git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@92310 82a268e6-3cf1-43bd-a215-b396298e98cf
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@ -1,12 +1,16 @@
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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.HashMap;
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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.configuration.AlgorithmConfiguration;
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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.netcdf.NetCDF;
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import org.gcube.dataanalysis.geo.connectors.table.Table;
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import org.gcube.dataanalysis.geo.connectors.table.TableMatrixRepresentation;
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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.gcube.dataanalysis.geo.interfaces.GISDataConnector;
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@ -16,21 +20,28 @@ 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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private AlgorithmConfiguration configuration;
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public static int maxSignalLength = 100000;
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public MatrixExtractor(String scope, String cfgDir) {
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public MatrixExtractor(AlgorithmConfiguration configuration) {
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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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gnInspector.setScope(configuration.getGcubeScope());
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this.configuration=configuration;
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}
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public GeoNetworkInspector getFeaturer(){
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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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public boolean isTable() {
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if (configuration.getParam(TableMatrixRepresentation.tableNameParameter) != null)
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return true;
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else
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return false;
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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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@ -50,62 +61,121 @@ public static List<Tuple<Double>> generateCoordinateTripletsInBoundingBox(double
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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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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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return getRawValuesInTimeInstantAndBoundingBox(layerTitle, time, coordinates3d, xL, xR, yL, yR, false);
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}
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private GISDataConnector currentconnector;
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private String layer;
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private String layerURL;
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protected List<Double> getRawValuesInTimeInstantAndBoundingBox(String layerTitle, int time, List<Tuple<Double>> coordinates3d, double xL, double xR, double yL, double yR, boolean saveLayer) throws Exception {
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// get the layer
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Metadata meta = gnInspector.getGNInfobyUUIDorName(layerTitle);
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Metadata meta = null;
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GISDataConnector connector = null;
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if (currentconnector != null && saveLayer)
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connector = currentconnector;
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else {
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if (isTable()) {
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AnalysisLogger.getLogger().debug("Extracting grid from table " + configuration.getParam(TableMatrixRepresentation.tableNameParameter));
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connector = new Table(configuration);
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currentconnector = connector;
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} else
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meta = gnInspector.getGNInfobyUUIDorName(layerTitle);
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}
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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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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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layerURL = "";
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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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} 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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} 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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currentconnector = connector;
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}
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if (connector!=null)
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//execute connector
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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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throw new Exception("ERROR: Connector not found for layer " + layerTitle + " - Cannot Rasterize!");
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}
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boolean log = true;
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public double[] takeSignalInTime(String layerTitle, double x, double y, double z, double resolution) throws Exception {
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// HashMap<Integer, Double> signal = new HashMap<Integer, Double>();
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double[] signal = new double[maxSignalLength];
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int t = 0;
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log=false;
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while (true) {
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try {
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if (t%100==0)
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AnalysisLogger.getLogger().debug("Matrix Extractor-> Extracting Time Instant " + t);
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double[][] values = takeTimeInstantMatrix(layerTitle, t, x, x, y, y, z, resolution, resolution, true);
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// signal.put(t,values[0][0]);
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signal[t]=values[0][0];
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t++;
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if (t==maxSignalLength)
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break;
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("Matrix Extractor-> No More Time Intervals!");
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break;
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}
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}
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// double[] dsignal = new double[signal.size()];
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double[] dsignal = new double[t];
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// int i = 0;
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// for (Double signald : signal.values()) {
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for (int i=0;i<t;i++){
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dsignal[i] = signal[i];
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i++;
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}
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log = true;
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return dsignal;
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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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return takeTimeInstantMatrix(layerTitle, timeInstant, x1, x2, y1, y2, z, xResolution, yResolution, false);
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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, boolean savelayer) throws Exception {
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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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if (layerTitle.toLowerCase().contains("MatrixExtractor->FAO aquatic species distribution map")) {
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AnalysisLogger.getLogger().debug("MatrixExtractor->FAO DISTRIBUTION LAYER ... TO APPY PATCH!");
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faolayer=true;
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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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if (log){
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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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}
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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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@ -120,76 +190,71 @@ public static List<Tuple<Double>> generateCoordinateTripletsInBoundingBox(double
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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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if (log)
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AnalysisLogger.getLogger().debug("Taking " + (ysteps + 1) + " values per " + (xsteps + 1) + "=" + (ysteps + 1 * xsteps + 1) + "...");
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// adjust the BB in the case of one single point
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if (x2 == x1) {
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x2 = x2 + (xResolution / 2d);
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x1 = x1 - (xResolution / 2d);
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}
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if (y2 == y1) {
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y2 = y2 + (yResolution / 2d);
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y1 = y1 - (yResolution / 2d);
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}
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if (log)
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AnalysisLogger.getLogger().debug("Bounding box: (" + x1 + "," + x2 + ";" + y1 + "," + y2 + ")");
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// long t0=System.currentTimeMillis();
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List<Double> timeValues = getRawValuesInTimeInstantAndBoundingBox(layerTitle, timeInstant, tuples, x1, x2, y1, y2, savelayer);
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// AnalysisLogger.getLogger().debug("Elapsed:"+(System.currentTimeMillis()-t0));
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if (log)
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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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// 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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// 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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// 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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} 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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// 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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} else
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g++;
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}
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// applyNearestNeighbor();
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//applyNearestNeighbor();
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AnalysisLogger.getLogger().debug("Features map: "+slice.length+","+slice[0].length);
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if (log)
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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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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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* AnalysisLogger.getLogger().debug("Applying nearest Neighbor to all the rows"); //apply nearest neighbor to each row AlgorithmConfiguration config = new AlgorithmConfiguration(); config.setConfigPath(configDir); boolean rapidinit = false;
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*
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*
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* for (int i=0;i<slice.length;i++){ // AnalysisLogger.getLogger().debug("Checking for unfilled values"); boolean tofill = false; for (int j=0;j<slice[i].length;j++) { if (new Double(slice[i][j]).equals(Double.NaN)) tofill = true; } if (tofill){ if (!rapidinit){ config.initRapidMiner(); rapidinit=true; } AnalysisLogger.getLogger().debug("Filling signal"); double[] ssliced = SignalProcessing.fillSignal(slice[i]); slice[i] = ssliced; } // else // AnalysisLogger.getLogger().debug("Signal yet complete"); }
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*/
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}
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}
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