gCubeSystem
/
ecological-engine
14
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@58915 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Gianpaolo Coro 2012-09-24 09:45:27 +00:00
parent 88186cea22
commit fb2cb3557b
14 changed files with 603518 additions and 225 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

602713
Analysis.log.1 Normal file
View File

File diff suppressed because one or more lines are too long

4
cfg/transducerers.properties
View File

@ -2,6 +2,10 @@ BIOCLIMATE_HSPEC=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPECTra
BIOCLIMATE_HCAF=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHCAFTransducer
BIOCLIMATE_HSPEN=org.gcube.dataanalysis.ecoengine.transducers.BioClimateHSPENTransducer
HCAF_INTERPOLATION=org.gcube.dataanalysis.ecoengine.transducers.InterpolationTransducer
HCAF_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HcafFilter
HSPEN_FILTER=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.HspenFilter
ABSENCE_CELLS_FROM_AQUAMAPS=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarineAbsencePointsFromAquamapsDistribution
PRESENCE_CELLS_GENERATION=org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors.MarinePresencePoints
OCCURRENCES_MERGER=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsMerger
OCCURRENCES_INTERSECTOR=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsIntersector
OCCURRENCES_INSEAS_ONEARTH=org.gcube.dataanalysis.ecoengine.transducers.OccurrencePointsInSeaOnEarth

BIN
neuralnetwork_Fis-30189_randomnative
View File

Binary file not shown.

BIN
neuralnetwork_Fis-30189_randomsuitable
View File

Binary file not shown.

BIN
neuralnetwork_Fis-30189_staticnative
View File

Binary file not shown.

BIN
neuralnetwork_Fis-30189_staticsuitable
View File

Binary file not shown.

4
src/main/java/org/gcube/dataanalysis/ecoengine/spatialdistributions/AquamapsNN.java
View File

@ -79,10 +79,10 @@ public class AquamapsNN extends AquamapsNative{
}
// double [] output = new double[1];
float probability = (float) output[0];
/*
if (probability>0.1)
AnalysisLogger.getLogger().debug(" Probability " + probability);
*/
// System.exit(0);
return probability;
}

446
src/main/java/org/gcube/dataanalysis/ecoengine/test/experiments/latimeria/ExperimentsForLatimeria.java
View File

@ -9,236 +9,182 @@ import org.gcube.dataanalysis.ecoengine.evaluation.DiscrepancyAnalysis;
import org.gcube.dataanalysis.ecoengine.interfaces.Evaluator;
import org.gcube.dataanalysis.ecoengine.interfaces.Generator;
import org.gcube.dataanalysis.ecoengine.interfaces.Modeler;
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
import org.gcube.dataanalysis.ecoengine.processing.factories.EvaluatorsFactory;
import org.gcube.dataanalysis.ecoengine.processing.factories.GeneratorsFactory;
import org.gcube.dataanalysis.ecoengine.processing.factories.ModelersFactory;
import org.gcube.dataanalysis.ecoengine.processing.factories.TransducerersFactory;
import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
import org.gcube.dataanalysis.ecoengine.utils.PresetConfigGenerator;
public class ExperimentsForLatimeria {
static String absenceRandom = "absence_data_latimeria_random";
static String absenceStatic = "absence_data_latimeria";
static String absenceRandomTable = "absence_data_latimeria_random";
static String absenceStaticTable = "absence_data_latimeria";
static String presenceTable = "presence_data_latimeria";
static String envelopeTable = "hspen_latimeria";
static String aquamapsSuitableTable = "hspec_suitable_latimeria_chalumnae";
static String aquamapsNativeTable = "hspec_native_latimeria_chalumnae";
static String nnsuitableTable = "hspec_suitable_neural_latimeria_chalumnae";
static String nnsuitableRandomTable = "hspec_suitable_neural_latimeria_chalumnae_random";
static String nnnativeTable = "hspec_native_neural_latimeria_chalumnae";
static String nnnativeRandomTable = "hspec_native_neural_latimeria_chalumnae_random";
static String hcaf= "hcaf_d";
static String filteredhcaf= "bboxed_hcaf_d";
private static AlgorithmConfiguration configAquamapsSuitable() {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_SUITABLE");
config.setParam("DistributionTable",aquamapsSuitableTable );
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", "hspen_latimeria");
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
return config;
}
private static AlgorithmConfiguration configAquamapsNative() {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_NATIVE");
config.setParam("DistributionTable", aquamapsNativeTable);
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", "hspen_latimeria");
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
return config;
}
private static AlgorithmConfiguration configAquamapsNNSuitable(String tableName,String username) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_SUITABLE_NEURALNETWORK");
config.setParam("DistributionTable", tableName);
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", "hspen_latimeria");
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
config.setParam("SpeciesName", "Fis-30189");
config.setParam("UserName", username);
return config;
}
private static AlgorithmConfiguration configAquamapsNNNative(String tableName,String username) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_NATIVE_NEURALNETWORK");
config.setParam("DistributionTable", tableName);
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", "hspen_latimeria");
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
config.setParam("SpeciesName", "Fis-30189");
config.setParam("UserName", username);
return config;
}
public static AlgorithmConfiguration configSuitableNeuralNetworkTraining(String absenceTable,String username) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPSNN");
config.setParam("AbsenceDataTable", absenceTable);
config.setParam("PresenceDataTable", "presence_data_latimeria");
config.setParam("SpeciesName", "Fis-30189");
config.setParam("UserName",username);
config.setParam("LayersNeurons", "100"+AlgorithmConfiguration.getListSeparator()+"2");
return config;
}
public static AlgorithmConfiguration configNativeNeuralNetworkTraining(String absenceTable,String username) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPSNN");
config.setParam("AbsenceDataTable", absenceTable);
config.setParam("PresenceDataTable", "presence_data_latimeria");
config.setParam("SpeciesName", "Fis-30189");
config.setParam("UserName", username);
config.setParam("LayersNeurons", "100");
return config;
}
public static AlgorithmConfiguration configQualityAnalysis(String table,String absenceTable){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("QUALITY_ANALYSIS");
config.setParam("PositiveCasesTable","presence_data_latimeria");
config.setParam("NegativeCasesTable",absenceTable);
config.setParam("PositiveCasesTableKeyColumn","csquarecode");
config.setParam("NegativeCasesTableKeyColumn","csquarecode");
config.setParam("DistributionTable",table);
config.setParam("DistributionTableKeyColumn","csquarecode");
config.setParam("DistributionTableProbabilityColumn","probability");
config.setParam("PositiveThreshold","0.8");
config.setParam("NegativeThreshold","0.3");
return config;
}
public static AlgorithmConfiguration configDiscrepancyAnalysis(String table1,String table2){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("DISCREPANCY_ANALYSIS");
config.setParam("FirstTable",table1);
config.setParam("SecondTable",table2);
config.setParam("FirstTableCsquareColumn","csquarecode");
config.setParam("SecondTableCsquareColumn","csquarecode");
config.setParam("FirstTableProbabilityColumn","probability");
config.setParam("SecondTableProbabilityColumn","probability");
config.setParam("ComparisonThreshold","0.1");
return config;
}
public static AlgorithmConfiguration configHRSAnalysis(String projectiontable,String absenceTable){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("HRS");
config.setParam("ProjectingAreaTable", projectiontable);
config.setParam("ProjectingAreaFeaturesOptionalCondition", "where oceanarea>0");
config.setParam("FeaturesColumns", "depthmean"+AlgorithmConfiguration.getListSeparator()+"depthmax"+AlgorithmConfiguration.getListSeparator()+"depthmin"+AlgorithmConfiguration.getListSeparator()+" sstanmean"+AlgorithmConfiguration.getListSeparator()+"sbtanmean"+AlgorithmConfiguration.getListSeparator()+"salinitymean"+AlgorithmConfiguration.getListSeparator()+"salinitybmean"+AlgorithmConfiguration.getListSeparator()+" primprodmean"+AlgorithmConfiguration.getListSeparator()+"iceconann"+AlgorithmConfiguration.getListSeparator()+"landdist"+AlgorithmConfiguration.getListSeparator()+"oceanarea");
config.setParam("PositiveCasesTable", "presence_data_latimeria");
config.setParam("NegativeCasesTable", absenceTable);
return config;
}
static String speciesID = "Fis-30189";
static String staticsuitable = "staticsuitable";
static String randomsuitable = "randomsuitable";
static String staticnative = "staticnative";
static String randomnative = "randomnative";
static int numberOfPoints = 34;
public static void trainNeuralNetworks() throws Exception{
List<Modeler> modelers = null;
modelers = ModelersFactory.getModelers(configSuitableNeuralNetworkTraining(absenceStatic,staticsuitable));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
modelers = ModelersFactory.getModelers(configSuitableNeuralNetworkTraining(absenceRandom,randomsuitable));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
modelers = ModelersFactory.getModelers(configNativeNeuralNetworkTraining(absenceStatic,staticnative));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
modelers = ModelersFactory.getModelers(configNativeNeuralNetworkTraining(absenceRandom,randomnative));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
}
static String nntablesuitable = "hspec_suitable_neural_latimeria_chalumnae";
static String nntablesuitableRandom = "hspec_suitable_neural_latimeria_chalumnae_random";
static String nntablenative = "hspec_native_neural_latimeria_chalumnae";
static String nntablenativeRandom = "hspec_native_neural_latimeria_chalumnae_random";
public static void generateAquamapsNativeSuitableNeuralNetwokrs() throws Exception{
List<Generator> generators = null;
generators = GeneratorsFactory.getGenerators(configAquamapsNNSuitable(nntablesuitable,staticsuitable));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
generators = GeneratorsFactory.getGenerators(configAquamapsNNSuitable(nntablesuitableRandom,randomsuitable));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
generators = GeneratorsFactory.getGenerators(configAquamapsNNNative(nntablenative,staticnative));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
generators = GeneratorsFactory.getGenerators(configAquamapsNNNative(nntablenativeRandom,randomnative));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
static float x1 = 95.346678f;
static float y1 = -9.18887f;
static float x2 = 125.668944f;
static float y2 = 12.983148f;
public static void generateHSPENTable() throws Exception{
System.out.println("*****************************HSPEN FILTER**********************************");
List<Transducerer> trans = null;
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configHSPENfilter(envelopeTable, speciesID));
trans.get(0).init();
Regressor.process(trans.get(0));
trans = null;
}
public static void generateAquamapsNativeSuitable() throws Exception{
List<Generator> generators = null;
generators = GeneratorsFactory.getGenerators(configAquamapsSuitable());
System.out.println("*****************************AQUAMAPS SUITABLE**********************************");
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsSuitable(aquamapsSuitableTable,envelopeTable));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
generators = GeneratorsFactory.getGenerators(configAquamapsNative());
System.out.println("*****************************AQUAMAPS NATIVE**********************************");
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsNative(aquamapsNativeTable,envelopeTable));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
}
public static void generatePresenceTable() throws Exception{
System.out.println("*****************************PRESENCE TABLE**********************************");
List<Transducerer> trans = null;
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configPresenceTable(presenceTable, -1, speciesID));
trans.get(0).init();
Regressor.process(trans.get(0));
trans = null;
}
public static void generateRandomAbsenceTable() throws Exception{
System.out.println("*****************************RANDOM ABSENCES**********************************");
List<Transducerer> trans = null;
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configAbsenceTable(true, absenceRandomTable, aquamapsNativeTable, numberOfPoints, speciesID));
trans.get(0).init();
Regressor.process(trans.get(0));
trans = null;
}
public static void generateAbsenceTable() throws Exception{
System.out.println("*****************************ABSENCES**********************************");
List<Transducerer> trans = null;
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configAbsenceTable(false, absenceStaticTable, aquamapsNativeTable, numberOfPoints, speciesID));
trans.get(0).init();
Regressor.process(trans.get(0));
trans = null;
}
public static void trainNeuralNetworks() throws Exception{
List<Modeler> modelers = null;
System.out.println("*****************************TRAINING NN SUITABLE WITH STATIC ABSENCES**********************************");
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configSuitableNeuralNetworkTraining(presenceTable,absenceStaticTable,staticsuitable,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2"));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
/*
System.out.println("*****************************TRAINING NN SUITABLE WITH RANDOM ABSENCES**********************************");
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configSuitableNeuralNetworkTraining(presenceTable,absenceRandomTable,staticsuitable,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2"));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
*/
System.out.println("*****************************TRAINING NN NATIVE WITH STATIC ABSENCES**********************************");
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configNativeNeuralNetworkTraining(presenceTable,absenceStaticTable,staticnative,speciesID,"100"));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
/*
System.out.println("*****************************TRAINING NN NATIVE WITH RANDOM ABSENCES**********************************");
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configNativeNeuralNetworkTraining(presenceTable,absenceRandomTable,staticsuitable,speciesID,"100"));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
*/
}
public static void trainSuitableNeuralNetworks() throws Exception{
List<Modeler> modelers = null;
System.out.println("*****************************TRAINING NN SUITABLE WITH STATIC ABSENCES**********************************");
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configSuitableNeuralNetworkTraining(presenceTable,absenceStaticTable,staticsuitable,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2"));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
}
public static void trainNativeNeuralNetworks() throws Exception{
System.out.println("*****************************TRAINING NN NATIVE WITH STATIC ABSENCES**********************************");
List<Modeler> modelers = null;
modelers = ModelersFactory.getModelers(PresetConfigGenerator.configNativeNeuralNetworkTraining(presenceTable,absenceStaticTable,staticnative,speciesID,"100"+AlgorithmConfiguration.getListSeparator()+"2"));
modelers.get(0).init();
Regressor.process(modelers.get(0));
modelers = null;
}
public static void generateAquamapsNativeSuitableNeuralNetwokrs() throws Exception{
List<Generator> generators = null;
System.out.println("*****************************GENERATING NN SUITABLE WITH STATIC ABSENCES**********************************");
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsNNSuitable(nnsuitableTable,staticsuitable,envelopeTable,speciesID));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
/*
System.out.println("*****************************GENERATING NN SUITABLE WITH RANDOM ABSENCES**********************************");
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsNNSuitable(nnsuitableRandomTable,randomsuitable,envelopeTable,speciesID));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
*/
System.out.println("*****************************GENERATING NN NATIVE WITH STATIC ABSENCES**********************************");
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsNNNative(nnnativeTable,staticnative,envelopeTable,speciesID));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
/*
System.out.println("*****************************GENERATING NN NATIVE WITH RANDOM ABSENCES**********************************");
generators = GeneratorsFactory.getGenerators(PresetConfigGenerator.configAquamapsNNNative(nnnativeRandomTable,randomnative,envelopeTable,speciesID));
generators.get(0).init();
Regressor.process(generators.get(0));
generators = null;
*/
}
public static void calcdiscrepancy(String table1,String table2) throws Exception{
System.out.println("*****************************DISCREPANCY: "+table1+" vs "+table2+"************************************");
List<Evaluator> evaluators = null;
evaluators = EvaluatorsFactory.getEvaluators(configDiscrepancyAnalysis(table1, table2));
evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configDiscrepancyAnalysis(table1, table2));
evaluators.get(0).init();
Regressor.process(evaluators.get(0));
PrimitiveType output = (PrimitiveType) evaluators.get(0).getOutput();
@ -247,9 +193,10 @@ public class ExperimentsForLatimeria {
evaluators = null;
}
public static void calcquality(String table1,String absenceTable) throws Exception{
public static void calcquality(String table,String presenceTable, String absenceTable) throws Exception{
System.out.println("*****************************QUALITY: "+table+" vs "+presenceTable+" and "+absenceTable+"************************************");
List<Evaluator> evaluators = null;
evaluators = EvaluatorsFactory.getEvaluators(configQualityAnalysis(table1, absenceTable));
evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configQualityAnalysis(presenceTable,absenceTable,table));
evaluators.get(0).init();
Regressor.process(evaluators.get(0));
PrimitiveType output = (PrimitiveType) evaluators.get(0).getOutput();
@ -258,10 +205,20 @@ public class ExperimentsForLatimeria {
evaluators = null;
}
static String hcaf= "hcaf_d";
public static void generateHCAFFilter() throws Exception{
System.out.println("*****************************HCAF FILTER ON : "+x1+","+y1+","+x2+","+y2+"************************************");
List<Transducerer> trans = null;
trans = TransducerersFactory.getTransducerers(PresetConfigGenerator.configHCAFfilter(filteredhcaf, x1, y1, x2, y2));
trans.get(0).init();
Regressor.process(trans.get(0));
trans = null;
}
public static void calcHRS(String hcaf,String absenceTable) throws Exception{
System.out.println("*****************************HRS: "+absenceTable+","+presenceTable+" vs "+hcaf+"************************************");
List<Evaluator> evaluators = null;
evaluators = EvaluatorsFactory.getEvaluators(configHRSAnalysis(hcaf, absenceTable));
evaluators = EvaluatorsFactory.getEvaluators(PresetConfigGenerator.configHRSAnalysis(filteredhcaf, absenceTable, presenceTable));
evaluators.get(0).init();
Regressor.process(evaluators.get(0));
PrimitiveType output = (PrimitiveType) evaluators.get(0).getOutput();
@ -270,34 +227,77 @@ public class ExperimentsForLatimeria {
evaluators = null;
}
public static void main1(String[] args) throws Exception{
//generate hspen table for the species
generateHSPENTable();
//generate Aquamaps distributions
generateAquamapsNativeSuitable();
//generate presence and absence hcafs
generatePresenceTable();
generateAbsenceTable();
generateHCAFFilter();
// generateRandomAbsenceTable(); NOTE: in this case the randoms are equal to the static
//train the neural networks on these tables
trainNeuralNetworks();
//project the neural networks
generateAquamapsNativeSuitableNeuralNetwokrs();
//Analysis
calcdiscrepancy(aquamapsSuitableTable, nnsuitableTable);
// calcdiscrepancy(aquamapsSuitableTable, nnsuitableRandomTable);
calcdiscrepancy(aquamapsNativeTable, nnnativeTable);
// calcdiscrepancy(aquamapsNativeTable, nnnativeRandomTable);
calcquality(aquamapsSuitableTable, presenceTable, absenceStaticTable);
// calcquality(aquamapsSuitableTable, presenceTable, absenceRandomTable);
calcquality(nnsuitableTable, presenceTable, absenceStaticTable);
// calcquality(nnsuitableTable, presenceTable, absenceRandomTable);
calcquality(nnsuitableRandomTable, presenceTable, absenceStaticTable);
// calcquality(nnsuitableRandomTable, presenceTable, absenceRandomTable);
//filter the hcaf on Indonesia
calcHRS(filteredhcaf,absenceStaticTable);
// calcHRS(filteredhcaf,absenceRandomTable);
}
public static void main(String[] args) throws Exception{
//generate hspen table for the species
// generateHSPENTable();
//generate Aquamaps distributions
// generateAquamapsNativeSuitable();
// trainNeuralNetworks();
//generate presence and absence hcafs
// generatePresenceTable();
// generateAbsenceTable();
// generateHCAFFilter();
//train the neural networks on these tables
// trainSuitableNeuralNetworks();
// trainNativeNeuralNetworks();
//project the neural networks
// generateAquamapsNativeSuitableNeuralNetwokrs();
//Analysis
/*
calcdiscrepancy(aquamapsSuitableTable, nntablesuitable);
calcdiscrepancy(aquamapsSuitableTable, nntablesuitableRandom);
calcdiscrepancy(aquamapsNativeTable, nntablenative);
calcdiscrepancy(aquamapsNativeTable, nntablenativeRandom);
calcdiscrepancy(aquamapsSuitableTable, nnsuitableTable);
calcdiscrepancy(aquamapsNativeTable, nnnativeTable);
calcquality(aquamapsSuitableTable, presenceTable, absenceStaticTable);
calcquality(nnsuitableTable, presenceTable, absenceStaticTable);
calcHRS(filteredhcaf,absenceStaticTable);
calcHRS(filteredhcaf,null);
*/
calcquality(aquamapsNativeTable, presenceTable, absenceStaticTable);
calcquality(nnnativeTable, presenceTable, absenceStaticTable);
/*
calcquality(aquamapsSuitableTable, absenceStatic);
calcquality(aquamapsSuitableTable, absenceRandom);
calcquality(nntablesuitable, absenceStatic);
calcquality(nntablesuitable, absenceRandom);
calcquality(nntablesuitableRandom, absenceStatic);
calcquality(nntablesuitableRandom, absenceRandom);
calcquality(nntablenative, absenceStatic);
calcquality(nntablenative, absenceRandom);
calcquality(nntablenativeRandom, absenceStatic);
calcquality(nntablenativeRandom, absenceRandom);
*/
calcHRS(hcaf,absenceStatic);
calcHRS(hcaf,absenceRandom);
}
}

105
src/main/java/org/gcube/dataanalysis/ecoengine/transducers/QueryExecutor.java Normal file
View File

@ -0,0 +1,105 @@
package org.gcube.dataanalysis.ecoengine.transducers;
import java.util.List;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.contentmanagement.lexicalmatcher.utils.DatabaseFactory;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.configuration.INFRASTRUCTURE;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.interfaces.Transducerer;
import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
import org.gcube.dataanalysis.ecoengine.utils.ResourceFactory;
import org.hibernate.SessionFactory;
//implements a creator of tables which simply executes a query
public class QueryExecutor implements Transducerer {
protected String query = "";
protected String finalTableName = "";
protected float status = 0;
protected AlgorithmConfiguration config;
@Override
public List<StatisticalType> getInputParameters() {
return null;
}
@Override
public String getResourceLoad() {
if ((status > 0) && (status < 100))
return ResourceFactory.getResources(100f);
else
return ResourceFactory.getResources(0f);
}
ResourceFactory resourceManager;
@Override
public String getResources() {
if (resourceManager == null)
resourceManager = new ResourceFactory();
return resourceManager.getResourceLoad(1);
}
@Override
public float getStatus() {
return status;
}
@Override
public INFRASTRUCTURE getInfrastructure() {
return INFRASTRUCTURE.LOCAL;
}
@Override
public StatisticalType getOutput() {
return null;
}
@Override
public void init() throws Exception {
}
@Override
public void setConfiguration(AlgorithmConfiguration config) {
this.config = config;
}
@Override
public void shutdown() {
}
@Override
public String getDescription() {
return null;
}
@Override
public void compute() throws Exception {
SessionFactory dbconnection = null;
try{
AnalysisLogger.getLogger().trace("Initializing DB Connection");
dbconnection = DatabaseUtils.initDBSession(config);
AnalysisLogger.getLogger().trace("Deleting Previous Table");
DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(finalTableName), dbconnection);
AnalysisLogger.getLogger().trace("Deleted");
AnalysisLogger.getLogger().trace("Executing query: "+query);
DatabaseFactory.executeSQLUpdate(query, dbconnection);
AnalysisLogger.getLogger().trace("Executed!");
} catch (Exception e) {
throw e;
} finally {
if (dbconnection != null)
dbconnection.close();
status = 100;
AnalysisLogger.getLogger().trace("Processing Finished and db closed");
}
}
}

72
src/main/java/org/gcube/dataanalysis/ecoengine/transducers/simplequeryexecutors/HcafFilter.java Normal file
View File

@ -0,0 +1,72 @@
package org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors;
import java.util.ArrayList;
import java.util.List;
import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.transducers.QueryExecutor;
public class HcafFilter extends QueryExecutor {
static String finalTable = "FINAL_TABLE_NAME";
static String bbx1 = "BOUNDING_BOX_LEFT_LOWER_LONG";
static String bbx2 = "BOUNDING_BOX_RIGHT_UPPER_LONG";
static String bby1 = "BOUNDING_BOX_LEFT_LOWER_LAT";
static String bby2 = "BOUNDING_BOX_RIGHT_UPPER_LAT";
String bbx1$;
String bbx2$;
String bby1$;
String bby2$;
String species;
@Override
public void init() throws Exception {
finalTableName = config.getParam(finalTable);
bbx1$ = config.getParam(bbx1);
bbx2$ = config.getParam(bbx2);
bby1$ = config.getParam(bby1);
bby2$ = config.getParam(bby2);
query = "select * into " + finalTableName + " from hcaf_d where (centerlat-0.25)>" + bby1$ + " and (centerlong-0.25)>" + bbx1$ + " and (centerlat+0.25)<" + bby2$ + " and (centerlong+0.25)<" + bbx2$;
}
@Override
public List<StatisticalType> getInputParameters() {
PrimitiveType p1 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.RANDOM, finalTable, "the name of the Filtered Hcaf", "hspen_filtered");
PrimitiveType p2 = new PrimitiveType(Float.class.getName(), null, PrimitiveTypes.NUMBER, bbx1, "the left lower longitude of the bounding box (range [-180,+180])", "0");
PrimitiveType p3 = new PrimitiveType(Float.class.getName(), null, PrimitiveTypes.NUMBER, bbx2, "the right upper longitude of the bounding box (range [-180,+180])", "0");
PrimitiveType p4 = new PrimitiveType(Float.class.getName(), null, PrimitiveTypes.NUMBER, bby1, "the left lower latitude of the bounding box (range [-90,+90])", "10");
PrimitiveType p5 = new PrimitiveType(Float.class.getName(), null, PrimitiveTypes.NUMBER, bby2, "the right upper latitude of the bounding box (range [-90,+90])", "10");
List<StatisticalType> parameters = new ArrayList<StatisticalType>();
parameters.add(p1);
parameters.add(p2);
parameters.add(p3);
parameters.add(p4);
parameters.add(p5);
return parameters;
}
@Override
public StatisticalType getOutput() {
List<TableTemplates> template = new ArrayList<TableTemplates>();
template.add(TableTemplates.HCAF);
return new OutputTable(template, finalTableName, finalTableName, "a HCAF table focusing on the selected Bounding Box");
}
@Override
public String getDescription() {
return "An algorithm producing a HCAF table on a selected Bounding Box";
}
}

56
src/main/java/org/gcube/dataanalysis/ecoengine/transducers/simplequeryexecutors/HspenFilter.java Normal file
View File

@ -0,0 +1,56 @@
package org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors;
import java.util.ArrayList;
import java.util.List;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveTypesList;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.transducers.QueryExecutor;
public class HspenFilter extends QueryExecutor {
static String finalTable = "FINAL_TABLE_NAME";
static String speciesCodes = "SPECIES_CODES";
String species;
@Override
public void init() throws Exception {
finalTableName = config.getParam(finalTable);
species = config.getParam(speciesCodes).replace(AlgorithmConfiguration.getListSeparator(), ",");
query = "select * into "+finalTableName+" from hspen where speciesid in ('"+species+"')";
}
@Override
public List<StatisticalType> getInputParameters() {
PrimitiveType p3 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.RANDOM, finalTable,"the name of the Filtered Hspen","hspen_filtered");
PrimitiveTypesList pl = new PrimitiveTypesList(PrimitiveTypes.STRING, speciesCodes, "A list of species codes (Fish Base Format) to take. E.g. Fis-30189", false);
List<StatisticalType> parameters = new ArrayList<StatisticalType>();
parameters.add(p3);
parameters.add(pl);
return parameters;
}
@Override
public StatisticalType getOutput() {
List<TableTemplates> template = new ArrayList<TableTemplates>();
template.add(TableTemplates.HCAF);
return new OutputTable(template, finalTableName, finalTableName, "a HSPEN table containing only selected species");
}
@Override
public String getDescription() {
return "An algorithm producing a HSPEN table with only some selected species";
}
}

75
src/main/java/org/gcube/dataanalysis/ecoengine/transducers/simplequeryexecutors/MarineAbsencePointsFromAquamapsDistribution.java Normal file
View File

@ -0,0 +1,75 @@
package org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors;
import java.util.ArrayList;
import java.util.List;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.transducers.QueryExecutor;
public class MarineAbsencePointsFromAquamapsDistribution extends QueryExecutor {
static String doRandom = "RANDOM_TAKE";
static String AquamapsHSpecTable = "AQUAMAPS_HSPEC";
static String finalTable = "FINAL_TABLE_NAME";
static String numberOfPoints = "NUMBER_OF_POINTS";
static String speciesCode = "SPECIES_CODE";
String dorandom;
String aquamapsTable;
String nPoints;
String species;
@Override
public void init() throws Exception {
dorandom = config.getParam(doRandom);
finalTableName = config.getParam(finalTable);
aquamapsTable= config.getParam(AquamapsHSpecTable);
nPoints= config.getParam(numberOfPoints);
species = config.getParam(speciesCode);
String dorandom$ = "";
if (Boolean.parseBoolean(dorandom))
dorandom$="order by random()";
query = "select * into "+finalTableName+" from hcaf_d as a where a.csquarecode in (select csquarecode from "+aquamapsTable+" where probability<=0.2 and speciesid='"+species+"'"+dorandom$+" limit "+nPoints+") and oceanarea>0";
}
@Override
public List<StatisticalType> getInputParameters() {
List<TableTemplates> templateHspec = new ArrayList<TableTemplates>();
templateHspec.add(TableTemplates.HSPEC);
InputTable p1 = new InputTable(templateHspec,AquamapsHSpecTable,"an Aquamaps table from which to produce the absence points","hspec");
PrimitiveType p2 = new PrimitiveType(Boolean.class.getName(), null, PrimitiveTypes.BOOLEAN, doRandom, "a flag for taking points randomly (true) or close together (false)","true");
PrimitiveType p3 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.RANDOM, finalTable,"Name of the HCAF table to produce containing Absence Cells","absence_hcaf");
PrimitiveType p4 = new PrimitiveType(Integer.class.getName(), null, PrimitiveTypes.NUMBER, numberOfPoints,"Number of points to take","20");
PrimitiveType p5 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, speciesCode,"the species code according to the Fish-Base conventions","Fis-30189");
List<StatisticalType> parameters = new ArrayList<StatisticalType>();
parameters.add(p1);
parameters.add(p2);
parameters.add(p3);
parameters.add(p4);
parameters.add(p5);
return parameters;
}
@Override
public StatisticalType getOutput() {
List<TableTemplates> template = new ArrayList<TableTemplates>();
template.add(TableTemplates.HCAF);
return new OutputTable(template, finalTableName, finalTableName, "a HCAF table containing Absence Points cells");
}
@Override
public String getDescription() {
return "An algorithm producing cells and features (HCAF) for a species containing absense points taken by an Aquamaps Distribution";
}
}

64
src/main/java/org/gcube/dataanalysis/ecoengine/transducers/simplequeryexecutors/MarinePresencePoints.java Normal file
View File

@ -0,0 +1,64 @@
package org.gcube.dataanalysis.ecoengine.transducers.simplequeryexecutors;
import java.util.ArrayList;
import java.util.List;
import org.gcube.dataanalysis.ecoengine.datatypes.OutputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.transducers.QueryExecutor;
public class MarinePresencePoints extends QueryExecutor {
static String finalTable = "FINAL_TABLE_NAME";
static String numberOfPoints = "NUMBER_OF_POINTS";
static String speciesCode = "SPECIES_CODE";
String nPoints;
String species;
@Override
public void init() throws Exception {
finalTableName = config.getParam(finalTable);
nPoints= config.getParam(numberOfPoints);
species = config.getParam(speciesCode);
String points = "";
if (Integer.parseInt(nPoints)>0){
points = "limit "+nPoints;
}
query = "select * into "+finalTableName+" from hcaf_d where csquarecode in (select csquarecode from occurrencecells where speciesid = '"+species+"' "+points+")";
}
@Override
public List<StatisticalType> getInputParameters() {
PrimitiveType p3 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.RANDOM, finalTable,"Name of the HCAF table to produce containing Presence Cells","presence_hcaf");
PrimitiveType p4 = new PrimitiveType(Integer.class.getName(), null, PrimitiveTypes.NUMBER, numberOfPoints,"Maximum number of points to take (-1 to take all)","-1");
PrimitiveType p5 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, speciesCode,"the species code according to the Fish-Base conventions","Fis-30189");
List<StatisticalType> parameters = new ArrayList<StatisticalType>();
parameters.add(p3);
parameters.add(p4);
parameters.add(p5);
return parameters;
}
@Override
public StatisticalType getOutput() {
List<TableTemplates> template = new ArrayList<TableTemplates>();
template.add(TableTemplates.HCAF);
return new OutputTable(template, finalTableName, finalTableName, "a HCAF table containing Presence Points cells");
}
@Override
public String getDescription() {
return "An algorithm producing cells and features (HCAF) for a species containing presence points";
}
}

204
src/main/java/org/gcube/dataanalysis/ecoengine/utils/PresetConfigGenerator.java Normal file
View File

@ -0,0 +1,204 @@
package org.gcube.dataanalysis.ecoengine.utils;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.test.regression.Regressor;
public class PresetConfigGenerator {
public static AlgorithmConfiguration configAquamapsSuitable(String aquamapsSuitableTable, String envelopeTable) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_SUITABLE");
config.setParam("DistributionTable",aquamapsSuitableTable );
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", envelopeTable);
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
return config;
}
public static AlgorithmConfiguration configAquamapsNative(String aquamapsNativeTable, String envelopeTable) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_NATIVE");
config.setParam("DistributionTable", aquamapsNativeTable);
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", envelopeTable);
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
return config;
}
public static AlgorithmConfiguration configAquamapsNNSuitable(String tableName,String username, String envelopeTable, String speciesID) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_SUITABLE_NEURALNETWORK");
config.setParam("DistributionTable", tableName);
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", envelopeTable);
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
config.setParam("SpeciesName", speciesID);
config.setParam("UserName", username);
return config;
}
public static AlgorithmConfiguration configAquamapsNNNative(String tableName,String username, String envelopeTable, String speciesID) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPS_NATIVE_NEURALNETWORK");
config.setParam("DistributionTable", tableName);
config.setParam("CsquarecodesTable", "hcaf_d");
config.setParam("EnvelopeTable", envelopeTable);
config.setParam("OccurrencePointsTable", "occurrencecells");
config.setParam("CreateTable", "true");
config.setParam("SpeciesName", speciesID);
config.setParam("UserName", username);
return config;
}
public static AlgorithmConfiguration configSuitableNeuralNetworkTraining(String presenceTable, String absenceTable,String username, String speciesID, String neuronsAndLayers) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPSNN");
config.setParam("AbsenceDataTable", absenceTable);
config.setParam("PresenceDataTable", presenceTable);
config.setParam("SpeciesName", speciesID);
config.setParam("UserName",username);
config.setParam("LayersNeurons", neuronsAndLayers);
return config;
}
public static AlgorithmConfiguration configNativeNeuralNetworkTraining(String presenceTable, String absenceTable,String username, String speciesID, String neuronsAndLayers) {
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(5);
config.setModel("AQUAMAPSNN");
config.setParam("AbsenceDataTable", absenceTable);
config.setParam("PresenceDataTable", presenceTable);
config.setParam("SpeciesName", speciesID);
config.setParam("UserName", username);
config.setParam("LayersNeurons", neuronsAndLayers);
return config;
}
public static AlgorithmConfiguration configQualityAnalysis(String presenceTable, String absenceTable, String table){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("QUALITY_ANALYSIS");
config.setParam("PositiveCasesTable",presenceTable);
config.setParam("NegativeCasesTable",absenceTable);
config.setParam("PositiveCasesTableKeyColumn","csquarecode");
config.setParam("NegativeCasesTableKeyColumn","csquarecode");
config.setParam("DistributionTable",table);
config.setParam("DistributionTableKeyColumn","csquarecode");
config.setParam("DistributionTableProbabilityColumn","probability");
config.setParam("PositiveThreshold","0.8");
config.setParam("NegativeThreshold","0.3");
return config;
}
public static AlgorithmConfiguration configDiscrepancyAnalysis(String table1,String table2){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("DISCREPANCY_ANALYSIS");
config.setParam("FirstTable",table1);
config.setParam("SecondTable",table2);
config.setParam("FirstTableCsquareColumn","csquarecode");
config.setParam("SecondTableCsquareColumn","csquarecode");
config.setParam("FirstTableProbabilityColumn","probability");
config.setParam("SecondTableProbabilityColumn","probability");
config.setParam("ComparisonThreshold","0.1");
return config;
}
public static AlgorithmConfiguration configHRSAnalysis(String projectiontable,String absenceTable, String presenceTable){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("HRS");
config.setParam("ProjectingAreaTable", projectiontable);
config.setParam("ProjectingAreaFeaturesOptionalCondition", "where oceanarea>0");
config.setParam("FeaturesColumns", "depthmean"+AlgorithmConfiguration.getListSeparator()+"depthmax"+AlgorithmConfiguration.getListSeparator()+"depthmin"+AlgorithmConfiguration.getListSeparator()+" sstanmean"+AlgorithmConfiguration.getListSeparator()+"sbtanmean"+AlgorithmConfiguration.getListSeparator()+"salinitymean"+AlgorithmConfiguration.getListSeparator()+"salinitybmean"+AlgorithmConfiguration.getListSeparator()+" primprodmean"+AlgorithmConfiguration.getListSeparator()+"iceconann"+AlgorithmConfiguration.getListSeparator()+"landdist"+AlgorithmConfiguration.getListSeparator()+"oceanarea");
config.setParam("PositiveCasesTable", presenceTable);
config.setParam("NegativeCasesTable", absenceTable);
return config;
}
public static AlgorithmConfiguration configAbsenceTable(boolean random, String absenceTable, String hspecTable, int numberOfPoints, String speciesCode){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("ABSENCE_CELLS_FROM_AQUAMAPS");
config.setParam("RANDOM_TAKE", ""+random);
config.setParam("FINAL_TABLE_NAME", absenceTable);
config.setParam("AQUAMAPS_HSPEC", hspecTable);
config.setParam("SPECIES_CODE", speciesCode);
config.setParam("NUMBER_OF_POINTS", ""+numberOfPoints);
return config;
}
public static AlgorithmConfiguration configPresenceTable(String presenceTable, int numberOfPoints, String speciesCode){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("PRESENCE_CELLS_GENERATION");
config.setParam("FINAL_TABLE_NAME", presenceTable);
config.setParam("SPECIES_CODE", speciesCode);
config.setParam("NUMBER_OF_POINTS", ""+numberOfPoints);
return config;
}
public static AlgorithmConfiguration configHCAFfilter(String table, float x1,float y1, float x2, float y2){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("HCAF_FILTER");
config.setParam("FINAL_TABLE_NAME", table);
config.setParam("BOUNDING_BOX_LEFT_LOWER_LONG", ""+x1);
config.setParam("BOUNDING_BOX_RIGHT_UPPER_LONG", ""+x2);
config.setParam("BOUNDING_BOX_LEFT_LOWER_LAT", ""+y1);
config.setParam("BOUNDING_BOX_RIGHT_UPPER_LAT", ""+y2);
return config;
}
public static AlgorithmConfiguration configHSPENfilter(String table, String speciesList){
AlgorithmConfiguration config = Regressor.getConfig();
config.setNumberOfResources(1);
config.setAgent("HSPEN_FILTER");
config.setParam("FINAL_TABLE_NAME", table);
config.setParam("SPECIES_CODES", speciesList);
return config;
}
}