protected boolean beginExecution(final IScope scope) throws GamaRuntimeException {
final IAgent agent = scope.getAgentScope();
if (scope.interrupted()) {
return false;
}
final Boolean enter = (Boolean) agent.getAttribute(ENTER);
Map<String, Object> memory = (Map) agent.getAttribute(STATE_MEMORY);
if (enter || memory == null) {
memory = new THashMap();
agent.setAttribute(STATE_MEMORY, memory);
} else {
for (final Map.Entry<String, Object> entry : memory.entrySet()) {
scope.addVarWithValue(entry.getKey(), entry.getValue());
}
}
if (enter) {
if (enterActions != null) {
enterActions.executeOn(scope);
}
if (agent.dead()) {
return false;
}
agent.setAttribute(ENTER, false);
}
return true;
}
private static Instances convertToInstances(
final IScope scope,
final IList<String> attributes,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents)
throws GamaRuntimeException {
FastVector attribs = new FastVector();
for (String att : attributes) {
attribs.addElement(new Attribute(att));
}
Instances dataset =
new Instances(scope.getAgentScope().getName(), attribs, agents.length(scope));
for (IAgent ag : agents.iterable(scope)) {
int nb = attributes.size();
double vals[] = new double[nb];
for (int i = 0; i < nb; i++) {
String attrib = attributes.get(i);
Double var = Cast.asFloat(scope, ag.getDirectVarValue(scope, attrib));
vals[i] = var;
}
Instance instance = new Instance(1, vals);
dataset.add(instance);
}
return dataset;
}
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;
}
protected String evaluateTransitions(final IScope scope) throws GamaRuntimeException {
final IAgent agent = scope.getAgentScope();
for (int i = 0; i < transitionsSize; i++) {
final FsmTransitionStatement transition = transitions.get(i);
if (transition.evaluatesTrueOn(scope)) {
final String futureState = transition.getName();
haltOn(scope);
transition.executeOn(scope);
scope.setAgentVarValue(agent, STATE, futureState);
return futureState;
}
}
if (!agent.dead()) {
scope.saveAllVarValuesIn((Map) agent.getAttribute(STATE_MEMORY));
}
return name;
}
@Override
public IPopulation getPopulation(final IScope scope) {
final IAgent a = scope.getAgentScope();
IPopulation result = null;
if (a != null) {
// AD 19/09/13 Patch to allow experiments to gain access to the simulation populations
result = a.getPopulationFor(this);
}
return result;
}
@operator(
value = {IKeyword.AT, "@"},
type = ITypeProvider.FIRST_CONTENT_TYPE)
@doc(
deprecated =
"The use of at on a species is deprecated, please use it one a population instead (list(species_name) instead of species_name)")
public static IAgent at(final IScope scope, final ISpecies s, final GamaPoint val)
throws GamaRuntimeException {
return scope.getAgentScope().getPopulationFor(s).getAgent(scope, val);
}
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 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 IList listValue(final IScope scope, final IType contentsType, final boolean copy)
throws GamaRuntimeException {
// return getPopulation(scope).listValue(scope, contentsType);
// hqnghi 16/04/14
IPopulation pop = getPopulation(scope);
if (pop == null) {
pop = scope.getSimulationScope().getPopulationFor(contentsType.getName());
}
return pop.listValue(scope, contentsType, false);
// end-hqnghi
}
@operator(
value = {"clustering_em"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by EM Algorithm based on the given attributes. Some paremeters can be defined: "
+ "max_iterations: the maximum number of iterations to perform;"
+ "num_clusters: the number of clusters; minStdDev: minimum allowable standard deviation",
examples = {
@example(
value =
"clustering_em([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"max_iterations\"::10, \"num_clusters\"::3])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_simple_kmeans",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringEM(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
EM em = new EM();
em.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("max_iterations")) {
em.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
}
if (parameters.containsKey("num_clusters")) {
em.setNumClusters(Cast.asInt(scope, parameters.get("num_clusters")));
}
if (parameters.containsKey("minStdDev")) {
em.setMinStdDev(Cast.asFloat(scope, parameters.get("minStdDev")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, em, attributes, agents);
return groupes;
}
@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;
}
@operator(
value = {"clustering_cobweb"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clusteredby CobWeb Algorithm based on the given attributes. Some paremeters can be defined: "
+ "acuity: minimum standard deviation for numeric attributes; "
+ "cutoff: category utility threshold by which to prune nodes seed",
examples = {
@example(
value =
"clustering_cobweb([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"acuity\"::3.0, \"cutoff\"::0.5)",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_simple_kmeans",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringCobweb(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
Cobweb cobweb = new Cobweb();
cobweb.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("acuity")) {
cobweb.setAcuity(Cast.asFloat(scope, parameters.get("acuity")));
}
if (parameters.containsKey("cutoff")) {
cobweb.setCutoff(Cast.asFloat(scope, parameters.get("cutoff")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, cobweb, attributes, agents);
return groupes;
}
public int getDate(IScope scope) {
return scope.getClock().getCycle();
}
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 = {"clustering_xmeans"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by X-Means Algorithm based on the given attributes. Some paremeters can be defined: bin_value: value given for true value of boolean attributes; cut_off_factor: the cut-off factor to use;"
+ "distance_f: The distance function to use. 4 possible distance functions: euclidean (by default) ; 'chebyshev', 'manhattan' or 'levenshtein'; "
+ "max_iterations: the maximum number of iterations to perform; max_kmeans: the maximum number of iterations to perform in KMeans; max_kmeans_for_children: the maximum number of iterations KMeans that is performed on the child centers;"
+ "max_num_clusters: the maximum number of clusters; min_num_clusters: the minimal number of clusters",
examples = {
@example(
value =
"clustering_xmeans([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\", \"is_male\"],[\"bin_value\"::1.0, \"distance_f\"::\"manhattan\", \"max_num_clusters\"::10, \"min_num_clusters\"::2])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_simple_kmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringXMeans(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters)
throws GamaRuntimeException {
XMeans xmeans = new XMeans();
xmeans.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
if (parameters.containsKey("bin_value")) {
xmeans.setBinValue(Cast.asFloat(scope, parameters.get("bin_value")));
}
if (parameters.containsKey("cut_off_factor")) {
xmeans.setCutOffFactor(Cast.asFloat(scope, parameters.get("cut_off_factor")));
}
if (parameters.containsKey("distance_f")) {
String distanceFct = Cast.asString(scope, parameters.get("distance_f"));
if (distanceFct.equals("chebyshev")) {
xmeans.setDistanceF(new ChebyshevDistance());
} else if (distanceFct.equals("manhattan")) {
xmeans.setDistanceF(new ManhattanDistance());
} else if (distanceFct.equals("levenshtein")) {
xmeans.setDistanceF(new EditDistance());
}
}
if (parameters.containsKey("max_iterations")) {
try {
xmeans.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
} catch (Exception e) {
}
}
if (parameters.containsKey("max_kmeans")) {
xmeans.setMaxKMeans(Cast.asInt(scope, parameters.get("max_kmeans")));
}
if (parameters.containsKey("max_kmeans_for_children")) {
xmeans.setMaxKMeansForChildren(
Cast.asInt(scope, parameters.get("max_kmeans_for_children")));
}
if (parameters.containsKey("max_num_clusters")) {
xmeans.setMaxNumClusters(Cast.asInt(scope, parameters.get("max_num_clusters")));
}
if (parameters.containsKey("min_num_clusters")) {
xmeans.setMinNumClusters(Cast.asInt(scope, parameters.get("min_num_clusters")));
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, xmeans, attributes, agents);
return groupes;
}
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);
}
}
}
}
}
}
@Override
public Object value(final IScope scope) {
// return scope.getSimulationScope();
IAgent sc = scope.getAgentScope();
return sc.getScope().getRoot().getScope().getSimulationScope();
}
@operator(
value = {"clustering_simple_kmeans"},
content_type = IType.LIST,
category = {IOperatorCategory.STATISTICAL},
concept = {IConcept.STATISTIC})
@doc(
value =
"A list of agent groups clustered by K-Means Algorithm based on the given attributes. Some paremeters can be defined: "
+ "distance_f: The distance function to use. 4 possible distance functions: euclidean (by default) ; 'chebyshev', 'manhattan' or 'levenshtein'; "
+ "dont_replace_missing_values: if false, replace missing values globally with mean/mode; max_iterations: the maximum number of iterations to perform;"
+ "num_clusters: the number of clusters",
examples = {
@example(
value =
"clustering_simple_kmeans([ag1, ag2, ag3, ag4, ag5],[\"size\",\"age\", \"weight\"],[\"distance_f\"::\"manhattan\", \"num_clusters\"::3])",
equals = "for example, can return [[ag1, ag3], [ag2], [ag4, ag5]]",
isExecutable = false)
},
see = {
"clustering_xmeans",
"clustering_em",
"clustering_farthestFirst",
"clustering_DBScan",
"clustering_cobweb"
})
public static IList<IList<IAgent>> primClusteringSimpleKMeans(
final IScope scope,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents,
final IList<String> attributes,
final GamaMap<String, Object> parameters) {
SimpleKMeans kmeans = new SimpleKMeans();
kmeans.setSeed(Cast.asInt(scope, scope.getRandom().getSeed()));
if (parameters != null) {
try {
if (parameters.containsKey("distance_f")) {
String distanceFct = Cast.asString(scope, parameters.get("distance_f"));
if (distanceFct.equals("chebyshev")) {
kmeans.setDistanceFunction(new ChebyshevDistance());
} else if (distanceFct.equals("manhattan")) {
kmeans.setDistanceFunction(new ManhattanDistance());
} else if (distanceFct.equals("levenshtein")) {
kmeans.setDistanceFunction(new EditDistance());
}
}
if (parameters.containsKey("dont_replace_missing_values")) {
kmeans.setDontReplaceMissingValues(
Cast.asBool(scope, parameters.get("dont_replace_missing_values")));
}
if (parameters.containsKey("max_iterations")) {
kmeans.setMaxIterations(Cast.asInt(scope, parameters.get("max_iterations")));
}
if (parameters.containsKey("num_clusters")) {
kmeans.setNumClusters(Cast.asInt(scope, parameters.get("num_clusters")));
}
} catch (Exception e) {
}
}
IList<IList<IAgent>> groupes = clusteringUsingWeka(scope, kmeans, attributes, agents);
return groupes;
}