git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/EcologicalEngineGeoSpatialExtension@75000 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
parent
c82d3636b1
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@ -1,8 +1,7 @@
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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.Collections;
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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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@ -12,10 +11,17 @@ 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.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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@ -88,18 +94,30 @@ public class GeoIntersector {
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}
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*/
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} else {
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//TODO: adjust WFS take
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AnalysisLogger.getLogger().debug("found a Geo Layer with title " + layerTitle + " and layer name " + layer);
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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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AnalysisLogger.getLogger().debug("Taking point: (" + x + "," + y + ")");
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LinkedHashMap<String, Double> features = new LinkedHashMap<String, Double>();
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features = getFeaturesFromWFS(featurer.getWFSLink(meta), layer, x, y);
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featuresSets.add(features);
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}
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*/
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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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AnalysisLogger.getLogger().debug("Intersecting "+triplets.size()+" vs "+featuresInTime.size() +" elements");
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for (Tuple<Double> triplet:triplets){
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GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326);
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CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(triplet.getElements().get(0),triplet.getElements().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.p.covers(po)){
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// System.out.println(po+" intersected by "+poly.p);
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features.add(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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if (!found)
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features.add(Double.NaN);
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}
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}
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}
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return features;
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@ -119,14 +137,21 @@ public class GeoIntersector {
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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 wfsUrl, String layer, double x, double y) {
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if (wfsUrl == null)
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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(wfsUrl, layer, x, y);
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return EnvDataExplorer.getFeatures(geoserverUrl, layer, x, y);
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}
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public double[][] takeLastTimeChunk(String layerTitle, double x1, double x2, double y1, double y2, double z, double xResolution, double yResolution) throws Exception {
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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 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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if ((x2 < x1) || (y2 < y1)) {
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AnalysisLogger.getLogger().debug("ERROR: BAD BOUNDING BOX!!!");
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@ -152,17 +177,17 @@ public class GeoIntersector {
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}
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AnalysisLogger.getLogger().debug("Taking " + ysteps + " values per "+xsteps+"="+(ysteps*xsteps)+ "...");
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List<Double> time = getFeaturesInTimeInstant(layerTitle, 0, tuples, x1, x2, y1,y2);
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AnalysisLogger.getLogger().debug("Taken " + time.size() + " values");
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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 = time.size();
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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 = time.get(t);
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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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@ -14,9 +14,9 @@ public class TestChunkization {
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long t0 = System.currentTimeMillis();
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AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile);
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GeoIntersector intersector = new GeoIntersector(null, cfg);
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// intersector.takeLastTimeChunk(layertitle, -180, 180, -10, 10, 0, 1, 1);
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intersector.takeLastTimeChunk(layertitle, -10, 10, -10, 10, 0,1, 1);
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// intersector.takeLastTimeChunk(layertitle, -180, 180, -90, 90, 0, 1, 1);
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// intersector.takeTimeSlice(layertitle, 0, -180, 180, -10, 10, 0, 1, 1);
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// intersector.takeTimeSlice(layertitle, 0, -10, 10, -10, 10, 0,1, 1);
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intersector.takeTimeSlice(layertitle, 0, -180, 180, -90, 90, 0, 0.5, 0.5);
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System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
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}
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}
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@ -0,0 +1,21 @@
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package org.gcube.dataanalysis.geo.test;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
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import org.gcube.dataanalysis.geo.retrieval.GeoIntersector;
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public class TestChunkizationLayer {
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static String cfg = "./cfg/";
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public static void main(String[] args) throws Exception{
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String layertitle = "MyDistributionMap";
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// String layertitle = "Mass Concentration of Chlorophyll in Sea Water in [03-30-13 01:00] (3D) {Mercator Ocean BIOMER1V1R1: Data extracted from dataset http://atoll-mercator.vlandata.cls.fr:44080/thredds/dodsC/global-analysis-bio-001-008-a}";
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// String layertitle = "Objectively Analyzed Climatology in [07-01-01 01:00] (3D) {World Ocean Atlas 09: Sea Water Temperature - annual: dods://thredds.research-infrastructures.eu/thredds/dodsC/public/netcdf/temperature_annual_1deg_ENVIRONMENT_OCEANS_.nc}";
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long t0 = System.currentTimeMillis();
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AnalysisLogger.setLogger(cfg+AlgorithmConfiguration.defaultLoggerFile);
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GeoIntersector intersector = new GeoIntersector(null, cfg);
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// intersector.takeTimeSlice(layertitle, 0, -10, 10, -10, 10, 0,1, 1);
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intersector.takeTimeSlice(layertitle, 0, -180, 180, -90, 90, 0, 0.5, 0.5);
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System.out.println("ELAPSED TIME: "+(System.currentTimeMillis()-t0));
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}
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}
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@ -1,18 +1,48 @@
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package org.gcube.dataanalysis.geo.utils;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.LinkedHashMap;
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import java.util.List;
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import org.gcube.contentmanagement.graphtools.utils.HttpRequest;
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import org.gcube.contentmanagement.lexicalmatcher.utils.AnalysisLogger;
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import org.gcube.dataanalysis.geo.meta.OGCFormatter;
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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.LinearRing;
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import com.vividsolutions.jts.geom.Point;
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import com.vividsolutions.jts.geom.Polygon;
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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 EnvDataExplorer {
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private static String callWFS(String geoServer, String layer, double x, double y) {
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float tolerance = 0.25f;
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String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, OGCFormatter.pointToBoundingBox(x, y, tolerance), 1, "json");
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String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, OGCFormatter.pointToBoundingBox(x, y, tolerance), 1, "json");
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Requesting URL: " + wfsURL);
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String returned = null;
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try {
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returned = HttpRequest.sendGetRequest(wfsURL, null);
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> ERROR " + e.getLocalizedMessage());
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}
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if (returned != null)
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Intersection: " + returned);
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else
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Found Nothing!");
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return returned;
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}
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private static String callWFS(String geoServer, String layer, double xL, double yL, double xR, double yR) {
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// String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, OGCFormatter.buildBoundingBox(xL, yL, xR, yR), 0, "json");
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// there is a bug in WFS in the retrieval according to a bounding box: y must be in the range -180;180. then I preferred to take all the features
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String wfsURL = OGCFormatter.getWfsUrl(geoServer, layer, null, 0, "json");
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Requesting URL: " + wfsURL);
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String returned = null;
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try {
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public static LinkedHashMap<String, Double> getFeatures(String geoserver, String layer, double x, double y) {
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try {
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AnalysisLogger.getLogger().debug("Calling WFS towards Geoserver:" + geoserver + " and layer:" + layer);
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String jsonString = callWFS(geoserver, layer, x, y);
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LinkedHashMap<String, Object> map = JsonMapper.parse(jsonString);
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LinkedHashMap<String, String> mapout = (LinkedHashMap<String, String>) ((HashMap<String, Object>) map.get("features")).get("properties");
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LinkedHashMap<String, Double> values = new LinkedHashMap<String, Double>();
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for (String key:mapout.keySet()){
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LinkedHashMap<String, Double> values = new LinkedHashMap<String, Double>();
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for (String key : mapout.keySet()) {
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values.put(key, Double.parseDouble(mapout.get(key)));
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}
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return values;
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return null;
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}
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}
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public static List<FeaturedPolygon> getFeatures(String geoserver, String layer, double xL, double yL, double xR, double yR) {
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try {
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AnalysisLogger.getLogger().debug("Calling WFS towards Geoserver:" + geoserver + " and layer:" + layer);
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String jsonString = callWFS(geoserver, layer, xL, yL, xR, yR);
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// System.out.println("JSON:"+jsonString);
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LinkedHashMap<String, Object> map = JsonMapper.parse(jsonString);
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List<FeaturedPolygon> fpolygons = new ArrayList<FeaturedPolygon>();
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FeaturedPolygon poly = null;
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for (String key : map.keySet()) {
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if (key.contains("features")) {
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HashMap<String, Object> propertiesMap = (HashMap<String, Object>) map.get(key);
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//cycle on all the properties
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for (String properties : propertiesMap.keySet()) {
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if (properties.contains("properties")) {
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if (poly==null)
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poly=new FeaturedPolygon();
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LinkedHashMap<String, String> props = (LinkedHashMap<String, String>) propertiesMap.get(properties);
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//fill the properties of the fpolygon
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for (String keyprop : props.keySet()) {
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try {
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//fulfill the FeaturedPolygon
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String value = props.get(keyprop);
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try{
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String lowcaseprop = keyprop.toLowerCase();
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if ((poly.value==null) &&
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!lowcaseprop.startsWith("id")&&
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!lowcaseprop.endsWith("id"))
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poly.setValue(Double.parseDouble(value));
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else
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poly.addFeature(keyprop, value);
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}catch (Exception e2){
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poly.addFeature(keyprop, value);
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}
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} catch (Exception e) {
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}
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}
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}
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else
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if (properties.contains("geometry") && !properties.contains("geometry_")) {
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if (poly==null)
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poly=new FeaturedPolygon();
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else if (poly.p!=null){
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if (poly.value==null)
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poly.value=Double.NaN;
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fpolygons.add(poly);
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poly=new FeaturedPolygon();
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}
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LinkedHashMap<String, String> props = (LinkedHashMap<String, String>) propertiesMap.get(properties);
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List<double[]> coords = WFS2Coordinates(props.toString());
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GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326);
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Polygon p = null;
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if (coords != null) {
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Coordinate[] coordarray = new Coordinate[coords.size()];
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int i=0;
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for (double[] pair:coords){
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coordarray[i] = new Coordinate(pair[0],pair[1]);
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i++;
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}
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CoordinateArraySequence coordseq = new CoordinateArraySequence(coordarray);
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LinearRing ring = new LinearRing(coordseq, factory);
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p = new Polygon(ring, new LinearRing[] {}, factory);
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}
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poly.setPolygon(p);
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}
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}
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}
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}// end for on all the wfs
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if (poly!=null){
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if (poly.value==null)
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poly.value=Double.NaN;
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fpolygons.add(poly);
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}
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return fpolygons;
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} catch (Exception e) {
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AnalysisLogger.getLogger().debug("EnvDataExplorer-> Error in getting properties");
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return null;
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}
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}
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public static List<double[]> WFS2Coordinates(String wfsgeometry) {
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// geometry935133b1-ba3c-493d-8e18-6fb496ced995={type=MultiPolygon, coordinates={966a275c-23aa-4a43-a943-7e1c7eaf5d65=[[[1.5,125.00000000000011],[1.5,124.5],[2.000000000000057,124.5],[2.000000000000057,125.00000000000011],[1.5,125.00000000000011]]]}},
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String[] coordinatePairs = null;
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List<double[]> dpairs = new ArrayList<double[]>();
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if (wfsgeometry.toLowerCase().contains("multipolygon")) {
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String coordString = "coordinates=";
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String coordinates = wfsgeometry.substring(wfsgeometry.indexOf(coordString) + coordString.length());
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coordinates = coordinates.substring(coordinates.indexOf("=")+1);
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coordinatePairs = coordinates.split("\\],\\[");
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for (String coord : coordinatePairs) {
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coord = coord.replaceAll("(\\[|\\]|\\}|\\{|)", "");
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String[] coordpair = coord.split(",");
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double[] dd = new double[2];
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//invert the coordinates as the final must be are long,lat
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dd[1] = Double.parseDouble(coordpair[0]);
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dd[0] = Double.parseDouble(coordpair[1]);
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dpairs.add(dd);
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}
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}
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return dpairs;
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}
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public static void main(String[] args) {
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String geom = "{type=MultiPolygon, coordinates={cce4daf3-966e-4b5f-adea-f88ea2b93d03=[[[-16,-146.49999999999997],[-16,-146.99999999999994],[-15.5,-146.99999999999994],[-15.5,-146.49999999999997],[-16,-146.49999999999997]]]}}";
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List<double[]> coords = WFS2Coordinates(geom);
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GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 4326);
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// GeometryFactory factory = new GeometryFactory(new PrecisionModel(), 0);
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/*
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* CoordinateArraySequence coords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(12.0, 34.23), new Coordinate(12.000, 54.555), new Coordinate(7, 8), new Coordinate(12.0, 34.23) }); LinearRing ring = new LinearRing(coords, factory); Polygon p = new Polygon(ring, null, factory); CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(12.0, 34.23),});
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*/
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// CoordinateArraySequence coords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(1.5, 125.00000000000011), new Coordinate(1.5, 124.5), new Coordinate(2.000000000000057, 124.5), new Coordinate(2.000000000000057, 125.00000000000011), new Coordinate(1.5, 125.00000000000011) });
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if (coords != null) {
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Coordinate[] coordarray = new Coordinate[coords.size()];
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int i=0;
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for (double[] pair:coords){
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coordarray[i] = new Coordinate(pair[0],pair[1]);
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i++;
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}
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CoordinateArraySequence coordseq = new CoordinateArraySequence(coordarray);
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LinearRing ring = new LinearRing(coordseq, factory);
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Polygon p = new Polygon(ring, new LinearRing[] {}, factory);
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// CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(-16,-146.49999999999997), });
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CoordinateArraySequence pcoords = new CoordinateArraySequence(new Coordinate[] { new Coordinate(-150,-16), });
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Point po = new Point(pcoords, factory);
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// po = p.getCentroid();
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System.out.println("contains: " + p.contains(po)+" boundary: "+p.covers(po));
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}
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}
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}
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@ -0,0 +1,28 @@
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package org.gcube.dataanalysis.geo.utils;
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import java.util.LinkedHashMap;
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|
||||
import com.vividsolutions.jts.geom.Polygon;
|
||||
|
||||
public class FeaturedPolygon {
|
||||
public Polygon p;
|
||||
public LinkedHashMap<String, String> features;
|
||||
public Double value;
|
||||
public FeaturedPolygon(){
|
||||
|
||||
}
|
||||
|
||||
public void setPolygon(Polygon p){
|
||||
this.p=p;
|
||||
}
|
||||
|
||||
public void setValue(Double v){
|
||||
this.value=v;
|
||||
}
|
||||
|
||||
public void addFeature(String key,String value){
|
||||
if (features==null)
|
||||
features = new LinkedHashMap<String, String>();
|
||||
features.put(key,value);
|
||||
}
|
||||
}
|
||||
|
|
@ -4,6 +4,7 @@ import java.util.Iterator;
|
|||
import java.util.LinkedHashMap;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.UUID;
|
||||
|
||||
import com.google.gson.JsonArray;
|
||||
import com.google.gson.JsonElement;
|
||||
|
|
@ -32,6 +33,9 @@ public class JsonMapper {
|
|||
parseMap(map, (JsonObject) element);
|
||||
}
|
||||
}
|
||||
else{
|
||||
map.put(UUID.randomUUID().toString(), element.toString());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -47,6 +51,10 @@ public class JsonMapper {
|
|||
Map.Entry<String, JsonElement> entry = iterator.next();
|
||||
String key = entry.getKey();
|
||||
JsonElement value = entry.getValue();
|
||||
if (map.get(key)!=null){
|
||||
key+=UUID.randomUUID();
|
||||
}
|
||||
|
||||
if (!value.isJsonPrimitive()) {
|
||||
map.put(key, parse(value.toString()));
|
||||
} else {
|
||||
|
|
|
|||
Loading…
Reference in New Issue