git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngine@51720 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
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@ -1,4 +1,4 @@
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name = EcologicalEngine
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package = org.gcube
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package = org.gcube.dataanalysis.ecologicalengine
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# Where the jar will be stored
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lib.dir = Dependencies/org.gcube.dataanalysis.ecologicalengine.jar
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@ -22,10 +22,28 @@ public class BioClimateAnalysis {
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private static String countHighProbabilityCells = "select count(*) from %1$s where probability>%2$s";
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private static String countSeaCells = "select count(*) from %1$s as a join %2$s as b on a.oceanarea>0 and a.csquarecode=b.csquarecode and ((a.iceconann<b.iceconann-%3$s or a.iceconann>b.iceconann+%3$s) or " + "(a.salinitymean<b.salinitymean-%3$s or a.salinitymean>b.salinitymean+%3$s) or (a.sstanmean<b.sstanmean-%3$s or a.sstanmean>b.sstanmean+%3$s))";
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private static String iceLeakage = "select count(*) from %1$s as a join %2$s as b on a.csquarecode=b.csquarecode and (a.iceconann<b.iceconann) and a.oceanarea>0";
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private static String takeRangeOfDepths= "select distinct depthmin, max(depthmax) from %1$s group by depthmin order by depthmin";
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private static String countNumberOfSpecies= "count(*) from %1$s where depthmin<%2$s and depthmin>=%3$s and depthmax<%4$s and depthmax>=%5$s";
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private static enum FIELD {
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iceconann, sstanmean, salinitymean
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};
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private static String takeAvgSelection = "select avg(%1$s),%2$s from %3$s %4$s group by %2$s order by %2$s";
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private static String [] selectionCriteria = {"faoaream", "lme"};
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private static String [] timeseriesNames = {"Ice Conc.", "Sea Surface Temperature","Salinity"};
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private static String [] quantitiesNames= {FIELD.iceconann.name(), FIELD.sstanmean.name(),FIELD.salinitymean.name()};
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private static String [] selectionFilters= {"where faoaream>0", "where lme>0"};
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private static String [] criteriaNames = {"FaoArea", "LME"};
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// private static String takeSubHspec = "select %1$s from #CLAUSE# order by %1$s";
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private static String meanVal = "select avg(%2$s) from %1$s where oceanarea>0";
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// private static String meanVal = "select %2$s from %1$s where csquarecode = '1311:478:4'";
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private String configPath;
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private String temporaryDirectory;
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@ -34,36 +52,33 @@ public class BioClimateAnalysis {
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private String[] csquareTable;
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private String[] finalDistributionTable;
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//hspec
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// hspec
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private int[] highProbabilityCells;
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private double[] discrepancies;
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//hcaf
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// hcaf
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private double[] avgIce;
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private double[] avgSST;
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private double[] avgSalinity;
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private Evaluator eval;
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private float status;
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private boolean liveRender;
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boolean doHcafAn;
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boolean doHspecAn;
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private LexicalEngineConfiguration config;
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private static enum FIELD {
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iceconann, sstanmean, salinitymean
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};
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static int width = 680;
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static int height = 420;
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public static void main(String[] args) throws Exception {
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String configPath = "./cfg/";
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String databaseUrl = "jdbc:postgresql://localhost/testdb";
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String databaseUser = "gcube";
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String databasePassword = "d4science2";
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BioClimateAnalysis bioClimate = new BioClimateAnalysis(configPath, configPath, databaseUrl, databaseUser, databasePassword,true);
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bioClimate.produceGraphs2D();
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BioClimateAnalysis bioClimate = new BioClimateAnalysis(configPath, configPath, databaseUrl, databaseUser, databasePassword, true);
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bioClimate.produceGraphs2D();
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}
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private static String[] SERIES = { "High Probability Cells Trend (>0.8)", "Number of Changing Cells", "Reducing Ice Concentration Trend", "Average Discrepancy Between Distributions", "Average Trends", "Ice Concentration", "Sea Surface Temperature", "Salinity" };
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@ -89,55 +104,52 @@ public class BioClimateAnalysis {
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return producedImages;
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}
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private void produceGraphs() throws Exception {
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private void produceGraphs(String [] csquareTableNames,String[] hspecTableNames) throws Exception {
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producedImages = new ArrayList<Image>();
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int numberOfTrends = highProbabilityCells.length;
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// create the datasets...
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DefaultCategoryDataset probabilityTrend = new DefaultCategoryDataset();
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DefaultCategoryDataset discrepanciesTrend = new DefaultCategoryDataset();
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DefaultCategoryDataset avgIceD = new DefaultCategoryDataset();
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DefaultCategoryDataset avgSSTD = new DefaultCategoryDataset();
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DefaultCategoryDataset avgSalinityD = new DefaultCategoryDataset();
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for (int i = 0; i < numberOfTrends; i++) {
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if (doHcafAn){
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avgIceD.addValue(avgIce[i], "Ice Conc.", csquareTable[i]);
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avgSSTD.addValue(avgSST[i], "SST", csquareTable[i]);
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avgSalinityD.addValue(avgSalinity[i], "Salinity", csquareTable[i]);
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if (doHcafAn) {
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avgIceD.addValue(avgIce[i], "Ice Conc.", csquareTableNames[i]);
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avgSSTD.addValue(avgSST[i], "SST", csquareTableNames[i]);
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avgSalinityD.addValue(avgSalinity[i], "Salinity", csquareTableNames[i]);
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}
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if (doHspecAn){
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probabilityTrend.addValue(highProbabilityCells[i], "Number Of Cells", finalDistributionTable[i]);
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if (doHspecAn) {
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probabilityTrend.addValue(highProbabilityCells[i], "Number Of Cells", hspecTableNames[i]);
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if (i > 0) {
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discrepanciesTrend.addValue(discrepancies[i], "Mean Discrepancy Respect to Prev. Distrib.", finalDistributionTable[i]);
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}
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}
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}
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int width = 680;
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int height = 420;
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if (doHspecAn){
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if (doHspecAn) {
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double min = Operations.getMin(discrepancies);
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discrepancies[0] = min;
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if (liveRender){
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BioClimateGraph lineg1 = new BioClimateGraph(SERIES[0], Operations.getMax(highProbabilityCells), Operations.getMin(highProbabilityCells));
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if (liveRender) {
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BioClimateGraph lineg1 = new BioClimateGraph(SERIES[0], Operations.getMax(highProbabilityCells), Operations.getMin(highProbabilityCells));
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BioClimateGraph lineg4 = new BioClimateGraph(SERIES[3], Operations.getMax(discrepancies), min);
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lineg4.render(discrepanciesTrend);
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lineg1.render(probabilityTrend);
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}
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producedImages.add(BioClimateGraph.renderStaticImgObject(width, height, probabilityTrend, SERIES[0], Operations.getMax(highProbabilityCells), Operations.getMin(highProbabilityCells)));
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producedImages.add(BioClimateGraph.renderStaticImgObject(width, height, discrepanciesTrend, SERIES[3], Operations.getMax(discrepancies), min));
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}
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if (doHcafAn){
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if (liveRender){
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if (doHcafAn) {
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if (liveRender) {
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BioClimateGraph lineg6 = new BioClimateGraph(SERIES[5], Operations.getMax(avgIce), Operations.getMin(avgIce));
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BioClimateGraph lineg7 = new BioClimateGraph(SERIES[6], Operations.getMax(avgSST), Operations.getMin(avgSST));
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BioClimateGraph lineg8 = new BioClimateGraph(SERIES[7], Operations.getMax(avgSalinity), Operations.getMin(avgSalinity));
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lineg7.render(avgSSTD);
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lineg8.render(avgSalinityD);
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}
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producedImages.add(BioClimateGraph.renderStaticImgObject(width, height, avgIceD, SERIES[5], Operations.getMax(avgIce), Operations.getMin(avgIce)));
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producedImages.add(BioClimateGraph.renderStaticImgObject(width, height, avgSSTD, SERIES[6], Operations.getMax(avgSST), Operations.getMin(avgSST)));
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producedImages.add(BioClimateGraph.renderStaticImgObject(width, height, avgSSTD, SERIES[6], Operations.getMax(avgSST), Operations.getMin(avgSST)));
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producedImages.add(BioClimateGraph.renderStaticImgObject(width, height, avgSalinityD, SERIES[7], Operations.getMax(avgSalinity), Operations.getMin(avgSalinity)));
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}
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AnalysisLogger.getLogger().trace("Produced All Images");
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}
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public void hcafEvolutionAnalysis(String[] hcafTable,String[] hcafTableNames) throws Exception {
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globalEvolutionAnalysis(hcafTable, null, hcafTableNames, null, null, null);
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}
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public void hspecEvolutionAnalysis(String[] hspecTables, String[] hspecTableNames, String probabilityColumn, String csquareColumn) throws Exception {
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globalEvolutionAnalysis(null, hspecTables, null, hspecTableNames, probabilityColumn, csquareColumn);
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}
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private List<Image> producedCharts;
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public void hcafEvolutionAnalysis(String[] hcafTable) throws Exception{
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evolutionAnalysis(hcafTable, null, null, null);
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}
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public void hspecEvolutionAnalysis(String[] hspecTables, String probabilityColumn, String csquareColumn) throws Exception{
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evolutionAnalysis(null, hspecTables, probabilityColumn, csquareColumn);
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public void produceCharts(HashMap<String,HashMap<String,double []>> GeoMap,String[] hcafTablesNames){
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//produce a char for each feature
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producedCharts = new ArrayList<Image>();
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for (String featurename:GeoMap.keySet()){
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DefaultCategoryDataset chart = new DefaultCategoryDataset();
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HashMap<String,double []> timeseries = GeoMap.get(featurename);
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double absmax = -Double.MAX_VALUE;
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double absmin = Double.MAX_VALUE;
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for (String timeserie:timeseries.keySet()){
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double[] points = timeseries.get(timeserie);
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for (int i=0;i<points.length;i++){
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if (points [i]>absmax)
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absmax = points[i];
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if (points [i]<absmin)
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absmin = points[i];
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chart.addValue(points[i], timeserie,hcafTablesNames[i]);
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}
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}
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if (liveRender) {
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BioClimateGraph lineg1 = new BioClimateGraph(featurename, absmax, absmin);
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lineg1.render(chart);
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}
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producedCharts.add(BioClimateGraph.renderStaticImgObject(width, height, chart, featurename, absmax, absmin));
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}
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}
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public void evolutionAnalysis(String[] hcafTable, String[] hspecTables, String probabilityColumn, String csquareColumn) throws Exception {
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public void geographicEvolutionAnalysis(String[] hcafTable,String []hcafTableNames) throws Exception {
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try {
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referencedbConnection = DatabaseFactory.initDBConnection(configPath + AlgorithmConfiguration.defaultConnectionFile, config);
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AnalysisLogger.getLogger().debug("ReferenceDB initialized");
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doHcafAn = true;
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doHspecAn = true;
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if (hcafTable == null)
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doHcafAn = false;
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if (hspecTables == null)
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doHspecAn = false;
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referencedbConnection = DatabaseFactory.initDBConnection(configPath + AlgorithmConfiguration.defaultConnectionFile, config);
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AnalysisLogger.getLogger().debug("ReferenceDB initialized");
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doHcafAn = true;
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doHspecAn = true;
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status = 0f;
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this.csquareTable = hcafTable;
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status = 0f;
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this.csquareTable = hcafTable;
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this.finalDistributionTable = hspecTables;
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int numbOfPoints = (hcafTable!=null)? hcafTable.length:hspecTables.length;
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highProbabilityCells = new int[numbOfPoints];
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discrepancies = new double[numbOfPoints];
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avgIce = new double[numbOfPoints];
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avgSST = new double[numbOfPoints];
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avgSalinity = new double[numbOfPoints];
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float statusstep = 80f / (float) numbOfPoints;
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int numbOfTables = (hcafTable != null) ? hcafTable.length : 0;
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if (numbOfTables > 0) {
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//a map for each feature. each sub map contains a trend for faoaream, lme etc.
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HashMap<String,HashMap<String,double []>> GeoMap= new HashMap<String, HashMap<String,double[]>>();
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float statusstep = 80f / (float) numbOfTables;
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//for each table
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for (int i = 0; i < numbOfTables; i++) {
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//for each criterion to apply: fao area, lme etc.
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for (int j=0;j<criteriaNames.length;j++){
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//for each quantity to display: ice concentration
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for (int k=0;k<quantitiesNames.length;k++){
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String query = String.format(takeAvgSelection, quantitiesNames[k],selectionCriteria[j],hcafTable[i],selectionFilters[j]);
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AnalysisLogger.getLogger().debug("Query to be executed : "+query);
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//take couples (avg,code)
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List<Object> quantityCriterion = DatabaseFactory.executeSQLQuery(query, referencedbConnection);
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//for each row
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for (Object element: quantityCriterion){
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Object [] row = (Object[]) element;
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//take avg value
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double value = (row[0]==null)?0:Double.parseDouble(""+row[0]);
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//take code for criterion
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String code = ""+row[1];
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String chartName = timeseriesNames[k]+" for "+criteriaNames[j]+"_"+code;
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//put the code and the value in the timeseries associated to the feature name
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HashMap<String,double []> submap = GeoMap.get(chartName);
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if (submap==null){
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submap = new HashMap<String, double[]>();
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GeoMap.put(chartName, submap);
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}
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String timeseries = criteriaNames[j]+"_"+code;
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double [] elements = submap.get(timeseries);
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if (elements==null){
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elements = new double[numbOfTables];
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submap.put(timeseries, elements);
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}
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elements[i] = value;
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}
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}
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}
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status = status + statusstep;
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}
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status = 80f;
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produceCharts(GeoMap,hcafTableNames);
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}
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} catch (Exception e) {
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e.printStackTrace();
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throw e;
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} finally {
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status = 100f;
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referencedbConnection.close();
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}
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}
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public void globalEvolutionAnalysis(String[] hcafTable, String[] hspecTables,String[] hcafTablesNames, String [] hspecTableNames, String probabilityColumn, String csquareColumn) throws Exception {
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try {
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referencedbConnection = DatabaseFactory.initDBConnection(configPath + AlgorithmConfiguration.defaultConnectionFile, config);
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AnalysisLogger.getLogger().debug("ReferenceDB initialized");
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doHcafAn = true;
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doHspecAn = true;
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if (hcafTable == null)
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doHcafAn = false;
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if (hspecTables == null)
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doHspecAn = false;
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status = 0f;
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this.csquareTable = hcafTable;
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this.finalDistributionTable = hspecTables;
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int numbOfPoints = (hcafTable != null) ? hcafTable.length : hspecTables.length;
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highProbabilityCells = new int[numbOfPoints];
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discrepancies = new double[numbOfPoints];
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avgIce = new double[numbOfPoints];
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avgSST = new double[numbOfPoints];
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avgSalinity = new double[numbOfPoints];
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float statusstep = 80f / (float) numbOfPoints;
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for (int i = 0; i < numbOfPoints; i++) {
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if (doHspecAn)
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highProbabilityCells[i] = calcHighProbabilityCells(hspecTables[i], 0.8);
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if (doHcafAn){
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if (doHcafAn) {
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avgIce[i] = avgValue(hcafTable[i], FIELD.iceconann.name());
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avgSST[i] = avgValue(hcafTable[i], FIELD.sstanmean.name());
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avgSalinity[i] = avgValue(hcafTable[i], FIELD.salinitymean.name());
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AnalysisLogger.getLogger().trace("(" + hcafTable[i] +"): " + " ICE " + avgIce[i] + " SST " + avgSST[i] + " SAL " + avgSalinity[i]);
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AnalysisLogger.getLogger().trace("(" + hcafTable[i] + "): " + " ICE " + avgIce[i] + " SST " + avgSST[i] + " SAL " + avgSalinity[i]);
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}
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if (doHspecAn) {
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if (i == 0) {
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discrepancies[i] = 1.0;
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} else {
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// OLD CALCULATION discrepancies[i] = MathFunctions.roundDecimal(calcDiscrepancy(configPath, temporaryDirectory, hspecTables[i], hspecTables[i - 1], probabilityColumn, csquareColumn, 0.1f), 5);
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// OLD CALCULATION discrepancies[i] = MathFunctions.roundDecimal(calcDiscrepancy(configPath, temporaryDirectory, hspecTables[i], hspecTables[i - 1], probabilityColumn, csquareColumn, 0.1f), 5);
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discrepancies[i] = MathFunctions.roundDecimal(calcOverDiscrepancy(configPath, temporaryDirectory, hspecTables[i], hspecTables[i - 1], probabilityColumn, csquareColumn, 0.1f), 5);
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}
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AnalysisLogger.getLogger().trace("(" + hspecTables[i] +"): DISCREPANCY " + discrepancies[i] +" HIGH PROB CELLS " + highProbabilityCells[i]);
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AnalysisLogger.getLogger().trace("(" + hspecTables[i] + "): DISCREPANCY " + discrepancies[i] + " HIGH PROB CELLS " + highProbabilityCells[i]);
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}
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// AnalysisLogger.getLogger().trace("(" + hcafTable[i] + "," + hspecTables[i] + "): HIGH PROB CELLS " + highProbabilityCells[i] + " DISCREPANCY " + discrepancies[i] + " ICE " + avgIce[i] + " SST " + avgSST[i] + " SAL " + avgSalinity[i]);
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// AnalysisLogger.getLogger().trace("(" + hcafTable[i] + "," + hspecTables[i] + "): HIGH PROB CELLS " + highProbabilityCells[i] + " DISCREPANCY " + discrepancies[i] + " ICE " + avgIce[i] + " SST " + avgSST[i] + " SAL " + avgSalinity[i]);
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status = status + statusstep;
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}
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status = 80f;
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produceGraphs();
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produceGraphs(hcafTablesNames,hspecTableNames);
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} catch (Exception e) {
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e.printStackTrace();
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@ -231,9 +336,8 @@ public class BioClimateAnalysis {
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}
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}
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// init connections
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public BioClimateAnalysis(String configPath, String persistencePath, String databaseURL, String databaseUserName, String databasePassword,boolean liveRender) throws Exception {
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public BioClimateAnalysis(String configPath, String persistencePath, String databaseURL, String databaseUserName, String databasePassword, boolean liveRender) throws Exception {
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this.configPath = configPath;
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this.temporaryDirectory = persistencePath;
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if (!configPath.endsWith("/"))
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@ -246,7 +350,7 @@ public class BioClimateAnalysis {
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config.setDatabaseURL(databaseURL);
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config.setDatabaseUserName(databaseUserName);
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config.setDatabasePassword(databasePassword);
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||||
|
||||
this.liveRender = liveRender;
|
||||
}
|
||||
|
||||
|
|
@ -254,10 +358,12 @@ public class BioClimateAnalysis {
|
|||
AnalysisLogger.getLogger().trace("Calculating High Prob Cells");
|
||||
List<Object> countage = DatabaseFactory.executeSQLQuery(String.format(countHighProbabilityCells, hspec, probabilty), referencedbConnection);
|
||||
int count = Integer.parseInt("" + countage.get(0));
|
||||
AnalysisLogger.getLogger().trace("Calc High Prob Cells: "+count);
|
||||
AnalysisLogger.getLogger().trace("Calc High Prob Cells: " + count);
|
||||
return count;
|
||||
}
|
||||
|
||||
|
||||
|
||||
public double avgValue(String hcaf1, String field) throws Exception {
|
||||
|
||||
List<Object> countage = DatabaseFactory.executeSQLQuery(String.format(meanVal, hcaf1, field), referencedbConnection);
|
||||
|
|
@ -287,26 +393,26 @@ public class BioClimateAnalysis {
|
|||
}
|
||||
|
||||
public double calcOverDiscrepancy(String configPath, String persistencePath, String firstTable, String secondTable, String probabilityColumnName, String csquareColumn, float comparisonThreshold) throws Exception {
|
||||
|
||||
List<Object> nelementsQ1 = DatabaseFactory.executeSQLQuery(DatabaseUtils.countElementsStatement(firstTable),referencedbConnection);
|
||||
int nelements = Integer.parseInt(""+nelementsQ1.get(0));
|
||||
AnalysisLogger.getLogger().trace("Number Of elements1: "+nelementsQ1);
|
||||
List<Object> nelementsQ2 = DatabaseFactory.executeSQLQuery(DatabaseUtils.countElementsStatement(secondTable),referencedbConnection);
|
||||
int nelements2 = Integer.parseInt(""+nelementsQ2.get(0));
|
||||
AnalysisLogger.getLogger().trace("Number Of elements2: "+nelementsQ1);
|
||||
|
||||
List<Object> sumFirst = DatabaseFactory.executeSQLQuery(DatabaseUtils.sumElementsStatement(firstTable,probabilityColumnName),referencedbConnection);
|
||||
double sum1 = Double.parseDouble(""+sumFirst.get(0));
|
||||
AnalysisLogger.getLogger().trace("Sum1: "+sum1);
|
||||
|
||||
List<Object> sumSecond = DatabaseFactory.executeSQLQuery(DatabaseUtils.sumElementsStatement(secondTable,probabilityColumnName),referencedbConnection);
|
||||
double sum2 = Double.parseDouble(""+sumSecond.get(0));
|
||||
AnalysisLogger.getLogger().trace("Sum2: "+sum1);
|
||||
|
||||
double d = (double)(sum2-sum1)/(double)(nelements+nelements2);
|
||||
|
||||
List<Object> nelementsQ1 = DatabaseFactory.executeSQLQuery(DatabaseUtils.countElementsStatement(firstTable), referencedbConnection);
|
||||
int nelements = Integer.parseInt("" + nelementsQ1.get(0));
|
||||
AnalysisLogger.getLogger().trace("Number Of elements1: " + nelementsQ1);
|
||||
List<Object> nelementsQ2 = DatabaseFactory.executeSQLQuery(DatabaseUtils.countElementsStatement(secondTable), referencedbConnection);
|
||||
int nelements2 = Integer.parseInt("" + nelementsQ2.get(0));
|
||||
AnalysisLogger.getLogger().trace("Number Of elements2: " + nelementsQ1);
|
||||
|
||||
List<Object> sumFirst = DatabaseFactory.executeSQLQuery(DatabaseUtils.sumElementsStatement(firstTable, probabilityColumnName), referencedbConnection);
|
||||
double sum1 = Double.parseDouble("" + sumFirst.get(0));
|
||||
AnalysisLogger.getLogger().trace("Sum1: " + sum1);
|
||||
|
||||
List<Object> sumSecond = DatabaseFactory.executeSQLQuery(DatabaseUtils.sumElementsStatement(secondTable, probabilityColumnName), referencedbConnection);
|
||||
double sum2 = Double.parseDouble("" + sumSecond.get(0));
|
||||
AnalysisLogger.getLogger().trace("Sum2: " + sum1);
|
||||
|
||||
double d = (double) (sum2 - sum1) / (double) (nelements + nelements2);
|
||||
return d;
|
||||
}
|
||||
|
||||
|
||||
public double calcDiscrepancy(String configPath, String persistencePath, String firstTable, String secondTable, String probabilityColumnName, String csquareColumn, float comparisonThreshold) throws Exception {
|
||||
|
||||
AlgorithmConfiguration config = new AlgorithmConfiguration();
|
||||
|
|
@ -327,14 +433,13 @@ public class BioClimateAnalysis {
|
|||
|
||||
config.setParam("ComparisonThreshold", "" + comparisonThreshold);
|
||||
|
||||
config.setParam("MaxSamples", ""+30000);
|
||||
|
||||
config.setParam("MaxSamples", "" + 30000);
|
||||
|
||||
eval = EvaluatorsFactory.getEvaluators(config).get(0);
|
||||
HashMap<String, String> out = eval.process(config);
|
||||
|
||||
Double d = Double.parseDouble(out.get("MEAN"));
|
||||
return d;
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue