git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@92163 82a268e6-3cf1-43bd-a215-b396298e98cf
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package org.gcube.dataanalysis.geo.retrieval;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.LinkedHashMap;
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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.signals.SignalProcessing;
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import org.gcube.dataanalysis.ecoengine.utils.Tuple;
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import org.gcube.dataanalysis.geo.meta.features.FeaturesManager;
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import org.gcube.dataanalysis.geo.utils.AscDataExplorer;
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import org.gcube.dataanalysis.geo.utils.EnvDataExplorer;
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import org.gcube.dataanalysis.geo.utils.FeaturedPolygon;
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import org.gcube.dataanalysis.geo.utils.ThreddsDataExplorer;
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import org.opengis.metadata.Metadata;
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import org.opengis.metadata.identification.Identification;
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import com.vividsolutions.jts.geom.Coordinate;
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import com.vividsolutions.jts.geom.GeometryFactory;
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import com.vividsolutions.jts.geom.Point;
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import com.vividsolutions.jts.geom.PrecisionModel;
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import com.vividsolutions.jts.geom.impl.CoordinateArraySequence;
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public class GeoIntersector {
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private FeaturesManager featurer;
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private String configDir;
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public GeoIntersector(String scope, String cfgDir) {
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featurer = new FeaturesManager();
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featurer.setScope(scope);
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this.configDir=cfgDir;
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}
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public FeaturesManager getFeaturer(){
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return featurer;
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}
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public LinkedHashMap<String, Double> getFeaturesInTime(String layerTitle, double x, double y) throws Exception {
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return getFeaturesInAllTimes(layerTitle, x, y, 0);
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}
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public LinkedHashMap<String, Double> getFeaturesInAllTimes(String layerTitle, double x, double y, double z) throws Exception {
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LinkedHashMap<String, Double> features = new LinkedHashMap<String, Double>();
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// get the layer
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// Metadata meta = featurer.getGNInfobyTitle(layerTitle);
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Metadata meta = featurer.getGNInfobyUUIDorName(layerTitle);
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// if the layer is good
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if (meta != null) {
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String layer = featurer.getLayerName(meta);
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if (layer == null)
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layer = layerTitle;
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// check if it is a NetCDF
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if (featurer.isThreddsFile(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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features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, x, y, z);
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} else {
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AnalysisLogger.getLogger().debug("found a Geo Layer with title " + layerTitle + " and layer name " + layer);
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features = getFeaturesFromWFS(featurer.getWFSLink(meta), layer, x, y);
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}
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}
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return features;
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}
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public List<Double> getFeaturesInTimeInstant(String layerTitle, int time, List<Tuple<Double>> triplets, double xL,double xR, double yL, double yR) throws Exception {
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List<Double> features = new ArrayList<Double>();
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// get the layer
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Metadata meta = featurer.getGNInfobyUUIDorName(layerTitle);
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// if the layer is good
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if (meta != null) {
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String layer = featurer.getLayerName(meta);
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if (layer == null)
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layer = layerTitle;
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// check if it is a NetCDF
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if (featurer.isThreddsFile(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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features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, time, triplets, xL,xR, yL, yR);
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/*
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for (Tuple<Double> triplet : triplets) {
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double x = triplet.getElements().get(0);
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double y = triplet.getElements().get(1);
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double z = 0;
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if (triplet.getElements().size() > 2)
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z = triplet.getElements().get(2);
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AnalysisLogger.getLogger().debug("Taking point: (" + x + "," + y + "," + z + ")");
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LinkedHashMap<String, Double> features = new LinkedHashMap<String, Double>();
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features = getFeaturesFromNetCDF(featurer.getOpenDapLink(meta), layer, x, y, z);
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AnalysisLogger.getLogger().debug("Got: (" + features + ")");
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featuresSets.add(features);
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}
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*/
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}
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else if (featurer.isAscFile(meta)){
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AnalysisLogger.getLogger().debug("managing ASC File");
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String remoteFile = featurer.getHttpLink(meta);
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AscDataExplorer asc = new AscDataExplorer(remoteFile);
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features = asc.retrieveDataFromAsc(triplets);
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AnalysisLogger.getLogger().debug("ASC File managed");
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}
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else {
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AnalysisLogger.getLogger().debug("found a Geo Layer with reference " + layerTitle + " and layer name " + layer);
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// AnalysisLogger.getLogger().debug("Taking point: (" + x + "," + y + ")");
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List<FeaturedPolygon> featuresInTime = new ArrayList<FeaturedPolygon>();
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AnalysisLogger.getLogger().debug("taking WFS features");
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featuresInTime = getFeaturesFromWFS(featurer.getGeoserverLink(meta), layer, xL,yL, xR, yR);
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int tsize = triplets.size();
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AnalysisLogger.getLogger().debug("Intersecting "+tsize+" vs "+featuresInTime.size() +" elements");
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int ttc= 0;
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Double[] featuresarray = new Double[tsize];
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int k=0;
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long t0=0;
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GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326);
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// Tuple[] tripletss = new Tuple[tsize];
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// tripletss = triplets.toArray(tripletss);
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// for (Tuple<Double> triplet:triplets){
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for (Tuple<Double> triplet:triplets){
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ArrayList<Double> elements = triplet.getElements();
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CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(elements.get(0),elements.get(1)),});
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Point po = new Point(pcoords, factory);
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boolean found = false;
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for (FeaturedPolygon poly:featuresInTime){
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if (poly!=null && poly.p!=null && poly.p.covers(po)){
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// System.out.println(po+" intersected by "+poly.p+ " assigning value "+poly.value);
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// features.add(poly.value);
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featuresarray[k] = poly.value;
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found = true;
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break;
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}
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}
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po = null;
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if (!found){
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// features.add(Double.NaN);
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featuresarray[k] = Double.NaN;
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}
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if (ttc%10000==0){
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AnalysisLogger.getLogger().debug("Status: "+((double)ttc*100d/(double)tsize));
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// System.out.println("::"+((System.currentTimeMillis()-t0)/1000));
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}
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ttc++;
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k++;
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// if (ttc%1000==0)
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// t0 = System.currentTimeMillis();
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}
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features = Arrays.asList(featuresarray);
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}
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}
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return features;
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}
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private List<Double> getFeaturesFromNetCDF(String opendapURL, String layer, int time, List<Tuple<Double>> triplets, double xL,double xR, double yL, double yR) {
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if (opendapURL == null)
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return null;
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return ThreddsDataExplorer.retrieveDataFromNetCDF(opendapURL, layer, time, triplets, xL,xR, yL, yR);
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}
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private LinkedHashMap<String, Double> getFeaturesFromNetCDF(String opendapURL, String layer, double x, double y, double z) {
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if (opendapURL == null)
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return null;
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return ThreddsDataExplorer.retrieveDataFromNetCDF(opendapURL, layer, x, y, z);
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}
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private LinkedHashMap<String, Double> getFeaturesFromWFS(String geoserverUrl, String layer, double x, double y) {
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if (geoserverUrl == null)
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return null;
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return EnvDataExplorer.getFeatures(geoserverUrl, layer, x, y);
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}
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private List<FeaturedPolygon> getFeaturesFromWFS(String geoserverUrl, String layer, double xL,double yL,double xR, double yR) {
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if (geoserverUrl == null)
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return null;
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return EnvDataExplorer.getFeatures(geoserverUrl, layer, xL,yL,xR, yR);
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}
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public static List<Tuple<Double>> generateCoordinateTriplets(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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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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public double[][] takeTimeSlice(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("fao aquatic species distribution map") )
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{
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AnalysisLogger.getLogger().debug("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("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("Building the points grid according to YRes:" + yResolution + " and XRes:" + xResolution);
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AnalysisLogger.getLogger().debug("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 = getFeaturesInTimeInstant(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 (Kolmogorov, forgive them for they know not what they do)
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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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/*
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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("Features map: "+slice.length+","+slice[0].length);
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return slice;
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}
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}
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