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ecological-engine
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git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@71681 82a268e6-3cf1-43bd-a215-b396298e98cf

This commit is contained in:
Gianpaolo Coro 2013-03-25 11:00:52 +00:00
parent b30615b560
commit 03f7f99d2b
6 changed files with 62 additions and 17 deletions
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5
src/main/java/org/gcube/dataanalysis/ecoengine/datatypes/PrimitiveType.java
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@ -1,6 +1,7 @@
package org.gcube.dataanalysis.ecoengine.datatypes;
import java.util.HashMap;
import java.util.LinkedHashMap;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
@ -49,8 +50,8 @@ public class PrimitiveType extends StatisticalType{
this.type = type;
}
public static HashMap<String,StatisticalType> stringMap2StatisticalMap(HashMap<String,String> stringmap){
HashMap<String,StatisticalType> map = new HashMap<String, StatisticalType>();
public static LinkedHashMap<String,StatisticalType> stringMap2StatisticalMap(HashMap<String,String> stringmap){
LinkedHashMap<String,StatisticalType> map = new LinkedHashMap<String, StatisticalType>();
for (String key:stringmap.keySet()){
String value = stringmap.get(key);
PrimitiveType string = new PrimitiveType(String.class.getName(), value, PrimitiveTypes.STRING, key,key);

42
src/main/java/org/gcube/dataanalysis/ecoengine/evaluation/ClimateImpactAnalysis.java Normal file
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@ -0,0 +1,42 @@
package org.gcube.dataanalysis.ecoengine.evaluation;
import java.util.ArrayList;
import java.util.List;
import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
public class ClimateImpactAnalysis extends DiscrepancyAnalysis {
protected String SpeciesListTable = "ReferenceHSPEN";
protected String LeftHSPEC = "LeftHSPEC";
protected String RightHSPEC = "RightHSPEC";
@Override
public List<StatisticalType> getInputParameters() {
List<TableTemplates> templatesHspen = new ArrayList<TableTemplates>();
templatesHspen.add(TableTemplates.HSPEN);
List<TableTemplates> templatesHspec = new ArrayList<TableTemplates>();
templatesHspec.add(TableTemplates.HSPEC);
InputTable hspec1 = new InputTable(templatesHspec,LeftHSPEC,"Left table containing a hspec distribution","hspen");
InputTable hspec2 = new InputTable(templatesHspec,RightHSPEC,"Right table containing a hspec distribution","hspen");
InputTable hspen = new InputTable(templatesHspen,SpeciesListTable,"Species List Table taken from envelopes","hspen");
List<StatisticalType> stlist = new ArrayList<StatisticalType>();
stlist.add(hspec1);
stlist.add(hspec2);
stlist.add(hspen);
DatabaseType.addDefaultDBPars(stlist);
return stlist;
}
}

9
src/main/java/org/gcube/dataanalysis/ecoengine/evaluation/DiscrepancyAnalysis.java
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@ -2,6 +2,7 @@ package org.gcube.dataanalysis.ecoengine.evaluation;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
@ -41,7 +42,7 @@ public class DiscrepancyAnalysis extends DataAnalysis {
int numberofvectors;
float maxerror;
String maxdiscrepancyPoint;
private HashMap<String, String> output;
private LinkedHashMap<String, String> output;
@Override
public List<StatisticalType> getInputParameters() {
@ -74,7 +75,7 @@ public class DiscrepancyAnalysis extends DataAnalysis {
@Override
public HashMap<String, String> analyze() throws Exception {
public LinkedHashMap<String, String> analyze() throws Exception {
String FirstTableCsquareColumn = config.getParam("FirstTableCsquareColumn");
String SecondTableCsquareColumn = config.getParam("SecondTableCsquareColumn");
@ -97,7 +98,7 @@ public class DiscrepancyAnalysis extends DataAnalysis {
if (FirstTable.equals(SecondTable)){
output = new HashMap<String, String>();
output = new LinkedHashMap<String, String>();
output.put("MEAN", "0.0");
output.put("VARIANCE", "0.0");
output.put("NUMBER_OF_ERRORS", "0");
@ -129,7 +130,7 @@ public class DiscrepancyAnalysis extends DataAnalysis {
analyzeCompareList(takePoints);
calcDiscrepancy();
output = new HashMap<String, String>();
output = new LinkedHashMap<String, String>();
output.put("MEAN", "" + MathFunctions.roundDecimal(mean,2));
output.put("VARIANCE", "" + MathFunctions.roundDecimal(variance,2));
output.put("NUMBER_OF_ERRORS", "" + numberoferrors);

8
src/main/java/org/gcube/dataanalysis/ecoengine/evaluation/DistributionQualityAnalysis.java
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@ -2,6 +2,7 @@ package org.gcube.dataanalysis.ecoengine.evaluation;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
@ -14,7 +15,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.DatabaseParameters;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.interfaces.DataAnalysis;
@ -42,7 +42,7 @@ public class DistributionQualityAnalysis extends DataAnalysis {
float acceptanceThreshold = 0.8f;
float rejectionThreshold = 0.3f;
double bestThreshold = 0.5d;
private HashMap<String, String> output;
private LinkedHashMap<String, String> output;
public List<StatisticalType> getInputParameters() {
List<StatisticalType> parameters = new ArrayList<StatisticalType>();
@ -138,7 +138,7 @@ public class DistributionQualityAnalysis extends DataAnalysis {
return points;
}
public HashMap<String, String> analyze() throws Exception {
public LinkedHashMap<String, String> analyze() throws Exception {
try {
acceptanceThreshold = Float.parseFloat(config.getParam("PositiveThreshold"));
@ -185,7 +185,7 @@ public class DistributionQualityAnalysis extends DataAnalysis {
double omissionrate = calculateOmissionRate(truePositives, falseNegatives);
double specificity = calculateSpecificity(trueNegatives, falsePositives);
output = new HashMap<String, String>();
output = new LinkedHashMap<String, String>();
output.put("TRUE_POSITIVES", "" + truePositives);
output.put("TRUE_NEGATIVES", "" + trueNegatives);
output.put("FALSE_POSITIVES", "" + falsePositives);

8
src/main/java/org/gcube/dataanalysis/ecoengine/evaluation/HabitatRepresentativeness.java
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@ -2,6 +2,7 @@ package org.gcube.dataanalysis.ecoengine.evaluation;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
@ -13,7 +14,6 @@ import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.DatabaseParameters;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
import org.gcube.dataanalysis.ecoengine.interfaces.DataAnalysis;
@ -30,7 +30,7 @@ public class HabitatRepresentativeness extends DataAnalysis {
String configPath = "./cfg/";
private HashMap<String, String> output;
private LinkedHashMap<String, String> output;
private static int minimumNumberToTake = 10000;
private float status;
private int currentIterationStep;
@ -191,7 +191,7 @@ public class HabitatRepresentativeness extends DataAnalysis {
private double currentHRSScore;
private double [] currentHRSVector;
public HashMap<String, String> analyze() throws Exception {
public LinkedHashMap<String, String> analyze() throws Exception {
try {
status = 0;
@ -220,7 +220,7 @@ public class HabitatRepresentativeness extends DataAnalysis {
status=Math.min(status+100f/maxTests,99f);
}
output = new HashMap<String, String>();
output = new LinkedHashMap<String, String>();
output.put("HRS_VECTOR", "" + Transformations.vector2String(meanHRSVector));
output.put("HRS", "" + org.gcube.contentmanagement.graphtools.utils.MathFunctions.roundDecimal(meanHRS,2));

7
src/main/java/org/gcube/dataanalysis/ecoengine/interfaces/DataAnalysis.java
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@ -1,6 +1,7 @@
package org.gcube.dataanalysis.ecoengine.interfaces;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
@ -26,7 +27,7 @@ public abstract class DataAnalysis implements Evaluator{
protected AlgorithmConfiguration config;
protected SessionFactory connection;
public abstract HashMap<String, String> analyze() throws Exception;
public abstract LinkedHashMap<String, String> analyze() throws Exception;
/**
* Processing skeleton : init-analyze-end
@ -34,10 +35,10 @@ public abstract class DataAnalysis implements Evaluator{
* @return
* @throws Exception
*/
HashMap<String, String> out;
LinkedHashMap<String, String> out;
public void compute() throws Exception{
status = 0;
out = new HashMap<String, String>();
out = new LinkedHashMap<String, String>();
try{
out = analyze();