private XYZDataset createDataSet(HashBasedTable<String, String, Double> data) {
MatrixSeries series =
new MatrixSeries(
"DataTable", roomToCodeMapping.keySet().size(), roomToCodeMapping.keySet().size());
for (String source : roomToCodeMapping.keySet()) {
Integer sourceId = roomToCodeMapping.get(source);
for (String destination : roomToCodeMapping.keySet()) {
Integer destinationId = roomToCodeMapping.get(destination);
if (!data.contains(source, destination)) {
series.update(sourceId, destinationId, -1.0);
} else {
double value;
if (type == MarkovDataDialog.HeatMapType.COMPARISON)
value = (data.get(source, destination) + 1.0) / 2; // Scale to 0 to 1 for comparison
else value = data.get(source, destination);
if (value < 0 || value > 1) {
System.out.println(
"***********Problem in value=" + value + "(" + source + "," + destination + ")");
}
series.update(sourceId, destinationId, value);
}
}
}
System.out.println("Room size = " + roomToCodeMapping.keySet().size());
return new MatrixSeriesCollection(series);
}
private static ArrayList<String> printData(HashBasedTable<String, String, Double> tbl1) {
// lstOut = output data
// sbl1 = current line
// rgs1 = list of row ids
// rgs2 = list of headers
ArrayList<String> lstOut;
StringBuilder sbl1;
String rgs1[];
String rgs2[];
lstOut = new ArrayList<String>();
rgs1 = tbl1.rowKeySet().toArray(new String[tbl1.rowKeySet().size()]);
rgs2 = new String[rgs1.length];
for (int i = 0; i < rgs1.length; i++) {
rgs2[i] = (new File(rgs1[i])).getName();
}
lstOut.add("SampleID" + "," + Joiner.on(",").join(rgs2));
for (String s : tbl1.columnKeySet()) {
sbl1 = new StringBuilder();
sbl1.append(s);
for (int i = 0; i < rgs1.length; i++) {
sbl1.append("," + tbl1.get(rgs1[i], s));
}
lstOut.add(sbl1.toString());
}
return lstOut;
}
@Test
public void calculateWeight_WeightsCalculated_WeightsCorrect() {
for (Integer i : tblWeight.rowKeySet()) {
for (Integer j : tblWeight.columnKeySet()) {
assertEquals(tblWeight.get(i, j), spw1.getWeight(spw1.getEdge(i, j)), 0.0000001);
}
}
}
private void handleIncomingConfirmableCoapRequest(ChannelHandlerContext ctx, MessageEvent me) {
InetSocketAddress remoteEndpoint = (InetSocketAddress) me.getRemoteAddress();
CoapMessage coapMessage = (CoapMessage) me.getMessage();
IncomingReliableMessageExchange newMessageExchange =
new IncomingReliableMessageExchange(remoteEndpoint, coapMessage.getMessageID());
IncomingMessageExchange oldMessageExchange =
ongoingMessageExchanges.get(remoteEndpoint, coapMessage.getMessageID());
// Check if there is an ongoing
if (oldMessageExchange != null) {
if (oldMessageExchange instanceof IncomingReliableMessageExchange) {
// if the old message exchange is reliable and the empty ACK was already sent send another
// empty ACK
if (((IncomingReliableMessageExchange) oldMessageExchange).isAcknowledgementSent())
writeEmptyAcknowledgement(remoteEndpoint, coapMessage.getMessageID());
}
// if the old message was unreliable and the duplicate message is confirmable send empty ACK
else writeEmptyAcknowledgement(remoteEndpoint, coapMessage.getMessageID());
// As the message is already being processed there is nothing more to do
return;
}
// try to add new reliable message exchange
boolean added = false;
synchronized (monitor) {
Long time = System.currentTimeMillis() + MIN_EMPTY_ACK_DELAY_MILLIS;
// Add message exchange to set of ongoing exchanges to detect duplicates
if (!ongoingMessageExchanges.contains(remoteEndpoint, coapMessage.getMessageID())) {
ongoingMessageExchanges.put(remoteEndpoint, coapMessage.getMessageID(), newMessageExchange);
added = true;
}
// If the scheduling of the empty ACK does not work then it was already scheduled
if (!emptyAcknowledgementSchedule.put(time, newMessageExchange)) {
log.error("Could not schedule empty ACK for message: {}", coapMessage);
ongoingMessageExchanges.remove(remoteEndpoint, coapMessage.getMessageID());
added = false;
}
}
// everything is fine, so further process message
if (added) ctx.sendUpstream(me);
}
private void initialize() {
// ert1 = earth geometry object
// dThreshold = threshold distance
// ranDist = distances range
// ranTime = time range
// ranDirect = directions range
// i1 = counter
// rgdSum = row sums
double dThreshold;
EarthGeometry ert1;
Range<Double> ranDist;
Range<Double> ranTime;
Range<Double> ranDirect;
int i1;
double rgdSum[];
// initializing mocked data
rgdLat = new double[] {45., 46., 47., 48.};
rgdLon = new double[] {-110., -109., -108., -107.};
rgdPoints = new double[rgdLat.length * rgdLat.length][2];
i1 = 0;
for (int i = 0; i < rgdLat.length; i++) {
for (int j = 0; j < rgdLat.length; j++) {
rgdPoints[i1][0] = rgdLat[i];
rgdPoints[i1][1] = rgdLon[j];
i1++;
}
}
rgdAbund = new double[2][rgdPoints.length];
tblWeight = HashBasedTable.create(4, 4);
dThreshold = 150.;
ert1 = new EarthGeometry();
rgdSum = new double[rgdPoints.length];
for (int i = 0; i < rgdPoints.length; i++) {
for (int j = 0; j < rgdPoints.length; j++) {
if (i != j
&& ert1.orthodromicDistanceWGS84(
rgdPoints[i][0], rgdPoints[i][1], rgdPoints[j][0], rgdPoints[j][1])
< dThreshold) {
tblWeight.put(i, j, 1.);
rgdSum[i] += 1.;
} else {
tblWeight.put(i, j, 0.);
}
}
rgdAbund[0][i] = ((double) i) / 20.;
rgdAbund[1][i] = (((double) i) % 4.) / 4.;
}
for (int i = 0; i < rgdPoints.length; i++) {
for (int j = 0; j < rgdPoints.length; j++) {
if (rgdSum[i] > 0) {
tblWeight.put(i, j, tblWeight.get(i, j) / rgdSum[i]);
}
}
}
// loading spatial weights object from file
ranDist = Range.closed(0., dThreshold);
ranTime = Range.closed(0., 12.);
ranDirect = Range.closed(0., 360.);
bio1 =
new BiomIO(
"/home/jladau/Desktop/Data/Microbial_Community_Samples/ValidationData.NA.NA.Ladau.biom");
try {
spw1 =
new SpatialWeightsMatrix(
bio1, ranDist, ranDirect, ranTime, "binary", "latitude-longitude", false);
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Returns the permitted option occurrence within a message with the given code
*
* @param optionNumber the options number
* @param messageCode the number corresponding to a message code
* @return the permitted option occurrence within a message with the given code
*/
public static Occurence getPermittedOccurrence(int optionNumber, int messageCode) {
Occurence result = OCCURENCE_CONSTRAINTS.get(messageCode, optionNumber);
return result == null ? NONE : result;
}
public void addCrossFeature(int i, int j, String f) {
if (!crossFactors.contains(i, j)) {
crossFactors.put(i, j, new Factor());
}
crossFactors.get(i, j).add(f);
}
