@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<EarthModel> modelP =
new ObjectParameter<>(
EarthModel.MODEL_ID, EarthModel.class, SphericalVincentyEarthModel.class);
if (config.grab(modelP)) {
model = modelP.instantiateClass(config);
}
ObjectParameter<IndexFactory<O, ?>> innerP =
new ObjectParameter<>(
ProjectedIndex.Factory.Parameterizer.INDEX_ID, IndexFactory.class);
if (config.grab(innerP)) {
inner = innerP.instantiateClass(config);
}
Flag materializeF = new Flag(ProjectedIndex.Factory.Parameterizer.MATERIALIZE_FLAG);
if (config.grab(materializeF)) {
materialize = materializeF.isTrue();
}
Flag norefineF = new Flag(ProjectedIndex.Factory.Parameterizer.DISABLE_REFINE_FLAG);
if (config.grab(norefineF)) {
norefine = norefineF.isTrue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
FileParameter fileP = new FileParameter(FILE_ID, FileParameter.FileType.INPUT_FILE);
if (config.grab(fileP)) {
file = fileP.getValue();
}
PatternParameter idP = new PatternParameter(ID_ID, ID_PATTERN_DEFAULT);
if (config.grab(idP)) {
idpattern = idP.getValue();
}
PatternParameter scoreP = new PatternParameter(SCORE_ID);
if (config.grab(scoreP)) {
scorepattern = scoreP.getValue();
}
Flag inverstedF = new Flag(INVERTED_ID);
if (config.grab(inverstedF)) {
inverted = inverstedF.getValue();
}
ObjectParameter<ScalingFunction> scalingP =
new ObjectParameter<>(SCALING_ID, ScalingFunction.class, IdentityScaling.class);
if (config.grab(scalingP)) {
scaling = scalingP.instantiateClass(config);
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter deltaP = new DoubleParameter(DELTA_ID);
if (config.grab(deltaP)) {
delta = deltaP.doubleValue();
}
deltaP.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE);
IntParameter nP = new IntParameter(N_ID, 1);
nP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
if (config.grab(nP)) {
n = nP.intValue();
}
DoubleParameter alphaP = new DoubleParameter(ALPHA_ID, 1.);
alphaP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_DOUBLE);
if (config.grab(alphaP)) {
alpha = alphaP.doubleValue();
}
ObjectParameter<Distribution> distP =
new ObjectParameter<>(DIST_ID, Distribution.class, UniformDistribution.class);
if (config.grab(distP)) {
dist = distP.instantiateClass(config);
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<NumberVectorDistanceFunction<?>> distanceFunctionP =
new ObjectParameter<>(
EvaluateSilhouette.Parameterizer.DISTANCE_ID,
NumberVectorDistanceFunction.class,
EuclideanDistanceFunction.class);
if (config.grab(distanceFunctionP)) {
distance = distanceFunctionP.instantiateClass(config);
}
EnumParameter<NoiseHandling> noiseP =
new EnumParameter<NoiseHandling>(
EvaluateSilhouette.Parameterizer.NOISE_ID,
NoiseHandling.class,
NoiseHandling.TREAT_NOISE_AS_SINGLETONS);
if (config.grab(noiseP)) {
noiseOption = noiseP.getValue();
}
if (noiseOption == NoiseHandling.IGNORE_NOISE) {
Flag penalizeP = new Flag(EvaluateSilhouette.Parameterizer.NO_PENALIZE_ID);
if (config.grab(penalizeP)) {
penalize = penalizeP.isFalse();
}
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter quantileP =
new DoubleParameter(QUANTILE_ID, 0.1) //
.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE) //
.addConstraint(CommonConstraints.LESS_EQUAL_ONE_DOUBLE);
if (config.grab(quantileP)) {
quantile = quantileP.doubleValue();
}
DoubleParameter samplingP =
new DoubleParameter(SAMPLING_ID) //
.addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE);
if (config.grab(samplingP)) {
sampling = samplingP.doubleValue();
}
Flag nozerosF = new Flag(NOZEROS_ID);
if (config.grab(nozerosF)) {
nozeros = nozerosF.isTrue();
}
RandomParameter randP = new RandomParameter(SEED_ID);
if (config.grab(randP)) {
rand = randP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
PatternParameter positiveClassNameP = new PatternParameter(POSITIVE_CLASS_NAME_ID);
positiveClassNameP.setOptional(true);
if (config.grab(positiveClassNameP)) {
positiveClassName = positiveClassNameP.getValue();
}
IntParameter binsP = new IntParameter(BINS_ID, 50);
binsP.addConstraint(CommonConstraints.GREATER_THAN_ONE_INT);
if (config.grab(binsP)) {
bins = binsP.getValue();
}
ObjectParameter<ScalingFunction> scalingP =
new ObjectParameter<>(SCALING_ID, ScalingFunction.class, IdentityScaling.class);
if (config.grab(scalingP)) {
scaling = scalingP.instantiateClass(config);
}
Flag splitfreqF = new Flag(SPLITFREQ_ID);
if (config.grab(splitfreqF)) {
splitfreq = splitfreqF.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter probP =
new DoubleParameter(PROB_ID) //
.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE) //
.addConstraint(CommonConstraints.LESS_EQUAL_ONE_DOUBLE);
if (config.grab(probP)) {
prob = probP.getValue().doubleValue();
}
RandomParameter rndP = new RandomParameter(SEED_ID);
if (config.grab(rndP)) {
rnd = rndP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final FileParameter MATRIX_PARAM =
new FileParameter(MATRIX_ID, FileParameter.FileType.INPUT_FILE);
if (config.grab(MATRIX_PARAM)) {
matrixfile = MATRIX_PARAM.getValue();
}
final ObjectParameter<DistanceParser> PARSER_PARAM =
new ObjectParameter<>(PARSER_ID, DistanceParser.class, AsciiDistanceParser.class);
if (config.grab(PARSER_PARAM)) {
parser = PARSER_PARAM.instantiateClass(config);
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<DistributionEstimator<D>> innerP =
new ObjectParameter<>(INNER_ID, DistributionEstimator.class);
if (config.grab(innerP)) {
inner = innerP.instantiateClass(config);
}
DoubleParameter trimP = new DoubleParameter(TRIM_ID);
trimP.addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE);
trimP.addConstraint(CommonConstraints.LESS_THAN_HALF_DOUBLE);
if (config.grab(trimP)) {
trim = trimP.doubleValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final IntParameter pK =
new IntParameter(K_ID) //
.addConstraint(CommonConstraints.GREATER_THAN_ONE_INT);
if (config.grab(pK)) {
k = pK.getValue();
}
final ObjectParameter<ReferencePointsHeuristic> refpP =
new ObjectParameter<>(
REFP_ID, ReferencePointsHeuristic.class, GridBasedReferencePoints.class);
if (config.grab(refpP)) {
refp = refpP.instantiateClass(config);
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<PrimitiveDistanceFunction<NumberVector>> distanceFunctionP =
new ObjectParameter<>(
DISTANCE_ID, PrimitiveDistanceFunction.class, EuclideanDistanceFunction.class);
if (config.grab(distanceFunctionP)) {
distance = distanceFunctionP.instantiateClass(config);
}
EnumParameter<NoiseHandling> noiseP =
new EnumParameter<NoiseHandling>(
NOISE_ID, NoiseHandling.class, NoiseHandling.TREAT_NOISE_AS_SINGLETONS);
if (config.grab(noiseP)) {
noiseHandling = noiseP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final Flag flag = new Flag(INVERT_ID);
if (config.grab(flag)) {
invert = flag.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final DoubleParameter param = new DoubleParameter(D_ID);
if (config.grab(param)) {
eps = param.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleArrayListParameter meansP = new DoubleArrayListParameter(INITIAL_MEANS);
if (config.grab(meansP)) {
initialMeans = meansP.getValue().toArray(new double[0][]);
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
IntParameter startP = new IntParameter(STARTK_ID, 3);
if (config.grab(startP)) {
startk = startP.intValue();
}
IntParameter maxkP = new IntParameter(MAXK_ID, 20);
if (config.grab(maxkP)) {
maxk = maxkP.intValue();
}
IntParameter samplesP = new IntParameter(SAMPLE_ID, 1000);
if (config.grab(samplesP)) {
samples = samplesP.intValue();
}
RandomParameter seedP = new RandomParameter(SEED_ID);
if (config.grab(seedP)) {
rnd = seedP.getValue();
}
IntParameter dimP = new IntParameter(DIM_ID);
if (config.grab(dimP)) {
dim = dimP.intValue();
}
EnumParameter<Aggregate> aggP =
new EnumParameter<>(AGGREGATE_ID, Aggregate.class, Aggregate.MED_MAD);
if (config.grab(aggP)) {
agg = aggP.getValue();
}
EnumParameter<OutputFormat> formatP =
new EnumParameter<>(FORMAT_ID, OutputFormat.class, OutputFormat.TABULAR);
if (config.grab(formatP)) {
format = formatP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<DistanceFunction<? super O>> distanceFunctionP =
makeParameterDistanceFunction(EuclideanDistanceFunction.class, DistanceFunction.class);
if (config.grab(distanceFunctionP)) {
distanceFunction = distanceFunctionP.instantiateClass(config);
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter palphaP = new DoubleParameter(EIGENPAIR_FILTER_PALPHA, DEFAULT_PALPHA);
palphaP.addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE);
palphaP.addConstraint(CommonConstraints.LESS_THAN_ONE_DOUBLE);
if (config.grab(palphaP)) {
palpha = palphaP.getValue();
}
DoubleParameter walphaP =
new DoubleParameter(
WeakEigenPairFilter.Parameterizer.EIGENPAIR_FILTER_WALPHA, DEFAULT_WALPHA);
walphaP.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_DOUBLE);
if (config.grab(walphaP)) {
walpha = walphaP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter dofP = new DoubleParameter(ChiSquaredDistribution.Parameterizer.DOF_ID);
if (config.grab(dofP)) {
dof = dofP.doubleValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final IntParameter param = new IntParameter(HISTOGRAM_BINS_ID, 100);
param.addConstraint(CommonConstraints.GREATER_THAN_ONE_INT);
if (config.grab(param)) {
numbins = param.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final DoubleParameter rmaxP = new DoubleParameter(RMAX_ID);
if (config.grab(rmaxP)) {
rmax = rmaxP.doubleValue();
}
final IntParameter nminP = new IntParameter(NMIN_ID, 20);
if (config.grab(nminP)) {
nmin = nminP.intValue();
}
final DoubleParameter alphaP = new DoubleParameter(ALPHA_ID, 0.5);
if (config.grab(alphaP)) {
alpha = alphaP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
EnumParameter<Linkage> linkageP = new EnumParameter<>(LINKAGE_ID, Linkage.class);
linkageP.setDefaultValue(Linkage.WARD);
if (config.grab(linkageP)) {
linkage = linkageP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
IntParameter portP = new IntParameter(PORT_ID, port);
portP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
portP.addConstraint(new LessEqualConstraint(65535));
if (config.grab(portP)) {
this.port = portP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
generator = config.tryInstantiate(GeneratorXMLDatabaseConnection.class);
// Output file
outputFile =
getParameterOutputFile(
config,
"The file to write the generated data set into, if the file already exists, the generated points will be appended to this file.");
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter sparsP = new DoubleParameter(SPARSITY_ID);
sparsP.setDefaultValue(3.);
sparsP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_DOUBLE);
if (config.grab(sparsP)) {
sparsity = sparsP.doubleValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
final IntParameter dimP =
new IntParameter(DIM_ID) //
.addConstraint(CommonConstraints.GREATER_EQUAL_ZERO_INT);
if (config.grab(dimP)) {
dim = dimP.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<ClusteringAlgorithm<?>> referencealgP =
new ObjectParameter<>(
REFERENCE_ID, ClusteringAlgorithm.class, ByLabelOrAllInOneClustering.class);
if (config.grab(referencealgP)) {
referencealg = referencealgP.instantiateClass(config);
}
Flag noiseSpecialHandlingF = new Flag(NOISE_ID);
if (config.grab(noiseSpecialHandlingF)) {
noiseSpecialHandling = noiseSpecialHandlingF.getValue();
}
Flag selfPairingF = new Flag(SELFPAIR_ID);
if (config.grab(selfPairingF)) {
selfPairing = selfPairingF.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
IntParameter param =
new IntParameter(K_ID) //
.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
if (config.grab(param)) {
k = param.intValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
input = config.tryInstantiate(InputStep.class);
// Distance function parameter
final ObjectParameter<DistanceFunction<O>> dpar =
new ObjectParameter<>(DISTANCE_ID, DistanceFunction.class);
if (config.grab(dpar)) {
distance = dpar.instantiateClass(config);
}
final IntParameter kpar = new IntParameter(K_ID);
kpar.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
if (config.grab(kpar)) {
k = kpar.intValue();
}
// Output file parameter
final FileParameter cpar = new FileParameter(CACHE_ID, FileParameter.FileType.OUTPUT_FILE);
if (config.grab(cpar)) {
out = cpar.getValue();
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
DoubleParameter epsilonP =
new DoubleParameter(EPSILON_ID) //
.addConstraint(CommonConstraints.GREATER_THAN_ZERO_DOUBLE);
if (config.grab(epsilonP)) {
epsilon = epsilonP.getValue();
}
IntParameter minptsP =
new IntParameter(MINPTS_ID) //
.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
if (config.grab(minptsP)) {
minpts = minptsP.getValue();
if (minpts <= 2) {
LOG.warning(
"DBSCAN with minPts <= 2 is equivalent to single-link clustering at a single height. Consider using larger values of minPts.");
}
}
}
@Override
protected void makeOptions(Parameterization config) {
super.makeOptions(config);
ObjectParameter<DimensionSelectingSubspaceDistanceFunction<V>> param =
new ObjectParameter<>(
DISTANCE_FUNCTION_ID,
DimensionSelectingSubspaceDistanceFunction.class,
SubspaceEuclideanDistanceFunction.class);
if (config.grab(param)) {
distance = param.instantiateClass(config);
}
DoubleParameter epsilonP = new DoubleParameter(EPSILON_ID);
if (config.grab(epsilonP)) {
epsilon = epsilonP.getValue();
}
IntParameter minptsP = new IntParameter(MINPTS_ID);
minptsP.addConstraint(CommonConstraints.GREATER_EQUAL_ONE_INT);
if (config.grab(minptsP)) {
minpts = minptsP.getValue();
}
}