From 95697b28e079fd8d1847256c82ce4a1b9a40ad43 Mon Sep 17 00:00:00 2001 From: Giancarlo Panichi Date: Tue, 19 Jan 2021 16:23:16 +0100 Subject: [PATCH] Removed marytts-d4science #20135 --- .../dataanalysis/geo/test/TestGeoTiff.java | 91 -------------- .../dataanalysis/geo/test/TestSignal.java | 111 ------------------ .../geo/test/TestSignalTable.java | 95 --------------- .../geo/test/TestWaterColumnGeoTiff.java | 36 ------ .../geo/test/TestWaterColumnTemperature.java | 37 ------ 5 files changed, 370 deletions(-) delete mode 100644 src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java delete mode 100644 src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java delete mode 100644 src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java delete mode 100644 src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java delete mode 100644 src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java diff --git a/src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java deleted file mode 100644 index 2e1c856..0000000 --- a/src/test/java/org/gcube/dataanalysis/geo/test/TestGeoTiff.java +++ /dev/null @@ -1,91 +0,0 @@ -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); - - } - -} diff --git a/src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java deleted file mode 100644 index 1e3e25b..0000000 --- a/src/test/java/org/gcube/dataanalysis/geo/test/TestSignal.java +++ /dev/null @@ -1,111 +0,0 @@ -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); - - } - -} diff --git a/src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java deleted file mode 100644 index bdb23a3..0000000 --- a/src/test/java/org/gcube/dataanalysis/geo/test/TestSignalTable.java +++ /dev/null @@ -1,95 +0,0 @@ -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); - } - -} diff --git a/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java deleted file mode 100644 index a1d50e1..0000000 --- a/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnGeoTiff.java +++ /dev/null @@ -1,36 +0,0 @@ -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"); - - } - -} diff --git a/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java b/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java deleted file mode 100644 index 1198a9b..0000000 --- a/src/test/java/org/gcube/dataanalysis/geo/test/TestWaterColumnTemperature.java +++ /dev/null @@ -1,37 +0,0 @@ -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"); - - } - -}