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ecological-engine
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fixed bugs on hspen filtering and AquaMaps ANNs 

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@86746 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Gianpaolo Coro 2013-12-09 14:31:18 +00:00
parent aeb215469a
commit 866d992515
3 changed files with 30 additions and 7 deletions
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18
src/main/java/org/gcube/dataanalysis/ecoengine/spatialdistributions/AquamapsNN.java
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@ -1,5 +1,6 @@
package org.gcube.dataanalysis.ecoengine.spatialdistributions; package org.gcube.dataanalysis.ecoengine.spatialdistributions;
import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.IOException; import java.io.IOException;
import java.io.ObjectInputStream; import java.io.ObjectInputStream;
@ -20,6 +21,11 @@ public class AquamapsNN extends AquamapsNative{
private Neural_Network neuralnet; private Neural_Network neuralnet;
@Override
public ALG_PROPS[] getProperties() {
ALG_PROPS [] p = {ALG_PROPS.SPECIES_VS_CSQUARE_FROM_DATABASE};
return p;
}
@Override @Override
public String getName() { public String getName() {
@ -36,7 +42,8 @@ public class AquamapsNN extends AquamapsNative{
List<StatisticalType> parameters = super.getInputParameters(); List<StatisticalType> parameters = super.getInputParameters();
PrimitiveType p1 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "SpeciesName","Name of the Species for which the distribution has to be produced","Fis-30189"); PrimitiveType p1 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "SpeciesName","Name of the Species for which the distribution has to be produced","Fis-30189");
PrimitiveType p2 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "NeuralNetworkName","The name of the Neural Network","neuralnet_"); // PrimitiveType p2 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "NeuralNetworkName","The name of the Neural Network","neuralnet_");
PrimitiveType p2 = new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "NeuralNetworkName","The file containing the Neural Network", "neuralnet_");
ServiceType p3 = new ServiceType(ServiceParameters.USERNAME, "UserName","LDAP username"); ServiceType p3 = new ServiceType(ServiceParameters.USERNAME, "UserName","LDAP username");
parameters.add(p1); parameters.add(p1);
@ -49,8 +56,15 @@ public class AquamapsNN extends AquamapsNative{
@Override @Override
public void init(AlgorithmConfiguration config, SessionFactory dbHibConnection) { public void init(AlgorithmConfiguration config, SessionFactory dbHibConnection) {
super.init(config,dbHibConnection); super.init(config,dbHibConnection);
AnalysisLogger.getLogger().debug("Initializing ANNs");
String persistencePath = config.getPersistencePath(); String persistencePath = config.getPersistencePath();
String filename = persistencePath + "neuralnetwork_" + config.getParam("SpeciesName") + "_" + config.getParam("UserName")+"_"+config.getParam("NeuralNetworkName").replace(" ", ""); // String filename = persistencePath + "neuralnetwork_" + config.getParam("SpeciesName") + "_" + config.getParam("UserName")+"_"+config.getParam("NeuralNetworkName").replace(" ", "");
String nnname = config.getParam("NeuralNetworkName");
AnalysisLogger.getLogger().debug("Init ANN in projection mode with filename: "+nnname);
String filename = new File(nnname).getAbsolutePath();
AnalysisLogger.getLogger().debug("ANN: using file name: "+filename);
if (filename!=null)
neuralnet = loadNN(filename); neuralnet = loadNN(filename);
} }

13
src/main/java/org/gcube/dataanalysis/ecoengine/spatialdistributions/AquamapsNNSuitable.java
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@ -1,5 +1,6 @@
package org.gcube.dataanalysis.ecoengine.spatialdistributions; package org.gcube.dataanalysis.ecoengine.spatialdistributions;
import java.io.File;
import java.io.FileInputStream; import java.io.FileInputStream;
import java.io.IOException; import java.io.IOException;
import java.io.ObjectInputStream; import java.io.ObjectInputStream;
@ -41,7 +42,8 @@ public class AquamapsNNSuitable extends AquamapsSuitable{
List<StatisticalType> parameters = super.getInputParameters(); List<StatisticalType> parameters = super.getInputParameters();
PrimitiveType p1 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "SpeciesName","Name of the Species for which the distribution has to be produced","Fis-30189"); PrimitiveType p1 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "SpeciesName","Name of the Species for which the distribution has to be produced","Fis-30189");
PrimitiveType p2 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "NeuralNetworkName","The name of the Neural Network","neuralnet_"); // PrimitiveType p2 = new PrimitiveType(String.class.getName(), null, PrimitiveTypes.STRING, "NeuralNetworkName","The name of the Neural Network","neuralnet_");
PrimitiveType p2 = new PrimitiveType(File.class.getName(), null, PrimitiveTypes.FILE, "NeuralNetworkName","The file containing the Neural Network", "neuralnet_");
ServiceType p3 = new ServiceType(ServiceParameters.USERNAME, "UserName","LDAP username"); ServiceType p3 = new ServiceType(ServiceParameters.USERNAME, "UserName","LDAP username");
parameters.add(p1); parameters.add(p1);
@ -53,9 +55,16 @@ public class AquamapsNNSuitable extends AquamapsSuitable{
@Override @Override
public void init(AlgorithmConfiguration config, SessionFactory dbHibConnection) { public void init(AlgorithmConfiguration config, SessionFactory dbHibConnection) {
AnalysisLogger.getLogger().debug("Initializing ANNs");
super.init(config,dbHibConnection); super.init(config,dbHibConnection);
String persistencePath = config.getPersistencePath(); String persistencePath = config.getPersistencePath();
String filename = persistencePath + "neuralnetwork_" + config.getParam("SpeciesName") + "_" + config.getParam("UserName")+"_"+config.getParam("NeuralNetworkName").replace(" ", "");
// String filename = persistencePath + "neuralnetwork_" + config.getParam("SpeciesName") + "_" + config.getParam("UserName")+"_"+config.getParam("NeuralNetworkName").replace(" ", "");
String nnname = config.getParam("NeuralNetworkName");
AnalysisLogger.getLogger().debug("Init ANN in projection mode with filename: "+nnname);
String filename = new File(nnname).getAbsolutePath();
AnalysisLogger.getLogger().debug("ANN: using file name: "+filename);
if (filename!=null)
neuralnet = loadNN(filename); neuralnet = loadNN(filename);
} }

2
src/main/java/org/gcube/dataanalysis/ecoengine/transducers/simplequeryexecutors/HspenFilter.java
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@ -25,7 +25,7 @@ public class HspenFilter extends QueryExecutor {
finalTableName = config.getParam(finalTable); finalTableName = config.getParam(finalTable);
finalTableLabel = config.getParam(finalTableLabel$); finalTableLabel = config.getParam(finalTableLabel$);
species = config.getParam(speciesCodes).replace(AlgorithmConfiguration.getListSeparator(), ","); species = config.getParam(speciesCodes).replace(AlgorithmConfiguration.getListSeparator(), "','");
query = "select * into "+finalTableName+" from hspen where speciesid in ('"+species+"')"; query = "select * into "+finalTableName+" from hspen where speciesid in ('"+species+"')";
} }