public static void Main(string[] args)
{
if (args.Length == 3)
{
ROOT_DIR = args[0];
NUM_TIMESERIES = int.Parse(args[1]);
NEWSPLITPOLICY = bool.Parse(args[2]);
}
InitalizeGlobalSettings();
//BaseIndex();
// Test 1 - Reading from GeneratedRawDataIndex
/*Index<RawDataFormat> testIndex = Index<RawDataFormat>.Load(Globals.IndexRootDir);
* Double[] query = Util.RandomWalk(2);
* IndexEntry result = testIndex.ApproximateSearch(query);
* List<RawDataFormat> timeSeries = testIndex.ReturnDataFormatFromTermEntry((TermEntry)result);*/
// Test 2 - Reading from FileRawDataLoader
//const string DATA_FILE = @"/Users/ppo/Documents/Thesis/test";
const string DATA_FILE = @"/Users/ppo/Dropbox/Thesis/datasets/SonyAIBORobotSurfaceII/SonyAIBORobotSurfaceII_TRAIN_SHAPELET_32_space";
Index <RawShapeletFormat> anotherIndex = new Index <RawShapeletFormat>(0, new IndexOptions("root"));
DataLoader dl = new FromFileRawShapeletLoader(anotherIndex, DATA_FILE, 10000);
InsertTimeSeries(dl);
Index <RawShapeletFormat> .Save(Globals.IndexRootDir, anotherIndex);
Index <RawShapeletFormat> loadBack = Index <RawShapeletFormat> .Load(Globals.IndexRootDir);
OutputIndex(loadBack, "root");
using (StreamWriter sw = new StreamWriter(Path.Combine(Globals.IndexRootDir, "indexOutput.csv"))) {
sw.Write(output);
}
/*foreach (IndexEntry i in anotherIndex.GetIndexEntries()) {
* if (i is TermEntry) {
* ((TermEntry)i).ToString();
* } else {
* foreach (IndexEntry j in ((SplitEntry<RawShapeletFormat>)i).GetIndexEntries())
* {
* if (j is TermEntry)
* {
* ((TermEntry)j).ToString();
* } else {
* ((SplitEntry<RawShapeletFormat>)j).GetIndexEntries();
* }
* }
* }
* }*/
for (int i = 0; i < 100; i++)
{
Double[] query = Util.RandomWalk(4);
IndexEntry result = anotherIndex.ApproximateSearch(query);
List <RawShapeletFormat> timeSeries = anotherIndex.ReturnDataFormatFromTermEntry((TermEntry)result);
}
//Console.WriteLine("Press Enter to exit program.");
//Console.ReadLine();
}
public static void TinyImagesExperiment()
{
Index <Meta1DataFormat> si = Index <Meta1DataFormat> .Load(Globals.IndexRootDir);
string queryFile = @"F:\Exp\TinyImages_256Len_8Word_2KThreshold\_queries\queries.txt";
List <double[]> queries = Util.ReadFiletoDoubleList(queryFile, false);
for (int i = 0; i < queries.Count; ++i)
{
queries[i] = Util.NormalizationHandler(Util.DownSample(queries[i], TinyImagesDataLoader.DOWNSAMPLERATE));
if (queries[i].Length != Globals.TimeSeriesLength)
{
throw new ApplicationException("queries[i].Length != Globals.TimeSeriesLength");
}
TermEntry res = si.ApproximateSearch(queries[i]);
Console.WriteLine("Query:{0} FileName:{1}", i, res.FileName);
List <Meta1DataFormat> metas = si.ReturnDataFormatFromTermEntry(res);
double bsf = Double.MaxValue;
Meta1DataFormat bsfMeta = new Meta1DataFormat();
foreach (Meta1DataFormat m in metas)
{
double dist = Util.EuclideanDistance(m.GetTimeSeries(), queries[i]);
if (dist < bsf)
{
bsf = dist;
bsfMeta = m;
}
}
Console.WriteLine("BsfDist:{0} LocMeta:{1}", bsf, bsfMeta.meta);
}
}
public static void InsectExperiment()
{
Index <Meta3DataFormat> si = Index <Meta3DataFormat> .Load(Globals.IndexRootDir);
string queryFile = @"C:\Temp\insect\queries.txt";
List <double[]> queries = Util.ReadFiletoDoubleList(queryFile, true);
using (StreamWriter sw = new StreamWriter(@"C:\Temp\insect\output.txt"))
{
for (int i = 0; i < queries.Count; ++i)
{
if (queries[i].Length != Globals.TimeSeriesLength)
{
throw new ApplicationException("queries[i].Length != Globals.TimeSeriesLength");
}
TermEntry res = si.ApproximateSearch(queries[i]);
Console.WriteLine("Query:{0} FileName:{1}", i, res.FileName);
List <Meta3DataFormat> metas = si.ReturnDataFormatFromTermEntry(res);
double bsf = Double.MaxValue;
Meta3DataFormat bsfMeta = new Meta3DataFormat();
foreach (Meta3DataFormat m in metas)
{
double dist = Util.EuclideanDistance(m.GetTimeSeries(), queries[i]);
if (dist < bsf)
{
bsf = dist;
bsfMeta = m;
}
}
Console.WriteLine("BsfDist:{0} Meta1:{1} Meta2:{2}", bsf, bsfMeta.meta1, bsfMeta.meta2);
sw.WriteLine(Util.ArrayToString(queries[i]));
sw.WriteLine(Util.ArrayToString(bsfMeta.GetTimeSeries()));
}
}
}
/// <summary>
/// Builds an index with randomly generated time series
/// </summary>
public static void BaseIndex()
{
DateTime startTime = DateTime.Now;
// index construction
Index <RawDataFormat> si = new Index <RawDataFormat>(0, new IndexOptions("root"));
DataLoader dl = new GeneratedRawDataLoader(si, Globals.TimeSeriesLength, NUM_TIMESERIES, SEED);
InsertTimeSeries(dl);
Console.WriteLine();
Console.WriteLine("Sequential Disk Accesses: " + DiskCost.seqcost);
Console.WriteLine("Random Disk Accesses: " + DiskCost.rancost);
Console.WriteLine("Read Disk Accesses: " + DiskCost.readcost);
Console.WriteLine("Saved cost in buffer: " + DiskCost.savedcost);
Console.WriteLine();
Index <RawDataFormat> .Save(Globals.IndexRootDir, si);
Index <RawDataFormat> si2 = Index <RawDataFormat> .Load(Globals.IndexRootDir);
DateTime endConstructionTime = DateTime.Now;
Console.WriteLine("Index Construction Time: {0}", endConstructionTime - startTime);
// generate some test queries
const int NUM_QUERIES = 10;
List <double[]> queries = new List <double[]>(NUM_QUERIES);
for (int i = 0; i < NUM_QUERIES; i++)
{
queries.Add(Util.RandomWalk(Globals.TimeSeriesLength));
}
// full sequential scan
Console.WriteLine("Performing full sequential scan.");
Console.WriteLine("--------------------------------");
List <IndexFileDist[]> nnInfo = si.KNearestNeighborSequentialScan(10, queries);
Console.WriteLine();
// query results
Console.WriteLine("Performing exact and approximate search.");
Console.WriteLine("----------------------------------------");
int counter = 0;
for (int i = 0; i < NUM_QUERIES; i++)
{
IndexFileDist exactResult;
si.ExactSearch(queries[i], out exactResult);
IndexFileDist approxResult = Index <RawDataFormat> .MinFileEucDist(queries[i],
si.ApproximateSearch(queries[i]).FileName);
Assert.IsTrue(exactResult == nnInfo[i][0]);
if (approxResult == exactResult)
{
counter++;
Console.WriteLine(approxResult);
}
}
Console.WriteLine("{0} approximate results == exact results.", counter);
Console.WriteLine();
}
public static void SearchQualityExperiment()
{
DateTime startTime = DateTime.Now;
// index construction
Index <RawDataFormat> si = new Index <RawDataFormat>(0, new IndexOptions("root"));
DataLoader dl = new GeneratedRawDataLoader(si, Globals.TimeSeriesLength, NUM_TIMESERIES, SEED);
InsertTimeSeries(dl);
Console.WriteLine();
Console.WriteLine("Sequential Disk Accesses: " + DiskCost.seqcost);
Console.WriteLine("Random Disk Accesses: " + DiskCost.rancost);
Console.WriteLine("Read Disk Accesses: " + DiskCost.readcost);
Console.WriteLine("Saved cost in buffer: " + DiskCost.savedcost);
Console.WriteLine();
Index <RawDataFormat> .Save(Globals.IndexRootDir, si);
Index <RawDataFormat> si2 = Index <RawDataFormat> .Load(Globals.IndexRootDir);
DateTime endConstructionTime = DateTime.Now;
Console.WriteLine("Index Construction Time: {0}", endConstructionTime - startTime);
// avg over queries
const int NUM_QUERIES = 100;
List <double[]> queries = new List <double[]>(NUM_QUERIES);
for (int i = 0; i < NUM_QUERIES; i++)
{
queries.Add(Util.RandomWalk(Globals.TimeSeriesLength));
}
// measured metrics
double approxSearchDist = 0;
double approxSearchNodeDist = 0;
double approxSearchNodeSize = 0;
CostCounter exactSearchCosts = new CostCounter();
for (int i = 0; i < queries.Count; ++i)
{
// exact search
IndexFileDist eRes;
exactSearchCosts += si.ExactSearch(queries[i], out eRes);
// approximate search
TermEntry approxNode = si.ApproximateSearch(queries[i]);
double mDist = double.MaxValue;
List <RawDataFormat> nodeEntries = si.ReturnDataFormatFromTermEntry(approxNode);
double sumDists = 0;
foreach (RawDataFormat rd in nodeEntries)
{
double dist = Util.EuclideanDistance(queries[i], rd.GetTimeSeries());
sumDists += dist;
if (dist < mDist)
{
mDist = dist;
}
}
approxSearchDist += mDist;
approxSearchNodeDist += sumDists / nodeEntries.Count;
approxSearchNodeSize += nodeEntries.Count;
}
approxSearchDist /= queries.Count;
approxSearchNodeDist /= queries.Count;
approxSearchNodeSize /= queries.Count;
using (StreamWriter sw = new StreamWriter(Path.Combine(ROOT_DIR, "searchQuality.txt")))
{
string baseFormat = string.Format("{0}:NumTs_{1}:Th_{2}:Wl_{3}:NewPolicy", NUM_TIMESERIES, Globals.IndexNumMaxEntries, Globals.TimeSeriesLength, Globals.NewSplitPolicy);
sw.WriteLine(baseFormat);
sw.WriteLine("ExactSearchNumIO {0}", exactSearchCosts.IO / (double)queries.Count);
sw.WriteLine("ExactSearchNumCalcuations {0}", exactSearchCosts.distance / (double)queries.Count);
sw.WriteLine("ApproxSearchDistance {0}", approxSearchDist);
sw.WriteLine("ApproxSearchAverageNodeDistance {0}", approxSearchNodeDist);
sw.WriteLine("ApproxSearchAverageNodeSize {0}", approxSearchNodeSize);
sw.WriteLine("ValidationString ");
foreach (double[] query in queries)
{
sw.Write("{0} ", query[1]);
}
sw.WriteLine();
}
}
public static void DnaExperiment()
{
Util.NormalizationHandler = new Util.Normalize(Util.MeanZero_Normalization);
// in-memory data, referenced by the index
const string DATAFOLDER = @"K:\Datasets\DNA\Dna2Ts\Monkey_Binary";
// load index
Index <Meta2DataFormat> si = Index <Meta2DataFormat> .Load(Globals.IndexRootDir);
// populate in-memory data
DnaDataLoader.LoadDnaToMetaBuffer(DATAFOLDER);
// generate queries
DateTime queryStart = DateTime.Now;
int numQueries = 0;
string[] humanChrs = Directory.GetFiles(@"K:\Datasets\DNA\Dna2Ts\Human_Binary", "*.dat");
Array.Sort(humanChrs, new NaturalStringComparer());
Dictionary <string, DnaChrResult> queryResult = new Dictionary <string, DnaChrResult>(humanChrs.Length);
for (int chrNo = 0; chrNo < humanChrs.Length; ++chrNo)
{
string chrFile = humanChrs[chrNo];
GC.Collect();
using (BinaryReader br = new BinaryReader(new FileStream(chrFile, FileMode.Open, FileAccess.Read)))
{
List <DnaSearchResult> qResults = new List <DnaSearchResult>();
// List<Meta2DataFormat> _queryApproxRes = new List<Meta2DataFormat>();
// List<double> _dists = new List<double>();
// List<int> _queryPos = new List<int>();
long fileLength = br.BaseStream.Length / sizeof(int);
int posShift = Globals.TimeSeriesLength / 4; // shift by quarters
double[] dnaChr = new double[(int)Math.Floor((fileLength / sizeof(int)) / (double)DnaDataLoader.SAMPLERATE)];
Console.WriteLine("F:{0} OrigLen:{1} newLen:{2} Shift:{3}", chrFile, fileLength, dnaChr.Length, posShift);
// downsample
int count = 0;
double sum = 0;
for (int i = 0; i < dnaChr.Length; ++i)
{
sum = 0;
count = 0;
while (count < DnaDataLoader.SAMPLERATE)
{
sum += br.ReadInt32();
count++;
}
dnaChr[i] = sum / DnaDataLoader.SAMPLERATE;
}
double[] ts = new double[Globals.TimeSeriesLength];
for (int pos = 0; pos < dnaChr.Length - Globals.TimeSeriesLength; pos += posShift)
{
numQueries += 2;
Array.Copy(dnaChr, pos, ts, 0, Globals.TimeSeriesLength);
double mean = Util.Mean(ts, 0, ts.Length - 1);
for (int k = 0; k < ts.Length; ++k)
{
ts[k] = ts[k] - mean;
}
TermEntry tEntry = si.ApproximateSearch(ts);
List <Meta2DataFormat> termNodeEntries = si.ReturnDataFormatFromTermEntry(tEntry);
double bsfDist = Double.MaxValue;
Meta2DataFormat bsfMeta = new Meta2DataFormat();
foreach (Meta2DataFormat m in termNodeEntries)
{
double dist = Util.EuclideanDistance(Util.NormalizationHandler(m.GetTimeSeries()), ts);
if (dist < bsfDist)
{
bsfDist = dist;
bsfMeta = m;
}
}
qResults.Add(new DnaSearchResult()
{
dist = bsfDist,
matchingChr = bsfMeta._chrNo,
matchingPos = bsfMeta._pos,
queryChr = chrNo,
queryPos = pos,
});
// reverse
ts = ts.Reverse().ToArray();
tEntry = si.ApproximateSearch(ts);
termNodeEntries = si.ReturnDataFormatFromTermEntry(tEntry);
bsfDist = Double.MaxValue;
bsfMeta = new Meta2DataFormat();
foreach (Meta2DataFormat m in termNodeEntries)
{
double dist = Util.EuclideanDistance(Util.NormalizationHandler(m.GetTimeSeries()), ts);
if (dist < bsfDist)
{
bsfDist = dist;
bsfMeta = m;
}
}
qResults.Add(new DnaSearchResult()
{
dist = bsfDist,
matchingChr = bsfMeta._chrNo,
matchingPos = bsfMeta._pos,
queryChr = chrNo,
queryPos = pos,
});
}
queryResult.Add(chrFile, new DnaChrResult()
{
results = qResults
});
}
}
DateTime queryStop = DateTime.Now;
Console.WriteLine("{0} Queries, {1} TimeElapsed.", numQueries, queryStop - queryStart);
//// print results
using (StreamWriter sw = new StreamWriter(Path.Combine(Globals.IndexRootDir, "queryOutput.txt")))
{
foreach (KeyValuePair <string, DnaChrResult> kvp in queryResult)
{
// Console.WriteLine("HumanChromosome:{0}", kvp.Key);
// Console.WriteLine("AverageDistance:{0}", kvp.Value.AverageDistance);
// Console.WriteLine();
foreach (DnaSearchResult sr in kvp.Value.results)
{
sw.WriteLine(sr.ToString());
}
}
}
//using (StreamWriter sw = new StreamWriter(Path.Combine(Globals.IndexRootDir, "queryOutputTop.txt")))
//{
// foreach (KeyValuePair<string, DnaChrResult> kvp in queryResult)
// {
// // Console.WriteLine("HumanChromosome:{0}", kvp.Key);
// // Console.WriteLine("AverageDistance:{0}", kvp.Value.AverageDistance);
// // Console.WriteLine();
// List<DnaSearchResult>sr = kvp.Value.results;
// sr.Sort();
// sr = sr.GetRange(0, 10);
// Console.WriteLine("For Human Chr:{0}", kvp.Key);
// var counts = from q in sr
// group q by q.matchingChr into g
// select new { Chr = g.Key, NumHits = g.Count() };
// foreach (var v in counts)
// Console.WriteLine("{0} : {1}", v.Chr, v.NumHits);
// }
// // //{
// // // for (int i = 0; i < kvp.Value.queryTs.Count; ++i)
// // // {
// // // sw.WriteLine(Util.ArrayToString(kvp.Value.queryTs[i]));
// // // sw.WriteLine(Util.ArrayToString(Util.NormalizationHandler(kvp.Value.queryApproxRes[i].GetTimeSeries())));
// // // }
// // // //foreach (double[] d in kvp.Value.queryTs)
// // // // sw.WriteLine(Util.ArrayToString(d));
//}
}
