git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@92162 82a268e6-3cf1-43bd-a215-b396298e98cf
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package org.gcube.dataanalysis.geo.matrixmodel;
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import java.util.ArrayList;
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import java.util.List;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.connectors.asc.ASC;
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import org.gcube.dataanalysis.geo.connectors.interfaces.GISDataConnector;
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import org.gcube.dataanalysis.geo.connectors.netcdf.NetCDF;
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import org.gcube.dataanalysis.geo.connectors.wfs.WFS;
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import org.gcube.dataanalysis.geo.infrastructure.GeoNetworkInspector;
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import org.opengis.metadata.Metadata;
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import org.opengis.metadata.identification.Identification;
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public class MatrixExtractor {
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private GeoNetworkInspector gnInspector;
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private String configDir;
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public MatrixExtractor(String scope, String cfgDir) {
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gnInspector = new GeoNetworkInspector();
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gnInspector.setScope(scope);
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this.configDir=cfgDir;
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}
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public GeoNetworkInspector getFeaturer(){
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return gnInspector;
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}
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public static List<Tuple<Double>> generateCoordinateTripletsInBoundingBox(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution){
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int ysteps = (int) ((y2 - y1) / yResolution);
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int xsteps = (int) ((x2 - x1) / xResolution);
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List<Tuple<Double>> tuples = new ArrayList<Tuple<Double>>();
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AnalysisLogger.getLogger().debug("Building the points grid according to YRes:" + yResolution + " and XRes:" + xResolution);
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// build the tuples according to the desired resolution
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for (int i = 0; i < ysteps + 1; i++) {
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double y = (i * yResolution) + y1;
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if (i == ysteps)
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y = y2;
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for (int j = 0; j < xsteps + 1; j++) {
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double x = (j * xResolution) + x1;
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if (j == xsteps)
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x = x2;
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tuples.add(new Tuple<Double>(x, y, z));
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}
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}
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return tuples;
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}
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protected List<Double> getRawValuesInTimeInstantAndBoundingBox(String layerTitle, int time, List<Tuple<Double>> coordinates3d, double xL,double xR, double yL, double yR) throws Exception {
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// get the layer
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Metadata meta = gnInspector.getGNInfobyUUIDorName(layerTitle);
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// if the layer is good
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if (meta != null) {
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String layer = gnInspector.getLayerName(meta);
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if (layer == null)
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layer = layerTitle;
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String layerURL = "";
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GISDataConnector connector = null;
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if (gnInspector.isNetCDFFile(meta)) {
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Identification id = meta.getIdentificationInfo().iterator().next();
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String title = id.getCitation().getTitle().toString();
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AnalysisLogger.getLogger().debug("found a netCDF file with title " + title + " and layer name " + layer);
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layerURL = gnInspector.getOpenDapLink(meta);
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connector = new NetCDF();
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}
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else if (gnInspector.isAscFile(meta)){
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AnalysisLogger.getLogger().debug("managing ASC File");
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layerURL = gnInspector.getHttpLink(meta);
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connector = new ASC();
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}
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else if (gnInspector.isWFS(meta)){
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AnalysisLogger.getLogger().debug("found a Geo Layer with reference " + layerTitle + " and layer name " + layer);
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layerURL = gnInspector.getGeoserverLink(meta);
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connector = new WFS();
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}
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if (connector!=null)
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return connector.getFeaturesInTimeInstantAndArea(layerURL, layer, time, coordinates3d, xL, xR, yL, yR);
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else
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throw new Exception("ERROR: Connector not found for layer "+layerTitle+" - Cannot Rasterize!");
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}
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else
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throw new Exception("ERROR: Metadata not found for layer "+layerTitle+" - Cannot Rasterize!");
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}
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public double[][] takeTimeInstantMatrix(String layerTitle, int timeInstant, double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution) throws Exception {
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AnalysisLogger.getLogger().debug("Bounding box: (" + x1 + "," + x2 + ";" + y1 + "," + y2 + ")");
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boolean faolayer = false;
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if (layerTitle.toLowerCase().contains("MatrixExtractor->FAO aquatic species distribution map") )
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{
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AnalysisLogger.getLogger().debug("MatrixExtractor->FAO DISTRIBUTION LAYER ... TO APPY PATCH!");
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faolayer=true;
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}
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if ((x2 < x1) || (y2 < y1)) {
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AnalysisLogger.getLogger().debug("MatrixExtractor->ERROR: BAD BOUNDING BOX!!!");
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return new double[0][0];
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}
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int ysteps = (int) ((y2 - y1) / yResolution);
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int xsteps = (int) ((x2 - x1) / xResolution);
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double[][] slice = new double[ysteps + 1][xsteps + 1];
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List<Tuple<Double>> tuples = new ArrayList<Tuple<Double>>();
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AnalysisLogger.getLogger().debug("MatrixExtractor->Building the points grid according to YRes:" + yResolution + " and XRes:" + xResolution);
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AnalysisLogger.getLogger().debug("MatrixExtractor->Points to reassign:" + (ysteps*xsteps));
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// build the tuples according to the desired resolution
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for (int i = 0; i < ysteps + 1; i++) {
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double y = (i * yResolution) + y1;
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if (i == ysteps)
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y = y2;
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for (int j = 0; j < xsteps + 1; j++) {
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double x = (j * xResolution) + x1;
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if (j == xsteps)
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x = x2;
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tuples.add(new Tuple<Double>(x, y, z));
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}
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}
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AnalysisLogger.getLogger().debug("Taking " + ysteps + " values per "+xsteps+"="+(ysteps*xsteps)+ "...");
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List<Double> timeValues = getRawValuesInTimeInstantAndBoundingBox(layerTitle, timeInstant, tuples, x1, x2, y1,y2);
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AnalysisLogger.getLogger().debug("Taken " + timeValues.size() + " values");
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// build back the values matrix
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int k = 0;
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int g = 0;
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int ntriplets = timeValues.size();
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//cycle on all the triplets to recontruct the matrix
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for (int t = 0; t < ntriplets; t++) {
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//take the corresponding (time,value) pair
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Double value = timeValues.get(t);
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//if there is value, then set it, otherwise set NaN
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//the layer is undefined in that point and a value must be generated
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//assign a value to the matrix
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//WARNING: PATCH FOR FAO LAYERS:. Probability can be equal to 2 for uncertainty
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if (faolayer && (value>1)){
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AnalysisLogger.getLogger().debug("APPLYING FAO PATCH!");
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slice[k][g] = 0.5;
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}
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else
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slice[k][g] = value;
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//increase the x step according to the matrix
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if (g == xsteps) {
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g = 0;
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k++;
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}
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else
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g++;
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}
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//applyNearestNeighbor();
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AnalysisLogger.getLogger().debug("Features map: "+slice.length+","+slice[0].length);
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return slice;
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}
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public void applyNearestNeighbor(){
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/*
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AnalysisLogger.getLogger().debug("Applying nearest Neighbor to all the rows");
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//apply nearest neighbor to each row
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AlgorithmConfiguration config = new AlgorithmConfiguration();
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config.setConfigPath(configDir);
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boolean rapidinit = false;
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for (int i=0;i<slice.length;i++){
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// AnalysisLogger.getLogger().debug("Checking for unfilled values");
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boolean tofill = false;
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for (int j=0;j<slice[i].length;j++) {
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if (new Double(slice[i][j]).equals(Double.NaN))
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tofill = true;
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}
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if (tofill){
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if (!rapidinit){
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config.initRapidMiner();
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rapidinit=true;
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}
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AnalysisLogger.getLogger().debug("Filling signal");
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double[] ssliced = SignalProcessing.fillSignal(slice[i]);
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slice[i] = ssliced;
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}
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// else
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// AnalysisLogger.getLogger().debug("Signal yet complete");
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}
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*/
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}
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}
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@ -0,0 +1,148 @@
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package org.gcube.dataanalysis.geo.matrixmodel;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.UUID;
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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.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.ecoengine.utils.DatabaseUtils;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.utils.CSquareCodesConverter;
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import org.hibernate.SessionFactory;
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/**
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* transforms a raster map into a table
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*
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* @author coro
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*
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*/
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public class RasterTable {
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private double valuesMatrix[][];
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double x1;
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double x2;
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double y1;
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double y2;
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double z;
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double xResolution;
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double yResolution;
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private AlgorithmConfiguration configuration;
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private String tablename = "rstr" + ("" + UUID.randomUUID()).replace("-", "");
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static String createTableStatement = "CREATE TABLE %1$s (id serial, csquarecode character varying, x real, y real, z real, probability real)";
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static String columnsnames = "csquarecode, x , y , z , probability";
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public static String csquareColumn = "csquarecode";
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public static String probabilityColumn = "probability";
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public static String idColumn = "id";
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public String getTablename() {
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return tablename;
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}
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public void setTablename(String tablename) {
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this.tablename = tablename;
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}
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public RasterTable(double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution, double[][] values, AlgorithmConfiguration configuration) {
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this.valuesMatrix = values;
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this.configuration = configuration;
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this.x1 = x1;
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this.x2 = x2;
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this.y1 = y1;
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this.y2 = y2;
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this.z = z;
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this.xResolution = xResolution;
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this.yResolution = yResolution;
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}
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public void dumpGeoTable() {
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// open the connection to the db
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SessionFactory dbconnection = DatabaseUtils.initDBSession(configuration);
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try {
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AnalysisLogger.getLogger().debug("Database Initialized");
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// create a table
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DatabaseFactory.executeSQLUpdate(String.format(createTableStatement, tablename), dbconnection);
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AnalysisLogger.getLogger().debug("Table " + tablename + " created");
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List<Tuple<Double>> coordinates = MatrixExtractor.generateCoordinateTripletsInBoundingBox(x1, x2, y1, y2, z, xResolution, yResolution);
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int triplets = coordinates.size();
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AnalysisLogger.getLogger().debug("Generated " + triplets + " coordinates triples");
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List<Double> values = associateValueToCoordinates(coordinates, valuesMatrix);
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AnalysisLogger.getLogger().debug("Association to values completed - fulfilling buffer");
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// for each element in the matrix, build the corresponding csquare code
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StringBuffer sb = new StringBuffer();
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for (int i = 0; i < triplets; i++) {
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// save the string in a buffer
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Tuple<Double> cset = coordinates.get(i);
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double x = cset.getElements().get(0);
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double y = cset.getElements().get(1);
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String csquare = CSquareCodesConverter.convertAtResolution(y,x, xResolution);
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Double value = values.get(i);
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//we do not use NaNs in this case every value will be filled
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if (value.isNaN())
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value = 0d;
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sb.append("('" + csquare + "'," + x + "," + y + "," + z + ",'" + value + "')");
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if (i % 5000 == 0) {
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// AnalysisLogger.getLogger().debug("Partial Inserting Buffer of " + sb.length() + " Values");
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String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnsnames, sb);
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DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection);
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// AnalysisLogger.getLogger().debug("Partial Insertion completed with Success!");
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sb = new StringBuffer();
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} else if (i < triplets - 1)
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sb.append(",");
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}
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AnalysisLogger.getLogger().debug("Inserting Final Buffer of " + sb.length() + " Values");
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// save all the strings on the table
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if (sb.length() > 0) {
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String insertStatement = DatabaseUtils.insertFromBuffer(tablename, columnsnames, sb);
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DatabaseFactory.executeSQLUpdate(insertStatement, dbconnection);
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AnalysisLogger.getLogger().debug("Insertion completed with Success!");
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}
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} catch (Exception e) {
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e.printStackTrace();
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AnalysisLogger.getLogger().debug("Error in dumping table: " + e.getLocalizedMessage());
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} finally {
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// close the connection
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DatabaseUtils.closeDBConnection(dbconnection);
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AnalysisLogger.getLogger().debug("Raster Geo Table DB closed!");
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}
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}
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public void deleteTable() {
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SessionFactory dbconnection = null;
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try {
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dbconnection = DatabaseUtils.initDBSession(configuration);
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DatabaseFactory.executeSQLUpdate(DatabaseUtils.dropTableStatement(tablename), dbconnection);
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} catch (Exception e) {
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e.printStackTrace();
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} finally {
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DatabaseUtils.closeDBConnection(dbconnection);
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}
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}
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public static List<Double> associateValueToCoordinates(List<Tuple<Double>> coordinates, double[][] data){
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List<Double> values = new ArrayList<Double>();
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int k = 0;
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int g = 0;
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int ntriplets = coordinates.size();
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int xsteps = data[0].length-1;
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for (int t = 0; t < ntriplets; t++) {
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values.add(data[k][g]);
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if (g == xsteps) {
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g = 0;
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k++;
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}
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else
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g++;
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}
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return values;
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}
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}
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