active (A) list
final int mbmax = max(mbmin, 1 + (n - 1) / nbmax); // max samples per block
final int nb = 1 + (n - 1) / mbmax; // number of blocks <= nbmax
final int mb = 1 + (n - 1) / nb; // evenly distribute samples per block
Parallel.loop(
nb,
new Parallel.LoopInt() { // for all blocks, ...
public void compute(int ib) {
if (bltask[ib] == null) { // if necessary for this block, make ...
dtask[ib] = new float[6]; // work array for tensor coefficients
bltask[ib] = new ActiveList(); // and an empty active list
}
int i = ib * mb; // beginning of block
int j = min(i + mb, n); // beginning of next block (or end)
for (int k = i; k < j; ++k) { // for each sample in block, ...
Sample s = al.get(k); // get k'th sample from A list
solveOne(t, m, times, marks, s, bltask[ib], dtask[ib]); // do sample
}
bltask[ib].setAllAbsent(); // needed when merging B lists below
}
});
// Merge samples from all B lists to a new A list. All samples
// in B lists are currently marked as absent in the A list. As
// samples in B lists are appended to the A list, their absent
// flags are set to false, so that no sample is appended more
// than once to the new A list.
al.clear();
for (int ib = 0; ib < nb; ++ib) {
if (bltask[ib] != null) {
al.appendIfAbsent(bltask[ib]);
bltask[ib].clear();
}
}
}
}
void appendIfAbsent(ActiveList al) {
if (_n + al._n > _a.length) growTo(2 * (_n + al._n));
int n = al._n;
for (int i = 0; i < n; ++i) {
Sample s = al.get(i);
if (s.absent) {
_a[_n++] = s;
s.absent = false;
}
}
}
/*
* Solves for times by sequentially processing each sample in active list.
*/
private void solveSerial(
ActiveList al, float[][][] t, int m, float[][][] times, int[][][] marks) {
float[] d = new float[6];
ActiveList bl = new ActiveList();
int ntotal = 0;
while (!al.isEmpty()) {
// al.shuffle(); // demonstrate that solution depends on order
int n = al.size();
ntotal += n;
for (int i = 0; i < n; ++i) {
Sample s = al.get(i);
solveOne(t, m, times, marks, s, bl, d);
}
bl.setAllAbsent();
al.clear();
al.appendIfAbsent(bl);
bl.clear();
}
trace("solveSerial: ntotal=" + ntotal);
trace(" nratio=" + (float) ntotal / (float) (_n1 * _n2 * _n3));
}
/*
* Processes one sample from the A list.
* Appends samples not yet converged to the B list.
*/
private void solveOne(
float[][][] t,
int m,
float[][][] times,
int[][][] marks,
Sample s,
ActiveList bl,
float[] d) {
// Sample indices.
int i1 = s.i1;
int i2 = s.i2;
int i3 = s.i3;
// Current time and new time computed from all four neighbors.
float ti = currentTime(t, i1, i2, i3);
float ci = computeTime(t, i1, i2, i3, K1S[6], K2S[6], K3S[6], d);
t[i3][i2][i1] = ci;
// If new and current times are close enough (converged), then ...
if (ci >= ti * ONE_MINUS_EPSILON) {
// Neighbors may need to be activated if computed time is small
// relative to the minimum time computed so far. The factor 1.5
// improves accuracy for large anisotropy. Cost increases as the
// square of this factor, so we do not want it to be too large.
boolean checkNabors = ci <= 1.5f * times[i3][i2][i1];
// If computed time less than minimum time, mark this sample.
if (ci < times[i3][i2][i1]) {
times[i3][i2][i1] = ci;
marks[i3][i2][i1] = m;
}
// If necessary, check the neighbors.
if (checkNabors) {
// For all six neighbors, ...
for (int k = 0; k < 6; ++k) {
// Neighbor sample indices; skip if out of bounds.
int j1 = i1 + K1[k];
if (j1 < 0 || j1 >= _n1) continue;
int j2 = i2 + K2[k];
if (j2 < 0 || j2 >= _n2) continue;
int j3 = i3 + K3[k];
if (j3 < 0 || j3 >= _n3) continue;
// Skip neighbor sample if computed time would be too big.
// if (!doComputeTime(t,times,j1,j2)) continue;
// Current and computed times for the neighbor.
float tj = currentTime(t, j1, j2, j3);
float cj = computeTime(t, j1, j2, j3, K1S[k], K2S[k], K3S[k], d);
// If computed time is significantly less than current time, ...
if (cj < tj * ONE_MINUS_EPSILON) {
// Replace the current time.
t[j3][j2][j1] = cj;
// Append neighbor to the B list, thereby activating it.
bl.append(_s[j3][j2][j1]);
}
}
}
}
// Else, if not converged, append this sample to the B list.
else {
bl.append(s);
}
}
/*
* Solves for times by processing samples in the active list in parallel.
*/
private void solveParallelX(
final ActiveList al,
final float[][][] t,
final int m,
final float[][][] times,
final int[][][] marks) {
int nthread = Runtime.getRuntime().availableProcessors();
ExecutorService es = Executors.newFixedThreadPool(nthread);
CompletionService<Void> cs = new ExecutorCompletionService<Void>(es);
ActiveList[] bl = new ActiveList[nthread];
float[][] d = new float[nthread][];
for (int ithread = 0; ithread < nthread; ++ithread) {
bl[ithread] = new ActiveList();
d[ithread] = new float[6];
}
final AtomicInteger ai = new AtomicInteger();
int ntotal = 0;
// int niter = 0;
while (!al.isEmpty()) {
ai.set(0); // initialize the shared block index to zero
final int n = al.size(); // number of samples in active (A) list
ntotal += n;
final int mb = 32; // size of blocks of samples
final int nb = 1 + (n - 1) / mb; // number of blocks of samples
int ntask = min(nb, nthread); // number of tasks (threads to be used)
for (int itask = 0; itask < ntask; ++itask) { // for each task, ...
final ActiveList bltask = bl[itask]; // task-specific B list
final float[] dtask = d[itask]; // task-specific work array
cs.submit(
new Callable<Void>() { // submit new task
public Void call() {
for (int ib = ai.getAndIncrement(); ib < nb; ib = ai.getAndIncrement()) {
int i = ib * mb; // beginning of block
int j = min(i + mb, n); // beginning of next block (or end)
for (int k = i; k < j; ++k) { // for each sample in block, ...
Sample s = al.get(k); // get k'th sample from A list
solveOne(t, m, times, marks, s, bltask, dtask); // process sample
}
}
bltask.setAllAbsent(); // needed when merging B lists below
return null;
}
});
}
try {
for (int itask = 0; itask < ntask; ++itask) cs.take();
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
// Merge samples from all B lists to a new A list. As samples
// are appended, their absent flags are set to false, so that
// each sample is appended no more than once to the new A list.
al.clear();
for (int itask = 0; itask < ntask; ++itask) {
al.appendIfAbsent(bl[itask]);
bl[itask].clear();
}
// ++niter;
}
es.shutdown();
// trace("solveParallel: ntotal="+ntotal);
// trace(" nratio="+(float)ntotal/(float)(_n1*_n2*_n3));
}