private static double[] computeXaXs(
final IScope scope,
final IAgentFilter filter,
final Map<Object, Integer> categoriesId,
final Map<IAgent, Integer> agsId,
final int valObsId,
final int valSimId,
final int valInitId,
final GamaMatrix<Double> fuzzytransitions,
final Double distance,
final IAgent agent,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final IContainer.Addressable<Integer, IAgent> agents,
final int nbCat) {
double xa = 0.0;
double xs = 0.0;
double[] XaXs = new double[2];
double sizeNorm = FastMath.sqrt(agent.getEnvelope().getArea());
List<IAgent> neighbors =
distance == 0 || filter == null
? new ArrayList<IAgent>()
: new ArrayList<IAgent>(
scope.getTopology().getNeighborsOf(scope, agent, distance, filter));
Map<IAgent, Double> distancesCoeff = new TOrderedHashMap<IAgent, Double>();
distancesCoeff.put(agent, 1.0);
for (IAgent ag : neighbors) {
double euclidDist = agent.getLocation().euclidianDistanceTo(ag.getLocation());
distancesCoeff.put(ag, 1 / (1.0 + euclidDist / sizeNorm));
}
for (IAgent ag : distancesCoeff.keySet()) {
int id = agsId.get(ag);
Object valI = valsInit.get(id);
Object valO = valsObs.get(id);
Object valS = valsSim.get(id);
int valOId = categoriesId.get(valO);
int valSId = categoriesId.get(valS);
int valIId = categoriesId.get(valI);
double dist = distancesCoeff.get(ag);
double valxatmp =
fuzzyTransition(scope, fuzzytransitions, nbCat, valInitId, valSimId, valIId, valOId)
* dist;
double valxstmp =
fuzzyTransition(scope, fuzzytransitions, nbCat, valInitId, valObsId, valIId, valSId)
* dist;
if (valxatmp > xa) {
xa = valxatmp;
}
if (valxstmp > xs) {
xs = valxstmp;
}
}
XaXs[0] = xa;
XaXs[1] = xs;
return XaXs;
}
@operator(
value = {"percent_absolute_deviation"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {IConcept.STATISTIC})
@doc(
value =
"percent absolute deviation indicator for 2 series of values: percent_absolute_deviation(list_vals_observe,list_vals_sim)",
examples = {
@example(
value = "percent_absolute_deviation([200,300,150,150,200],[250,250,100,200,200])",
isExecutable = false)
})
public static double percentAbsoluteDeviation(
final IScope scope, final IList<Double> vals1, final IList<Double> vals2) {
if (vals1 == null || vals2 == null) {
return 1;
}
int nb = vals1.size();
if (nb != vals2.size()) {
return 0;
}
double sum = 0;
double coeff = 0;
for (int i = 0; i < nb; i++) {
double val1 = Cast.asFloat(scope, vals1.get(i));
double val2 = Cast.asFloat(scope, vals2.get(i));
coeff += val1;
sum += FastMath.abs(val1 - val2) * 100.0;
}
if (coeff == 0) {
return 0;
}
return sum / coeff;
}
@Override
public IList copy() {
IList result = new AListSingle();
for (int i = 0; i < index; ++i) {
result.addEnd(arr[i]);
}
return result;
}
@Override
public void addWorker(String worker) {
heartbeat.put(worker, System.currentTimeMillis());
if (!workers.contains(worker)) {
log.info("Adding worker " + worker);
workers.add(worker);
log.info("Number of workers is now " + workers.size());
}
}
@Override
public IList<ISpecies> getMicroSpecies() {
final IList<ISpecies> retVal = GamaListFactory.create(Types.SPECIES);
retVal.addAll(microSpecies.values());
final ISpecies parentSpecies = this.getParentSpecies();
if (parentSpecies != null) {
retVal.addAll(parentSpecies.getMicroSpecies());
}
return retVal;
}
@Override
public IList<ISpecies> getSubSpecies(final IScope scope) {
IList<ISpecies> subspecies = GamaListFactory.create(Types.SPECIES);
GamlModelSpecies model = (GamlModelSpecies) scope.getModel().getSpecies();
for (ISpecies s : model.getAllSpecies().values()) {
if (s.getParentSpecies() == this) {
subspecies.add(s);
}
}
return subspecies;
}
@Override
public GamaMap mapValue(
final IScope scope, final IType keyType, final IType contentsType, final boolean copy)
throws GamaRuntimeException {
final IList<IAgent> agents = listValue(scope, contentsType, false);
// Default behavior : Returns a map containing the names of agents as keys and the agents
// themselves as values
final GamaMap result =
GamaMapFactory.create(Types.STRING, scope.getModelContext().getTypeNamed(getName()));
for (final IAgent agent : agents.iterable(scope)) {
result.put(agent.getName(), agent);
}
return result;
}
@Test
public void testHazelcastInstances() {
assertNotNull(map1);
assertNotNull(map2);
assertNotNull(multiMap);
assertNotNull(queue);
assertNotNull(topic);
assertNotNull(set);
assertNotNull(list);
assertNotNull(executorService);
assertNotNull(idGenerator);
assertNotNull(atomicLong);
assertNotNull(atomicReference);
assertNotNull(countDownLatch);
assertNotNull(semaphore);
assertNotNull(lock);
assertEquals("map1", map1.getName());
assertEquals("map2", map2.getName());
assertEquals("testMultimap", multiMap.getName());
assertEquals("testQ", queue.getName());
assertEquals("testTopic", topic.getName());
assertEquals("set", set.getName());
assertEquals("list", list.getName());
assertEquals("idGenerator", idGenerator.getName());
assertEquals("atomicLong", atomicLong.getName());
assertEquals("atomicReference", atomicReference.getName());
assertEquals("countDownLatch", countDownLatch.getName());
assertEquals("semaphore", semaphore.getName());
}
@Override
public boolean addJobToCurrent(Job j) throws Exception {
IAtomicReference<Job> r = h.getAtomicReference("job-" + j.getWorkerId());
if (r.get() != null || !r.isNull()) {
boolean sent = false;
while (!sent) {
// always update
for (String s : workers()) {
if (jobFor(s) == null) {
log.info(
"Redirecting worker "
+ j.getWorkerId()
+ " to "
+ s
+ " due to work already being allocated");
r = h.getAtomicReference("job-" + s);
j.setWorkerId(s);
sent = true;
}
}
}
}
r.set(j);
// iterate over jobs without the work/data
j.setWork(null);
jobs.add(j);
return true;
}
/**
* Adds an update to the current mini batch
*
* @param id the id of the worker who did the update
* @param update the update to add
*/
@Override
public void addUpdate(String id, E update) {
try {
updateSaver().save(id, update);
} catch (Exception e) {
throw new RuntimeException(e);
}
updates.add(id);
}
private static void computeXYCrispVector(
final IScope scope,
final Map<Object, Integer> categoriesId,
final List<Object> categories,
final IList<Object> vals1,
final IList<Object> vals2,
final GamaMatrix<Double> fuzzycategories,
final int nbCat,
final int nb,
final double[][] crispVector1,
final double[][] crispVector2,
final double[] X,
final double[] Y,
final boolean[] sim,
final IList<Object> weights) {
for (int j = 0; j < nbCat; j++) {
X[j] = 0;
Y[j] = 0;
}
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
Object val1 = vals1.get(i);
Object val2 = vals2.get(i);
int indexVal1 = categoriesId.get(val1);
int indexVal2 = categoriesId.get(val2);
X[indexVal1] += weight;
Y[indexVal2] += weight;
for (int j = 0; j < nbCat; j++) {
crispVector1[i][j] = Cast.asFloat(scope, fuzzycategories.get(scope, indexVal1, j));
crispVector2[i][j] = Cast.asFloat(scope, fuzzycategories.get(scope, indexVal2, j));
}
if (val1.equals(val2)) {
sim[i] = true;
} else {
sim[i] = false;
}
}
for (int j = 0; j < nbCat; j++) {
X[j] /= total;
Y[j] /= total;
}
}
private static int buildRings(
final IScope scope,
final IAgentFilter filter,
final Double distance,
final List<Double> rings,
final Map<Double, Integer> ringsPn,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents) {
IList<ILocation> locs = GamaListFactory.create(Types.POINT);
for (IAgent ag : agents.iterable(scope)) {
locs.add(ag.getLocation());
}
ILocation centralLoc = (ILocation) Stats.getMean(scope, locs);
IAgent centralAg = scope.getTopology().getAgentClosestTo(scope, centralLoc, filter);
List<IAgent> neighbors =
distance == 0 || filter == null
? new ArrayList<IAgent>()
: new ArrayList<IAgent>(
scope.getTopology().getNeighborsOf(scope, centralAg, distance, filter));
for (IAgent ag : neighbors) {
double dist = centralLoc.euclidianDistanceTo(ag.getLocation());
if (dist == 0) {
continue;
}
if (!rings.contains(dist)) {
rings.add(dist);
ringsPn.put(dist, 1);
} else {
ringsPn.put(dist, 1 + ringsPn.get(dist));
}
}
Collections.sort(rings);
for (int i = 1; i < rings.size(); i++) {
double dist = rings.get(i);
double dist1 = rings.get(i - 1);
ringsPn.put(dist, ringsPn.get(dist) + ringsPn.get(dist1));
}
return rings.size();
}
@Override
public void removeWorker(String worker) {
workers.remove(worker);
if (jobFor(worker) != null) {
try {
clearJob(worker);
} catch (Exception e) {
log.warn("Unable to clear job for worker with id" + worker);
}
}
}
protected void handleListAddMany(String[] args) {
int count = 1;
if (args.length > 1) count = Integer.parseInt(args[1]);
int successCount = 0;
long t0 = Clock.currentTimeMillis();
for (int i = 0; i < count; i++) {
boolean success = getList().add("obj" + i);
if (success) successCount++;
}
long t1 = Clock.currentTimeMillis();
println("Added " + successCount + " objects.");
println("size = " + list.size() + ", " + successCount * 1000 / (t1 - t0) + " evt/s");
}
private static double computePo(
final IScope scope,
final IAgentFilter filter,
final Map<Object, Integer> categoriesId,
final GamaMatrix<Double> fuzzytransitions,
final Double distance,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final int nbCat,
final int nb,
final IList<Double> similarities,
final IList<Object> weights) {
Map<IAgent, Integer> agsId = new TOrderedHashMap<IAgent, Integer>();
for (int i = 0; i < agents.length(scope); i++) {
agsId.put(agents.get(scope, i), i);
}
for (int i = 0; i < nb; i++) {
Object valObs = valsObs.get(i);
Object valSim = valsSim.get(i);
Object valInit = valsInit.get(i);
int valObsId = categoriesId.get(valObs);
int valSimId = categoriesId.get(valSim);
int valInitId = categoriesId.get(valInit);
IAgent agent = agents.get(scope, i);
double[] XaXs =
computeXaXs(
scope,
filter,
categoriesId,
agsId,
valObsId,
valSimId,
valInitId,
fuzzytransitions,
distance,
agent,
valsInit,
valsObs,
valsSim,
agents,
nbCat);
similarities.add(FastMath.min(XaXs[0], XaXs[1]));
}
double meanSimilarity = 0;
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
double val = weight * similarities.get(i);
total += weight;
meanSimilarity += val;
}
meanSimilarity /= total;
return meanSimilarity;
}
@Override
public void clearJob(String id) throws Exception {
if (id == null) {
log.warn("No job to clear; was null, returning");
return;
}
IAtomicReference<Job> jRef = h.getAtomicReference("job-" + id);
if (jRef.isNull()) return;
jRef.clear();
log.info("Destroyed job ref " + id);
Job remove = null;
for (Job j : jobs) {
if (j.getWorkerId().equals(id)) {
remove = j;
break;
}
}
jobs.remove(remove);
}
@Override
public void addTopic(String topic) throws Exception {
topics.add(topic);
}
/**
* Tracks worker ids that need state replication
*
* @param workerId the worker id to replicate
* @return the list of worker ids that need state replication
*/
@Override
public boolean needsReplicate(String workerId) {
return replicate.contains(workerId);
}
/**
* Adds a worker to the list to be replicate d
*
* @param workerId the worker id to add
*/
@Override
public void addReplicate(String workerId) {
if (!replicate.contains(workerId)) replicate.add(workerId);
}
@Override
public int numWorkers() {
int num = workers.size();
return num;
}
private static void computeXaXsTransitions(
final IScope scope,
final IAgentFilter filter,
final GamaMatrix<Double> fuzzytransitions,
final Double distance,
final IContainer<Integer, IAgent> agents,
final int nbCat,
final Map<List<Integer>, Map<Double, Double>> XaPerTransition,
final Map<List<Integer>, Map<Double, Double>> XsPerTransition,
final Set<Double> Xvals) {
IList<ILocation> locs = GamaListFactory.create(Types.POINT);
for (IAgent ag : agents.iterable(scope)) {
locs.add(ag.getLocation());
}
ILocation centralLoc = (ILocation) Stats.getMean(scope, locs);
if (filter != null) {
IAgent centralAg = scope.getTopology().getAgentClosestTo(scope, centralLoc, filter);
List<IAgent> neighbors =
distance == 0
? new ArrayList<IAgent>()
: new ArrayList<IAgent>(
scope.getTopology().getNeighborsOf(scope, centralAg, distance, filter));
double sizeNorm = FastMath.sqrt(centralAg.getEnvelope().getArea());
Map<IAgent, Double> distancesCoeff = new TOrderedHashMap<IAgent, Double>();
distancesCoeff.put(centralAg, 1.0);
for (IAgent ag : neighbors) {
double euclidDist = centralAg.getLocation().euclidianDistanceTo(ag.getLocation());
double dist = 1 / (1.0 + euclidDist / sizeNorm);
distancesCoeff.put(ag, dist);
}
for (int i = 0; i < nbCat; i++) {
for (int j = 0; j < nbCat; j++) {
for (int k = 0; k < nbCat; k++) {
List<Integer> ca = new ArrayList();
ca.add(i);
ca.add(j);
ca.add(k);
double xa = 0;
double xs = 0;
for (IAgent ag : distancesCoeff.keySet()) {
double dist = distancesCoeff.get(ag);
double xatmp = fuzzyTransition(scope, fuzzytransitions, nbCat, i, k, i, j) * dist;
double xstmp = fuzzyTransition(scope, fuzzytransitions, nbCat, i, j, i, k) * dist;
if (xatmp > xa) {
xa = xatmp;
}
if (xstmp > xs) {
xs = xstmp;
}
}
if (xa > 0) {
Map<Double, Double> mapxa = XaPerTransition.get(ca);
if (mapxa == null) {
mapxa = new TOrderedHashMap<Double, Double>();
mapxa.put(xa, 1.0);
XaPerTransition.put(ca, mapxa);
} else {
if (mapxa.containsKey(xa)) {
mapxa.put(xa, mapxa.get(xa) + 1.0);
} else {
mapxa.put(xa, 1.0);
}
}
Xvals.add(xa);
}
if (xs > 0) {
Map<Double, Double> mapxs = XsPerTransition.get(ca);
if (mapxs == null) {
mapxs = new TOrderedHashMap<Double, Double>();
mapxs.put(xs, 1.0);
XsPerTransition.put(ca, mapxs);
} else {
if (mapxs.containsKey(xa)) {
mapxs.put(xs, mapxs.get(xs) + 1.0);
} else {
mapxs.put(xs, 1.0);
}
}
Xvals.add(xs);
}
}
}
}
}
}
private static double computeSimilarity(
final IScope scope,
final IAgentFilter filter,
final Double distance,
final IList<Object> vals1,
final IList<Object> vals2,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final int nbCat,
final int nb,
final double[][] crispVector1,
final double[][] crispVector2,
final boolean[] sim,
final double[][] fuzzyVector1,
final double[][] fuzzyVector2,
final IList<Double> similarities,
final IList<Object> weights) {
Map<IAgent, Integer> agsId = new TOrderedHashMap<IAgent, Integer>();
for (int i = 0; i < agents.length(scope); i++) {
agsId.put(agents.get(scope, i), i);
}
for (int i = 0; i < nb; i++) {
if (sim[i]) {
similarities.add(1.0);
} else {
IAgent agent = agents.get(scope, i);
// double sizeNorm = agent.getPerimeter() / 4.0;
double sizeNorm = FastMath.sqrt(agent.getEnvelope().getArea());
List<IAgent> neighbors =
distance == 0 || filter == null
? new ArrayList<IAgent>()
: new ArrayList<IAgent>(
scope.getTopology().getNeighborsOf(scope, agent, distance, filter));
Map<IAgent, Double> distancesCoeff = new TOrderedHashMap<IAgent, Double>();
distancesCoeff.put(agent, 1.0);
for (IAgent ag : neighbors) {
double euclidDist = agent.getLocation().euclidianDistanceTo(ag.getLocation());
distancesCoeff.put(ag, 1 / (1.0 + euclidDist / sizeNorm));
}
for (int j = 0; j < nbCat; j++) {
double max1 = 0.0;
double max2 = 0.0;
for (IAgent ag : neighbors) {
int id = agsId.get(ag);
double val1 = crispVector1[id][j] * distancesCoeff.get(ag);
double val2 = crispVector2[id][j] * distancesCoeff.get(ag);
if (val1 > max1) {
max1 = val1;
}
if (val2 > max2) {
max2 = val2;
}
}
fuzzyVector1[i][j] = max1;
fuzzyVector2[i][j] = max2;
}
double s1Max = -1 * Double.MAX_VALUE;
double s2Max = -1 * Double.MAX_VALUE;
for (int j = 0; j < nbCat; j++) {
double s1 = FastMath.min(fuzzyVector1[i][j], crispVector2[i][j]);
double s2 = FastMath.min(fuzzyVector2[i][j], crispVector1[i][j]);
if (s1 > s1Max) {
s1Max = s1;
}
if (s2 > s2Max) {
s2Max = s2;
}
}
similarities.add(FastMath.min(s1Max, s2Max));
}
}
double meanSimilarity = 0;
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
double val = weight * similarities.get(i);
total += weight;
meanSimilarity += val;
}
meanSimilarity /= total;
return meanSimilarity;
}
@operator(
value = {"kappa"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {})
@doc(
value =
"kappa indicator for 2 map comparisons: kappa(list_vals1,list_vals2,categories, weights). Reference: Cohen, J. A coefficient of agreement for nominal scales. Educ. Psychol. Meas. 1960, 20. ",
examples = {
@example(
value =
"kappa([cat1,cat1,cat2,cat3,cat2],[cat2,cat1,cat2,cat1,cat2],[cat1,cat2,cat3], [1.0, 2.0, 3.0, 1.0, 5.0])",
isExecutable = false)
})
public static double kappa(
final IScope scope,
final IList<Object> vals1,
final IList<Object> vals2,
final List<Object> categories,
final IList<Object> weights) {
if (vals1 == null || vals2 == null) {
return 1;
}
int nb = vals1.size();
if (nb != vals2.size()) {
return 0;
}
int nbCat = categories.size();
double[] X = new double[nbCat];
double[] Y = new double[nbCat];
double[][] contigency = new double[nbCat][nbCat];
for (int j = 0; j < nbCat; j++) {
X[j] = 0;
Y[j] = 0;
for (int k = 0; k < nbCat; k++) {
contigency[j][k] = 0;
}
}
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
Object val1 = vals1.get(i);
Object val2 = vals2.get(i);
int indexVal1 = categoriesId.get(val1);
int indexVal2 = categoriesId.get(val2);
X[indexVal1] += weight;
Y[indexVal2] += weight;
contigency[indexVal1][indexVal2] += weight;
}
for (int j = 0; j < nbCat; j++) {
X[j] /= total;
Y[j] /= total;
for (int k = 0; k < nbCat; k++) {
contigency[j][k] /= total;
}
}
double po = 0;
double pe = 0;
for (int i = 0; i < nbCat; i++) {
po += contigency[i][i];
pe += X[i] * Y[i];
}
if (pe == 1) {
return 1;
}
return (po - pe) / (1 - pe);
}
public BaseHazelCastStateTracker(String connectionString, String type, int stateTrackerPort)
throws Exception {
log.info(
"Setting up hazelcast with type "
+ type
+ " connection string "
+ connectionString
+ " and port "
+ stateTrackerPort);
if (type.equals("master") && !PortTaken.portTaken(stateTrackerPort)) {
// sets up a proper connection string for reference wrt external actors needing a reference
if (connectionString.equals("master")) {
String host = InetAddress.getLocalHost().getHostName();
this.connectionString = host + ":" + stateTrackerPort;
}
this.hazelCastPort = stateTrackerPort;
config = hazelcast();
h = Hazelcast.newHazelcastInstance(config);
h.getCluster()
.addMembershipListener(
new MembershipListener() {
@Override
public void memberAdded(MembershipEvent membershipEvent) {
log.info("Member added " + membershipEvent.toString());
}
@Override
public void memberRemoved(MembershipEvent membershipEvent) {
log.info("Member removed " + membershipEvent.toString());
}
@Override
public void memberAttributeChanged(MemberAttributeEvent memberAttributeEvent) {
log.info("Member changed " + memberAttributeEvent.toString());
}
});
} else if (type.equals("master") && PortTaken.portTaken(stateTrackerPort))
throw new IllegalStateException(
"Specified type was master and the port specified was taken, please specify a different port");
else {
setConnectionString(connectionString);
log.info("Connecting to hazelcast on " + connectionString);
ClientConfig client = new ClientConfig();
client.getNetworkConfig().addAddress(connectionString);
h = HazelcastClient.newHazelcastClient(client);
}
this.type = type;
jobs = h.getList(JOBS);
workers = h.getList(WORKERS);
// we can make the assumption workers isn't empty because
// the master node by default comes with a applyTransformToDestination of workers
if (!this.type.equals("master")) {
while (workers.isEmpty()) {
log.warn("Waiting for data sync...");
Thread.sleep(1000);
}
log.info("Workers is " + workers.size());
}
begunTraining = h.getAtomicReference(BEGUN);
miniBatchSize = h.getAtomicReference(INPUT_SPLIT);
workerEnabled = h.getMap(WORKER_ENABLED);
replicate = h.getList(REPLICATE_WEIGHTS);
topics = h.getList(TOPICS);
updates = h.getList(UPDATES);
heartbeat = h.getMap(HEART_BEAT);
master = h.getAtomicReference(RESULT);
isPretrain = h.getAtomicReference(IS_PRETRAIN);
numTimesPretrain = h.getAtomicReference(NUM_TIMES_RUN_PRETRAIN);
numTimesPretrainRan = h.getAtomicReference(NUM_TIMES_PRETRAIN_RAN);
done = h.getAtomicReference(DONE);
validationEpochs = h.getAtomicReference(VALIDATION_EPOCHS);
improvementThreshold = h.getAtomicReference(IMPROVEMENT_THRESHOLD);
bestLoss = h.getAtomicReference(BEST_LOSS);
earlyStop = h.getAtomicReference(EARLY_STOP);
patience = h.getAtomicReference(PATIENCE);
patienceIncrease = h.getAtomicReference(PATIENCE_INCREASE);
numBatches = h.getAtomicReference(NUM_BATCHES_SO_FAR_RAN);
// applyTransformToDestination defaults only when master, otherwise, overrides previous values
if (type.equals("master")) {
begunTraining.set(false);
saver = createUpdateSaver();
numTimesPretrainRan.set(0);
numTimesPretrain.set(1);
isPretrain.set(true);
done.set(false);
resource = new StateTrackerDropWizardResource(this);
bestLoss.set(Double.POSITIVE_INFINITY);
earlyStop.set(true);
patience.set(40.0);
patienceIncrease.set(2.0);
improvementThreshold.set(0.995);
validationEpochs.set((int) Math.min(10, patience() / 2));
numBatches.set(0);
}
}
@Override
public void availableForWork(String id) {
if (!workers.contains(id)) workers.add(id);
}
@operator(
value = {"fuzzy_kappa_sim"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {IConcept.MAP})
@doc(
value =
"fuzzy kappa simulation indicator for 2 map comparisons: fuzzy_kappa_sim(agents_list,list_vals1,list_vals2, output_similarity_per_agents,fuzzy_transitions_matrix, fuzzy_distance, weights). Reference: Jasper van Vliet, Alex Hagen-Zanker, Jelle Hurkens, Hedwig van Delden, A fuzzy set approach to assess the predictive accuracy of land use simulations, Ecological Modelling, 24 July 2013, Pages 32-42, ISSN 0304-3800, ",
examples = {
@example(
value =
"fuzzy_kappa_sim([ag1, ag2, ag3, ag4, ag5], [cat1,cat1,cat2,cat3,cat2],[cat2,cat1,cat2,cat1,cat2], similarity_per_agents,[cat1,cat2,cat3],[[1,0,0,0,0,0,0,0,0],[0,1,0,0,0,0,0,0,0],[0,0,1,0,0,0,0,0,0],[0,0,0,1,0,0,0,0,0],[0,0,0,0,1,0,0,0,0],[0,0,0,0,0,1,0,0,0],[0,0,0,0,0,0,1,0,0],[0,0,0,0,0,0,0,1,0],[0,0,0,0,0,0,0,0,1]], 2,[1.0,3.0,2.0,2.0,4.0])",
isExecutable = false)
})
public static double fuzzyKappaSimulation(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final IList<Double> similarities,
final List<Object> categories,
final GamaMatrix<Double> fuzzytransitions,
final Double distance,
final IList<Object> weights) {
if (agents == null) {
return 1;
}
int nb = agents.length(scope);
if (nb < 1) {
return 1;
}
similarities.clear();
int nbCat = categories.size();
double[] nbObs = new double[nbCat];
double[] nbSim = new double[nbCat];
double[] nbInit = new double[nbCat];
double[][] nbInitObs = new double[nbCat][nbCat];
double[][] nbInitSim = new double[nbCat][nbCat];
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
Map<List<Integer>, Map<Double, Double>> XaPerTransition =
new TOrderedHashMap<List<Integer>, Map<Double, Double>>();
Map<List<Integer>, Map<Double, Double>> XsPerTransition =
new TOrderedHashMap<List<Integer>, Map<Double, Double>>();
Set<Double> Xvals = new HashSet<Double>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
for (int i = 0; i < nbCat; i++) {
nbInit[i] = 0;
nbObs[i] = 0;
nbSim[i] = 0;
for (int j = 0; j < nbCat; j++) {
nbInitObs[i][j] = 0;
nbInitSim[i][j] = 0;
}
}
IAgentFilter filter = In.list(scope, agents);
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
int idCatInit = categoriesId.get(valsInit.get(i));
int idCatObs = categoriesId.get(valsObs.get(i));
int idCatSim = categoriesId.get(valsSim.get(i));
nbInit[idCatInit] += weight;
nbSim[idCatSim] += weight;
nbObs[idCatObs] += weight;
nbInitObs[idCatInit][idCatObs] += weight;
nbInitSim[idCatInit][idCatSim] += weight;
}
double po =
computePo(
scope,
filter,
categoriesId,
fuzzytransitions,
distance,
valsInit,
valsObs,
valsSim,
agents,
nbCat,
nb,
similarities,
weights);
double pe = 0;
computeXaXsTransitions(
scope,
filter,
fuzzytransitions,
distance,
agents,
nbCat,
XaPerTransition,
XsPerTransition,
Xvals);
for (int i = 0; i < nbCat; i++) {
for (int j = 0; j < nbCat; j++) {
for (int k = 0; k < nbCat; k++) {
List<Integer> ca = new ArrayList<Integer>();
ca.add(i);
ca.add(j);
ca.add(k);
Map<Double, Double> pmuXa = XaPerTransition.get(ca);
Map<Double, Double> pmuXs = XsPerTransition.get(ca);
double emu = 0;
for (Double xval : Xvals) {
double XaVal = pmuXa == null || !pmuXa.containsKey(xval) ? 0 : pmuXa.get(xval);
double XsVal = pmuXs == null || !pmuXs.containsKey(xval) ? 0 : pmuXs.get(xval);
double proba = xval * XaVal * XsVal;
emu += proba;
}
double poas = nbInit[i] == 0 ? 0 : nbInitObs[i][j] / nbInit[i] * nbInitSim[i][k] / total;
pe += emu * poas;
}
}
}
if (pe == 1) {
return 1;
}
return (po - pe) / (1 - pe);
}
@operator(
value = {"fuzzy_kappa"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {})
@doc(
value =
"fuzzy kappa indicator for 2 map comparisons: fuzzy_kappa(agents_list,list_vals1,list_vals2, output_similarity_per_agents,categories,fuzzy_categories_matrix, fuzzy_distance, weights). Reference: Visser, H., and T. de Nijs, 2006. The map comparison kit, Environmental Modelling & Software, 21",
examples = {
@example(
value =
"fuzzy_kappa([ag1, ag2, ag3, ag4, ag5],[cat1,cat1,cat2,cat3,cat2],[cat2,cat1,cat2,cat1,cat2], similarity_per_agents,[cat1,cat2,cat3],[[1,0,0],[0,1,0],[0,0,1]], 2, [1.0,3.0,2.0,2.0,4.0])",
isExecutable = false)
})
public static double fuzzyKappa(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<Object> vals1,
final IList<Object> vals2,
final IList<Double> similarities,
final List<Object> categories,
final GamaMatrix<Double> fuzzycategories,
final Double distance,
final IList<Object> weights) {
if (agents == null) {
return 1;
}
int nb = agents.length(scope);
if (nb < 1) {
return 1;
}
int nbCat = categories.size();
similarities.clear();
boolean[] sim = new boolean[nb];
double[][] crispVector1 = new double[nb][nbCat];
double[][] crispVector2 = new double[nb][nbCat];
double[][] fuzzyVector1 = new double[nb][nbCat];
double[][] fuzzyVector2 = new double[nb][nbCat];
double[] X = new double[nbCat];
double[] Y = new double[nbCat];
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
IAgentFilter filter = In.list(scope, agents);
computeXYCrispVector(
scope,
categoriesId,
categories,
vals1,
vals2,
fuzzycategories,
nbCat,
nb,
crispVector1,
crispVector2,
X,
Y,
sim,
weights);
double meanSimilarity =
computeSimilarity(
scope,
filter,
distance,
vals1,
vals2,
agents,
nbCat,
nb,
crispVector1,
crispVector2,
sim,
fuzzyVector1,
fuzzyVector2,
similarities,
weights);
List<Double> rings = new ArrayList<Double>();
Map<Double, Integer> ringsPn = new TOrderedHashMap<Double, Integer>();
int nbRings = buildRings(scope, filter, distance, rings, ringsPn, agents);
double similarityExpected = computeExpectedSim(nbCat, X, Y, nbRings, rings, ringsPn);
if (similarityExpected == 1) {
return 1;
}
return (meanSimilarity - similarityExpected) / (1 - similarityExpected);
}
@operator(
value = {"kappa_sim"},
content_type = IType.FLOAT,
category = {IOperatorCategory.MAP_COMPARAISON},
concept = {})
@doc(
value =
"kappa simulation indicator for 2 map comparisons: kappa(list_valsInits,list_valsObs,list_valsSim, categories, weights). Reference: van Vliet, J., Bregt, A.K. & Hagen-Zanker, A. (2011). Revisiting Kappa to account for change in the accuracy assessment of land-use change models, Ecological Modelling 222(8)",
examples = {
@example(
value =
"kappa([cat1,cat1,cat2,cat2,cat2],[cat2,cat1,cat2,cat1,cat3],[cat2,cat1,cat2,cat3,cat3], [cat1,cat2,cat3],[1.0, 2.0, 3.0, 1.0, 5.0])",
isExecutable = false)
})
public static double kappaSimulation(
final IScope scope,
final IList<Object> valsInit,
final IList<Object> valsObs,
final IList<Object> valsSim,
final List<Object> categories,
final IList<Object> weights) {
if (valsInit == null || valsObs == null || valsSim == null) {
return 1;
}
int nb = valsInit.size();
if (nb != valsObs.size() || nb != valsSim.size()) {
return 0;
}
int nbCat = categories.size();
double[] O = new double[nbCat];
double[][] contigency = new double[nbCat][nbCat];
double[][] contigencyOA = new double[nbCat][nbCat];
double[][] contigencyOS = new double[nbCat][nbCat];
for (int j = 0; j < nbCat; j++) {
O[j] = 0;
for (int k = 0; k < nbCat; k++) {
contigency[j][k] = 0;
contigencyOA[j][k] = 0;
contigencyOS[j][k] = 0;
}
}
Map<Object, Integer> categoriesId = new TOrderedHashMap<Object, Integer>();
for (int i = 0; i < nbCat; i++) {
categoriesId.put(categories.get(i), i);
}
double total = 0;
for (int i = 0; i < nb; i++) {
double weight = weights == null ? 1.0 : Cast.asFloat(scope, weights.get(i));
total += weight;
Object val1 = valsObs.get(i);
Object val2 = valsSim.get(i);
Object valO = valsInit.get(i);
int indexVal1 = categoriesId.get(val1);
int indexVal2 = categoriesId.get(val2);
int indexValO = categoriesId.get(valO);
O[indexValO] += weight;
contigency[indexVal1][indexVal2] += weight;
contigencyOA[indexValO][indexVal1] += weight;
contigencyOS[indexValO][indexVal2] += weight;
}
for (int j = 0; j < nbCat; j++) {
for (int k = 0; k < nbCat; k++) {
contigency[j][k] /= total;
if (O[j] > 0) {
contigencyOA[j][k] /= O[j];
contigencyOS[j][k] /= O[j];
}
}
O[j] /= total;
}
double po = 0;
double pe = 0;
for (int j = 0; j < nbCat; j++) {
po += contigency[j][j];
double sum = 0;
for (int i = 0; i < nbCat; i++) {
sum += contigencyOA[j][i] * contigencyOS[j][i];
}
pe += O[j] * sum;
}
if (pe == 1) {
return 1;
}
return (po - pe) / (1 - pe);
}
/**
* Updates the status of the worker to not needing replication
*
* @param workerId the worker id to update
*/
@Override
public void doneReplicating(String workerId) {
replicate.remove(workerId);
}