Exemple #1
0
      @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);
      }
    }
Exemple #3
0
    @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);
      }
    }
Exemple #9
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    @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();
      }
    }
Exemple #12
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 @Override
 protected void makeOptions(Parameterization config) {
   super.makeOptions(config);
   final Flag flag = new Flag(INVERT_ID);
   if (config.grab(flag)) {
     invert = flag.getValue();
   }
 }
Exemple #13
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 @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();
      }
    }
Exemple #18
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    @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();
   }
 }
Exemple #20
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    @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();
   }
 }
Exemple #22
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 @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();
   }
 }
Exemple #23
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 @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();
   }
 }
Exemple #26
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    @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();
      }
    }
Exemple #27
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    @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();
   }
 }
Exemple #29
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    @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.");
        }
      }
    }
Exemple #30
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    @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();
      }
    }