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ecological-engine-geospatial-extensions
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Removed marytts-d4science #20135

This commit is contained in:
Giancarlo Panichi 2021-01-19 16:23:16 +01:00
parent 0e12b0890d
commit 95697b28e0
5 changed files with 0 additions and 370 deletions
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91
src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java
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package org.gcube.dataanalysis.geo.test;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector;
import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor;
import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor;
public class TestGeoTiff {
static String cfg = "./cfg/";
public static void main(String[] args) throws Exception{
String layertitle = "WorldClimBioWCS2";
long t0 = System.currentTimeMillis();
AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile);
AlgorithmConfiguration config = new AlgorithmConfiguration();
config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab");
config.setConfigPath(cfg);
TimeSeriesExtractor intersector = new TimeSeriesExtractor(config);
// intersector.takeTimeSlice(layertitle, 0, -180, 180, -10, 10, 0, 1, 1);
// intersector.takeTimeSlice(layertitle, 0, -10, 10, -10, 10, 0,1, 1);
// intersector.takeTimeInstantMatrix(layertitle, 0, -180, 180, -90, 90, 0, 0.5, 0.5);
double signal[] = intersector.extractT(layertitle, 0d, 0d,0d,0.5);
// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal");
System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
System.out.println("Signal: "+signal.length);
BufferedWriter bw = new BufferedWriter(new FileWriter(new File("signal.txt")));
for (double si: signal){
bw.write(si+",");
}
bw.close();
PeriodicityDetector pd = new PeriodicityDetector();
double F = pd.detectFrequency(signal,true);
System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]");
System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]");
System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength+" "+pd.getPeriodicityStregthInterpretation());
}
public static void main1(String[] args) throws Exception{
takeSignal();
}
public static void takeSignal() throws Exception{
BufferedReader br = new BufferedReader(new FileReader(new File("signal.txt")));
String line = br.readLine();
double[] signal = null;
while (line!=null){
String [] el = line.split(",");
signal=new double[el.length];
int i=0;
for (String e:el){
signal[i]=Double.parseDouble(e);
i++;
}
line = null;
}
br.close();
// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal");
PeriodicityDetector pd = new PeriodicityDetector();
// signal = pd.produceNoisySignal(2000, 1, 0.1f, 0f);
//float freq=1;//signal.length;
// double F = pd.detectFrequency(signal, (int)freq, 0, freq, 1f,true);
double F = pd.detectFrequency(signal,true);
System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]");
System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]");
System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength);
}
}

111
src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java
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package org.gcube.dataanalysis.geo.test;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector;
import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
import org.gcube.dataanalysis.geo.matrixmodel.MatrixExtractor;
import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor;
public class TestSignal {
static String cfg = "./cfg/";
public static void main(String[] args) throws Exception{
// String layertitle = "Statistical Mean in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}";
// String layertitle = "Mass Concentration of Chlorophyll in Sea Water in [03-30-13 01:00] (3D) {Mercator Ocean BIOMER1V1R1: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-analysis-bio-001-008-a}";
// String layertitle = "Objectively Analyzed Climatology in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}";
//temperature anomaly: long signal
//String layertitle = "be24800d-7583-4efa-b925-e0d8760e0fd3";
//temperature short periodic signal
// String layertitle = "dffa504b-dbc8-4553-896e-002549f8f5d3";
// String layertitle = "afd54b39-30f7-403a-815c-4f91c6c74c26";
// String layertitle = "6411b110-7572-457a-a662-a16e4ff09e4e";
//wind stress
// String layertitle = "255b5a95-ad28-4fec-99e0-5d48112dd6ab";
//wind speed
// layertitle = "a116c9bc-9380-4d40-8374-aa0e376a6820";
//nitrates
// layertitle = "b1cd9549-d9d0-4c77-9532-b161a69fbd44";
//ASC
// String layertitle = "2c2304d1-681a-4f3a-8409-e8cdb5ed447f";
//WFS
// String layertitle = "0aac424b-5f5b-4fa6-97d6-4b4deee62b97";
//Chlorophyll
String layertitle = "c565e32c-c5b3-4964-b44f-06dc620563e9";
long t0 = System.currentTimeMillis();
AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile);
AlgorithmConfiguration config = new AlgorithmConfiguration();
config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab");
config.setConfigPath(cfg);
TimeSeriesExtractor intersector = new TimeSeriesExtractor(config);
// intersector.takeTimeSlice(layertitle, 0, -180, 180, -10, 10, 0, 1, 1);
// intersector.takeTimeSlice(layertitle, 0, -10, 10, -10, 10, 0,1, 1);
// intersector.takeTimeInstantMatrix(layertitle, 0, -180, 180, -90, 90, 0, 0.5, 0.5);
double signal[] = intersector.extractT(layertitle, 0d, 0d,0d,0.5);
// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal");
System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
System.out.println("Signal: "+signal.length);
BufferedWriter bw = new BufferedWriter(new FileWriter(new File("signal.txt")));
for (double si: signal){
bw.write(si+",");
}
bw.close();
PeriodicityDetector pd = new PeriodicityDetector();
double F = pd.detectFrequency(signal,true);
System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]");
System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]");
System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength+" "+pd.getPeriodicityStregthInterpretation());
}
public static void main1(String[] args) throws Exception{
takeSignal();
}
public static void takeSignal() throws Exception{
BufferedReader br = new BufferedReader(new FileReader(new File("signal.txt")));
String line = br.readLine();
double[] signal = null;
while (line!=null){
String [] el = line.split(",");
signal=new double[el.length];
int i=0;
for (String e:el){
signal[i]=Double.parseDouble(e);
i++;
}
line = null;
}
br.close();
// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal");
PeriodicityDetector pd = new PeriodicityDetector();
// signal = pd.produceNoisySignal(2000, 1, 0.1f, 0f);
//float freq=1;//signal.length;
// double F = pd.detectFrequency(signal, (int)freq, 0, freq, 1f,true);
double F = pd.detectFrequency(signal,true);
System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]");
System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]");
System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength);
}
}

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src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java
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package org.gcube.dataanalysis.geo.test;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileReader;
import java.io.FileWriter;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.signals.PeriodicityDetector;
import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
import org.gcube.dataanalysis.geo.matrixmodel.TimeSeriesExtractor;
public class TestSignalTable {
static String cfg = "./cfg/";
public static void main(String[] args) throws Exception{
AlgorithmConfiguration config = new AlgorithmConfiguration();
config.setConfigPath("./cfg/");
config.setPersistencePath("./");
config.setParam("DatabaseUserName", "utente");
config.setParam("DatabasePassword", "d4science");
config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
config.setParam("DatabaseDriver", "org.postgresql.Driver");
// vessels
config.setParam(TableMatrixRepresentation.tableNameParameter, "generic_id037d302d_2ba0_4e43_b6e4_1a797bb91728");
// config.setParam(TableMatrixRepresentation.xDimensionColumnParameter, "x");
// config.setParam(TableMatrixRepresentation.yDimensionColumnParameter, "y");
// config.setParam(zDimensionColumnParameter,"");
config.setParam(TableMatrixRepresentation.timeDimensionColumnParameter, "datetime");
config.setParam(TableMatrixRepresentation.valueDimensionColumnParameter, "speed");
config.setParam(TableMatrixRepresentation.filterParameter, "speed<2");
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab");
config.setConfigPath(cfg);
TimeSeriesExtractor intersector = new TimeSeriesExtractor(config);
long t0 = System.currentTimeMillis();
// double signal[] = intersector.takeSignalInTime("table", -47.14, 44.52, 0d, 0.5);
double signal[] = intersector.extractT("table");
// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal");
System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
System.out.println("Signal: "+signal.length);
PeriodicityDetector pd = new PeriodicityDetector();
double F = pd.detectFrequency(signal,true);
System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]");
System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]");
System.out.println("Detected Periodicity Strength:"+pd.periodicityStrength);
}
public static void main1(String[] args) throws Exception{
takeSignal();
}
public static void takeSignal() throws Exception{
BufferedReader br = new BufferedReader(new FileReader(new File("signal.txt")));
String line = br.readLine();
double[] signal = null;
while (line!=null){
String [] el = line.split(",");
signal=new double[el.length];
int i=0;
for (String e:el){
signal[i]=Double.parseDouble(e);
i++;
}
line = null;
}
br.close();
// SignalProcessing.displaySignalWithGenericTime(signal, 0, 1, "signal");
PeriodicityDetector pd = new PeriodicityDetector();
// signal = pd.produceNoisySignal(2000, 1, 0.1f, 0f);
//float freq=1;//signal.length;
// double F = pd.detectFrequency(signal, (int)freq, 0, freq, 1f,true);
double F = pd.detectFrequency(signal,true);
System.out.println("Detected Frequency:"+F+" indecision ["+pd.lowermeanF+" , "+pd.uppermeanF+"]");
System.out.println("Detected Period:"+pd.meanPeriod+" indecision ["+pd.lowermeanPeriod+" , "+pd.uppermeanPeriod+"]");
System.out.println("Detected Period Strength:"+pd.periodicityStrength);
}
}

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src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java
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package org.gcube.dataanalysis.geo.test;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
import org.gcube.dataanalysis.ecoengine.utils.Tuple;
import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor;
public class TestWaterColumnGeoTiff {
public static void main(String[] args) throws Exception{
AlgorithmConfiguration config = new AlgorithmConfiguration();
config.setConfigPath("./cfg/");
config.setPersistencePath("./");
String layertitle = "WorldClimBioGeoTiffTest2";
// layertitle = "WorldClimBioWCS2";
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab");
ZExtractor extractor = new ZExtractor(config);
long t0 = System.currentTimeMillis();
double watercolumn[] = extractor.extractZ(layertitle, 18.620429d,20.836419d,0, 0);
System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
System.out.println("Signal: "+watercolumn.length);
System.out.println("Signal first element: "+watercolumn[0]);
SignalProcessing.displaySignalWithGenericTime(watercolumn, 0, 1, "signal");
}
}

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src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java
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package org.gcube.dataanalysis.geo.test;
import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
import org.gcube.dataanalysis.ecoengine.signals.SignalProcessing;
import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
import org.gcube.dataanalysis.geo.matrixmodel.ZExtractor;
public class TestWaterColumnTemperature {
public static void main(String[] args) throws Exception{
AlgorithmConfiguration config = new AlgorithmConfiguration();
config.setConfigPath("./cfg/");
config.setPersistencePath("./");
String layertitle = "6411b110-7572-457a-a662-a16e4ff09e4e";
/*
layertitle = "be24800d-7583-4efa-b925-e0d8760e0fd3";
layertitle = "320652c8-e986-4428-9306-619d9014822a";
layertitle = "0aac424b-5f5b-4fa6-97d6-4b4deee62b97";
*/
AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
config.setGcubeScope("/d4science.research-infrastructures.eu/gCubeApps/BiodiversityLab");
ZExtractor extractor = new ZExtractor(config);
long t0 = System.currentTimeMillis();
double watercolumn[] = extractor.extractZ(layertitle, 0,0, 0, 100);
System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
System.out.println("Signal: "+watercolumn.length);
SignalProcessing.displaySignalWithGenericTime(watercolumn, 0, 1, "signal");
}
}