/**
* Center the values around the median per column.
*
* @param result the input and output matrix where the first dimension are rows and the second
* columns.
*/
private static void centerAroundColumnMedian(final double[][] result) {
for (int i = 0; i < result[0].length; i++) {
final DescriptiveStatistics stats = new DescriptiveStatistics();
for (final double[] aResult : result) {
stats.addValue(aResult[i]);
}
final double median = stats.getPercentile(50);
for (int j = 0; j < result.length; j++) {
result[j][i] -= median;
}
}
}
protected void autoCorrelation() {
DescriptiveStatistics descriptiveStatistics = new DescriptiveStatistics(simulations);
double mean = descriptiveStatistics.getMean();
double variance = descriptiveStatistics.getVariance();
int numberOfAutocorrelations = simulations.length / 2;
double[] autoCorrelations = new double[numberOfAutocorrelations];
for (int i = 1; i <= numberOfAutocorrelations; ++i) {
autoCorrelations[i - 1] = autoCovariance(i, mean) / variance;
}
plot("Auto Correlations", autoCorrelations);
}
/**
* @param args
* @throws IOException
*/
public void results(String[] f) throws IOException {
String[] indicators = {"EPSILON", "IGD", "SPREAD", "HV"};
String[] operators = {"BLX", "SBX"
// ,"DEX"
};
int runs = 15;
double aux = 0;
String str = "";
BufferedReader br = null;
Vector<PrintWriter> pw = new Vector<PrintWriter>();
DescriptiveStatistics d = new DescriptiveStatistics();
for (int i = 0; i < operators.length; i++) {
for (int j = 0; j < indicators.length; j++) {
pw.add(
new PrintWriter(
"C:\\Users\\9dgonzalezg\\Desktop\\workspace\\GA\\GA"
+ "\\resultsMyNSGAIIExperiment\\data\\"
+ new String(f[i])
+ "_"
+ indicators[j]
+ ".res"));
for (int k = 0; k < runs; k++) {
br =
new BufferedReader(
new FileReader(
"C:\\Users\\9dgonzalezg"
+ "\\Desktop\\workspace\\GA\\GA\\resultsMyNSGAIIExperiment\\"
+ "data\\"
+ f[i]
+ "\\"
+ new Integer(k).toString()
+ "\\"
+ indicators[j]));
str = br.readLine();
while (str != null) {
aux = Double.parseDouble(str);
d.addValue(aux);
str = br.readLine();
}
br.close();
pw.get(j).println(d.getMean());
d.clear();
}
pw.get(j).close();
}
pw.clear();
}
}
@Override
public void execute() {
double util = 0;
double power = 0;
double prevSlavWork;
double prevWork;
// store current work and SLA violated work values
prevSlavWork = totalSlavWork;
prevWork = totalWork;
// reset total work values
totalSlavWork = 0;
totalWork = 0;
totalPower = 0;
for (Host host : dc.getHosts()) {
// store host CPU utilization
if (!hostUtil.containsKey(host)) {
hostUtil.put(host, new DescriptiveStatistics());
}
hostUtil.get(host).addValue(host.getCpuManager().getCpuInUse());
util += host.getCpuManager().getCpuInUse();
// get VM SLA values
for (VMAllocation vmAlloc : host.getVMAllocations()) {
totalSlavWork += vmAlloc.getVm().getApplication().getTotalSLAViolatedWork();
totalWork +=
vmAlloc
.getVm()
.getApplication()
.getTotalIncomingWork(); // NOTE: This ONLY works with SINGLE TIERED applications.
// For multi-tiered applications, this will count incoming
// work multiple times!!
}
// get power consumption
power += host.getCurrentPowerConsumption();
totalPower += host.getPowerConsumed();
}
dcUtil.addValue(util);
dcPower.addValue(power);
dcPowerEfficiency.addValue(util / power);
double optimalPowerConsumption = calculateOptimalPowerConsumption(util);
dcOptimalPower.addValue(optimalPowerConsumption);
dcOptimalPowerEfficiency.addValue(util / optimalPowerConsumption);
dcOptimalPowerRatio.addValue((util / optimalPowerConsumption) / (util / power));
// records the total fraction of SLA violated incoming work since the last time interval
dcSla.addValue((totalSlavWork - prevSlavWork) / (totalWork - prevWork));
}
private double calcSTDev(
HashMap<Integer, String> singleGeneCaseValueMap, String groupType, String profileStableId) {
switch (groupType) {
case "altered":
DescriptiveStatistics stats_altered = new DescriptiveStatistics();
for (Integer alteredSampleId : alteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(alteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_altered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_altered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(alteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_altered.getStandardDeviation();
case "unaltered":
DescriptiveStatistics stats_unaltered = new DescriptiveStatistics();
for (Integer unalteredSampleId : unalteredSampleIds) {
if (singleGeneCaseValueMap.containsKey(unalteredSampleId)) {
if (profileStableId.indexOf("rna_seq") != -1) {
try {
stats_unaltered.addValue(
Math.log(Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)))
/ Math.log(2));
} catch (NumberFormatException e) {
e.getStackTrace();
}
} else {
try {
stats_unaltered.addValue(
Double.parseDouble(singleGeneCaseValueMap.get(unalteredSampleId)));
} catch (NumberFormatException e) {
e.getStackTrace();
}
}
}
}
return stats_unaltered.getStandardDeviation();
default:
return Double.NaN; // error
}
}
@Test
public void testDataJsonConsumption() throws Exception {
JsonArray ginzburg = createJson("ginzburg", 1, 10);
assertEquals(ginzburg.size(), 1);
BasicSampleExtractor extractor = new BasicSampleExtractor();
JsonObject jsonObject = ginzburg.getJsonObject(0);
Optional<SampleData> sampleData = extractor.extractSample(jsonObject);
assertTrue(sampleData.isPresent());
assertEquals(sampleData.get().getPublishId(), "ginzburg");
assertFalse(sampleData.get().getTime().isEmpty());
double[] readings = extractor.extractReadings(jsonObject.getString(READINGS));
assertEquals(readings.length, 10);
DescriptiveStatistics stats = new DescriptiveStatistics(readings);
double median = stats.getPercentile(50);
assertEquals(sampleData.get().getMedian(), median);
}
/**
* Normalize (standardize) the sample, so it is has a mean of 0 and a standard deviation of 1.
*
* @param sample Sample to normalize.
* @return normalized (standardized) sample.
* @since 2.2
*/
public static double[] normalize(final double[] sample) {
DescriptiveStatistics stats = new DescriptiveStatistics();
// Add the data from the series to stats
for (int i = 0; i < sample.length; i++) {
stats.addValue(sample[i]);
}
// Compute mean and standard deviation
double mean = stats.getMean();
double standardDeviation = stats.getStandardDeviation();
// initialize the standardizedSample, which has the same length as the sample
double[] standardizedSample = new double[sample.length];
for (int i = 0; i < sample.length; i++) {
// z = (x- mean)/standardDeviation
standardizedSample[i] = (sample[i] - mean) / standardDeviation;
}
return standardizedSample;
}
public Vector<double[]> getMeanSd(svm_node[][] node) {
// TODO Auto-generated method stub
DescriptiveStatistics statistics = new DescriptiveStatistics();
int nAttr = node[0].length;
int nSample = node.length;
double[] meanValues = new double[nAttr];
double[] sdValues = new double[nAttr];
for (int i = 0; i < nAttr; i++) {
statistics.clear();
for (int j = 0; j < nSample; j++) {
statistics.addValue(node[j][i].value);
}
// 获取中值及标准差
meanValues[i] = statistics.getMean();
sdValues[i] = statistics.getStandardDeviation();
}
Vector<double[]> meanSd = new Vector<double[]>();
meanSd.add(meanValues);
meanSd.add(sdValues);
return meanSd;
}
/**
* Construct a new DCUtilizationMonitor
*
* @param simulation
* @param frequency The frequency in milliseconds to run this monitor
* @param windowSize The number of historical values to use in calculations
* @param dc
*/
public DCUtilizationMonitor(
Simulation simulation, long frequency, int windowSize, DataCentre dc) {
super(simulation, frequency);
this.windowSize = windowSize;
this.dc = dc;
dcUtil.setWindowSize(windowSize);
dcSla.setWindowSize(windowSize);
dcPower.setWindowSize(windowSize);
dcOptimalPower.setWindowSize(windowSize);
dcPowerEfficiency.setWindowSize(windowSize);
dcOptimalPowerEfficiency.setWindowSize(windowSize);
dcOptimalPowerRatio.setWindowSize(windowSize);
// initialize host values
for (Host host : dc.getHosts()) {
hostUtil.put(host, new DescriptiveStatistics(windowSize));
}
}
/**
* Returns summary statistics for all attributes.
*
* @param listwiseDeletion A flag enabling list-wise deletion
* @return
*/
@SuppressWarnings({"unchecked", "rawtypes"})
public <T> Map<String, StatisticsSummary<?>> getSummaryStatistics(boolean listwiseDeletion) {
Map<String, DescriptiveStatistics> statistics = new HashMap<String, DescriptiveStatistics>();
Map<String, StatisticsSummaryOrdinal> ordinal = new HashMap<String, StatisticsSummaryOrdinal>();
Map<String, DataScale> scales = new HashMap<String, DataScale>();
// Detect scales
for (int col = 0; col < handle.getNumColumns(); col++) {
// Meta
String attribute = handle.getAttributeName(col);
DataType<?> type = handle.getDataType(attribute);
// Scale
DataScale scale = type.getDescription().getScale();
// Try to replace nominal scale with ordinal scale based on base data type
if (scale == DataScale.NOMINAL && handle.getGeneralization(attribute) != 0) {
if (!(handle.getBaseDataType(attribute) instanceof ARXString)
&& getHierarchy(col, true) != null) {
scale = DataScale.ORDINAL;
}
}
// Store
scales.put(attribute, scale);
statistics.put(attribute, new DescriptiveStatistics());
ordinal.put(
attribute,
getSummaryStatisticsOrdinal(
handle.getGeneralization(attribute),
handle.getDataType(attribute),
handle.getBaseDataType(attribute),
getHierarchy(col, true)));
}
// Compute summary statistics
for (int row = 0; row < handle.getNumRows(); row++) {
// Check, if we should include this row
boolean include = true;
if (listwiseDeletion) {
for (int col = 0; col < handle.getNumColumns(); col++) {
if (handle.isSuppressed(row) || DataType.isNull(handle.getValue(row, col))) {
include = false;
break;
}
}
}
// Check
checkInterrupt();
// If yes, add
if (include) {
// For each column
for (int col = 0; col < handle.getNumColumns(); col++) {
// Meta
String value = handle.getValue(row, col);
String attribute = handle.getAttributeName(col);
DataType<?> type = handle.getDataType(attribute);
// Analyze
if (!value.equals(handle.getSuppressionString()) && !DataType.isNull(value)) {
ordinal.get(attribute).addValue(value);
if (type instanceof DataTypeWithRatioScale) {
statistics
.get(attribute)
.addValue(((DataTypeWithRatioScale) type).toDouble(type.parse(value)));
}
}
}
}
}
// Convert
Map<String, StatisticsSummary<?>> result = new HashMap<String, StatisticsSummary<?>>();
for (int col = 0; col < handle.getNumColumns(); col++) {
// Check
checkInterrupt();
// Depending on scale
String attribute = handle.getAttributeName(col);
DataScale scale = scales.get(attribute);
DataType<T> type = (DataType<T>) handle.getDataType(attribute);
ordinal.get(attribute).analyze();
if (scale == DataScale.NOMINAL) {
StatisticsSummaryOrdinal stats = ordinal.get(attribute);
result.put(
attribute,
new StatisticsSummary<T>(
DataScale.NOMINAL,
stats.getNumberOfMeasures(),
stats.getMode(),
type.parse(stats.getMode())));
} else if (scale == DataScale.ORDINAL) {
StatisticsSummaryOrdinal stats = ordinal.get(attribute);
result.put(
attribute,
new StatisticsSummary<T>(
DataScale.ORDINAL,
stats.getNumberOfMeasures(),
stats.getMode(),
type.parse(stats.getMode()),
stats.getMedian(),
type.parse(stats.getMedian()),
stats.getMin(),
type.parse(stats.getMin()),
stats.getMax(),
type.parse(stats.getMax())));
} else if (scale == DataScale.INTERVAL) {
StatisticsSummaryOrdinal stats = ordinal.get(attribute);
DescriptiveStatistics stats2 = statistics.get(attribute);
boolean isPeriod = type.getDescription().getWrappedClass() == Date.class;
// TODO: Something is wrong with commons math's kurtosis
double kurtosis = stats2.getKurtosis();
kurtosis = kurtosis < 0d ? Double.NaN : kurtosis;
double range = stats2.getMax() - stats2.getMin();
double stddev = Math.sqrt(stats2.getVariance());
result.put(
attribute,
new StatisticsSummary<T>(
DataScale.INTERVAL,
stats.getNumberOfMeasures(),
stats.getMode(),
type.parse(stats.getMode()),
stats.getMedian(),
type.parse(stats.getMedian()),
stats.getMin(),
type.parse(stats.getMin()),
stats.getMax(),
type.parse(stats.getMax()),
toString(type, stats2.getMean(), false, false),
toValue(type, stats2.getMean()),
stats2.getMean(),
toString(type, stats2.getVariance(), isPeriod, true),
toValue(type, stats2.getVariance()),
stats2.getVariance(),
toString(type, stats2.getPopulationVariance(), isPeriod, true),
toValue(type, stats2.getPopulationVariance()),
stats2.getPopulationVariance(),
toString(type, stddev, isPeriod, false),
toValue(type, stddev),
stddev,
toString(type, range, isPeriod, false),
toValue(type, range),
stats2.getMax() - stats2.getMin(),
toString(type, kurtosis, isPeriod, false),
toValue(type, kurtosis),
kurtosis));
} else if (scale == DataScale.RATIO) {
StatisticsSummaryOrdinal stats = ordinal.get(attribute);
DescriptiveStatistics stats2 = statistics.get(attribute);
// TODO: Something is wrong with commons math's kurtosis
double kurtosis = stats2.getKurtosis();
kurtosis = kurtosis < 0d ? Double.NaN : kurtosis;
double range = stats2.getMax() - stats2.getMin();
double stddev = Math.sqrt(stats2.getVariance());
result.put(
attribute,
new StatisticsSummary<T>(
DataScale.RATIO,
stats.getNumberOfMeasures(),
stats.getMode(),
type.parse(stats.getMode()),
stats.getMedian(),
type.parse(stats.getMedian()),
stats.getMin(),
type.parse(stats.getMin()),
stats.getMax(),
type.parse(stats.getMax()),
toString(type, stats2.getMean(), false, false),
toValue(type, stats2.getMean()),
stats2.getMean(),
toString(type, stats2.getVariance(), false, false),
toValue(type, stats2.getVariance()),
stats2.getVariance(),
toString(type, stats2.getPopulationVariance(), false, false),
toValue(type, stats2.getPopulationVariance()),
stats2.getPopulationVariance(),
toString(type, stddev, false, false),
toValue(type, stddev),
stddev,
toString(type, range, false, false),
toValue(type, range),
range,
toString(type, kurtosis, false, false),
toValue(type, kurtosis),
kurtosis,
toString(type, stats2.getGeometricMean(), false, false),
toValue(type, stats2.getGeometricMean()),
stats2.getGeometricMean()));
}
}
return result;
}
public static void main(String[] args) {
// TEST MEASURE
// Point p1 = new Point(-1d, -1d);
// Point p2 = new Point(2d, 3d);
// System.out.println(measure.d(p1, p2));
// System.out.println(measure.s(p1, p2));
// return;
Double[][] data = FileHandler.readFile(fileName);
// cannot display points if dimension is > 2
if (data[0].length != 2) canDisplay = false;
// build graphic points from coords' array
buildPointsFromData(data);
Config.computeBoundingRect(points);
// init display
if (canDisplay) {
disp = new Display();
disp.setVisible(true);
for (Point p : points) {
disp.addObject(p);
}
}
testResults = new double[nbTests];
for (int t = 0; t < nbTests; ++t) {
// define K clusters and K temporary centres
clusters = new ArrayList<Cluster>();
for (int i = 0; i < K; ++i) {
clusters.add(new Cluster());
}
setRandomCenters();
for (Cluster c : clusters) {
System.out.println("center for cluster " + c + ": " + c.getCenter());
}
if (canDisplay) pause(1000);
// variables used in for loops
double minDist, currDist, diff;
Double[] prevCoords, newCoords;
Cluster alloc;
Point newCenter;
for (int i = 0; i < maxIter; ++i) {
if (canDisplay) {
disp.setLabel("[ iteration #" + (i + 1) + " ]");
} else {
System.out.println("------> iteration #" + (i + 1));
}
// allocate points to group which center is closest
for (Point p : points) {
minDist = Config.MAX;
alloc = clusters.get(0); // default initialization
for (Cluster c : clusters) {
currDist = measure.d(p, c.getCenter());
if (currDist < minDist) {
minDist = currDist;
alloc = c;
}
}
alloc.addPoint(p);
}
// recenter: calculate gravity centers for formed groups
diff = 0;
prevCoords = null;
for (Cluster c : clusters) {
// delete previous center if it not a Point of the Cluster
if (canDisplay && !c.getPoints().contains(c.getCenter())) {
disp.removeObject(c.getCenter());
}
if (stopOnConverge) {
prevCoords = c.getCenter().getCoords();
}
newCenter = c.makeGravityCenter();
if (stopOnConverge) {
newCoords = c.getCenter().getCoords();
for (int k = 0; k < prevCoords.length; ++k) {
diff += Math.abs(prevCoords[k] - newCoords[k]);
}
}
if (canDisplay) {
disp.addObject(newCenter);
} else {
// System.out.println("\tcenter for " + c + ": " + c.getCenter());
System.out.println(c.getCenter());
}
} // loop over clusters
if (canDisplay) {
disp.repaint();
}
// if Clusters' centers don't change anymore, then stop (algorithm converged)
if (diff == 0 && stopOnConverge) {
testResults[t] = (double) i;
if (canDisplay) {
disp.setLabel("[ Converged at iteration #" + (i) + " ]");
disp.repaint();
} else {
System.out.println("[ Converged at iteration #" + (i) + " ]");
}
break;
}
pause(100);
} // loop over iterations
if (testResults[t] == 0) {
System.out.println("!!!!!!!!!! Test #" + t + " did not converge.");
if (stopOnConverge) return;
}
// reset display
if (canDisplay && t + 1 < nbTests) {
for (Point p : points) p.setCluster(null);
for (Cluster c : clusters) disp.removeObject(c.getCenter());
}
} // loop over tests
// display test results and compute means
DescriptiveStatistics stats = new DescriptiveStatistics(testResults);
System.out.println("=========> Results:");
for (int t = 0; t < nbTests; ++t) {
System.out.println("--> [ " + testResults[t] + " ]");
}
System.out.println("=========> Means: " + stats.getMean());
System.out.println("=========> Std dev: " + stats.getStandardDeviation());
}