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;
}
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;
}
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 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;
}
}
/**
* Method createFrom() Method used to read initial values and attributes from a CSV values
* descring a synthetic population
*
* @author Vo Duc An
* @since 04-09-2012
* @see msi.gama.common.interfaces.ICreateDelegate#createFrom(msi.gama.runtime.IScope,
* java.util.List, int, java.lang.Object)
*/
@Override
public boolean createFrom(
final IScope scope,
final List<Map> inits,
final Integer max,
final Object source,
final Arguments init,
final CreateStatement statement) {
final IList<Map> syntheticPopulation = (IList<Map>) source;
final int num =
max == null
? syntheticPopulation.length(scope) - 1
: CmnFastMath.min(syntheticPopulation.length(scope) - 1, max);
// the first element of syntheticPopulation a string (i.e.,
// "genstar_population")
for (int i = 1; i < num; i++) {
final Map genstarInit = syntheticPopulation.get(i);
statement.fillWithUserInit(scope, genstarInit);
// mix genstar's init attributes with user's init
inits.add(genstarInit);
}
return true;
}
public void updateXValues(IScope scope, int chartCycle, int targetNb) {
Object xval, xlab;
if (this.useXSource || this.useXLabels) {
if (this.useXSource) {
xval = xsource.resolveAgainst(scope).value(scope);
} else {
xval = xlabels.resolveAgainst(scope).value(scope);
}
if (this.useXLabels) {
xlab = xlabels.resolveAgainst(scope).value(scope);
} else {
xlab = xsource.resolveAgainst(scope).value(scope);
}
if (xval instanceof GamaList) {
IList xv2 = Cast.asList(scope, xval);
IList xl2 = Cast.asList(scope, xlab);
if (this.useXSource && xv2.size() > 0 && xv2.get(0) instanceof Number) {
XSeriesValues = new ArrayList<Double>();
Xcategories = new ArrayList<String>();
for (int i = 0; i < xv2.size(); i++) {
XSeriesValues.add(new Double(Cast.asFloat(scope, xv2.get(i))));
Xcategories.add(Cast.asString(scope, xl2.get(i)));
}
} else {
if (xv2.size() > Xcategories.size()) {
Xcategories = new ArrayList<String>();
for (int i = 0; i < xv2.size(); i++) {
if (i >= XSeriesValues.size()) {
XSeriesValues.add(new Double(getXCycleOrPlusOneForBatch(scope, chartCycle)));
}
Xcategories.add(Cast.asString(scope, xl2.get(i)));
}
}
}
if (xv2.size() < targetNb) {
throw GamaRuntimeException.error(
"The x-serie length ("
+ xv2.size()
+ ") should NOT be shorter than any series length ("
+ targetNb
+ ") !",
scope);
}
} else {
if (this.useXSource && xval instanceof Number) {
double dvalue = Cast.asFloat(scope, xval);
String lvalue = Cast.asString(scope, xlab);
XSeriesValues.add(new Double(dvalue));
Xcategories.add(lvalue);
}
if (targetNb == -1 && !this.forceNoXAccumulate) targetNb = XSeriesValues.size() + 1;
while (XSeriesValues.size() < targetNb) {
XSeriesValues.add(new Double(getXCycleOrPlusOneForBatch(scope, chartCycle)));
Xcategories.add(Cast.asString(scope, xlab));
}
}
}
if (!this.useXSource && !this.useXLabels) {
if (targetNb == -1 && !this.forceNoXAccumulate && commonXindex >= XSeriesValues.size())
targetNb = XSeriesValues.size() + 1;
while (XSeriesValues.size() < targetNb) {
addCommonXValue(scope, getXCycleOrPlusOneForBatch(scope, chartCycle));
}
}
}
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);
}
@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 = {"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);
}
