private void setup()
{
this.Length = _values.Count;
this.WarpingWindow = calculateWarpingWindow(this.Length, _warpingWindow);
_sortingBuffer = new OrderedVector[this.Length];
BaseValues = new MDVector[this.Length];
OrderedValues = new MDVector[this.Length];
Ordered = new int[this.Length];
_envelope = new LemireEnvelope(this.Length, this.WarpingWindow, _dimensions);
OrderedUpperEnvelope = new MDVector[this.Length];
OrderedLowerEnvelope = new MDVector[this.Length];
for (int i = 0; i < this.Length; i++)
{
this.BaseValues[i] = _values[i];
_sortingBuffer[i] = new OrderedVector()
{
Vector = _values[i], Index = i
};
OrderedValues[i] = new MDVector(_dimensions);
OrderedUpperEnvelope[i] = new MDVector(_dimensions);
OrderedLowerEnvelope[i] = new MDVector(_dimensions);
}
}
public DTWResult warp(Query query)
{
//prepare/reset knn search:
jumpsize = query.Length;
wk = 0;
_wk = 0;
lastloc = 0;
for (int tmpk = 0; tmpk < bestk; tmpk++)
{
_kvec[tmpk] = double.PositiveInfinity;
_lvec[tmpk] = 0;
}
double bsf; // best-so-far
MDVector[] t; // data array
MDVector[] tz, cb, cb1, cb2;
MDVector d;
int i, j;
int dataIndex = 0;
int matchIndex = 0;
int kim = 0, keogh = 0, keogh2 = 0;
double distance = 0;
// prepare query object
query.process();
cb = new MDVector[query.Length];
cb1 = new MDVector[query.Length];
cb2 = new MDVector[query.Length];
t = new MDVector[query.Length * 2];
for (i = 0; i < t.Length; i++)
{
t[i] = new MDVector(_dimensions);
}
tz = new MDVector[query.Length];
for (i = 0; i < tz.Length; i++)
{
tz[i] = new MDVector(_dimensions);
}
// Initialize the cummulative lower bound
for (i = 0; i < query.Length; i++)
{
cb[i] = new MDVector(_dimensions);
cb[i].set(0);
cb1[i] = new MDVector(_dimensions);
cb1[i].set(0);
cb2[i] = new MDVector(_dimensions);
cb2[i].set(0);
}
// Initialize
bsf = double.PositiveInfinity;
i = 0; /// current index of the data in current chunk of size EPOCH
j = 0; /// the starting index of the data in the circular array, t
ex.set(0);
ex2.set(0);
bool done = false;
int it = 0, ep = 0, k = 0;
int I; /// the starting index of the data in current chunk of size EPOCH
LemireEnvelope lemireEnvelope = new LemireEnvelope(EPOCH, query.WarpingWindow, _dimensions);
DTWCalculator dtwCalculator = new DTWCalculator(query.Length, query.WarpingWindow, _dimensions);
while (!done)
{
// Read first query.Length-1 points
ep = 0;
if (it == 0)
{
for (k = 0; k < query.Length - 1; k++)
{
if (dataIndex < _data.Count)
{
buffer[k].set(_data[dataIndex++]);
}
}
}
else
{
for (k = 0; k < query.Length - 1; k++)
{
buffer[k].set(buffer[EPOCH - query.Length + 1 + k]);
}
}
// Read buffer of size EPOCH or when all data has been read.
ep = query.Length - 1;
while (ep < EPOCH)
{
if (dataIndex >= _data.Count)
{
break;
}
buffer[ep].set(_data[dataIndex++]);
ep++;
}
// Data are read in chunk of size EPOCH.
// When there is nothing to read, the loop is end.
if (ep <= query.Length - 1)
{
done = true;
}
else
{
lemireEnvelope.process(buffer, ep);
/// Do main task here..
ex.set(0);
ex2.set(0);
for (i = 0; i < ep; i++)
{
// A bunch of data has been read and pick one of them at a time to use
d = buffer[i];
// Calcualte sum and sum square
ex = MDVector.add(ex, d, ex);
result = MDVector.multiply(d, d, result);
ex2 = MDVector.add(ex2, result, ex2);
// t is a circular array for keeping current data
t[i % query.Length].set(d);
// double the size for avoiding using modulo "%" operator
t[(i % query.Length) + query.Length].set(d);
// Start the task when there are more than query.Length-1 points in the current chunk
if (i >= query.Length - 1)
{
mean = MDVector.divide(ex, query.Length, mean);
std = MDVector.divide(ex2, query.Length, std);
mean2 = MDVector.multiply(mean, mean, mean2);
std = MDVector.subtract(std, mean2, std);
std.sqrt();
// compute the start location of the data in the current circular array, t
j = (i + 1) % query.Length;
// the start location of the data in the current chunk
I = i - (query.Length - 1);
// Use a constant lower bound to prune the obvious subsequence
lb_kim = _kimLb.hierarchy(t, query.BaseValues, j, query.Length, mean, std, bsf);
if (lb_kim < bsf)
{
// Use a linear time lower bound to prune; z_normalization of t will be computed on the fly.
// uo, lo are envelop of the query.
lb_k = _keoghLb.cumulative(query.Ordered, t, query.OrderedUpperEnvelope, query.OrderedLowerEnvelope, cb1, j, query.Length, mean, std, bsf);
if (lb_k < bsf)
{
// Take another linear time to compute z_normalization of t.
// Note that for better optimization, this can merge to the previous function.
for (k = 0; k < query.Length; k++)
{
tz[k] = Utilities.normalize(t[(k + j)], mean, std, tz[k]);
}
// Use another lb_keogh to prune
// qo is the sorted query. tz is unsorted z_normalized data.
// l_buff, u_buff are big envelop for all data in this chunk
lb_k2 = _keoghLb.dataCumulative(query.Ordered, query.OrderedValues, cb2, lemireEnvelope.Lower, lemireEnvelope.Upper, I, query.Length, mean, std, bsf);
if (lb_k2 < bsf)
{
// Choose better lower bound between lb_keogh and lb_keogh2 to be used in early abandoning DTW
// Note that cb and cb2 will be cumulative summed here.
if (lb_k > lb_k2)
{
cb[query.Length - 1].set(cb1[query.Length - 1]);
for (k = query.Length - 2; k >= 0; k--)
{
cb[k] = MDVector.add(cb[k + 1], cb1[k], cb[k]);
}
}
else
{
cb[query.Length - 1].set(cb2[query.Length - 1]);
for (k = query.Length - 2; k >= 0; k--)
{
cb[k] = MDVector.add(cb[k + 1], cb2[k], cb[k]);
}
}
// Compute DTW and early abandoning if possible
distance = dtwCalculator.distance(tz, query.BaseValues, cb, bsf);
if (distance < bsf)
{
// Update bsf
// loc is the real starting location of the nearest neighbor in the file
matchIndex = (it) * (EPOCH - query.Length + 1) + i - query.Length + 1;
if (bestk == 1)
{
_kvec[0] = bsf;
_lvec[0] = matchIndex;
bsf = distance;
}
else
{
bsf = ucr_set_knn(distance, matchIndex);
}
}
}
else
{
keogh2++;
}
}
else
{
keogh++;
}
}
else
{
kim++;
}
// Reduce absolute points from sum and sum square
ex = MDVector.subtract(ex, t[j], ex);
result = MDVector.multiply(t[j], t[j], result);
ex2 = MDVector.subtract(ex2, result, ex2);
}
}
// If the size of last chunk is less than EPOCH, then no more data and terminate.
if (ep < EPOCH)
{
done = true;
}
else
{
it++;
}
}
}
Array.Sort(_kvec, _lvec);
return(new DTWResult()
{
Locations = _lvec, Distances = _kvec
});
}
