deploy of charts and little correction on Gaussian charts
git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@112129 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
af8419ac0f
commit
937d559ae4
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@ -94,7 +94,7 @@ public class GaussianDistributionGraph extends GenericStandaloneGraph {
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protected JFreeChart createChart(Dataset dataset) {
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String label = "mean:"+mean+" variance:"+variance;
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String label = "mean:"+mean+" std dev:"+variance;
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if (label.length()>30)
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label = label.substring(0,30)+"...";
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@ -114,9 +114,9 @@ public class GaussianDistributionGraph extends GenericStandaloneGraph {
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return jfreechart;
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}
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public static JFreeChart createStaticChart(Dataset dataset, double mean, double variance) {
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public static JFreeChart createStaticChart(Dataset dataset, double mean, double stddev) {
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String label = "mean:"+mean+" variance:"+variance;
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String label = "mean:"+mean+" std dev:"+stddev;
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if (label.length()>30)
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label = label.substring(0,30)+"...";
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@ -0,0 +1,59 @@
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package org.gcube.dataanalysis.ecoengine.test;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.transducers.charts.QuantitiesAttributesChartsTransducerer;
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import org.gcube.dataanalysis.ecoengine.transducers.charts.TimeSeriesChartsTransducerer;
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public class ChartsTests {
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public static void main(String[] args) throws Exception{
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AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile);
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath("./cfg/");
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config.setPersistencePath("./");
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config.setParam("DatabaseUserName", "utente");
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config.setParam("DatabasePassword", "d4science");
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config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
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config.setParam("DatabaseDriver", "org.postgresql.Driver");
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config.setParam("InputTable", "hspen_mini");
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// config.setParam("Attributes", "speciesid#lifestage#faoareas");
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config.setParam("Quantities", "depthmax#speccode");
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config.setGcubeScope("/gcube/devsec/devVRE");
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QuantitiesAttributesChartsTransducerer cscreator = new QuantitiesAttributesChartsTransducerer();
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cscreator.setConfiguration(config);
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cscreator.compute();
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System.out.println("DONE! "+cscreator.getOutput());
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}
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public static void main1(String[] args) throws Exception{
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AnalysisLogger.setLogger("./cfg/" + AlgorithmConfiguration.defaultLoggerFile);
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath("./cfg/");
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config.setPersistencePath("./");
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config.setParam("DatabaseUserName", "utente");
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config.setParam("DatabasePassword", "d4science");
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config.setParam("DatabaseURL", "jdbc:postgresql://statistical-manager.d.d4science.research-infrastructures.eu/testdb");
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config.setParam("DatabaseDriver", "org.postgresql.Driver");
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config.setParam("InputTable", "timeseries_id4dd368bf_63fb_4d19_8e31_20ced63a477d");
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config.setParam("Attributes", "country#area");
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// config.setParam("Attributes", "");
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config.setParam("Quantities", "quantity");
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config.setParam("Time", "time");
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config.setGcubeScope("/gcube/devsec/devVRE");
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TimeSeriesChartsTransducerer cscreator = new TimeSeriesChartsTransducerer();
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cscreator.setConfiguration(config);
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cscreator.compute();
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System.out.println("DONE! "+cscreator.getOutput());
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}
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}
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@ -0,0 +1,156 @@
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package org.gcube.dataanalysis.ecoengine.transducers.charts;
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import java.awt.Image;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import org.gcube.contentmanagement.graphtools.data.conversions.ImageTools;
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import org.gcube.contentmanagement.lexicalmatcher.analysis.core.LexicalEngineConfiguration;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.datatypes.PrimitiveType;
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import org.gcube.dataanalysis.ecoengine.datatypes.StatisticalType;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.PrimitiveTypes;
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import org.gcube.dataanalysis.ecoengine.interfaces.StandardLocalExternalAlgorithm;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.hibernate.SessionFactory;
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import org.jfree.chart.JFreeChart;
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public abstract class AbstractChartsProducer extends StandardLocalExternalAlgorithm {
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static String inputTableParameter = "InputTable";
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static String attributesParameter = "Attributes";
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static String quantitiesParameter = "Quantities";
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static String timeParameter = "Time";
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public HashMap<String, Image> producedImages = new HashMap<String, Image>();
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public boolean displaycharts = true;
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static int maxSeries = 10;
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SessionFactory connection = null;
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@Override
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protected abstract void setInputParameters();
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@Override
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public StatisticalType getOutput() {
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PrimitiveType images = new PrimitiveType(HashMap.class.getName(), producedImages, PrimitiveTypes.IMAGES, "images", "Charts");
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LinkedHashMap<String, StatisticalType> outputmap = new LinkedHashMap<String, StatisticalType>();
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outputmap.put("Images", images);
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PrimitiveType output = new PrimitiveType(HashMap.class.getName(), outputmap, PrimitiveTypes.MAP, "ResultsMap", "Results Map");
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return output;
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}
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@Override
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public void init() throws Exception {
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AnalysisLogger.getLogger().debug("ChartsProducer Initialized");
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}
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@Override
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public abstract String getDescription();
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public String[] getDimensions() {
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String dimensionS = IOHelper.getInputParameter(config, attributesParameter);
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String[] dimensions = null;
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try{dimensions = dimensionS.split(AlgorithmConfiguration.getListSeparator());}catch(Exception e){}
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if (dimensions!=null && dimensions.length==1 && dimensions[0].trim().length()==0)
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dimensions = null;
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return dimensions;
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}
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public String[] getQuantities() {
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String quantitieS = IOHelper.getInputParameter(config, quantitiesParameter);
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String[] quantities = quantitieS.split(AlgorithmConfiguration.getListSeparator());
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return quantities;
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}
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public String getTimeDimension(){
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String timeS = IOHelper.getInputParameter(config, timeParameter);
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return timeS;
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}
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public String InfoRetrievalQuery(String table, String[] dimensions, String quantity,String time) {
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if (time!=null){
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if (dimensions!=null && dimensions.length>0)
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return "select * from (select distinct " + Arrays.toString(dimensions).replace("[", "").replace("]", "") + " , " + quantity +","+time+" from "+table+" order by " + quantity + " limit " + maxSeries+") as a order by "+time;
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else
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return "select * from (select distinct " +quantity +","+time+" from "+table+" order by " + quantity + " limit " + maxSeries+") as a order by "+time;
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}
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else{
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if (dimensions!=null && dimensions.length>0)
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return "select distinct " + Arrays.toString(dimensions).replace("[", "").replace("]", "") + " , " + quantity +" from "+table+" order by " + quantity + " limit " + maxSeries;
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else
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return "select distinct row_number() over(), " + quantity +" from "+table+" order by " + quantity + " limit " + maxSeries;
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}
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}
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@Override
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protected void process() throws Exception {
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status = 0;
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AnalysisLogger.setLogger(config.getConfigPath() + AlgorithmConfiguration.defaultLoggerFile);
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long t0 = System.currentTimeMillis();
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try {
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AnalysisLogger.getLogger().debug("ChartsProducer started");
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String driver = config.getParam("DatabaseDriver");
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String username = config.getParam("DatabaseUserName");
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String pwd = config.getParam("DatabasePassword");
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String url = config.getParam("DatabaseURL");
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String table = IOHelper.getInputParameter(config, inputTableParameter);
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AnalysisLogger.getLogger().debug("ChartsProducer: Driver: " + driver + " User " + username + " URL " + url + " Table: " + table);
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connection = DatabaseUtils.initDBSession(config);
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AnalysisLogger.getLogger().debug("ChartsProducer: Connection initialized");
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LexicalEngineConfiguration conf = new LexicalEngineConfiguration();
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conf.setDatabaseUserName(username);
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conf.setDatabasePassword(pwd);
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conf.setDatabaseDriver(driver);
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conf.setDatabaseURL(url);
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conf.setDatabaseDialect("org.hibernate.dialect.PostgreSQLDialect");
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String[] dimensions = getDimensions();
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String[] quantities = getQuantities();
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String time = getTimeDimension();
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//one quantity for each chart
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for (String quantity : quantities) {
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//produce chart with dimensions,quantity, time
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String query = InfoRetrievalQuery(table,dimensions,quantity,time);
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AnalysisLogger.getLogger().debug("ChartsProducer: Query for retrieving information "+query);
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List<Object> values = DatabaseFactory.executeSQLQuery(query, connection);
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JFreeChart[] charts= createCharts(dimensions,quantity,time,values,displaycharts);
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for (JFreeChart chart:charts){
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if (chart!=null){
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Image image= ImageTools.toImage(chart.createBufferedImage(680, 420));
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producedImages.put("Charts focused on "+quantity, image);
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}
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}
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}
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AnalysisLogger.getLogger().debug("ChartsProducer: finished");
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} catch (Throwable e) {
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e.printStackTrace();
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throw new Exception(e.getMessage());
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} finally {
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shutdown();
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status = 100;
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}
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}
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public abstract JFreeChart[] createCharts(String[] dimensions,String quantity,String time,List<Object> rows, boolean displaychart);
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@Override
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public void shutdown() {
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AnalysisLogger.getLogger().debug("ChartsProducer shutdown");
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DatabaseUtils.closeDBConnection(connection);
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}
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}
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@ -0,0 +1,126 @@
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package org.gcube.dataanalysis.ecoengine.transducers.charts;
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import java.util.ArrayList;
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import java.util.List;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.GaussianDistributionGraph;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.HistogramGraph;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.RadarGraph;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.ScatterGraphGeneric;
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import org.gcube.contentmanagement.graphtools.utils.MathFunctions;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.contentmanagement.lexicalmatcher.utils.DatabaseFactory;
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import org.gcube.dataanalysis.ecoengine.datatypes.ColumnTypesList;
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import org.gcube.dataanalysis.ecoengine.datatypes.DatabaseType;
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import org.gcube.dataanalysis.ecoengine.datatypes.InputTable;
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import org.gcube.dataanalysis.ecoengine.datatypes.enumtypes.TableTemplates;
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import org.gcube.dataanalysis.ecoengine.utils.IOHelper;
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import org.jfree.chart.JFreeChart;
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import org.jfree.data.category.DefaultCategoryDataset;
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import org.jfree.data.function.NormalDistributionFunction2D;
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import org.jfree.data.general.DatasetUtilities;
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import org.jfree.data.xy.XYSeriesCollection;
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public class QuantitiesAttributesChartsTransducerer extends AbstractChartsProducer {
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@Override
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protected void setInputParameters() {
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List<TableTemplates> templates = new ArrayList<TableTemplates>();
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templates.add(TableTemplates.GENERIC);
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InputTable tinput = new InputTable(templates, inputTableParameter, "The input table");
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inputs.add(tinput);
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ColumnTypesList p1 = new ColumnTypesList(inputTableParameter, attributesParameter, "The dimensions to consider in the charts", true);
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ColumnTypesList p2 = new ColumnTypesList(inputTableParameter, quantitiesParameter, "The numeric quantities to visualize ", false);
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inputs.add(p1);
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inputs.add(p2);
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DatabaseType.addDefaultDBPars(inputs);
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}
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@Override
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public String getDescription() {
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return "An algorithm producing generic charts of attributes vs. quantities. Charts are displayed per quantity column. Histograms, Scattering and Radar charts are produced for the top ten quantities. A gaussian distribution reports overall statistics for the quantities.";
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}
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@Override
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public JFreeChart[] createCharts(String[] dimensions, String quantity, String time, List<Object> rows, boolean displaychart) {
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if (dimensions==null)
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dimensions=new String[0];
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DefaultCategoryDataset datasetHisto = new DefaultCategoryDataset();
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for (Object row : rows) {
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Object[] array = (Object[]) row;
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Double q = null;
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try {
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q = Double.parseDouble("" + array[array.length - 1]);
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} catch (Exception e) {
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}
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if (q != null) {
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int dimIdx = 0;
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for (String dimension : dimensions) {
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String dimensionValue = "";
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if (array[dimIdx]!=null)
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dimensionValue = ""+array[dimIdx];
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if (dimensionValue.length()>0)
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datasetHisto.addValue(q, dimensionValue, dimension);
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dimIdx++;
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}
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}
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}
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List<Object> meanvar = DatabaseFactory.executeSQLQuery("select avg("+quantity+"), variance("+quantity+") from "+IOHelper.getInputParameter(config, inputTableParameter), connection);
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Object[] meanvarsrow = (Object[]) meanvar.get(0);
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double mean = MathFunctions.roundDecimal(Double.parseDouble(""+meanvarsrow[0]),2);
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double variance = MathFunctions.roundDecimal(Math.sqrt(Double.parseDouble(""+meanvarsrow[1])),2);
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AnalysisLogger.getLogger().debug("QuantitiesAttributesCharts: " + mean + " and variance:" + variance);
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NormalDistributionFunction2D normaldistributionfunction2d = new NormalDistributionFunction2D(mean, variance);
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org.jfree.data.xy.XYSeries gaussianxyseries = DatasetUtilities.sampleFunction2DToSeries(normaldistributionfunction2d, (mean - (2 * variance)), (mean + (2 * variance)), 121, "Distribution of "+quantity);
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XYSeriesCollection gaussianxyseriescollection = new XYSeriesCollection();
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gaussianxyseriescollection .addSeries(gaussianxyseries);
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JFreeChart charthisto = null;
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JFreeChart chartscattering = null;
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JFreeChart chartradar = null;
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if (dimensions.length>0){
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charthisto = HistogramGraph.createStaticChart(datasetHisto);
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chartscattering = ScatterGraphGeneric.createStaticChart(datasetHisto);
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chartradar = RadarGraph.createStaticChart(datasetHisto);
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}
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JFreeChart chartgaussian = GaussianDistributionGraph.createStaticChart(gaussianxyseriescollection, mean, variance);
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if (displaychart){
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HistogramGraph tsg = new HistogramGraph("QuantitiesAttributesHistogram");
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tsg.render(datasetHisto);
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ScatterGraphGeneric scatter = new ScatterGraphGeneric("QuantitiesAttributesScattering");
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scatter.render(datasetHisto);
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RadarGraph radar = new RadarGraph("QuantitiesAttributesRadar");
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radar.render(datasetHisto);
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GaussianDistributionGraph gaussian = new GaussianDistributionGraph("Gaussian");
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gaussian.mean=mean;
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gaussian.variance=variance;
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gaussian.render(gaussianxyseriescollection);
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}
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JFreeChart [] charts = new JFreeChart[4];
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charts [0] = charthisto;
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charts [1] = chartscattering;
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charts [2] = chartradar;
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charts [3] = chartgaussian;
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return charts;
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}
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}
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@ -0,0 +1,139 @@
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package org.gcube.dataanalysis.ecoengine.transducers.charts;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.List;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.LineGraph;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.TimeSeriesGraph;
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import org.gcube.contentmanagement.graphtools.plotting.graphs.TransectLineGraph;
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import org.gcube.contentmanagement.graphtools.utils.DateGuesser;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.datatypes.ColumnType;
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import org.jfree.chart.JFreeChart;
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import org.jfree.data.category.DefaultCategoryDataset;
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import org.jfree.data.time.FixedMillisecond;
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import org.jfree.data.time.TimeSeries;
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import org.jfree.data.time.TimeSeriesCollection;
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import com.sun.org.apache.bcel.internal.generic.LNEG;
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public class TimeSeriesChartsTransducerer extends QuantitiesAttributesChartsTransducerer {
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@Override
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protected void setInputParameters() {
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super.setInputParameters();
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ColumnType p = new ColumnType(inputTableParameter, timeParameter, "The column containing time information", "year", false);
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inputs.add(p);
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}
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@Override
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public String getDescription() {
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return "An algorithm producing time series charts of attributes vs. quantities. Charts are displayed per quantity column and only the top ten quantities are reported.";
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}
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String timepattern = "";
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SimpleDateFormat formatter = null;
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Date sampleTime = null;
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public Date getTime(String timel) {
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timel = timel.replace("time:", "");
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try {
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if (formatter == null) {
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timepattern = DateGuesser.getPattern(timel);
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AnalysisLogger.getLogger().debug("Time pattern: " + timepattern);
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formatter = new SimpleDateFormat(timepattern);
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sampleTime = formatter.parse(timel);
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}
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return formatter.parse(timel);
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} catch (ParseException e) {
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e.printStackTrace();
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return null;
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}
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}
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public String getChartPattern(Date time) {
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if (timepattern.equals("s") || DateGuesser.isJavaDateOrigin(time)) {
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return "HH:mm:ss:SS";
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} else {
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if (timepattern.length() == 4)
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return "yyyy";
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else
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||||
return "MM-dd-yy";
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public JFreeChart[] createCharts(String[] dimensions, String quantity, String time, List<Object> rows, boolean displaychart) {
|
||||
|
||||
if (dimensions==null)
|
||||
dimensions = new String[0];
|
||||
|
||||
TimeSeriesCollection dataset = new TimeSeriesCollection();
|
||||
TimeSeries series = null;
|
||||
if (dimensions.length>0)
|
||||
series = new TimeSeries("Trend of " + quantity + " for " + Arrays.toString(dimensions).replace("[", "").replace("]", ""));
|
||||
else
|
||||
series = new TimeSeries("Trend of " + quantity);
|
||||
dataset.addSeries(series);
|
||||
|
||||
DefaultCategoryDataset[] linedatasets = new DefaultCategoryDataset[dimensions.length];
|
||||
|
||||
for (Object row : rows) {
|
||||
Object[] array = (Object[]) row;
|
||||
Double q = null;
|
||||
Date timeD = null;
|
||||
String timel = "" + array[array.length - 1];
|
||||
try {
|
||||
q = Double.parseDouble("" + array[array.length - 2]);
|
||||
timeD = getTime(timel);
|
||||
} catch (Exception e) {
|
||||
}
|
||||
|
||||
if (q != null && timeD != null) {
|
||||
FixedMillisecond ms = new FixedMillisecond(timeD);
|
||||
series.add(ms, q);
|
||||
|
||||
for (int dimIdx=0;dimIdx<dimensions.length;dimIdx++) {
|
||||
String dimensionValue = "";
|
||||
if (array[dimIdx] != null)
|
||||
dimensionValue = "" + array[dimIdx];
|
||||
if (dimensionValue.length() > 0) {
|
||||
DefaultCategoryDataset lineds = linedatasets[dimIdx];
|
||||
if (lineds == null){
|
||||
lineds = new DefaultCategoryDataset();
|
||||
linedatasets[dimIdx]=lineds;
|
||||
}
|
||||
lineds.addValue(q, "singlets", timel + ";[" + dimensionValue + "]");
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
JFreeChart chartTS = TimeSeriesGraph.createStaticChart(dataset, getChartPattern(sampleTime), "Variations of " + quantity);
|
||||
|
||||
if (displaychart) {
|
||||
TimeSeriesGraph tsg = new TimeSeriesGraph("Variations of " + quantity);
|
||||
tsg.timeseriesformat = getChartPattern(sampleTime);
|
||||
tsg.render(dataset);
|
||||
for (int i = 0; i < dimensions.length; i++) {
|
||||
TransectLineGraph tlg = new TransectLineGraph("Variations of " + dimensions[i]);
|
||||
tlg.render(linedatasets[i]);
|
||||
}
|
||||
}
|
||||
|
||||
JFreeChart[] charts = new JFreeChart[1 + dimensions.length];
|
||||
charts[0] = chartTS;
|
||||
for (int i = 0; i < dimensions.length; i++) {
|
||||
JFreeChart linechartTS = LineGraph.createStaticChart(linedatasets[i], "Variations of " + dimensions[i]);
|
||||
charts[i+1] = linechartTS;
|
||||
}
|
||||
return charts;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue