public void doRFileEvaluate(final IScope scope, final IContainer param) {
int size = param.length(scope);
// if ( size == 0 ) { throw GamaRuntimeException.error("Missing Parameter Exception", scope); }
final String RFile = getPath();
try {
// Call R
RCaller caller = new RCaller();
String RPath = GamaPreferences.LIB_R.value(scope).getPath();
caller.setRscriptExecutable(RPath);
double[] vectorParam = new double[param.length(scope)];
int k = 0;
for (Object o : param.iterable(scope)) {
vectorParam[k++] = Cast.asFloat(scope, o);
}
RCode c = new RCode();
// Adding the parameters
c.addDoubleArray("vectorParam", vectorParam);
// Adding the codes in file
List<String> R_statements = new ArrayList<String>();
// tmthai.begin----------------------------------------------------------------------------
String fullPath = FileUtils.constructAbsoluteFilePath(scope, RFile, true);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.RScript:" + RPath);
GuiUtils.debug("Stats.R_compute_param.Param:" + vectorParam.toString());
GuiUtils.debug("Stats.R_compute_param.RFile:" + RFile);
GuiUtils.debug("Stats.R_compute_param.fullPath:" + fullPath);
}
// FileReader fr = new FileReader(RFile);
FileReader fr = new FileReader(fullPath);
// tmthai.end----------------------------------------------------------------------------
BufferedReader br = new BufferedReader(fr);
String statement;
while ((statement = br.readLine()) != null) {
c.addRCode(statement);
R_statements.add(statement);
// java.lang.System.out.println(statement);
}
br.close();
fr.close();
caller.setRCode(c);
GamaMap<String, IList> result = GamaMapFactory.create(Types.STRING, Types.LIST);
String var = computeVariable(R_statements.get(R_statements.size() - 1).toString());
caller.runAndReturnResult(var);
// DEBUG:
// java.lang.System.out.println("Name: '" + R_statements.length(scope) + "'");
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.R_statements.length: '" + R_statements.size() + "'");
}
for (String name : caller.getParser().getNames()) {
String[] results = null;
results = caller.getParser().getAsStringArray(name);
// java.lang.System.out.println("Name: '" + name + "'");
if (DEBUG) {
GuiUtils.debug(
"Stats.R_compute_param.caller.Name: '"
+ name
+ "' length: "
+ results.length
+ " - Value: "
+ results.toString());
}
result.put(name, GamaListFactory.create(scope, Types.NO_TYPE, results));
}
if (DEBUG) {
GuiUtils.debug("Stats.R_compute_param.return:" + result.serialize(false));
}
setBuffer(result);
} catch (Exception ex) {
throw GamaRuntimeException.error("RCallerExecutionException " + ex.getMessage(), scope);
}
}
private static IList<IList<IAgent>> clusteringUsingWeka(
final IScope scope,
final Clusterer clusterer,
final IList<String> attributes,
final IAddressableContainer<Integer, IAgent, Integer, IAgent> agents)
throws GamaRuntimeException {
Instances dataset = convertToInstances(scope, attributes, agents);
try {
clusterer.buildClusterer(dataset);
IList<IList<IAgent>> groupes = GamaListFactory.create(Types.LIST.of(Types.AGENT));
for (int i = 0; i < clusterer.numberOfClusters(); i++) {
groupes.add(GamaListFactory.<IAgent>create(Types.AGENT));
}
for (int i = 0; i < dataset.numInstances(); i++) {
Instance inst = dataset.instance(i);
int clusterIndex = -1;
clusterIndex = clusterer.clusterInstance(inst);
IList<IAgent> groupe = groupes.get(clusterIndex);
groupe.add(agents.get(scope, i));
}
return groupes;
} catch (Exception e) {
return null;
}
}
@Override
public IList value(final IScope scope) throws GamaRuntimeException {
if (isConst && computed) {
return GamaListFactory.createWithoutCasting(getType().getContentType(), values);
}
for (int i = 0; i < elements.length; i++) {
if (elements[i] == null) {
computed = false;
return GamaListFactory.EMPTY_LIST;
}
values[i] = elements[i].value(scope);
}
computed = true;
// Important NOT to return the reference to values (but a copy of it).
return GamaListFactory.createWithoutCasting(getType().getContentType(), values);
}
@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;
}
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<String> getAttributeNames(final IScope scope) {
return GamaListFactory.create(scope, Types.STRING, getVarNames());
}
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);
}
}
}
}
}
}
public void doRFileEvaluate(final IScope scope) {
final String RFile = getPath();
try {
// Call R
RCaller caller = new RCaller();
String RPath = GamaPreferences.LIB_R.value(scope).getPath();
caller.setRscriptExecutable(RPath);
// caller.setRscriptExecutable("\"" + RPath + "\"");
// if(java.lang.System.getProperty("os.name").startsWith("Mac"))
// {
// caller.setRscriptExecutable(RPath);
// }
RCode c = new RCode();
List<String> R_statements = new ArrayList<String>();
// tmthai.begin----------------------------------------------------------------------------
String fullPath = FileUtils.constructAbsoluteFilePath(scope, RFile, true);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute.RScript:" + RPath);
GuiUtils.debug("Stats.R_compute.RFile:" + RFile);
GuiUtils.debug("Stats.R_compute.fullPath:" + fullPath);
}
// FileReader fr = new FileReader(RFile);
FileReader fr = new FileReader(fullPath);
// tmthai.end----------------------------------------------------------------------------
BufferedReader br = new BufferedReader(fr);
String statement;
while ((statement = br.readLine()) != null) {
c.addRCode(statement);
R_statements.add(statement);
// java.lang.System.out.println(statement);
if (DEBUG) {
GuiUtils.debug("Stats.R_compute.statement:" + statement);
}
}
fr.close();
br.close();
caller.setRCode(c);
GamaMap<String, IList> result = GamaMapFactory.create(Types.STRING, Types.LIST);
String var = computeVariable(R_statements.get(R_statements.size() - 1).toString());
caller.runAndReturnResult(var);
for (String name : caller.getParser().getNames()) {
Object[] results = null;
results = caller.getParser().getAsStringArray(name);
// for (int i = 0; i < results.length; i++) {
// java.lang.System.out.println(results[i]);
// }
if (DEBUG) {
GuiUtils.debug(
"Stats.R_compute_param.caller.Name: '"
+ name
+ "' length: "
+ results.length
+ " - Value: "
+ results.toString());
}
result.put(name, GamaListFactory.createWithoutCasting(Types.NO_TYPE, results));
}
if (DEBUG) {
GuiUtils.debug("Stats.R_compute.return:" + result.serialize(false));
}
// return result;
setBuffer(result);
} catch (Exception ex) {
throw GamaRuntimeException.error("RCallerExecutionException " + ex.getMessage(), scope);
}
}